Intelligent Design

Bad math: Why Larry Moran’s “I’m not a Darwinian” isn’t a valid reply to Meyer’s argument

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Professor Larry Moran has written a response to my post, A succinct case for Intelligent Design. Unfortunately, Professor Moran gets his facts wrong from the get-go. He writes:

It seems to me that the [Intelligent Design creationist] movement concentrates on criticizing evolution (and materialism) and doesn’t really present much of a case for believing that the history of life was directed by gods.

Now, it’s no skin off my nose if Professor Moran wants to call us creationists. Frankly, I couldn’t care less. But the Intelligent Design movement has never claimed to have scientific evidence that the history of life was “directed by gods.” What we claim is that certain highly specific, functional systems which are found in living things were designed by some intelligent agent or agents. By “intelligent,” I don’t mean “humanlike”; rather, what I mean is: capable of engaging in abstract reasoning, when selecting suitable means to achieve one’s goals. In the most clear-cut Intelligent Design cases, the agent has to engage in mathematical reasoning – whether it be about squares (in the case of the monolith on the Moon in the movie 2001, whose sides are in the ration 1:4:9) or about digital code (in the case of the DNA we find in living things), or about which complex geometrical arrangements of amino acid chains will prove to be capable of performing a biologically useful task (in the case of protein design).

When I speak of the agent’s “goals,” I don’t mean the agent’s personal motives for doing something, which we have no way of inferring from the products they design; rather, I simply mean the task that the agent was attempting to perform, or the problem that they were trying to solve. Beyond that, there is nothing more that we could possibly infer about the agent, unless we were acquainted with them or with other members of their species. For instance, we cannot infer that the designer of an artifact was a sentient being (since the ability to design doesn’t imply the ability to feel) , or a material being (whatever that vague term means), or a physical entity (since there’s no reason why a designer needs to exhibit law-governed behavior), or even a complex or composite entity. To be sure, all the agents that we are familiar with possess these characteristics, but we cannot infer them from the products designed by an agent. Finally, the fact that an agent is capable of performing a variety of functions does not necessarily imply that the agent is composed of multiple detachable parts. We simply don’t know that. In short: the scientific inferences we can make about non-human designers are extremely modest.

Moran’s verdict: “No case for Intelligent Design”

After quoting the 123-word passage from Meyer’s book which I highlighted in my original post, summarizing the four fundamental problems with unguided evolution, Professor Moran accuses Dr. Meyer of claiming that Intelligent Design must be true because Darwinism is false:

This passage merely affirms what we all know to be true; namely that there is no case for Intelligent Design Creationism. It’s just a bunch of whining about the inadequacies of the IDiot version of evolution. That version assumes that all of evolution is due to natural selection acting on random mutations and this gives rise to the appearance of design.

I don’t believe in that version of evolution and I don’t think that most species look as though they were designed. Does that mean that I’m an Intelligent Design Creationist? Of course not. Meyers (and Torley) have fallen for the trap of the false dichotomy.

Even if all four of Stephen Meyer’s critiques were correct, he still isn’t offering an alternative explanation and he still isn’t showing us evidence for an intelligent designer—or any other kind of designer.

As anyone who has read Darwin’s Doubt knows, this is a complete travesty of Meyer’s argument. Professor Moran is displaying his ignorance here.

The evidence for an intelligent designer, in a nutshell

Dr. Meyer’s case for an intelligent designer is spelt out with admirable lucidity in an Evolution News and Views post titled, Does Darwin’s Doubt Commit the God-of-the-Gaps Fallacy? (October 16, 2013). The argument proceeds as follows:

Premise One: Despite a thorough search and evaluation, no materialistic causes or evolutionary mechanisms have demonstrated the power to produce large amounts of specified or functional information (or integrated circuitry).

Premise Two: Intelligent causes have demonstrated the power to produce large amounts of specified/functional information (and integrated circuitry).

Conclusion: Intelligent design constitutes the best, most causally adequate, explanation for the specified/functional information (and circuitry) that was necessary to produce the Cambrian animals…

In fact, the argument for intelligent design developed in Darwin’s Doubt constitutes an “inference to the best explanation” based upon our best available knowledge….[A]n inference to the best explanation …asserts the superior explanatory power of a proposed cause based upon its established — its known — causal adequacy, and based upon a lack of demonstrated efficacy, despite a thorough search, of any other adequate cause. The inference to design, therefore, depends on present knowledgee of the causal powers of various materialistic entities and processes (inadequate) and intelligent agents (adequate).

Meyer’s argument can also be found in chapters 17 and 18 of his book, Darwin’s Doubt. Sadly, Professor Moran evinces no sign of having read those chapters. One wonders whether he merely skimmed Dr. Meyer’s book.

Why the neutral theory of evolution won’t remedy the deficiencies of neo-Darwinism

But let us return to Professor Moran’s remarks about natural selection. In his introduction to The Origin of Species, Charles Darwin wrote: “I am convinced that Natural Selection has been the main but not the exclusive means of modification.” In a similar vein, Richard Dawkins famously declared: “Evolution by natural selection is the only workable theory ever proposed that is capable of explaining life, and it does so brilliantly.”

Professor Moran does not share these views. He rejects the view that “evolution is due to natural selection acting on random mutations and this gives rise to the appearance of design,” forthrightly asserting: “I don’t believe in that version of evolution.” He maintains that “a huge number of mutations are neutral and there are far more neutral mutations fixed by random genetic drift that there are beneficial mutations fixed by natural selection.” This, he declares, is what modern-day evolutionists believe. In an earlier post, he complains that “you have to read very carefully to find any mention of modern evolutionary theory in Meyer’s book – he prefers to focus his attack on mutation + natural selection.”

What Professor Moran does not tell us here is that Dr. Stephen Meyer wrote a detailed and extensive critique of the neutral theory of evolution in his book, Darwin’s Doubt. In his critique, Dr. Meyer focuses on the ground-breaking work of Dr. Michael Lynch, a geneticist who espouses the neutral theory of evolution. Meyer argues that this theory is incapable of accounting for the origin of new animal body plans, because it is built on faulty mathematical assumptions (bolding mine – VJT):

Michael Lynch, a geneticist at Indiana University, … proposes a neutral or “non-adaptive” theory of evolution in which natural selection plays a largely insignificant role…

Lynch argues that in small populations, animal genomes will inevitably grow over time as nonprotein-coding sections of DNA (as well as gene duplicates) accumulate due to the weakness of natural selection. He thinks that these neutral mutations drive the evolution of animals.

… [F]or Lynch’s theory to explain the origin of new and functional genes and proteins (and the anatomical complexities that depend on them), his theory would have to solve the problem of combinatorial inflation… He would have to show that random mutations could efficiently search the relevant combinatorial space of possible sequences corresponding to a given novel functional gene or protein.

Nevertheless, Lynch does not even address the problem of combinatorial inflation or the closely related problem of the rarity of genes and proteins in sequence space…

Lynch does argue in one paper that neutral evolutionary processes can generate new complex adaptations – adaptations requiring multiple coordinated mutations – within realistic waiting times. In particular, writing in a recent paper with colleague Adam Abegg of St. Louis University, he argues that “conventional population genetic mechanisms” such as random mutation and genetic drift can cause the “relatively rapid emergence of specific complex adaptations.” …

But some things are just too good to be true, and it turns out that Lynch and Abegg made a subtle but fundamental mathematical error in coming to their conclusion. Appropriately, perhaps, the first person to demonstrate that Lynch’s incredible claim was problematic was Douglas Axe… In the end, he traced Lynch and Abegg’s claims to two erroneous equations, both of which were based on erroneous assumptions. In essence, Lynch and Abegg assumed that organisms will acquire a given complex adaptation by traversing a direct path to the new anatomical structure. Each mutation would build on the previous one in the most efficient manner possible – with no setbacks, false starts, aimless wandering, or genetic degradation – until the desired structure or system (or gene) is constructed. Thus, they formulated an undirected model of evolutionary change, and one that assumes, moreover, that there is no mechanism available (such as natural selection) that can lock in potentially favorable mutational changes on the way to some complex advantageous structure….

Yet nothing in Lynch’s neutral model ensures that potentially advantageous mutations will remain in place while other mutations accrue. As Axe explains, “Productive changes cannot be ‘banked,’ whereas Equation 2 [one of Lynch’s equations] presupposes that they can.” Instead, Axe shows, mathematically, that degradation (the fixation of mutational changes that make the complex adaptation less likely to arise) will occur much more rapidly than constructive mutations, causing the expected waiting time to increase exponentially.
(2013, pp. 321, 322, 326, 327-328)

Quoting Marshall – but missing the big picture

In another post, Professor Moran quotes with relish from a critical review of Dr. Meyer’s book by the eminent UC paleontologist, Professor Charles Marshall:

…when it comes to explaining the Cambrian explosion, Darwin’s Doubt is compromised by Meyer’s lack of scientific knowledge, his “god of the gaps” approach, and selective scholarship that appears driven by his deep belief in an explicit role of an intelligent designer in the history of life.

However, Dr. Meyer has responded at length to Professor Marshall’s criticisms, in a four-part series. Meyer’s most telling points can be found in his second post, which is titled, To Build New Animals, No New Genetic Information Needed? More in Reply in Charles Marshall. I’ll quote a few brief excerpts (bolding mine – VJT):

…Marshall simply assumes that most of the genetic information necessary to build the Cambrian animals already existed before the Cambrian explosion. In fact, he seems to presuppose the existence of what Susumu Ohno called a “pananimalian genome,”16 a nearly complete set of the genes necessary to build Cambrian animals within some phenotypically simpler, ur-metazoan ancestor. Thus, he states the new animal phyla “emerged through the rewiring of the gene regulatory networks (GRNs) of already existing genes.”17 …

Nevertheless, this question-begging assumption does not solve the central problem posed by Darwin’s Doubt — that of the origin of the genetic (and epigenetic) information necessary to produce the Cambrian animals. It merely pushes the problem back several tens or hundreds of millions of years, assuming that such a universal genetic toolkit ever existed.

Readers of the book will recall my discussion, in Chapters 9 and 10, of recent mutagenesis experiments. These experiments have established the extreme rarity of functional genes and proteins among the many (combinatorially) possible ways of arranging nucleotide bases or amino acids within their corresponding “sequence spaces.” … This extreme rarity also helps to explain why mathematical biologists, using standard population genetics models, are calculating exceedingly long waiting times (well in excess of available evolutionary time) for the production of new genes and proteins when producing such genes or proteins requires even a few coordinated mutations.20

For these reasons, defining the Cambrian explosion as a 25 million year event, as Marshall does, instead of a 10 million year event, as many other Cambrian experts do (and as I do in Darwin’s Doubt), makes no appreciable difference in solving the problem of the origin of genetic information — such is the extreme rarity of functional bio-macromolecules within their relevant sequence spaces. Nor, for that matter, does positing the origin of a complete set of genes (that is, many more than just one) for building all the Cambrian animals 100 million years before the Cambrian explosion. That merely pushes the problem back…In any case, the experimentally based calculations in Darwin’s Doubt show that neither ten million, nor several hundred million years would afford enough opportunities to produce the genetic information necessary to build even a single novel gene or protein, let alone all the new genes and proteins needed to produce new animal forms.

Nobody would question Professor Marshall’s expertise in paleontology, but the argument in Dr. Stephen Meyer’s book, Darwin’s Doubt, is ultimately a mathematical one. Until evolutionists demonstrate that they can grapple with the mathematics in Meyer’s argument, their criticisms of his book will continue to miss the mark.

Reading the critical reviews of Meyer’s book reinforced my conviction that many contemporary biologists fail to grasp that the scientific case for unguided evolution is built on a foundation of faulty math. As a philosopher of science, Dr. Meyer is to be congratulated for having the courage to publicly declare that the emperor has no clothes.

Finally, here’s what Harvard geneticist George Church (who isby no means an Intelligent Design theorist) said about Darwin’s Doubt:

Stephen Meyer’s new book Darwin’s Doubt represents an opportunity for bridge-building, rather than dismissive polarization — bridges across cultural divides in great need of professional, respectful dialog — and bridges to span evolutionary gaps.

Readers can find many more comments on this Web page by highly qualified scientists praising Darwin’s Doubt. Professor Moran is welcome to call them all “idiots” if he likes. But somehow I don’t think he’ll do that. Or will he?

670 Replies to “Bad math: Why Larry Moran’s “I’m not a Darwinian” isn’t a valid reply to Meyer’s argument

  1. 1
    JimFit says:

    If ID means IDiot people then Professor Moran is a Moron.

  2. 2
    Box says:

    VJT:
    It merely pushes the problem back several tens or hundreds of millions of years, assuming that such a universal genetic toolkit ever existed.

    Solving a problem by pushing a problem back seems to be the atheist’s favorite “solution”.
    The multiverse concept is another example of such a “solution”. And when we then ask: “From whence came the Multiverse?”, they get all whipped up in a frenzy:

    The multiverse theory seems to provide an opportunity seized upon by wishful thinkers, theologians, and their fellow travelers among the physicists and philosophers. First they ask, “If our universe is just one of many in a multiverse, where did the multiverse come from? And where did the multiverse’s cause come from, and where did its cause come from?” And so on, ad infinitum. Once they have convinced themselves and others that this series of questions has no stopping point in physics, they play what they imagine is a trump card, a question whose only answer they think has to be the God hypothesis.

    [A.Rosenberg, ‘The Atheist’s Guide to Reality’, ch.2]

  3. 3
    RexTugwell says:

    JF: I’ve often thought that Moran is pretty brave calling us IDiots when his own name screams for its own point mutation.

  4. 4
    Silver Asiatic says:

    Moran: “It’s just a bunch of whining about the inadequacies of the IDiot version of evolution. That version assumes that all of evolution is due to natural selection acting on random mutations and this gives rise to the appearance of design.”

    Richard Dawkins famously declared: “Evolution by natural selection is the only workable theory ever proposed that is capable of explaining life, and it does so brilliantly.”

    So, Dawkins believes in the idiot version of evolution.

    That’s very good to know.

  5. 5
    OldArmy94 says:

    Moran: Ain’t no god, so all of you IDiots are wrong.

    That’s his “argument” in a nutshell. He is a shrill, bigoted little man, and that makes him, ultimately, irrelevant.

  6. 6
    johnnyb says:

    I have a feeling that Dr. Moran agrees with us but can’t bring himself to say it. You all might be interested in a response I gave to another article by Dr. Moran which talked more about neutral theory. My summation of it was this:

    At the end of the day, if you read Dr. Moran’s article really closely, what is really true is that the ID’ers are actually using language quite correctly and legitimately, but it bothers Dr. Moran that they are not fitting into his stereotype of their behavior. ID is not attacking a straw man precisely because its arguments are aimed at Darwinian evolution, and not evolutionary theory as a whole. ID’ers opt for precision of language, specifying exactly what it is that is being disagreed with. The only way that ID-skeptics like Dr. Moran can criticize is by pretending that we mean something other than what we precisely specify.

    His problem isn’t that we are wrong, but that we are right, and we don’t fit into his stereotypes where he wants us to be.

    In another post, Moran agrees that a certain type of mutation is triggered by the conditions that necessitate the mutation, but can’t bring himself to say that they were guided. So he invented a straw-man version of what I was saying in order to claim victory.

    In other words, Moran seems to be well aware of what our arguments are, and what they imply, but he can’t bring himself to pull all of it together and admit the obvious (that, at the very least, our criticisms are on-track), and so instead he invents straw-man versions of whatever he reads and handily defeats them.

  7. 7
    Mung says:

    As anyone who has read Darwin’s Doubt knows, this is a complete travesty of Meyer’s argument. Professor Moran is displaying his ignorance here.

    I don’t think Larry Moran is ignorant, I think he’s just biased. Hard to tell the two apart at times.

  8. 8
    Larry Moran says:

    As anyone who has read Darwin’s Doubt knows, this is a complete travesty of Meyer’s argument. Professor Moran is displaying his ignorance here.

    Vincent Torley posted a quotation from Darwin’s Doubt and said that it “struck me as the best case I’ve ever seen for Intelligent Design, in 200 words or less.”

    I responded by pointing out that the quotation was nothing more than an attack on evolution—or at least Meyer’s strawman version of evolution. It did not present any case at all for ID except by implication assuming that evolution is wrong and ID is the only other choice.

    Aside from that major flaw, the strawman version of evolution is the adaptationist view popularized by Richard Dawkins who is specifically mentioned in the quotation. Not only that, the sentences immediately after the quotation refers to The God Delusion and the “New Atheist philosophy” so we know what Meyer has in mind.

    Now Vincent wants to move the goalposts and discuss a different version of Stephen Meyer’s defense of Intelligent Design Creationism. One that can be found elsewhere in the book and in other writings by Meyer.

    Does that mean he no longer stands by his original post as “A Succinct Case for Intelligent Design”?

  9. 9
    Larry Moran says:

    johnnyb said,

    ID is not attacking a straw man precisely because its arguments are aimed at Darwinian evolution, and not evolutionary theory as a whole. ID’ers opt for precision of language, specifying exactly what it is that is being disagreed with. The only way that ID-skeptics like Dr. Moran can criticize is by pretending that we mean something other than what we precisely specify.

    Let’s see if I understand you.

    What you (and Meyer) are saying is that if the false Darwinian version of evolution is wrong then Intelligent Design Creationism is correct. You say this even though you know full well that there’s another possibility; namely, that the real, complete, version of evolutionary theory might be correct.

    Is that what you mean?

    That seems like a very strange way to behave since you have been told time and time again that the version of evolution you are attacking is not the version that most scientists accept.

    Well, I least I can thank you for being honest about the fact that you know that what you are doing is deceptive and stupid.

  10. 10
    Mung says:

    Dr. Moran:

    Genetic Load
    Every newborn human baby has about 100 mutations not found in either parent. If most of our genome contained functional sequence information, then this would be an intolerable genetic load. Only a small percentage of our genome can contain important sequence information suggesting strongly that most of our genome is junk.

    Genetic load is a number between 0 and 1 and it measures the extent to which the average individual in a population is inferior to the best possible kind of individual.

    https://www.blackwellpublishing.com/ridley/a-z/Genetic_load.asp

    What is the best possible kind of human?

    Presumably each parent of the baby also had 100 mutations not found in either parent. So why is either parent better than their child?

  11. 11
    Barry Arrington says:

    Moran,

    What you (and Meyer) are saying is that if the false Darwinian version of evolution is wrong then Intelligent Design Creationism is correct. You say this even though you know full well that there’s another possibility; namely, that the real, complete, version of evolutionary theory might be correct.

    For someone who purports to have an understanding of ID solid enough to critique it, you display a remarkable inability to articulate its basic claims.

  12. 12
    Mung says:

    Larry M:

    You say this even though you know full well that there’s another possibility; namely, that the real, complete, version of evolutionary theory might be correct.

    Well, no. There is no such thing as “the real, complete, version of evolutionary theory,” so it cannot be a possibility. Nice try though.

  13. 13
    Larry Moran says:

    johnnyb says,

    In other words, Moran seems to be well aware of what our arguments are, and what they imply, but he can’t bring himself to pull all of it together and admit the obvious (that, at the very least, our criticisms are on-track) …

    Some of your criticisms are on track. Indeed, I agree with some of them, especially some of the points raised by Michael Behe.

    I certainly agree with the main IDiot criticism of evolution; namely, that random mutations and natural selection cannot account for all of evolution. But just about every knowledgeable evolutionary biologist would agree with that so it’s hardly big news today. (It may have been big news fifty years ago.)

  14. 14
    bFast says:

    Dr.Larry Moran (evolution be praised) is a painfully disrespectful human being who doesn’t understand his own theory.

    I tried to have a dialog with him recently where I charge that Neutral Theory is simply a subset of neo-Darwinian theory. In the conversation he asked me to explain why positive mutations sometimes don’t get fixed in a population. I provided a correct answer for him, causing him to label me an IDiot.

    If a college professor treats online bloggers this way, I am sure that he treats his students at the University of Toronto the same way. If this interaction, calling a student an idiot, had been in the context of a University of Toronto program, I would have filed a formal complaint.

    Mr. Moran — you were wrong sir! My answer was correct, and you responded to it by calling me an IDiot. That makes you an idiot, does it not? I challenge you to prove that the answer I provided to you which produced your rant was wrong. I challenge you that if you cannot do so, you give up the label “IDiot” forever (in public and private).

  15. 15
    Barry Arrington says:

    Moran,

    “IDiot”? Really. Aren’t you an adult? You look like an adult in that picture on the homepage of your blog. But you kinda sound like a second grader.

    I’m not asking you to stop though. I mean if credentialed evolutionary biologists like yourself think such infantile tactics are necessary to make your case, by all means keep doing it. Somehow, I can’t imagine Newton, Einstein or Godel calling their opponents poopyheads.

  16. 16
    Barry Arrington says:

    Moran, Lewis was probably thinking about someone like you:

    What inclines me now to think that you may be right in regarding [evolution] as the central and radical lie in the whole web of falsehood that now governs our lives, is not so much your arguments against it as the fanatical and twisted attitudes of its defenders.

    C.S. Lewis, Collected Letters, to Bernard Acworth, 13 September 1951

  17. 17
    Mapou says:

    You know. I don’t get it. Why do we argue with a dishonest, inconsequential, and insulting imbecile like Larry Moran?

  18. 18
    Mung says:

    We’re not arguing with him, we’re trying to infect him with a meme that he will inadvertently pass on to his students.

  19. 19
    Silver Asiatic says:

    BA

    I mean if credentialed evolutionary biologists like yourself think such infantile tactics are necessary to make your case, by all means keep doing it. Somehow, I can’t imagine Newton, Einstein or Godel calling their opponents poopyheads.

    LOL – exactly. Keep up the little temper tantrums. We couldn’t ask for a better example of our opposition.

    Great argument – we’re IDiots and ‘creationists’. Ooooh, that just hurts too much and we’re going to have to run home to mommy now.

  20. 20
    Larry Moran says:

    Dear bFast,

    Please provide a link to the discussion where you were right about modern evolutionary theory and I was wrong.

    I’m more than happy to apologize if what you say is correct.

  21. 21
    bFast says:

    Moran, “I certainly agree with the main IDiot criticism of evolution; namely, that random mutations and natural selection cannot account for all of evolution.”

    Like, what do you propose beyond random mutations and natural selection? It appears that your entire claim is that natural selection plays very little role. Your entire claim, therefore, seems to be that random mutations account for all of evolution. Or do you have a thought that is deeper than “neutral theory”?

    Oh yea, you have the tought that it is appropriate to call people idiots, even when you are wrong.

  22. 22
    Larry Moran says:

    Barry Arrington says,

    I mean if credentialed evolutionary biologists like yourself think such infantile tactics are necessary to make your case, by all means keep doing it.

    Mapou says,

    Why do we argue with a dishonest, inconsequential, and insulting imbecile like Larry Moran?

  23. 23
  24. 24
    Larry Moran says:

    bFast says,

    Like, what do you propose beyond random mutations and natural selection?

    Do you honestly not know the answer to this question after I’ve spent 25 years explaining it to IDiots like you?

    It appears that your entire claim is that natural selection plays very little role.

    Natural selection plays a dominant role in adaptation and in the evolution of many, but not all, complex structures. However, it’s only responsible for a tiny percentage of all fixations during evolution.

    But I think you already know that. Maybe you’ve forgotten?

    Or do you have a thought that is deeper than “neutral theory”?

    Yes, I have at least three other thoughts.

    1. Random genetic drift

    2. Evolution by Accident

    3. Mutationism

    HTH HAND

  25. 25
    Larry Moran says:

    bFast,

    You linked to a comment where you said.

    The topic of this post is whether there is anything to the theory of evolution beyond random variation and natural selection. I contend that there is not

    Do you still believe that?

    If you do, then you are an IDiot.

  26. 26
    ppolish says:

    “Third Way Evolution” now up to 51 members from 14 countries. Just FYI
    http://www.thethirdwayofevolution.com/people/P0
    Lot of smart cookies who know Modern Synthesis = FAIL

  27. 27
    sean samis says:

    Dr. Meyer’s case for intelligent design is badly flawed.

    In Premise One, the thoroughness of the search for materialistic causes is exaggerated. Our current understanding of how the genetic code works and drives development is too incomplete and too young to have been “thoroughly searched”.

    Premise Two is basically irrelevant.

    The Conclusion should be that intelligent design constitutes an intellectually defective explanation because it relies on the permanence of our current ignorance of natural processes and offers not even a tentative way to test for the existence of a designing intelligence. ID seems causally adequate but it is also scientifically sterile: it’s an intellectual dead-end; it provides no avenues forward; it makes no actionable predictions; it cannot even suggest how to find the most critical evidence for it: the designing intelligence.

    Dependency on “present knowledge” is the key weakness. Dr Meyers give us essentially an argument from ignorance. Because present knowledge is always changing, any theory predicated on our continuing ignorance is never the “best explanation”.

    If all that is true (it is.) then this question might appear to have no “best explanation”; if so what do we do? Lacking a “best explanation” would mean we should continue exploring all explanations until one distinguishes itself. But given this situation, the distinguishing feature of evolution comes to the fore: it provides research targets; it requires and predicts things to look for and experiments to perform.

    sean s.

  28. 28
    Mung says:

    bFast, I have to agree with Larry on this one. Everyone know that natural selection alone isn’t enough, even Larry:

    Nobody is denying that natural selection is important but many of us think that natural selection alone cannot account for the complexity and variety of life that we see around us today.

    Natural selection alone is not enough. All the leading textbooks on evolutionary biology say so.

  29. 29
    Mung says:

    sean samis:

    Our current understanding of how the genetic code works and drives development is too incomplete and too young…

    What’s this nonsense about some “genetic code.” Is it like the Bible Code?

  30. 30
    ppolish says:

    Mung, “Natural Selection” is s concept that needs to be retired. Not just an overrated concept, but a wrong one.

  31. 31
    bFast says:

    Mr. Moran,

    I have decided to mirror your bad behavior. Every future time you post in a dialog with me, if you use the derogatory term (you know which one I mean) to reference me, any of my colleagues, or us as a group, then I will use a similar derogatory term in reference to you.

    Moderator: Please either take the position of welcoming this “turn about is fair play” approach, or simply delete every pejorative entry on Mr. Moran’s part. Please do not block Mr. Moran altogether.

    Mr. Moran, you seem to confuse IDers holding your pet theories with the same respect as you do, with us not understanding them. I assure you, I have a pretty reasonable grasp of these theories that you site.

    Wikipedia defines “neutral theory” as follows: “The neutral theory of molecular evolution holds that at the molecular level most evolutionary changes and most of the variation within and between species is not caused by natural selection but by random drift of mutant alleles that are neutral.” I would define neutral theory as “the study of what happens to genetic mutation that are neither promoted nor deterred by natural selection.”

    In one of your links you said, “Whenever you hear someone denying the role of chance in evolution you can be certain they are ignoring random genetic drift.” The ID community, in general, very much recognizes that the current synthesis is a chance-driven theory. But what is the role of chance? For the current synthesis* to be true, chance must be a very foresighted magician.

    “Random Genetic Drift”, the study of changes in allele frequency when natural selection neither promotes, nor deters the allele. According to my definition, therefore, Random Genetic Drift is a subset of “Neutral Theory.”

    “Evolution by Accident”. This is a term I have not heard before. It appears to be a tight simile to Gould’s “contingency” view. It is as it is because it happens to be that way — no strategy involved. In my understanding of the current synthesis, all mutations are accidental. Most mutations have no effect on the phenotype of the organism (because according to the theory 90% of DNA is junk). Those mutations that do have an affect on the phenotype of an organism often change the organism in a way that makes no substantive difference to the organism’s ability to survive. Again, they follow the rules of neutral theory. Some make a very small difference to the organism’s ability to survive. These are put in a camp that I understand gets called “near neutral theory”.

    Mutationism — there is a term I have not encountered before. Wikipedia says, “Mutationism refers to historical and contemporary views of evolution that emphasize the role of mutation and that are understood as alternatives to Darwinism. In the mutationist view, change may occur in discrete jumps.” ‘Sounds like foresighted mutations happening, to me. I like mutationism. I find that it fits with my view of what actually happened. You may call it “goddidit”.

    * I use the term “current synthesis” to include all of the twists and variations on naturalistic evolution that have been developed over the years.

  32. 32
    bFast says:

    ‘Love this term “mutationist”. It fits my grid. My view of how life got from stew to you is that at many points along the way someone interjected groups of mutations into existing organism. (Yes, I hold to universal common descent.) According to Mr. Moran, that makes me a “mutationist”. I accept his accusation. I am a mutationist, but I can change — if evidence leads me elsewhere.

  33. 33
    bFast says:

    Oh, does “neutral theory” have any meaningful explanatory power? I think it does. I think that it is the best explanation that the naturalists have put forth to explain Haldane’s dilemma.

  34. 34
    bornagain77 says:

    As to Neutral Evolution:

    Kimura (1968) developed the idea of “Neutral Evolution”. If “Haldane’s Dilemma” is correct, the majority of DNA must be non-functional.

    Neutral theory was not developed because of any empirical observation, but was developed because it was forced upon Darwinism by the mathematics. (i.e. neutral theory is actually the result of a theoretical failure of Darwinism within mathematics!)

    Haldane’s Dilemma
    Excerpt: Haldane was the first to recognize there was a cost to selection which limited what it realistically could be expected to do. He did not fully realize that his thinking would create major problems for evolutionary theory. He calculated that in man it would take 6 million years to fix just 1,000 mutations (assuming 20 years per generation).,,, Man and chimp differ by at least 150 million nucleotides representing at least 40 million hypothetical mutations (Britten, 2002). So if man evolved from a chimp-like creature, then during that process there were at least 20 million mutations fixed within the human lineage (40 million divided by 2), yet natural selection could only have selected for 1,000 of those. All the rest would have had to been fixed by random drift – creating millions of nearly-neutral deleterious mutations. This would not just have made us inferior to our chimp-like ancestors – it surely would have killed us. Since Haldane’s dilemma there have been a number of efforts to sweep the problem under the rug, but the problem is still exactly the same. ReMine (1993, 2005) has extensively reviewed the problem, and has analyzed it using an entirely different mathematical formulation – but has obtained identical results.
    John Sanford PhD. – “Genetic Entropy and The Mystery of the Genome” – pg. 159-160

    Walter ReMine on Haldane’s Dilemma – interview
    http://kgov.com/Walter-ReMine-on-Haldanes-Dilemma

    Kimura’s Quandary
    Excerpt: Kimura realized that Haldane was correct,,, He developed his neutral theory in response to this overwhelming evolutionary problem. Paradoxically, his theory led him to believe that most mutations are unselectable, and therefore,,, most ‘evolution’ must be independent of selection! Because he was totally committed to the primary axiom (neo-Darwinism), Kimura apparently never considered his cost arguments could most rationally be used to argue against the Axiom’s (neo-Darwinism’s) very validity.
    John Sanford PhD. – “Genetic Entropy and The Mystery of the Genome” – pg. 161 – 162

    A graph featuring ‘Kimura’s Distribution’ being ‘properly used’ is shown in the following video:

    Evolution Vs Genetic Entropy – Andy McIntosh – video
    https://vimeo.com/91162565

    John Sanford has indeed backed up his claim that the mathematics of population genetics could be used to argue against the very validity of Darwinism.

    Using Numerical Simulation to Test the Validity of Neo-Darwinian Theory – 2008
    Abstract: Evolutionary genetic theory has a series of apparent “fatal flaws” which are well known to population geneticists, but which have not been effectively communicated to other scientists or the public. These fatal flaws have been recognized by leaders in the field for many decades—based upon logic and mathematical formulations. However population geneticists have generally been very reluctant to openly acknowledge these theoretical problems, and a cloud of confusion has come to surround each issue.
    Numerical simulation provides a definitive tool for empirically testing the reality of these fatal flaws and can resolve the confusion. The program Mendel’s Accountant (Mendel) was developed for this purpose, and it is the first biologically-realistic forward-time population genetics numerical simulation program. This new program is a powerful research and teaching tool. When any reasonable set of biological parameters are used, Mendel provides overwhelming empirical evidence that all of the “fatal flaws” inherent in evolutionary genetic theory are real. This leaves evolutionary genetic theory effectively falsified—with a degree of certainty which should satisfy any reasonable and open-minded person.
    http://www.icr.org/i/pdf/techn.....Theory.pdf

    Using Numerical Simulation to Better Understand Fixation Rates, and Establishment of a New Principle – “Haldane’s Ratchet” – Christopher L. Rupe and John C. Sanford – 2013
    Excerpt: We then perform large-scale experiments to examine the feasibility of the ape-to-man scenario over a six million year period. We analyze neutral and beneficial fixations separately (realistic rates of deleterious mutations could not be studied in deep time due to extinction). Using realistic parameter settings we only observe a few hundred selection-induced beneficial fixations after 300,000 generations (6 million years). Even when using highly optimal parameter settings (i.e., favorable for fixation of beneficials), we only see a few thousand selection-induced fixations. This is significant because the ape-to-man scenario requires tens of millions of selective nucleotide substitutions in the human lineage.
    Our empirically-determined rates of beneficial fixation are in general agreement with the fixation rate estimates derived by Haldane and ReMine using their mathematical analyses. We have therefore independently demonstrated that the findings of Haldane and ReMine are for the most part correct, and that the fundamental evolutionary problem historically known as “Haldane’s Dilemma” is very real.
    Previous analyses have focused exclusively on beneficial mutations. When deleterious mutations were included in our simulations, using a realistic ratio of beneficial to deleterious mutation rate, deleterious fixations vastly outnumbered beneficial fixations. Because of this, the net effect of mutation fixation should clearly create a ratchet-type mechanism which should cause continuous loss of information and decline in the size of the functional genome. We name this phenomenon “Haldane’s Ratchet”.
    http://media.wix.com/ugd/a704d.....fa9c20.pdf

    Here is a recent article, not associated with Dr. Sanford, that also found a insurmountable barrier in the theoretical framework of Darwinism:

    Neo-Darwinism’s Catch-22: Before Evolving New Features, Organisms Would Be Swamped by Genetic Junk – Casey Luskin – April 10, 2015
    Excerpt: A new peer-reviewed paper in the journal Complexity presents a computational model of evolution which shows that evolving new biological structures may be deterred by an unavoidable catch-22 problem.,,,
    This is a bit complex — let’s go over it again. Darwinian evolution either (1) produces nothing new, or (2) it’s destined to produce boatloads of deadly junk. In the case of (2), the reward for trying new things is high compared to the cost of building new structures. But in order for the ratio to be high enough for complexity to increase, the cost of building new things must be negligible. Novelties proliferate, but the fraction,, that’s vestigial grows, and the organism is eventually swamped and overwhelmed by harmful vestigial features. However, if you try to avoid the problem of (2) by making the reward-to-cost ratio lower, as in (1), then nothing new ever evolves.
    The authors think real biological organisms are closer to position (1). Indeed, study in the field of systems biology increasingly finds that biological systems contain very little junk.,,,
    per ENV

    There are also other strong theoretical and empirical reasons to believe neutral theory is incorrect:

    Unexpectedly small effects of mutations in bacteria bring new perspectives – November 2010
    Excerpt: Most mutations in the genes of the Salmonella bacterium have a surprisingly small negative impact on bacterial fitness. And this is the case regardless whether they lead to changes in the bacterial proteins or not.,,, using extremely sensitive growth measurements, doctoral candidate Peter Lind showed that most mutations reduced the rate of growth of bacteria by only 0.500 percent. No mutations completely disabled the function of the proteins, and very few had no impact at all. Even more surprising was the fact that mutations that do not change the protein sequence had negative effects similar to those of mutations that led to substitution of amino acids. A possible explanation is that most mutations may have their negative effect by altering mRNA structure, not proteins, as is commonly assumed.
    http://www.physorg.com/news/20.....teria.html

    “Moreover, there is strong theoretical reasons for believing there is no truly neutral nucleotide positions. By its very existence, a nucleotide position takes up space, affects spacing between other sites, and affects such things as regional nucleotide composition, DNA folding, and nucleosome building. If a nucleotide carries absolutely no (useful) information, it is, by definition, slightly deleterious, as it slows cell replication and wastes energy.,, Therefore, there is no way to change any given site without some biological effect, no matter how subtle.”
    – John Sanford – Genetic Entropy and The Mystery of The Genome – pg. 21 – Inventor of the ‘Gene Gun’

    etc.. etc..

    here are some supplemental comments/quips as to neutral theory:

    Majestic Ascent: Berlinski on Darwin on Trial – David Berlinski – November 2011
    Excerpt: The publication in 1983 of Motoo Kimura’s The Neutral Theory of Molecular Evolution consolidated ideas that Kimura had introduced in the late 1960s. On the molecular level, evolution is entirely stochastic, and if it proceeds at all, it proceeds by drift along a leaves-and-current model. Kimura’s theories left the emergence of complex biological structures an enigma, but they played an important role in the local economy of belief. They allowed biologists to affirm that they welcomed responsible criticism. “A critique of neo-Darwinism,” the Dutch biologist Gert Korthof boasted, “can be incorporated into neo-Darwinism if there is evidence and a good theory, which contributes to the progress of science.”
    By this standard, if the Archangel Gabriel were to accept personal responsibility for the Cambrian explosion, his views would be widely described as neo-Darwinian.
    http://www.evolutionnews.org/2.....53171.html

    With the adoption of the ‘neutral theory’ of evolution by many prominent Darwinists, and the casting under the bus of Natural Selection as a major player in evolution, William J Murray quipped,,,

    “One wonders what would have become of evolution had Darwin originally claimed that it was simply the accumulation of random, neutral variations that generated all of the deeply complex, organized, interdependent structures we find in biology? Would we even know his name today?
    What exactly is Darwin really famous for now? Advancing a really popular, disproven idea (of Natural Selection), along the lines of Luminiferous Aether?
    Without the erroneous but powerful meme of “survival of the fittest” to act as an opiate for the Victorian intelligentsia and as a rationale for 20th century fascism, how might history have proceeded under the influence of the less vitriolic maxim, “Survival of the Happenstance”?”
    – William J Murray

    Ann Gauger on genetic drift – August 2012
    Excerpt: The idea that evolution is driven by drift has led to a way of retrospectively estimating past genetic lineages. Called coalescent theory, it is based on one very simple assumption — that the vast majority of mutations are neutral and have no effect on an organism’s survival. (For a review go here.) According to this theory, actual genetic history is presumed not to matter. Our genomes are full of randomly accumulating neutral changes. When generating a genealogy for those changes, their order of appearance doesn’t matter. Trees can be drawn and mutations assigned to them without regard to an evolutionary sequence of genotypes, since genotypes don’t matter.
    http://www.uncommondescent.com.....tic-drift/

    Here is a Completely Different Way of Doing Science – Cornelius Hunter PhD. – April 2012
    Excerpt: But how then could evolution proceed if mutations were just neutral? The idea was that neutral mutations would accrue until finally an earthquake, comet, volcano or some such would cause a major environmental shift which suddenly could make use of all those neutral mutations. Suddenly, those old mutations went from goat-to-hero, providing just the designs that were needed to cope with the new environmental challenge. It was another example of the incredible serendipity that evolutionists call upon.
    Too good to be true? Not for evolutionists. The neutral theory became quite popular in the literature. The idea that mutations were not brimming with cool innovations but were mostly bad or at best neutral, for some, went from an anathema to orthodoxy. And the idea that those neutral mutations would later magically provide the needed innovations became another evolutionary just-so story, told with conviction as though it was a scientific finding.
    Another problem with the theory of neutral molecular evolution is that it made even more obvious the awkward question of where these genes came from in the first place.
    http://darwins-god.blogspot.co.....ay-of.html

    as to drift specifically

    Thou Shalt Not Put Evolutionary Theory to a Test – Douglas Axe – July 18, 2012
    Excerpt: “For example, McBride criticizes me for not mentioning genetic drift in my discussion of human origins, apparently without realizing that the result of Durrett and Schmidt rules drift out. Each and every specific genetic change needed to produce humans from apes would have to have conferred a significant selective advantage in order for humans to have appeared in the available time (i.e. the mutations cannot be ‘neutral’). Any aspect of the transition that requires two or more mutations to act in combination in order to increase fitness would take way too long (greater than 100 million years).
    My challenge to McBride, and everyone else who believes the evolutionary story of human origins, is not to provide the list of mutations that did the trick, but rather a list of mutations that can do it. Otherwise they’re in the position of insisting that something is a scientific fact without having the faintest idea how it even could be.”
    – Doug Axe PhD.
    per Evolution News and Views

    Natural Selection Struggles to Fix Advantageous Traits in Populations – Casey Luskin – October 23, 2014
    Excerpt: Michael Lynch, an evolutionary biologist at Indiana University,, writes that “random genetic drift can impose a strong barrier to the advancement of molecular refinements by adaptive processes.”2 He notes that the effect of drift is “encouraging the fixation of mildly deleterious mutations and discouraging the promotion of beneficial mutations.”3 Likewise, Eugene Koonin, a leading scientist at the National Institutes of Health, explains that genetic drift leads to “random fixation of neutral or even deleterious changes.”4
    http://www.evolutionnews.org/2.....90571.html

  35. 35
    bornagain77 says:

    Of related note to Sanford’s work:

    Biological Information – Mutation Count & Synergistic Epistasis (mutation accumulation) 1-17-2015 by Paul Giem – video
    https://www.youtube.com/watch?v=6gdoZk_NbmU

  36. 36
    Mung says:

    Excuse me, but isn’t Dr. Moran being just a bit disingenuous, perhaps even hypocritical?

    While berating IDiots for being too selectionist minded, his arguments against ID and for junk DNA are, guess what?

    If you said selectionist, you win.

  37. 37
    bFast says:

    Larry Moran,

    “The topic of this post is whether there is anything to the theory of evolution beyond random variation and natural selection. I contend that there is not

    Do you still believe that?”

    Mr. Moran, there is nothing to the theory of “genetic drift” but random variation. That this the beginning and the end of the theory.

    Of everything you have sited so far, the only thing that may step beyond “random variation and natural selection” is mutationism. Mutationism steps beyond random variation only if those mutations are foresighted. If they are foresighted, then who had the foresight?

    Mr Moran, there is nothing to the theory of evolution beyond random variation and natural selection. Prove me wrong, rather than name calling.

  38. 38
    Mung says:

    bfast, apparenly Dr. Moran read you as having written:

    …there is nothing to the theory of evolution beyond random variation plus natural selection.

    The “and” you used led him to believe the two terms were always connected. Might be a Canadian thing.

    Think of it s a truth table. Evolution is true only if random variation and natural selection is true.

    What you should have said is:

    The role of selection is far less important in modern evolutionary theory now than in the past. It is now a well known fact, taught in all the leading textbooks on evolutionary biology, that chance is the dominant factor in evolution. However, there is still some role for selection, especially when arguing against IDiots.

  39. 39
    Mung says:

    It’s no mystery. When an IDiot argues that evolution is chance-based haul out selection. When an IDiot hauls out selection say chance did it. Either way the IDiot is wrong, and that’s whey they are IDiots.

  40. 40
    Daniel King says:

    In short: the scientific inferences we can make about non-human designers are extremely modest.

    Hopefully, those inferences, scientific or not, resemble nothing like human design. Let’s have those inferences!

  41. 41
    mike1962 says:

    Larry Moran: I certainly agree with the main IDiot criticism of evolution;

    Just curious, but why must you refer to ID proponents as “IDiots?” Do you really think they are idiots? Are you suffering from constipation? Did your dog just die? Are you just an asshat? What?

    And do you call people “IDiots” to their faces?

    Have a nice weekend.

  42. 42
    Mung says:

    Who cares why Larry calls people IDiots? My theory is that he gets a twinge in a certain part of his anatomy. But that’s neither here nor there.

    Does he have an argument? Someone can be a complete [certain part of the male anatomy] and still have an argument.

    His argument seems to be that IDiots argue against Darwinian evolution for the wrong reason, or that they argue as if evolution is Darwinian, which it isn’t [unless it is].

  43. 43
    ppolish says:

    I was once a Theistic Evolutionist – the largest denomination of evolutionists on the globe. Largest and most complete/explanatory too btw.

    I suppose Larry would have called me an idiot. But now Larry considers me an IDiot. I like the new insult a lot better. Heck, it isn’t really even an insult when you get right down to it.

  44. 44
    Mapou says:

    ‘IDiot’ is an insult. ‘Evotard’ is an insult. ‘Creationist’ is an insult only in the mind of an evotard. But do not fear, creationists. Soon, ‘evolutionist’ will also be an insult. Then the Darwin era will be known as the era of dumb science and will become just a footnote in the annals of science history.

  45. 45
    bFast says:

    Mung (39), you hit the proverbial nail on the head! A bit of a dangerous context for a typo (whey should be why).

    Mapou, “evotard”, love it! I began to search it on google when I realized what you were saying. Oh man! Its already in the urban dictionary.

  46. 46
    Mapou says:

    Evotard. Yeah, I wish I could take credit for inventing it. It’s brilliant. It’s almost shakespearean. 😀

  47. 47
    Jim Smith says:

    the first person to demonstrate that Lynch’s incredible claim was problematic was Douglas Axe… In the end, he traced Lynch and Abegg’s claims to two erroneous equations, both of which were based on erroneous assumptions

    Is there a reference for Douglas Axe’s work on neutral theory, and any subsequent replies to critics?

    Thanks

  48. 48
    Larry Moran says:

    bFast says,

    Mr. Moran, there is nothing to the theory of “genetic drift” but random variation. That this the beginning and the end of the theory.

    How can you spend so much time and effort criticising evolution when you clearly don’t understand it?

    Only an IDiot would do that.

    Why don’t you read an introductory textbook on evolution before you embarrass yourself any further?

  49. 49
    Larry Moran says:

    mike1962 asks,

    Just curious, but why must you refer to ID proponents as “IDiots?” Do you really think they are idiots?

    Hmmm … many of you have had the opportunity on this thread to demonstrate that you are capable of learning something about evolution and why the word “Darwinist” is an insult.

    You have declined that opportunity. After reading the comments, and the posts on the leading ID blogs, the only logical conclusion is that the vast majority of you are, indeed, IDiots.

    I suspect that there may be one or two Intelligent Design Creationists out there who understand the science they are criticising but they are afraid to speak up. Your movement will never be credible until you start policing yourselves and eliminate the kooks who give ID such a bad reputation.

  50. 50
    bornagain77 says:

    of related interest:

    Anthony Jack, Why Don’t Psychopaths Believe in Dualism? – video (14 minute 20 seconds mark)
    http://www.youtube.com/watch?l.....zOk#t=862s

    Why Don’t Psychopaths Believe in Dualism?
    The Role of Opposing Brain Networks Anthony Jack (Case Western Reserve University, Cognitive Science, Cleveland, OH
    In a theoretical paper linking the attribution of phenomenal consciousness to moral cognition, Robbins and Jack (Philosophical Studies, 2006) predicted that psychopaths would not perceive the problem of consciousness. New experimental evidence is presented which supports this claim: in a group of undergraduates it was found that support for a naturalistic view of the mind is positively correlated with the primary psychopathic trait of callousness.
    http://www.sonoran-sunsets.com/goinggreen.html

    Christians respond better to psychiatric treatment than atheists: – July 21, 2013
    Excerpt: “Our work suggests that people with a moderate to high level of belief in a higher power do significantly better in short-term psychiatric treatment than those without, regardless of their religious affiliation. Belief was associated with not only improved psychological well-being, but decreases in depression and intention to self-harm,” explained Rosmarin.
    The study looked at 159 patients, recruited over a one-year period. Each participant was asked to gauge their belief in God as well as their expectations for treatment outcome and emotion regulation, each on a five-point scale. Levels of depression, well being, and self-harm were assessed at the beginning and end of their treatment program.
    http://www.uncommondescent.com.....are-crazy/

    Christians happier than atheists – on Twitter – June 28 2013
    Excerpt: Two doctoral students in social psychology and an adviser analyzed the casual language of nearly 2 million tweets from more than 16,000 active users to come up with their findings, which were published in Social Psychological and Personality Science.
    The team identified subjects by finding Twitter users who followed the feeds of five prominent public figures. In the case of Christians, those select five were Pope Benedict XVI, Joel Osteen, Rick Warren, conservative political commentator Dinesh D’Souza and Joyce Meyer, an evangelical author and speaker.
    In the case of atheists, the five followed feeds included Richard Dawkins, Sam Harris, Christopher Hitchens, Monica Salcedo and Michael Shermer – the latter two respectively being a self-described “fiercely outspoken atheist” blogger, and a science writer who founded The Skeptics Society.
    With the help of a text analysis program, the researchers found that Christians tweet with higher frequency words reflecting positive emotions,,,,
    Christians, they found, are more likely to use words like “love,” “happy” and “great”; “family,” “friend” and “team.”
    Atheists win when it comes to using words like “bad,” “wrong,” and “awful”,,,
    http://religion.blogs.cnn.com/.....n-twitter/

    Atheism and health
    A meta-analysis of all studies, both published and unpublished, relating to religious involvement and longevity was carried out in 2000. Forty-two studies were included, involving some 126,000 subjects. Active religious involvement increased the chance of living longer by some 29%, and participation in public religious practices, such as church attendance, increased the chance of living longer by 43%.[4][5]
    http://www.conservapedia.com/Atheism_and_health

  51. 51
    daveS says:

    BA77,

    support for a naturalistic view of the mind is positively correlated with the primary psychopathic trait of callousness.
    http://www.sonoran-sunsets.com/goinggreen.html

    That “Going Green” page is certainly interesting (I don’t use, but I am also in favor of marijuana legalization).

    Has the Anthony Jack work on dualism and psychopaths been published yet?

  52. 52
    CJYman says:

    Just a quick comment for Larry from an IDiot willing to learn:

    I think it would do everyone well to define the key term here … ‘random.’ I understand that ‘random’ is usually used in reference to fitness. However, ‘random’ is a word with some equivocation potential. In the context of fitness does it merely mean ‘unguided’ (in either a teleological sense or in a law-like sense) or ‘equal probability’ or something else? Which genetic variations according to modern evolutionary theory are non-random? Are these variations then ‘guided’ by the structure of life itself? If so, does this begin to approach the idea that life engineers its own evolution?

    Is ‘random’ to be equated with ‘chance?’ Here is a list of how chance can be popularly used:

    1. Referencing a lack of correlation
    2. Describing a lack of knowledge (measure of ignorance)
    3. Description of ignorance of variables (part of #2)
    4. Reference to a uniform probability distribution (equilibrium state)

    Or, is something else meant by ‘random’ and what is the demarcation criteria for determining random vs. non-random variations? How is a variation tested for ‘randomness?’ And, in the end, what significant difference does ‘random’ or ‘non-random’ make to any theory of evolution Darwinian or otherwise?

    Please do carry on with the educational portion of the show.

  53. 53
    bornagain77 says:

    The Phenomenal Stance Revisited – Anthony I. Jack & Philip Robbins – 2012
    Abstract: In this article, we present evidence of a bidirectional coupling between moral concern and the attribution of properties and states that are associated with experience (e.g., conscious awareness, feelings). This coupling is also shown to be stronger with experience than for the attribution of properties and states more closely associated with agency (e.g., free will, thoughts). We report the results of four studies. In the first two studies, we vary the description of the mental capacities of a creature, and assess the effects of these manipulations on moral concern. The third and fourth studies examine the effects of variations in moral concern on attributions of mindedness. Results from the first two studies indicate that moral concern depends primarily on the attribution of experience, rather than the attribution of agency. The results of the latter two studies demonstrate that moral concern increases attributions of mindedness, and that this effect is stronger for attributions of experience than for attributions of agency.
    http://philpapers.org/rec/JACTPS

    The phenomenal stance – Philip Robbins & Anthony I. Jack – 2006
    Abstract: Cognitive science is shamelessly materialistic. It maintains that human beings are nothing more than complex physical systems, ultimately and completely explicable in mechanistic terms. But this conception of humanity does not fit well with common sense. To think of the creatures we spend much of our day loving, hating, admiring, resenting, comparing ourselves to, trying to understand, blaming, and thanking — to think of them as mere mechanisms seems at best counterintuitive and unhelpful. More often it may strike us as ludicrous, or even abhorrent.,,,
    http://philpapers.org/rec/ROBTPS

  54. 54
    daveS says:

    Thanks, BA77.

  55. 55
    JimFit says:

    I think real randomness can exist only in a state of Nothingness, why? Because something random by definition is something that isn’t determined by anything nor determines something, randomness can exist only in the abscence of everything since there would be no cause to break the law. Randomness doesn’t exist, what it exists is the lack of information for an event, that’s pseudorandomness not randomness.

  56. 56
    Mung says:

    CJYman,

    When the word random is used to describe mutation events what is meant is random with regard to fitness. And fitness is a selectionist term. So at it’s core, all evolution is selectionist.

    When random is used with respect to genetic drift. it simply means stochastic. Refer to sampling theory.

    Hope that helps.

  57. 57
    Jim Smith says:

    http://tonyjack.org/files/2013.....lism%20(1).pdf

    Uncorrected Proof. Jack, A.I. (2013) A scientific case for conceptual dualism 1
    A scientific case for conceptual dualism: The problem of consciousness and
    the opposing domains hypothesis.
    Anthony I. Jack
    Department of Cognitive Science, Case Western Reserve University
    To appear in:
    J. Knobe, T. Lombrozo & S. Nichols (Eds.)
    Oxford Studies in Experimental Philosophy (Vol. 1)
    Oxford University Press.

    we predicted that psychopaths
    would not be able to perceive the problem of consciousness.

    In a series of five experiments (Jack, in
    preparation), we found a highly replicable and robust negative correlation (r~-0.34) between
    belief in dualism and the primary psychopathic trait of callous affect7.

    Clearly these findings fit well with the hypothesis (Robbins and Jack, 2006) that
    psychopaths can’t see the problem of consciousness8. Taking these finding together with other
    work on dehumanization and the anti-social effects of denying the soul and free will, they
    present a powerful picture. When we see persons, that is, when we see others as fellow humans,
    then our percept is of something essentially non-physical nature. This feature of our psychology
    appears to be relevant to a number of other philosophical issues, including the tension between
    utilitarian principles and deontological concerns about harming persons (Jack et al., accepted),
    the question of whether God exists (Jack et al., under review-b), and the problem of free will9.

    Anthony Jack is a physicalist. In trying to develop a physical theory of consciousness he proposes that for most people the problem of consciousness, the appearance of dualism, is caused by different brain networks used for thinking about mechanisms (ie how the brain works) and for understanding social situations (ie how people feel). According to Jack, it isn’t a natural gap but a gap due to brain physiology and psychopaths lack social thinking (are callous) so they don’t see the problem.

  58. 58
    Mung says:

    For the record, I don’t think Larry Moran is a psychopath.

    Are you sure you’re in the right thread Jim?

    Dr. Moran, do you accept or reject the central tenet of Darwinian theory that variation is random with respect to fitness?

  59. 59
    ppolish says:

    Larry, Evotards should read an introductory textbook on probability. Unlike an introductory textbook on evolution, it is not fiction.

  60. 60
    daveS says:

    Jim Smith,

    Thanks for the helpful summary.

  61. 61
    bornagain77 says:

    Thanks Jim Smith for clearing that up. The papers I found didn’t seem quite right for the claim made in the video (i.e. people who do not believe in a soul are more psychopathic).

    Here are some, IMHO, well researched videos that make a strong case for the reality of the soul

    The Case for the Soul – InspiringPhilosophy – (4:03 minute mark, Brain Plasticity including Schwartz’s work) – Oct. 2014 – video
    The Mind is able to modify the brain (brain plasticity). Moreover, Idealism explains all anomalous evidence of personality changes due to brain injury, whereas physicalism cannot explain mind.
    https://www.youtube.com/watch?v=oBsI_ay8K70

    The Case for the Soul: Refuting Physicalist Objections – video
    Computers vs. Qualia, Libet and ‘Free won’t’, Split Brain (unified attention of brain despite split hemispheres, visual and motion information is shared between the two hemispheres despite the hemispheres being split),
    https://www.youtube.com/watch?v=GB5TNrtu9Pk

    Also, in direct contrast to ‘the selfish gene’, the following study shows that we are not nearly such helpless ‘victims of our genes’ as materialists would presuppose

    Scientists Finally Show How Your Thoughts Can Cause Specific Molecular Changes To Your Genes, – December 10, 2013
    Excerpt: “To the best of our knowledge, this is the first paper that shows rapid alterations in gene expression within subjects associated with mindfulness meditation practice,” says study author Richard J. Davidson, founder of the Center for Investigating Healthy Minds and the William James and Vilas Professor of Psychology and Psychiatry at the University of Wisconsin-Madison.
    “Most interestingly, the changes were observed in genes that are the current targets of anti-inflammatory and analgesic drugs,” says Perla Kaliman, first author of the article and a researcher at the Institute of Biomedical Research of Barcelona, Spain (IIBB-CSIC-IDIBAPS), where the molecular analyses were conducted.,,,
    the researchers say, there was no difference in the tested genes between the two groups of people at the start of the study. The observed effects were seen only in the meditators following mindfulness practice. In addition, several other DNA-modifying genes showed no differences between groups, suggesting that the mindfulness practice specifically affected certain regulatory pathways.
    http://www.tunedbody.com/scien.....ges-genes/

    also of interest to the reality of the soul:

    The insurmountable problem of ‘form/shape’ for neo-Darwinian explanations has now been demonstrated by a few different methods. (May 2015)
    http://www.uncommondescent.com.....ent-563822

  62. 62
    bFast says:

    Larry Moron (49)

    How can you spend so much time and effort criticising evolution when you clearly don’t understand it?

    Only an IDiot would do that.

    You, sir, claim to have the ability to articulate. Please articulate for me. I learn very well from examples and scenarios. Please show me an example, a scenario that shows genetic drift to be something more than random variation.

    Larry Moron, “the word “Darwinist” is an insult.” Huh? You may see it as such, but others don’t. ( http://www.thefreedictionary.com/Darwinism )
    I have oft pleaded with y’all to provide a better single term that differentiates between those who hold to naturalistic evolution and those who hold to UCD, as I do, but not to the naturalistic form. None has been forthcoming. Your brilliant colleagues can only come up with loaded terms like “evolutionist” or “scientist”.

    Larry Moron, if you think that our use of the term Darwinist (usually neo-Darwinist to respect random genetic variation) entitles you to use the term “IDiot”, well, by the same source as sited above, ( http://www.thefreedictionary.com/idiot )
    these two “insults” aren’t in the same camp. Rather, “idiot” is about equivalent to moron ( http://www.thefreedictionary.com/moron ) In fact, according to thefreedictionary, moron is less of an insult (person w/ mental age of 7) than idiot is (age < 3).

  63. 63
    KevNick says:

    I have said it before I will just repeat it again:

    Larry Moran uses name calling, especially his favorite “IDiot” as a substitution for the lack of scientific evidence any logically thinking and arguing scientist should and would provide. It is so easy to figure out his pattern. Each time Larry makes and argument for which he has no scientific evidence for instead of a link to it, he will bluff; this means that “… all knowledgeable scientists have known IT for x number of years”. If one investigates Larry’s claims, like I did, most if his so-called “…all knowledgeable scientists…” don’t agree with him. Larry pins stuff and his beliefs on other scientists and when exposed, he moves on to another one without remorse.

  64. 64
    dl says:

    Dr. Moran seems to be preaching to the choir. He keeps saying “IDiots” and Intelligent Design Creationists. He certainly knows that none of us are idiots. He almost certainly knows the difference between Intelligent Design and Creationism and is deliberately trying to conflate the two.

    Dr. Moran is probably trying to score points with people that believe name calling is a win. Its hard to take him seriously.

    Just to be clear, it just as hard to take pro-ID name callers serious too.

  65. 65
    bFast says:

    Larry Moron,

    How can you spend so much time and effort criticising evolution when you clearly don’t understand it?
    Only an IDiot would do that.

    I found some more IDiots for you:
    http://evolution.berkeley.edu/.....eory.shtml

    The main point of the neutral theory is simply that when we see several versions of a gene in a population, it is likely that their frequencies are simply drifting around.

    http://evolution.berkeley.edu/.....cle/evo_24

    Genetic drift affects the genetic makeup of the population but, unlike natural selection, through an entirely random process. So although genetic drift is a mechanism of evolution, it doesn’t work to produce adaptations.

    FOLKS, DON’T GO TO UC BERKELEY! THEY ARE idIOTS THERE, LARRY MORON SAYS SO.

  66. 66
    bFast says:

    dl, “Just to be clear, it just as hard to take pro-ID name callers serious too.”

    I presume you are referring to me in this. Please consider my name calling in light of my post #31 above. The moment I discover that Larry Moran can communicate without name calling, my mirroring will come to a screeching halt. I think, however, that he is a stone thrower that lives in a glass house.

  67. 67
    dl says:

    bfast

    I was not referring to you in my post. It was a general statement.

    From what I have seen, unlike Dr Moran’s posts, your posts have relevant information. I think that name calling in general undermines the impact of the posts. Just my opinion.

  68. 68
    Larry Moran says:

    bFast asks,

    You, sir, claim to have the ability to articulate. Please articulate for me. I learn very well from examples and scenarios. Please show me an example, a scenario that shows genetic drift to be something more than random variation.

    As I stated in my blog post on Random genetic drift [Random Genetic Drift], it is a stochastic process that affects the frequencies of alleles in a population. It results in the eventual fixation of alleles and the elimination of others. In fact, almost all of molecular phylogeny is based on nearly neutral alleles that have become fixed by accident in different populations.

    Random genetic drift is also responsible for the elimination of most beneficial alleles before they can become fixed by natural selection. Not only that, it can result in the fixation of detrimental alleles in a process that’s the exact opposite of natural selection.

    Variation in a population is due to mutation but the fact that most populations contain a lot of variation is, indeed, due to the fact that random genetic drift is a much slower process than natural selection. What this tells us is that most of the variation is nearly neutral.

    The really important point, however, is that random genetic drift eventually results in FIXATION of alleles and, therefore, the elimination of variation. Over time, species evolve more by random genetic drift. This process opens up new possibilities for future evolution including future adaptations.

    This is one of the many things that most Intelligent Design Creationists don’t understand. It may take many mutations to evolve a given structure or phenotype and most ID proponents think that requires many simultaneous mutations because they think that a stepwise evolution won’t work. It won’t work, according to them, because some of the intermediates may not be adaptive and may even be detrimental.

    Once you understand that neutral and detrimental mutations can easily be fixed by drift, you will understand a lot more about evolution. You will understand why Darwinism can’t achieve the goal but a proper understanding of modern evolutionary theory can.

    I gave you several references in my blog post but you can also find all this information in any textbook on introductory evolutionary biology, especially one that focuses on population genetics. It’s probably a good idea to familiarize yourself with the basic concepts of evolution before criticising it.

  69. 69
    Larry Moran says:

    bFast says,

    Larry Moron, “the word “Darwinist” is an insult.”

    Yes, the way it is used by most creationists it is an insult. Most of them portray Darwinists as evil men and women who are responsible for the holocaust and eugenics and a host of other vile things. They use the word to mean people who worship the nineteenth views of Charles Darwin.

  70. 70
    Larry Moran says:

    Mung asks,

    Dr. Moran, do you accept or reject the central tenet of Darwinian theory that variation is random with respect to fitness?

    No, not in the way that you mean it. It’s okay to use the word “random” in colloquial speech but evolutionary biologists know that there are any factors that influence mutations. In fact, we know pretty accurately how transitions differ from transversions and how various repeats can be expanded or reduced. We also know that certain sites are more susceptible to damage caused by x-rays or UV light.

    In additions to all those complications, there are certain sites in some genomes that are specifically mutated at high frequency (directed mutations).

    HTH HAND

  71. 71
    Mung says:

    But Darwinists are evil. And Christian Darwinists are more evil than others.

    😉

  72. 72
    Mapou says:

    Moran:

    bFast says,

    Larry Moron, “the word “Darwinist” is an insult.”

    Yes, the way it is used by most creationists it is an insult. Most of them portray Darwinists as evil men and women who are responsible for the holocaust and eugenics and a host of other vile things. They use the word to mean people who worship the nineteenth views of Charles Darwin.

    Strange. I believe the entire universe, including life on earth, was intelligently designed and created for a purpose. I guess that makes me a creationist, right? Yes but I certainly do not use the term ‘Darwinist’ to mean what you claim. I use it to mean a dirt worshipper who believes that complex self-replicating organisms emerged from dirt over millions of years all by themselves. IOW, a Darwinist is a deeply religious and superstitious person, not unlike a voodooist. 😀

  73. 73
    Mung says:

    This is the “EVOLUTION BY ACCIDENT” website containing essays and articles by Larry Moran who is solely responsible for all errors, omissions, and conceptual confusion.

    heh

    Genetic drift affects the genetic makeup of the population but, unlike natural selection, through an entirely random process. So although genetic drift is a mechanism of evolution, it doesn’t work to produce adaptations.

    http://evolution.berkeley.edu/.....cle/evo_24

    Larry Moran:

    Over time, species evolve more by random genetic drift. This process opens up new possibilities for future evolution including future adaptations.

  74. 74
    Larry Moran says:

    dl says,

    He almost certainly knows the difference between Intelligent Design and Creationism and is deliberately trying to conflate the two.

    On Describing IDiots as Creationists

    How Do Intelligent Design Creationists Define “Creationism”?

    The “Intelligent Design” Version of Creationism

    Theistic Evolution: How Does God Do It?

    Creationism Continuum

    Part of the problem here is that some people think that the word “creationist” should be reserved for Young Earth Creationists only. That’s pretty common in the USA but it’s not a universal way to define creationism, even in the USA. The more general, and more accurate, definition is that a creationist is anyone who believes in a creator god. (See the Wikipedia article on Creationism.) That definition applies to all proponents of Intelligent Design. (Don’t quibble about David Berlinski.)

    It’s true that ID proponents like to pretend that their “theory” could apply to space aliens but the reality is quite different. All you have to do is examine the posts on Uncomon Descent and Evolution News & Views to see how many refer to gods—especially the Christian gods.

  75. 75
    Mung says:

    Larry Moran:

    Part of the problem here is that some people think that the word “creationist” should be reserved for Young Earth Creationists only.

    Most of us in fact understand the distinction, whereas you seem to be doing your utmost to pretend it doesn’t exist.

    Creationism and Its Critics in Antiquity

    You object to the characterization of Darwinists as Nazis. Well, many of us object to the characterization of ID as Creationism. But that doesn’t stop you.

    And the basis for your moral outrage?

  76. 76
    Mapou says:

    Moran @74,

    So what if ALL ID proponents believed that the entire universe and life on earth were created? IDists are Christians, therefore what? What is your scientific point? You make it sound as if we are trying to disguise our religious inclinations. Why should we do that and why do you think it makes your own beliefs indistinguishable from religion?

    Oh, I get it. It’s that silly Darwinist reasoning style again. IDists are Christians, therefore evolution is true. Yeah, right.

  77. 77
    vjtorley says:

    Professor Moran:

    Thank you for your comments. Re the case for Intelligent Design: you keep harping on the fact that the original 123-word quote I supplied from Dr. Meyer did not supply a positive case for Intelligent Design. But I acknowledged this in a comment (#4) on my original post where I wrote:

    Actually, Dr. Meyer explains this elsewhere in his book, but I can sum it up in two words: causal adequacy. Intelligent Design can do the job; all the unguided mechanisms that we know of cannot.

    And in my next comment (#5), I added:

    While we’re talking about the explanatory superiority of Intelligent Design, I might also add that living things exhibit certain features (such as digital code, functional specified information and top-down organization) which are the hallmark traits of intelligent agency.

    Considering that I made these remarks shortly after putting up my original post, I can hardly be accused of suddenly “shifting the goalposts.”

    In a follow-up post (which I know you’ve read, because you borrowed the title in one of your recent posts), I also quoted another short passage from Meyer’s book (H/T Mung; bolding mine – VJT):

    …[E]ach of the features of the Cambrian animals and the Cambrian fossil record that constitute negative clues – clues that render neo-Darwinism and other materialistic theories inadequate as causal explanations – also happen to be features of systems known from experience to have arisen as the result of intelligent activity. In other words, standard materialistic evolutionary theories have failed to identify an adequate mechanism or cause for precisely those attributes of living forms that we know from experience only intelligence – conscious rational activity – is capable of producing. That suggests, in accord with the method of historical scientific reasoning elucidated in the previous chapter, the possibility of making a strong historical inference to intelligent design as the best explanation for the origin of those attributes.

    Darwin’s Doubt, p. 358

    This post of mine went up several hours before you wrote your post, The best case for Intelligent Design Creationism. You cannot justly accuse me of changing the subject, with regard to Meyer’s argument for Intelligent Design.

    Your complaint that the passage I quoted did not specifically address the version of evolution which you espouse was a just one, and I have attempted to remedy that defect in my latest post. But instead of defending Professor Lynch’s neutral theory of evolution, you focus your remarks on gods and on whether Intelligent Design qualifies as creationism.

    I had expected a meaty, mathematical response. I haven’t received one. What does that tell me about the present condition of modern evolutionary theory? Clearly, it’s not in very good shape, if this is the best defense it can manage.

  78. 78
    bFast says:

    Larry Moran, “Most of them portray Darwinists as evil men and women who are responsible for the holocaust and eugenics and a host of other vile things.”

    If you check out this link: http://www.uncommondescent.com.....ent-559349
    you will see that I do not. I agree with you that the ID community’s view of morality within a naturalistic framework is a painfully narrow one. I do, however, understand the “creationist”‘s prospective that one’s frame of reference affects ones moral code. I even understand their fear that loosing a Christian frame of reference is going to result in what they would view as evil.

    Mr. Moran, you use the term “creationist” quite often. You load it with a certain amount of critical baggage, do you not? So both terms Darwinist (or neo-Darwinist) and creationist do carry some baggage, I call ’em equal.

  79. 79
    bFast says:

    Larry Moran (68), thanks for a thoughtful response.

    I have read it carefully, and I have read your link carefully.

    I had read your findings that the amount of genetic difference between human and chimp can be fully accounted for by the neutral theory alone. This is pretty impressive.

    I think that the only known tool to develop genetic diversity is the neutral theory. Genetic diversity is an interesting and powerful force. I look at my little Pomeranian dog, and recognize that its ancestors were wolves. Though I understand that the small breed dogs have picked up a few post-wolf mutations, for the most part wolves carry the genetic makeup of the pomeranian. Its pretty amazing.

    I can also see that this tool of genetic diversity allows for a whole bunch of little potentials to build up for later use by natural selection. This may prove handy for all living things as our world warms up.

    On the topic of mutations being fixed and lost, well, I have my own familiarity with this topic. I did some simulations a few years ago. It was something to watch as I embedded a positive mutation into an organism, and saw it spread. In my 1000 entity environment, if there were less than 50 of the mutations, there was still a really good chance that it would be purged. Once it got past about 50, it began to have a good chance of fixing — even though it was designed to be beneficial.

    While it is true that drift will fix mutations, it is very good at generating them, as so many of the mutations are near neutral. It is the fact that it generates them faster than it fixes and purges them that makes it the universal tool for development of genetic diversity, yes?

    I also agree with you that drift accounts for more speciation than natural selection does. If two populations get isolated, the genetic makeup of each population will drift around — with periodic near-neutral alleles fixing. Eventually the two will truly qualify as separate species, even if both are well tuned for their environments, so have little effect from natural selection.

  80. 80
    Box says:

    Larry Moran: Once you understand that neutral and detrimental mutations can easily be fixed by drift, you will understand a lot more about evolution. You will understand why Darwinism can’t achieve the goal but a proper understanding of modern evolutionary theory can.

    From this I understand that neutral theory of evolution (NTE) offers many possible steps—even detrimental ones—between non-flagellum and flagellum. NTE offers all sorts of non-functional structures that are either ‘neutral’, ‘nearly-neutral’ or even ‘detrimental’ which on a good day can form a fully functional flagellum.
    However there are infinite ways to build non-functional structures. And this reminds me of something Dawkins wrote:

    It is true that there are quite a number of ways of making a living – flying, swimming, swinging through the trees, and so on. But, however many ways there may be of being alive, it is certain that there are vastly more ways of being dead, or rather not alive. You may throw cells together at random, over and over again for a billion years, and not once will you get a conglomeration that flies or swims or burrows or runs, or does anything, even badly, that could remotely be construed as working to keep itself alive.

    Now my question is: the alleged junk-DNA aside, do we see nature littered with non-functional structures?

  81. 81
    vjtorley says:

    Professor Moran,

    I wonder if you would care to comment on this passage from Dr. Meyer’s book, Darwin”s Doubt (Harper One, 2013, p. 328, square brackets mine – VJT):

    Lynch and Abegg assumed [in their paper] that organisms will acquire a given complex adaptation by traversing a direct path to the new anatomical structure. Each mutation would build on the previous one in the most efficient manner possible – with no setbacks, false starts, aimless wandering, or genetic degradation – until the desired structure or system (or gene) is constructed. Thus, they formulated an undirected model of evolutionary change, and one that assumes, moreover, that there is no mechanism available (such as natural selection) that can lock in potentially favorable mutational changes on the way to some complex advantageous structure….

    Yet nothing in Lynch’s neutral model ensures that potentially advantageous mutations will remain in place while other mutations accrue. As Axe explains [in his reply to Lynch], “Productive changes cannot be ‘banked,’ whereas Equation 2 [one of Lynch’s equations] presupposes that they can.” Instead, Axe shows, mathematically, that degradation (the fixation of mutational changes that make the complex adaptation less likely to arise) will occur much more rapidly than constructive mutations, causing the expected waiting time to increase exponentially.

    Are you claiming that Dr. Axe and Dr. Meyer have misconstrued the nature of random genetic drift?

  82. 82
    dl says:

    Professor Moran,

    Thanks for the response. I read the articles you linked to and I think I have a better understanding of why you use the term Intelligent Design Creationists.

    From my reading of your articles and posts, it seems that you believe that a belief in intelligent design depends on a belief in a creator. That is (in my opinion) not quite correct, but its understandable. I think its safe to say though, that the intelligent design movement is looking at evidence of design from a scientific perspective. Calling an intelligent design proponent a “creationist” is going to make most people think of religion, and its just a way to portray intelligent design as a religious endeavor.

    There are undoubtedly some intelligent design proponents who “pretend” to think that aliens could have been the intelligent designers. There are bad apples in any group. Intelligent design itself doesn’t deal with the identity of the designers, so that is a valid perspective. Another possibility is the scenario described by James Gardner in his book “The Intelligent Universe”. He explicitly distances himself from intelligent design, but his claims that the universe displays some sort of intelligence is right in line with a belief in intelligent design without a creator.

  83. 83
    JimFit says:

    Moron

    see how many refer to gods—especially the Christian gods.

    God is one because He is eternal, you can’t use plural on something infinite, its stupid and illogical.

    If God doesn’t exist then the Universe came out of Nothingness, assembled itself throught Randomness and we are here due to Luck, can you please prove me that Nothingness, Randomness and Luck exist?

  84. 84
    bFast says:

    JimFit, Larry Moran has begun to communicate in a respectful manner. Let us reciprocate by not using offensive terms in reference to him.

  85. 85
    JimFit says:

    bFast i see only arrogance and mockery from this random cosmic accident that nothingness spewed, not respect.

  86. 86
    Mung says:

    Larry Moran:

    All you have to do is examine the posts on Uncomon Descent and Evolution News & Views to see how many refer to gods—especially the Christian gods.

    UD is unabashedly anti-materialism.

    Edward Feser writes:

    …the debate over materialism has arguably never been more than tangentially concerned with how best to explain physical phenomena … Rather, the debate has, for two and a half millennia, focused primarily on three fundamental metaphysical issues: the nature of the mind and its relation to the body, the ontological and epistemological status of mathematical and other apparently abstract objects, and the question of the existence of God.

    Give the constant influx of materialists here, it is no wonder that god talk appears along with them. Consider your own example.

  87. 87
    bFast says:

    JimFit, the last 5 posts by Larry Moran have been respectful and informative. He was asked to stop his name calling. That didn’t work, so he was subjected to matching name calling. He now seems to have given up that game. We need to too!

    IOW, your vitriol is simply not Christian (Matt 5:44).

  88. 88
    Mung says:

    Name calling is pointless and juvenile. That’s why I love it!

  89. 89
    Querius says:

    The appearance of an ad hominem attack by your opponent is a tacit admission of defeat, that your opponent has no additional cogent arguments to counter yours. As a Christian, I don’t want to respond in kind, preferring instead to point out the bankruptcy of such an assertion. However, I also don’t feel compelled to be diplomatic or coddle someone like this, and I’ve teased such people to push back a little, hopefully to get them to abandon or at least reconsider their arrogant pretensions.

    For example, there was a guy here who claimed that Behe’s math was wrong and that he’d worked professionally using probability and statistics. Then, when challenged by a simple probability problem, he got it wrong. Even wd400 gently suggested that he recheck his calculations, but instead of admitting he made a mistake, he blamed it on a typo. So I teased him.

    Or a few days ago, I gently teased Professor Moran that he got the date of the King & Jukes paper off by a year, but I didn’t lambast him for it (although he hasn’t admitted to his mistake). Anybody can make a mistake, math, spelling, or a date. But when Professor Moran doubles down on junk DNA, or tries to assert that something different than was understood historically, it’s fair to call him on it, especially since the position seems to be a rhetorical one resulting from what seems to be ideological bias (hence his use of the pejorative label, Idiots).

    But I’m not calling him names.

    -Q

  90. 90
    Mapou says:

    You know. I don’t care what the rest of you say. I will always be disrespectful to Darwinists, whoever they are. I will attack them relentlessly and with glee.

    What is going on here is not a debate, folks. It’s a war. Moran and his kind can kiss my asteroid. All over the place. 😀

  91. 91
    Mapou says:

    There is nothing more pathetic and disgusting than a Darwinist with a PhD attached to his or her name. Just one man’s opinion.

  92. 92
    bFast says:

    Larry Moran:

    The more general, and more accurate, definition is that a creationist is anyone who believes in a creator god. (See the Wikipedia article on Creationism.) That definition applies to all proponents of Intelligent Design.

    Actually, Larry, I agree with you. There might be a couple of alternative opinions floating around, but nearly all of us are theists, and most of us are Christian. As such, I am not prepared to quibble about the “Creationist” title, even though I recognize that the term is used with some amount of “young earth” baggage attached.

    You seem to carry an implication, however, that is not correct for me. While I am Christian, I also hold to common descent. As such, I must abandon the belief in a literal Adam and Eve. This forces a major shift in how the Biblical interpreted. Once this shift occurs, however, true Theistic Evolution (there is only laws of nature, and those laws naturally produce life) has a lot to be said for. The question becomes, If God needs to interfere with nature to make life, does that mean that he is incapable of creating a set of laws that will do it without interference? If so, are we not limiting the capacity of God when we suggest that he is unable to do something?

    It is an elegant argument. If I could see nature to be the product of natural law alone, I would accept it. It is in looking into the details about the nature of life that I keep seeing stuff that could not possibly have developed via law alone.

    Therefore — therefore my ID position is held by the evidence alone, not by my philosophy or theology. This cannot be said for those with a non-theist commitment.

  93. 93
    Querius says:

    Lol, Mapou.

    But as our brother Paul reminds us, our war is not against flesh and blood . . . “but against the spirituals of the wickedness in the heavenlies.” (literal Greek translation)

    God loves Professor Moran and wants to rescue him from his anger, frustration, and eventual judgment. You won’t be helping him if you, like Peter in the garden of Gethsemane, cut his ear off. 😮

    -Q

  94. 94
    Querius says:

    bornagain77 @ 34 –

    Thanks for the great references and commentary, which I really appreciated!

    -Q

  95. 95
    Mapou says:

    Querius @93,

    There is a time for everything. There is a time for turning the other cheek and there is a time for kicking ass and taking names. The way I see it, we are entering the start of the ass-kicking period. Get ready to live in interesting times. LOL.

  96. 96
    Larry Moran says:

    bFast says,

    It is in looking into the details about the nature of life that I keep seeing stuff that could not possibly have developed via law alone.

    It’s called the argument from ignorance. When I see things that I can’t explain, I say, “Isn’t that interesting. I don’t know how that works.”

    The difference between you and me is that you say, “I don’t know how that works. God must have done it so it’s evidence that god(s) exist.”

    That’s pretty much the essence of Intelligent Design Creationism in spite of the fact that all ID proponents will go to great lengths to deny it.

  97. 97
    Larry Moran says:

    Mapou says,

    There is nothing more pathetic and disgusting than a Darwinist with a PhD attached to his or her name. Just one man’s opinion.

    I agree. I been fighting them for years trying to get them to understand modern evolutionary theory. In fact, I’ll be meeting Richard Dawkins in a few weeks for another round. Wish me luck.

  98. 98
    Larry Moran says:

    Querius says.

    Or a few days ago, I gently teased Professor Moran that he got the date of the King & Jukes paper off by a year, but I didn’t lambast him for it (although he hasn’t admitted to his mistake).

    Sorry, I didn’t notice. My bad.

    Anybody can make a mistake, math, spelling, or a date. But when Professor Moran doubles down on junk DNA, or tries to assert that something different than was understood historically, it’s fair to call him on it, …

    Well, I WAS there in the late 1960s so I do have a perspective that you probably don’t share.

    More importantly, I’ve been debating this point about the history of junk DNA for about 25 years and during that time I’ve had lots of feedback and corrections. If there’s some thing you’d like to “call me on” then go for it.

  99. 99
    Mung says:

    Larry Moran:

    I’ll be meeting Richard Dawkins in a few weeks for another round. Wish me luck.

    So now you know how we feel when Dawkins decides to critique religion.

    Dawkins got infected by the selfish meme some time back, but

    Good luck!

  100. 100
    Cross says:

    Larry Moran @ 96

    “The difference between you and me is that you say, “I don’t know how that works. God must have done it so it’s evidence that god(s) exist.””

    Whereas yourself and many scientists insist God must not exist and thus there must be a materialist answer. Materialist of the gaps.

    Cheers

  101. 101
    Mapou says:

    Moran is just pretending not to be a Darwinist but that is exactly what he is.

  102. 102
    JimFit says:

    Larry

    The difference between you and me is that you say, “I don’t know how that works. God must have done it so it’s evidence that god(s) exist.”

    God has done it but that doesn’t make the how mystical to humans, the fact that we humans can undestand how it works proves that we are the images of God, equal in understanding.

  103. 103
    Querius says:

    Larry Moran @ 98,

    Thank you for gentle answers.

    Yes, I have no doubt that you not only have a historical perspective that I don’t have, including correspondence with key contributors. Also, I respect the fact that you’ve had 25 years of debate with students, colleagues, and others.

    You could still be wrong. This is actually likely to some degree considering how much scientific understanding changes over time.

    As a scientist you’ve assumed a responsibility not only to refute weak objections, but also to challenge weak rationalizations.

    One version of ID is defined as a paradigm that pragmatically assumes poorly understood biological structures and processes have an underlying design—without necessarily postulating a designer. Considering “junk” DNA, which approach would more likely succeed in advancing scientific progress in the areas that are poorly understood:

    A Larry Moran that assumes that the majority of human junk DNA does not have any important function?

    or

    A Larry Moran that assumes that the majority of human junk DNA has an important, unknown function?

    Thanks for listening.

    -Q

  104. 104
    bpragmatic says:

    Larry says:
    “The difference between you and me is that you say, “I don’t know how that works. God must have done it so it’s evidence that god(s) exist.””

    This is what I have observed, over time, to be a fundamental flaw in the unguided evolutionists’ philosophy (that is really all it is, a philoshopy). Understanding of how biological systems “work” are observed and in scientific fashion described very well with a high degree of certainty. A theory of “evolution” need not be invoked for this kind of scientific work. Where these people run into difficulty is conflating the observable “how it works” with the largely conjectural and undemonstrable conjecture as to “how these functions developed”.

    Other than scant quantitative methods in comparison to what is required to get beyond the conjectural aspects of the assertions just doesnt exist in the “evolutionists” bag of “demonstrations”.

    Stop whining about the “Intelligent Design Creationists”, get off of your butts and come up with some convincing empirical evidence that actually, in a material sense, supports your conjecture. After all the evolution industry has had decades of public funding to come up with something other than a bunch of “just so stories” but, when it comes down to it, that is all it has to show for it.

  105. 105
    Cross says:

    bpragmatic @ 104

    “Stop whining about the “Intelligent Design Creationists”, get off of your butts and come up with some convincing empirical evidence that actually, in a material sense, supports your conjecture. After all the evolution industry has had decades of public funding to come up with something other than a bunch of “just so stories” but, when it comes down to it, that is all it has to show for it.”

    Indeed. In particular, come up with a plausible, or even better, testable “Origin Of Live” without the need for intelligent agency, can’t see how you can claim materialist evolution without first proving you can start it without help. If you can’t, it’s a gap you are carefully (fearfully?) avoiding.

    Cheers

  106. 106
    bFast says:

    Larry Moran(96)

    It’s called the argument from ignorance. When I see things that I can’t explain, I say, “Isn’t that interesting. I don’t know how that works.”

    Honestly, Larry, I don’t believe that you stop there.

    The difference between you and me is that you say, “I don’t know how that works. God must have done it so it’s evidence that god(s) exist.”

    Now, for honesty. You say, we don’t know how that works — yet. (but I’m sure that however it exists, it couldn’t possibly be because god did it.”) If you honestly held to methodological, but not philosophical, naturalism you would say, “hmmm, we don’t know how that works, maybe god did it, maybe not. We’ll continue to follow the “not” hypothesis.) In my opinion, it is just as unscientific to declare “no way god did it” as it is to declare “goddidit.”

    That’s pretty much the essence of Intelligent Design Creationism in spite of the fact that all ID proponents will go to great lengths to deny it.

    Please understand, I am a civilian, a non-scientist. As such, I must walk through life in the real world. I cannot bear to wear the proper scientific “methodological naturalism” hat all of the time. That is my obligation as a human being. As a person, living life, I must put my faith somewhere, either “I don’t know how this works therefore God did it” or “I don’t know how this works, but I am sure that God didn’t do it”.

    As my extra-scientific pursuits have clearly confirmed for me that God does stuff, I bend towards “God did it”.

    (To be continued in a new comment, because this is a really important bit.)

  107. 107
    bFast says:

    Larry Moran, now for the important bit.

    I remember listening to a philosopher of science (he was actually a physicist talking about biology) sharing how in the past scientists have seen that which was not understood, and declared “God did it”. Lo and behold, later discoveries brought mechanism to the picture, and virtually all of the “God did it” claim in that context disappeared. His general thesis was, as is yours, that we were too quick to cry “God did it”.

    I took something very different from his treatise, however. It seemed to me that the best antidote for “God did it” is an adequate explanation. “God did it” persists until an adequate explanation is found.

    I see data — life. I see the textbook explanation for that life: Random Variation + natural selection. I see this explanation get better over time — neutral theory, etc. However, I still see an explanation that seems woefully inadequate! The model you have espoused does not seem to have any ability to create the wonderfully complex, intricate, cascading systems that are found in life, (among a dozen other major inadequacies.)

    When an adequate explanation for life as we know it is found and revealed to me, I’ll abandon “God did it” for that one. Until then, I would rather wrongly declare that God did it (because after all he did do it, even if indirectly) than to wrongly declare that he did not.

  108. 108
    kairosfocus says:

    LM:

    I passed by for a moment, saw BFast, and tracked back to 96:

    [BF:] It is in looking into the details about the nature of life that I keep seeing stuff that could not possibly have developed via law alone.

    [LM:] It’s called the argument from ignorance. When I see things that I can’t explain, I say, “Isn’t that interesting. I don’t know how that works.”

    The difference between you and me is that you say, “I don’t know how that works. God must have done it so it’s evidence that god(s) exist.”

    That’s pretty much the essence of Intelligent Design Creationism in spite of the fact that all ID proponents will go to great lengths to deny it.

    Pardon, but on fair comment you are here projecting, caricaturing by setting up a strawman, stereotyping and likely scapegoating as “Creationism” is in this context a loaded term, just a tad less extreme in import than X-deniers — a propaganda term that seems to be increasingly resorted to, which is laced with the aura of holocaust denialism. This seems similar to what I have encountered at your own blog on occasion and spoken to for record on finding myself addressed, including when you have in effect enabled others who have take to stalking behaviour. (Which FYI, is now, quite likely, on the ground.)

    I suggest to you that you have a duty of care to accuracy and fairness to adjust your thought and assertions, and accordingly will make a few notes in response to the just clipped. (I also point onwards to the UD summary on what ID is, and to the weak argument corrective responses under the resources tab, top of this and every UD page.)

    On steps of thought:

    1 –> First, the design inference is not either an appeal to ignorance nor a “god of the gaps” argument, as should be long since acknowledged. Instead, it is an inductive inference to best current explanation on long since known patterns of causal factors.

    2 –> For instance, it is that Bible thumping fundy — NOT — Plato, who in the Laws Bk X documented 2350 years ago, that we commonly find chance, necessity of nature and art or intelligently directed configuration as common causal patterns. You likely know of Monod’s Chance and Necessity, c 1970, which builds on that frame.

    3 –> The reasonable, empirical issue is: do such patterns of causation leave traces that we may profitably study on an empirical basis. To which the patent answer is yes.

    4 –> Considering an object, phenomenon or process etc on an aspect by aspect basis (it matters not what colour the cord or bob are in assessing the behaviour of a simple pendulum) we may readily see what Galileo saw as a student so long ago now: natural regularities tracing to mechanical necessities that may be observed and reduced to laws, e.g. that of the simple pendulum, or of a heavy falling object, then onwards to say the scheme of Newtonian dynamics and the four core laws that have bridged terrestrial and celestial phenomena so powerfully, riveting the concept of universality of natural law. All with the aid of a falling apple and a moon swinging by in orbit.

    5 –> Subsequently, in dealing with things like molecular behaviour, it was found that there are phenomena that it makes sense to study statistically, and onwards to inject the ideas of chance and randomness (think, quantum-stochastic phenomena such as alpha particle decay). Laplace’s demon who from initial conditions could calculate the trajectory of the whole cosmos, has long been out of a job. That is, radical contingency leading to drastically dissimilar behaviour on closely similar initial circumstances, has been recognised.

    6 –> A classic, simple case is the dropping, rolling and settling of a fair die. It reliably falls at 9.8 N/kg under typical circumstances, due to mechanical necessity of gravity, which we can right off use to weigh the earth, starting with size estimates tracing to Eratosthenes and his shadow observations at Summer Solstice in Egypt. But, patently, thanks to eight corners and twelve edges, the die is chaotic and radically contingent, yielding the well known flat distribution of outcomes from the set {1, 2, . . . 6}

    7 –> But also, as the Houses in Las Vegas know, there is another form of contingent behaviour that may affect dice: loading, by purposeful manipulation of many possible mechanisms. Ranging in effect from slight bias to imposed certainty at will.

    8 –> Where of course, such agency — purposeful, intelligent action similar to the configuration of our very different comments in this thread as text-strings in English — may also use constrained randomness or chance, e.g. the use of dice in games.

    9 –> So, already, we see that different aspects of and/or patterns of outcomes in a situation may reasonably point to mechanical necessity manifested as natural regularities, or in highly contingent outcomes that may trace to chance and/or design. Where the presence of aspects exhibiting necessity or chance does not rule out the possibility of design as also acting.

    10 –> The empirical observation anchored design inference asks and seeks to answer a reasonable question: can we reliably, on empirical observation, identify intelligently and presumably purposefully directed configuration, as opposed to what we may expect from the other highly contingent factor, blind chance?

    11 –> The answer, obviously, is yes. In at least certain cases, it is a commonplace that stochastic patterns yield expected outcomes that if sufficiently violated in what we observe point away from chance. Dice that significantly and conveniently diverge from fair dice point to design. Classic, Fisher based statistical inference testing allows us to conclude that it is unreasonable to assign a chance based null hyp to an outcome, etc. Such is not even seriously controversial.

    12 –> In telecommunications, too, we routinely identify signals and noise based on statistical and other factors, using metrics such as signal to noise ratio as key indicia. Indeed, this ratio plays a vital role in this field of science, which of course studies technological systems and is directly applicable to say DNA.

    13 –> This already establishes a filtering process on a per aspect basis, that distinguishes natural regularity, chance and design as relevant and often detectable causal processes/ patterns.

    14 –> In studying origins linked phenomena, we see a further factor; temporal remoteness. We cannot directly observe the remote past of origins, we may only study traces and produce reconstructions as models that may have more or less of reasonable plausibility.

    15 –> None of us saw the origin of the cosmos we observe or the solar system, or of life or of multicellular organisms with major body plans, or of continents and islands, or of humans. We are here in the province of historical sciences that seek to reconstruct the plausible past of origins.

    16 –> Newton, in his four rules of reasoning, championed what has come to be termed the vera causa principle, which was picked up by Lyell and Darwin: in explaining traces of the unobservable past or remote reaches of space etc, we should use factors actually observed to be adequate to causally explain materially similar effects in the here and now.

    17 –> This is glorified common sense. What is demonstrably capable is a better explanation than what is merely speculative guesswork not anchored to adequate explanation per demonstration.

    18 –> Reinforcing, when of candidate explanations E1, E2, . . . En, some Ei is uniquely empirically adequate to account for the observed facts F1, F2, . . . Fm, is coherent logically and dynamically and is explanatorily elegant (neither simplistic nor an ad hoc patchwork), it is clearly the explanation to beat. The best current one.

    19 –> When it comes to the relevant aspects of origin of cell based life and of key body plan features, the dominant explanations are typically rooted in a priori evolutionary materialist scientism, typically presented as a seemingly “reasonable” imposition of methodological naturalism as opposed to admitting the chaotic “supernatural” in the door of “Science.”

    20 –> This is already an ideological loading that begs questions and often closes minds.

    21 –> But the matter is deeper than that. For, there is another empirically relevant dichotomy for explaining highly contingent phenomena that has been on the table since Plato and which is there already in all sorts of contexts; so that we have no good epistemic right to lock it out ideologically on origins science issues: namely, the natural (= chance and/or necessity) vs the ART-ificial.

    22 –> So, when I see talking points such as I clipped above, I see an ideological lock-out on fear of admitting the much despised shadow of God on the doorstep of the halls of Science. Perhaps, “Behold, I stand at the door and knock . . . ” has a relevance that we may need to heed.

    23 –> But, more to the point, cosmological fine tuning, functionally specific, complex organisation and/or associated information [= FSCO/I for short], algorithms, codes and co-ordinated typically irreducibly complex arrays of communication and execution machinery in the heart of cell based life, the presence of such in even the integrated von Neumann kinematic self-replication facility [= vNSR for short] that enables cells to reproduce and more raise serious questions about the causal adequacy of blind chance and mechanical necessity [= BC + MN, for short].

    24 –> Nor is this a mere negative argument: we are very familiar with such phenomena and their causes . . . on trillions of directly observed cases in point, such phenomena reliably, consistently trace to intelligently directed configuration as observed cause. Where, we simply do not have credible observation of such beyond a reasonable threshold of complexity, coming about by blind chance and/or mechanical necessity.

    25 –> So, we have met both halves of the inference to best explanation requisites.

    26 –> Whether or not you are inclined to agree makes little difference. FSCO/I — including that in the vNSR at the heart of cell based life — strongly points to design as vera causa adequate, observed and known cause of such phenomena.

    27 –> Where, we may summarise this as that FSCO/I etc are reliable signs of design as best current causal explanation of relevant phenomena.

    28 –> As Meyer, responding to Falk’s critique of Signature in the Cell, summarised:

    The central argument of my book is that intelligent design—the activity of a conscious and rational deliberative agent—best explains the origin of the information necessary to produce the first living cell. I argue this because of two things that we know from our uniform and repeated experience, which following Charles Darwin I take to be the basis of all scientific reasoning about the past. First, intelligent agents have demonstrated the capacity to produce large amounts of functionally specified information (especially in a digital form). Second, no undirected chemical process has demonstrated this power. Hence, intelligent design provides the best—most causally adequate—explanation for the origin of the information necessary to produce the first life from simpler non-living chemicals. In other words, intelligent design is the only explanation that cites a cause known to have the capacity to produce the key effect in question . . . . In order to [[scientifically refute this inductive conclusion] Falk would need to show that some undirected material cause has [[empirically] demonstrated the power to produce functional biological information apart from the guidance or activity a designing mind. Neither Falk, nor anyone working in origin-of-life biology, has succeeded in doing this . . . .

    29 –> Similarly, in Darwin’s Doubt, he summarised negatively:

    “This book has presented four separate scientific critiques demonstrating the inadequacy of the neo-Darwinian mechanism, the mechanism that Dawkins assumes can produce the appearance of design without intelligent guidance. It has shown that the neo-Darwinian mechanism fails to account for the origin of genetic information because: (1) it has no means of efficiently searching combinatorial sequence space for functional genes and proteins and, consequently, (2) it requires unrealistically long waiting times to generate even a single new gene or protein. It has also shown that the mechanism cannot produce new body plans because: (3) early acting mutations, the only kind capable of generating large-scale changes, are also invariably deleterious, and (4) genetic mutations cannot, in any case, generate the epigenetic information necessary to build a body plan.” (pp. 410-411)

    . . . and, positively:

    [E]ach of the features of the Cambrian animals and the Cambrian fossil record that constitute negative clues – clues that render neo-Darwinism and other materialistic theories inadequate as causal explanations – also happen to be features of systems known from experience to have arisen as the result of intelligent activity. In other words, standard materialistic evolutionary theories have failed to identify an adequate mechanism or cause for precisely those attributes of living forms that we know from experience only intelligence – conscious rational activity – is capable of producing. That suggests, in accord with the method of historical scientific reasoning elucidated in the previous chapter, the possibility of making a strong historical inference to intelligent design as the best explanation for the origin of those attributes. (p. 358)

    30 –> Now, let us pause. Above, at no material point in my argument have I made reference to a scriptural religious tradition as a primary source or control [typically presented as record by the one who was there, our Creator], nor is such implicit, in fact this line of argument builds on the likes of a Plato, not a Moses. In short, my reasoning here is NOT Creationism, as the Creationists themselves sometimes object.

    31 –> The dismissive, loaded tag, Intelligent Design Creationism, is thus exposed as inappropriate namecalling. This should cease, in the name of basic fairness; on pain of exposure of a propagandistic agenda rather than a concern for duties of care on accuracy and fairness.

    32 –> Back on focus, I actually no longer care what determined, aggressive objectors who insistently resort to all sorts of fallacies and tactics that will not stand the cold light of day say or think. For, adequate warrant has been shown for why the design inference, limited as it is, is made. And, why it is warranted as best current explanation of OOL and OOBP [= origin of body plans].

    33 –> Serious objectors need to show cause why blind chance and mechanical necessity do meet the vera causa test, to be seriously considered further.

    34 –> First, for OOL, the root of the tree of life as commonly taught. With particular reference to the origin of a gated, encapsulated metabolic automaton based on molecular nanotechnologies using C-chemistry in aqueous medium, and embedding an integrated code and algorithm-using vNSR, i.e. the living cell.

    35 –> Second, for OOBP. Dozens of times over and within a reasonable window of time and atomic resources, here on earth. I care not whether neo-darwinist mechanisms or the various alternatives now put forth are placed in the relations:

    chance variations in life forms [CV] +

    culling by differential reproductive success in niches [CBDRS] –>

    descent with incremental modifications [DWIM] –>

    branching tree evolution [BTE] –>

    tree of life pattern [ToL]

    36 –> Vera causa must be met, or we have a patent case of inappropriately grossly extrapolating adaptation mechanisms within islands of function based on FSCO/I [start with proteins in AA sequence space to see what such islands look like and why they will be deeply isolated and pose blind search needle in haystack search challenges] to cover how one finds and arrives at shores of such deeply isolated islands in the relevant life form config spaces.

    37 –> In short, one needs to show adequate cause to bridge micro to OOBP level macro evolution, with of course the Cambrian fossil revolution as case study no 1.

    38 –> Third, one needs to credibly account for origin of mind [OOM] or even OOM & Morals [OOM&M], i/l/o say Haldane:

    “It seems to me immensely unlikely that mind is a mere by-product of matter. For if my mental processes are determined wholly by the motions of atoms in my brain I have no reason to suppose that my beliefs are true. They may be sound chemically, but that does not make them sound logically. And hence I have no reason for supposing my brain to be composed of atoms. In order to escape from this necessity of sawing away the branch on which I am sitting, so to speak, I am compelled to believe that mind is not wholly conditioned by matter.” [“When I am dead,” in Possible Worlds: And Other Essays [1927], Chatto and Windus: London, 1932, reprint, p.209.]

    39 –> That is, one of the phenomena in play is scientists who use reason and evidence to warrant claims including theories of origins. Thus such theories are inherently self-referential. At minimum, they must avoid self-falsification through self-contradiction; which is clearly on the table.

    40 –> Likewise, to imply that our inescapable sense of moral accountability and governance is in effect delusional, is to imply grand delusion in mindedness, leading to self referential incoherence.

    41 –> BTW, that is a part of where I would reason to God and to ethical theism. As, there is but one serious candidate that accounts for such a circumstance: the inherently good creator God, a necessary and maximally great being who is worthy of service by doing the good. Who, in the heavens above, has left evidence adequate to point to design. Starting with a credible beginning [implies, begin-ner] and extending to multiple convergent lines of observations pointing to carefully balanced fine tuning. Which, as this sets up the physical requisites of C-chemistry aqueous medium life, then raises the matter of credible candidates to be designer. (One needs not have specific candidates in mind to infer burglary or arson etc, or even loaded dice.) All of which is multiplied by historical evidence and the living testimony of millions who have encountered and been transformed by God. (Not that such matters much to those utterly, stubbornly, selectively hyperskeptically determined to reject the reality of God, but I simply note for completeness: my confidence in the reality of God is separate from my confidence in the significance of signs of design in the world of life.)

    _______________

    So, there is a reasonable case to infer design in the world of life and similar design of the observed cosmos. Regardless of what those determined to object may say.

    I therefore suggest that a focus on the merits is indicated.

    KF

  109. 109
    Larry Moran says:

    Querius asks,

    Considering “junk” DNA, which approach would more likely succeed in advancing scientific progress in the areas that are poorly understood:

    A Larry Moran that assumes that the majority of human junk DNA does not have any important function?

    or

    A Larry Moran that assumes that the majority of human junk DNA has an important, unknown function?

    Back around 1970, when most of us became aware of the problem, we wondered what possible purpose all that extra DNA could serve. Almost everyone thought that it must have some kind of function.

    Much of this speculation about possible function was based on a misunderstanding of evolution—the same misunderstanding that still exists today, especially among creationists. We thought that natural selection would have eliminated any DNA that did not have a function.

    Gradually, over the next few years, more and more evidence accumulated that most of that excess DNA in large genomes was, actually, nonfunctional. It was junk DNA.

    Larry Moran began by assuming that the DNA had a function because that’s what his (my) flawed understanding of evolution suggested. By 1970 the evidence for junk was too good to ignore and my views on evolution had been corrected by people like King, Jukes, Ohno, and Kimura.

    There are still many scientists who argue against junk DNA. Almost all of them have a flawed “Darwinian” view of evolution that doesn’t allow for junk DNA. In that sense they are allied with the Intelligent Design Creationists. “Darwinist” scientists don’t believe in junk DNA but you would never know that from reading creationist literature.

    If you want to think of evolution in the same way that Charles Darwin did then that’s fine by me. However, if you are arguing from that perspective you MUST take into account the views of your opponents and portray them accurately.

    And you MUST get the history right. If you are caught lying about the history then nobody’s going to believe anything else you say.

    Intelligent Design Creationists lie about the history in a way that suits their purpose. They make it look like scientists were really stupid to believe that all noncoding DNA was junk. Scientists were not stupid back then and they are not stupid now. You are never going to be taken seriously if non-scientist ID proponents continue to insist that they know more about evolution than the experts who study it for their entire working lives.

    Learn about evolution. Learn about junk DNA. There’s plenty of serious science that we could debate and discuss if you would only make the effort to understand what you are rejecting.

  110. 110
    Larry Moran says:

    Cross says,

    Indeed. In particular, come up with a plausible, or even better, testable “Origin Of Live” without the need for intelligent agency, can’t see how you can claim materialist evolution without first proving you can start it without help. If you can’t, it’s a gap you are carefully (fearfully?) avoiding.

    I have no idea how life began. I have never avoided that issue.

    If you have a detailed explanation of how life began then please share it with the world. It has to fit with all the known scientific facts. If you postulate that aliens—or any other intelligent agency—were involved then please include the scientific evidence for their existence and their motives.

    You might want to include something about THEIR origins.

  111. 111
    Larry Moran says:

    bFast says,

    If you honestly held to methodological, but not philosophical, naturalism you would say, “hmmm, we don’t know how that works, maybe god did it, maybe not. We’ll continue to follow the “not” hypothesis.) In my opinion, it is just as unscientific to declare “no way god did it” as it is to declare “goddidit.”

    I teach a course on critical thinking and we spend a lot of time discussing how to argue. One of the most important lessons is on learning to understand the point of view of your opponents. You can really have a good debate if you don’t understand what your opponents are saying.

    I don’t believe in the existence of gods. Why in the world would I say, ““hmmm, we don’t know how that works, maybe god did it”? That would be like you saying, “hmmm, we don’t know how that works, maybe aliens from Vega did it.”

    Your understanding of the distinction between methodological naturalism and philosophical naturalism is flawed. You seem to think that people practicing methodological naturalism have to consider the possibility that gods exists. That’s not correct.

    In fact, there really is no distinction. Many philosophers have rejected the claim that science is restricted to a form of methodological naturalism that allows for the presence of gods.

    Many scientists do not say, “no way god did it” because they don’t believe in god. You need to try harder to put yourself in the minds of your opponents when you make an argument.

  112. 112
    Silver Asiatic says:

    Larry Moran

    You are never going to be taken seriously if non-scientist ID proponents continue to insist that they know more about evolution than the experts who study it for their entire working lives.

    In fairness, there’s a man who was or is …

    – Chair for the Public Understanding of Science at the University of Oxford
    – Editorial advisor to the Encarta Encyclopedia and the Encyclopedia of Evolution.
    – President of the Biological Sciences section of the British Association for the Advancement of Science.
    Simonyi Professor for the Public Understanding of Science at Oxford
    – Doctor of Science degree by the University of Oxford in 1989. He holds honorary doctorates in science from the University of Huddersfield, University of Westminster, Durham University,[133] the University of Hull, the University of Antwerp, and the University of Oslo,[134] and honorary doctorates from the University of Aberdeen,[135] Open University, the Vrije Universiteit Brussel,[11] and the University of Valencia.[136]
    – He also holds honorary doctorates of letters from the University of St Andrews and the Australian National University (HonLittD, 1996), and was elected Fellow of the Royal Society of Literature in 1997 and the Royal Society in 2001.[11]
    – His other awards include the Zoological Society of London’s Silver Medal (1989), the Finlay Innovation Award (1990), the Michael Faraday Award (1990), the Nakayama Prize (1994), the fifth International Cosmos Prize (1997), the Kistler Prize (2001), the Medal of the Presidency of the Italian Republic (2001), and the Nierenberg Prize for Science in the Public Interest (2009).[137]
    In 2005, the Hamburg-based Alfred Toepfer Foundation awarded him its Shakespeare Prize in recognition of his “concise and accessible presentation of scientific knowledge”.
    – He won the Lewis Thomas Prize for Writing about Science for 2006, as well as the Galaxy British Book Awards’s Author of the Year Award for 2007.[141]
    In the same year, he was listed by Time magazine as one of the 100 most influential people in the world in 2007,[142] and he was ranked 20th in The Daily Telegraph’s 2007 list of 100 greatest living geniuses.[143]

    … who you think holds the Idiot view of evolution.

    So, where’s the problem – with ID? or with the evolutionary biological community itself?

    If studying evolution for 25 years leads to the conclusion that the most awarded evolutionary theorist in the world is an idiot — what does that say about so-called ‘evolutionary theory’ itself?

  113. 113
    Cross says:

    Larry Moran @ 110

    “I have no idea how life began. I have never avoided that issue.”

    With respect, all materialists avoid OOL because they have no plausible explanation of self reproducing life from non-life.

    They try to keep it out of any materialist evolution debate (making it a separate issue rather than a core tenet of materialist evolution) because if life cannot spring from non-life without intervention by God or some intelligent agent then you cannot guarantee that intervention has not been made to the progression of evolution as you see it.

    Can I remind you that materialist evolutionists are the ones claiming that life has created itself and then evolved into man, this is an extraordinary claim that OOL scientists have so far made zero progress on.

    Like most scientists today you persist in the idea that “science” is the only arbiter of knowledge and “materialist only” causes are the only possibilities. The materialist co option of science means that you limit whole other possibilities and science is all the poorer for it.

    Cheers

  114. 114
    Silver Asiatic says:

    LM

    Why in the world would I say, ““hmmm, we don’t know how that works, maybe god did it”? That would be like you saying, “hmmm, we don’t know how that works, maybe aliens from Vega did it.”

    Not really. It has to do with causality – ultimate causes and the origin of things.
    Why would you conclude that the only causes of things are physical/mechanical processes? Your own thoughts and rational deliberations are evidence of non-physical causes.

    Intelligence an intention cause things. Why rule out immaterial essences?

  115. 115
    Larry Moran says:

    kairosfocus says,

    The dismissive, loaded tag, Intelligent Design Creationism, is thus exposed as inappropriate namecalling. This should cease, in the name of basic fairness; on pain of exposure of a propagandistic agenda rather than a concern for duties of care on accuracy and fairness.

    The whole point of the intelligent design movement is to provide “scientific” evidence for the existence of a creator.

    This mostly consists of attacking evolution on the grounds that if evolution can be discredited then that leaves room for creator gods.

    It’s ironic that an Intelligent Design Creationist would accuse be of engaging in a propaganda war. Have you read the posts on the main ID blogs?

  116. 116
    kairosfocus says:

    LM, wrong. I do not need ID as a reason to believe in God, nor do most people, it is not design in life so God is real. If anything, it was that many took evidence on origins of life to try to put God out of a job, dressed up in a lab coat; something that still comes out in Lewontin’s a priori materialism which has been embedded in origins science via methodological naturalism, which is epistemically question-begging; and which silences evidence and diverts from the big challenge. Namely, vera causa — there is not empirically warranted adequate cause rooted in chance and necessity that explains on observation OOL or OOBP given the need to account for complex, functionally specific organisation and associated information; including that in the code and algorithm using vNSR in the heart of the cell — starting with DNA. And, that for the requisite proteins and regulatory networks and programmes to build body plans. But if such materialism is ideologically imposed and institutionalised, it locks out the evidence to the contrary that exposes the weaknesses I just pointed to. I take the design inference on especially the world of life, seriously, because it is empirically evident and warranted and because I see no good reason to let materialist ideological question begging faze me, even if institutionalised. If you had real answers I am sure you would not be playing around with schoolyard tagging games, but would lay out the Nobel prize winning evidence on OOL and OOBP that has been decisive for decades. Instead I am the one pointing to the implications of evidence that won Nobel prizes starting with unravelling of DNA’s secrets from 1953 on. In short, tellingly, you are here indulging in motive mongering on an issue that instead pivots on inductive warrant, that is going to make it all but impossible for those who buy into the ideology to hear the voice of the evidence and logic. This rather reminds me of what it was like to try to reason with the indoctrinated Marxists in my Uni back in the days before the system collapsed. And, it looks a lot to me like, that is what is going to have to happen. Took 60 years from von Mises’ analysis on valuation and the like, but that is what told in the end. KF

    PS: Maybe it has not dawned on you that you are here speaking to someone who has been targetted for years of stalking and enabling, now likely on the ground as well.

  117. 117
    Larry Moran says:

    Silver Asatic asks,

    So, where’s the problem – with ID? or with the evolutionary biological community itself?

    There is a very interesting debate among evolutionary biologists concerning the importance of natural selection and other issues. Richard Dawkins and I may disagree on some of these issues but we do not disagree about the fact of evolution.

    Furthermore, Dawkins understands very well the position of his critics and those critics recognize the validity of many of his arguments. That’s why the debate among evolutionary biologists is so interesting and informative.

    It’s nothing like the debate I see here. There are only two or three Intelligent Design Creationists who could participate in those debates with any credibility. Most of them haven’t got a clue about the major issues in evolutionary biology. They simply reject evolution out of hand because it conflicts with their religion.

    That’s a shame because there really are interesting things to discuss about evolution.

  118. 118
    Larry Moran says:

    Cross says,

    With respect, all materialists avoid OOL because they have no plausible explanation of self reproducing life from non-life.

    They try to keep it out of any materialist evolution debate …

    If you are willing to admit that once life began then evolution can explain the subsequent history without resorting to gods, then we can discuss the origin of life.

    Are you willing? If so, then stop attacking evolution as though you reject it.

    As for the “debate” on the origin of life, I have no detailed materialistic explanation. Do you have a detailed nonmaterialistic explanation of are you just bluffing?

  119. 119
    Larry Moran says:

    Silver Asiatic asks,

    Why would you conclude that the only causes of things are physical/mechanical processes?

    Because there’s no evidence of any other kind of causes. Maybe you believe in these other causes (gods) but you have to demonstrate in some manner that they exist. That brings us to a discussion about the existence of supernatural beings and that’s exactly what Intelligent Design Creationism is all about.

  120. 120
    Larry Moran says:

    kaiosfocus says,

    LM, wrong. I do not need ID as a reason to believe in God, nor do most people …

    I know that. You start with a belief in supernatural beings of some sort then develop ID as a way of confirming your belief and dealing with the obvious conflicts between your beliefs and science. It’s a form of apologetics.

    Nobody ever came to accept gods via the arguments of Intelligent Design Creationists.

    Thank-you for making that clear.

    If anything, it was that many took evidence on origins of life to try to put God out of a job, dressed up in a lab coat ….

    First, I do not claim to know how life originated and I don’t know any scientists who make such a claim. None of us would ever use “evidence” on the origin of life as an argument against the existence of gods. That does not prevent us from trying to refute believers who use the absence of evidence as proof of the existence of gods.

    Second, you have to believe in God in the first place in order to put him out of a job. What you are doing is confirming my view that from the ID perspective this entire debate is about the existence of gods and whether materialism is the correct view of the universe.

    That’s exactly what Philip Johnson said in the beginning. Why do you keep trying to pretend that this is just a scientific debate about the design inference?

  121. 121
    kairosfocus says:

    LM,

    nope; failed motive mongering again . . . rather like how it was trying to discuss with marxists who were forever projecting “reaction” and the like.

    Do you want for me to project to you motivation on materialist worldview and conclude to dismiss all you say on that?

    That would go nowhere but a might and manipulation make right, truth, knowledge etc power struggle.

    Pointless.

    I have excellent reason to recognise that God has acted into my life in many ways, which are utterly independent of the reasons why I have come to believe as a matter of inductive, scientific inference, that there are empirically reliable signs of design as key causal factor that may be empirically detected. Starting with a certain miracle of guidance in answer to my mom’s prayer of surrender; that saved my life over 40 years ago from death due to a chronic, life-threatening lung disease.

    No, the reason I have come to accept the design inference in the world of life is tied to the reasons why I respect and studied the sciences. It makes good inductive, observationally anchored sense.

    Those reasons, first are anchored in my studies in the logic of induction, then in my studies of information theory and communication systems cross-fertilised by studies in thermodynamics and mathematics tied to that. Some of that I outlined faintly above, starting with let’s think about dice and signal to noise ratio and what it implies. Now, ponder for a moment that in the heart of the living cell, we find coded algorithmic info, support nanotech and execution systems, e.g. protein synthesis. That got my attention bigtime. Contrast that with Darwin’s pond and other pre-life scenarios. Blind, highly contingent, needle in haystack search driven by chemical kinetics and the statistical phenomena at the root of thermodynamics since Gibbs, Boltzmann et al.

    I find from this, strong reason to infer to the empirically warranted best explanation of such phenomena, intelligently directed configuration.

    And, once there is good reason to see the reasonableness of a design inference at the root of the tree of life, OOL, that decisively shifts estimation of what is a reasonable explanation of OOBP thereafter. As SA pointed out a little above.

    The same functionally specific complex organisation and associated information is to be explained.

    I can find no solid, empirically anchored basis for seeing the implied blind needle in haystack search to arrive at OOBP dozens of times over, as feasible on blind chance plus mechanical necessity:

    CV + CBDRS [in various proportions] –> DWIM –>BTE –> ToL

    is not grounded in vera causa, adequate observed cause on blind watchmaker mechanisms. Too much haystack, vastly to little atomic-temporal resources to search it, no credible short cuts to put us at the shorelines of islands of functioon implied by the constraints of the right parts put together in the right way, for exceedingly complex and functionally specific entities.

    Pretty much the same reason why I accept the stat form of the second law of thermodynamics: statistical weights of clusters of microstates.

    Some “lotteries” are unwinnable, and a winnable lottery is carefully designed.

    Design makes good sense from the roots up, in short, and I have no a priori commitment against design, whether explicit or implicit. So, when I see that FSCO/I is per a trillion case observational base best explained on design, I go with that.

    So, nope, it’s not motive, save that to go with the weight of empirically anchored evidence that makes sense.

    KF

  122. 122
    Silver Asiatic says:

    SA: Why would you conclude that the only causes of things are physical/mechanical processes?

    LM: Because there’s no evidence of any other kind of causes.

    We observe purposeful causes. Mechanism is deterministic – not purposeful. So, we do have evidence of other causes.

  123. 123
    Silver Asiatic says:

    LM

    There is a very interesting debate among evolutionary biologists concerning the importance of natural selection and other issues. Richard Dawkins and I may disagree on some of these issues but we do not disagree about the fact of evolution.

    ID is part of the debate. IDist may disagree with both you and Richard Dawkins but do not disagree about ‘the fact of evolution’ – as an event giving evidence of Intelligent Design.

    As for ‘evolutionary theory’ – it’s laughable. You and Dawkins can “disagree” but supposedly there are ‘no weaknesses in evolutionary theory’. Let’s face it, there is no theory.

  124. 124
    kairosfocus says:

    SA, In a pause after a call and after setting up a networking connexion earlier this morning. I would also put chance in the mix (including the quantum version that seems to be genuinely random on the whole e.g. RA decay) but that too is distinct from purposeful, rational cause. If you want, try cosmic rays hitting H2O molecules and triggering mutations as a yardstick, or the like. Chance and/or mechanical necessity are non-rational, blindly natural factors. Which BTW can be used by purposeful agents when suitable. As in, dice based games. KF

  125. 125
    kairosfocus says:

    F/N: I should add that there is a design inference argument that does point beyond the observed cosmos. That, on fine tuning that sets up a cosmos fitted for C-Chemistry, aqueous medium terrestrial planet life. And yes, that then backs up the inferences to design on OOL and OOBP. But, that is not where the main debates circulate. From the beginnings of the modern design school of thought in Thaxton et al TMLO, 1984, it was openly acknowledged that design evidence on OOL (antecedent to that on OOBP) does not in itself point to designers as within or beyond the cosmos. Nope, the issue is an inductive one and linked to that questioning of an ideological imposition on science that seems to be begging questions. Namely a priori evolutionary materialism. To answer this, the challenge is that a proper application of the uniformity, like causes like, principle would show adequate cause of FSCO/I in the here-now before projecting empirically uncontrolled explanatory constructs on the remote past of origins. Where, the only empirically warranted cause for such — on a trillion member observational base — is intelligently directed configuration, aka design. Which, recall, speaks to both OOL and OOBP. KF

    PS: Young Earth Creationists are most unlikely to point to fine tuning linked to big bang cosmology. Old Earth ones do, but again are typically caught up in debates on textual interpretation and the like, which is just not a significant debate here. This should help the onlooker see for himself just how off-base the sort of tagging being used is. And, it matters but little whether Dr Moran is more inclined to stress chance variation mechanisms and de-emphasise certain aspects of culling on differential reproductive success, there still is not an adequate, observationally warranted explanation for FSCO/I per blind chance and mechanical necessity at OOL and OOBP. Where, OOL is the ROOT of the ToL. No roots . . .

  126. 126
    Larry Moran says:

    Silver Asiatic says,

    As for ‘evolutionary theory’ – it’s laughable. You and Dawkins can “disagree” but supposedly there are ‘no weaknesses in evolutionary theory’. Let’s face it, there is no theory.

    Please try to distinguish between evolution as a fact and evolutionary theory and how they both differ from the history of life.

    It’s not that hard as long as you open your eyes to the possibility that you might be confused.

    Once you’ve managed those basic ideas and concepts you will be able to make an intelligent contribution to this discussion. Until that time, you can’t.

    No evolutionary biologist would ever say that there are “weaknesss” in evolutionary theory but they would all say that it’s not complete. On the other hand, no evolutionary biologist would ever deny that chimpanzees and humans evolved from a common ancestor over a period of several million years (about five million years).

    Do you accept the scientific fact that humans and chimps share a common ancestor or do you reject that fact?

    Intelligent Design Creationists need to make up their minds whether common descent is required in order to believe in intelligent design. They need to decide whether evolution happened, but it is guided or planned by gods, or whether they deny evolution.

    I know that many accept evolution and common descent. It’s time for them to speak up whenever someone denies evolution. Can a Young Earth Creationist really be part of the movement when they claim that all of science is wrong about the age of the Earth?

  127. 127
    Box says:

    LM: Do you accept the scientific fact that humans and chimps share a common ancestor or do you reject that fact?

    It’s a hypothesis, right? Or is there actual evidence that officially elevated it to a fact?
    If so, which evidence? Please be specific.

  128. 128
    mike1962 says:

    Larry Moran: Do you accept the scientific fact that humans and chimps share a common ancestor or do you reject that fact?

    With regards to human origins, there are at least three possibilities:

    1. Humans were created from scratch without any ancestor.

    2. Humans evolved via non-telic processes from an ancestor that is common with chimpanzees. Humans are an accident of nature.

    3. Humans were brought about by a creator by deliberately modifying an ancestor that is common with chimpanzees. This modification may have been done in several steps.

    Setting aside option #1,

    Questions:

    To what degree of precision does the Modern Synthesis confirm option #2?

    To what degree of precision does the Modern Synthesis rule out option #3?

  129. 129
    Silver Asiatic says:

    LM

    Please try to distinguish between evolution as a fact and evolutionary theory and how they both differ from the history of life.

    It’s not that hard as long as you open your eyes to the possibility that you might be confused.

    There’s quite a lot to be confused about in those concepts. You’re claiming that Mr. Dawkins himself is confused about the theory. As for what the term ‘evolution’ actually means, that is also an area of confusion. I’d like to think that you have all the right answers to these things, but yours is merely one opinion among many conflicting views within biology.

    Once you’ve managed those basic ideas and concepts you will be able to make an intelligent contribution to this discussion. Until that time, you can’t.

    I think it’s pretty clear to most of us that you’re not well-informed about what ID is. Beyond that, I think its easy to see that you’re unsure about evolution itself.

    Do you accept the scientific fact that humans and chimps share a common ancestor or do you reject that fact?

    First, I deny that it is a fact. Secondly, sharing a common ancestor is as much evidence for ID as for any other view.

    Intelligent Design Creationists need to make up their minds whether common descent is required in order to believe in intelligent design.

    As above, this is incorrect. You don’t understand the ID proposal. “There is evidence of intelligent design in nature”. One does not need to affirm or deny common descent. You should consider that you might be confused about what ID proposes.

    They need to decide whether evolution happened, but it is guided or planned by gods, or whether they deny evolution.

    Again, this is irrelevant. “Evidence of design” – that’s what it’s about. Your claim would be like me insisting that all evolutionists have to come to a conclusion about Origin of Life theories. It’s outside of the scope of that research. The same with ID and implications of evolutionary theory.

    I know that many accept evolution and common descent. It’s time for them to speak up whenever someone denies evolution.

    Again, irrelevant. “Evidence of intelligent design in nature” doesn’t require a position on common descent.

    Can a Young Earth Creationist really be part of the movement when they claim that all of science is wrong about the age of the Earth?

    ID is a scientific research project. It’s not a ‘movement’.

    So, as I said – it’s clear that you don’t know the topic you’re attempting to critique.

  130. 130
    Mung says:

    Larry Moran then:

    You say this even though you know full well that there’s another possibility; namely, that the real, complete, version of evolutionary theory might be correct.

    Larry Moran now:

    No evolutionary biologist would ever say that there are “weaknesss” in evolutionary theory but they would all say that it’s not complete.

  131. 131
    Carpathian says:

    kairosfocus:

    I can find no solid, empirically anchored basis for seeing the implied blind needle in haystack search to arrive at OOBP dozens of times over, as feasible on blind chance plus mechanical necessity:

    It is not a blind search.

    Physics is a filter that does not allow simply any combination of matter.

    It also has the means to enforce certain configurations.

    Take two bar magnets and put them side by side, N pole to S pole.

    Now try putting them together N pole to N pole and you will find it doesn’t work.

    An intelligent designer is also limited by nature as to what he can do.

    Any designer that can organize matter despite the laws of nature is by definition supernatural.

    If the designer in ID is supernatural, then ID cannot be considered science.

  132. 132
    mike1962 says:

    Carpathian: If the designer in ID is supernatural, then ID cannot be considered science.

    Then it would follow if it turns out that human consciousness is supernatural, then analyzing human artifacts cannot be considered science. How far are you willing to commit to your anti-supernatural stance?

    Moreover, there are more options that you apparently have not considered. For example, perhaps the creator of the universe is completely supernatural, and the creator(s) of life on earth are partly natural and partly supernatural, like humans might be, working within the universe.

  133. 133
    Carpathian says:

    mike1962:

    Then it would follow if it turns out that human consciousness is supernatural, then analyzing human artifacts cannot be considered science.

    While human consciousness might be supernatural, our artifacts are not.

    Not one single law of nature was violated for anything humans have constructed.

    My point was that the intelligent designer must be limited by nature in the sense that he cannot violate the laws of nature when designing.

    In the event that the laws of nature do not apply to the designer, we are no longer debating in a scientific manner.

    If the designer is not limited by nature, for any reason, we are talking about religious creationism.

  134. 134
    mike1962 says:

    Carpathian: While human consciousness might be supernatural, our artifacts are not.

    Which means that just because something is supernatural, or partly supernatural, it doesn’t necessarily follow that it is non-scientific to study it’s artifacts.

    Not one single law of nature was violated for anything humans have constructed.

    You should say that it is not known that any laws of nature are violated when humans construct things.

    My point was that the intelligent designer must be limited by nature in the sense that he cannot violate the laws of nature when designing.

    Not necessarily. “Laws of nature” is merely a moniker we give things in nature that appear to us to operate in a regular manner. Consciousness, even human consciousness, it if it is supernatural, would necessarily violate the “laws of nature” every time it acted upon matter. You may be violating the “laws of nature” every time you willfully move your little finger. It’s an open question.

    In the event that the laws of nature do not apply to the designer, we are no longer debating in a scientific manner.

    Not necessarily. We might be able to rule out that a given artifact is achieveable by anything except a supernatural entity arranging objects within nature in a way nothing else could.

    If the designer is not limited by nature, for any reason, we are talking about religious creationism.

    A supernatural entity need not have anything to do with “religion.” All religions could be the invention of humans, and yet a supernatural intelligence capable of creating the universe, and interfering and intervening with natural objects within it could conceivably exist.

  135. 135
    Mung says:

    T. Ryan Gregory believes “it is important to distinguish evolution as fact, theory, and path.”

    An example of why it is important to distinguish evolution as fact, theory, and path.

    Larry seems to have difficulty separating the three.

  136. 136
    Carpathian says:

    mike1962:

    Which means that just because something is supernatural, or partly supernatural, it doesn’t necessarily follow that it is non-scientific to study it’s artifacts.

    We could certainly try to study it but how far could you get with the scientific method when you apply it to something supernatural in origin.

    The problem with ID is that if we determine something is natural in origin when it is in fact supernatural in origin, we cannot come to the conclusion that there is any design involved even though there may be.

    This means a scientific study of this artifact is impossible since we would only see non-design.

    This makes ID impossible if supernatural forces were actually involved.

    This creates a paradox in the sense that we see “natural” design, not intelligent design, despite the fact that there is a designer in the background, a designer whose presence ID is trying to prove with scientific methods, as people like Dembski are trying to do.

    You cannot scientifically prove the supernatural with naturalistic science.

    This what I see ID trying to do.

  137. 137
    bFast says:

    Larry Moran,

    I teach a course on critical thinking and we spend a lot of time discussing how to argue.

    You say the darndest things. I watch your behavior, and don’t see someone qualified to teach such a course. I would strongly suggest that you rework your course from the ground up. I would strongly suggest that you eliminate the term “argue” from its vocabulary, and replace it with dialog and discuss.

    The approach I take to blogging is that of the student-teacher. I seek to learn, and I have learned from you. I also seek to teach. You leave me with the impression that you see yourself as teacher — one who has nothing to learn. You may have a qualification to teach evolutionary biology, and biology in general. However, you have shown that you are really badly lacking in dialoging skills.

    One of the most important lessons is on learning to understand the point of view of your opponents. You can really have a good debate if you don’t understand what your opponents are saying.

    Larry Moran, another weird thing for you to say. Have you understood the ID perspective? I think you think you have, but you have not demonstrated so with feedback. Instead, you have been the master of blasting people with derogatory terminology, and being dismissive of their perspective. You don’t teach the art of winning arguments by throwing insults, do you?

    The other behavior I have seen from you very often is abandoning the loosing topic. You bounce from one thought line to another whenever you think that you may be loosing one. This may be a good strategy for arguing, but it is not a good strategy for a dialog that supports mutual growth.

  138. 138
    mike1962 says:

    CarpathianWe could certainly try to study it but how far could you get with the scientific method when you apply it to something supernatural in origin.

    Take, for example, a Rubic’s Cube. When the cube is “solved”, each side of the cube has a uniform color. By turning the sub-blocks on the axes, you can scramble the colors on each side of the cube so that the sides do not have a uniform color. By turning the sub-blocks on the axes, if you know how, you can always undo the scrambling and go back the uniform colors on each side.

    Now, I, by circumventing the “normal rules of the game”, can peel the stickers off and put them back on in such a way that you could never achieve by simply turning the sub-blocks on the axes. If you ever ran across one of my special cubes, you can try and try and never get it back to uniform colors. If you analyzed it you could figure out why: the scrambled starting point was not possible under the normal rules. Analysis could be carried out in a perfectly normal and scientific way to determine that somebody intervened in an unusual way, in a way not possible using normal rules. A “miracle” occurred.

    The problem with ID is that if we determine something is natural in origin when it is in fact supernatural in origin, we cannot come to the conclusion that there is any design involved even though there may be.

    Sure you could. You could come to an inference that intervention occurred, if given the normal operating rules of the system, the artifact is impossible. You could come to a reasonable inference that such a thing occurred, if given the normal operating rules, the artifact is exceedingly unlikely.

    The only reason someone might have to resist such a reasonable inference would not be because of “science”, but because of some prior philosophical commitment.

  139. 139
    mike1962 says:

    CarpathianWe could certainly try to study it but how far could you get with the scientific method when you apply it to something supernatural in origin.

    Take, for example, a Rubic’s Cube. When the cube is “solved”, each side of the cube has a uniform color. By turning the sub-blocks on the axes, you can scramble the colors on each side of the cube so that the sides do not have a uniform color. By turning the sub-blocks on the axes, if you know how, you can always undo the scrambling and go back the uniform colors on each side.

    Now, I, by circumventing the “normal rules of the game”, can peel the stickers off and put them back on in such a way that you could never achieve by simply turning the sub-blocks on the axes. If you ever ran across one of my special cubes, you can try and try and never get it back to uniform colors. If you analyzed it you could figure out why: the scrambled starting point was not possible under the normal rules. Analysis could be carried out in a perfectly normal and scientific way to determine that somebody intervened in an unusual way, in a way not possible using normal rules. A “miracle” occurred.

    The problem with ID is that if we determine something is natural in origin when it is in fact supernatural in origin, we cannot come to the conclusion that there is any design involved even though there may be.

    Sure you could. You could come to an inference that intervention occurred, if given the normal operating rules of the system, the artifact is impossible. You could come to a reasonable inference that such a thing occurred, if given the normal operating rules, the artifact is exceedingly unlikely.

    The only reason someone might have to resist such a reasonable inference would not be because of “science”, but because of some prior philosophical commitment.

  140. 140
    mike1962 says:

    Admin please delete the double post.

  141. 141
    sean samis says:

    At #129, Silver Asiatic wrote, among other things, “ID is a scientific research project. It’s not a ‘movement’.

    Really? And pray tell us how these “scientists” are experimenting to identify even the category of creatures which includes our intelligent designer? And what experiments are being pursued to explain how our designer can be a naturally occurring life form but we cannot be? There are so many questions, it’s hard to pick the best ones!

    What peer-reviewed biology journals are publishing their papers?

    sean s.

  142. 142
    Cross says:

    Larry Moran @ 118

    “If you are willing to admit that once life began then evolution can explain the subsequent history without resorting to gods, then we can discuss the origin of life.

    Are you willing? If so, then stop attacking evolution as though you reject it.

    As for the “debate” on the origin of life, I have no detailed materialistic explanation. Do you have a detailed nonmaterialistic explanation of are you just bluffing?”

    Dr Moran, I have never “attacked” evolution as such. It is true, I am a creationist (not young earth) but I am open to God using in part, evolution as part of the plan. In fact, like most creationists, I have no problem with micro evolution or as it would better be described as, built in adaption. I think that there is very little real evidence for macro evolution, but I am open to be convinced.

    However, I believe God created life and you would need to provide a plausible non-life to reproducing life explanation for me to abandon that belief.

    My “attack” is on bad science and bad scientists that reject any possibility other than a materialist one. Claiming that science requires this, they have co-opted science from the history of many great scientists that were believers in God.

    You have already stated that you don’t believe in God, thus, you are already closed to a whole range of evidence, this is bad science.

    I am not bluffing, I am not the one claiming that life created itself, it is you and any other scientist, that claims this without ANY plausible way for this to start, that is bluffing.

    Cheers

  143. 143
    Larry Moran says:

    Silver Asiatic says,

    Again, irrelevant. “Evidence of intelligent design in nature” doesn’t require a position on common descent.

    Are there any Young Earth Creationists here? What do you thinks of Stephen Meyer’s book Darwin’s Doubt? Do you agree with him that many species of animals appear in the fossil record over a relatively short period of time about 500 million years ago?

    If not, how can you believe anything else he writes in that book?

  144. 144
    bFast says:

    Larry Moran (111)

    Your understanding of the distinction between methodological naturalism and philosophical naturalism is flawed. In fact, there really is no distinction.

    Others seem to have a different perspective than you do on this. Consider this from Stanford University ( http://plato.stanford.edu/entr.....sm/#MetNat )

    ‘methodological naturalism’ asserts that religious commitments have no relevance within science: natural science itself requires no specific attitude to religion, and can be practised just as well by adherents of religious faiths as by atheists or agnostics

    Many philosophers have rejected the claim that science is restricted to a form of methodological naturalism that allows for the presence of gods. Great! I know that Richard Dawkins is of this mind. I wish the 3rd way crowd (you remember them, the guys with good cridentials that say that RV+NS (including neutral theory) is woefully inadequate to explain life on earth, then go off on wild tangents grasping to find some naturalistic straw to hold on to.)

    One way is Creationism that depends upon intervention by a divine Creator. That is clearly unscientific because it brings an arbitrary supernatural force into the evolution process.

    ( thetheirdwayofevolution.org )

    Lastly, philosophical naturalism should properly be prohibited from the American school system. It is a religious position — one that is disclusive of other respected, even dominant, religious perspectives.

  145. 145
    Larry Moran says:

    Silver Asiatic says,

    As for what the term ‘evolution’ actually means, that is also an area of confusion. I’d like to think that you have all the right answers to these things, but yours is merely one opinion among many conflicting views within biology.

    It’s true that there are different opinions about the meaning of the word “evolution” but there’s a pretty good consensus if you read the textbooks.

    Here’s my definition …

    What Is Evolution?

    Whenever I talk about evolution you will know that this is what I mean. I can’t do better than that.

    What’s your definition? What’s the standard ID definition and how does it compare with those in the evolutionary biology textbooks?

    Do you deny that evolution occurs according to my definition? Do you deny that it occurs according to your definition? Do Young Earth Creationists agree?

  146. 146
    Larry Moran says:

    @Box

    Do you deny that humans and chimpanzees share a common ancestor or are you really interested in knowing about the evidence?

    If you deny it, then it’s likely that you aren’t interested in scientific evidence so I’ll be wasting my time.

    Maybe some ID proponents would like to step in and educate Box? You’d be doing him/her a favor.

  147. 147
    Larry Moran says:

    Cross says,

    You have already stated that you don’t believe in God, thus, you are already closed to a whole range of evidence, this is bad science.

    There are about 1000 different gods. You probably don’t believe in 999 of them. Does that mean you are closed to a whole range of evidence? What about leprechauns? Are you closed to that evidence as well?

    There are decent philosophers who post here. They would point out the flaw in your logic but there’s an unwritten rule that creationists will never criticize other creationists. That’s a shame.

  148. 148
    Larry Moran says:

    bFast says,

    Lastly, philosophical naturalism should properly be prohibited from the American school system. It is a religious position — one that is disclusive of other respected, even dominant, religious perspectives.

    How are students ever going to learn about atheism if it isn’t taught in school?

    I support teaching the controversy. Do you?

  149. 149
    Cross says:

    Larry Moran @ 147

    “There are about 1000 different gods. You probably don’t believe in 999 of them. Does that mean you are closed to a whole range of evidence? What about leprechauns? Are you closed to that evidence as well?

    There are decent philosophers who post here. They would point out the flaw in your logic but there’s an unwritten rule that creationists will never criticize other creationists. That’s a shame.”

    Typical deflection of the issue. I never claim to be a philosopher and my belief in the Christian God is a separate issue not related to ID, much as kairosfocus has stated.

    The issue is not which God or anything about God, it is that you reject ANY God and thus do not accept any possibility outside materialist causes, this is bad science.

    Are you open to evidence of any God? I am open to you proving God does not exist, just form life from non-life without intervention.

    Cheers

  150. 150
    Larry Moran says:

    bFast is correct that there are differing views on whether science is restricted to methodological naturalism. The consensus these days seem to be tilting against this claim.

    If you are going to use the term “methodological naturalism” then you have to understand that not everyone agrees with you.

    Here are some blog posts …

    Can Science Test Supernatural Worldviews?

    Is Science Restricted to Methodologial Naturalism?

    Here Be Dragons

    http://sandwalk.blogspot.com/2.....ot-to.html“>Methodological Naturalism – How Not to Attack Intelligent Design Creationism

  151. 151
    Larry Moran says:

    Cross asks,

    Are you open to evidence of any God?

    Yes, of course.

    I’ve been saying this on the internet for 26 years.

    I have not seen any convincing evidence for gods so I don’t believe in any of them. I am an atheist.

  152. 152
    Mung says:

    Larry, long before you showed up claiming Darwin’s Doubt (2013) was a problem for YEC I pointed out that The Privileged Planet (2004) posed problems for YEC. You’re not even original.

    I guess when you say Intelligent Design Creationism you’re not really attempting to equate ID with YEC, because in all honesty you know they are not the same.

    …but there’s an unwritten rule that creationists will never criticize other creationists.

    LoL. You really should spend more time here.

  153. 153
    Mung says:

    I have not seen any convincing evidence for gods so I don’t believe in any of them. I am an atheist.

    The gods are stalking you. You just need to grow eyes in the back of your head to see them.

  154. 154
    Cross says:

    Larry Moran @ 151

    “Are you open to evidence of any God?

    Yes, of course.”

    Well Dr Moran, you at least have a sense of humor. I suspect that if they analysed your DNA and found in the “junk” section a sequence which when converted to ascii said” larry moran, made by God” you would still not believe it.

    I have read some of your blog, does not strike me as written by someone with an open mind.

    Cheers

  155. 155
    Mung says:

    Dr. Moran,

    Would you believe it to be a fact that humans and chimps share a common ancestor lacking a theory that is capable of explaining the evidence you must believe exists and upon which you believe it has been established to be a fact?

    Or is the theory of evolution irrelevant to the fact of evolution?

  156. 156
    Barry Arrington says:

    Moran:

    There are about 1000 different gods. You probably don’t believe in 999 of them.

    Sigh. You justify your atheism with an assertion that would get any freshman theology student flunked if he wrote it on exam. How are we supposed to take you seriously.

    Here’s why this statement is so facile.

  157. 157
    bFast says:

    Larry Moran, “I support teaching the controversy. Do you?” Yes, I support teaching the controversy. I support dialoguing about the controversy respectfully. I even very strongly support clarifying that alternative views such as ID are not mainstream. I will say that I am surprised that you are willing to give the ID community this card.

  158. 158
    Querius says:

    Larry Moran @ 109 recalled,

    Back around 1970, when most of us became aware of the problem, we wondered what possible purpose all that extra DNA could serve. Almost everyone thought that it must have some kind of function.

    This is exactly the position of the ID paradigm (with the emphasis on design and taking no position on any designer). I guess back in 1970, you and your colleagues were IDiots like us (but you know better now). 😉

    Does that also answer my question of which Larry Moran would more likely succeed in advancing scientific progress in the areas that are poorly understood? After all, in your view you were able to falsify the assumption of design in “junk” DNA, right?

    If you are willing to admit that once life began then evolution can explain the subsequent history without resorting to gods, then we can discuss the origin of life.

    But you’re simply substituting series of probabilistic miracles for the results of an astounding biochemical programming language that we’re only starting to understand. Some cosmologists try to do the same with the origin of the universe, using quantum fluctuation as their “god,” not realizing that probability doesn’t exist without space-time.

    Since you need an external agency to pop the universe into existence from non-existence, and that external agency is not subject to the laws of the previously non-existent nature, it’s not much of a stretch to wonder whether the same agency popped an astounding biochemical language into existence along with life itself. If that were true, and I know you believe it isn’t, it doesn’t affect scientific investigation in the slightest except for an amazing sense of awe about discovering the hidden mechanisms of life.

    You’re looking for a naturalistic way that life adapts to its environment—as of course you should—but this has no relevance regarding belief in God. The people who believe in an immaterial God don’t need material proof, the people who choose not to believe in an immaterial God don’t want a material proof.

    -Q

  159. 159
    bFast says:

    Larry Moran (146)

    @Box

    Do you deny that humans and chimpanzees share a common ancestor or are you really interested in knowing about the evidence?

    I’ll take this one on. There is one piece of evidence that compels me to hold to common ancestry of human and chimp. It is my understanding that both have about 80 shared disease producing mutations floating around in their genome. Which is to say that there are about 80 diseases which have been traced back to specific mutant alleles where both humans and chimps have those alleles in the same genes.

    If this one piece of evidence can be reasonably challenged, I will become much more open minded on this matter.

    However, Larry Moran, I would like to have an honest, complete, debate with you about the characteristics of the HAR1F rna gene. Everything I can see in this gene says that it must have taken multiple simultaneous mutations — something that cannot realistically happen in a naturalistic model.

  160. 160
  161. 161
    Box says:

    LM: Do you accept the scientific fact that humans and chimps share a common ancestor or do you reject that fact?

    Box: It’s a hypothesis, right? Or is there actual evidence that officially elevated it to a fact?
    If so, which evidence? Please be specific.

    LM: Do you deny that humans and chimpanzees share a common ancestor or are you really interested in knowing about the evidence?

    [Translation:] There is no evidence that officially elevates the hypothesis ‘humans and chimps share a common ancestor’ into a scientific fact. I would certainly reference such evidence if it existed, however it does not. You caught me bluffing.

  162. 162
    kairosfocus says:

    Carpathian:

    Just for info:

    It is not a blind search.

    Physics is a filter that does not allow simply any combination of matter.

    It also has the means to enforce certain configurations.

    Unless something is highly contingent it has low information storage potential. That is why it is vital to understand, say how the 4-state possibilities GCAT/U for D/RNA are independent of the chaining chemistry. If it were not, the ability to store info would be reduced. Further to this, the very existence of variant codes and the creation of artificial variants shows that the R/DNA code is not driven by mechanical necessity. I also pointed out long since how the CCA tip of the tRNA is a universal link, it is what for short we can call loading enzymes that put particular AAs on particular tRNAs. The contingency involved is patent.

    This has already been pointed out to you but it obviously does not fit your ideology.

    Further to this, in an AA chain, the peptide bond is not the only feasible one, and the distribution of proteins in AA sequence space is clumped and sparse with many small domains.

    Under blind watchmaker circumstances, that does pose a blind, needle in haystack search challenge to the assembly of first cell based life and onward to the clusters of proteins needed to form fresh tissue types for organs required for organisation of body plans. Mix in embryological requisites and the regulatory challenge greatly compounds the issue as the bricks have to be correctly assembled.

    Again, I do not expect this to break through your ideological shield, but I am fairly confident that it will point out to others the gap between what you seem forced to assert and easily confirmed facts.

    KF

  163. 163
    kairosfocus says:

    BA,

    on 999 vs 1 vs 0 etc, it seems to me the key issue is to understand roots and modes of being.

    For, non-being, utter nothingness, if it ever was, as such cannot have causal capacity, would forever obtain. Thus, a first phil qn is, why is there something instead of nothing. Linked is of course the issue of the one and the many: coherent unity amidst diversity in a cosmos not a chaos.

    Such q’s are prior to science, which makes them but little reflected on even by the highly credentialled in our day.

    Going on, we see that there are possible vs impossible beings [square circles have mutually incoherent core requisites and cannot be formed] and of possible beings, many are contingent, causally dependent on prior enabling factors. As, a fire depends on heat, fuel, oxidiser and an un- interfered- with chain reaction [as in Halon extinguishers]. That dependence is why such can begin, end and it is how they are sustained. By contrast we consider beings with no such dependencies, i.e. candidate necessary beings. Things like two-ness exist and must exist in any possible world, being embedded in root structures.

    From such, we see that if something now is, a unified diverse world, something always was. Something eternal and necessary.

    It is then easy to see that a serious candidate necessary being will be world-foundational, will be either impossible or else actual, and therefore it is reasonable to consider a unifying root being who grounds reality; God.

    Consider also our own status as morally governed, i/l/o the valid part of Hume’s guillotine, namely that the IS to ground OUGHT must be in the root of reality. Where, the notion that in effect the sense of moral obligation is delusional, would let loose general delusion and would bring rationally contemplative mindedness into self-referential incoherence.

    After centuries of debates, there is but one serious candidate IS to ground OUGHT: the inherently good creator-God, a necessary and maximally great being worthy of service by doing the good.

    In short, the God of generic ethical theism is reasonable.

    And, the nature of God is also sufficiently clear and is utterly diverse from the small-g gods that are being trotted out as though paganism is a sufficient objection to dismiss theism. (Once such is baldly stated, its sophomoric character is obvious.)

    There are of course debates about God and his interventions among us.

    The same fact of deep disputes and diverse views holds on practically any subject of significance, and our possibilities of error will not change the fundamental realities that exist. Instead, we should cultivate the path of seeking truth and right, turning from error and darkness to truth and light. (And of course, my recent response to AS will help clarify: http://www.uncommondescent.com.....of-theism/ )

    The upshot of this, is that too many new atheists are not thinking about God beyond superficial dismissive rhetoric.

    They need to think again, starting with the implications of modes and roots of being and the point that God is a serious candidate necessary being. As in, unless they can show that God is in fact not a serious candidate NB [a bit hard given that eternality, unity and self-sufficiency are core attributes for the very idea of God], he will either be impossible or actual. And, since the failure of objections on the problem of evil, it is hard to even see where to begin such a project.

    In short, it is not unreasonable or irrational to take the reality of God seriously, and the transforming experience of encounter with God on the part of millions across the world and down the ages should give serious pause.

    Where, of course, it should be fairly plain that such thinking is simply independent of the question of there being observationally evident signs such as functionally specific complex organisation and associated information that — on a trillion member base of observations of actual cause — reliably indicate intelligently directed configuration as key causal factor.

    Which, I notice, is being consistently ducked, distracted from or twisted into strawman caricatures, or else blandly asserted away.

    Interesting.

    KF

  164. 164
    Silver Asiatic says:

    sean s

    Really? And pray tell us how these “scientists” are experimenting to identify even the category of creatures which includes our intelligent designer?

    As I said, that’s like asking how evolutionists are experimenting to find the origin of life. ID researches evidence of intelligent design in nature. It does not propose a theory about who the designer is.

    And what experiments are being pursued to explain how our designer can be a naturally occurring life form but we cannot be?

    You’re thinking about some other scientific project (or something), not ID.

    What peer-reviewed biology journals are publishing their papers?

    http://www.discovery.org/id/peer-review/

  165. 165
    Larry Moran says:

    Box says,

    [Translation:] There is no evidence that officially elevates the hypothesis ‘humans and chimps share a common ancestor’ into a scientific fact. I would certainly reference such evidence if it existed, however it does not. You caught me bluffing.

    Oops! Caught again.

    I was trying to hide the fact that there is no scientific evidence whatsoever that humans and chimpanzees share a common ancestor.

    It’s all just a massive ruse perpetuated by scientists in order to fool creationists into accepting evolution.

    I’m off to church.

    IDiot.

  166. 166
    Larry Moran says:

    bFast says,

    I’ll take this one on. There is one piece of evidence that compels me to hold to common ancestry of human and chimp.

    The total evidence comes from shared similarities, the fossil record, and molecular phylogeny.

    Since I’m mostly interested in molecular evolution, I share your interest in that data. It’s solid evidence for the fact that humans and chimps share a common ancestor.

    Did you read my posts on the comparison of the human and chimp genomes? Not only does that comparison demonstrate shared ancestry, it also confirms that most mutations are neutral and fixed by random genetic drift.

    I haven’t seen any response from creationists that offers an alternative explanation.

    How do you explain the differences between chimpanzees. humans, and macaques?

    Why are the human and chimpanzee/bonobo genomes so similar?

    On the frustration of trying to educate IDiots

    bFast, why do you suppose that Young Earth Creationists ignore all the evidence for common descent but still support ID? Most of the ID arguments against evolution rely on the assumption of common descent and the fact that evolution of some sort occurs.

  167. 167
    Silver Asiatic says:

    Larry Moran @ 145

    It’s true that there are different opinions about the meaning of the word “evolution” but there’s a pretty good consensus if you read the textbooks.

    Here’s my definition …

    What Is Evolution?

    That’s an interesting post. You put some considerable analysis into the variety of definitions. In the end, you offer your opinion on what ‘evolution’ is supposed to mean, in so doing, you claim dictionary definitions, textbook explanations of the term, and definitions offered by fellow biologists are “are simply wrong”, and “not how one should define evolution”.

    Again, interesting opinions. Of course, nobody owns the definition of the term, as much as you might think you do (or it appears that way).

    You have already used (or used in that very blog post) several different/conflicting ideas under the term ‘evolution’ – and this includes supposed ‘fact of’, ‘theory of’ (which should be ‘theories of’), microevolution and macroevolution … as well as, my favorite, “the idiot version of evolution” which is what Richard Dawkins believes in.

    So for me, its enough to see that there is widespread confusion within the biological community about what evolution is. That’s nothing new and is no surprise. The same evolutionary community, dishonestly claims that “evolution is a fact”, without specifying that all they mean is “organisms have shown some genetic change over time”.

    Those of us who have been debating this topic for a while know the deceptive nature of that little game – the bait and switch. Evolution means one minimal thing when pressed for evidence. Evolution means “the single explanation for the development of all lifeforms and every feature of every lifeform through the entire history of earth’s biosphere. That’s the dishonest little game that is played with the public. But we’ve known all that for a long time.

    You anticipated this objection in your post:

    Anti-evolutionists often claim scientists are being dishonest when they talk about evolution.

    You might ask yourself why anti-evolutionists arrived at that conclusion. I gave you some hints above.

    As for my own personal definition of the term, I find that an absurd request. Your definition conflicts with what we find even among other scientists. The term means various contradictory things. That’s what it is.

    For my understanding, evolution is an ambiguous term used to manipulate various outcomes. I wouldn’t try to claim that there is ‘one correct definition’ – on the contrary, there are contradictory definitions that are all perfectly ‘correct’. Evolution cannot be falsified because one can always change the definition of the term.

    “Evolution” can equally be said to be: “the intelligently designed process that explains the emergence of biological forms over the history of life on earth”.

    In general however, it means: “Evolution is a process that sometimes results in heritable changes in a population (or not) spread over many generations or a few, primarily through natural selection acting on random mutations and primarily through genetic drift and the accumulation of neutral mutations and primarily through unknown, blind, unintelligent, undirected, processes, and through self-organization, which through the process of emergence caused everything in life to be what it is today, and which proves that God doesn’t exist and he wouldn’t have done things this way anyway.”

    That’s the concise version. There’s a lot more detailed version that one can piece together from hundreds of sources.

  168. 168
    Silver Asiatic says:

    LM

    … humans and chimps share a common ancestor.

    There is no directly observed evidence of that. None.

    It’s not a demonstrable fact.

  169. 169
    Larry Moran says:

    bFast asks,

    However, Larry Moran, I would like to have an honest, complete, debate with you about the characteristics of the HAR1F rna gene

    I don’t know anything about this possible gene. There doesn’t seem to have been much work on it in the past few years.

    Is it known to have a function or is it just junk RNA? Do you have a reference to a paper showing that the RNA has an actual function?

  170. 170
    Box says:

    Larry M: I was trying to hide the fact that there is no scientific evidence whatsoever that humans and chimpanzees share a common ancestor.

    So, instead of referencing extraordinary conclusive evidence, which officially elevates the hypothesis ‘humans and chimps share a common ancestor’ to a scientific fact, you are moving the goalposts. You now pretend that it is my position that “there is no scientific evidence whatsoever that humans and chimpanzees share a common ancestor”. To be clear, it is my position that there is supportive evidence for this hypothesis.

    However it is your explicit claim that ‘humans and chimps share a common ancestor’ is a scientific FACT.
    I’m not letting you get away with it: retract your claim or reference the extraordinary conclusive evidence to back up your claim.

  171. 171
    Barry Arrington says:

    K @ 165:

    The upshot of this, is that too many new atheists are not thinking about God beyond superficial dismissive rhetoric.

    Such as Larry Moran. He shows up and presents himself as the pure light of intellect in which we poor benighted rubes can bask as the shackles of our ignorance fall from our hands. And then he makes an argument that any educated teenager could rebut in five minutes.

    Larry, I beseech you, truly I do. Try to understand our arguments. If you don’t believe them after that, fair enough. But setting up straw men and knocking them down does neither you nor us any good, wouldn’t you agree?

  172. 172
    Larry Moran says:

    Silver Aiatic says,

    In general however, [evolution] means: “Evolution is a process that sometimes results in heritable changes in a population (or not) spread over many generations or a few, primarily through natural selection acting on random mutations and primarily through genetic drift and the accumulation of neutral mutations and primarily through unknown, blind, unintelligent, undirected, processes, and through self-organization, which through the process of emergence caused everything in life to be what it is today, and which proves that God doesn’t exist and he wouldn’t have done things this way anyway.”

    Great! You and I agree that evolution is false, using your definition of evolution.

    That was easy.

    Wanna talk about the Stanley Cup playoffs?

    IDiot.

  173. 173
    Larry Moran says:

    Barry Arrington says,

    Try to understand our arguments. If you don’t believe them after that, fair enough.

    I’m trying. Really I am.

    It’s not easy. Just look at all the comments above and see what I mean. You guys are all over the map.

    I suggest you try and clean up your acts before pointing fingers at others. Do you or do you not believe in common descent? Is that required in ID or not? Is everything in ID consistent with the spontaneous creation of all kinds less than 10,000 years ago?

  174. 174
    Silver Asiatic says:

    Nice job, Larry. We couldn’t ask for a better exemplar of the angry atheist/evolutionist. Keep up the good work!

  175. 175
    Larry Moran says:

    Querius says,

    The people who believe in an immaterial God don’t need material proof, …

    I know, and that’s a problem.

    I means we can never have a serious discussion about evolution and intelligent design because we don’t agree on the fundamental rules of scientific debate.

    … the people who choose not to believe in an immaterial God don’t want a material proof.

    Yes we do. Science is a way of knowing that relies on evidence. If you want to know whether gods exist, you need evidence. But you’ve already denied that evidence is important so we can’t discuss that either.

    However, we can conclude that science and religion are in conflict.

  176. 176
    Larry Moran says:

    When I said that humans and chimps share a common ancestor, Silver Asiatic said,

    There is no directly observed evidence of that. None.

    Nice job, Silver Asiatic. We couldn’t ask for a better exemplar of the IDiot in action. Keep up the good work!

    What astonishes me about the ID world is that we have people right here on this thread who accept the evidence for a common ancestor of humans and chimps.

    Yet they never, ever dispute the words of another creationist. Why is that?

    What am I supposed to believe about ID? Do I believe that ID denies common descent or accepts it? Do I believe that ID rejects all evidence of evolution, some of it, or none of it?

  177. 177
    Barry Arrington says:

    Moran:

    Do you or do you not believe in common descent?

    Surely you know that leading ID theorist Michael Behe believes in common descent. Why would you ask such a question?

  178. 178
    mike1962 says:

    Larry Moran,

    Are you going to answer my questions @128?

  179. 179
    Barry Arrington says:

    Moran:

    You guys are all over the map.

    Are you suggesting that unless everyone who subscribes to a theory agrees on every particular then the theory is false?

    Because if that is what you are suggesting you just tossed modern evolutionary theory out the window. Talk about all over the map. As I recently demonstrated, there is not a single core principle upon which all proponents of modern evolutionary theory agree.

    I suspect that is not what you mean. I suspect you are saying that’s a problem for thee, but not for me.

  180. 180
    Silver Asiatic says:

    SA

    There is no directly observed evidence of that. None.

    LM:

    Yet they never, ever dispute the words of another creationist. Why is that?

    Nobody disputes that because they can’t.

    Well, of course, there’s your devastating argument: “I’ll call you an IDiot”.

    Wow – brilliant.

  181. 181
    Silver Asiatic says:

    BA

    Are you suggesting that unless everyone who subscribes to a theory agrees on every particular then the theory is false?

    Professor Moran is already on record in opposing Richard Dawkins’ view as “the idiot version of evolution”.

    But we’re supposedly, all over the map.

  182. 182
    Silver Asiatic says:

    LM

    What am I supposed to believe about ID?

    Perhaps someone could help you create a strawman version of it so you could refute that? Or on the other hand, you could accept that ID is about evidence of design in nature.

    Do I believe that ID denies common descent or accepts it?

    Does evolutionary theory accept abiogenesis or reject it? Oh, it’s a study that is not directed to that question? Interesting. Ok, let me ask again then – does evolutionary theory accept abiogenesis or reject it? I can’t seem to get an answer here!!!

    Do I believe that ID rejects all evidence of evolution, some of it, or none of it?

    Some aspects of nature show evidence of having been designed by intelligence.

    Wait a second! Does evolution have a position on abiogenesis or not?

  183. 183
    Larry Moran says:

    Mung asks,

    Would you believe it to be a fact that humans and chimps share a common ancestor lacking a theory that is capable of explaining the evidence you must believe exists and upon which you believe it has been established to be a fact?

    Or is the theory of evolution irrelevant to the fact of evolution?

    That’s an important question and the answer is something that creationists need to understand.

    It’s best to use an analogy. I think we can all agree that gravity is a fact. Right?

    There are several theories of gravitation that explain the fact of gravity. The theories may turn out to be right or wrong but as Stephen Jay Gould pointed out in his essay, humans don’t float off the ground while the theory is being worked out.

    The evidence that humans and chimpanzees share a common ancestor is so strong that it is considered a fact of science. We have a fairly robust evolutionary theory that explains how this could happen. However, the fact exists independent of any theoretical explanation.

    The converse is not really true. Evolutionary theory has to be consistent with the facts or it doesn’t count as a scientific theory.

    When arguing with creationists it’s sometimes very hard to figure out whether they accept scientific facts or whether they reject all facts that conflict with their religious views.

    Young Earth Creationists fall into the latter category. It’s pointless, really, to debate evolution with them since they reject all the evidence for a universe that’s billions of years old. They are completely outside of science so there’s no point in presenting evidence to back up my case. They reject it out of hand without batting an eyelash.

    That’s why I want to know whether someone accepts common descent before having a discussion with them.

    Note how Barry Arrington avoided the question. That’s why I won’t continue any discussion with him.

    How about you, Mung, do you accept the evidence for common descent and agree that evolution is a fact? (Possibly a fact that is not a COMPLETE explanation of life but a fact nevertheless.)

  184. 184
    Larry Moran says:

    Barry Arrington says,

    Because if that is what you are suggesting you just tossed modern evolutionary theory out the window. Talk about all over the map. As I recently demonstrated, there is not a single core principle upon which all proponents of modern evolutionary theory agree.

    I’m wondering how many ID proponents actually agree with Barry Arrington that there’s not a single core principle upon which all evolutionary biologist agree?

    Speak up right now. How many of believe that there are evolutionary biologists who reject natural selection, mutation, random genetic drift, common descent, allopatric speciation, recombination, genes, and variation within populations?

    I agree with Barry that evolution is a difficult topic and that there is considerable scientific controversy within evolutionary biology. I’m doing my best to explain the scientific consensus and which topics are really controversial. I’m trying to explain MY view and MY definitions so that all of you can understand where I’m coming from.

    All I ask is that you guys do the same. Tell me which parts of ID are genuine and which parts are not. Here’s a simple question. Is Stephen Meyer’s book compatible with Young Earth Creationism? If not, is his book a statement about the ID position or just a personal opinion?

  185. 185
    Larry Moran says:

    mike1962 asks,

    2. Humans evolved via non-telic processes from an ancestor that is common with chimpanzees. Humans are an accident of nature.

    To what degree of precision does the Modern Synthesis confirm option #2?

    I don’t support the Modern Synthesis as I’ve explained many times on my blog.

    However, scientific theories do not CONFIRM facts. They explain them and are consistent with them.

    In this case, I don’t know what you mean by “non-telic” but it’s not part of any evolutionary theory that I know of. I also don’t know of any evolutionary theory that requires humans to be “an accident of nature.”

    3. Humans were brought about by a creator by deliberately modifying an ancestor that is common with chimpanzees. This modification may have been done in several steps.

    To what degree of precision does the Modern Synthesis rule out option #3?

    No scientific theory can rule out the existence of gods. Surely you knew that already?

    Or were you just being an IDiot?

  186. 186
    Larry Moran says:

    bFast says,

    I will say that I am surprised that you are willing to give the ID community this card.

    I believe that the only way to educate citizens is to expose them to critical thinking. In this case, there are many people who believe in ID but, as we see in this thread, they have very little experience dealing with objections to their views and very little understanding of science and evolution.

    I would help a great deal if we teach students the pros and cons of major controversies within society. For example, students in public schools could discuss the evidence for and against the idea that Earth is 4.5 billion years old. At the same time they would be exposed to the nature of science and how it works.

    Obviously I think that Young Earth Creationism will not survive this strategy of teaching the controversy but I’m willing to take my chances.

    Same for all other versions of creationism including Intelligent Design Creationism.

  187. 187
    Silver Asiatic says:

    LM

    For example, students in public schools could discuss the evidence for and against the idea that Earth is 4.5 billion years old.

    It certainly would be interesting to explore the theological evidence for or against Biblical Creationism as well as the theological foundations of Darwinism.

    I don’t think that would be permitted, legally, in American public schools though.

  188. 188
    Larry Moran says:

    Cross says at #154

    I have read some of your blog, does not strike me as written by someone with an open mind.

    Really? Does it strike you as written by someone who is skeptical?

    What do you think of Uncommon Descent and Evolution News & Views? Are they written by people with a much more open mind because they are all believers in the Judeo-Christian gods?

  189. 189
    Larry Moran says:

    Cross said in #142

    You have already stated that you don’t believe in God, thus, you are already closed to a whole range of evidence, this is bad science.

    I replied that if this were true then Cross is also guilty of bad science and close-mindedness because there are lots of other gods that he/she doesn’t believe in.

    Barry Arrington jumps in at #156 with,

    Sigh. You justify your atheism with an assertion that would get any freshman theology student flunked if he wrote it on exam. How are we supposed to take you seriously.

    Is it any wonder that I sometimes call you IDiots? You can’t even read for comprehension.

  190. 190
    Barry Arrington says:

    Moran:

    Is Stephen Meyer’s book compatible with Young Earth Creationism?

    Seriously? Have you even read the book? Meyer constantly talks about “millions of years.”

  191. 191
    Barry Arrington says:

    Moran:

    Speak up right now. How many of believe that there are evolutionary biologists who reject natural selection . . .

    I’ll take the first item on your list as just one example

    No one — not even the young earth creationists — rejects natural selection in the sense that it exists and can account for at least some limited data sets (e.g., antibiotic resistance). Lots of people — including materialist proponents of modern evolutionary theory — are skeptical that it is of more than trivial importance to evolutionary theory.

    This is not news. Apparently you don’t get out much. You can read the linked article I provided if you want more examples.

  192. 192
    Barry Arrington says:

    Moran @ 189: And you make gobsmackingly stupid comments like “there are lots of other gods Christians don’t believe in” as if you don’t understand the massive category error such a statement implies. Sigh, again.

  193. 193
    Mung says:

    LM: How about you, Mung, do you accept the evidence for common descent and agree that evolution is a fact?

    See, even you can’t avoid conflating the two.

    Larry Moran:

    That’s why I think it’s important to explain the real biological definition of evolution as a change in the heritable characteristics of a population over time. We can explain that this is a minimal definition, and that there’s more to evolution than this, but we shouldn’t back away from the real meaning of the term since it conveys some important messages. If we cave into pressure from the general public to make evolution into something they can understand, with all their biases, then we will have lost the battle before we even begin.

    The amazing thing about the minimal definition of biological evolution is that it doesn’t carry any baggage concerning the history of life or its future.

    Yes, I accept that evolution is a fact. Even YEC’s accept evolution as a fact. What’s more, YEC’s even accept common descent.

    You seem to be fully cognizant of the need for subtle distinctions within your own field but then utterly lose sight of that when talking about the views of others.

    The problem isn’t that YEC’s don’t believe in evolution, it’s that they believe in hyper-accelerated evolution. It’s not that the earth is 6,000 years old, but that all extant life evolved from a very small population which came off an ark even less than 6,000 years ago.

  194. 194
    Mung says:

    Larry Moran:

    Is Stephen Meyer’s book compatible with Young Earth Creationism?

    No. Neither was The Privileged Planet, another ID book.

    If not, is his book a statement about the ID position or just a personal opinion?

    I assume you’re talking about the age of the earth and how long life has been present on earth. The “minimal definition” of ID “doesn’t carry any baggage concerning the history of life or its future.”

    Surely you can understand.

  195. 195
    Andre says:

    This is the best post ever! Larry Moran identifies the materialist designers, time, chance, natural selection, drift and random mutations. Scientific evidence has shown time and again that these designers are inadequate to account for life or its diversity. Larry knows this all too well but that does not seem to stop him from selling his inadequate designers as fact.

    There is only one idiot posting here.

  196. 196
  197. 197
    Carpathian says:

    mike1962:

    Now, I, by circumventing the “normal rules of the game”, can peel the stickers off and put them back on in such a way that you could never achieve by simply turning the sub-blocks on the axes. If you ever ran across one of my special cubes, you can try and try and never get it back to uniform colors. If you analyzed it you could figure out why: the scrambled starting point was not possible under the normal rules. Analysis could be carried out in a perfectly normal and scientific way to determine that somebody intervened in an unusual way, in a way not possible using normal rules. A “miracle” occurred.

    The Rubik’s cube is a good analogy.

    If however, scientists actually ran into a real-life situation such as this, how could you trust science afain?

    You would never be sure if your measurements described the true configuration or history of what you were analyzing.

    I can’t imagine any being powerful enough to dismiss the laws of physics as not being able to make nature itself create any configuration he could imagine.

    We live in a natural world, not a supernatural one and there is no need for the two to overlap.

    Only if the designer were not the creator of the universe would he run into the problems facing biological design.

    If the designer can’t control the environment, his new design will probably fail as the the environment and ecology of any local area changes constantly and sometimes dramatically.

    Just as IDists bring up the statistical improbability of macro evolution, a designer would face the same problem with hitting a target environment for his design.

  198. 198
    Carpathian says:

    kairosfocus:

    Under blind watchmaker circumstances, that does pose a blind, needle in haystack search challenge to the assembly of first cell based life and onward to the clusters of proteins needed to form fresh tissue types for organs required for organisation of body plans.

    Biology is not blindly random.

    Applying statistics for benign objects such as cards does not translate to systems.

    Whether a being started life or not, that system is not bound by the same probabilities as discrete objects are.

    Take a handful of bar magnets and try to build any configuration of them.

    You will find out you can’t.

    Thanks to sexual reproduction, biology is very fast.

    Bit patterns are a combination of parents and ancestors and new biological configurations contain mutations from all of those ancestors and thus you are not restricted to single element changes.

    When talking about biology, configurations that do not function well in their environment are eliminated. Those DNA deltas that got them eliminated are now gone making room for configurations that can survive in that environment.

    Biology does not allow certain things just as magnets do not allow certain configurations.

    The needle is simply the current environment and any configuration that survives in it has found it.

  199. 199
    JimFit says:

    Larry

    they are all believers in the Judeo-Christian gods

    God is one because He is eternal, you can’t use plurality on something infinite. As for your claim about the ethnicity of God, well, the Bible clearly states that there are other races but the Bible focuses on the Jews, it doesn’t say that God is Jew. Even Jesus states at John 8:58 “Before Abraham Was, I Am” to stress out that His teachings are universal to all people and not objective only to Jews.

    Your belief that you are a random cosmic accident that nothingness spewed without free will or purpose isn’t scientific since Randomness Nothingness and Luck doesn’t exist in science but on nihilism.

  200. 200
    Mung says:

    Larry quotes S.J. Gould:

    I don’t mention these differences to lament, or complain, or to criticize astronomical usage. After all, their concept of ‘evolution’ remains more faithful to etymology and the original English definition; whereas our Darwinian reconstruction has virtually reversed the original meaning. In this case, since neither side will or should give up its understanding of “evolution”—astronomers because they have retained an original and etymologically correct meaning, evolutionists because their redefinition expresses the very heart of their central and revolutionary concept of life’s history—our best solution lies simply in exposing and understanding the legitimate differences, and in explaining the good reasons behind the disparity of use.

  201. 201
    JimFit says:

    Larry

    Because there’s no evidence of any other kind of causes. Maybe you believe in these other causes (gods) but you have to demonstrate in some manner that they exist. That brings us to a discussion about the existence of supernatural beings and that’s exactly what Intelligent Design Creationism is all about.

    No. We all agree that God is a Cosmic Consciousness that caused the Universe and unfolded to create life, Consciousness is fundamental for matter to exist, you must start to ask yourself “What is matter?” “What do we get if we keep reducing matter?”

    https://www.youtube.com/watch?v=4C5pq7W5yRM

    Your own transcendent consciousness is the cause for matter to exist so when you are asking to present other causes you have the answer on yourself, you are the transcendent cause of matter.

    Four intersecting lines of experimental evidence from quantum mechanics that shows that consciousness precedes material reality (Wigner’s Quantum Symmetries, Wheeler’s Delayed Choice, Leggett’s Inequalities, Quantum Zeno effect):

    https://docs.google.com/document/d/1G_Fi50ljF5w_XyJHfmSIZsOcPFhgoAZ3PRc_ktY8cFo/edit

  202. 202
    kairosfocus says:

    Carpathian,

    the first challenge is to account for OOL through blind watchmaker chance plus necessity i/l/o the implications of codes, protein isolation in AA sequence space and much more. That imposes a blind — non purposeful — needle in haystack search.

    Where, just 500 – 1,000 bits would swamp atomic and temporal search resources for the sol system and the observed cosmos. At 500 bits and 10^57 atoms trying new binary configs for 500 bits at 10^13 – 14/s, we are looking at a search of 1 straw sampled from a stack comparably thick as our galaxy. At 1,000 bits per atom for 10^80 atoms, the stack would swallow up our observed cosmos.

    That is the sort of search challenge that is a toy search compared to the real ones.

    The 10 – 100+ mn bases of additional bio info to account for proteins, tissue types and organ systems plus regulatory info, to get to major body plans imposes a further major challenge to blind watchmaker, non purposeful non-intelligent chance and necessity. Even, were there a smoothly incremental ever improving path across a tree of life network, pop sizes, mut rates would long since have exhausted available time on the usual timelines.

    But in fact there is no good actually observed evidence that

    CV + CBDRS –> DWIM

    can reasonably account for novel body plans. We have tiny adaptations grossly extrapolated in a context constrained by ideological imposition.

    Likewise, the sort of ToL that SHOULD result, would be dominated by transitional forms. After 1/4+ mn fossil species, millions of museum specimens and billions more seen in the ground, these are still consistently missing over 100 yrs after Darwin.

    The only empirically warranted, known source of FSCO/I is design.

    KF

  203. 203
    Carpathian says:

    kairosfocus:

    the first challenge is to account for OOL through blind watchmaker chance plus necessity i/l/o the implications of codes, protein isolation in AA sequence space and much more. That imposes a blind — non purposeful — needle in haystack search.

    If the first lifeform were created, that would not necessarily impact on how it evolves.

    Secondly, you keep insisting on blind unrestricted randomness when it comes to biology.

    That is clearly not so.

    Try to get A to randomly bind with T, C or G.

    It doesn’t happen.

    The laws of physics restrict certain configurations of matter depending on its elements.

    Blind randomness in biology just doesn’t happen.

    Where, just 500 – 1,000 bits would swamp atomic and temporal search resources for the sol system and the observed cosmos.

    Since not all configurations are allowed in biology, your 500 bit barrier does not apply.

  204. 204
    Carpathian says:

    kairosfocus:

    Here is output from a program I am developing.

    carp /lLog.log /s /p64 /g16 /i10 /c6 /d /m5

    Population Size = 64
    Fitness String Len = 16
    Pop Len/Fit Len = 4.000000
    No Change = 1
    PosChange = 16
    NegChange = 0
    Multiple Change = 4
    % MultiBit changes = 30.77
    Number of generations = 13

    With a population of 64, a 16 bit “target” combination can be found in only 13 generations when each two parents have a 6 child family.

    30% of those 13 generations had multi-character gains despite the fact that mutation only targets a single char in each generation.

    This is due to sexual reproduction and shows why statistics have to be applied to the system as a whole and not simply to each member of the population.

  205. 205
    kairosfocus says:

    Carpathian, targetted search, designed, starting with a search within island of function and with scope of search that is nothing like what is needed. Now, if your program were to assemble itself out of molecular noise and the same for the executing machinery, that might be saying something. KF

    PS: the design of a first life form drastically shifts estimation of onward design. Design, from root on up.

  206. 206
    Carpathian says:

    kairosfocus:

    Now, if your program were to assemble itself out of molecular noise and the same for the executing machinery, that might be saying something. KF

    Untrue.

    An oscilloscope that can’t design itself is just as useful as one that is assembled in a factory.

    There is no other scientific debate where modularization is not allowed by the participants.

    Evolution can be broken down into components and investigated separately.

    Again, biology is not something that can be statistically treated as random.

    Show me A binding randomly with T, C and G.

    It doesn’t happen and your 500 bit limit does not apply to biology.

    Every successful lifeform is itself “the needle in the haystack”.

    There is no target and no “search”.

  207. 207
    Andre says:

    Carpathian

    So evolution is unguided but not really, so you can have your cake and eat it.

  208. 208
    Carpathian says:

    Andre:

    Evolution does what Joe says in that it eliminates those that cannot survive in their local environment.

    That is the only “guidance” and it’s enough.

  209. 209
    bFast says:

    Larry Moran (189)

    Cross said in #142

    You have already stated that you don’t believe in God, thus, you are already closed to a whole range of evidence, this is bad science.

    I think that both of you have this wrong. I think that one’s world view affects our threshold of believability. Consider near death experiences, for instance. Surely one who starts from an atheistic perspective is going to be very suspicious that such stories are nothing more than stories. When scientists suggest a possible explanation, such as games minds play when oxygen deprived, the atheist will have a lower threshold of believability than I will.

    However, the bigger area of difference between the worldviews is how we respond to the “I don’t know”s of the world. The atheists are quick to accuse us of a “god of the gaps” position. In truth, they are correct. We see the inexplicable and conclude that God did this. The atheist, however, seems oblivious of the fact that their position, “I don’t know, but it definitely wasn’t god”, is every bit as presumptuous as ours is.

  210. 210
    Carpathian says:

    kairosfocus:

    Here is a 500 bit “search”

    carp /lLog.log /c6 /d /g250 /p64 /m5 /n /s

    Population Size = 64
    Fitness String Len = 250
    Pop Len/Fit Len = 0.256000
    No Change = 162
    PosChange = 250
    NegChange = 0
    Multiple Change = 44
    % MultiBit changes = 11.99
    Number of generations = 367

    Note that it is 367 generations for a 500 bit “search”.

  211. 211
    bFast says:

    Larry Moran (186)

    Obviously I think that Young Earth Creationism will not survive this strategy of teaching the controversy but I’m willing to take my chances.

    My YEC perspective was not able to stand in light of the evidence. I tried classical OEC (the earth is old, Adam and Eve were Biblically young.) The evidence against this position I also find overwhelming.

    Same for all other versions of creationism including Intelligent Design Creationism.

    I surely know a heck of a lot more than the average high school will teach about evolutionary theory. I have recently been taught much about neutral theory. I have learned, for instance, that neutral theory is a better tool for explaining speciation than “survival of the fittest” is. However, I have no temptation whatsoever to abandon my ID position. I find it to be the hands down winner from an evidence perspective.

  212. 212
    kairosfocus says:

    Carpathian, again you have substituted an intelligently guided and fine tuned hill-climbing exercise within an island of function for the real challenge, to find islands of function by blind search starting in a sea of overwhelmingly non-functional configs where you do not get an oracle until you are on a shoreline of function. You are trying to use cases of intelligent design to suggest that ID is not the observed cause of FSCO/I; as in, red herring led away to strawman . . . but computer sims like this have been repeatedly rhetorically persuasive ever since Weasel, never mind the abundant clues as to why they are irrelevant. I point out, simply by designing and coding, you actually demonstrate what you keep shutting your eyes to — intelligent design at work creating FSCO/I, which also happens when you compose your comments. A is A, sir. And, it is precisely to remove the indoctrinated substitutions that I keep pointing to the root of the ToL, OOL. self replication based on code using von Neumann kinematic self replicator, is part of what needs to be accounted for. KF

  213. 213
    Carpathian says:

    kairosfocus:

    Again you dodge the point.

    If physics is blind and random, you should be able to randomly drop some magnets and end up with a blind random configuration of magnets.

    The pile doesn’t do that because physics prohibits certain configurations.

    You seem to not want to address this fact.

    Biology is not blindly random.

  214. 214
    soundburger says:

    Larry Moran, both here and countless times on his own site, likes to end his posts with some variation of the question, “Now do you see why I call (you/them) IDiots?

    He writes this in mock exasperation, as if the option to resort to insulting and disparaging language to make a sweeping/generalizing condemnation is somehow forced upon him.

    Which, of course, we know is not the case. The choice to use, and continually reinforce, his own pet insult -an exceedingly childish one, at that – so as to encourage its dissemination, is his and his alone.

    Thus, the question, “Now do you see why I call them Idiots?” is, like so many things with Moran, a cheap dodge. Yes, Larry, we do. And it speaks volumes about you, yourself, and very little about anyone or anything else.

  215. 215
    kairosfocus says:

    Carpathian, I really don’t have time for a rhetorical circles game. I point you to 108 above and its steps of thought, which answer on the merits, at this stage mostly for the interested onlooker and for record: http://www.uncommondescent.com.....ent-565372 , including by extension the reasons why the relevant molecules of life — D/RNA and proteins especially will be highly contingent in chain sequence which specifies prerequisites of function in ways that are well known, and how contingency is not accounted for on mechanical necessity. Instead, we must attend to chance and/or design and thus lead on to how FSCO/I poses a blind needle in haystack challenge to chance and necessity. Also, I point you to protein synthesis again and note to you that tRNAs have a CCA universal joint to which the AAs to be chained are loaded thus demonstrating high contingency at a critical step. In short, you are trying to compare guavas with bicycles. KF

  216. 216
    kairosfocus says:

    PS: Clipping:

    http://www.ncbi.nlm.nih.gov/books/NBK21603/

    >> The function of tRNA molecules, which are 70?–?80 nucleotides long, depends on their precise three-dimensional structures. In solution, all tRNA molecules fold into a similar stem-loop arrangement that resembles a cloverleaf when drawn in two dimensions (Figure 4-26a). The four stems are short double helices stabilized by Watson-Crick base pairing; three of the four stems have loops containing seven or eight bases at their ends, while the remaining, unlooped stem contains the free 3? and 5? ends of the chain. Three nucleotides termed the anticodon, located at the center of one loop, can form base pairs with the three complementary nucleotides forming a codon in mRNA. As discussed later, specific aminoacyl-tRNA synthetases recognize the surface structure of each tRNA for a specific amino acid and covalently attach the proper amino acid to the unlooped amino acid acceptor stem. The 3? end of all tRNAs has the sequence CCA, which in most cases is added after synthesis and processing of the tRNA are complete. [–> This bonds to the COOH end of the amino aced loaded to the tRNA, which in the ribosome is then used to load to the elongating protein chain, notice the universal joint and the “recognition” protocol that leads to correct loading.] Viewed in three dimensions, the folded tRNA molecule has an L shape with the anticodon loop and acceptor stem forming the ends of the two arms >>

  217. 217
    mike1962 says:

    Carpathian @197

    You obviously miss the point. Please re-read what I wrote and think about it more, then actually address my point. (Then you may also see the pointlessness of your last reply.)

  218. 218
    Larry Moran says:

    bFast says,

    The atheist, however, seems oblivious of the fact that their position, “I don’t know, but it definitely wasn’t god”, is every bit as presumptuous as ours is.

    That is not the standard atheist position. Many people (you?) think that an atheist is someone who denies that gods exist. That’s not the version of atheism that most of us prefer. We prefer to define an atheist as someone who has not been convinced that gods exist.

    My kind of atheist would never say what you said. I’m open to the possibility that gods exist although the probability has to be very low because nobody has come up with any convincing evidence even when I ask for it.

    Be careful when you attribute positions to atheists because the word may not mean what you think it means. It’s the same problem I face when I use the word “creationist.” I have to make it clear what meaning I’m using.

  219. 219
    Larry Moran says:

    JinFit says,

    God is one because He is eternal, you can’t use plurality on something infinite

    I’m not an expert on your version of religion. Where does Satan fit in? Is he a god? If not, what it he?

    What about the angels like Michael and Gabriel? Are they gods, minor gods, or some other kind of supernatural being?

    What’s the status of Mary if you are Roman Catholic? I think she still performs miracles, doesn’t she? Does that make her a god (goddess) or something else?

  220. 220
    Mung says:

    Larry, you should probably stick with what you know. You’re close to making as much a fool of yourself as Dawkins has made a fool of himself when attempting to address religious issues. Really, you just expose your ignorance when you pose such questions.

  221. 221
    kairosfocus says:

    LM, passed by. JF is alluding to God as ontological root of being, which is strictly speaking philosophy in answer to the first question, why is there something rather than nothing and the question of the one and the many — unity and diversity in a coherent cosmos as opposed to a chaos, which is of like rank. Such point to questions of being, non being, possible vs impossible being and necessary vs contingent being thence the root of a unified reality. These issues are strictly prior to questions like the particular theology taught in a scriptural tradition and validation of that tradition. Add in implications of our being inescapably under moral government, demanding a world-foundational IS that properly bears the weight of OUGHT. The questions also point to the profound reasonableness of a generic ethical theism, despite the commonly encountered dismissive and even contempt-laced rhetoric and outright hostility to “religion” — a convenient grab-bag, often stereotypical term, that — that are ever so common in our day of rhetoric over reason. I suggest you look at the remarks in 163 above: http://www.uncommondescent.com.....ent-565505 When these issues are sorted out then issues of particular traditions can be addressed. And yes, these are waaay before inductive logic questions as to whether there are empirically reliable signs that point to intelligently directed configuration as key causal factor for certain classes of objects and phenomena etc. As just one marker of this, contingent, possible beings are in key part explained on causal factors, and in particular dependence on enabling factors, similar to the dependence of a fire on heat, fuel, oxidiser and a chain reaction. KF

  222. 222
    Larry Moran says:

    Mung says,

    Really, you just expose your ignorance when you pose such questions.

    Okay. So I admit I was just being provocative. I’m surprised that you object since it’s pretty similar to your behavior.

    But can you answer the questions? What is the status of Satan and the archangels? If they aren’t gods then what are they? They are definitely supernatural, right?

  223. 223
    kairosfocus says:

    LM, cart before horse [cf 221 just above: http://www.uncommondescent.com.....ent-565596 and onward 163 further above as linked], and in a context that given your rhetoric of contempt and taunting terms as you have repeatedly used here and elsewhere, points to red herrings led away to strawman caricatures soaked in ad hominems to be set alight to cloud, confuse, poison and polarise the atmosphere. The proper focal issue is the design inference on inductive signs, and as you have raised issues that require it, foundational philosophical issues that set a context for a responsible view of matters scientific and theological alike. The phil horse must pull the issues cart — including incidental systematics theology issues as you try to raise without due context and basis, I am afraid. KF

    PS: A Typical short introductory systematics work will be easily 1,000 pp. A full bore one typically will be 4,000 – 10,000. The Angelic Doctor’s classic and unfinished is about 3,000. In that context I will briefly note that angels are not gods and will not accept attempted worship. Satan, a rebel angel is called god of this world, but that simply means attempted usurper and is a mark of his perversity. As should be commonly understood.

  224. 224
    Mung says:

    ok Larry, I don’t particularly want to discuss religion with you, but I’ll make an exception. 🙂

    The New Testament records two occasions, one in which a man was worshiped as God and another in which a man began to worship an angel. I’ll not bother quoting the passages, but neither one supports the idea that man or angels ought to be worshiped as God, in fact they support just the opposite.

    I trust that addresses at least two of your questions. Would you have asked the same questions if you were visiting a site on Judaism or Islam?

    As far as Satan, I may not be the best person to ask about that as I doubt my views on Satan would qualify as orthodox. I don’t believe Satan is a god, or even godlike. There may be no such being.

    As far as the supernatural, I believe in a necessary being, a being who by His very nature cannot not exist. This being is therefore the most natural being that can possibly exist, for existence is His nature. To refer to such a being as supernatural is a category error.

    You, me, the material world; we are what are not natural. We have things exactly backwards.

    You have your minimalist definition of evolution and expect us to respect it [and rightly so]. Likewise, we have our minimalist definition of intelligent design and would just like to see it respected in turn.

    I am sure many of us would love to discuss evolution and ID with you. But that would require a bit of mutual respect and understanding. We can both hope.

  225. 225
    Cross says:

    bFast @ 209

    Hi bFast. I have never doubted that my belief in God, my worldview, effects the way I see the evidence for evolution. I am biased (for many reasons not related to ID or evolution) and I know it. If fact, one thing that should not be in dispute, is that we all are.

    I am though, genuinely open to the evidence, if it is compelling enough. I am yet to be convinced about macro/evolution, because of a number of reasons like irreducible complexity in life, the maths of probabilities and the lack of transitional fossil evidence. OOL requires a Designer and no other plausible materialist explanation is on the table.

    However, the view often pushed by scientists is that they are unbiased and open to all possibilities, even if it disproves their pet theories. The truth is, this is not so. Dr Moran, in his posts has claimed to be open to God existing, but this is not really true. His other responses and his blog show this. I am only pointing out his bias and real lack of openness.

    You will notice that Dr Moran has claimed no knowledge of HAR1F, do you not think that odd, since his field is biochemistry and HAR1F directly relates to the common ancestor of chimp and human. The problem is, it is evidence against this transition in only 5-7 million years. Does not fit in with his worldview so he ignores it.

    BTW, I posted a link in 160 about HAR1F, he wont like the source but the references are a good start if Dr Moran is actually interested.

    Cheers

  226. 226
    bFast says:

    Larry Moran,

    Many people (you?) think that an atheist is someone who denies that gods exist. That’s not the version of atheism that most of us prefer. We prefer to define an atheist as someone who has not been convinced that gods exist.

    This gets awfully close to the position of agnostic — the position that I believe that “science” must hold. (Even if the individual scientists hold different beliefs, it seems imperative that their scientist hat be agnostic.)

    Reading between the lines of your opinion about the unknown, however, it appears that “I don’t know, but it definitely wasn’t god” is darn close to your view. Your view might delete the “definitely”, but that’s about all.

  227. 227
    bFast says:

    Larry Moran (189), “Is it any wonder that I sometimes call you IDiots?”

    Larry, you know who says the darndest things? The “other”. Democrats see Republicans saying the stupidest things all the time. They nearly never see other Democrats doing the same. Republicans — them too. If Protestants are debating Catholics — yup, there too. You debating Richard Dawkins — if he is on the other side of the table he is much more likely to say really stupid things than if you and he are working together to correct the guy with the IDiotic prospective.

    This is the nature of human nature. In fact, I have found it so true that I have realized that the only person who never says the darndest things is me. Well, I used to, sometimes, but not any more.

  228. 228
    Larry Moran says:

    Mung says,

    You have your minimalist definition of evolution and expect us to respect it [and rightly so]. Likewise, we have our minimalist definition of intelligent design and would just like to see it respected in turn.

    Vincent Torley posted something resembling a minimalist definition of ID in his post ….

    A succinct case for Intelligent Design

    I responded to that succinct case at …

    The best case for Intelligent Design Creationism

    I pointed out that Torley’s “succinct case” was simply “four separate scientific critiques demonstrating the inadequacy of the neo-Darwinian mechanism.” That’s not really a case for ID, is it?

    In this post (top) Torley retreats and claims that I should have read other parts of Meyer’s book in order to understand the real “succinct case” for ID.

    It’s all very confusing. Perhaps you could give me your version of a minimalist definition of intelligent design? Please make sure that the other ID proponents in this thread agree with you.

  229. 229
    Larry Moran says:

    bFast says,

    This gets awfully close to the position of agnostic …

    An agnostic is a person who says you can never know for sure if gods exist or not. (See Agnostic.)

    I am an atheist agnostic and so is Richard Dawkins (see The God Delusion). I used to teach a course with a Jesuit Priest who is a theist agnostic (his own description of himself).

    This is another one of those words where different people use different definitions but in this case the common usage doesn’t conform very closely to the dictionary definition.

  230. 230
    Mung says:

    Hi Larry,

    I know the posts are coming fast and furious so I can understand you missing it or not connecting the dots if you did see it. See my linked @ 196. It was meant to immediately follow my @ 194 where I bring up the minimalist definition of ID, but another post appeared in between.

    Here it is again:

    ID Defined

    I am not talking about the case for ID like you weren’t talking about the case for evolution when you came up with your minimalist definition of evolution. We’re talking about terms that define the essence of our positions.

    I hope you don’t mind my quoting you to make my case. You can always accuse me of quote-mining.

    Please make sure that the other ID proponents in this thread agree with you.

    All I can do is say it’s how ID is understood here at UD.

  231. 231
    Mung says:

    Larry Moran:

    Please make sure that the other ID proponents in this thread agree with you.

    Like you went out and made sure all biologists agreed with your minimalist definition of evolution?

    You make me laugh.

  232. 232
    Mung says:

    Dear Dr. Moran,

    If you understand your position, it is that evolution occurs at the level of the population and there really is no evolution at the level of the organism.

    Don’t many biologists have difficulty with a theory of evolution that does not explain how organisms evolve?

    The Changing Role of the Embryo in Evolutionary Thought

    Isn’t it that case that it is organisms that must be capable of evolving and that any theory of evolution that fails to explain how this can be the case is seriously deficient?

  233. 233
    Querius says:

    Larry Moran noted @ 175,

    Q: The people who believe in an immaterial God don’t need material proof, …
    LM: I know, and that’s a problem.

    No, it’s the opposite of a problem. My proof, as for many other Christians, is both immaterial and personal. For example, what is the weight of profound inner peace measured in kilograms? What is the depth of overflowing love and joy measured in meters? What is the frequency of wisdom and self control in megahertz? Surely you know. 😉

    LM: I(t) means we can never have a serious discussion about evolution and intelligent design because we don’t agree on the fundamental rules of scientific debate.

    Not at all. I don’t disagree with evolution because of my faith in Jesus Christ, I disagree with it because I think it’s lousy science. I’m not sure that scientific debate is fundamentally any different than any other rational discussion, excepting of course that you can feel free to continue calling me an IDiot. 😉

    Q: … the people who choose not to believe in an immaterial God don’t want a material proof.
    LM: Yes we do. Science is a way of knowing that relies on evidence. If you want to know whether gods exist, you need evidence. But you’ve already denied that evidence is important so we can’t discuss that either.

    Do you really? What would it mean to you personally if such proof came into your life and you experienced the profound transformation that authentic Christians experience? Speaking for yourself, do you think you would stop your research or do you think that you would be re-energized in your intensity to understand the spectacular things that God initiated?

    LM: However, we can conclude that science and religion are in conflict.

    Speaking as a Christian, I’d say that science and the Christian faith are not at all in conflict. I’m delighted with scientific observation, rigorous investigation, and discovery. As I alluded to earlier, if I thought evolution made sense, particularly from a chemical perspective that didn’t require so many miracles, I’d have no trouble believing it. The Bible says God created the heavens and the earth, and history records that Alexander the Great conquered the known world at one time. Certainly historians are not intending to imply that Alexander didn’t use trained armies and diplomacy, but just ran out there by himself like some naked Hercules. Exactly HOW Alexander achieved what he did is of great interest to historians! So when I read that God created the heavens and the earth, I assume that there’s a process and structure waiting to be discovered.

    Furthermore, did you know that the first scientific experiment is recorded in the Bible? You can read about it here in the first chapter of Daniel:
    https://www.biblegateway.com/passage/?search=Daniel+1&version=NIV

    The experiment includes a hypothesis, an experimental group, a control group, well-defined parameters, an independent evaluation, and a written record. The events described occurred around 600 B.C. (and even the most cynical scholars admit that the book was indeed written well before Christ).

    Kind regards,

    -Q

  234. 234
    Cross says:

    Querius @ 233

    “Speaking as a Christian, I’d say that science and the Christian faith are not at all in conflict. I’m delighted with scientific observation, rigorous investigation, and discovery. As I alluded to earlier, if I thought evolution made sense, particularly from a chemical perspective that didn’t require so many miracles, I’d have no trouble believing it. The Bible says God created the heavens and the earth, and history records that Alexander the Great conquered the known world at one time. Certainly historians are not intending to imply that Alexander didn’t use trained armies and diplomacy, but just ran out there by himself like some naked Hercules. Exactly HOW Alexander achieved what he did is of great interest to historians! So when I read that God created the heavens and the earth, I assume that there’s a process and structure waiting to be discovered.”

    Amen, and well put.

    Cheers

  235. 235
    Andre says:

    Larry Moran

    I know you keep saying that there is no evidence for gods and that is fair, but let me ask you this?

    Do you accept that molecular nano-tech machines inside living cells are the result of blind purposeless chance and luck forces?

    If you do then please tell me why you even bother with science? What’s the point if it has no meaning or no purpose?

  236. 236
    Mung says:

    Dr. Moran, you wrote:

    Over time, species evolve more by random genetic drift. This process opens up new possibilities for future evolution including future adaptations.

    Do you agree that random genetic drift does not and cannot explain adaptations?

    Genetic drift affects the genetic makeup of the population but, unlike natural selection, through an entirely random process. So although genetic drift is a mechanism of evolution, it doesn’t work to produce adaptations.

    here

    Do you really believe that the debate over ID is about whether some locus in DNA not under selection becomes fixed due to random sampling?

    When debating adaptations with IDiots (or evolutionists for that matter) do you don your Darwinist cap? Or do you have a non-Darwinian explanation for adaptations?

    Do you really believe that a process which you yourself admit creates new possibilities for adaptation would pose some problem to a theory of intelligent design?

    What is it you think ID is afraid of?

  237. 237
    Mung says:

    Larry Moran:

    Over time, species evolve more by random genetic drift.

    Do you mean by this that within a given population more alleles become fixed due to random sampling than due to selection?

    Or do you mean that more new species arise due to random genetic drift than due to selection?

    Both?

    I am assuming the former. If the former, in the context of the debate over ID, so what? Creationists have long maintained (rightly or wrongly) that chance is the predominating element in mechanistic theories of evolution.

    They are consistently told they are wrong, of course. You can even see this right here in this very thread.

  238. 238
    bFast says:

    Larry Moran (229) Atheist agnostic vs. theistic agnostic. Interesting. I have not heard this conjunction before. I have heard Richard Dawkins say approximately, “there probably isn’t a god, so let’s stop worrying about it.” The “probably” is the agnostic bit, I presume.

    I presume, then, that your perspective is that you cannot know if there is a god or not, but in light of evidence to the contrary, you will go with the “no god” hypothesis. The theist agnostic goes with the “god” hypothesis, though he lacks “knowing”.

    I, for one, am not agnostic. I am rather confident that there is a God. I have a hypothesis about him, however, which I do hold loosely. Though I came up with the hypothesis on my own, I found that Max Planck espoused a similar hypothesis. Could it be that the quanta (possibly the strings) is a mighty, conscious, brain? The question, of course, is how to test it.

  239. 239
    bFast says:

    Mung (236) “Do you agree that random genetic drift does not and cannot explain adaptations?”
    Dr. Moran, let me answer this one. Let me see if I understand your theory correctly.

    Genetic drift produces genetic diversity. Drift finds numerous variations that are “good enough”. It saves ’em away in the toolbox. Sometimes it’ll fix one “good enough” option — eliminating the others in the same space. But mostly it develops a variety of workable options.

    Consider our friend the wolf. It built up a whole bunch of alleles that all work. Now, when we apply selective pressure, this build-up of alleles becomes the bank of options from which selection can select. If you want a short legged “wolf” that can poke its nose into badger holes, well, the genetic options to pull that off exist.

    Drift doesn’t in itself create adaptations, but it builds the kit of options that can be used later by selection to produces adaptations.

  240. 240
    Mung says:

    bFast:

    Drift doesn’t in itself create adaptations, but it builds the kit of options that can be used later by selection to produces adaptations.

    So if I am a clockmaker, I just need to wait for the clock-making toolkit to arrive?

  241. 241
    Mung says:

    Carpathian:

    Here is a 500 bit “search”

    carp /lLog.log /c6 /d /g250 /p64 /m5 /n /s

    Why did you choose only six children?

    Why did you choose a length 250 for your candidate strings?

    Why did you choose a population size of 64?

    Design. Design. Design.

  242. 242
    Andre says:

    Mung at @241

    So if I am a clockmaker, I just need to wait for the clock-making toolkit to arrive?

    Priceless!

  243. 243
    kairosfocus says:

    LM, 228:

    I see your assertion of a “retreat” on VJT’s part.

    I think that is a loaded, almost sophomoric rhetorically dismissive description of something that is more nuanced and contextual than you suggest.

    First, it has long been trumpeted far and wide as scientific consensus that Darwinian and linked mechanisms suffice to explain the appearance of design in the functionally specific complex organisation and associated information (FSCO/I for short). This in turn implies that the appearance of specified complexity does create a strong impression of design, on our experience of observed cases. This, is therefore implicit.

    So, if there is a breakdown of the claim then that returns the alternative to its status as best explanation.

    Meyer, as VJT outlined and cited, argues that on the case of the Cambrian life fossils, there is such a breakdown at a crucial and longstanding case in point:

    “This book has presented four separate scientific critiques demonstrating the inadequacy of the neo-Darwinian mechanism, the mechanism that Dawkins assumes can produce the appearance of design without intelligent guidance. It has shown that the neo-Darwinian mechanism fails to account for the origin of genetic information because: (1) it has no means of efficiently searching combinatorial sequence space for functional genes and proteins and, consequently, (2) it requires unrealistically long waiting times to generate even a single new gene or protein. It has also shown that the mechanism cannot produce new body plans because: (3) early acting mutations, the only kind capable of generating large-scale changes, are also invariably deleterious, and (4) genetic mutations cannot, in any case, generate the epigenetic information necessary to build a body plan.” (pp. 410-411)

    On fair comment, these four objections to the proposed macro-evolutionary mechanisms have not been cogently answered, but have been repeatedly distracted from or brushed aside or twisted into strawman caricatures. And in particular no actually observed blind watchmaker chance-necessity mechanism shown capable of macro-level changes required for body plan origination has ever been shown.

    Further to this, on a trillion case observational base, FSCO/I routinely and reliably comes about by design, by intelligently directed configuration. This includes posts in this thread of comments.

    So, what we may have is a half statement of a case that needs to be further filled in. Which, is a legitimate objection, but that is to presentation rather than substance.

    And, when such was raised by MF, VJT presented in a fresh, headlined post (I would prefer in thread reply or at least a link so something is in the chain of comments, then headlining) the longstanding positive side of Meter’s case, using a further clip — which, on fair comment, you have never cogently responded to:

    [E]ach of the features of the Cambrian animals and the Cambrian fossil record that constitute negative clues – clues that render neo-Darwinism and other materialistic theories inadequate as causal explanations – also happen to be features of systems known from experience to have arisen as the result of intelligent activity. In other words, standard materialistic evolutionary theories have failed to identify an adequate mechanism or cause for precisely those attributes of living forms that we know from experience only intelligence – conscious rational activity – is capable of producing. That suggests, in accord with the method of historical scientific reasoning elucidated in the previous chapter, the possibility of making a strong historical inference to intelligent design as the best explanation for the origin of those attributes. (2013, p. 358)

    Notice, Meyer’s explicit abductive, inference to best explanation, inductive approach applied to sciences of natural history that seek to reconstruct the deep past of origins. He is also using the associated vera causa principle, that explanations of traces from what is not directly observable, should be based on observed adequate cause.

    The observed adequate cause of FSCO/I is design.

    To overthrow this, advocates of evolutionary materialism need to demonstrate that blind chance and mechanical necessity can create such. And recall, this also includes the explanation of the code using, von Neumann kinematic self replication that is at the heart of cellular self-replication and therefore reproduction.

    Recent attempts to disparage the phenomenon, FSCO/I — as common as text in this thread, or fishing reels, PCs used to read this, and in things like oil refineries, protein synthesis in the cell, wider metabolism and much more across the world of life — suggest that objectors do not have such a proper counter to Meyer’s point.

    I draw to your attention, also, an earlier case, where Meyer responded to Falk’s critical review of Signature in the Cell, and in so doing amplified the above significantly:

    The central argument of my book is that intelligent design—the activity of a conscious and rational deliberative agent—best explains the origin of the information necessary to produce the first living cell. I argue this because of two things that we know from our uniform and repeated experience, which following Charles Darwin I take to be the basis of all scientific reasoning about the past. First, intelligent agents have demonstrated the capacity to produce large amounts of functionally specified information (especially in a digital form). Second, no undirected chemical process has demonstrated this power. Hence, intelligent design provides the best—most causally adequate—explanation for the origin of the information necessary to produce the first life from simpler non-living chemicals. In other words, intelligent design is the only explanation that cites a cause known to have the capacity to produce the key effect in question . . . . In order to [[scientifically refute this inductive conclusion] Falk would need to show that some undirected material cause has [[empirically] demonstrated the power to produce functional biological information apart from the guidance or activity a designing mind. Neither Falk, nor anyone working in origin-of-life biology, has succeeded in doing this . . . .

    The central problem facing origin-of-life researchers is neither the synthesis of pre-biotic building blocks (which Sutherland’s work addresses) or even the synthesis of a self-replicating RNA molecule (the plausibility of which Joyce and Tracey’s work seeks to establish, albeit unsuccessfully . . . [[Meyer gives details in the linked page]). Instead, the fundamental problem is getting the chemical building blocks to arrange themselves into the large information-bearing molecules (whether DNA or RNA) . . . .

    For nearly sixty years origin-of-life researchers have attempted to use pre-biotic simulation experiments to find a plausible pathway by which life might have arisen from simpler non-living chemicals, thereby providing support for chemical evolutionary theory. While these experiments have occasionally yielded interesting insights about the conditions under which certain reactions will or won’t produce the various small molecule constituents of larger bio-macromolecules, they have shed no light on how the information in these larger macromolecules (particularly in DNA and RNA) could have arisen. Nor should this be surprising in light of what we have long known about the chemical structure of DNA and RNA. As I show in Signature in the Cell, the chemical structures of DNA and RNA allow them to store information precisely because chemical affinities between their smaller molecular subunits do not determine the specific arrangements of the bases in the DNA and RNA molecules. Instead, the same type of chemical bond (an N-glycosidic bond) forms between the backbone and each one of the four bases, allowing any one of the bases to attach at any site along the backbone, in turn allowing an innumerable variety of different sequences. This chemical indeterminacy is precisely what permits DNA and RNA to function as information carriers. It also dooms attempts to account for the origin of the information—the precise sequencing of the bases—in these molecules as the result of deterministic chemical interactions . . . .

    [[W]e now have a wealth of experience showing that what I call specified or functional information (especially if encoded in digital form) does not arise from purely physical or chemical antecedents [[–> i.e. by blind, undirected forces of chance and necessity]. Indeed, the ribozyme engineering and pre-biotic simulation experiments that Professor Falk commends to my attention actually lend additional inductive support to this generalization. On the other hand, we do know of a cause—a type of cause—that has demonstrated the power to produce functionally-specified information. That cause is intelligence or conscious rational deliberation. As the pioneering information theorist Henry Quastler once observed, “the creation of information is habitually associated with conscious activity.” And, of course, he was right. Whenever we find information—whether embedded in a radio signal, carved in a stone monument, written in a book or etched on a magnetic disc—and we trace it back to its source, invariably we come to mind, not merely a material process. Thus, the discovery of functionally specified, digitally encoded information along the spine of DNA, provides compelling positive evidence of the activity of a prior designing intelligence. This conclusion is not based upon what we don’t know. It is based upon what we do know from our uniform experience about the cause and effect structure of the world—specifically, what we know about what does, and does not, have the power to produce large amounts of specified information . . . .

    [[In conclusion,] it needs to be noted that the [[now commonly asserted and imposed limiting rule on scientific knowledge, the] principle of methodological naturalism [[ that scientific explanations may only infer to “natural[[istic] causes”] is an arbitrary philosophical assumption, not a principle that can be established or justified by scientific observation itself. Others of us, having long ago seen the pattern in pre-biotic simulation experiments, to say nothing of the clear testimony of thousands of years of human experience, have decided to move on. We see in the information-rich structure of life a clear indicator of intelligent activity and have begun to investigate living systems accordingly. If, by Professor Falk’s definition, that makes us philosophers rather than scientists, then so be it. But I suspect that the shoe is now, instead, firmly on the other foot. [[Meyer, Stephen C: Response to Darrel Falk’s Review of Signature in the Cell, SITC web site, 2009. (Emphases and parentheses added.)]

    The same basic argument extends to the origin of body plans, as outlined.

    There is a positive case for design in life, based on inference to best current, observationally answered, vera causa tested explanation. That case also requires pointing out the causal inadequacy of a long dominant alternative, but which on closer examination has not passed vera causa but has instead been ideologically established and entrenched.

    Such needs to also be faced.

    VJT may not have presented the matter completely at the first, but that does not mean that it was not substantially there. And, when challenged, he did not retreat from the point of causal inadequacy but pointed to what else passes the vera causa test.

    I suggest you need to restructure your own presentation to more accurately reflect that.

    KF

  244. 244
    Larry Moran says:

    @bFast #239

    Random genetic drift does not produce genetic diversity. It reduces genetic diversity by eliminating some alleles and fixing others. In the absence of mutation (an impossible situation, to be sure) a population would eventually become homozygous due to drift and selection.

    This is not rocket science. I don’t understand why it’s so difficult for people to understand the basic concepts of population genetics and evolution.

    Perhaps you are confused about the difference between the process of random genetic drift and whether alleles can be neutral (i.e. Neutral Theory)?

    The fact that neutral alleles can be fixed in a population by drift means that a population can explore sequence space in a way that would be impossible if all alleles had to be either beneficial or detrimental. For example, this explains how chloroquine resistance arose in Plasmodium when it requires that several different mutations become fixed in the population.

    That, by the way, refutes most of Behe’s argument in The Edge of Evolution.

    Many of the adapations in Richard Lenski’s long term evolution experiment were preceded by fixing neutral alleles that opened up further possibilities for beneficial alleles to arise. Those “permissive” alleles were absolutely essential for the final adaptation but they were neutral when they were first fixed in the population.

    This is not theory. It has been demonstrated and proved many times. The important point here is neutral alleles, not drift. Drift also affects detrimental and beneficial alleles.

  245. 245
    phoodoo says:

    Soundburger has already done a pretty good job of chopping this moron, er sorry Moran, into mincemeat, but I guess I can do a bit more.

    Larry’s take is that, well, you see, if enough meaningless, arbitrary, useless, things are thrown into a body plan, that makes a great foundation to build up a more useful one. Holy fricking cow, how desperate does one’s logic need to be to believe this?

    Its like this, if you have a fully functioning car, but then you accidentally put a big crack in your axle that doesn’t completely tear it in two, and then you also slap on a bunch of bent horseshoes onto the outside of the engine block, well, one day those will be great places to bolt on some wings to turn your car into a flying spaceship with a retractable afterburners.

    If soundburger didn’t explain clearly enough what an idiot this guy is, well, now it should be abundantly clear.

    Oh, but we don’t understand population genetics!

  246. 246
    kairosfocus says:

    Folks, can I suggest that we not allow ourselves to be drawn into a schoolyard taunt down-spiral to the gutter. KF

  247. 247
    kairosfocus says:

    F/N: Let us observe VJT showing a template for a refutation of the design inference on the world of life:

    What I was looking for was a short scientific rebuttal of Dr. Meyer’s arguments, something along these lines (I’m making this stuff up):

    Contrary to Dr. Meyer’s claim that the combinatorial sequence space for functional genes and proteins is too large to be searched within the time available, scientists have calculated that functional proteins as short as 50 amino acids could have been generated within the space of 100 million years on the primordial Earth, within proto-cells near hydrothermal vents, and they have recently created artificial life-forms requiring only short amino-acid chains. What’s more, it turns out that the pathways between various proteins domains were in fact much shorter than previously believed, making the origin of the various proteins found in organisms today from a much smaller subset mathematically plausible. Scientists have also created a workable model of a developmentally plastic genome in which early acting mutations are nowhere near as harmful as in modern organisms. Finally, cell biologists have recently sketched a plausible hypothesis as to how the epigenetic information in the cell may have arisen, step-by-step. (Insert references here.)

    That is what a proper reply to an Intelligent Design argument looks like. Maybe we’ll see one, in a decade or two. Who knows? But I’m not holding my breath. The case for Intelligent Design is built on cutting-edge science. The case for life having arisen by an unguided natural process is built on conjectures and castles in the air. That’s why we call it “promissory materialism.”

    Can Dr Moran or any other of our objectors fill in the blanks and provide the references — including especially Nobel Prize response speeches?

    Let us see.

    Failing that, is is not reasonable to infer that the best explanation for the FSCO/I in the world of life — from the gated, encapsulated, metabolic C-chemistry aqueous medium nanotech automaton with integral von Neumann, code using kinematic self replicator we term the cell on up — is the same as a trillion case observational base leads us to expect . . . intelligently directed configuration (aka, design)?

    Why or why not, on what grounds?

    KF

  248. 248
    Silver Asiatic says:

    From a post last year:

    VJT: Reading Professor Moran’s post, I was struck by its muted tone. Moran believes that “some evolution at the morphological level can be attributed to … random genetic drift,” including “neutral morphological changes and a small percentage of detrimental morphological changes.” He admits that “Neutral Theory and random genetic drift … are not very good at explaining most adaptations,” adding that “the vast majority of complex structures seem to be adaptations of one sort of another.” He then tentatively proposes that “there are many ‘functions’ and ‘behaviors’ that are neutral,” but concedes that “it’s difficult to rule out any adaptive component.” He finally acknowledges that “natural selection plays an important role in the origin of most complex structures and novel adaptive morphological features,” but goes on to suggest that “there are likely to [be] many ‘novel morphological features’ that are non-adaptive.” However, since Professor Moran has already conceded that “the vast majority of complex structures seem to be adaptations of one sort of another,” it is difficult to know what to make of his last suggestion.

    http://www.uncommondescent.com.....evolution/

  249. 249
    Box says:

    Larry,

    You will probably call me an IDiot again, but here it is:

    What is an organism?

    If it’s fermions and bosons all the way down why is it that things don’t fall completely apart—as they do, in fact, at the moment of death. What power holds off that moment—precisely for a lifetime, and not a moment longer?
    Why do fermions and bosons act in concert to form an organism? We both know that fermions and bosons couldn’t care less about the organisms that they constitute.
    So, please tell me, what is an ‘organism’ if it’s fermions and bosons all the way down?

  250. 250
    Andre says:

    Phoodoo

    That is about the best analogy one could use, this snake oil Prof Moran is peddling is nonsense and as much as he likes he has not refuted Behe nor has Lenski’s experiments shown what he is claiming, Lenski’s e-coli are sick, they are not fit for purpose because under constrained conditions they shed information to survive……

    Prof Moran will never have my respect and here is why, when I asked him a question all he had to say was; “You don’t understand evolution”

    It’s clear he knows nothing either.

  251. 251
    soundburger says:

    kairosfocus, I appreciate that you are doing your best to keep this on a certain plane, and that is commendable. On the other hand, I would suggest that there actually IS no ‘down-spiral to the gutter’; rather, there are legitimate grievances to be had with Larry Moran’s demeanor, just as there are re his scientific assertions.

    He actually has numerous things to answer for. To take one example, he has mentioned that he teaches a course in Critical Thinking at his university.

    One can definitely wonder if he has the right credentials and expertise to teach such a course. For example, if a student came up to a professor in such a course, saying that he liked a certain writer, and it was revealed that the writer used juvenile put downs (such as IDiot), and numerous charges of stupidity, etc, toward those he disagreed with, what would a GOOD Critical Thinking prof do?

    He would warn the student off such a writer, surely. He would explain that the writer was poisoning the well, and thus should be held suspect in terms of the level of confidence he actually held regarding his own position. He would explain that a critical thinker must be able to recognize such dishonest techniques of persuasion, and hold it against one who uses them.

    Is it really, therefore, a ‘down-spiral’ merely to point such things out? IS Larry Moran a good teacher of a critical thinking course, or even the right person to be teaching such a course? And, if not, could we not go from there to at least reserve judgment in terms of what sort of techniques he uses to sell his own opinions and pass them off as fact in OTHER teaching venues?

  252. 252
    Larry Moran says:

    @Silver Asiatic #248

    Instead of posting Vincent Torley’s version of my views why not quote me instead?

    Better still, ask me for clarification if you are still confused about modern evolutionary theory.

  253. 253
    computerist says:

    What evolutionists (like Larry) are saying, is that
    evolution works regardless, because mutations
    will pile up, and eventually become useful (aka: have a selective/fitness advantage).

    In computer lingo, say for example we have this binary string:

    101010[100101]001010101[01010]10010101

    The subsets within the brackets, represent/translate into non-functional sequences.
    They’re simply “disregarded” for the moment.
    The other subsets, are functional and have some sort of selective/fitness advantage.
    The “compiler” will step-through sub-sequences and try to compile them.

    Now, say the first non-functional subset, incurs a mutation later down the road.

    101010100100001010101[01010]10010101

    Now it has become useful, translates into a functional sequence.

    It has now “integrated” with the first and second functional block into a more sophisticated
    functional state.

    Evolution works! Blind undirected processes all the way 🙂

  254. 254
    Larry Moran says:

    Andre #250 says,

    That is about the best analogy one could use, this snake oil Prof Moran is peddling is nonsense and as much as he likes he has not refuted Behe nor has Lenski’s experiments shown what he is claiming, Lenski’s e-coli are sick, they are not fit for purpose because under constrained conditions they shed information to survive……

    Prof Moran will never have my respect and here is why …

    If it’s any comfort to you, you will never have my respect either if you keep spouting such nonsense. It’s clear that you have never read Lenski’s papers and it’s clear that you have not followed the debate over Behe’s claims.

    In spite of your lack of knowledge of these issues, you come across as someone who is absolutely certain that he is right and I am the one spouting nonsense.

    I challenge you to a one-on-one debate over on Sandwalk concerning your claim that, “… nor has Lenski’s experiments shown what he is claiming, Lenski’s e-coli are sick, they are not fit for purpose because under constrained conditions they shed information to survive……”

    If you accept, I’ll start the thread today and you can post the first round as a guest author without any comment or interference from me. Start by proving that Lenski’s experiments do not show what I was claiming. I will reply in the next post.

    Put up or shut up. (Or weasel out by making some excuse.) You will earn my respect if you agree to the debate.

    Here’s some reading material so you can prepare for the debate.

    Richard Lenski answers questions about the long-term evolution experiment (LTEE)

    Vincent Torley tries to understand fixation

    On the unpredictability of evolution and potentiation in Lenski’s long-term evolution experiment

    Lenski’s long-term evolution experiment: the evolution of bacteria that can use citrate as a carbon source

    Elizabeth Pennisi writes about Richard Lenski’s long-term evolution experiment

    How do creationists interpret Lenski’s long-term evolution experiment?

  255. 255
    Larry Moran says:

    computerist #253 says,

    What evolutionists (like Larry) are saying, is that
    evolution works regardless, because mutations
    will pile up, and eventually become useful (aka: have a selective/fitness advantage).

    I have patiently explained in this thread what I actually meant. I have explained it in greater detail on my blog and provided numerous references. In addition, there are six or seven very good introductory evolutionary biology textbooks that explain it very well.

    I spite of all this, you post a ridiculous summary of what you think I said without doing any of the homework one would expect of some intelligent person attempting to understand a difficult concept for the first time.

    I have a favorite word for people like you, can you guess what it is?

  256. 256
    kairosfocus says:

    S-B,

    As it turns out, I have taught the UK/Caribbean equivalent of a critical thinking etc course, the A Level General Studies/Paper.

    Your basic point on that is well taken, there is a need to move away from pathos and blind adherence to authority to focus on facts and logic. and atmosphere poisoning based on red herrings, led away to strawmen soaked in ad hominems and set alight to cloud, confuse, poison and polarise the atmosphere does little good. (I think this triple-threat approach is a bit more instructive than poisoning the well.)

    My particular concern in the thread has been the shoot back in kind, which I had hoped was over.

    But it is not.

    I have noticed that so soon as I took time to put the phil horse before the issues cart, the red herring on angelology and demonology has vanished. Similarly, there is a tippy-toes around the OOL-FSCO/I origins and vera causa issues. Similarly, neutral evo does not seem to answer adequately to OOBP-FSCO/I issues.

    Most recently, I think LM needs to retract his “retreat” strawman caricature of VJT’s citations of Meyer and the core ID case. Likewise, it would be very interesting indeed to see a serious fleshing out of VJT’s skeletal outline of a refutation of the ID case.

    For this last, I asked for esp Nobel Prize lectures, as those typically will make the major points on breakthrough achievements at the ultimate forum for recognition. Never mind, that the arguments stand on their merits.

    My thought is, if you have the merits, stand there.

    KF

  257. 257
    computerist says:

    I have patiently explained in this thread what I actually meant. I have explained it in greater detail on my blog and provided numerous references. In addition, there are six or seven very good introductory evolutionary biology textbooks that explain it very well.

    Six or seven intros? Is evolution so simple that one textbook is not enough?

    I spite of all this, you post a ridiculous summary of what you think I said without doing any of the homework one would expect of some intelligent person attempting to understand a difficult concept for the first time.

    I’m just trying to help, Larry. As someone who designs and builds complex functional systems for a living, I thought I would help out a fellow evolutionist.

  258. 258
    Larry Moran says:

    kairosfocus #243 says,

    First, it has long been trumpeted far and wide as scientific consensus that Darwinian and linked mechanisms suffice to explain the appearance of design in the functionally specific complex organisation and associated information (FSCO/I for short). This in turn implies that the appearance of specified complexity does create a strong impression of design, on our experience of observed cases. This, is therefore implicit.

    So, if there is a breakdown of the claim then that returns the alternative to its status as best explanation.

    I agree that you have described the essence of Intelligent Design Creationism.

    You begin by setting up a dichotomy where there are two, and only two, possible explanations for something in the natural world that appears designed. (“I don’t know” isn’t an option.)

    Then you comb through the scientific literature to find some examples of apparent design where evolutionary biologists do not have a detailed enough explanation that satisfies you. Examples like bacterial flagella and the Cambrian Explosion.

    You then declare that the only other possibility is that gods did it.

    When evolutionary biologists challenge you to provide a few more details—just what you ask of them—you say that this isn’t part of your scientific explanation. Maybe aliens did it.

    It’s a pretty good strategy. If evolutionary biologists ever did come up with a good explanation for, say, the Cambrian Explosion, with lots of supporting evidence, then you will just concede that this is one more case where evolution works and move on to some other example.

    I’m sure you will agree that Intelligent Design Creationism will not be falsified if we come up with an explanation of the Cambrian Explosion, right?

    And I’m sure that Intelligent Design Creationists will continue to insist that they have no obligation to describe the designer and how he/she/it works because that’s not part of their scientific theory. On the other hand, they are perfectly willing to nitpick to death all the details, theories, hypotheses, and speculations of evolutionary biologists because, unlike you, they are obliged to give you plenty of details about the history of life.

  259. 259
    Larry Moran says:

    bFast @ #238 says,

    I presume, then, that your perspective is that you cannot know if there is a god or not, but in light of evidence to the contrary, you will go with the “no god” hypothesis. The theist agnostic goes with the “god” hypothesis, though he lacks “knowing”

    Yes, that’s correct. Atheists know that it’s impossible to prove a negative (gods don’t exist) so it’s really pretty silly to adopt such a firm position on gods.

    Unfortunately, the same rule applies to Santa Claus and the tooth fairy but nobody ever declares themselves to be agnostic about them.

    The same thing applies to (almost) extinct gods like Zeus and Thor. I’m sure you are very confident that these gods don’t exist and so am I. However, if you are debating a philosopher then you will have to concede that you cannot ever prove their nonexistence.

    BTW, I’m pretty sure that there were people in the past who were as confident about the existence of their gods as you are about yours. You are happy to declare that they were misguided, or even delusional. Does this bother you in any way?

  260. 260
    Larry Moran says:

    Mung @ #237 asks,

    Do you mean by this that within a given population more alleles become fixed due to random sampling than due to selection?

    Or do you mean that more new species arise due to random genetic drift than due to selection?

    Both?

    It’s a fact that within a given population more alleles become fixed by random genetic drift than by natural selection.

    The issue is more complicated when it comes to speciation. Some of us believe that the evolution of reproductive incompatibility is largely due to chance events. Others, including Jerry Coyne, think that natural selection plays an important role.

  261. 261
    computerist says:

    @259

    It’s assuming that if we can explain x phenomenon, that therefore x phenomenon is not special anymore.

    The “it’s just nature” mentality, is why atheists/evos (like Larry Moran) are confused.

  262. 262
    Larry Moran says:

    Mung asks,

    Do you agree that random genetic drift does not and cannot explain adaptations?

    It’s not that simple.

    The fixation of nearly neutral alleles can be an essential precursor to some important adaptations. So in that sense the fixation of neutral alleles by random genetic drift can explain some adaptations.

    In addition I agree with Michael Lynch that some complex structures and processes could arise entirely by accident. Random genetic drift is a key component of such a process.

    These complex structures—he uses the spliceosome as an example—then become essential over time as additional layers of mutations and fixations add to their function. You end up with something that looks designed but, in fact, began as an historical accident.

    These are important issues in the Intelligent Design debate but it takes quite a bit of effort to understand them. Unfortunately, very few Intelligent Design Creationists are willing to make the effort because their minds are already made up. They know that evolution is impossible because it conflicts with their religious beliefs.

    These are the people who mock and disrespect evolutionary biologists by calling them Darwinists and claiming that they are responsible for eugenics and the holocaust.

    It’s hard for us to respect those creationists.

  263. 263
    kairosfocus says:

    LM,

    This is beginning to be predictable, so I will speak for record.

    First, you know or should know that the design inference is not equal to “creationism” in any reasonable sense of the word.

    Second, the context of reasoning about origins science is that form of inductive reasoning that can be described as abductive inference to the best current explanation. Promissory IOUs and blank checks and willful obtuse refusal to acknowledge what we know on a trillion member observational base do not cut it. Namely, functionally specific, complex organisation and associated information have well known causes. Reliably, intelligently directed configuration, AKA design.

    So, if we meet a phenomenon that exhibits FSCO/I, we are entitled epistemically to inductively infer that its best explanation is design.

    Especially, when the proposed alternatives have never been credibly observed to actually reliably cause FSCO/I and in fact have been demonstrably ideologically imposed via so-called methodological naturalism. Where, had you bothered to attend to the per aspect design inference filter approach, you would have seen that mechanical necessity comes first as default and is broken based on high contingency. The default for high contingency outcomes is chance, and this is broken where something like FSCO/I shows per needle in haystack search challenge, that it is maximally implausible as an explanation. In cases like FSCO/I we know through a trillion member base of direct observations, that it is a reliable result of intelligently directed configuration. So, design is the inductively warranted causal factor at work, and is strongly supported.

    To overthrow it, show that blind chance and/or mechanical necessity are observed capable of causing FSCO/I. Repeatedly, claimed cases of such — for years — have turned out to be design.

    Third, at no point have I inferred on the world of life that God did it, as a design inference on FSCO/I. Your resentment of a capital letter for God also speaks sad volumes, and your insistent loaded strawman caricature in the teeth of repeated patient explanation does not speak well of your approach either.

    FYI, I have long been on record that I agree with Thaxton et al from the beginnings of the modern design school of thought: FSCO/I in cells and onwards in body plans points to intelligently directed configuration (even as suspicious accelerants point to arson) but that does not in itself suffice to conclude as to who or what said designer or designers is/are. Indeed, I have specifically stated that a molecular nanotech lab some generations beyond Venter et al would credibly be enough. I have suggested that across this century we will likely achieve a similar result with implications for Industrial Revo 3.0, self replicating technologies, pointing onwards to development transformation and Solar System colonisation.

    It would be quite obvious, that a demonstration that FSCO/I can be and is formed by blind watchmaker chance and necessity would decisively undermine an inference to design as inductively warranted explanation for it. A demonstration of 72 ASCII characters in coherent English — or, better, compilable, running and functional Java code — coming about by blind chance and mechanical necessity would devastate the design inference on FSCO/I etc. So, long before we come to a demonstration of a blind watchmaker chance and necessity mechanism observed capable of creating body plans, the design inference is quite testable and falsifiable.

    (There is a different context of design inference on fine tuning that does not pivot on FSCO/I etc that would have to be addressed on another level, but that would be irrelevant to a demonstration that meets the vera causa test that establishes neo-darwinist or rival schools as fairly substantiating the blind watchmaker thesis. Such a demonstration — not done after 150 years and not in prospect — would have the same impact as convincing demonstration of a reliable perpetuum mobile of the 2nd kind would for thermodynamics. I am not holding my breath for that to be done, either.)

    I have no duty to try to prop up your strawman caricature of the design inference or to try to defend such. Instead, I expose it for what it is, a caricature set up to be knocked over by someone who insists on misrepresentation in the teeth of repeated correction.

    I call on you to deal with design thought as it is on its merits, not with a cooked up strawman caricature.

    As for your evident hostility to God, and for why I and many others hold that it is a reasonable and responsible worldview to accept God as the root necessary being behind reality, that speaks volumes. I point to 163 for a summary: http://www.uncommondescent.com.....ent-565505

    Again.

    Finally, I draw attention to VJT’s outline format for a real refutation of the design inference on the world of life. If you cannot readily flesh that out, why should I ignore the trillion member observation base that establishes as a firm inductively grounded conclusion, that FSCO/I is best explained on intelligently directed configuration as causal process?

    Why should I then not further infer that the FSCO/I in cell based life is evidence of life having been designed from the first cell on?

    Why should I not then infer yet further, that a designer of life is to be expected, as designers produce designs?

    And, why should I not integrate that with the evidence long since also in hand of a fine tuned cosmos set up for terrestrial planet, C-Chemistry based aqueous medium life? Pointing, onward to a cosmos designer (even through multiverse speculations)?

    The time for dismissive, loaded caricatures and namecalling of supporters of design thought, and of the substance of our thinking, is over.

    Long since over.

    KF

    PS: Your distortions on the history of ideas and ideological then policy consequences since the late C19, also needs severe revision. The Eugenics movement did grow up in Darwinist soil, and it did have devastating consequences as did wider scientific racism, evolutionary materialistic scientism dressed up in the lab coat, associated amorality, radical relativism and nihilism. Refusal to face that history frankly and refusal to learn from what was bought at the price of blood and tears, as 100+ million ghosts remind us, is utterly unwise. But then Santayana long since taught us that history teaches that those who refuse lessons of sound history are doomed to relive its worst chapters, and by and large we refuse the lessons. Hence Marx’s remark about history repeating twice, first as tragedy then as farce. And, FYI, I have to live with the shadow of the mushroom cloud brought to you courtesy physics and physicists. Let us learn from grim history, lest we relive it. And one step to that is a sound, history and ethics anchored, key case study based science in society professionalism course for science majors in training. Likewise, engineers and computer scientists. It is time to face up to our responsibilities.

  264. 264
    Larry Moran says:

    soundburger at #251 says,

    For example, if a student came up to a professor in such a course, saying that he liked a certain writer, and it was revealed that the writer used juvenile put downs (such as IDiot), and numerous charges of stupidity, etc, toward those he disagreed with, what would a GOOD Critical Thinking prof do?

    I’ll tell you what I do. Maybe that will help.

    I would point out that there’s a difference between critical thinking and rhetorical devices. In order to survive in the real world you have to learn about both. Critical thinking involves making sure you understand sound logic and the facts.

    How you deliver that information effectively in a modern society often involves additional skills.

    We use Jonathan Wells’ book Icons of Evolution as an example. We learn that his put down of evolutionary biologists by charging them with stupidity is a very effective strategy for his audience. We learn that the creationists, in general, are very good at this sort of thing and it works.

    I show them that if you want to really engage in a debate then it’s pretty ineffective to just rely on evidence and critical thinking. No politician will ever do this. Sometimes you have to be provocative and annoying in order to attract attention and get your message out. That’s how the real world works.

    For example, many evolutionary biologist have written about random genetic drift, Neutral Theory, etc. etc. but they have been ignored. As soon as I start calling ID proponents IDiots I get an entire thread with my name on it and I get a chance to actually educate some of them.

  265. 265
    bFast says:

    Larry Moran (259)

    I’m pretty sure that there were people in the past who were as confident about the existence of their gods as you are about yours. You are happy to declare that they were misguided, or even delusional. Does this bother you in any way?

    Larry Moran, has it dawned on you that your statement can be put back at you? You are (fairly) confident that there is no god. When you discover that there is (our conjecture is that you will) does it bother you that you shot down one God too many.

    If ever there is evidence for the existence of God, it is the big bang. (I am sure you presume that our physicist friends are right about that.) We have found the moment of creation. It is amazing! It is incredible! Most importantly, physicists believe that it is almost unfathomably precise. Honestly, Larry Moran, I find it inconceivable to look at the big bang and say “just happened” — don’t know how yet, but “just happened”.

    Oh, in my opinion the big bang also falsifies all polytheistic religious perspectives. (It also falsifies YEC, which is why YEC views the big bang a yet another scientific error.)

    If “big bang” then it is the product of “one”, or none if we have very stretchy imaginations.

  266. 266
    Mung says:

    Larry Moran:

    On the other hand, they [Intelligent Design Creationists] are perfectly willing to nitpick to death all the details, theories, hypotheses, and speculations of evolutionary biologists because, unlike you, they are obliged to give you plenty of details about the history of life.

    This is one of those things where they made their own bed.

    Evolutionary biologists are for the most part opposed to things just poofing into existence [except when they aren’t]. Remember, it’s just too improbable that it just appeared fully formed.

    So it must have arisen via some historical process.

    What’s more, that process must have been mechanical.

    If one is going to insist that organisms are machines and can be explained in mechanistic terms that does sort of come with the territory. Crying foul isn’t really an option.

  267. 267
    CJYman says:

    LM:
    “BTW, I’m pretty sure that there were people in the past who were as confident about the existence of their gods as you are about yours. You are happy to declare that they were misguided, or even delusional. Does this bother you in any way?”

    Not in the slightest. They were not wholly misguided nor were they all any more delusional than we are today in reference to ‘what we know.’

    And I’m pretty sure that there were people in the past who were as confident about their model of evolution as you are about yours. You are happy to declare that they were misguided, or even IDiots. Does this bother you in any way?

    Furthermore, ‘Creation’ & ‘Design’ are not synonymous terms in this debate. ‘Creationist’ refers to those who believe in ‘creation ex nihilo.’ ‘Intelligent Design’ merely refers to teleology in nature — the target design guiding the physical/mechanical implementation of said design. Thus, some people could be labelled as ID Creationists, but others most definitely not. This is why it can be offensive to some of us especially those who accept the mechanisms of evolution as agreed upon by the scientific community.

    I at least speak for myself when I say that I am an ID proponent that does not believe in Divine intervention, sees evolutionary mechanisms as playing no role in my acceptance or rejection of ID Theory, and I even go so far as to accept that, from a logical perspective, some sort of abiogenesis must have occurred. What I take issue with is the ‘unguided’ language. I am thus more of a ‘Guidance-ist’ than a ‘Creationist.’ I presume this applies to many more people than myself. It is your attachment of ‘creationist’ to ID that is both unnecessary and actually incorrect on the same level as calling you a ‘Darwinian evolutionist.’

  268. 268
    Carpathian says:

    kairosfocus:

    Carpathian, I really don’t have time for a rhetorical circles game.

    Neither do I so please address the statements I actually make.

    Biology is concerned with reality not immaterial statistics.

    You cannot use your blind random needle in the haystack argument when it comes to biology or any issue dealing with physics.

    The OOL question deals with reality, i.e. physics, and blind random chance is limited to the range that the laws of physics allows.

    Because randomness in physics is limited, any configuration of X bits in the real world, will be less than 2 raised to the power of X. How much is dependent on the situation.

    Secondly, there is more than 1 “searcher” looking for that needle in biology, there is actually a population searching.

    If a million people start “searching” for a needle that could be in a million places, it is likely that one of those people will find it in the first place they look
    Thirdly, in biology, each member of the population need only find a portion of the “needle” and thanks to sexual reproduction, that needle will appear as a descendant.

  269. 269
    Carpathian says:

    kairosfocus:

    A demonstration of 72 ASCII characters in coherent English — or, better, compilable, running and functional Java code — coming about by blind chance and mechanical necessity would devastate the design inference on FSCO/I etc.

    Biological evolution doesn’t work like this.

    In biology, not all genetic configurations manage to reproduce themselves.

    A roll of the dice though, will result in one of six configurations with no bias on any particular one.

    Biology does not work like dice.

  270. 270
    kairosfocus says:

    Carpathian, it is obvious that the information – needle in haystack search challenge is overwhelming and that you have no answer than to try desperately to wish or sweep it away. That is good enough for the astute onlooker who recognises the existence of coded, algorithmic information in protein synthesis, or the significance of the CCA universal tip for tRNA that attaches to the COOH end of AA’s to be chained. And, so much more. KF

    PS: I suggest to you that those who teach chance variation as source of mutations, and those who have long concluded that random processes are strongly connected to molecular phenomena may have some’at to say to you. Nor do my considerations pivot on flat random distributions. You will find, further, that I gave a simple easily done test that, long before we get to Darwin’s pond or the like would potentially falsify the design inference. If you were not content to snip and snipe, you would see that I then went on to OOL — the root of ToL, and OOBP by the branching tree models usually put forth.

  271. 271
    bFast says:

    Carpathian:

    Biology is concerned with reality not immaterial statistics.

    You cannot use your blind random needle in the haystack argument when it comes to biology or any issue dealing with physics.

    Huh? You do recognize that your position invalidates at least 50% of the Biology and Physics studies, do you not? Statistics is a perfectly valid mathematical form.

  272. 272
    Carpathian says:

    Mung:

    Carpathian: Here is a 500 bit “search”

    carp /lLog.log /c6 /d /g250 /p64 /m5 /n /s

    Mung: Why did you choose only six children?

    Why did you choose a length 250 for your candidate strings?

    Why did you choose a population size of 64?

    Design. Design. Design.

    For the same reason a technician would inject a 1 KHz signal into an electronic circuit and that would be to see how the circuit responds.

    The technician might then “choose” a 10 KHz signal in order to see how the circuit responds to a different frequency.

    My program works much like an oscilloscope in a lab. It allows me to make measurements.

    In this case, I am watching to see how the “system” responds.

    It is amazing that virtually every ID proponent has trouble with finding the dividing line between the test equipment and the device being tested.

    If I use a “designed” ruler to measure the length of a blade of grass, I have not corrupted the grass with “design”.

    The grass is the device under test, the ruler, despite being “designed”, is not a part of the grass.

    Do you disagree?

  273. 273
    Silver Asiatic says:

    LM

    I agree with Michael Lynch that some complex structures and processes could arise entirely by accident … he uses the spliceosome as an example

    It’s difficult to explain the origin of a complex molecular machine like that via the supposed, non-random mutation-selection process, but entirely by accident? I wouldn’t think the theory would generate that level of credibility.

    Sometimes you have to be provocative and annoying in order to attract attention and get your message out. That’s how the real world works.

    For example, many evolutionary biologist have written about random genetic drift, Neutral Theory, etc. etc. but they have been ignored. As soon as I start calling ID proponents IDiots I get an entire thread with my name on it and I get a chance to actually educate some of them.

    I’m not sure if you were being serious, but if so, that seems honest and admirable on that account.

    Yes, it’s a good way to get attention, I’ll agree — and you could have a positive effect. There’s the risk also that you could make things worse by giving people less reason to trust the evolutionary-biology community.

    Nick Maske, for example, certainly did that in his appearances here — lots of bluster, insults, contempt and dodging-issues from him, made it seem like biologists are, basically, evil (with a few exceptions).

    Some of the other anti-ID regulars here come across in the same way (to a much lesser extreme) – pedantic, nit-picking on details of various papers while completely ignoring the bigger issues. When they’re proven incorrect (which happens frequently) they simply lose credibility for the evolutionary view. That’s the gamble that they take.

    But anyway, if you can win respect or even win some small points from this audience, I think you will have achieved something for your point of view.

    It might not seem like it, but I appreciate hearing your arguments.

  274. 274
    Carpathian says:

    bfast:

    Statistics is a perfectly valid mathematical form.

    Of course it is but applied incorrectly its as bad as trying add apples and oranges.

    If I have a set of 4 numbers; [1,2,3,4,5,6,7,8], the chances of 1 coming up is 1 in 8 just as it is for any other number in the set.

    If however, my set looks like this, [1,1,1,1,2,2,4,8], the odds of me getting a 1 is 2 to 1 despite the fact the index into the set is still a 1 of 8 possibility.

    In both cases statistics can be applied but the results have to make sense.

    Some configurations in physics are not possible and are therefore not in the “set”.

    In reality, because of physics, the restrictions are more complex than saying, X is not in the set as even the “selection” of an index into the set may be restricted.

    That’s why you cannot apply statistics in a purely numerical scope when it comes to biology.

    It’s not a perfect analogy but the idea is you cannot treat the real world in a purely numerically random manner.

  275. 275
    kairosfocus says:

    LM,

    At risk of turnabout blame the victim rhetorical cheap shots, I will quietly note that resort to incivility through namecalling etc as seen above has not helped.

    Specifically, all you have succeeded in doing is convincing me that I would not want to entrust any person I cared about to your tutelage; which means essentially anyone. Abusive namecalling, willful distortion of people and ideas, schoolyard bully level taunting and the like tell me you are an enabler of the fever swamp extremists who take it to the next level, stalking.

    Further, you have convinced me that you are not capable of teaching sound, straight thinking, but would be very likely to resort to indoctrination, intimidation and outright bullying to push an ideological agenda.

    Worse, for cause as seen above, you have come across repeatedly as speaking in disregard to truth and fairness, in evident hope that what you say or suggest will be taken as substantially true.

    I trust that, one day, you will come to realise what has been going on and will turn from it before it is too late.

    KF

  276. 276
    Andre says:

    Prof Moran

    Last night as I read your posts I had a thought….. Is Keith S and Larry Moran the same person? Your ignorance and arrogance is just about on par, but when you invited me over to Sandwalk to come and debate you I knew you are cut from the same cloth, please don’t take this personal but visiting your site is second to being the worst after TSZ, diogenes, your favorite lapdog makes me sick to my stomach, you can tell the world I won’t come and debate on your site, that much is true, I tried before and your best effort ever was….You don’t understand evolution…

    So crow on your victory, but you ain’t getting me ever to visit your awful blog full of foul tempered ignoramuses.

  277. 277
    bFast says:

    Carpathian, “That’s why you cannot apply statistics in a purely numerical scope when it comes to biology.”

    As far as I know, there is exactly one tool in biology that doesn’t blindly follow the flow of statistics. That is natural selection. Virtually all cases where the ID community apply statistics begin with “natural selection cannot work here, therefore …”. If this argument is in error, if natural selection can work in the provided context — present such. If natural selection is not able to act within the presented context, well, statistics fully apply. Your next defense is to show that the metric upon which the statistics have been applied is invalid. But your blanket “That’s why you cannot apply statistics in a purely numerical scope when it comes to biology” statement is, well, hogwash.

  278. 278
    Carpathian says:

    kairosfocus:

    Carpathian, it is obvious that the information – needle in haystack search challenge is overwhelming and that you have no answer than to try desperately to wish or sweep it away.

    It is very obvious that you don’t want to address this challenge.

    Take a cold spoon and a hot spoon and put them together.

    Physics will take care of the “configuration” and it won’t be random.

    You will never end up with 1 hot spoon and 1 cold one, or 2 cold ones or two hot ones.

    What you will always end up with is two warm ones regardless of any statistical analysis you perform.

    If you can’t show me that physics and thus biology are purely random, you can’t you use your needle in a haystack argument.

    I haven’t swept the the challenge away, I’ve addressed it.

    Now you address it by showing me why a “search” for a biological “target” is purely random.

  279. 279
    Mung says:

    Carpathian:

    My program works much like an oscilloscope in a lab. It allows me to make measurements.

    In this case, I am watching to see how the “system” responds.

    Why? You don’t plan to tinker with the settings do you, Mr. Intelligent Designer?

    It is amazing that virtually every ID proponent has trouble with finding the dividing line between the test equipment and the device being tested.

    If I use a “designed” ruler to measure the length of a blade of grass, I have not corrupted the grass with “design”.

    The grass is the device under test, the ruler, despite being “designed”, is not a part of the grass.

    Do you disagree?

    It is amazing that you would rather talk about grass than your program and how it functions and why it does what it does.

    Do you disagree?

  280. 280
    bFast says:

    BTW, even when natural selection is at work, statisticians are not unemployed. Natural selection offers a twist on statistics, but doesn’t bar the mathematical form altogether.

    Moderator: I tried to edit my post above, but it said I don’t have permission. The clock said I did. Whassup?

  281. 281
    Mung says:

    Carpathian:

    If I have a set of 4 numbers; [1,2,3,4,5,6,7,8], the chances of 1 coming up is 1 in 8 just as it is for any other number in the set.

    😀

  282. 282
    Carpathian says:

    Mung, good eye!

  283. 283
    bFast says:

    Carpathian, “Now you address it by showing me why a “search” for a biological “target” is purely random.”

    Carpathian, let me help you out here for a minute:

    1 – We refer to islands of functionality. This is not a point of functionality, but a 3 dimensional object of functionality. Parts of the island are very near sea-level, ie, a wee bit of functionality happens, but not much. In any case, there is some reason to believe that once an enzyme is found that can catalyze a particular reaction a little bit (in the common case), natural selection is able to optimize the enzyme to find the maximum point on the island (or possibly a false high on a nearby peak with multi-peaked islands.)

    2 – The islands of functionality reside in a sea of dysfunction. Any protein sequence that is not able to usefully catalyze anything is in that sea. Natural selection offers this enzyme no directionality at all. It is subject to simple statistics.

    3 – The dynamic fitness landscape — The sea level isn’t a constant. Just as in the development of the earth we see where sea levels were very high, and very low. We see land bridges between Asia and America. We recognize that just because something is under sea-level at the moment, in different circumstances it may not be.

    4 – Lastly, when analyzing the point where island meets sea, one must respect Larry Moran’s “neutral theory”‘s perspective which suggests that Natural Selection is actually a very weak force. His theory, therefore, raises the sea-level quite a bit.

  284. 284
    Carpathian says:

    bFast:

    But your blanket “That’s why you cannot apply statistics in a purely numerical scope when it comes to biology” statement is, well, hogwash.

    Show me it’s hogwash.

    Natural selection is not “selection” at all, it is elimination.

    Any configuration of “data”, i.e. organism, that does not reproduce has its “data” removed from the “database”, i.e. population.

    This is not a pre-meditated decision by “nature”, it is simply a case of the environment you find yourself in, too difficult to survive.

  285. 285
    computerist says:

    This is not rocket science. I don’t understand why it’s so difficult for people to understand the basic concepts of population genetics and evolution.

    Is it possible Professor Larry Moran, can you create or provide a flowchart for how you think evolution creates apparent design/FCSI? I don’t think this should be too much trouble and it would be super helpful for IDiots such as myself. You’re obviously far more informed evolutionist than most, and you can “close the loop” (so to speak) on this issue atleast from your end. Much appreciated.

  286. 286
    Andre says:

    Prof Moran

    One last thing if talking about Lenski’s experiment made you huff and puff and make your hair stand up like a Rhodesian Ridgeback all things considered you don’t really have anything and that is a statement of fact unless of course you can prove facts wrong……

  287. 287
    bFast says:

    Larry Moran (244)

    This is not rocket science. I don’t understand why it’s so difficult for people to understand the basic concepts of population genetics and evolution.

    This is not an issue of not understanding evolution. Most of us have a pretty darn accurate picture of evolution — we get caught up in the semantics of which term references which subset of said theory, that’s all. And you make it your hobby to point out these issues of semantics so that you can hold to your theory that anyone who understands the theory will obviously accept it.

    Let me encapsulate the entire theory in a single thought.

    DNA is a long chain of information. Some of this information is in the form of protein coding genes. (These things are enormously complex in Eukaryotas, much simpler in bacteria.) Much of this information is presumed to be, well, noise. Another good chunk (bigger than the “protein coding genes” chunk) is active, but not being converted through RNA to protein.

    Especially in the process of duplication, noise is added to the DNA. We call that mutation. There are patterns to this noise such as insertions, deletions, inversions, and even horizontal gene transfer. Each of these is noise. The most common form, however, is the point mutation. While this insertion of noise is not exactly random, it is not strategic. (There is the exception that possibly organisms have developed strategic patterns of mutation, such as in our immunity system. These strategies on the part of the organism are presumably developed through the non-foresighted process described above.)

    When a mutation happens in a “gene”, the segment of DNA that codes for protein (and sometimes just for enzymic RNA), a new allele is born. Thats where all variety comes from. (I am not sure what mutations in active, non-gene, DNA is called, but it is obviously part of the variety as well. Further, presumably junk DNA takes on a mutation that re-activates it. This too is part of the non-foresighted mutation source of variety.)

    This new allele can become more or less common based solely on forces that have nothing to do with the allele. The lucky/unlucky ride. If the frequency of the allele becomes 0, then that allele is purged from the DNA. Albeit it may be resurrected again by another instance of the same mutation.

    As the allele rides on the sea of chance, it has its influence on the organism. It may make the organism fundamentally dysfunctional, or infertile. If so, it is purged from the gene pool in one generation. If it offers some dysfunction or some advantage, it will have statistically poorer or better odds of spreading in the gene pool. If its disadvantage or advantage is minor, the variation of statistical odds is very small.

    If the winds of chance blow in favor of a particular allele often enough, it will become the universal allele within the species — it will be fixed. Even if an allele has slight disadvantages, it can still be fixed.

    Because alleles get fixed in populations purely because of chance, if you separate two communities of organisms long enough, they will become separate species. Sometimes when a group of alleles get together in a community of the same organism the organism takes on an adaptive advantage. The alleles involve increase in frequency, and an adaptive advantage is born.

    When an organism encounters a fundamentally different environment or opportunity, natural selection may use the alleles floating around to carve out a unique sort of organism — adaptation happens.

    That is a very long winded description of the evolutionary process. This is a demonstration of a vastly richer understanding of evolution than 98% of the evolution-believing population has!

    Larry Moran — you seem to have an “if they understand the theory, they will believe the theory” belief. It is not true! I would contend that the opposite is true. If you understood the challenges to evolutionary theory that ID presents, you would see evolutionary theory to be vastly inadequate.

  288. 288
    bFast says:

    Caparthian, “Show me it’s hogwash.” Caparthian, oi. I just discussed the scenarios where natural selection plays no role, and you went on to try to correct me on my definition of natural selection.

    Please repeat this mantra: “If a mutation does not affect an organism’s phenotype, natural selection plays no role.”

  289. 289
    Andre says:

    bFast

    @ 287 from your lips to Prof Moran’s ears….. and I’m not using it sarcastically……

  290. 290
    Evolve says:

    ///The theory of intelligent design (ID) holds that certain features of the universe and of living things are best explained by an intelligent cause rather than an undirected process such as natural selection. ///
    http://www.uncommondescent.com/id-defined/

    This definition itself is flawed. ID “theory” has not shown that design can ONLY come from intelligence and there cannot be any other source for design. Life itself is proof that nature can produce design on its own with no intelligent intervention.

  291. 291
    Mung says:

    Evolve:

    ID “theory” has not shown that design can ONLY come from intelligence and there cannot be any other source for design.

    So?

  292. 292
    Andre says:

    Evolve

    Life is proof that nature can produce design? Extraordinary claims require extraordinary evidence. Do you have any that nature can design life?

  293. 293
    Larry Moran says:

    kairosfocus at #275 sys,

    Specifically, all you have succeeded in doing is convincing me that I would not want to entrust any person I cared about to your tutelage; which means essentially anyone. Abusive namecalling, willful distortion of people and ideas, schoolyard bully level taunting and the like tell me you are an enabler of the fever swamp extremists who take it to the next level, stalking.

    Further, you have convinced me that you are not capable of teaching sound, straight thinking, but would be very likely to resort to indoctrination, intimidation and outright bullying to push an ideological agenda.

    Worse, for cause as seen above, you have come across repeatedly as speaking in disregard to truth and fairness, in evident hope that what you say or suggest will be taken as substantially true.

    I have never been as mean, disrespectful, and despicable as kaisosfocus.

  294. 294
    kairosfocus says:

    Ev, just passing by. Show us a credible case on actual observation of functionally specific complex organisation and/or associated information of at least 500 bits of complexity coming about by blind chance and mechanical necessity. There is a trillion member base of cases of such FSCO/I arising due to intelligently directed configuration. Backed up by the needle in haystack search challenge. Until you can pass this test, we can be inductively highly confident that FSCO/I is a reliable sign of design as cause, on grounds that are a commonplace of scientific reasoning. KF

  295. 295
    Larry Moran says:

    CJYman at #267 asks,

    And I’m pretty sure that there were people in the past who were as confident about their model of evolution as you are about yours. You are happy to declare that they were misguided, or even IDiots. Does this bother you in any way?

    Yes, of course it does. I worry that my current view of evolution might be incorrect. It’s a real concern because I have changed my views and perspective several times already when new data and new information becomes available. In fact, there are experts on Sandwalk who correct me just about every week.

    However, because I have thought about it and been taught by others, I know which parts of evolutionary theory are wrong. I’m trying to teach you guys so you won’t persist in making simple errors when you launch your attacks on evolution.

    When you criticize something that thousands of expert scientists have studied for decades and reveal that you don’t understand it well enough to have an informed opinion, it makes you look like …. well, you know.

  296. 296
    computerist says:

    Professor Larry Moran goes on about Thor, Zeus and other gods, but under the atheist framework, which implies that in order to get beyond the probabilistic hurdles required to get a life supporting finely tuned universe it must invoke superstitious multiverse hypothesis or an eternal universe.

    In which case, given the infinite amount of time and infinite amount of possibilities that the atheist framework must posit, an easter bunny, flying spaghetti monster, tooth fairy, Thor, Zeus etc… more than likely exist. Or perhaps already the flying spaghetti monster is the one who created the universe.

  297. 297
    bFast says:

    Larry Moran, “I have never been as mean, disrespectful, and despicable as kaisosfocus.”

    You’ve got to be kidding! I agree that Kaisosfocus is sharp of tongue. I certainly believe him to often be too sharp of tongue for his own good.

    However, you have made it a habit of calling people idiots. You have lashed out with the term idiot to people (me) even when those people (me) have provided the evolutionary correct answer (though possibly not using the ideal terminology.)

    Larry Moran, “I have never been as mean, disrespectful, and despicable as kaisosfocus.” Talk about the pot calling the kettle black!

  298. 298
    Andre says:

    What exactly are you trying to teach us Prof Moran? That the accidental blind workings of matter is responsible for the diversity of life? Really? Do you honestly in your heart believe that?

  299. 299
    kairosfocus says:

    LM, I am going to underscore in response to your latest, that it is a fair and accurate summary that you have continually resorted to schoolyard taunting name calling [IDiot, Intelligent Design Creationists etc], invidious association [here, Creationism in the teeth of evidence that such is inappropriate], strawman caricatures in the teeth of repeated correction, speech with reckless disregard to truth and fairness, all repeatedly and readily documented above and elsewhere across UD in recent days. I therefore stand by my conclusion that I would not recommend anyone I care about to your tutelage, in critical thinking or any other subject; the risks I highlighted earlier would be too high. You have tripped too many warning flags and have willfully ignored repeated, justified correctives from multiple directions. I think on fair comment you need to look back at what you have done and how you have tried to justify it, including now shoot at the messenger. Please, do better next time. KF

  300. 300
    Andre says:

    Prof Moran

    Do you know when you become a critical thinker? The day you realize how much magic the materialist version of evolution requires for it to work.

  301. 301
    bFast says:

    Andre, “The day you realize how much magic the materialist version of evolution requires for it to work.” Preach it brother!

  302. 302
    CJYman says:

    Larry Moran @ 295,

    I appreciate your answer. It makes sense. I’m just wondering how you have determined that evolution is an unguided process? Is there a scientific approach that you have used to distinguish between guided and unguided processes? Not looking for a huge debate at the moment since I don’t have time for such. I would appreciate just a basic thought on the matter.

    As well, what are your thoughts on my thoughts re: ‘Creationist’ as an incorrect description for many if not most IDers?

  303. 303
    Larry Moran says:

    CJYman at #302 asks

    I appreciate your answer. It makes sense. I’m just wondering how you have determined that evolution is an unguided process?

    I don’t believe in any gods. That doesn’t leave much choice unless I attribute the guiding to lepechauns. In order to believe that evolution is guided, you pretty much have to start with the belief in a guider.

    As well, what are your thoughts on my thoughts re: ‘Creationist’ as an incorrect description for many if not most IDers?

    See #74 above. The word “creationist” can have much broader meaning than you think. That’s the definition I use.

  304. 304
    Larry Moran says:

    Andre says,

    Do you know when you become a critical thinker? The day you realize how much magic the materialist version of evolution requires for it to work.

    Says the man (boy?) who makes ridiculous statements then runs away when challenged to defend them.

    And you wonder why I call some of you IDiots?

  305. 305
    Larry Moran says:

    kairosfocus at #299 says,

    I am going to underscore in response to your latest, that it is a fair and accurate summary that you have continually resorted to schoolyard taunting name calling [IDiot, Intelligent Design Creationists etc], …

    Schoolyard taunting, as you call it, is just that. It’s good clean fun and it pales in comparison to your mean spirited comments about me.

    .. invidious association [here, Creationism in the teeth of evidence that such is inappropriate],

    I have explained why I use the word “creationist.” Many evolutionary biologists have described themselves as creationists and so has Philip Johnson and other ID proponents who are not necessarily Young Earth Creationists. I gave you a link to the Wikipedia definition, which is similar to mine.

    That’s hardly “invidious.”

    … strawman caricatures in the teeth of repeated correction, …

    I try very hard not to do that but sometimes what you see as a “correction” is merely a difference of opinion.

    … speech with reckless disregard to truth and fairness, …

    I do not believe that is correct. I may make mistakes from time to time but I never, ever, disregard the truth, recklessly or otherwise. As for “fairness,” I try to be fair but I admit that from time to time I get a bit exasperated with you guys and your taunting.

  306. 306
    Mung says:

    Dr. Moran, further on the subject of genetic drift.

    At what population size does genetic drift pretty much swamp out selection? Are there other factors that need to be taken into consideration in answering such a question, other than population size?

  307. 307
    Larry Moran says:

    bFast at #297 says,

    However, you have made it a habit of calling people idiots. You have lashed out with the term idiot to people (me) even when those people (me) have provided the evolutionary correct answer (though possibly not using the ideal terminology.)

    Larry Moran, “I have never been as mean, disrespectful, and despicable as kaisosfocus.” Talk about the pot calling the kettle black!

    I have, indeed, referred to ID proponents as IDiots and I’ve even called some of them “idiots.”

    I have never launched a mean-spirited personal attack on the integrity of any of you and brought up your personal life (i.e. your job).

    Like this …

    Further, you have convinced me that you are not capable of teaching sound, straight thinking, but would be very likely to resort to indoctrination, intimidation and outright bullying to push an ideological agenda.

    If you don’t see the difference than I have no further use for you.

  308. 308
    Mung says:

    Larry Moran:

    In order to believe that evolution is guided, you pretty much have to start with the belief in a guider.

    How about the organism as guider?

    Why doesn’t evolutionary theory consider the organism itself as an actor rather than just the unlucky recipient of genetic accidents.

    CJYman: I’m just wondering how you have determined that evolution is an unguided process?

    Larry Moran: I don’t believe in any gods. That doesn’t leave much choice unless I attribute the guiding to lepechauns.

    That’s not a reason why evolution must be unguided. It’s basically a statement of faith. But thanks for being honest.

    As Cornelius Hunter would say: Religion drives science.

  309. 309
    Cross says:

    Mung @ 308

    “and it matters”

    cheers

  310. 310
    bFast says:

    Unfortunately, Larry Moran, I understand kaisosfocus’ sentiment: “Further, you have convinced me that you are not capable of teaching sound, straight thinking, but would be very likely to resort to indoctrination, intimidation and outright bullying to push an ideological agenda.”

    It is very obvious to me that you would be incapable of handing out an A to someone who was clear about not holding to your philosophical/religious position. That is your position in its entirety: “I don’t believe in any gods. That doesn’t leave much choice.”

    If my child were taking a course from you, I would ask them to hold their personal perspective very carefully. I would suggest to them that they spit out the answers that you want. Ideally, I would have them seek a different professor. Sorry, but that’s how people behave when selecting who to have in authority over them.

    As per “I have, indeed, referred to ID proponents as IDiots and I’ve even called some of them “idiots.”” There really is no difference between IDiots and idiots. You may want to pretend that there is, but there is not.

  311. 311
    bFast says:

    Larry Moran, “Schoolyard taunting, as you call it, is just that. It’s good clean fun” No it is not! It is bullying! It is mean and vicious!

  312. 312
    Mung says:

    The Bully Card? Really? Some people need to be bullied.

  313. 313
    Andre says:

    Prof Moran

    I did not rum away, I’m still here bit I won’t go to Sandwalk, I use to but you never tried to enlighten then why now? Change of heart?

  314. 314
    Querius says:

    Amid all this “good clean fun,” I got distracted into thinking about the complexity of some of the chemical cycles maintained in living cells such as those involved in vision, energy storage and release, and even in the complexity embodied in the codes and feedback mechanisms.

    1. Given 100 identical earth-like planets over 4.5 billion years or so, can we support an estimate as to how many of them we might expect to see evolve complex life at or beyond that present on earth?

    2. Let’s flip this on its head. Could we predict how complex life could be before the driving mechanisms of evolution would prove inadequate in the time given (4.5 billion years)?

    For example, let’s say that each chemical cycle required double the number of steps (not just double the number of reactions). Would evolution in the time available be inadequate to result in higher animals? How about ten times as many steps? Could this estimate be supported beyond simple speculation?

    3. The evolutionary models that have been described here, only described two actors: a drifting genome and a drifting physical environment. What if we added in a typical number of species required for a stable, self-contained ecosystem, each drifting as well. Would we expect this scenario to trend towards a monoculture or toward greater diversity? How fast would the environment need to drift before genetic variability of each species wouldn’t be able to keep up with the environment and resulting in a mass extinction?

    Just some musings.

    -Q

  315. 315
    kairosfocus says:

    LM,

    With all due respect, your onward response is sadly telling, and fully justifies some plain speaking as it seems you have never learned the lesson in an old story on what the frog said to the boy approaching it, stone in hand: “fun” for you, is death to me.

    First, when you imagine that personal attack and loaded false accusation, also insisting on setting up loaded strawman caricatures in the teeth of correction as “fun,” you are taking delight in slandering, abusing a privileged position, enabling the lunatic fringe who go on to stalking and worse. Which, as I have had to speak to for record, is something that is personally happening to me (now, credibly reaching to on the ground stalking involving remotely connected persons that I have had to bring to the attention of local authorities); I pause to express appreciation to Dr Felsenstein for a different spirit.

    Second, such an uncivil pattern fully justifies the concern that the moral and psycho-social firewalls that would restrain abusive behaviours such as twisting critical thinking and learning science etc into indoctrination, manipulation, intimidation and worse, are breaking down or have broken down. In effect, you just tripped further warning flags and so: no, I would not have you in loco parentis, nor would I recommend you for that role to other parents of prospective college or school students.

    Further to this, it is patent that it would be dangerous to be a research student or junior colleague who does not reflexively toe the evolutionary materialist scientism and likely linked political progressivism as well as radical secularism, statism and the like partyline in a department or faculty where people with the attitudes and behaviour patterns shown above and already red flagged have a significant presence. This brings out the core concerns about abusive Faculty and breakdown of the core university ethos of responsible academic freedom that others have raised here at UD and elsewhere.

    I strongly suggest to you that you need to pause, take serious stock on what you and too many others of your ilk have been doing, and amend the patterns that are evident above and it seems, elsewhere.

    Finally, shooting at the messenger through invidious motive-mongering and projective turnabout accusation is a classic retaliatory behaviour pattern against what I have actually done, which is to blow the whistle: wake up, take stock and do better. That sort of behaviour implies resistance to reform, implying institutionalisation of the rot.

    Mix in the long-term pervasive influence of the university and its professors in our civilisation, and one readily sees the implications for entire societies.

    It is not for nothing that Plato long since warned in the Laws Bk X 2350 years past:

    Ath. . . .[The avant garde philosophers and poets, c. 360 BC] say that fire and water, and earth and air [i.e the classical “material” elements of the cosmos], all exist by nature and chance, and none of them by art . . . [such that] all that is in the heaven, as well as animals and all plants, and all the seasons come from these elements, not by the action of mind, as they say, or of any God, or from art, but as I was saying, by nature and chance only [ –> that is, evolutionary materialism is ancient and would trace all things to blind chance and mechanical necessity] . . . .

    [Thus, they hold] that the principles of justice have no existence at all in nature, but that mankind are always disputing about them and altering them; and that the alterations which are made by art and by law have no basis in nature, but are of authority for the moment and at the time at which they are made.- [ –> Relativism, too, is not new; complete with its radical amorality rooted in a worldview that has no foundational IS that can ground OUGHT.] These, my friends, are the sayings of wise men, poets and prose writers, which find a way into the minds of youth. They are told by them that the highest right is might [ –> Evolutionary materialism — having no IS that can properly ground OUGHT — leads to the promotion of amorality on which the only basis for “OUGHT” is seen to be might (and manipulation: might in “spin”)], and in this way the young fall into impieties, under the idea that the Gods are not such as the law bids them imagine; and hence arise factions [ –> Evolutionary materialism-motivated amorality “naturally” leads to continual contentions and power struggles influenced by that amorality at the hands of ruthless power hungry agendas], these philosophers inviting them to lead a true life according to nature, that is,to live in real dominion over others [ –> such amoral factions, if they gain power, “naturally” tend towards ruthless abuse], and not in legal subjection to them.

    Those who refuse to learn from history are doomed to repeat its worst chapters.

    KF

    PS: Your pretence that trying to label design theory as a species of Creationism is innocent and justified by pointing out that some Creationists have been involved with or support design thought, speaks inadvertent culture war volumes.

  316. 316
    kairosfocus says:

    bFast, thank you. KF

  317. 317
    soundburger says:

    LM writes, #264

    “How you deliver that information effectively in a modern society often involves additional skills.”

    That’s understandable and of course true. But I doubt that many would agree that using and promoting a poisonous term (poisonous in the sense of belittling an entire group) should NOT be considered a ‘skill’, but a cheat.

    Furthermore, I would be surprised to learn that in Jonathan Wells, in the book you mention, actually calls biologists ‘stupid’ as you say, but will gladly look at your citation.

    So although it is well to teach students about certain propaganda ‘skills’ that have been proven to be effective, even though they are dishonest, polarizing, mean-spirited, etc. (such as most political campaigns employ),
    I still maintain that you put yourself in an odd position when you are both a teacher who wishes to alert students to such techniques while being someone who uses them.

    Remembering of course that, in standard philosophical teaching, those who are fooled by poisoning the well, and other such techniques, are as culpable as those who employ them; thus the purpose of a critical thinking course would be to help them see through manipulative techniques, not embrace them.

  318. 318
    Larry Moran says:

    bFASt says,

    No it is not! It is bullying! It is mean and vicious!

    Calling you guys IDiots is bullying, mean, and vicious?

    Get a life. This is the internet.

  319. 319
    soundburger says:

    apologies for the numerous syntax errors in my comment above. My computer was oddly giving me only half a screen to work with so I wrote on the fly, and this site appears not to have an edit function.

  320. 320
    Larry Moran says:

    bFASt says,

    It is very obvious to me that you would be incapable of handing out an A to someone who was clear about not holding to your philosophical/religious position. That is your position in its entirety: “I don’t believe in any gods. That doesn’t leave much choice.”

    If my child were taking a course from you, I would ask them to hold their personal perspective very carefully. I would suggest to them that they spit out the answers that you want. Ideally, I would have them seek a different professor. Sorry, but that’s how people behave when selecting who to have in authority over them.

    THAT’S an example of something that’s mean and vicious.

  321. 321
    Larry Moran says:

    soundburger at #317 writes

    I still maintain that you put yourself in an odd position when you are both a teacher who wishes to alert students to such techniques while being someone who uses them.

    Everybody uses those techniques. Just look at the comments in this thread. The trick is to teach students what they are and when, if ever, they are necessary. Any teacher who stands up in front of a class and acts like they would never use rhetorical devices in public discourse is either lying or incredibly stupid. You would not want your child to take a course with such a professor, would you?

    Remembering of course that, in standard philosophical teaching, those who are fooled by poisoning the well, and other such techniques, are as culpable as those who employ them; thus the purpose of a critical thinking course would be to help them see through manipulative techniques, not embrace them.

    I taught the course with a philosophy professor and we discussed that very topic. My students got lots of practice recognizing what critical thinking and logical arguments look like and how to use them.

    They also learned how to recognize practices that look scientific and seem like critical thinking, but are, in fact, something else. This is where ethics, morality, and religion enter the picture.

    It’s perfectly okay to argue from your personal ethical/moral/religious views as long as you don’t try to disguise them as examples of science or critical thinking. We used abortion and human cloning as examples.

    It would be nice to live in an ideal world where nobody watched FOX News or MSNBC because they all recognized that facts are more important than rhetoric. But I’ll let you in on a little secret ….. we don’t live in that world.

    Leading Intelligent Design Creationists are very skilful at this kind of argument (rhetoric). Just look at Barry Arrington’s posts on eugenics and the holocaust, for example. Does anyone really believe that evolution must be wrong because it was used to support eugenics and the holocaust? Is that critical thinking?

    Just look at the abuse I’ve been subjected to on this very thread. Just look at how many people here claim to be defending the true “science” behind ID but soon bring up religion, atheism, and materialism, which are the real enemies they are fighting. That’s a very clever trick and it was deliberately designed by the founders of ID in order to disguise their religious purpose.

    If you don’t know how to play that game you are going to be ignored, like CNN. I want to make sure my students are armed with all the skills necessary to survive in the 21st century.

    On the other hand, I do sympathize with some of the religious parents on this blog. I understand why they would not want to put their children in one of my classes. Their children might actually learn something about critical thinking and rhetoric and that could only end badly.

    Oh, BTW, some Young Earth Creationists have gotten an “A+” in my course. There aren’t many and most don’t do very well. Other creationists get about the same grades as the nonbelievers. (More than half the students at my university are nonbelievers.)

    For the first seven years of the course my co-instructor was a Jesuit priest. That helped ensure that all views were treated fairly. This is a major concern in all courses. I tell my students that all professors have strong opinions on all sorts of things and they need to learn how to cope with that. I tell them that the only thing worse than a professor with opinions is one who pretends that he/she doesn’t have opinions and everything in the course is pure fact.

    We use evolution courses as an example of that kind of behavior. Most of my students took an evolution course where they never learned of any scientific controversies or disputes within evolutionary biology. That’s crazy and it’s not how one should teach critical thinking. (The title of the course is “Scientific Misconceptions and Controversies.”)

    Some of my students even write essays on the bad teaching they’ve encountered in science courses.

  322. 322
    kairosfocus says:

    LM, Would you be willing to call people — let’s say, a fairly upset father whose child just got a questionably low grade in a critical thinking class who has come to you with an attorney by his side — idiots, illegal conspirators to subvert the US Constitution [that’s the political agenda behind insistence on “Creationists in cheap tuxedos”), and worse to their faces? This is not “get a life,” which is itself, further tripping warning flags on defiant resistance to correction. KF

  323. 323
    Larry Moran says:

    soundburger says,

    Furthermore, I would be surprised to learn that in Jonathan Wells, in the book you mention, actually calls biologists ‘stupid’ as you say, but will gladly look at your citation.

    Wells is too clever to actually say that scientists are stupid. Instead, he pretends that his “icons” are the pillars of support for evolution then proceeds to dismantle them pointing out that expert scientists were not clever enough to see that their most important evidence for evolution could be so easily refuted by an amateur. The implication is obvious. (It’s a clever rhetorical device.)

    He claims that some of these expert scientists were deliberately deceiving the general public while others were just blinded by their lack of critical thinking skills.

    We examined all those claims in my class to see if they were true. (Some were, most weren’t.)

  324. 324
    Larry Moran says:

    Darn. I completely forgot about another leading Intelligent Design Creationist who posts regularly on this blog. Denyse O’Leary’s writings are 99% rhetoric and less than 1% critical thinking. (And 0% science.)

    You do realize, I hope, that because of Barry Arrington and Denyse O’Leary this blog is viewed by most scientists as the FOX News of blogging. It’s to be enjoyed (sometimes) but never taken seriously.

  325. 325
    kairosfocus says:

    LM,

    Wells is too clever to actually say that scientists are stupid. Instead, he pretends that his “icons” are the pillars of support for evolution then proceeds to dismantle them pointing out that expert scientists were not clever enough to see that their most important evidence for evolution could be so easily refuted by an amateur. The implication is obvious.

    In short, you admit you have misrepresented Wells.

    Now, I just pulled my copy.

    Let’s do a short case study.

    The cover says:

    Icons of evolution
    Science or myth?
    Why much of what we teach about evolution is wrong

    That is, the clear primary context is science education regarding the world of life and its origins. His preface begins with his undergrad studies but obviously he also means to engage the high school biology class and textbook. So, the context is the teaching icons commonly appearing in textbooks c 2000 and used to make the neo-darwinian synthesis and associated models seem plausible to students. (That already shows that your dismissal of his argument sets up and knocks over a strawman.)

    His listed icons are:

    The Miller-Urey experiment
    Darwin’s Tree of Life
    Homology in vertebrate limbs
    Haeckel’s embryos
    Archaeopteryx as a key missing link
    Peppered moths
    Darwin’s finches
    Four-winged fruit flies
    Fossil horses
    From Apes to Human

    Onlookers may wish to see his essay at the time, survival of the fakest: http://www.discovery.org/artic.....Fakest.pdf This has subtitle: “SCIENCE NOW KNOWS THAT MANY OF THE PILLARS OF DARWINIAN THEORY ARE EITHER FALSE OR MISLEADING. YET BIOLOGY TEXTS CONTINUE TO PRESENT THEM AS FACTUAL EVIDENCE OF EVOLUTION. WHAT DOES THIS IMPLY ABOUT THEIR SCIENTIFIC STANDARDS?”

    Such clearly distinguishes between the textbook icons and the state of scientific research, then addresses the textbooks. Indeed, at the end of the article, ten then popular biology texts used in High School are identified and graded with comments on how grades were given. None gets as high as a C-.

    From p. 249 of Icons, he provides a much expanded discussion, with sub-grades and standards. The textbooks have copyright dates 1998 or later, consistent with currency c 2000.

    So, Wells is explicitly not primarily addressing Scientists but the state of science education as manifested in what is in textbooks. Of course, if a textbook author is a Scientist, the remarks address that scientist in his role as educator. But a problem with Scientist A does not imply one with B, C, D etc, save insofar as the profession should police itself. For which the Haeckel case is a capital example of evident misrepresentation sustained for over a century.

    That does not speak to stupidity, but to ideological domination and resulting abuse of the education system and key authorities — textbooks — to indoctrinate.

    So, per fair comment, the conclusion is plainly that the dismissal of Wells itself exemplifies a strawman caricature fallacy on your part.

    One, that trips further warning flags.

    KF

    PS: The Fox News comparison is inadvertently revealing also. Fox News is not materially different from other major news agencies in terms of level of coverage and proneness to get things wrong and to be sensational etc, but because it is out of line with the standard liberal-progressive line, it is targetted as somehow a pariah and is dismissed instead of soberly addressed on substance. The truth is, that all news does need improvement but there seems to be a widespread blindness to the dominant pattern of biases.

  326. 326
    Larry Moran says:

    kairosfocus says,

    LM, Would you be willing to call people — let’s say, a fairly upset father whose child just got a questionably low grade in a critical thinking class who has come to you with an attorney by his side — idiots, illegal conspirators to subvert the US Constitution [that’s the political agenda behind insistence on “Creationists in cheap tuxedos”), and worse to their faces?

    First, my university has a policy of treating university students as adults. They speak for themselves. We don’t listen to parents. That’s for kindergarten. We also don’t listen to lawyers. The university has it’s own policy for dealing with complaints and lawyers are not permitted.

    Second, I don’t call students IDiots. Believe it or not, I know the difference between how to behave in a classroom and how to behave on the internet.

    Third, I am a Canadian and I teach in a Canadian university. I don’t give a damn about your constitution.

    Fourth, I DO teach my students that religion is behind Intelligent Design Creationism and my university would back me 100% on that just as they (and I) would back a theistic professor who advocated intelligent design. (I suspect you don’t know very much about universities.)

    Fifth, even in the USA, universities do not have to keep religion out of the classroom. Perhaps you’ve heard of Liberty University and Notre Dame? Even public universities have religion departments and courses on the existence of gods. You can’t teach critical thinking if some subjects are banned.

    This is not “get a life,” which is itself, further tripping warning flags on defiant resistance to correction. KF

    Get a life. Or stop your defiant resistance to my corrections.

  327. 327
    Larry Moran says:

    kairosfocus says,

    So, per fair comment, the conclusion is plainly that the dismissal of Wells itself exemplifies a strawman caricature fallacy on your part.

    OMG! You are actually serious, aren’t you?

    Just read what you wrote.

  328. 328
    kairosfocus says:

    LM, your problem is showing, and that is tripping further warning flags. I suggest you do take a moment to compare what Wells actually did with what you wrote and what you pivoted to on being challenged. KF

  329. 329
    Silver Asiatic says:

    LM

    Calling you guys IDiots is bullying, mean, and vicious?

    Ok, I get it. All it means is “I disagree with you”. You’ve called enough people IDiots now that we can see that it’s an insult that’s not supposed to be taken seriously. Your tentative and subjective opinions on what evolution is and how it works, conflicts with the ID view, and so you refer to the people you disagree with as IDiots. Ok, not a big deal as I see it. As I said before, I can actually appreciate an attention-getting mechanism as long as you’re honest about it (which on that you have been so far).

    I think it’s fair, however, to look for a higher level of critical thinking from you. There’s quite a lot to be skeptical about within the claims of materialism and evolutionary theory.

    As for intelligently guided ‘evolution’ – we have directly observed evidence of it (artificial selection).

    Someone mentioned human accelerated regions as a challenge to common descent also – you might want to respond to that some time.

    Also, you claim to have no evidence of ‘gods’ but on the same basis, you have no direct observations of humans descending from chimplike ancestors. You make an inference based on fossil and genetic similarities. You even posit ancestors that are invisible (at least for now).

    We have no evidence of non-humans giving birth to humans. But you’re so convinced that it did happen, you call it a fact.

    At the same time, you find zero evidence in the entire history of theological arguments, of the existence of ‘gods’.

    If only one testimonial report supporting the existence of the supernatural and/or of ‘gods’ is true, then what you’re denying evidence of does exist.

    Since you’re open to the question (agnostic?), I’d think you’d want to know quite a lot about it. There’s quite a lot of evidence to consider.

  330. 330
    CJYman says:

    Larry Moran,

    I am interested in what your response will be to Mung @ 308.

    Larry Moran @ 303:
    “The word “creationist” can have much broader meaning than you think. That’s the definition I use.”

    Likewise with ‘Darwinian’ as in Darwinian Evolution … no? In the end I don’t really care how people use terms so long as they define their terms and are consistent in both how they define terms and in application. Who determines the broader meaning behind terms and why should it matter if someone has a definition of Darwinian that entails varying degrees of RV+NS? You’ve already made it clear you do not believe in evolution being guided, thus according to the ‘not-guided’ definition of ‘random,’ you believe in nothing more than ‘RV+NS’ to varying degrees — even if the majority of variation were random with no NS in operation, eventually NS must kick in at some point to produce the wonders of life. Thus your position is at the very least ‘neo-Darwinian’ according to how some people here define the term.

    And just to be sure … you would be a ‘creationist’ in respect to the origin of human artifacts, correct?

  331. 331
    Larry Moran says:

    CJYman asks

    Likewise with ‘Darwinian’ as in Darwinian Evolution … no?

    Yes, to a certain extent. Among evolutionary biologists there’s no substantive disagreement about “Darwinian evolution.” It means evolution by natural selection.

    There’s also the general view that a Darwinist is someone who places a great deal of emphasis on natural selection, often to the exclusion of other mechanisms.

    Creationists get into trouble when they say, for example, that Darwinists believe in junk DNA. That’s very misleading since true Darwinists actually reject the idea of junk DNA.

    In most cases, creationists are using the term “Darwinist” as a synonym for “materialist” and that’s really confusing.

    You may not like the term Intelligent Design Creationist but it’s very clear who I’m referring to. That’s not true with “Darwinist.”

    In any case, if you agree that “Darwinist” in intended as an insult then that’s okay by me as long as you are up front about it.

  332. 332
    Silver Asiatic says:

    LM

    You may not like the term Intelligent Design Creationist but it’s very clear who I’m referring to.

    It’s less clear than ID proponent (or even IDist). The term Creationist has multiple meanings. Adding it to intelligent design muddies what you’re saying, not clarifies it.

  333. 333
    Evolve says:

    Andre,

    ///Extraordinary claims require extraordinary evidence.///

    The burden of evidence is on you people who make the extraordinary claim that intelligence created life on earth with no evidence for such a thing. All you have is “design inference” – living things look designed, therefore it was created by a designer. And you brand this trope “science”!

    KF,

    ///There is a trillion member base of cases of such FSCO/I arising due to intelligently directed configuration.///

    It only shows that humans have designed those configurations. It doesn’t automatically lead to the conclusion that ONLY an intelligent being can create every information out there. How has ID “theory” excluded the possibility that nature can create information on its own through chemical & physical processes? Because you don’t see it happening now? Any new life form arising now will be instantly gobbled up by existing life forms. But the early earth was sterile allowing prebiotic chemistry to proceed for hundreds of millions of years.

  334. 334
    CJYman says:

    Larry Moran:
    “You may not like the term Intelligent Design Creationist but it’s very clear who I’m referring to. That’s not true with ‘Darwinist.'”

    It only clear to the extent that you are a ‘creationist’ in respect to the origin of human artifacts. And then, I have no problem with the term ‘creationist;’ it merely becomes redundant.

    Otherwise, it brought up YEC or OEC connotations until you explained exactly what you meant by the term. And the implied connection with those ‘creationist’ groups makes a lot of sense since they both use the big ‘C’ word right in their label and theirs was the main use of the term ‘Creationist’ as in ‘ex nihilo’ until ID grew up to be a more prominent player in this game.

    Of course you weren’t confused about your definition of ‘creationist’ but others who knew the difference between the YEC & OEC groups and ID proper sure were confused. Were they IDiots for being confused about your use of the term or are you the only one allowed the privilege of a little confusion now and again?

    Larry Moran:
    “In any case, if you agree that “Darwinist” in intended as an insult then that’s okay by me as long as you are up front about it.”

    Nah, I never really cared much for labeling others without carrying on an open conversation about what exactly they ‘believe;’ and insults are just bad form, Internet or otherwise.

    But I guess Mung does have a point. Sometimes the only choice is to respond in like manner. Meh … to each his own I guess.

  335. 335
    computerist says:

    It’s a scary thought how one must bow down before materialist ideology within academia to be accepted.

    I sense Larry Moran (based on his comments here and his ramblings on his blog) is one of those ideologues one must be super duper careful with.

  336. 336
    Carpathian says:

    bFast:

    bFast:
    But your blanket “That’s why you cannot apply statistics in a purely numerical scope when it comes to biology” statement is, well, hogwash.

    Caparthian, “Show me it’s hogwash.” Caparthian, oi. I just discussed the scenarios where natural selection plays no role, and you went on to try to correct me on my definition of natural selection.

    You have not shown that you can apply statistics purely randomly, you’ve shown you can’t.

    Notice also that your statement applies to natural selection, not statistics.

  337. 337
    CJYman says:

    In response to Evolve @ 333, I say …

    Larry Moran, since you presumably are familiar with ID’s arguments, would you use your teaching skills to explain to Evolve how he is off base with his analysis of both ID and science (especially in reference to the ‘no evidence’ and ‘excluded the possibility’ bit). Thanks.

    Now, for the sake of argument, let’s take Evolve’s perspective of ID Theory as true. At the very least even in Evolve’s mind, ID has the appearance of design going for it (which is why I don’t understand the ‘no evidence’ bit) and we all know that science is founded upon observation and repeatability. Conversely, what is the observable method that determines these type of designs actually result from unguided processes. How do we determine that evolution is unguided and if it is not repeatable, how do we call it science? For the record, I am an ID proponent that does not believe in Divine intervention, sees evolutionary mechanisms as playing no role in my acceptance or rejection of ID Theory, and I even go so far as to accept that, from a logical perspective, some sort of abiogenesis must have occurred. Oh, and I do see the study of evolution as perfectly scientific.

    I would just rather see Evolve actually engage in some deeper thought for a second. Larry Moran, as a teacher, maybe you would be kind enough to help a fellow traveler?

    Also, I would still like to see a response from Larry Moran to Mung @ 308.

  338. 338
    Evolve says:

    ///Conversely, what is the observable method that determines these type of designs actually result from unguided processes. ///

    There’s plenty of observational evidence all strongly pointing to the fact that living things evolved and diversified from the simplest to the most complex entirely on their own through crosstalk with the environment and with no external intervention. Every new evidence still confirms this fact.

    There’s not even a single piece of evidence that confirms some abrupt interference by an external agency. Now if ID claims there was intelligent intervention, that position is on a weak footing (putting it mildly) because (1) you don’t have any evidence that a designer exists at all, let alone the mechanism by which he acted where, when & how and (2) you also have to explain why all available evidence points to the unguided evolution of living things.

  339. 339
    Andre says:

    Evolve

    How do you even test unguided evolution?

  340. 340
    CJYman says:

    Thank you Andre.

    Evolve, I wish I had something more to say, but you have responded to neither my position nor my question as laid out in my last comment.

    Maybe you could learn something from what Larry Moran is attempting to teach us here … don’t go spouting off [nonsense] until you understand your opponents position.

  341. 341
    Mung says:

    Evolve, How do you even test unguided evolution?

    He doesn’t. It’s a fact. No testing required.

  342. 342
    bFast says:

    Larry Moran, “Second, I don’t call students IDiots. Believe it or not, I know the difference between how to behave in a classroom and how to behave on the internet.”

    No sir, you don’t. You may know how to behave in a classroom, I haven’t checked. But it hasn’t dawned on you yet that your resume is written by your internet blogging. It also hasn’t dawned on you that students employ their professors to provide them with education. As the professor’s employer, they have the right to be selective. As the professor’s employer, they have the right to peruse the internet to aid them in making that decision. As the professor’s employer, if they know that the professor refers to them as “idiot” behind their back, if the internet evidence suggests that the student (employer) must not only understand the evidence presented, but must also come to the same methodological conclusion (even if the case is not logical but ontological) then the employer may choose to pass up on this candidate.

    Making such a choice is not an evil or despicable act. I would be quite happy to recommend such an approach from the pulpit.

  343. 343
    kairosfocus says:

    bFast, I add that with the cost being as it is these days, the buy centre involved is the family. KF

  344. 344
    kairosfocus says:

    Ev, the evidence is, humans are examples of intelligent designers. The evidence that humans exhaust the list of possible designers, zip. The evidence that blind chance and mechanical necessity can create FSCO/I, zip. The evidence that it is produced by intelligently directed configuration, trillions of observed cases — making FSCO/I a strong inductive sign of design. Which, is what you tried to side track focus from. KF

  345. 345
    bFast says:

    Oh, and, Larry Moran, this ball does bounce both ways. I am rather sure that many are advised to avoid Behe. On the other hand, I bet that many choose Lehigh University simply because he teaches there. I bet bones that if you checked the position of students entering his class, there would be a much higher percentage that support ID than support materialistic evolution (note my new term, for me it permanently replaces Darwinist and neo-Darwinist.)

    This is natural selection at work.

  346. 346
    KevNick says:

    Larry,

    I’m challenging you to provide all the scientific evidence for ALL the reasons WHY you became so convinced that life arose by chance. I will set up a blog and you and your buddies like Coyne, Horsham, PZ. Myers and others can upload their favorite empirical proof… I’m fine even if one of you provides ONLY ONE EMPIRICAL EVIDENCE. If that actually ever happens, I will publically declare who I am and I will become one of you. I will disclose my identity and I will buy ALL OF JERRY’S BOOKS…
    I don’t think any scientist can object to that …

    Larry, if you don’t answer this challenge, I will make you pay for it… and I mean it…

  347. 347
    kairosfocus says:

    bFast, there is a reason why I normally speak to evolutionary materialism. KF

  348. 348
    Cross says:

    KevNick @ 346

    “Larry, if you don’t answer this challenge, I will make you pay for it… and I mean it…”

    I don’t know if you are serious, but this is no place for making threats, regardless of Dr Moran’s views.

    Please withdraw or explain yourself.

    Cheers

  349. 349
    soundburger says:

    Cross, exactly. What KevNick has given Larry an (perfectly good) excuse to do is go back to Sandwalk and complain to his fans, who are always ready to reduce the members of this site, in toto, to its lowest common denominator, about the uncivilized treatment he received as thanks for putting so much time in here. Way to go, KN.

  350. 350
    kairosfocus says:

    S-Bu & Cross (attn KN); While I doubt KN meant his remarks as a threat, they can be read that way. KN, do explain. KF

  351. 351
    KevNick says:

    I didn’t mean to threaten Larry. It may have came across as such because of the nature of the challenge I presented him with. I’m sorry if it was understood like that. It is obviously a misunderstanding.

    I meant that if Larry doesn’t respond to the challenge, I will “make him pay” for his arrogance, name calling and lack of respect of others’ views by exposing it (his lack of evidence for the origins of life) on the internet, blogs and such.

    I hope this helps.

  352. 352
    Andre says:

    Kevnick

    All you’ll get out of Larry Man is this;

    “You don’t understand evolution”

    nothing more and nothing less.

  353. 353
    JimFit says:

    Larry i am curious why you think evolution disproves God when Evolution couldn’t happen without the Fine Tuned Constants of the Universe.
    Lets say that i throw you a rock, will you blame the rock, the physics or my will to throw you the rock? Since my will was the source of this chain of events you will blame my will. God wills and the Universe is created after a chain of deterministic events, evolution is part of these chain of events and for that reason is deterministic.

    If God didn’t created the Universe there was no intention behind our existence, that means that the Universe popped out of Nothingness (or existed past eternally), assembled itself through Randomness and we are here due to Luck, where does science supports Randomness Nothingness and Luck? Science works with Determinism but Determinism requires an act and act requires consciousness. Can you tell me why my reasoning is false?

  354. 354
    Mung says:

    I don’t think Larry thinks evolution disproves God.

  355. 355
    Mung says:

    Dr. Moran, you’re convinced of the fact of evolution. But as was pointed out earlier, even young earth creationists accept the fact of evolution and accept common descent.

    I hope you are not portraying the ID and Creationist positions as consisting of evolution-denial and fact-denial in your writings.

    That said, how about the fact of organic codes?

    …the word code has largely been used in a metaphorical sense… It is imperative, therefore, to realise that there are organic codes which are not metaphorical but real… Sooner or later, therefore, biologists will have to come to terms with the theoretical implications of this extraordinary fact.

    – Marcello Barbieri, The Organic Codes: An Introduction to Semantic Biology

    How has modern evolutionary theory come to terms with these facts, or is it still in fact-denial mode?

  356. 356
    Carpathian says:

    JimFit:

    Larry i am curious why you think evolution disproves God when Evolution couldn’t happen without the Fine Tuned Constants of the Universe.

    Fine tuning would make a great thread for discussion.

    I myself don’t think fine tuning exists as there doesn’t seem to be any evidence to support that the universe does not balance itself as a running system.

  357. 357
    Upright BiPed says:

    #356

    Darwinian evolution doesn’t occur without a semiotic system to establish prescriptive control over matter. It requires irreducible complexity to establish a genome and organize a heterogeneous living cell. These are requirements for Darwinian evolution, not the products of Darwinian evolution. (If A requires B for A to exist, then A cannot be the sourtce of B).

  358. 358
    Carpathian says:

    Upright BiPed:

    Darwinian evolution doesn’t occur without a semiotic system to establish prescriptive control over matter. It requires irreducible complexity to establish a genome and organize a heterogeneous living cell. These are requirements for evolution, not the products of evolution.

    I don’t agree that IC is required. By definition, evolution builds on previous structures.

    A construction that appears to be IC in a current configuration may have served a different purpose in a previous one.

    Secondly, applying symbols to something is not required for that thing’s operation.

    A semiotic code is something we apply in order to communicate something’s operations or attributes.

    No labels are required for an organisms operation.

    Claiming a “semiotic system” is required implies that an intelligent designer is required, but that is what the debate is about, so it cannot be assumed to be true beforehand.

  359. 359
    Box says:

    Carpathian: I don’t agree that IC is required. By definition, evolution builds on previous structures.

    In order for evolution to build on previous structures a ‘semiotic system to establish prescriptive control over matter’ needs to be in place.

  360. 360
    Eugen says:

    You’ll never convince Mr.Moran….

    “It is difficult to get a man to understand something, when his salary depends on his not understanding it.”

    –Upton Sinclair

  361. 361
    Carpathian says:

    Box:

    In order for evolution to build on previous structures a ‘semiotic system to establish prescriptive control over matter’ needs to be in place.

    Semiotic refers to the study of symbols. The “code” in our cells is only semiotic due to our applying symbols to its components.

    Only chemical “codes” are actually required for operation, not semiotic ones.

    While semiotic codes imply a designer, chemical “codes” don’t.

  362. 362
    EugeneS says:

    Carpathian –

    “A construction that appears to be IC in a current configuration may have served a different purpose in a previous one.”

    “May have served a different purpose” already assumes the existence of a semiotic system as a prerequisite.

    I think you disregard the fact that for exaptation to occur you need a decision making block whose function is to decide when to switch over one existing function to another existing function. But first you need to have functionality to start with.

    Evolution (by definition unguided) chooses from among existing functions, not for future functions.

  363. 363
    Carpathian says:

    EugeneS:

    “May have served a different purpose” already assumes the existence of a semiotic system as a prerequisite.

    A semiotic system is concerned with symbols.

    A, T, C and G are symbols that we humans have applied to chemistry in the cell.

    There is no function added to the operation of a cell when we name its components.

    The “code” works chemically, not symbolically.

    Therefore, a semiotic system is not required.

    The distinction is necessary as claiming a semiotic code is present allows the introduction of a “code-maker” when none is really required.

    The “code” is a direct, physical and chemical one, not a “code” with indirection.

  364. 364
    Mung says:

    Carpathian: A semiotic system is concerned with symbols

    Give the man a cigar. So is your GA program. You’ve gone and confused the territory with the map again.

  365. 365
    Carpathian says:

    Mung, you are the master of irony.

  366. 366
    Mung says:

    Carpathian: The “code” works chemically, not symbolically.

    Priceless.

  367. 367
    Carpathian says:

    I’m shocked you didn’t dispute it.

    There may be hope for you Mung.

  368. 368
    JimFit says:

    Carpathian

    doesn’t seem to be any evidence to support that the universe does not balance itself as a running system.

    What do you mean by this? I don’t understand.

  369. 369
    Carpathian says:

    JimFit,

    What I mean is that it is due to the forces of physics, that we have stable systems that make sense. It is not due to any “fine-tuning” of those forces.

    Planets are in their orbits because of “untuned” physics, not because of fine-tuning of gravity to ensure those orbits.

    Our weather was not fine-tuned for us, rather our bodies have adapted to our climate and those that failed to function in their climate died off.

  370. 370
    JimFit says:

    But there were no physics prior to the Big Bang to determine the balance of these physics, your argument is based on a wrong idea, that the Universe is past eternal. The constants and quantities are independent of the laws of nature.

  371. 371
    EugeneS says:

    Carpathian,

    You simply are not exposed to the subject. I don’t claim that I am an expert but as far as I know the fact of the tuning (i.e. the fact that the stability zone in the phase space of the many parameters that ‘shape’ the world is extremely narrow) is not in question. What is in question is why this is so.

    On the point of biosemiosis you are disagreeing with a whole school of thought brought up by hard core thinkers whose scientific contribution is beyond any dispute. I am not blindly appealing to their authority. I am rather pointing out that this is serious science.

    ‘Just chemistry did it’ is no longer a plausible explanation. It has not stood the test of time. Sign and its processing are irreducible to physics and are the basis of all life. Life is symbolically controlled matter.

    JimFit,

    Spot on. According to Pattee, the biggest impact of sir Isaac Newton in science is the understanding of the need for a clear conceptual separation of the laws of nature from the initial conditions.

  372. 372
    Mung says:

    And the Morse “code” works electrically, not symbolically.

    Uh huh.

  373. 373
    StephenB says:

    I mistakenly posted a response to another thread on this thread, so I deleted it.

  374. 374
    Mung says:

    Are the silly evolutionists playing word games again?

    [always]

  375. 375
    Mung says:

    And yet the idea of evolution was born precisely in this way: as a theory that we need to explain not the fossils but what we see today around us. One cannot insist enough on this point: the theory of evolution was not proposed to explain the past, but to understand the present.

    – Marcello Barbieri

    And what is it about the present that needs to be explained? Adaptation. So why do claims of “I’m not a Darwinist” ring just a little hollow?

  376. 376
    JimFit says:

    You also said

    Our weather was not fine-tuned for us, rather our bodies have adapted to our climate and those that failed to function in their climate died off.

    Humans were created (since evolution is a deterministic process it doesn’t contradict the definition of a creation) for tropical zones (paradise), we adapted in different zones with our immaterial minds, not with our material bodies. We invented cloths, structures and so on to survive…
    Humans adapted on this Universe but this Universe adapted in what exactly? Nothingness? Your argument doesn’t make sense in a Universe with a beginning, you need something first for the evolution of the Universe to take place and this something must be also fine tuned. You must have fine tuning all the way down to infinity, of course that’s wrong since everything physical began to exist and that makes the existence of the values an immediate event.

  377. 377
    Upright BiPed says:

    Carp,

    I’ve returned and read your comments carefully. I can assure you that your conclusions are based on being misinformed and unaware. It is not readily apparent which of these factors is most pronounced in your case.

    I started to write out a lengthy detailed response, but I have decided to just ask you a couple of questions and perhaps you can lead yourself out of the morass you hold as evident.

    During protein synthesis, when the triplet GAU is presented to the ribosome via mRNA, leucine will be presented for binding to the newly forming polypeptide. If GAU is not presented, then leucine will not appear for binding. And then yet again, if GAU is eventually presented, leucine will surely appear for binding. Very obviously, the pattern GAU is a causal object in the system that presents leucine for binding at a certain point in time.

    But, ’present leucine for binding at a certain point in time’ is not a physical effect that can be derived from the thermodynamic properties of the triplet GAU (or any other arrangement of matter). The cell doesn’t do it that way, you cannot do it that way, and no one else can either. That is simply not the way reality works. Instead, the timely and systematic presentation of leucine is in a class of physical effects that can only be brought into existence by the translation of an informational medium. In other words, to cause something like present leucine now to happen, a system is required to utilize two arrangments of matter in a very special (well-defined) way. One arrangement must serve as a medium to evoke the effect, while the other must physically establish (determine) what the effect will be. Why? – because you can’t derive the effect from the medium. Moreover, the system must establish the effect from the arrangement of the medium while simultaneously preserving the natural discontinuity between them (which the cell does quite nicely).

    So here is my question: Can you cause (determine) the ’presentation of leucine at a certain point in time’ based merely on the dynamic properties of the triplet GAU, or does it have to be translated?

    And if you now understand that it must be translated (and therefore IC) do you understand why the system must preserve the discontinuity between them?

  378. 378
    Mung says:

    And not just bad math.

    Larry Moran:

    We don’t really care if the Bible is viewed as literal truth, poetry, or metaphor. It’s still a fairy tale because it describes beings that don’t exist.

    Therefore science is likewise a fairy tale, because it also describes things which do not exist.

  379. 379
    Mung says:

    And not just bad mathematicians:

    Larry Moran:

    It’s really just an amazing coincidence that all Intelligent Design Creationists believe in gods. There’s not a single one who thinks that the universe was designed by a bunch of immaterial, nonsentient, mathematicians who were just fooling around after the bar closed.

    Apparently they designed the universe and then it just magically popped into existence without any cause.

    So who needs them?

    Yes, Prof. Moran, IDists are capable of using Ockham’s Razor too.

  380. 380
    Mung says:

    Dear Dr. Moran,

    Given that neutral mutations are, by definition, adaptively indifferent, how can neutral theory be said to explain adaptation?

    The basic mechanism of adaptive evolution is without doubt natural selection.

    – Motoo Kimura

    What’s left? Adaptive evolution of selectively non-neutral mutations via genetic drift?

    Why can’t one be a Darwinist and still accept neutral theory and genetic drift? Are they not compatible?

    After all, gradualism is compatible with a fossil record in which evidence of gradualism is lacking, and two contradictory statements are compatible in the sense in that taken together they show themselves to be incompatible.

    Why can’t you be a Darwinist?

  381. 381
    kairosfocus says:

    Carpathian, please again reflect on the way tRNAs load AAs. With a universal CCA tip that binds to the COOH carboxylic end of the AA. Chaining is of course NH2 end to COOH end of preceding, repeat. The loading of tRNA is not chemically deterministic, the chaining of AAs in proteins is not deterministic, the sequence is predicated on a future effect, folding and agglomeration plus activation to function. Even the folding is not strongly controlled in many cases, cf chaperonin that guides functional folds vs prions as mis-folded MORE STABLE states. If you compare the ISO layer-cake OSI comms model, the physical layer fulfills requisites of higher layers but these also have their own protocols. And protocol, a convention linked to a coding system is language and is a strong index of design. KF

  382. 382
    Silver Asiatic says:

    Eugen @ 360

    That quote is a keeper – thanks! I’m going to post it at my desk at work as a healthy reminder about how the world works.

  383. 383
    Upright BiPed says:

    Carp,

    Re-reading my response at 377, I sure sounded sharp. My apologies. I was in a big hurry to get away for the long weekend, I really should have saved it for when I had more time.

    sorry

  384. 384
    Upright BiPed says:

    e-gads

    When I shortened my response, I switched my example from aspartate and leucine to just leucine. How embarrassing. But hopefully you get the point.

  385. 385
    EugeneS says:

    Mung,

    More on Occam’s Razor. Let them demonstrate that Leo Tolstoy was causally necessary for “War and Peace” to appear. I wonder if they could. Because, after all, a Leo Tolstoy is just a gene carrier machine 😉

    Evolutionism is a total bluff.

  386. 386
    Carpathian says:

    JimFit:

    But there were no physics prior to the Big Bang to determine the balance of these physics, your argument is based on a wrong idea, that the Universe is past eternal. The constants and quantities are independent of the laws of nature.

    We know nothing of the physics before the big bang, only what came after.

    The “laws of nature” as we call them is the interaction of matter and the forces that affect matter.

    From that, we derived the constants and quantities we use to describe nature.

    We can also see the flaws in our description as we have no way of expressing PI mathematically. We can keep converging on the value, but we can never reach an absolute value with our math showing that math is an invention of man.

    We have a certain proportion of oxygen in our atmosphere due to physics, not because of fine-tuning.

    If the Earth had been fine-tuned our atmosphere would not always be changing.

  387. 387
    Carpathian says:

    kairosfocus:

    If you compare the ISO layer-cake OSI comms model, the physical layer fulfills requisites of higher layers but these also have their own protocols. And protocol, a convention linked to a coding system is language and is a strong index of design. KF

    The communications model is a good analogy.

    At the level of the “codes” in our DNA, the body plan of an organism is so well “encoded”, that I have not only the body-plan of a human, but also look a lot like my father.

    In that sense, the DNA “code” has defined me so completely that from that viewpoint, there is very little room for randomness.

    That points to a very tight relationship to the “code” in my inherited DNA.

    This points to a much less complex relationship than a “protocol” would suggest. The relationship is more like a look-up table which points to a mapping, not a protocol type of process.

    As per your analogy, I would expect an intelligent interaction between DNA and its environment but I see only “decoding”, no “exchange” of information between DNA and another “communications node”.

    I see no protocol and the semiotic component comes from us.

  388. 388
    Carpathian says:

    JimFit:

    Humans were created (since evolution is a deterministic process it doesn’t contradict the definition of a creation) for tropical zones (paradise), we adapted in different zones with our immaterial minds, not with our material bodies.

    The Sherpas in Nepal are conditioned to high altitudes after centuries of living there, the Inuit are conditioned to living in the cold and the Hopi Indians living in the U.S southwest, can gain weight on what would be a starvation diet for us.

    These are all physical changes that come from bodies being fine-tuned to their environment.

  389. 389
    Carpathian says:

    EugeneS:

    You simply are not exposed to the subject. I don’t claim that I am an expert but as far as I know the fact of the tuning (i.e. the fact that the stability zone in the phase space of the many parameters that ‘shape’ the world is extremely narrow) is not in question. What is in question is why this is so.

    There is no question that different locations on Earth have different ecosystems.

    In a sense, each one could be said to be “fine-tuned” to its inhabitants but a better answer would be that organisms either adapt to the environment they’re in or they die off.

  390. 390
    Carpathian says:

    Upright BiPed:

    Carp,

    Re-reading my response at 377, I sure sounded sharp. My apologies. I was in a big hurry to get away for the long weekend, I really should have saved it for when I had more time.

    sorry

    You response sounded just fine so no offense taken!

    Instead, the timely and systematic presentation of leucine is in a class of physical effects that can only be brought into existence by the translation of an informational medium.

    A statement like this I have no problem with.

    A translation is exactly what I see, but I don’t see a protocol or semiotic system.

    A protocol is a predetermined set of messages exchanged between two intelligent communication nodes.

    I don’t see protocols anywhere in biology, only translation.

  391. 391
    Mung says:

    Carpathian, you don’t see “translation” either.

  392. 392
    EugeneS says:

    KF,

    Nice comment. I like the OSI analogy, too. Darwin did not know that the falsification of his theory was right in front of him. But our contemporary Darwinists have no excuse. They know it.

  393. 393
    Mung says:

    Carpathian, you can drop the scare quotes around the word code.

    The genetic code appeared on Earth at the origin of life, and the codes of culture arrived almost four billion years later. For a long time it has been assumed that these are the only codes that exist in Nature, and if that were true we would have to conclude that codes are extraordinary exceptions that appeared only at the beginning and at the end of the history of life. In reality, various other organic codes have been discovered in the past few decades and it is likely that more will come to light in the future. The existence of many organic codes in Nature is therefore an experimental fact, but also more than that. It is one of those facts that have extraordinary implications. In this book it is shown that the genetic code was a precondition for the origin of the first cells, the signal transduction codes divided the first cells into three primary kingdoms (Archaea, Bacteria and Eukarya), the splicing codes were instrumental to the origin of the eukaryotic nucleus, the histone code provided a new regulation system in eukaryotic genomes, and the cytoskeleton codes allowed the Eukarya to perform internal movements, including those of mitosis and meiosis. It is shown, furthermore, that organic codes had a key role in multicellular life, in particular in the origin of animals, the origin of mind and the origin of language. The great events of macroevolution, in other words, were associated with the appearance of new organic codes, and we can easily understand why. The reason is that a new code brings into existence something that has never existed before because it creates arbitrary associations, relationships that are not determined by physical necessity. Another outstanding implication is the fact that codes involve meaning and we need therefore to introduce in biology, with the standard methods of science, not only the concept of biological information but also that of biological meaning. The research on biological codes, in conclusion, is bringing to light new mechanisms in evolution and new fundamental concepts in science. This research is the field of Code Biology, the study of all codes of life, from the genetic code to the codes of culture, from the origin of life to the origin of man.

    http://link.springer.com/book/.....19-14535-8

  394. 394
    Upright BiPed says:

    Carp,

    Semiosis occurs when one thing signifies or represents another thing within a system. It ultimately refers to the physical process by which information is exchanged and translated in the living kingdom. In many ways, understanding semiosis is predicated on understanding what is required for a representation to be a representation.

    To confirm an instance of translated information, you have to find 4 interdependent material conditions. 1) representation: an arrangement of matter to evoke an effect within a system, where the arrangement of the medium and the effect it evokes are physicochemically arbitrary. 2) protocol: an arrangement of matter to physical establish the otherwise non-existent relationship between the arrangement of the medium and its post-translation effect. 3) discontinuity: the discontinuity between the arrangement of the medium and its post-translation effect must be preserved by the system. 4) unambiguous function: the effect of translation creates function in the process of being and/or survival of a living organism (i.e. life and semiosis are coextensive).

    These conditions remain true regardless of the content of the information or the system in which it’s found. Specifically in the genetic translation system, the representation is the codon, and the protocol is the aaRS (which charge the tRNA while preserving the discontinuity required by the system’s function). In others words, the effect of genetic translation is not determined by the structure of the nucleic codon that evokes the effect, instead it is determined by the structure of the aaRS that charge the tRNA. The system establishes a set of relationships (systematic regularities) that we now call the Genetic Code.

    But that is not all. Life is made up of heterogeneous self-replicators with the capacity of open-ended evolution (non physically-restricted memory). This places specific additional requirements on the system. The set of representational objects in the system will need to be independent of the minimum total potential energy state of their medium (i.e. thermodynamically inert). They can accomplish this by having a non-dynamic spatial orientation. This dimensional property simultaneously enables two capacities that are most critical to evolution. It enables the efficient open-ended memory that evolution requires (i.e. unrestricted variation), as well as the capacity to transcribe those representational objects between mediums (i.e. heredity). However, this also creates significant additional demands on the organization of the system. Such a system can only operate in the presence of other critical systematic regularities, which are themselves independent of local dynamics. Without these things there is no heterogeneous self-replicator and there is no Darwinian evolution. And as a final kick in the pants – all these things need to rise together from a non-information (inanimate) environment, with the details of the system’s construction simultaneously encoded in the very information that the system itself makes possible.

    You may also be interested to know that the unique physical conditions entailed in the genetic translation system make that type of system exclusively identifiable among all other physical systems. It can only be identified elsewhere in the recording of language and mathematics into memory, making it a measurable correlate of intelligence.

  395. 395
    kairosfocus says:

    Mung:

    The fear to recognise object code at work in the cell is diagnostic of the collapse of the materialist paradigm.

    Let’s clip:

    http://codebiology.org/

    >> Can we actually prove the existence of codes at the molecular level? The answer comes from the fact that any code is a set of rules that establish a correspondence between the objects of two independent worlds, which means that it is necessarily implemented by structures – called adaptors – that perform two independent recognition processes at each step. The genetic code, for example, is a set of rules that link the world of nucleotides to the world of amino acids, and its adaptors are the transfer-RNAs, molecules that recognize codons at one site and amino acids at a different one. The adaptors are required because there is no necessary link between the two worlds, and a set of adaptors is therefore a system that is implementing a set of coding rules.

    The adaptors, in short, are the key molecules in all organic codes. They are the molecular fingerprints of the codes, and their presence in a biological process is a sure sign that that process is based on a real code. This gives us an objective criterion for the discovery of the organic codes, and their existence is no longer a matter of speculation. It is, first and foremost, a genuine scientific problem.

    The existence of many organic codes in Nature is therefore an experimental fact – let us never forget this – but also more than that. It is one of those facts that have extraordinary theoretical implications.

    The first is the role that the organic codes played in the history of life. The genetic code was a precondition for the origin of the first cells, the signal transduction codes divided the common ancestor into the three primary kingdoms of Archaea, Bacteria and Eukarya, the splicing codes were essential to the origin of the nucleus, the histone code provided the working rules of chromatin, and the cytoskeleton codes allowed the eukarya to perform internal movements, including those of mitosis and meiosis (Barbieri 2003). All great events of macroevolution, in short, were associated with the appearance of new organic codes, and this gives us a completely new reconstruction of the history of life. >>

    Of course they go on to express the view that things evolve based on lucky copying errors, in effect. (If we could only get that lucky in coding!)

    KF

  396. 396
    kairosfocus says:

    Dr Selensky, thanks. I find it astonishing how hard some try not to see the patent reality of object codes at work in life systems, especially protein synthesis. KF

  397. 397
    Carpathian says:

    Upright Biped:

    Semiosis occurs when one thing signifies or represents another thing within a system. It ultimately refers to the physical process by which information is exchanged and translated in the living kingdom.

    I see semiosis as an immaterial human venture not something nature uses.

    It is at it’s simplest, our attempts to understand our labeling of real-world and immaterial objects.

    Semiosis (from the Greek: ?????????, s?meí?sis, a derivation of the verb ??????, s?meiô, “to mark”) is any form of activity, conduct, or process that involves signs, including the production of meaning. Briefly – semiosis is sign process. The term was introduced by Charles Sanders Peirce (1839–1914) to describe a process that interprets signs as referring to their objects,

    Whether we label a real world material process or not, it continues to function without regard to how it is labelled.

    You are suggesting that since we see a correlation between what we have labeled as the genetic code and the results of its chemical processing, that the processing must have somehow been guided by semiosis.

    2) protocol: an arrangement of matter to physical establish the otherwise non-existent relationship between the arrangement of the medium and its post-translation effect.

    This is not a definition of protocol. A protocol is the dynamic relationship between intelligent nodes, it is not the static relationship between unintelligent matter.

    Here is an example of a protocol:

    (query node 10) —
    — (OK node 10)
    (send data node 10) —
    — ( data node 10)
    (ERROR node 10) —
    — (resend data node 10)
    (OK node 10) —

    Here is an example of a translation:
    if A
    …….
    else if B
    ……

    I don’t see evidence of this higher level of intelligence that a protocol would require.

    The label PI is semiotic from the point of view of humans. Despite the label, the relationship between a circle’s circumference and it’s diameter, is in itself not semiotic.

    The chemical codes in DNA are chemical not semiotic.

  398. 398
    Mung says:

    Semiosis is a labeling process. LoL.

  399. 399
    Mung says:

    Carpathian:

    The chemical codes in DNA are chemical not semiotic.

    What is a chemical code?

  400. 400
    Carpathian says:

    Mung:

    Semiosis is a labeling process. LoL.

    You mean the originator of the term is wrong?

    Logic in its widest sense he identified with semiotics, the general theory of signs. He laboured over the distinction between two kinds of action: sign action, or semiosis, and dynamic, or mechanical, action. His major work, unfinished, was to have been entitled A System of Logic, Considered as Semiotic.

  401. 401
    Carpathian says:

    Mung:

    What is a chemical code?

    It’s the label we humans have applied to a chemical construction.

    It’s our immaterial symbolic reference to something that is material.

    The two are not related in any way except by us.

  402. 402
    kairosfocus says:

    Carpathian, object code in a specialised machine language. KF

  403. 403
    Carpathian says:

    kairosfocus:

    Carpathian, object code in a specialised machine language. KF

    That is a much better analogy than a protocol.

    As far as being semiotic, it is semiotic only in the sense that we have labeled the components.

  404. 404
    Upright BiPed says:

    Carp,

    I see semiosis as an immaterial human venture not something nature uses.

    Don’t tell that to the ants with their silly pheromones. They act like they are communicating. 🙂

    (it is an anthropocentric fallacy to suggest that only humans use representations)

    It is at it’s simplest, our attempts to understand our labeling of real-world and immaterial objects.

    Whether we label a real world material process or not, it continues to function without regard to how it is labelled.

    You are correct. Whether we label the system or not, it continues to function. It needs nothing from us to demonstrate the physical entailments of translation.

    I get it that you really want to isolate the use of representations as a human invention, but that just doesn’t hold water. Humans did not invent representations. When you see the sun come up in the morning, it is not ‘the sun’ traveling through your optical nerves; it’s a representation. That representation has nothing to do with the cognition of daylight, but it will evoke that effect based on the protocols in your brain that reflect your experience. The same thing goes for your dog.

    You are suggesting that since we see a correlation between what we have labeled as the genetic code and the results of its chemical processing, that the processing must have somehow been guided by semiosis.

    Try again. There is nothing whatsoever difficult about what I am saying. I gave you the four material conditions required for translation, along with unambiguous definitions of the terms.

    This is not a definition of protocol. A protocol is the dynamic relationship between intelligent nodes, it is not the static relationship between unintelligent matter.

    What would you say if you were me, using the word “protocol” in the blatantly obvious sense of a convention to be followed for correct function (and also gave a specific definition as well), and suddenly an electrician came to UD to tell you that you had the definition of “protocol” all wrong. “A protocol”, he says, “is where the white wire is the common, the black is hot, and the green is ground”. Or maybe instead it’s an office worker, who tells you that the protocol is that the top copy goes to shipping, yellow goes to accounting, green goes to legal, and white go to the front office. What would you say?

    Your objection is a non-starter.

    The chemical codes in DNA are chemical not semiotic.

    These conclusions of yours are divorced from physical reality. I suggest you read up and do some discovery. If you choose not to, that is your privilege.

    Howard Pattee

    cheers…

  405. 405
    Charles says:

    Upright BiPed @ 394

    3) discontinuity: the discontinuity between the arrangement of the medium and its post-translation effect must be preserved by the system.

    Would you elaborate on this point, please?

    Could you describe, specifically, which parts of the transcription process are “discontinuous” from each other and how does the discontinuity manifest as you intend the meaning? Do you mean logical, physiochemical, spatial, temporal?

    And, what would go wrong if there was no discontinuity?

    I’m not arguing, I’m asking.

  406. 406
    Mung says:

    Hi Charles.

    DNA consists of a sequence of nucleotides. A protein consists of a sequence of amino acids. These are two discontinuous domains. Two independent worlds of molecules.

    There is no necessary link between these two worlds. You cannot link together any configuration of nucleotides and obtain a configuration of amino acids, or vice versa.

    There must be a bridge between the two worlds, something that establishes a relationship.

    Lacking this, there is no confirmed instance of translated information.

    Can you imagine what the result would be inside the cell if bases running around loose in the cell started causing amino acids to clump together?

    There must be a break or gap (discontinuity) between the two worlds and it must be maintained or chaos would ensue.

  407. 407
    Silver Asiatic says:

    Charles @ 405

    I’ve read Upright BiPed’s view several times and I think I’ve got it — but perhaps not. In any case, I’d like to try because I think it’s a great argument. I just can’t seem to put it into terms which are clearer for me. (So, UB, please correct where I’m wrong).

    The key concept is the one you quoted:

    3) discontinuity: the discontinuity between the arrangement of the medium and its post-translation effect must be preserved by the system.

    I always get a bit confused by ‘discontinuity’. But in my terms, it’s like this …

    There is an “arrangement of matter” which causes an effect.
    Most simply, there’s a signal. The signal is communicated through a medium in the system. The protocol is what establishes the relationship between signal and effect.
    However, if all of this was “continuous”, or that’s something like “hard-coded” or “deterministic”. Then signal, medium and effect would be locked in. There wouldn’t be any translation or need for protocol.

    As UB says:

    the effect of genetic translation is not determined by the structure of the nucleic codon that evokes the effect

    So, the signal (information), medium and effect are ‘discontinuous’ – or non-determined, non-physically linked to each other.

    The reason for that is because the system has to […do something …] that requires [… something like decision, analyze, process …] with the information in order to […something…] the function.

    I think it’s like an information circuit with symbol set, protocol, sender, medium, translation, receiver and function.

    If all of those things were “continuous” (hard-coded, determined, linked), then there wouldn’t be need for most of it. A cloud doesn’t communicate information to raindrops. There’s no need for symbol-set, translation or protocol. There’s a ‘medium’ (sky/air) but the effect is determined physically.

    I hope I haven’t done a bad job with UB’s argument — I was just using the opportunity to explore it and hopefully gain more understanding about it.

  408. 408
    soundburger says:

    It’s really odd how the materialist position (MP) always seems to argue out of both sides of its mouth.

    On the one hand, the MP blithely states that there is nothing special about human consciousness. It is, if anything, merely an ’emergent’ property and a straightforward result of the laws of the universe playing out. It is chemicals and neuro-electrical processes, nothing more; and some day (perhaps soon), programmers and software engineers will create an AI system which functions exactly as, or even superior to, our own brains.

    But, THEN. When one argues that the workings inside genes, specifically DNA, is clearly a ‘code’, the MP then switches over completely. Nonsense! Codes are human constructs, human explanations.

    Well, which is it? If the human brain is nothing more than chemicals, why should our ‘codes’ be any different than the ‘codes’ operating in nature? Our brains are nothing other than nature in operation, right?

    Or, even more weirdly, is the MP that our brains, our logic, etc. IS something that can be reduced to knowable, observable material processes, but that DNA ISN’T, because we can’t use any of our own words to describe it properly?

    Dance, dance, dance.

  409. 409
    JimFit says:

    Carpathian

    We know nothing of the physics before the big bang, only what came after.

    There were no physics prior to the Big Bang, there was nothing physical prior to the big bang since there was no time or space. The word before doesn’t make sense.
    The constants were an immediate event and therefor a creation. You can’t have infinite past causes even if you are an atheist-materialist.
    The notion of an infinite causal regress providing a proper explanation is fallacious.Even if the succession of causes is infinite, the whole chain still requires a cause. To explain this, suppose there exists a causal chain of infinite contingent beings. If one asks the question, “Why are there any contingent beings at all?”, it won’t help to be told that “There are contingent beings because other contingent beings caused them.” That answer would just presuppose additional contingent beings. An adequate explanation of why some contingent beings exist would invoke a different sort of being, a necessary being that is not contingent.

    The “laws of nature” as we call them is the interaction of matter and the forces that affect matter.
    From that, we derived the constants and quantities we use to describe nature.

    The constants and quantities are independent of the laws of nature.

    We can also see the flaws in our description as we have no way of expressing PI mathematically. We can keep converging on the value, but we can never reach an absolute value with our math showing that math is an invention of man.

    The value of pi is 100% absolute.

    We have a certain proportion of oxygen in our atmosphere due to physics, not because of fine-tuning.
    If the Earth had been fine-tuned our atmosphere would not always be changing.

    The atmosphere on earth is linked to the first cause. Of course it is linked to the Fine Tuning of the Universe. Universe means everything that exists. Atmosphere = physics.

    The Sherpas in Nepal are conditioned to high altitudes after centuries of living there, the Inuit are conditioned to living in the cold and the Hopi Indians living in the U.S southwest, can gain weight on what would be a starvation diet for us.

    These are all physical changes that come from bodies being fine-tuned to their environment.

    They had to survive first artificially before nature help them to adapt better.

  410. 410
    bFast says:

    Carpathian(386)

    We can keep converging on the value, but we can never reach an absolute value with our math showing that math is an invention of man.

    Sheut No! We come up with pi to the 3 millionth digit, and we know that we still haven’t got it right! How can this be if math is the invention of man. What stupid inventor came up with this idiocy. When the guy invented pi why didn’t he just invent it as 3. He would have saved us so much misery with our lack of precision.

    You know why he didn’t use the number 3? Oh yea — because it doesn’t work in the real world! Hmmm, pi is pi because it works in the real world, not because somebody declared it.

  411. 411
    Mung says:

    There are no perfect circles, and PI is 3 or 4, but closer to 3. I call it Mung’s Law.

  412. 412
    kairosfocus says:

    Mung,

    Nope.

    I suggest

    x^2 + y^2 = r^2

    and shifted versions etc define absolutely perfect circles.

    Of course, we cannot physically create such with atomic matter but that is a different matter.

    And in this case we can deduce pi to perfect specification as the ratio of circumference to diameter.

    Of course a power series rep on any reasonable whole number base — the place value system is a power series in disguise:

    3.1415926539 . . . = 3 *10^0 + 1*10^-1 + 4*10^-2 + . . . — will if finite be an approximation.

    KF

  413. 413
    Carpathian says:

    Upright BiPed:

    Try again. There is nothing whatsoever difficult about what I am saying. I gave you the four material conditions required for translation, along with unambiguous definitions of the terms.

    I have no problem understanding what you said, I am simply disagreeing and don’t accept your conclusion that chemical/mechanical/physical processes are semiotic in any way except by our use of symbols.

    What would you say if you were me, using the word “protocol” in the blatantly obvious sense of a convention to be followed for correct function (and also gave a specific definition as well), and suddenly an electrician came to UD to tell you that you had the definition of “protocol” all wrong. “A protocol”, he says, “is where the white wire is the common, the black is hot, and the green is ground”.

    That is not a “protocol”, it is an electrical standard. While the electrician might make a simple statement that laymen understand, it does not change the actual meaning of the term protocol.

    When scientists and technicians use terms to communicate ideas to each other, they use the formal recognized definition of those terms in order that there are no misunderstandings.

    Your use of the term protocol is not accurate.

  414. 414
    Mung says:

    Let the definitional games begin! That’s certainly one way to avoid the argument. “You’re not using the word the way I want you to use the word” is not a rebuttal.

    http://en.wikipedia.org/wiki/Protocol

    http://www.thesaurus.com/browse/protocol

  415. 415
    Mung says:

    Carpathian: I have no problem understanding what you said…

    ok, then.

  416. 416
    kairosfocus says:

    Mung (attn Carpathian):

    Wiki puts it well:

    In telecommunications, a communication protocol is a system of rules that allow two or more entities of a communication system to communicate between them to transmit information via any kind of variation of a physical quantity. These are the rules or standard that defines the syntax, semantics and synchronization of communication and possible error recovery methods. Protocols may be implemented by hardware, software, or a combination of both.[1]

    Communicating systems use well-defined formats (protocol) for exchanging messages. Each message has an exact meaning intended to elicit a response from a range of possible responses pre-determined for that particular situation. The specified behavior is typically independent of how it is to be implemented. Communication protocols have to be agreed upon by the parties involved.[2] To reach agreement, a protocol may be developed into a technical standard. A programming language describes the same for computations, so there is a close analogy between protocols and programming languages: protocols are to communications as programming languages are to computations.[3]

    UB is of course quite correct in his usage. There is an underlying protocol involved in say protein synthesis operations, and yes that points strongly to design.

    KF

  417. 417
    Carpathian says:

    kairosfocus:

    Communicating systems use well-defined formats (protocol) for exchanging messages. Each message has an exact meaning intended to elicit a response from a range of possible responses pre-determined for that particular situation.

    Where is there an exchange of messages?

    UB is of course quite correct in his usage.

    He is wrong in his usage since there is no exchange of messages.

    Your original analogy was closer, that of processing object code, but to say that it is a protocol is incorrect.

  418. 418
    Carpathian says:

    For a protocol, you must have two or more intelligent agents.

    That doesn’t exist at the biological level we are discussing.

    While humans can exchange intelligent messages, cellular machinery does not.

    Show me an exchange of intelligent messages at that level.

  419. 419
    Mung says:

    kf: UB is of course quite correct in his usage.

    Yeah, I don’t know how he does it, lol. I bet if he used some other term, such rule or code or convention they would argue over that too.

    Ever notice how none of the critics can suggest the appropriate term to use, but only object to the one that was used? I wonder why (not really).

  420. 420
    Mung says:

    Carpathian: For a protocol, you must have two or more intelligent agents.

    Says who? Is the Morse code a protocol? Why can’t a single individual develop a protocol?

    Are you a dualist? Are your two intelligent agents non-physical? So perhaps what you really meant to say was for a protocol you must have two or more physical systems. Which deserves a big so what. That’s basically what Upright BiPed said.

  421. 421
    Carpathian says:

    Mung:

    Why can’t a single individual develop a protocol?

    One person can develop it but two or more intelligent agents are required to use it.

    Ever notice how none of the critics can suggest the appropriate term to use, but only object to the one that was used? I wonder why (not really).

    I’ve said it before and I’ll say it again just for you Mung; the most appropriate term is a “look-up table”.

    As KF mentioned, it is more like executing object code.

    The object code is not an intelligent agent.

    There is no protocol.

  422. 422
    soundburger says:

    Mung #419

    that’s exactly it. No other term. We are supposedly just to attribute it to ‘nature stuff’.

    Which is exactly what materialists will argue that human language/human consciousness/human intelligence is, except when it serves their purpose to draw a line between ‘nature stuff’ and humans using language to represent something.

    If EVERYTHING is ‘nature stuff’, then why should our representations be of a different nature than what we are representing? Somewhere along the line, whether its language, symbolism, human consciousness, etc, you have to account for our ‘immaterial’ world of representations being different from the material world. And if all you can fall back on is ’emergence’ you are not answering the question.

  423. 423
    Mung says:

    soundburger,

    Yes. The genetic code has been around for millions of years, but it didn’t really exist, because two intelligent humans weren’t there to label it or use it.

  424. 424
    computerist says:

    While humans can exchange intelligent messages, cellular machinery does not.

    That all depends how you define “exchange”.
    Protocols, as in network protocols, are based on client-server model architecture. As data is packaged accordingly (moved through the OSI layers) encoded and then decoded on the opposite end within context (HTTP, etc..).
    However, protocols are simply processes that perform some sort of translation.
    For example, in software concepts such as serialization, de-serialization, normalization etc.. I can say that these are also protocols because they perform certain translation within the context of the software.
    Binary, JSON, XML protocols etc…
    Two “nodes” operating within the context of software can be a database/file and memory, the defined rules within this program can be classified as a type of protocol.
    Secondly, this idea that protocols are absent within biological processes, is not a very good one. The translation-transcription process from DNA -> RNA -> Amino Acids -> Proteins, can be considered a protocol. You’re exempting biological systems from the use of protocols because you assume they could not have been formed. This is expected because blind undirected processes (which you promote), could not form protocols, but ID can. As a former CCNP network engineer, I have identified many protocols within biological systems analogous to what I would consider a protocol. It comes down to whether you think it’s an *actual* protocol.

  425. 425
    Mung says:

    Carpathian:

    One person can develop it [a protocol] but two or more intelligent agents are required to use it.

    Don’t be silly. I could develop a protocol to allow two computers to exchange data. No other humans needed.

    Carpathian: I’ve said it before and I’ll say it again just for you Mung; the most appropriate term is a “look-up table”.

    You mean like a dictionary, map, hash, hashmap, associative array. Stuff like that? How do you look things up in a look-up table? What’s the protocol?

    Is that what you think the genetic code is, a look-up table?

  426. 426
    soundburger says:

    Mung, yes, the code didn’t ‘exist’ until people came around to represent it in words. And, further to that, it was that very same code-that-isn’t-a-code that eventually gave rise to, and was the sole mechanism responsible for, human intelligence creating language, symbols, translation and transcription.

    But, of course, there is no connection between the processes that led to our development of language and language itself.

    One is material, the other is representative. Simple as that.

  427. 427
    Mung says:

    Meanwhile, today I learned that ribosomes of different species can contain very different proteins, and yet all function as ribosomes.

    Does anyone know where I can view the phylogenetic tree generated from comparing the protein composition of ribosomes?

  428. 428
    computerist says:

    ribosomes of different species can contain very different proteins, and yet all function as ribosomes.

    exactly.

  429. 429
    Upright BiPed says:

    Hi Charles, sorry for the delay. (holiday weekend)

    Could you describe, specifically, which parts of the transcription process are “discontinuous” from each other and how does the discontinuity manifest as you intend the meaning? Do you mean logical, physiochemical, spatial, temporal?

    Thanks for the question. I refer to it as a physicochemical discontinuity. The function of the system depends on its capacity to specify certain amino acids among alternatives. It accomplishes this by being able to recognize the spatial orientation of the nucleotides in codons, and relating those patterns to individual amino acids. But there is nothing about the spatial arrangement of three nucleotides that relates it to any amino acid. That relationship is determined solely by the aaRS, which loads the correct amino acid to the tRNA in temporal and spatial isolation from the actual translation. This type of organization establishes a set of relationships (the genetic code) while preserving the discontinuity that the system requires. If the effects of translation had to be determined by the arrangement of a medium, then they would be so by the forces of inexorable law, and those forces would limit the system to only those effects that can actually be determined by the physical properties of the medium. This would lock the system into local determinism and would make the specification of a particular amino acid (by the spatial arrangement of three nucleotides) impossible to obtain.

  430. 430
    Upright BiPed says:

    Would you elaborate on this point, please?

    In my opinion, the heart of the issue has to do with the type of effect being produced. You might think of it in terms of the old physicist’s question about living things — where does all the variety come from? It’s the kind of question (as Pattee suggests) that the physicists worry about, while the biologists aren’t overly concerned. I’ll probably butcher the argument, but it goes something like this: The laws of nature are the same on Saturn and Mercury as they are on Earth and Pluto, and so we see wide natural variations in form, even within the constraints of inexorable law. But nothing even comes close to the variety of form found in the living kingdom. Working from inside the same inexorable laws as the entire remainder of the cosmos, where did all the astonishing variety come from in living things? The physicist wonders — are we waiting for an atom to veer off its lawful course?

    The answer, of course, is translation. Having a certain amino acid bound in a certain location at a certain point in time is not a physical effect that can be determined by the dynamic properties of a codon. It can however be systematically produced by translation – an apparatus that divides the production of an effect into just two arrangements of matter that collectively harness the laws of physics to produce the effect. One arrangement serves as a representational medium to evoke the effect, while the other determines what the effect will be. From such an organization, the system establishes prescriptive control. This control immediately expands the range of effects that can be produced. And this greatly expanded set of possibilities is the physicochemical basis of both the origin and diversity of form in the living kingdom.

    That is my own view, but a physicist like Pattee would probably go on to talk about the dividing line in the system being the real distinction between energy-degenerate rate-independent symbol structures and the rate-dependent construction they control. A logician like Von Neuman might talk about the fundamental requirement of a physical description (measurement) separate from the system of assembly. And a biologist/bloodhound like Crick might even regale the group with the necessities behind his famous adapter hypothesis.

    In any case, the whole thing seems to turns on what is required for an arrangement of matter to be a representation. It doesn’t gain that status from its dynamic properties. A representation doesn’t exist until there is a separate arrangement to physically establish what is being represented in a system.

  431. 431
    Upright BiPed says:

    Carp,

    I am simply disagreeing and don’t accept your conclusion that chemical/mechanical/physical processes are semiotic in any way

    The thing about this response is that it perfectly mirrors all the other responses you’ve written. Over the course of three or four posts, you’ve told me time and again what you “don’t see” and what you disagree with. Yet, you haven’t actually addressed any of the physical observations I’ve made, as if merely asserting disagreement is sufficient. It isn’t. If you should choose to address the observations, then I’ll be happy to respond. Until that time, you haven’t given me anything to respond to.

  432. 432
    Charles says:

    Upright BiPed @ 430; Mung @ 406; Silver Asiatic @ 407

    Your posts help, thank you all, especially Upright BiPed.

    I had scanned Pattee’s paper that Upright BiPed linked, looking for “discon” to see if he mentioned “discontinuity”, but there weren’t any hits.

    Because I’m lazy 🙂 (and frankly I’m not sure I’d recognize a valid reference) I’ll just ask: Does Pattee discuss the same concept but using different terminology, and if so, what terms in Pattee’s paper correspond to “discontinuity”?

  433. 433
    Upright BiPed says:

    Hi Charles,

    Pattee identifies it through physics, and refers to it as the “epistemic cut”.

    The Physics of Symbols: bridging the epistemic cut

    Evolution requires the genotype–phenotype distinction, a primeval epistemic cut that separates energy-degenerate, rate-independent genetic symbols from the rate-dependent dynamics of construction that they control. This symbol–matter or subject–object distinction occurs at all higher levels where symbols are related to a referent by an arbitrary code.

  434. 434
    kairosfocus says:

    Carpathian, where there is communication using code and/or modulation, there must be protocols that allow transmitters and receivers to reliably work together. In the cell we have just such coded communication, as is exemplified by protein synthesis. Note, tRNAs have a universal CCA coupler that would chemically bind to ANY AA at its COOH end . . . and even that chemistry in preference to other possibilities has to be set up. The assignment by the loading enzyme, as long since noted, is the point where the code is fully locked in. The variant possibilities, natural (about 2 dozen) and artificial, show the high contingency. This points to adequate cause for the systems, codes and protocols, and that strongly points to design; on sign. KF

  435. 435
    Charles says:

    Upright BiPed @ 433

    “epistemic cut” Of course! What was I thinking. :-/

    Thanks…. later

  436. 436
    Upright BiPed says:

    Charles, if my #429 was unable to satisfy your curiosity about my use of the word “discontinuous”, I do apologize.

  437. 437
    Charles says:

    Upright BiPed, not your fault.

    The entire subject of semiosis as it applies to DNA transcription and amino acid production, interests me, but the point about “discontinuity” is an aspect I hadn’t considered. Intuitively I get the need to prevent uncontrolled or unintended chemical reactions, and cause only translational/transcription reactions. I’m trying to plug your general terminology into specifics of how aaRS works (my rudimentary understanding largely gleaned from watching videos), but I might be overthinking it.

    But at present my time is scattered and I think I have enough explanations now to piece it all together, but I need to reread them all and see if I can answer my own question.

  438. 438
    Upright BiPed says:

    Charles, if you contact me, perhaps I can send you something that will be useful to you.

    contact (at) complexitycafe (dot) com

  439. 439
    Mung says:

    Hi Charles,

    Take Morse code for example.

    There is nothing that follows from physical necessity that requires letters from the English alphabet to map to dots and dashes or vice versa.

    There is nothing that follows from physical necessity that requires dots and dashes to map to electrical states on a telegraph wire or vice versa.

    These are strictly by convention (protocol).

    The specific claim is that in the case of Morse code this discontinuity is a requirement and must be maintained in order for the code to have the desired effect.

    The generalization is that this same logic applies to any transfer of recorded information.

    The observation is that we find the exact same conditions within the cell, so we have good reason to believe we are observing actual codes and actual transmission of information and these terms are not being used metaphorically.

  440. 440
    Mung says:

    Further on Meyer’s argument:

    Some scholars have suggested that the Cambrian explosion too was an adaptive radiation, but this idea would put us before an insurmountable difficulty. Both phyletic gradualism and punctuated equilibria require, as a theoretical necessity, that the higher the taxon, the higher the number of speciations, and this means that changes at the phylum level must have taken longer times than changes at lower levels. In the case of the Cambrian explosion, however, this theoretical requirement contrasts with the evidence, and all classical mechanisms of adaptive radiations are incapable of explaining the phenomenon.

    – Marcello Barbieri

    Sounds entirely too Meyeresque. I can hear Elizabeth now. This Barbieri guy is no paleontologist.

  441. 441
    EugeneS says:

    UB, Mung,

    Great Posts 406, 430-431, 439.

    Many Thanks for the clarification on discontinuity. Correct me if I am wrong. As far as I understand, basically discontinuity makes sure it is possible to send “0” or “1” over the channel without locking it to its local dynamics. Discontinuity enables specification, i.e. makes sure that the information carrying capacity of the system is > 0. This is possible only in wide enough dynamic equilibrium zones.

    Abel treats it a little differently, i.e. from the point of decision theory. If you have multiple physico-chemically indeterminate indistinguishable states (dynamic equilibria) you as a decision maker have freedom to assign to certain equilibrium configurations pragmatic utility. Chess is his chosen example, where each chessman is in an equilibrium position when placed on a horizontal static board. It does not matter from physic’s perspective what position a chessman occupies on the board. However the position of a chessman is very important in the context of the game (i.e. has different pragmatic utility).

    I like the paper by Pattee that was cited in the thread. It has very many insights. What I find particularly enlightening is why the molecules of life is what they are.

    Rapid folding and stability of a protein requires steep energy landscapes, while optimization of function requires fine tuning of the folded shape of the protein by small changes in genetic sequences. This requires a relatively smooth energy landscape. Balancing these requirements is eased by large enough molecules so that major folding conditions are buffered from local fine-tuning changes in sequences

  442. 442
    Silver Asiatic says:

    Continuity would mean a locked-in determinate hard-coding from signal to receptor to effect/function. Rocks, hill, gravity are continuous, locked to create rock pile at bottom of hill.

    Discontinuity would mean indeterminancy, not locked by a physical configuration. A logic switch, intelligent response from several options.

  443. 443
    EugeneS says:

    Silver Asiatic #442,

    Exactly.

  444. 444
    Carpathian says:

    Mung:

    These are strictly by convention (protocol).

    Why don’t you simply use the term convention instead of protocol if you really mean convention?

    Don’t be silly. I could develop a protocol to allow two computers to exchange data. No other humans needed.

    The two computers are intelligent agents.

    Each side of the communications link is intelligent.

    [data] — )))
    ((( — [NAK]

  445. 445
    Carpathian says:

    Mung:

    The observation is that we find the exact same conditions within the cell, so we have good reason to believe we are observing actual codes and actual transmission of information and these terms are not being used metaphorically.

    We don’t see anything close to data exchange.

    We don’t even see data going one way.

    What we see are chemical reactions.

    A closer analogy would be a vinyl record.

    The grooves in the record physically move the needle to produce an electrical charge in the tone arm’s cartridge.

    There is no immaterial data component or exchange of data which would be required by a protocol.

    Everything that happens with a vinyl record happens with DNA.

    It is purely physical and no immaterial data is required or produced.

    If I’m wrong, show me the information that is received by the DNA.

    Show me some protocol where data is exchanged equivalent to a communications exchange between computers.

  446. 446
    Carpathian says:

    kairosfocus:

    Carpathian, where there is communication using code and/or modulation, there must be protocols that allow transmitters and receivers to reliably work together. In the cell we have just such coded communication, as is exemplified by protein synthesis. Note, tRNAs have a universal CCA coupler that would chemically bind to ANY AA at its COOH end . . . and even that chemistry in preference to other possibilities has to be set up. The assignment by the loading enzyme, as long since noted, is the point where the code is fully locked in. The variant possibilities, natural (about 2 dozen) and artificial, show the high contingency. This points to adequate cause for the systems, codes and protocols, and that strongly points to design; on sign. KF

    You have described the “physical layer” not “link” or “transport”.

    If I completely describe an RS-232 connection I have not in any way described a communications protocol.

    There is no way to have a protocol without having two way communications.

    Again, a “convention”, “look-up table” or “object code” are not examples of a protocol.

  447. 447
    Carpathian says:

    Upright BiPed:

    Carpathian: I have no problem understanding what you said, I am simply disagreeing and don’t accept your conclusion that chemical/mechanical/physical processes are semiotic in any way except by our use of symbols.

    Upright BiPed: The thing about this response is that it perfectly mirrors all the other responses you’ve written. Over the course of three or four posts, you’ve told me time and again what you “don’t see” and what you disagree with. Yet, you haven’t actually addressed any of the physical observations I’ve made, as if merely asserting disagreement is sufficient. It isn’t. If you should choose to address the observations, then I’ll be happy to respond. Until that time, you haven’t given me anything to respond to.

    Again, I am addressing your claims that there is a protocol involved and you haven’t shown me that a protocol is actually involved.

    You used the term “convention” to better describe your use of the term “protocol”.

    Why don’t you just use that term if it more accurately reflects what you mean?

    If you can show me an immaterial exchange of data, I would tend to agree with you but you have instead described only the physical layer of what might be a protocol.

    If there is no exchange of immaterial data, there is no protocol.

    It is your claim that there is one, so show me the protocol, not the physical layer.

    I don’t know how I could be clearer that you haven’t proven a case you’re trying to make.

    As far as there being semiotic code, you haven’t shown it.

    I have looked up Peirce, the originator of the term, and his description does not agree with yours.

    Peirce looked at symbols and signs. In one case, he stated that a footprint left by a human was semiotic.

    Notice that the semiotic attribute applies after the fact in that the person making the footprint had no intention of using a code.

    Semiosis deals with immaterial data, not physical data.

    I have not seen him refer to semiosis as having a mechanical or physical use.

  448. 448
    Mung says:

    Carpathian: If there is no exchange of immaterial data, there is no protocol.

    Thanks for getting there ahead of me. Saved me having to lead you to it. I figured this was your stance.

    So you’re not a materialist. You accept the existence of immaterial entities.

  449. 449
    kairosfocus says:

    Carpathian, the ISO OSI layercake model is not the only possible layercake, indeed the UK proposal on which it is based had five layers, and IIRC html protocols have 4. The issue is layered arrangements. Start and stop instructions with serial codes etc are similar. Which of course appear in life systems. KF

  450. 450
    Mung says:

    Is Carpathian confusing the map with the territory again?

    http://en.wikipedia.org/wiki/I.....ocol_suite

  451. 451
    Upright BiPed says:

    Again, I am addressing your claims that there is a protocol involved and you haven’t shown me that a protocol is actually involved.

    #429

    To confirm an instance of translated information, you have to find 4 interdependent material conditions. 1) representation: an arrangement of matter to evoke an effect within a system, where the arrangement of the medium and the effect it evokes are physicochemically arbitrary. 2) protocol: an arrangement of matter to physical establish the otherwise non-existent relationship between the arrangement of the medium and its post-translation effect. 3) discontinuity: the discontinuity between the arrangement of the medium and its post-translation effect must be preserved by the system. 4) unambiguous function: the effect of translation creates function in the process of being and/or survival of a living organism (i.e. life and semiosis are coextensive).

    These conditions remain true regardless of the content of the information or the system in which it’s found. Specifically in the genetic translation system, the representation is the codon, and the protocol is the aaRS (which charge the tRNA while preserving the discontinuity required by the system’s function). In others words, the effect of genetic translation is not determined by the structure of the nucleic codon that evokes the effect, instead it is determined by the structure of the aaRS that charge the tRNA. The system establishes a set of relationships (systematic regularities) that we now call the Genetic Code.

    Oxford Journals, Nucleic Acids Research:

    The aminoacyl-tRNA synthetases (AARS) are a diverse group of enzymes that ensure the fidelity of transfer of genetic information from DNA into protein. They catalyse the attachment of amino acids to transfer RNAs and thereby establish the rules of the genetic code by virtue of matching the nucleotide triplet of the anticodon with its cognate amino acid.

    Your complaining about my use of the word protocol is a distraction, made particularly obvious by the fact that I specifically defined my terms when I used them. C’mon. It’s 2015 in a post-industrial information society. Everybody on the surface of the planet knows that there are thousands of different kinds of protocols, and they know that all of them center around an agreement, or set of agreements, that preserves proper function.

    And they know it’s silly for you to continue to behave otherwise. Give it a rest.

  452. 452
    Mung says:

    Surely there is a proper protocol to getting someone to “give it a rest.”

  453. 453
    Charles says:

    Mung @ 439; Upright Biped:

    The specific claim is that in the case of Morse code this discontinuity is a requirement and must be maintained in order for the code to have the desired effect.

    I construe “discontinuity” in either the mathematical sense, for example given *all* integers 1 through 10: 1 2 3 4 7 8 9 10, the absence of 5 & 6 are a discontinuity. If they were charted, the line graph would have missing segments; or in the physical sense, for example the boundary between an ice cube and the water in which it floats is a discontinuity where the phase has changed from solid to liquid.

    A discontinuity is where something is missing or different when compared to its regular condition. A fracture is a discontinuity. A gap is a discontinuity.

    That said, let’s take the case of morse code; let’s take the specific case of an S-O-S encoded in some medium (small or large rocks, long or short sticks, cans viewed lengthwise or end-on). The arrangement or representation must be 3 dots 3 dashes 3 dots, or 3 short 3 long 3 short, or 3 small 3 large 3 small, or 3 round 3 straight 3 round… etc.

    The encoder (who needs help) arranges the medium to encode the S-O-S information and the rescuer interprets the information in the medium as a cry for help.

    Where is the discontinuity?

  454. 454
    Upright BiPed says:

    Charles,

    There is nothing about the physical properties of rocks or sticks that relates them to a message. The fact that you can use either rocks or sticks or cans demonstrates this point. There is a physicochemical discontinuity between them. The message is not a physical or chemical property of the medium, and it is not related to (or determined by) any physical or chemical property of the medium. This is what Pattee was referring to in his opening remarks. Physical reactions are described by the exchange of energy and the rates of exchange of energy. There is a distinction between the rate-independent symbol structure, and the rate-dependent effects they control.

  455. 455
    EugeneS says:

    Carpathian,

    “Each side of the communications link is intelligent”

    Not necessarily. An agent may receive signals from the outer world and still interpret them as data. But invariably it will need to have rules (not constraints) about how to interpret. No interpreter means no data.

    If it had only physical constraints, there would be no information processing capacity. Constraints imply law-like regular cause-effect relationships without freedom.

    Rules imply freedom from law-like necessity. Once you have that freedom (owing to contingency i.e. a multiplicity of physically equivalent states), you have the potential to create intelligent systems.

    Intelligence is about rules, which are about pragmatic choice between physically equivalent states. Note that non-linear physical phenomena like bifurcations are not choice themselves. They only provide alternatives to choose from. But designing intelligent systems involves choices that must be made in order to achieve an end result which has some pragmatic value.

    Life is about rules, not constraints, even though it is realized as a material system subject to the laws of nature. But the essence of it is rules of symbol interpretation.

  456. 456
    Carpathian says:

    EugeneS:

    Carpathian: “Each side of the communications link is intelligent”

    EugeneS: Not necessarily.

    You are correct when it comes to simply interpreting data, but to implement a protocol, both sides must be intelligent in order to interpret and acknowledge or reject messages.

    Any message received by either side must be inspected for data integrity before the data is even accepted for further processing.

    If it had only physical constraints, there would be no information processing capacity. Constraints imply law-like regular cause-effect relationships without freedom.

    I agree here and that is the problem I have with labeling biological processes as “semiotic”.

    Both Upright Biped and kairosfocus have described only the chemical physical layer, not any upper layers where the protocol and data would be processed.

    These upper layers have never been located and/or described in all our exchanges.

    Intelligence is about rules, which are about pragmatic choice between physically equivalent states.

    When it comes to biology, and here I don’t mean at the level of a brain/mind, physical states are the data in the sense that what you call “choices” are made at the material level.

    I still have not seen a protocol layer which is divorced from the physical, which I agree with you must exist if we are talking “intelligence”.

  457. 457
    Carpathian says:

    Upright BiPed:

    Everybody on the surface of the planet knows that there are thousands of different kinds of protocols, and they know that all of them center around an agreement, or set of agreements, that preserves proper function.

    Every one of these different agreements about protocols are about dynamic systems.

    These “protocol standards” apply to the coordinated exchange of information, not to static systems such as the definitions of codes.

    Your complaining about my use of the word protocol is a distraction, made particularly obvious by the fact that I specifically defined my terms when I used them.

    This is hopefully a scientific discussion, and on that level the terms we use should accurately describe what we are talking about.

    In a protocol, both sides must be intelligent in order to to reject, accept or properly build immaterial messages.

    You have taken the term protocol instead of the term convention, thereby changing its previously accepted meaning.

    Why would you change the meaning of a term that is already accepted?

    There is a huge difference between what happens in a protocol exchange and what happens when we adopt a convention.

    Why don’t you simply use the word convention if that’s what you mean?

    And they know it’s silly for you to continue to behave otherwise. Give it a rest.

    Every single example you have made is about the physical layer, not a higher level protocol.

    If I’m wrong, show me the immaterial data exchange. This is required for a protocol.

    Your use of protocol is different from that which is accepted by IT departments around the world.

    Your use of semiosis is not in agreement with that of Peirce who first came up with the term.

    So you’re in disagreement not with just me, but everyone whose terms you have used incorrectly.

  458. 458
    Mung says:

    Hi Charles,

    I am not sure I understand your question.

    Are you saying you see no discontinuity between S and . . . or between O and _ _ _ or between those and electrical impulses traveling along a telegraph wire?

    How would you describe the regular condition of a telegraph wire?

    I would describe the regular condition of a telegraph wire as not carrying any dits or dahs. If the regular condition of a telegraph wire was one of carrying pulses of dits and dahs how would you propose using it as a medium for sending morse coded messages?

  459. 459
    Carpathian says:

    kairosfocus:

    Carpathian, the ISO OSI layercake model is not the only possible layercake, indeed the UK proposal on which it is based had five layers, and IIRC html protocols have 4. The issue is layered arrangements.

    I agree but I don’t see layers being defined by Upright BiPed. He describes only the physical layer.

    Start and stop instructions with serial codes etc are similar. Which of course appear in life systems. KF

    Start and stop codes happen at the physical layer with RS-232 so that’s not a helpful analogy.

  460. 460
    Mung says:

    Carpathian: Any message received by either side must be inspected for data integrity before the data is even accepted for further processing.

    Even if this is true, so what? Are you saying no error checking takes place within the cell?

  461. 461
    Mung says:

    Carpathian:

    Both Upright Biped and kairosfocus have described only the chemical physical layer, not any upper layers where the protocol and data would be processed.

    These upper layers have never been located and/or described in all our exchanges.

    LoL. I repeat, you are suffering from map/territory confusion.

    Also, do you think the layers above the physical later are non-physical? Seriously?

  462. 462
    Carpathian says:

    Mung:

    How would you describe the regular condition of a telegraph wire?

    Probably marking as in RS-232 or a current loop.

    Almost all systems will be in the marking state so that a break in the line would be an exceptional condition in order to alert someone that messages are no longer possible..

  463. 463
    Upright BiPed says:

    Both Upright Biped and kairosfocus have described only the chemical physical layer, not any upper layers where the protocol and data would be processed.

    Perhaps you’ve wondered why I describe the physical implementation of the protocol?

    Here’s a hint:

    Semiosis occurs when one thing signifies or represents another thing within a system. It ultimately refers to the physical process by which information is exchanged and translated in the living kingdom.

    and what was your reply to this?

    I see semiosis as an immaterial human venture not something nature uses

    good grief.

    Since you refuse to open your eyes, maybe I should just start asking you to explain yourself until you figure out that in a material universe ALL communication is physical, and that ALL messages are independent of their medium, and therefore they ALL require material protocols to establish what their physical effects will be.

    What is an “immaterial human venture”?

  464. 464
    Carpathian says:

    Mung:

    Carpathian: Any message received by either side must be inspected for data integrity before the data is even accepted for further processing.

    Mung: Even if this is true, so what? Are you saying no error checking takes place within the cell?

    Again, the error checking done by a protocol relates to messages sent in both directions.

    The physical layer is a separate issue.

    In the RS-232 definition, a char can have a parity bit that can be checked for an error in a single char code, but the protocol error checks are applied both to complete packets of information and also the sequence of message types plus the timing between packets.

    Protocols are much more complex than simple code definitions.

    Also, do you think the layers above the physical later are non-physical? Seriously?

    Yes. That’s why protocols named the physical layer the physical layer.

    The layers above them are immaterial data.

    This is the same sort of distinction ID makes about the mind/brain, i.e, the brain is material and the mind isn’t.

  465. 465
    Upright BiPed says:

    #457

    If I’m wrong, show me the immaterial data exchange. This is required for a protocol.

    facepalm

  466. 466
    Upright BiPed says:

    #457

    Your use of protocol is different from that which is accepted by IT departments around the world.

    The world’s first computer science program began at Cambridge in 1953. The word “protocol” has been in use since the 1500’s. I wonder if there is only one accepted definiton of a protocol?

  467. 467
    Charles says:

    Upright BiPed @ 454:

    The fact that you can use either rocks or sticks or cans demonstrates this point. There is a physicochemical discontinuity between them.

    I suspect that perhaps a better word for “discontinuity” might be “independence”?

    “Discontinuity” implies a break or difference from what is otherwise “continuous”. But absent any rocks or sticks or cans, there is no medium and nothing in which “continuity” would be observed and nothing against which a “discontinuity” could be compared.

    The message is not a physical or chemical property of the medium, and it is not related to (or determined by) any physical or chemical property of the medium.

    Yes, the message is “intangible”, while the medium is “tangible”. You might even argue the “intangibility” of the information is “discontinuous” from the “tangibility” of the medium”, but one could allude to the physical arrangment of rocks or sticks or cans and legitimately describe rock and not-rock as a discontinuity as well, or stick and not-stick, can and not-can as discontinuities. But such discontinuities are not the point you are making about the message information. The presence of any single rock immediately and unavoidably is distinct from all the surrounding not-rock, and indeed establishes a discontinuity, but such a discontinuity is more like a “spandrel” (the space between two arches) in which the arches are necessary to supporting the roof while the space between them (the “spandrel”) is a mere consequent artifact. Spandrels are not “necessary” any more than the discontinuity between rock and not-rock is necessary, unavoidable consequence yes, but not “necessary”.

    The distinction I’m drawing, again, is that “discontinuity” implies something that was otherwise continuous, but your explanation correcly emphasizes the arbitrariness of the medium from the information in the representation.

    What is “necessary” is that the medium be an arbitrary arrangement to encode the information. It is arbitrary whether the medium be rocks or sticks or cans, and even their arrangement is arbitrary (provided the message sender and receiver agree on what represents information).

    A word similar in meaning to “arbitrary” but with the added connotation of the information being unaffected by the medium is “independent”.

    You could explain, with better rigor and precision:

    The fact that you can use either rocks or sticks or cans demonstrates this point. There is a physicochemical independence among them.

    or

    The fact that you can use either rocks or sticks or cans demonstrates this point. There is no physicochemical dependence among them.

    and

    The message is not a physical or chemical property of the medium, and it is not dependent on (or determined by) any physical or chemical property of the medium.

    and back in your post 394:

    3) independence: the independence of the arrangement of the medium from its post-translation effect must be preserved by the system.

    I also think the many excellent explanations of yours I’ve read as to the “arbitrariness” of the medium and the representation would be helpful to incorporate.

    In hindsight, the word “discontinuity” in the context of being “required” implied a break in something that was otherwise continuous, and I was lost down the rabbit hole.

    Required to be preserved, yes, but at least for me (personally) “independence” correctly conveys what I think you mean instead of “discontinuity”.

  468. 468
    Carpathian says:

    Upright BiPed:

    Semiosis occurs when one thing signifies or represents another thing within a system. It ultimately refers to the physical process by which information is exchanged and translated in the living kingdom.

    This is in contradiction to Peirce’s use of semiosis.

    From http://plato.stanford.edu/entr.....semiotics/

    The sign is the molehill, and the object of this sign is the mole. The mole determines the sign, in as much as, if the molehill is to succeed as a sign for the mole it must show the physical presence of the mole. If it fails to do this, it fails to be a sign of that object.

    Notice that semiosis is seen as after the fact. It is not a mechanism.

    What I mean is that Peirce viewed semiosis as an immaterial explanation not a material cause of an object.

    This is what I mean by immaterial human venture.

    Peirce as a human being came up with his concept of semiosis to help him explain the world around him. Semiosis is not a mechanism or even a description of a mechanism for causation.

    Since you refuse to open your eyes, maybe I should just start asking you to explain yourself until you figure out that in a material universe ALL communication is physical,..

    Agreed.

    ..and that ALL messages are independent of their medium,..

    Agreed.

    ..and therefore they ALL require material protocols to establish what their physical effects will be

    Here I disagree.

    There is no need for a message to have any physical effect at all.

    Secondly, a protocol is not used to establish the meaning of any message outside of transporting that message.

    The job of the internet is to send and receive messages without regard to their meaning by the sender or receiver.

    This is not the case in the cell.

    A cell is concerned directly with chemical reactions, nothing else.

    There are no high level messages of the type that occur in protocols.

  469. 469
    Upright BiPed says:

    #457,

    Your use of semiosis is not in agreement with that of Peirce who first came up with the term.

    International Society for Biomeiostic Studies:

    Biosemiotics is an interdisciplinary research agenda investigating the myriad forms of communication and signification found in and between living systems. It is thus the study of representation, meaning, sense, and the biological significance of codes and sign processes, from genetic code sequences to intercellular signaling processes to animal display behavior to human semiotic artifacts such as language and abstract symbolic thought.

    Such sign processes appear ubiquitously in the literature on biological systems. Up until very recently, however, it had been implicitly assumed that the use of such terms as “message” “signal” “code” and “sign” was ultimately metaphoric, and that such terms could someday effectively be reduced to the mere chemical and physical interactions underlying such processes. As the prospects for such a reduction become increasingly untenable, even in theory, the interdisciplinary research project of biosemiotics is attempting to re-open the dialogue …

  470. 470
    Carpathian says:

    Upright BiPed:

    The world’s first computer science program began at Cambridge in 1953. The word “protocol” has been in use since the 1500’s. I wonder if there is only one accepted definiton of a protocol?

    You are using the term protocol as it relates to the processing of information.

    Why would you think that I or anyone else would use a definition different than that?

  471. 471
    Carpathian says:

    Upright BiPed:

    Biosemiotics is an interdisciplinary research agenda investigating the myriad forms of communication and signification found in and between living systems

    This is not semiosis.

    They have coined their own term and I have no problem with that.

    No one would be confused that what they are concerned with is not semiosis, but rather a biological concept of their own.

    If they in any way use it to describe codes or signs as causation, they would be very far from Peirce’s semiosis but I have no problem with that since they have coined their own term.

    I would however have a problem with anyone taking their term and applying a different meaning to it, just as I have a problem with anyone applying their own meanings to any accepted terms.

  472. 472
    Upright BiPed says:

    #470

    Carp: You are using the term protocol as it relates to the processing of information.

    Why would you think that I or anyone else would use a definition different than that?

    #457

    Carp: Your use of protocol is different from that which is accepted by IT departments around the world.

    It might have occurred to you by now that the processing of information didn’t begin with an “IT Department” and neither did the use of the word protocol to describe a set of rules for proper function.

  473. 473
    Upright BiPed says:

    #471

    Please read a book.

  474. 474
    kairosfocus says:

    Carpathian, passive echo radar and sonar based on reflected echoes. KF

  475. 475
    Mung says:

    Meanwhile in the real world:

    discontinuous

    Consisting of distinct or unconnected elements

    As in, the codons in mRNA are distinct from and not connected to the amino acids in a polypeptide.

    Messenger RNA (mRNA) is a large family of RNA molecules that convey genetic information from DNA to the ribosome, where they specify the amino acid sequence of the protein products of gene expression. Following transcription of primary transcript mRNA (known as pre-mRNA) by RNA polymerase, processed, mature mRNA is translated into a polymer of amino acids: a protein, as summarized in the central dogma of molecular biology.

    As in DNA, mRNA genetic information is in the sequence of nucleotides, which are arranged into codons consisting of three bases each. Each codon encodes for a specific amino acid, except the stop codons, which terminate protein synthesis. This process of translation of codons into amino acids requires two other types of RNA: Transfer RNA (tRNA), that mediates recognition of the codon and provides the corresponding amino acid, and ribosomal RNA (rRNA), that is the central component of the ribosome’s protein-manufacturing machinery.

    http://en.wikipedia.org/wiki/Messenger_RNA

  476. 476
    Charles says:

    Carpathian @ 468

    A cell is concerned directly with chemical reactions, nothing else.

    And a CPU is concerned directly with instruction excution, nothing else

    There are no high level messages of the type that occur in protocols.

    But in a computer, the higher level message is in the software that the CPU is executing, instruction by instruction. At the instruction level, the CPU is not “messaging at a high level”, it is merely executing discrete steps at one the lowest levels possible.

    But the overall calculation being performed at a higher application level (say an integral or a sort) indeed generates a message (albeit not a self-replicating message) in the form of the answer to the integral or the sorted list.

    Likewise in a cell, the ribosome is executing the instructions, codon by codon, but the ribosome does not “message at a higher level”, rather that high level message is the genetic blueprint for making amino acids and assembling them into proteins in the DNA molecule.

    Consider by analogy an old assembly line using Numerical Controlled machines into which are fed a punch tape of holes that each machine reads and performs a specific funtion. One machine reads in a punch tape (in a repetitive loop) and positions a piece of work and drills holes in it. The next machine on the line similarly reads its tape and positions the work and cuts screw threads into the holes. While the next machine screws bolts into the threaded holes. No single NC machine at the lowest level generates the finished product, but at the highest level, the master NC punch tape contains the instructions for every machine on the line to perform its step in making the designed product, which design is implicit in the information on the punch tape.

    All are purely mechanical operations driven by mechanical punch tapes, wherein the position of the holes is the design information. The high level message is in the master NC punch tape, the protocols in how each machine is built to move depending on what hole(s) are present or not on its NC punch tape.

    Similarly in the cell, the master NC punch tape is the DNA molecule, and the NC controlled machines are the ribosomes, etc.

    The “protocol” in the NC controlled assembly line is the mechanical motions of the machines depending on where the holes are in the punch tape.

    The “protocol” in the cell is the physicochemical molecular bonds that form or are rejected as dictated by the tRNA when a ribosome interacts with it, based on the high level message in the DNA molecule.

    Hopefully that helps Upright Biped’s explanations rather than mangles them 🙂

  477. 477
    EugeneS says:

    Carpathian,

    Mung is right, you are confusing the map with the territory. In any existing information system, all its bits are material by necessity and yet their different roles are recognizable as each component produces what is required for the joint function of the whole system. You are conflating the formal with the physical. Physical things can comply with formal requirements, but they are different. Physicality causally depends upon formality, not the other way around.

    Semiosis is an objective phenomenon. It is the basis of any information exchange. Science is good at recognizing objective phenomena, of which semiosis is an example. The objectivity of semiosis is a fact.

    Your position is in disagreement with the established scientific result as regards semiosis. What then stops you from questioning the objectivity of, say, chemical reactions themselves to which you are appealing?

    If your position were tenable, it would invalidate science as a whole.

  478. 478
    Mung says:

    Not only is Carpathian confusing the map with the territory, but he also has the cart before the horse.

    The major contributions of the OSI Reference Model have been:

    1. to identify the collection of functions that are fundamental to providing reliable, cost-effective, secure and transparent communication between systems,

    2. to give a precise definition of each function without necessarily providing details of how the functionality is to be achieved,

    3. to define the concept of layered architecture in terms of services, functions and protocols, and

    4. to specify the seven-layer layer OSI architecture in terms of the functionality of each layer.

    The concept of services is central to the description of the OSI architecture. It is an abstract specification of the interface between subsystems in two adjacent layers. Each layer in OSI provides a set of services to subsystems in the layer above. Further, in providing these services, a layer uses the services made available by the layer(s) below. In order to bridge the gap between the services available to a layer and those that it provides, several functions have to be implemented. This collection of functions, and a mechanism to realize each of them, is specified by a protocol.

    Open Systems Interconnection: It’s Architecture and Protocols

  479. 479
    Mung says:

    2.2.3 Protocols

    A major concern of OSI is with communication between peer entities (of the same rank). For the case where peer entities reside within the same open system, there may exist a direct path or an interface between between them, in which case such communication is considered to be outside the scope of OSI.

    Open Systems Interconnection: It’s Architecture and Protocols

  480. 480
    Evolve says:

    Upright Biped is wrong and I have told him that before.
    He is essentially saying that a codon is not physically linked to an amino acid, it merely represents it.
    God has decided which codon should represent which amino acid, much like how humans have decided which given set of symbols should uniquely represent which alphabet in Morse Code.

    But this argument fails due to two reasons

    (1) It disregards the biochemistry.
    Morse Code has no chemistry, but the cell does! Note how Upright Biped fails to mention the Watson-Crick base pairing between a codon and its anticodon. This chemical interaction physically links the codon to its corresponding amino acid-bearing tRNA. To say that the codon and amino acid are disconnected is simply wrong. In Morse Code, there’s no such chemical link, therefore comparing it to biological translation is meaningless.

    (2) UB’s argument is erroneously based on teleological reasoning.
    As with most creationist arguments, UB implies that God decided such and such amino acids should be encoded by such and such codons and He set up a system to realize His vision. But in reality, the genetic code is a “frozen accident” where specific amino acids were “allocated to” specific codons by sheer chance contingent on physico-chemical properties and interactions of the molecules involved.

  481. 481
    Mung says:

    2.2.3 Protocols (continued)

    To provide services, the two entities themselves need to communicate with each other. Either the two (N)-entities communicate directly (outside the OSI environment), or they do so using (N-1)-services. In the latter case, communication between the peer entities is governed by a set of rules and formats that each entity must adhere to in order to provide services or implement functions. This set of rules and formats (semantics, syntax, and timing) is referred to as (N)-protocol.

    Open Systems Interconnection: It’s Architecture and Protocols

  482. 482
    Evolve says:

    Similarly, JimFit’s declaration above that the universe is fine-tuned is also wrong. Another bogus argument from teleological reasoning.

    His argument goes like this:
    The universe has life – the constants are precisely suitable for life – therefore the constants were set by God to allow life (i.e the universe was fine-tuned).

    But he fails to see the alternative.
    The universe began with a random set of constants – stars, planets & life are mere consequences, mere fallouts, of the values the universe started off with.

    Once you abandon teleology, the alternative becomes clear and the concept of fine-tuning itself erodes away.

  483. 483
    Mung says:

    And once you abandon reason there’s not much purpose to thinking.

  484. 484
    Mung says:

    Evolve is just another closet dualist.

  485. 485
    EugeneS says:

    Evolve #482

    Observation: narrow stability zones of universal constants;
    Explanation: just because it so happens.

    Not only does the universe have a set of properties, one out of infinitely many possible ones. These properties are stable that leads to remarkable regularities which enable science.

    Of course, it just so happens…

  486. 486
    EugeneS says:

    Evolve #480

    You are not seeing the wood for the trees.

    ‘Teleological reasoning’ in this case is the only option because in order to have such a ‘frozen accident’ there had to be many things available. And not only that, there should have happened a whole sequence of ‘frozen accidents’ at the right times at the right place with the right rate, with the right chemical gradients, pressures, temperatures, etc. And last but not least, with all those prerequisites in place it had to be ‘frozen’ at the right time. Your loose terminology gives away reasoning that lacks rigor. ‘Frozen’ means controlled. That is exactly the thing you need to demonstrate, i.e. the emergence of control all the way up from molecules to the formation of macro-molecules to the formation of replicators to the formation of the cell that replicates and metabolically controls its own life cycle, reacts to stimuli and makes decisions to adapt to changing environment.

    I suspect you don’t fully appreciate the complexity of things necessary for life.

    I am always amazed when people say “in reality” as if they saw what really happened before a human observer was even available. No reasoning is good enough for them. They know what really happened.

    Ultimately, it is a matter of faith, of course. I can accept that but what I do not accept is attempts to pretend that such a system of beliefs is purely scientific.

  487. 487
    Upright BiPed says:

    Evolve,

    #1
    If you are going to misrerepsent me, at least get the biochemistry right. Watson-Crick base pairing does not establish the Genetic Code. The aaRS does.

    See the inset box from Oxford in post #451

    #2
    It’s not really a matter of sheer chance that the genetic code came together in a “frozen accident”, because the actual coding protocol is only a part of the system that needs to be “frozen”. Remember that the patterns in the code are one-dimensional, meaning that they have a spatial orientation that must be incorporated into the function of the system. Therefore not only would the many individual relationships of the coding protocols have to “freeze” together (which is reason enough to ignore the notion of a frozen accident) but the additional systematic protocols required for system function (such as how many nucelotides constitute a single represenation, where to start reading along a sequence, where to stop, in what direction is the sequence to be read, etc) would also need to “freeze” at the same time, and moreover, become encoded in the very sequences that the coding structure makes possible.

    – – – – – – – – – – –

    An honest man, armed with all the knowledge available to us now, could only state that in some sense, the Origin of Life appears at the moment to be almost a miracle, so many are the conditions which would have to be satisfied to get it going. – Francis Crick (the man who first offered the “frozen accident” thesis)

  488. 488
    Charles says:

    Evolve @ 480:

    Here is the equation for the chemical reaction of Sodium and Chlorine to product salt:
    2 Na + Cl2 -> 2 NaCl

    2 molecules of monatomic sodium (solid) combine with 1 molecule of diatomic chlorine (gaseous) to yield 2 molecules of sodium chloride (salt)

    Note the reactants and products balance:
    Reactants:
    2 molecules Na having 1 atom each molecule
    1 molecule CL2 having 2 atoms each molecule
    equals:
    2 Na atoms
    2 Cl atoms

    Products:
    2 molecules of Sodium Chloride having 1 Na atom and 1 Cl atom for each molecule
    equals:
    2 Na atoms
    2 Cl atoms

    This chemical interaction physically links the codon to its corresponding amino acid-bearing tRNA.

    So show us the balanced chemical interaction equation for a codon that produces its corresponding amino acid.

    As Carpathian explains, it’s all just chemical reactions at the cell level, so he likely can help you with the equation that shows a specific codon being physically linked to its product amino acid.

  489. 489
    soundburger says:

    Carpathian, I, and Mung as well, are interested in your use of the word ‘immaterial’ but you have seemed reluctant to touch on that thus far.

    Would you please describe what you mean by ‘immaterial’? Do you believe that only humans are capable of pondering ‘immaterial’ things? If you believe that, why? Do you attribute it to some sort of lucky accident along our evolutionary course?

    Do other animals also possess this ability? For example, when birds build nests, do you believe they have a concept of what the nest will look like when finished? If so, would that also be ‘immaterial’ in your view?

    If you believe that only humans have ‘immaterial’ thoughts, how do you account for that? Why would something that would obviously have benefits to any number of species have only appeared in just one, out of millions?

    And if you believe that others, such as builders like birds and beavers, also run ‘immaterial’ concepts through their brains, what are the origins of ‘immateriality’? How do you account for it? Is it pervasive, and if so, why do you exclude it from the idea of genetic activity?

    I am very interested to learn how you demarcate between that which is material and that which isn’t.

  490. 490
    steveO says:

    KF:

    As it turns out, I have taught the UK/Caribbean equivalent of a critical thinking etc course, the A Level General Studies/Paper.

    Sorry, off topic, but KF I didn’t see any resources for teaching critical teaching on your website. Do you have any pointers? I think this is a very important topic for students. A generation is being duped but there’s always hope for the next!

  491. 491
    kairosfocus says:

    SO, There are resources on my reference web, e.g.

    1: Critical Thinking 15 minute primer: http://www.angelfire.com/pro/k.....inking.pdf

    2: Media spin — how to grade the media: http://www.angelfire.com/pro/k.....r_spin.htm

    3: On selective hyperskepticism (a major problem of today’s skeptics): http://www.angelfire.com/pro/k.....ticism.htm

    4: Phil toolkit (a course unit): http://www.angelfire.com/pro/k.....oolkit.htm

    5: Ac 27 and democracy in the hands of the manipulators: http://kairosfocus.blogspot.co.....-year.html

    (I am maxed-out on links more or less so in that RH col of my personal blog, make sure to watch the vid on the parable of Plat’s cave. This one is an eye-opening must-see that sets up specifics.)

    A look in the RH col of my blog will turn up much more:

    http://kairosfocus.blogspot.com/

    KF

    PS: Beyond I highly recommend Internet Encyclopedia of Philosophy for its fallacies page. Too often, fallacies pages or references are themselves biased or loaded with subtle fallacies tied to bias. Nizkor takes that up to the level of dealing with outright agitprop.

  492. 492
  493. 493
    steveO says:

    KF,

    Thank you. A wealth of information as always.

    My experience is that young people are being bombarded with one-sided liberal and materialistic propaganda and fallacies from many sources – TV, Internet, Hollywood, publishing houses, ideologues posturing as scientists and on and on..

    Equipping them with the ability to recognize this is essential!

    Apologies again for the off-topic subject matter.

  494. 494
    Mung says:

    Yes, Carpathian, I also would like to know at which point in the OSI model the data becomes immaterial, and where does it go while immaterial, and then at which layer it becomes material again, and how it transitions from immaterial to material.

    Obviously at the physical layer it must be material, right?

    And the transport layer, I can’t imagine why we would need a transport layer for immaterial data, so that must be material data.

    Does it perhaps go from material to immaterial and back again multiple times depending on the layer?

  495. 495
    kairosfocus says:

    SO, I think it is always present as background. For instance there is a thin line between legitimate appeal to credible conclusions of science (which may require considerable background to properly trace and test) and a fallacious ideological appeal to dominant or just domineering schools of thought. Having a critical thinking context makes a big difference. From your concern maybe the most helpful resource is the one on spin tactics as that allows people to draw conclusions about general trustworthiness, quality and integrity of sources that hold media power. As a good case in point, follow up the WUWT case on Wikipedia: http://wattsupwiththat.com/201.....tle-scary/ and the current tactic of abusing the term “denier” as a general smear: http://www.populartechnology.n.....niers.html also, notice this on dirty tactics when Alinskyite radical hyperskeptics take over a medium of influence: notice the case in point: http://wikipediawehaveaproblem.....le-begins/ also: http://wikipediawehaveaproblem.....asy-steps/ As at now, Wikipedia deserves to be ring fenced off and red flagged as vulnerable to or under the control of angry nihilistic radicals and cranks, sometimes in gangs; except on utterly innocuous topics where the media spin grid gives a pass. A pity, I recently had to go a long way around to find a better reference on difference equations in macro-economics, for instance even though the Wiki section was fit for purpose — given potential polarised rhetoric I had to walk away. Much the same attitudes and tactics target design thinkers or contributors at blogs, and design theory in general. Wiki’s hatchet job on ID has to be seen to be believed. KF

  496. 496
    kairosfocus says:

    Mung, the information proper is not material but the accompanying signal is; when you move to the software (remember, software proper is inherently abstract) that rides on the hardware and the physical behaviour we term signals, we have moved into the world of the abstract and beyond, that of the mental. Protocols are organised, informational, functionally specific and complex — FSCO/I, so it is no wonder that information dismissers will be tempted to play at hyperskeptical games to reject what so patently cuts clean across their cramped vision of the world. KF

    PS: Dictionary.com:

    >>
    software
    [sawft-wair, soft-]

    Examples
    Word Origin

    noun
    1.
    Computers. the programs used to direct the operation of a computer, as well as documentation giving instructions on how to use them.
    Compare hardware (def 5).
    2.
    anything that is not hardware but is used with hardware, especially audiovisual materials, as film, tapes, records, etc.:
    a studio fully equipped but lacking software. >>

  497. 497
  498. 498
    Evolve says:

    UB,

    You’re the one misrepresenting me. I was not talking about the establishment of the genetic code, rather I was saying that there’s no physical discontinuity between the codon and the effect it evokes – the amino acid.
    You claim things like:

    “There is nothing about the physical properties of rocks or sticks that relates them to a message.” – with respect to Morse Code

    “the effect of genetic translation is not determined by the structure of the nucleic codon that evokes the effect”

    This is dead wrong. The physical properties and structure of the codon is what determines its interaction with the anticodon on the corresponding tRNA, which in turn results in the addition of an amino acid to the growing polypeptide chain. Unlike Morse code and computer programs, THERE ARE physical and chemical interactions in the genetic system. The genetic system is decidedly different from man-made codes and there’s no need to invoke intelligence to explain it.

    You further say:
    “not only would the many individual relationships of the coding protocols have to “freeze” together…but the additional systematic protocols required for system function…would also need to “freeze” at the same time”

    No, everything doesn’t have to freeze together. Components could have had a pre-translational origin, for e.g tRNA and the genetic code itself may have originated before translation was in place, see:

    http://www.biologydirect.com/content/6/1/14

    And these components may have co-evolved until an optimally working system was eventually frozen:

    http://www.ncbi.nlm.nih.gov/pubmed/16838217
    http://onlinelibrary.wiley.com.....b.146/full

    Glycine tRNA is interpreted to be the first tRNA to originate and it supports the frozen accident model:
    http://www.biologydirect.com/content/3/1/53

    Ribozymes capable of performing the aaRS function of loading amino acids onto tRNAs have been generated by in vitro evolution, suggesting that RNA could have preceded aaRS before protein synthesis was established:
    http://www.nature.com/nsmb/jou.....00_28.html

    In short, you don’t need all systems to arise at once.

  499. 499
    kairosfocus says:

    Ev, show us actual organisms, please. KF

  500. 500
    CJYman says:

    Evolve:
    Unlike Morse code and computer programs, THERE ARE physical and chemical interactions in the genetic system.

    Where are the non-physical interactions in the application of the Morse code and in computer programs?

  501. 501
    kairosfocus says:

    CJY, layercake, with the physical one the lowest. The software interaction is peer to peer and protocol driven, code/rule/ convention based, but there is a physical level signal, there is hardware, there are natural law and mechanism controlled interactions. However, in principle there will be different possible or actual physical ways to carry out the upper level interactions. This is the sense where there is a cut, a distinction, a discontinuity between the upper stories and the physical one. For just one instance it so happens that tRNAs use a CCA-tip to couple to the COOH end of amino acids and in principle any tRNa could physically hold any AA. Specific enzymes match the configs of different tRNAs and load them appropriately. Variations are possible and are instantiated. This has been pointed out in this thread, just ignored. I should note that things like start and stop codes are also very significant in many ways.. KF

  502. 502
    CJYman says:

    Thanks KF, and I fully understand that, but my question is rhetorical in nature. I still am awaiting a response from Evolve, since Evolve appears to think that the substantial difference between Morse code and computer programs vs the program of life is in ‘non-physical’ interactions. I am extremely curious about what he means by ‘non-physical’ interactions and where specifically they take place within a computer program.

  503. 503
    Andre says:

    KF

    can you please embed a flowchart of how communication works for Evolve…

    You know the one that goes like this

    input encoder medium decoder output.

    I don’t think evolve understands the problems such a system has with accidental processes nor does he understand IC. Please KF. With a little bit of luck a light bulb might go on for him.

  504. 504
    Mung says:

    CJYman, you just don’t understand.

    There is nothing non-physical going on in the cell.
    Therefore everything occurs at the physical layer.
    Therefore there are no protocols.

    Unlike in computers,
    Where non-physical stuff goes on all the time.
    Therefore protocols are required.
    Except in the physical layer.
    There it’s all just physical stuff

  505. 505
    Mung says:

    Evolve: You’re the one misrepresenting me.

    This cracks me up. You’re the one who claimed that “God has decided which codon should represent which amino acid…” represents what UB said.

    Where did he ever say that?

  506. 506
    Mung says:

    Evolve, if there were no discontinuity between the codon and the amino acid there would be no need for an adaptor.

  507. 507
    Andre says:

    Evolve

    Your supposed objections are noted but are laughable. Accidents don’t build protocols.

  508. 508
    kairosfocus says:

    Andre, took a bit of work to put in all I eventually thought advisable, but here it is:

    http://www.uncommondescent.com.....ork-model/

    I bet you it will make little difference to those determined to dismiss the idea that coded information and linked communication systems are involved in the living cell.

    But, that itself will speak volumes on what is really going on.

    KF

  509. 509
    Andre says:

    KF

    You are a scholar and a gentleman. Thank you.

    Evolve apply our mind on the problem of why accidental processes, can’t have any success in building any type of communication system, to think it can is absurd. Are you absurd?

  510. 510
    EugeneS says:

    KairosFocus #499,

    I haven’t read a wiki article on the RNA world in English, but in Russian it is hilarious. The most interesting bits go like this:

    -“after the emergence of protein synthesis…” (bingo!)
    -“when a more reliable mechanism for information storage appeared…”
    -“having separated themselves from the world by a lipid membrane”
    – “were obtained by way of artificial evolution” (by far the best of all)

    It is an amusing “just so happened” kind of read.

    BTW, one of the two reviewers of the first reference given by Evolve is Eugene Koonin, the author of the multiverse concept. I gather he fully understands the issue with plausibility.

  511. 511
    kairosfocus says:

    Andre, I have added a generic layer-cake model, for completeness. KF

  512. 512
    kairosfocus says:

    Dr Selenski, yup, the discomfort is palpable. Reality is knocking at the door: behold, I stand at the door and knock — how does that read in Russian, BTW. KF

  513. 513
    EugeneS says:

    KF,

    Unfortunately, Cyrillic symbols are not displayed correctly when posted here due to encoding problems (here we go, protocols again 🙂 Apologies. BTW, a very nice note on OSI and the cell. Thanks. It must be discomforting.

  514. 514
    groovamos says:

    Carpathian: The grooves in the record physically move the needle to produce an electrical charge in the tone arm’s cartridge.

    There is no immaterial data component or exchange of data which would be required by a protocol.

    Everything that happens with a vinyl record happens with DNA.

    It is purely physical and no immaterial data is required or produced.

    If I’m wrong, show me the information that is received by the DNA.

    Show me some protocol where data is exchanged equivalent to a communications exchange between computers.

    See this is what happens when there is confusion about what is the nature of information. It would be totally silly to maintain that there is no useful information in that vinyl record. And the protocol for the information on the vinyl is composed of the engineering specifications for all of the hardware including all of the mechanical, electrical and electromechanical specs, e.g. 33-1/3 rpm (electromechanical), 20~20kHz (electrical), groove dimensions and maximum deflection (mechanical). These specs are themselves information as are comm protocols.

    Before there can be useful information there must be a mind to deem it useful. Every modern communication system is built along an analog channel, the only exceptions being very short distance pulsed links like memory buses, expansion buses, ATA disk interfaces USB, RS-232, etc. All of those are strictly digital pulsed. Ethernet and all comm links over a controlled channel or band are digitally encoded analog link (biphasic, QAM etc) as are all telecom links.

    So to say an analog process does not convey information is totally bogus, anything using antennae and rf channels are being conveyed over real world conditions and the real world is analog. Light entering your camera lens is real world, and the CMOS or CCD sensor chip at the heart of your camera is analog even though people are accustomed to saying “digital camera”.

    Anything that can be put to use by a mind is information. Your belief that analog processes cannot convey information is itself information; you put it into characters showing up on our screens. But your fingers moved to do that and your fingers are analog like that phono needle. And it is your opinion that the belief is useful information, my opinion is that your belief is useful for something other than the use to which you put to it.

    You may however possess information that I do not have regarding how information is processed in the cell and it may be very useful to me, because like the engineering data to build the phonograph, the cell is also built using information.

    I have a textbook by Carlson (Introduction To Signals and Noise in Electrical Communication) which devotes one chapter to information theory. (here: http://posterwall.com/blog_att.....1318295130) The very next chapter specifically sets out to apply insights from the previous regarding digital commmunications, applied to strictly analog systems like broadcast FM. Playing hit vinyl records.

  515. 515
    kairosfocus says:

    Dr Selenski, let us see how our friends interact with what was put up. I decided to pull together a more specific layer-cake diagram, which makes the matter fairly generic. Of course, Yockey is showing a second transmit side process with the loading of tRNA’s and shows mis-loading as a noise source. That one is actually a complicated process as it seems the loading enzymes respond to overall config, not the anticodon. KF

    PS: I was wondering how the usual Russian rendering translates directly, literally.

  516. 516
    kairosfocus says:

    F/N: Carpathian, look up RIAA equalisation — something I have not thought about in literally 30 years: http://en.wikipedia.org/wiki/RIAA_equalization

    KF

  517. 517
    Carpathian says:

    groovamos:

    It would be totally silly to maintain that there is no useful information in that vinyl record.

    I never said there was no information, I said there was no protocol.

    You never ACK or NAK any information coming from a vinyl record.

    A protocol operates above the level of data.

    For instance, you can send TCP/IP packets over any physical medium and you can even embed this protocol as data carried by another protocol.

    My problem with Upright BiPed’s use of the term protocol is that he applies it in a static non-intelligent environment.

    How can a record ACK my request for a data packet?

    This sort of bi-directional communication is required for a protocol.

    You need intelligence on both ends of the link.

    A vinyl record does not possess a protocol to even establish the link.

  518. 518
    Carpathian says:

    groovamos:

    Every modern communication system is built along an analog channel, the only exceptions being very short distance pulsed links like memory buses, expansion buses, ATA disk interfaces USB, RS-232, etc.

    There are actually no exceptions at all but the data carried by the medium, is completely unrelated to how it is delivered.

    This again in no way suggests that a protocol is present.

    The presence of information is not related in any way to the protocol.

  519. 519
    kairosfocus says:

    Carpathian, RIAA is a classic example of a protocol, as are AM, FM, SSB, etc. in the context of radio. KF

    PS: Note, Wiki:

    The RIAA equalization curve was intended to operate as a de facto global industry standard for records since 1954. However, it is almost impossible to say when the change actually took place.[1]

    Before then, especially from 1940, each record company applied its own equalization; there were over 100 combinations of turnover and rolloff frequencies in use, the main ones being Columbia-78, Decca-U.S., European (various), Victor-78 (various), Associated, BBC, NAB, Orthacoustic, World, Columbia LP, FFRR-78 and microgroove, and AES.

    This illustrates how co-ordination and convention are relevant to protocols. And obviously, those grooves are not a simple analogue of the vibrations impressed into electrical form by a microphone . . . . which itself implies protocols on mike design and recording head design, much less playback cartridge, it’s not “simple” transducer action, there is a lot of analogue signal processing.

  520. 520
    kairosfocus says:

    PPS: Note this further on RIAA:

    >> RIAA equalization is a form of pre-emphasis on recording and de-emphasis on playback. A recording is made with the low frequencies reduced and the high frequencies boosted, and on playback the opposite occurs. The net result is a flat frequency response, but with attenuation of high frequency noise such as hiss and clicks that arise from the recording medium. Reducing the low frequencies also limits the excursions the cutter needs to make when cutting a groove. Groove width is thus reduced, allowing more grooves to fit into a given surface area, permitting longer recording times. This also reduces physical stresses on the stylus which might otherwise cause distortion or groove damage during playback.

    A potential drawback of the system is that rumble from the playback turntable’s drive mechanism is amplified by the low frequency boost that occurs on playback. Players must therefore be designed to limit rumble, more so than if RIAA equalization did not occur.

    RIAA equalization is not a simple low-pass filter. It defines transition points in three places: 75 µs, 318 µs and 3180 µs, which correspond to 2122 Hz, 500 Hz and 50 Hz (rounded values).[2] Implementing this characteristic is not especially difficult, but is more involved than a simple amplifier.[3] In the past, almost all hi-fi preamplifiers, integrated amplifiers, and receivers had a built-in phono preamplifier with the RIAA characteristic, but it is often omitted in modern designs, due to the gradual obsolescence of vinyl records. Add-on phono preamplifiers with the RIAA equalization curve are available; these adapt a magnetic phono cartridge to an unbalanced ?10 dB consumer line-level RCA input. Some modern turntables feature built-in preamplification to the RIAA standard. Special preamplifiers are also available for the various equalization curves used on pre-1954 records.

    Digital audio editors often feature the ability to equalize audio samples using standard and custom equalization curves, removing the need for a dedicated hardware preamplifier when capturing audio with a computer. However, this can add an extra step in processing a sample, and may amplify audio quality deficiencies of the sound card being used to capture the signal.>>

  521. 521
    kairosfocus says:

    PPPS: More, on the background:

    >> Equalization practice for electrical recordings dates to the beginning of the art. In 1926 Joseph P. Maxwell and Henry C. Harrison from Bell Telephone Laboratories disclosed that the recording pattern of the Western Electric “rubber line” magnetic disc cutter had a constant velocity characteristic. This meant that as frequency increased in the treble, recording amplitude decreased. Conversely, in the bass as frequency decreased, recording amplitude increased. Therefore, it was necessary to attenuate the bass frequencies below about 250 Hz, the bass turnover point, in the amplified microphone signal fed to the recording head. Otherwise, bass modulation became excessive and overcutting took place, with the cutter into the next record groove. When played back electrically with a magnetic pickup having a smooth response in the bass region, a complementary boost in amplitude at the bass turnover point was necessary. G. H. Miller in 1934 reported that when complementary boost at the turnover point was used in radio broadcasts of records, the reproduction was more realistic and many of the musical instruments stood out in their true form.

    West in 1930 and later P. G. H. Voight (1940) showed that the early Wente-style condenser microphones contributed to a 4 to 6 dB midrange brilliance or pre-emphasis in the recording chain. This meant that the electrical recording characteristics of Western Electric licensees such as Columbia Records and Victor Talking Machine Company had a higher amplitude in the midrange region. Brilliance such as this compensated for dullness in many early magnetic pickups having drooping midrange and treble response. As a result, this practice was the empirical beginning of using pre-emphasis above 1,000 Hz in 78 and 331?3 rpm records, some 29 years before the RIAA curve.

    Over the years a variety of record equalization practices emerged and there was no industry standard. For example, in Europe, for many years recordings required playback with a bass turnover setting of 250 to 300 Hz and a treble rolloff at 10,000 Hz ranging from 0 to ?5 dB, or more. In the United States there were more varied practices and a tendency to use higher bass turnover frequencies, such as 500 Hz, as well as a greater treble rolloff like ?8.5 dB, and more. The purpose was to record higher modulation levels on the record.>>

  522. 522
    kairosfocus says:

    PPPPS: Standardisation:

    Evidence from the early technical literature concerning electrical recording suggests that it was not until the 1942–1949 period that there were serious efforts to standardize recording characteristics within an industry. Before this time, electrical recording technology from company to company was considered a proprietary art all the way back to the 1925 Western Electric licensed method first used by Columbia and Victor. For example, what Brunswick-Balke-Collender (Brunswick Corporation) did was different from the practices of Victor.

    Broadcasters were faced with having to adapt daily to the varied recording characteristics of many sources: various makers of “home recordings” readily available to the public, European recordings, lateral cut transcriptions, and vertical cut transcriptions. Efforts were started in 1942 to standardize within the National Association of Broadcasters (NAB), later known as the National Association of Radio and Television Broadcasters (NARTB). The NAB, among other items, issued recording standards in 1949 for laterally and vertically cut records, principally transcriptions. A number of 78 rpm record producers as well as early LP makers also cut their records to the NAB/NARTB lateral standard . . . .

    Between 1953 and 1956 (before the stereo LP in 1958) several standards bodies around the world adopted the same playback curve—identical to the RCA Victor New Orthophonic curve—which became standard throughout the national and international record markets.[6] However, although these standards were all identical, no universal name was used. One of the standard was called simply “RIAA”, and it is likely that this name was eventually adopted because it was memorable.

    It is possible that some niche record cutters were still using EQ curves other than the RIAA well into the 1970s. As a result, some audio manufacturers today produce Phono Equalizers with selectable EQ curves, including options for Columbia, Decca, CCIR, and TELDEC’s Direct Metal Mastering.

    For convenience, again, Wiki:

    In telecommunications, a communication protocol is a system of rules that allow two or more entities of a communication system to communicate between them to transmit information via any kind of variation of a physical quantity. These are the rules or standard that defines the syntax, semantics and synchronization of communication and possible error recovery methods. Protocols may be implemented by hardware, software, or a combination of both.[1]

    Communicating systems use well-defined formats (protocol) for exchanging messages. Each message has an exact meaning intended to elicit a response from a range of possible responses pre-determined for that particular situation. The specified behavior is typically independent of how it is to be implemented. Communication protocols have to be agreed upon by the parties involved.[2] To reach agreement, a protocol may be developed into a technical standard. A programming language describes the same for computations, so there is a close analogy between protocols and programming languages: protocols are to communications as programming languages are to computations.[3]

  523. 523
    kairosfocus says:

    Andre, notice how almost studiously divergent matters being raised are to what was shown at your request a little earlier:

    http://www.uncommondescent.com.....ork-model/

    KF

    PS: I guess in a digital age, it is important to point out that very similar cases obtain for analogue systems.

    PPS: Notice, what Crick wrote to his son.

  524. 524
    Mung says:

    Carpathian:

    How can a record ACK my request for a data packet?

    This sort of bi-directional communication is required for a protocol.

    And then there are the connection-less protocols such as IP and UDP.

    Connectionless Protocol – techopedia

    A connectionless protocol is a form of data transmission in which an IT signal goes out automatically without determining whether the receiver is ready, or even whether a receiver exists. Connectionless protocol is an alternative to some conventional connection-based forms of data transmission, which often involve setting up dedicated handshaking or device connectivity checks.

    Sorry Carpathian, but you’re obviously not the only nerd present, so you can’t jsut continue to make things up and expect to get away with it.

    🙂

    I wonder if the aliens will need to set up a handshaking protocol before they can send us message.

  525. 525
    Mung says:

    …the noise reducing operations of source coding and channel coding are unproblematic when the messages consist of discrete characters, or digits, but it is virtually impossible to remove noise from analog signals, and it is for this reason that industry and media have steadily moved from analog to digital technologies.

    – Marcello Barbieri, Code Biology: A New Science of Life

    Wait for it … yes … more biosemiotics. aaarrrgghhh!

    Information Theory and Error-Correcting Codes In Genetics and Biological Evolution

    Be sure to read the abstract. Maybe I will post it.

  526. 526
    Carpathian says:

    Mung: UDP packets have a protocol.

    The link that must be established must still be there for a UDP packet.

    UDP packets do not require an ACK.

    That does not mean that they don’t have to adhere to a protocol.

  527. 527
  528. 528
    Mung says:

    Carpathian: UDP packets have a protocol.

    Uh, yeah. That’s sort of the point sir!

  529. 529
    Carpathian says:

    kairosfocus:

    Carpathian, RIAA is a classic example of a protocol, as are AM, FM, SSB, etc. in the context of radio. KF

    No it’s not an example of a protocol at all.

  530. 530
    Carpathian says:

    Mung:

    Carpathian: UDP packets have a protocol.

    Mung: Uh, yeah. That’s sort of the point sir!

    And biology doesn’t.

    You are my best ally.

  531. 531
    Carpathian says:

    Mung:

    And the transport layer, I can’t imagine why we would need a transport layer for immaterial data, so that must be material data.

    I believe you should get some help from kairosfocus since you don’t seem to be able to understand what a protocol stack is.

  532. 532
    kairosfocus says:

    Carpathian, RIAA is an industry standard for communication, based on agreements such that what is stored in the grooves of a typical LP is NOT a direct, simple result of transducer action; where also, the imposed pattern is embedded in the physical medium and can in principle be inferred from it by examination of the frequency-linked characteristics. That makes it a protocol in an analogue context; especially given the existence of other alternative standards. I am responding to your earlier claims that clearly suggested such. KF

  533. 533
    kairosfocus says:

    Andre, notice the pattern? KF

    PS: Again, so it’s not conveniently buried: http://www.uncommondescent.com.....ork-model/

  534. 534
    Mung says:

    Carpathian: I believe you should get some help from kairosfocus since you don’t seem to be able to understand what a protocol stack is.

    You never learn do you. First you claimed I didn’t know anything about programming, now you claim I don’t know anything about what a protocol stack is. Funny.

    Sent any immaterial data lately? Did you use *magical poof* to make sure it reached the intended destination?

  535. 535
    CJYman says:

    Carpathian you are making stuff up as you go along. It is blindingly obvious to those of us who are even somewhat familiar with communications protocols.

    Carpathian:
    “My problem with Upright BiPed’s use of the term protocol is that he applies it in a static non-intelligent environment.

    How can a record ACK my request for a data packet?

    This sort of bi-directional communication is required for a protocol.”

    …and then …

    Carpathian:
    “UDP packets do not require an ACK.

    That does not mean that they don’t have to adhere to a protocol.”

    So which is it? Handshakes are required or handshakes are not required as per the definition of a communications protocol?

  536. 536
    Mung says:

    In the 1960s, Howard Pattee pointed out that the theory of self-replicating machines developed by John von Neumann in the 1950s throws an important light on the genetic code. Von Neumann had shown that a self-replicating system must contain a description of itself, and such a description must be categorically different [Mung: think discontinuity] from the system (‘the map is not the territory’). The description of a system, on the other hand, is necessarily made of entities that represent or, ‘stand for’, its material components, and function therefore as signs or symbols. According to von Neumann, in short, a self-replicating system must be a physical system controlled by symbols, or, more precisely, by a program, by the rules of a code.

    – Marcello Barbieri

  537. 537
    Carpathian says:

    CJYman:

    So which is it? Handshakes are required or handshakes are not required as per the definition of a communications protocol?

    It is intelligence at both sides of a link that is required for a protocol.

    Even though an ACK may not be required, the data and header in a UDP packet is still determined by a protocol.

  538. 538
    Mung says:

    Carpathian: … the data and header in a UDP packet is still determined by a protocol.

    How is the data determined?

    http://tools.ietf.org/html/rfc768

  539. 539
    Carpathian says:

    Mung:

    You never learn do you. First you claimed I didn’t know anything about programming, now you claim I don’t know anything about what a protocol stack is. Funny.

    You don’t.

    If you had enough programming experience with communications and protocols, you wouldn’t come up with the statements you do.

  540. 540
    Carpathian says:

    Mung:

    Carpathian: … the data and header in a UDP packet is still determined by a protocol.

    Mung: How is the data determined?

    The protocol defines the location of the data, along with any integrity checks. The protocol will also define the char set.

    0 7 8 15 16 23 24 31
    +——–+——–+——–+——–+
    | Source | Destination |
    | Port | Port |
    +——–+——–+——–+——–+
    | | |
    | Length | Checksum |
    +——–+——–+——–+——–+
    |
    | data octets …
    +—————- …

    User Datagram Header Format

  541. 541
    CJYman says:

    Carpathian:
    “It is intelligence at both sides of a link that is required for a protocol.”

    But before you stated that an ack was required for a protocol to exist. That was obviously incorrect. According to what definition is intelligence required and how do you define intelligence, and how does someone reading this know you aren’t just making it up as you go.

    Where would be the best resource to double check on your facts and definitions? You seem to be extremely sure that you know the one correct definition of ‘protocol’ as it relates to communication. Thus I’m sure you are aware of the few different definitions contained in the IEEE standards definition database, correct?

  542. 542
    Mung says:

    Carpathian,

    1. how does the specification of the location of the data determine the data? You claimed the data is determined by a protocol. That is obviously wrong.

    2. Where and how does the UDP protocol define the char set? Why does the char set even matter?

    Let me answer those for you so we don’t waste any more time on idiotic assertions. 1) It doesn’t. 2) It doesn’t.

  543. 543
    Carpathian says:

    Mung:

    1. how does the specification of the location of the data determine the data? You claimed the data is determined by a protocol. That is obviously wrong.

    You cannot simply put data anywhere you want.
    The protocol tells you where you put your data, the restrictions on that data and any data integrity you must apply to that data.

    The data IN the packet, provided it meets the standard is up to you.

    That is not what we see in biology. The “data” is one time chemically fixed.

    UDP is not a protocol, it’s a data packet type.

    It stands for Unacknowledged Data Packet.

    That’s why we don’t ACK, i.e. acknowledge the packet.

    I believe you have very little experience working with protocols, otherwise you wouldn’t ask these sort of basic questions.

  544. 544
    Mung says:

    Carpathian, at this point I must conclude that you pay no attention to what you write. It’s strictly fire and forget.

    You cannot simply put data anywhere you want.

    If course I can. I can bury it in the back yard if I so choose. I can feed it to my cat.

    The data IN the packet, provided it meets the standard is up to you.

    Of course it is. And if I choose to put no data in the packet I can do that too.

    But in your post @ 537 you said the data was determined by the protocol. So that was false. Untrue.

    UDP is not a protocol, it’s a data packet type.

    False. Untrue.

    The User Datagram Protocol (UDP) is one of the core members of the Internet protocol suite. The protocol was designed by David P. Reed in 1980 and formally defined in RFC 768

    I even provided a link to it.

    It [UDP] stands for Unacknowledged Data Packet.

    lol. Does IDP stand for Immaterial Data Packet?

  545. 545
    mike1962 says:

    Carpathian: [UDP] stands for Unacknowledged Data Packet.

    Milk. Through. Nose.

    http://en.wikipedia.org/wiki/U.....m_Protocol

    Of course, UDP is a protocol. A protocol is the set of rules by which communications are governed between entities whether we’re talking about bowing before the queen before she acknowledges your existence, or sending data from one computer process to another. This is going from bad to loony.

    Mung, you have the patience of Job.

    Mung: Does IDP stand for Immaterial Data Packet?

    Haha.

  546. 546
    Andre says:

    Carpathian

    UDP is a protocol and its part of the TCP/IP suite, it is not called Unacknowledged Data Packet it is in fact called;User Datagram Protocol

    UDP (User Datagram Protocol) is a communications protocol that offers a limited amount of service when messages are exchanged between computers in a network that uses the Internet Protocol (IP). UDP is an alternative to the Transmission Control Protocol (TCP) and, together with IP, is sometimes referred to as UDP/IP.

    You are correct that it does not require an ACK and its because its a broadcasting protocol in the TCP/IP stack.

  547. 547
    kairosfocus says:

    Carpathian,

    I will continue a bit on protocols as a functional, descriptive term for

    “a system of rules that allow two or more entities of a communication system to communicate between them to transmit information via any kind of variation of a physical quantity. These are the rules or standard that defines the syntax, semantics and synchronization of communication and possible error recovery methods . . . protocols are to communications as programming languages are to computations”

    . . . by going on to stereophonic vinyl records and the appropriate write/read heads.

    My point is, that “protocol” is not an arbitrary brand name that may be restricted by fiat, but denotes the need for standard frameworks for communication systems to work to move information from point A to point B, including via storage.

    And, the track of an LP is a spiralled, linear analog string with a built in temporal sequencing . . . likely rooted in the way a cam and cam follower work, which immediately implies that this technology can be used for process, sequence or servo system control and even coded information storage. In addition, two channels of information are modulated into the variation of two orthogonal sides of a v-shaped groove that is fitted to a needle that excites two transducers that extract the information as it is advanced at the specified rate of 33 1/3 RPM. That rate being enforced by use of a stroboscopic pattern on the side of the platter. Even the central spindle is a part of the specification.

    For that matter, the choice of stereo with two-track records was set up to sufficiently mimic the natural temporal displacement of sounds reaching our ears that gives spatial directivity.

    This was then set up to be recorded by allowing the depth and lateral displacement of two orthogonal sides of a V-track to vary, putting the two transducers at 45 degrees to vertical . . . a technical compromise.

    Cf: http://www.harryshifi.com/imag.....torial.pdf

    Notice, the tech requirements here:

    http://www.megaton.si/Technica.....-vinyl.pdf

    This of course leads logically to FM stereo, AM stereo and the vestigial sideband analogue TV signal (esp. colour!) in multiple formats, most significantly NTSC and PAL/SECAM.

    My point is, that whether one is on the digital encoding or the analogue modulation side of things, communication systems are irreducibly complex purposefully functional arrangements of correct, mutually adapted components with associated standards. Standards may often be stated verbally and/or pictorially — and engineering drawings have their own protocols — but are also necessarily embedded in the objective system components, the hardware and software. And protocol clusters and stacks are relevant. Including those for storage media.

    All of this points straight back to the significance of functionally specific, complex [quite often, with an irreducible core] organisation and associated information — FSCO/I. (A descriptive term.)

    In this context I should note that there are multiple modalities in communication, broadcast, intermediate use of storage, half and full duplex come to mind, with always the issue of mutual standards and need for initiation to set up the receive side to adequately capture what was sent on the transmit side.

    Protocols are everywhere — think even dictionaries, and together with associated FSCO/I, point strongly to co-ordinated design.

    KF

  548. 548
    kairosfocus says:

    Andre, notice what seems to studiously not be on the table:

    http://www.uncommondescent.com.....ork-model/

    KF

  549. 549
    Mung says:

    We reach in this way the conclusion that every living cell contains all four components of semiosis (signs, meanings, code and codemaker) and is therefore a real semiotic system.

    – Marcello Barbieri, Code Biology: A New Science of Life

  550. 550
    Carpathian says:

    Andre:

    UDP is a protocol and its part of the TCP/IP suite, it is not called Unacknowledged Data Packet it is in fact called;User Datagram Protocol

    You are absolutely right.

    Every now and then my fallible memory shows itself.

    It’s been years since I’ve done any work with this stuff.

    This however in no way means that the cell has a protocol involved.

    My memory failings don’t change science.

    The cell has no protocol and semiosis is not used before the fact.

  551. 551
    Carpathian says:

    Mung:

    Here is a part of what it takes to implement a protocol driver.

    #define HDLC_EscapeBit 0x20

    unsigned HDLC_State;

    enum { HDLC_State_AwaitingOpeningFlag
    , HDLC_State_AwaitingClosingFlag
    , HDLC_State_ReceivedFrame
    };

    unsigned PPP_State;

    enum { PPP_State_LinkDead
    , PPP_State_LinkEstablishment
    , PPP_State_LCP_LocalOptions
    , PPP_State_LCP_LocalOptions_AwaitResp
    , PPP_State_LCP_LocalOptions_AwaitResp_2
    , PPP_State_LCP_LocalOptions_AwaitResp_3
    , PPP_State_LCP_LocalOptions_AwaitResp_4
    , PPP_State_AuthenticationPhase
    , PPP_State_NetworkLayerProtocolPhase
    , PPP_State_LinkTerminationPhase
    };

    Here’s more:

    HDLC_fcs = PPPINITFCS16;

    if( uiLen && pSrc && pDest && (uiLen > 8) ^ fcstab[(HDLC_fcs ^ HDLC_AllStationsAddress) & 0xff];

    pDest[TxCount++] = HDLC_Control_Esc;
    pDest[TxCount++] = HDLC_Control_Field ^ HDLC_EscapeBit;

    HDLC_fcs = (HDLC_fcs >> 8) ^ fcstab[(HDLC_fcs ^ HDLC_Control_Field) & 0xff];

    ..and more:

    while( pFrame->State != HDLC_State_ReceivedFrame )
    {

    if( SerialRead( pConnection->uiHandle, &ucHDLC_Octet, 1 ) == 0 )
    {
    break;
    }

    switch( pFrame->State )
    {
    case HDLC_State_AwaitingOpeningFlag:
    pFrame->EscapeFlag = 0;
    pFrame->Count = 0;
    pFrame->State = HDLC_State_AwaitingClosingFlag;
    pFrame->fcs = PPPINITFCS16;

    if( ucHDLC_Octet == HDLC_FlagSequence )
    {
    break;
    }

    case HDLC_State_AwaitingClosingFlag:

    if( ucHDLC_Octet == HDLC_FlagSequence)
    {
    if( pFrame->Count == 0 )
    {
    pFrame->EscapeFlag = 0;
    pFrame->fcs = PPPINITFCS16;

    break;
    }

    Nothing like this happens in the cell.

  552. 552
    mike1962 says:

    Carpathian: Nothing like this happens in the cell.

    Nothing like a subject of the Crown bowing before the Queen or a servant pouring wine in a glass happens in a cell either. So what? Protocols can be implemented in numerous ways, in numerous media. What makes a protocol a protocol is a previously agreed upon set of rules governing communication.

    What’s going on in a cell and protein synthesis is wildly more ingenious and interesting than your C code above. And if you don’t think the codon/ribosome protein synthesis system utilizes a protocol (e.g, why precisely three nucleotides to a codon, and what the hell does a stop-codon do?) then that’s your problem.

  553. 553
    mike1962 says:

    Carpathian: Every now and then my fallible memory shows itself. It’s been years since I’ve done any work with this stuff.

    What does your fallible memory have to do with that fact that the point you were trying to make was patently wrong. You didn’t merely get the name wrong, you claimed UDP is not a protocol. Your memory of the name of the protocol has nothing to do with the fact that you denied UDP is a protocol.

  554. 554
    Mung says:

    I bet there’s no C compiler in the cell either. So therefore no code. No RAM chips, so no memory in the cell. And no CPU in the cell either. Therefore no processing.

    I could go on and on.

  555. 555
    groovamos says:

    carpathian: There are actually no exceptions at all but the data carried by the medium, is completely unrelated to how it is delivered.

    No exceptions to non-baseband digital communications links such as ethernet exist? How so? point us to some knowledgeable source on that please.

    This again in no way suggests that a protocol is present.

    ????

    The presence of information is not related in any way to the protocol.

    why the hang up on protocols? This is nothing but deflection. I made a wide angle view statement that all machinery around the exchange of information is itself built on information. Whether that machinery is built on software/hardware or hardware only should present no either/or scenario to grapple with. This is all obfuscation based around software engineering which can be dispensed with. You made the statement that, vague as it reads, seems to say that a phonograph record and playback apparatus is not used in information transfer. Which if that is what is being said, is bogus.

    Making the argument dependent on a software engineering point of view is obfuscation.

  556. 556
    Mung says:

    the stereochemical hypothesis

    …the first models of the genetic code were all based on the stereochemical hypothesis, the idea that the coding rules are dictated by chemical relationships in three dimensions, whereas language is made of arbitrary conventions. Eventually, however, the stereochemical hypothesis had to be abandoned because it became clear that the rules of the genetic code are not the result of chemical necessity. In this sense they are as arbitrary as the rules of language, and this makes us realize that at the molecular level there is not only recursion but also arbitrariness.

    – Marcello Barbieri, Code Biology

  557. 557
    Andre says:

    Do people know what protocol actually mean or are we going to differ on its meaning?

  558. 558
    Mung says:

    Hi Andre, We’re trying to define a protocol for how we will go about defining the meaning of protocol.

    Any suggestions?

  559. 559
    kairosfocus says:

    Andre,

    the general and relevant meanings are readily accessible and clips have been given. Relevant here is a Wiki clip:

    In telecommunications, a communication protocol is a system of rules that allow two or more entities of a communication system to communicate between them to transmit information via any kind of variation of a physical quantity. [–> notice, generality, which goes beyond particular discrete-state cases, albeit such cases are particularly important in creating the concept behind the term] These are the rules or standard that defines the syntax, semantics and synchronization of communication and possible error recovery methods. Protocols may be implemented by hardware, software, or a combination of both.[1]

    Communicating systems use well-defined formats (protocol) for exchanging messages. [–> Format, of course extends beyond discrete state, and in fact all real world signals are analogue [consider impacts of power supply glitches and the role of decoupling capacitors if you doubt me], certain imposed standards and thresholds. Each message has an exact meaning intended to elicit a response from a range of possible responses pre-determined for that particular situation. The specified behavior is typically independent of how it is to be implemented. Communication protocols have to be agreed upon by the parties involved.[2] To reach agreement, a protocol may be developed into a technical standard. A programming language describes the same for computations, so there is a close analogy between protocols and programming languages: protocols are to communications as programming languages are to computations.[3]

    In recent times digital comms has dominated and handshaking too, so I think there is a tendency of overly specific focus. The blunder above by an objector, on User Datagram PROTOCOL (it’s right there in the name) is emblematic.

    Wiki is again instructive, speaking against known ideological bias:

    The User Datagram Protocol (UDP) is one of the core members of the Internet protocol suite. The protocol was designed by David P. Reed in 1980 and formally defined in RFC 768.

    UDP uses a simple connectionless transmission model with a minimum of protocol mechanism. It has no handshaking dialogues, and thus exposes any unreliability of the underlying network protocol to the user’s program. There is no guarantee of delivery, ordering, or duplicate protection. UDP provides checksums for data integrity, and port numbers for addressing different functions at the source and destination of the datagram.

    With UDP, computer applications can send messages, in this case referred to as datagrams, to other hosts on an Internet Protocol (IP) network without prior communications to set up special transmission channels or data paths. UDP is suitable for purposes where error checking and correction is either not necessary or is performed in the application, avoiding the overhead of such processing at the network interface level. Time-sensitive applications often use UDP because dropping packets is preferable to waiting for delayed packets, which may not be an option in a real-time system.[1] If error correction facilities are needed at the network interface level, an application may use the Transmission Control Protocol (TCP) or Stream Control Transmission Protocol (SCTP) which are designed for this purpose.

    The protocol context is that of interaction and a standardised programme of correct behaviour. That’s why the term was borrowed from the context of diplomacy, courts of law and royal courts. There is no reason to confine it to discrete state cases — which in reality are also analogue anyway.

    As my response to your diagram request shows, the logic of what is going on is primary, attached labels, secondary:

    1 –> To communicate there must be a co-ordinated in-commonness of corresponding elements . . . hence

    2 –> the natural emergence of layered peer units in the comms system. As well,

    3 –> we naturally have start point and destination and wish to send an understandable message.

    4 –> This leads to standards, specifications and co-ordination regarding:

    – transduction,

    – modulation and/or encoding,

    – ports/interfaces [at all sorts of levels, well do I recall incoming/outgoing specs for TTL, CMOS & ECL logic and for UARTs],

    – power amplification and coupling to a channel/medium,

    – detection of a message at the receiving end,

    – demod and decoding,

    – presentation to the sink.

    5 –> All of this naturally leads to a need for standards within a comms system, and standardisation naturally tends to spread where there is an incentive to be in mutual communication, e.g. the spreading of AM radio and stereophonic records [the fate of quadraphonic records is instructive on failure to meet reasonable accord]

    6 –> Terms for such standards, such as codes, modulation systems and protocols are secondary to the underlying realities they describe.

    7 –> The dividing line here is that

    – codes address content that uses discrete state elements [e.g. alphanumeric characters, codons for genes, binary digits],

    – protocols are concerned with setting up co-ordinated communication with due regard to the natural layer-cake effect, and

    – mod/demod is concerned with encapsulating, sending, propagating and receiving then recovering signals in the midst of noise (and having regard to bandwidth and channel capacity issues).

    8 –> The upshot is, that once communication becomes a significant, non-trivial task, standards and a complex framework of specific rules embedded in the organisation of functional elements leads to a system that is in itself information-rich.

    9 –> That is, any complex communication system implies functionally specific complex [irreducibly so in fact — all of the core has to be there and has to be right for the whole to work] organisation and associated information, FSCO/I.

    10 –> FSCO/I, per trillions of observed cases, has just one empirically known source, design; a point backed up by the needle-in-haystack blind chance and necessity search challenge. Regardless of dismissive rhetoric to the contrary.

    11 –> And in the discrete signal case, we further deal with code, which is a manifestation of a phenomenon that in itself strongly points to verbalising intelligence as root cause.

    12 –> Where, when we come across entities that manifest FSCO/I like this, the underlying FSCO/I is embedded in the organisation of the system and

    13 –> it can therefore in principle be retrieved and measured by analysing the system and subsystems on node-arc networks and devising a reasonable structured chain of Y/N q’s to specify the description.

    14 –> The chain length of y/n q’s then is an index in functionally specific bits, of the info content of the organisation.

    15 –> Such holds for hardware and for software insofar as the latter is embedded in moving or stored signals.

    So, we see how the underlying logic of communication systems of any significant complexity points to design as credible source, due to the embedded FSCO/I.

    In the world of the cell, as Yockey summarised in his diagram (cf. the just linked) and as we can see in action in other diagrams and a video there, the protein synthesis system embeds a communication system pivoting on D/RNA as string data structure coded elements that hold regulatory and assembly instructions as well as the content of such.

    Where, too, the proteins, functional RNAs etc that come from the code further show FSCO/I that is remote from the physical-chemical action steps involved in the communication and assembly process. (Think, string chaining –> folding –> agglomeration and activation –> biofunction.)

    Next, for proteins and proteinaceous enzymes [I here distinguish ribozymes], the functionally relevant configs are deeply isolated in AA sequence space, and for that matter AA-AA peptide bonds are themselves not the only chemically relevant possibilities in play.

    Now, it is quite evident that cumulatively such strongly points to intelligently directed highly skilled configuration as cause, i.e. design.

    But, it is predictable that such a conclusion will be stoutly resisted by all sorts of rhetorical artifices, due to a priori commitment to evolutionary materialism.

    If you doubt me, note Lewontin in his notorious 1997 NYRB remark:

    It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes [[–> another major begging of the question . . . ] to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute [[–> i.e. here we see the fallacious, indoctrinated, ideological, closed mind . . . ], for we cannot allow a Divine Foot in the door. [Those tempted to cry the accusation, quote-mining should see the annotated fuller cite as linked]

    Until that ideological bewitchment is exposed, highlighted as a crude fallacy, and becomes utterly untenable as a violation of the vision of seeking empirically warranted truth that gave science the credibility it had, there will be no willingness to receive anything counter to such ideological closed-mindedness, no matter how compelling.

    Hence my emphasis on showing the facts and inviting the reasonable onlooker to see for him- or her- self what is going on.

    KF

  560. 560
    Andre says:

    KF

    Thank you for that. The question was probably directed incorrectly this is more for the hyper sceptics. Bit yes in a nutshell protocols in communication systems in its simplest form is a set of rules. Do our interlocutors agree with the meaning?

  561. 561
    kairosfocus says:

    Andre, I added the above exchange to the headlined FYI-FTR:

    http://www.uncommondescent.com.....ork-model/

    KF

    PS: I see Evolve seems to be absent, and has been once the FYI-FTR was put up. Let’s see if there is a return on the weekend.

  562. 562
    kairosfocus says:

    Andre, the underlying logic of standardised peer-peer formatting at multiple levels within a communication system — let’s just call it the layer-cake protocol effect [LCPE] — is patent, and links to what happens in royal courts etc just beg to be used: e.g. peers. A necessity if it is to work. Such can properly be described as a protocol. Once we extend beyond one-off level to cases where we want networks of interacting units, broadcast, simplex, half duplex, full duplex modes, the natural tendency is for standards to spread out, and the need for documentation then becomes obvious. But already at the one-off level, the FSCO/I and IC pointing strongly to design are present. KF

    PS: I am beginning to think part of what we are facing is the Wikipedia, domineering selectively hyperskeptical, rhetorically manipulative ideological faction subculture spreading out across the web. Complete, with conclusion- and- sentence- already- in- hand- just- find- a- plausible- peg- to- hang- on witch-hunts for heretics such as we here at UD represent. Cyber-stalking and even on the ground stalking naturally follow from such a mentality.

  563. 563
    Carpathian says:

    groovamos:

    You made the statement that, vague as it reads, seems to say that a phonograph record and playback apparatus is not used in information transfer. Which if that is what is being said, is bogus.

    What I said, as vague as it reads, is that there is no protocol, i.e., a bi-directional transfer of information that is required for protocol.

    As an example, you cannot send a NAK to the phonograph record nor can you send a NAK to the cartridge.

    The vinyl record analogy is exactly what we see in regards to the workings of a cell.

    The DNA is for all intents and purposes static.

    Like the grooves in a vinyl record, the DNA simply gets copied.

    There is no other high-level “IT-like” communications happening.

    I handle correction well.

    Show me a protocol exists as Upright BiPed claims.

    There is nothing even close to a high-level two way communications as is required for a protocol.

  564. 564
    Carpathian says:

    Andre:

    Bit yes in a nutshell protocols in communication systems in its simplest form is a set of rules. Do our interlocutors agree with the meaning?

    I agree but you don’t go far enough.

    A protocol defines rules for at least two ends in a communications systems.

    In a multi-drop environment, you usually have one master and many slaves, with every single one of them being an intelligent node. In this scenario, the protocol also defines who is allowed to transmit messages at any given time.

    None of this multiple intelligent communications happens in the cell.

    Everything anyone has presented so far has been at the physical layer.

    Mung mentions during his Morse code example something he calls “discontinuity”.

    I think what he means is “independence” of data.

    In other words, the data on the telegraph wires is time and position independent.

    Any char could at any time occupy a place on the data stream.

    This does not happen with DNA.

    It is fixed like the groove on a vinyl record and it is copied the same way.

  565. 565
    Carpathian says:

    kairosfocus:

    The protocol context is that of interaction and a standardised programme of correct behaviour.

    The interaction is from at least two intelligent parties.

    A man walks into a room, bows before a king, who then says a few words, an then taps the man on the shoulders with a sword.

    That is an example of protocol.

    Two intelligent agents are required for a protocol.

    Where are there at least two intelligent agents in the cell?

    Show me the intelligent agents required for a protocol that exist in the cell.

  566. 566
    Carpathian says:

    kairosfocus:

    7 –> The dividing line here is that

    – codes address content that uses discrete state elements [e.g. alphanumeric characters, codons for genes, binary digits],

    – protocols are concerned with setting up co-ordinated communication with due regard to the natural layer-cake effect, and

    – mod/demod is concerned with encapsulating, sending, propagating and receiving then recovering signals in the midst of noise (and having regard to bandwidth and channel capacity issues).

    Where are the two sides of this co-ordinated communication in the cell?

    Can you give me a cellular equivalent to the link layer?

    Can you give me a cellular equivalent to the transport layer?

  567. 567
    Carpathian says:

    mike1962:

    What does your fallible memory have to do with that fact that the point you were trying to make was patently wrong. You didn’t merely get the name wrong, you claimed UDP is not a protocol. Your memory of the name of the protocol has nothing to do with the fact that you denied UDP is a protocol.

    I got the acronym wrong.

    In x.25 and other protocols, packets can remain unacknowledged for a period of time, i.e. the sending end will not require an ACK for packet before it send the next but will send a block of up to n packets before the receiving end has to start ACKing.

  568. 568
    kairosfocus says:

    Carpathian, in any communicative situation, there naturally are two sides, transmission and reception. That such an irreducibly complex entity should arise by blind chance and mechanical necessity is utterly implausible indeed, and such would have to be acting on the TX side and the Rx side withut correlation given the high contingency and lack of unifying purpose. However, for a protocol to correlate the two sides can be the product of an individual designer or a team or as a result of a negotiated standard for research or industry is a well known matter of fact. In short, you were looking at the design inference in action through the wrong end of the telescope. KF

  569. 569
    Carpathian says:

    mike1962:

    And if you don’t think the codon/ribosome protein synthesis system utilizes a protocol (e.g, why precisely three nucleotides to a codon, and what the hell does a stop-codon do?) then that’s your problem.

    That is not a protocol, it is a translation.

    A protocol requires two intelligent nodes.

    Show me two intelligent nodes exchanging information in a cell.

    If by “protocol”, ID means “translation”, then use the term “translation”.

    If by “protocol” ID means mean “convention”, then use the term “convention”.

    Protocol has already been defined outside of ID, and in information technology, can be defined as the rules of communication between at least two intelligent agents.

    Where are the intelligent agents in the cell?

  570. 570
    Carpathian says:

    Mung:

    I could go on and on.

    And you probably will.

  571. 571
    Carpathian says:

    kairosfocus:

    Carpathian, in any communicative situation, there naturally are two sides, transmission and reception.

    But where are they in the cell?

    That is the question that requires an answer in order for Upright BiPed to be correct that there is a protocol when it comes to cellular activity.

    I am easily corrected when I make a mistake.

    I don’t see two intelligent node in the cell.

    Show me where they are and I will agree with Upright BiPed that there is a protocol at work in the cell.

    From what you written about layered communications, I think you agree with me that a “look-up” table does not qualify as a protocol.

  572. 572
    Carpathian says:

    groovamos:

    Making the argument dependent on a software engineering point of view is obfuscation.

    That is exactly what ID is doing.

    The claim is that “information” is being processed.

    Upright BiPed claims a “protocol” is at work along with a “code”.

    kairosfocus talks about a “von neumann” replicator.

    Biology is about chemistry, not software engineering.

  573. 573
    mike1962 says:

    Carpathian: Protocol has already been defined outside of ID, and in information technology, can be defined as the rules of communication between at least two intelligent agents. Where are the intelligent agents in the cell?

    If I write a program to generate random data and send it to unused IP addresses using a pre-defined UDP protocol, where is the intelligent receiver? These is none even though the UDP protocol is employed refuting your demand that a protocol necessarily requires a receiver in any given instance of utilization.

    But to answer your question with regards to cells, the sending agent is the cell that built DNA strand, the receiving agent is the cell that interprets it and builds proteins. All utilizing a predetermined protocol defined as tri-nucleotide codons with two stop codons.

    That is not a protocol, it is a translation.

    The format of the transference of information is not arbitrary. The protocol exist by the fact that codons are always composed of three nucleotides each and the existence of two stop codons. This protocol is more fundamental than the data that is conveyed. That’s enough to qualify as a protocol. But by all means keep on denying the obvious.

  574. 574
    Upright BiPed says:

    No on can be this dense. Seven days of it.

  575. 575
    Carpathian says:

    Upright BiPed:

    No on can be this dense. Seven days of it.

    I would never call you dense, but you have failed to meet kairosfocus’s definition of what a protocol is.

    There is a “look-up table”, no protocol.

    Match up what happens in a cell with kairosfocus’s protocol.

    Shut me up by showing that.

    You can’t because there is no equivalent in a cell.

    Your semiotic argument is also wrong.

    Peirce, the originator of the term, says a footprint in the mud is semiotic as it is a “sign” of human activity.

    Putting a footprint in the mud to signify that there was human activity is not semiotic.

    It’s because of you that I have looked at Peirce.

    What he says does not agree with your interpretation.

    Semiotic codes are not used to produce a result as you claim.

    Show me where Peirce claims that semiosis is a mechanism for producing a result.

  576. 576
    Carpathian says:

    mike1962:

    The protocol exist by the fact that codons are always composed of three nucleotides each and the existence of two stop codons. This protocol is more fundamental than the data that is conveyed. That’s enough to qualify as a protocol.

    No it’s not.

    Convince kairosfocus that it is enough to qualify as a protocol as he described it.

  577. 577
    Upright BiPed says:

    Carp, please hold a record album up to your ear.

    Hear anything?

    The reason you don’t hear the album is because there are no vibrations in air pressure coming from it. You need vibrations in air pressure, right around your head, and that’s your big problem. How do you get from grooves in a vinyl disc to vibrations in air pressure around your head?

    What on earth would be required for that?

    My best guess is that you might need something very particular. Most probably, something very particular to the way the grooves are arranged on the disc in the first place. It seems to me that the method for retrieving the information off the disc would have to be in some sort of substantial prior agreement with the way the disc was made.

    you have failed to meet kairosfocus’s definition of what a protocol is

    I gave you a material definition of my terms at the point I used the word. You have ignored that definition and set out to obfuscate the material issue behind the word. I won’t be enabling you. It’s an embarrassment.

    As always, it doesn’t matter what you call it, and thats the real point here.

    Bye.

  578. 578
    kairosfocus says:

    Carpathian, have you looked at the diagrams I have put up? If not, kindly cf Yockey’s mapping of protein synthesis. Note the encoding process to RNA code (including snipping and splicing] then transfer through nuclear ports to the ribosome, where there is a decoding driven, 3-letter codon framing process that is used to create the protein chain, terminating of course with a stop codon. KF

  579. 579
    Carpathian says:

    kairosfocus:

    Carpathian, have you looked at the diagrams I have put up? If not, kindly cf Yockey’s mapping of protein synthesis. Note the encoding process to RNA code (including snipping and splicing] then transfer through nuclear ports to the ribosome, where there is a decoding driven, 3-letter codon framing process that is used to create the protein chain, terminating of course with a stop codon. KF

    Kairosfocus, I accept your description of a mapping which causes a problem for Upright BiPed.

    What I’d like to see from you, is an example of a protocol in the cell just as you defined it with your layered communications protocol.

    Where in the cell does this occur?

    I don’t see two intelligent agents in the cell.

    I don’t see even one.

  580. 580
    Carpathian says:

    Upright BiPed:

    I gave you a material definition of my terms at the point I used the word. You have ignored that definition and set out to obfuscate the material issue behind the word. I won’t be enabling you. It’s an embarrassment.

    Why would you use an established term such as “protocol” and redefine it to mean “convention”?

    There is no reason to do that.

    Simply use terms as they are already defined.

    Kairosfocus’s description of “protocol” does not match yours.

  581. 581
    Carpathian says:

    Upright BiPed:

    My best guess is that you might need something very particular. Most probably, something very particular to the way the grooves are arranged on the disc in the first place. It seems to me that the method for retrieving the information off the disc would have to be in some sort of substantial prior agreement with the way the disc was made.

    That is a standard, it is not a protocol.

    Read kairosfocus’s definition of protocol.

  582. 582
    Carpathian says:

    Upright BiPed,

    Mung posted a good example when he talked about Morse code.

    In it he uses the term “discontinuity”.

    I think a better term might be independence.

    This means that the data on on the telegraph line is not dependent on where or when in the data stream it occurs.

    Any “position” in the data stream could be any character.

    This independence is not seen in the DNA “code”.

  583. 583
    kairosfocus says:

    Carpathian, again, did you notice the matched encoding/decoding pair? Now, consider a simple AM modulator, based on modifying Power supply amplitude in a transistor oscillator ckt that directly feeds an Antenna element. Then, again, compare a cartridge in a groove feeding magnetic elements then an amplifier-speaker embedding RIAA de-emphasis which then goes to your ear. The spiral groove, the motor, the head, all are blended together across the model. This goes to show that the elements of a Comms sys may blend aspects of the system model — it is abstract. KF

    PS: D/RNA strands are string data structures, which hold info values based on prong height. The transcribed, snipped and spliced mRNA blends coding, and transmission there is a physical transfer. Decoding depends on tRNA’s and a supporting loading process. The Ribosome-tRNA system again blends elements but aspects can be identified.

  584. 584
    Carpathian says:

    kairosfocus:

    Carpathian, again, did you notice the matched encoding/decoding pair? Now, consider a simple AM modulator, based on modifying Power supply amplitude in a transistor oscillator ckt that directly feeds an Antenna element. This goes to show that the elements of a Comms sys may blend aspects of the system model — it is abstract. KF

    You keep bringing up translation.

    Your definition of protocol goes far beyond simple translation.

    Show the “protocol”, not simple “translation”.

    It is you that showed the protocol layers.

    If you understand what you have posted you realize that “translation” and “protocol” are not equivalent terms.

    Point to the two intelligent agents involved in the protocol in the cell.

    I am familiar with Am modulation, FM modulation, pulse width modulation, etc.

    That is not the issue.

    Show me the intelligent agents involved in the “protocol” in the cell.

  585. 585
    kairosfocus says:

    F/N: To aid in understanding, I have updated the FTR to include an annotated form of Shannon’s 1948 diagram, just below Yockey’s analysis of the protein synthesis system for the living cell:

    http://www.uncommondescent.com.....ork-model/

    While such will not stop objections and tangents, it will provide a reference context that will readily show the matching.

    It should also be evident how the expansions that explicitly distinguish code and/or modulation units and transmission/reception units are directly related.

    KF

    PS: It should be fairly obvious why for didactic and operational purposes I and others — I even found much the same in Duncan, an A Level Physics text — have found it useful to open up Shannon’s black boxes and show specific components.

  586. 586
    kairosfocus says:

    Carpathian,

    protocols are standards that frame specs for messages and correlated encoders, modulators and transmission units in transmitters, as well as correlated receivers, demodulators and decoders in receivers. They may also address channel issues. Coders and Decoders may be multilevel, with peers in virtual direct contact at matching levels. Protocols also are directly linked to codes.

    Being embedded in the system they can be at least in part identified through reverse engineering exercises, as has been ongoing in molecular biology, winning several Nobel Prizes along the way.

    And it is patent that once a comms system is present by which signals are created, transferred to a receiver and then decoded and put to use, requisite protocols and codes are present. By the sheer logic of the process.

    As, in protein synthesis.

    I also know you are likely to want to object to our recognition of object code stored in D/RNA strings and back-traceable in part from protein AA chains. But, again, codes there are, as Crick recognised in the Mar 19 1953 letter that I have highlighted a snapshot of. That is who you need to answer to, not me.

    But the overall issue is not wranglings over hair-splitting differences on meanings of words that in the end only serve to confuse the onlooker, the issue is that once a communication system is present, there will be several well-matched, tightly correlated elements in an irreducibly complex array, that is functionally specific and information-rich.

    Thus, we see both IC and FSCO/I implying a massive needle in haystach blind search issue for any proposed blind watchmaker account of origin of cell based life. One that is nowhere near being solved.

    Worse, protein synthesis is at the heart of the operations of the living cell.

    And, there is but one empirically warranted, needle in haystack challenge plausible cause of FSCO/I. Intelligently directed configuration, AKA design.

    KF

  587. 587
    Carpathian says:

    kairosfocus:

    But the overall issue is not wranglings over hair-splitting differences on meanings of words that in the end only serve to confuse the onlooker, the issue is that once a communication system is present, there will be several well-matched, tightly correlated elements in an irreducibly complex array, that is functionally specific and information-rich.

    There is no hair-splitting here since I’m accepting your definition of layered protocol.

    Where in the cell do those two sides of the communication protocol exist?

    Show me the agents that demonstrate your explanation of a layered protocol.

    A simple translation is not a protocol.

    Your examples of physical, link, transport layers etc. are fine.

    Where in the cell are these shown to exist?

  588. 588
    kairosfocus says:

    Carpathian, You have been shown. Kindly cf the post here, including the diagrams, the infographic summary on protein synthesis and video:

    http://www.uncommondescent.com.....ork-model/

    Then particularly note the comparison of Yockey and Shannon. What you ask yet again has been presented and is there to be seen. As just one point of relevance, cf here on how researchers have sought to extend to a further base pair, NaM and 5SICS — or X and Y for simplicity:

    http://www.scripps.edu/news/pr.....sberg.html

    >> Romesberg and his lab have been trying to find a way to extend the DNA alphabet since the late 1990s. In 2008, they developed the efficiently replicating bases NaM and 5SICS, which come together as a complementary base pair within the DNA helix, much as, in normal DNA, the base adenine (A) pairs with thymine (T), and cytosine (C) pairs with guanine (G).

    The following year, Romesberg and colleagues showed that NaM and 5SICS could be efficiently transcribed into RNA in the lab dish. But these bases’ success in mimicking the functionality of natural bases was a bit mysterious. They had been found simply by screening thousands of synthetic nucleotide-like molecules for the ones that were replicated most efficiently. And it had been clear immediately that their chemical structures lack the ability to form the hydrogen bonds that join natural base pairs in DNA. Such bonds had been thought to be an absolute requirement for successful DNA replication?—a process in which a large enzyme, DNA polymerase, moves along a single, unwrapped DNA strand and stitches together the opposing strand, one complementary base at a time.

    An early structural study of a very similar base pair in double-helix DNA added to Romesberg’s concerns. The data strongly suggested that NaM and 5SICS do not even approximate the edge-to-edge geometry of natural base pairs—termed the Watson-Crick geometry, after the co-discoverers of the DNA double-helix. Instead, they join in a looser, overlapping, “intercalated” fashion. “Their pairing resembles a ‘mispair,’ such as two identical bases together, which normally wouldn’t be recognized as a valid base pair by the DNA polymerase,” said Denis Malyshev, a graduate student in Romesberg’s lab who was lead author along with Karin Betz of Marx’s lab.

    Yet in test after test, the NaM-5SICS pair was efficiently replicable. “We wondered whether we were somehow tricking the DNA polymerase into recognizing it,” said Romesberg. “I didn’t want to pursue the development of applications until we had a clearer picture of what was going on during replication.”

    Edge to Edge

    To get that clearer picture, Romesberg and his lab turned to Dwyer’s and Marx’s laboratories, which have expertise in finding the atomic structures of DNA in complex with DNA polymerase. Their structural data showed plainly that the NaM-5SICS pair maintain an abnormal, intercalated structure within double-helix DNA—but remarkably adopt the normal, edge-to-edge, “Watson-Crick” positioning when gripped by the polymerase during the crucial moments of DNA replication.

    “The DNA polymerase apparently induces this unnatural base pair to form a structure that’s virtually indistinguishable from that of a natural base pair,” said Malyshev.

    NaM and 5SICS, lacking hydrogen bonds, are held together in the DNA double-helix by “hydrophobic” forces, which cause certain molecular structures (like those found in oil) to be repelled by water molecules, and thus to cling together in a watery medium. “It’s very possible that these hydrophobic forces have characteristics that enable the flexibility and thus the replicability of the NaM-5SICS base pair,” said Romesberg. “Certainly if their aberrant structure in the double helix were held together by more rigid covalent bonds, they wouldn’t have been able to pop into the correct structure during DNA replication.”

    An Arbitrary Choice?

    The finding suggests that NaM-5SICS and potentially other, hydrophobically bound base pairs could some day be used to extend the DNA alphabet. It also hints that Evolution’s choice of the existing four-letter DNA alphabet—on this planet—may have been somewhat arbitrary. “It seems that life could have been based on many other genetic systems,” said Romesberg.

    He and his laboratory colleagues are now trying to optimize the basic functionality of NaM and 5SICS, and to show that these new bases can work alongside natural bases in the DNA of a living cell.

    “If we can get this new base pair to replicate with high efficiency and fidelity in vivo, we’ll have a semi-synthetic organism,” Romesberg said. “The things that one could do with that are pretty mind blowing.” >>

    Notice that key word, arbitrary?

    It is the echo of a protocol.

    Progress since has been to get an X-Y pair into a bacterium. Later, functions are intended, leading to a base of 2^6 = 176 possibilities for codons, assuming the codon triplet convention continues to hold.

    Likewise, the 3-letter codons and their tRNA assignments reflect protocols, as does the fact that the CCA-COOH coupler used to tie tRNA and AA is universal and independent of the actual AA side-branch. This is a context on which as was long since pointed out to you, thereare some two dozen variant codes and artificial assignments have been made.

    All of this shows that we are dealing with a co-ordinated system of formatting standards and frameworks, not fixed, forced inevitabilities.

    In that context, codes and protocols are plainly subject to being chosen, not given by the mere laws of physics and chemistry and linked natural forces.

    KF

  589. 589
    Carpathian says:

    kairosfocus:

    In this, we see how at different layers, there is a virtual direct communication between peers but this is actually accomplished by interfaces up and down the stacks with physical transmission being at the lowest level.

    The above are your words from your post.

    You have not shown an example of this.

    You have instead focused on translation.

    There is no point in my asking again if you can’t answer the questions that I’m asking.

    So here it is for a last time.

    Where is the immaterial communication?

    Where are the two immaterial ends?

    An example of a physical translation that does not include the higher levels of a protocol is not good enough to prove your own examples of what constitutes a protocol.

  590. 590
    Eugen says:

    Carpathian

    I’m from South Europe. We hear that some people from Carpathian mountains are little dense.

  591. 591
    Mung says:

    Carpathian wants to see the immaterial components in the cell and if we cannot show them to him they do not exist.

    And Morse code doesn’t actually work for communication because it doesn’t have all seven layers of the OSI model.

  592. 592
    kairosfocus says:

    Carpathian, you can see signals, which have been shown. Information rests in configurations or patterns of variation expressed in those signals and linked meanings that influence consequences and are meaningful, but it is not itself visible, just as energy is not itself visible or time is not itself visible. In a classic reference, wind proper is not visible too — just its effects. KF

    PS, an oopsie, apparently there are 172 candidate AAs out there. 6^3 = 216 will cover that.

  593. 593
    Evolve says:

    People like KF and Andre don’t grasp the point. Nobody disputes that there’s a flow of information from DNA-mRNA-Protein. You can make all these fancy flowcharts and compare it to man-made information flow. OK fine. But, in man-made systems such information flow happens specifically through purpose-built transmitting units, channels & receiving units whose underlying operation is not driven by their physicochemical or structural crosstalk. In life, however, information flow is the net result of a plethora of dynamic reactions and interactions among chemical molecules. Since chemistry can operate by itself there’s no need to assign this to any intelligence. By drawing crude analogies, you’re only providing ad hoc explanations for the problem at hand instead of trying to determine how such a system may have arisen.

    Consider this example:
    Birds have wings, aeroplanes also have wings.
    Both look awfully similar and serve pretty much the same purpose.
    Since aeroplane wings are designed, bird wings must also be designed!

    This sort of argument is bound to fail.
    Explore deeply and you’ll see that the bird wing shares homology with your hand and even with fins of fossil fishes! Their developmental patterns establish this relationship firmly. Now look at the fossil record and you’ll see how dinosaur arms transformed into bird wings. All this evidence also fits with other evidence for bird origins. We now have a much more comprehensive picture that has immense explanatory power than the ad hoc design explanation.

  594. 594
    Evolve says:

    KF asks:

    “Ev, show us actual organisms, please”

    If we succeed in producing cells from scratch you will claim that it was a result of intelligent design. If we fail to do so you will still claim that the failure validates ID’s position that the cell is so complex and it can’t be synthesized (coin a fancy phrase for complexity : FSCO/I :-)).

    Heads I win, tails you lose! That’s your position.

  595. 595
    Mung says:

    Control systems and coordination protocols of the secretory pathway

    HT: Dionisio

    Contrary to Carpathian’s assertions, Upright BiPed is not abusing the term “protocol” and protocols do not require the consent of two intelligent agents.

    Those are just red herrings to avoid discussing the issue that’s on the table.

  596. 596
    Evolve says:

    Mung,

    “Evolve, if there were no discontinuity between the codon and the amino acid there would be no need for an adaptor.”

    Yes, indeed one hypothesis holds that protein synthesis initially originated without any adaptor. There are codon or anticodon-like triplets in RNA molecules that can bind some amino acids directly! Thus amino acid polymerisation could have occurred on RNA templates where these binding sites are sequentially present. The current adaptor may have evolved later. See:
    http://www.ncbi.nlm.nih.gov/pubmed/15952885
    http://www.ncbi.nlm.nih.gov/pubmed/19795157

  597. 597
    Mung says:

    People like Evolve don’t grasp the point.

    Nobody disputes that there’s a flow of information from DNA-mRNA-Protein.

    Some people dispute whether there’s information at all.

    But the point is, the one you fail to grasp, is the question of the requirements for the transfer of recorded information (recorded in a physical medium) and it’s conversion into a physical effect.

    The best you and Carpathian have managed is “it just happens, that’s all.”

    … in man-made systems such information flow happens specifically through purpose-built transmitting units, channels & receiving units whose underlying operation is not driven by their physicochemical or structural crosstalk.

    Are you saying something non-physical (immaterial) is going on in these man-made physical systems? Are you, like Carpathian, a dualist?

    In life, however, information flow is the net result of a plethora of dynamic reactions and interactions among chemical molecules.

    Handwaving. Science wants to know the cause or causes. The result is merely what requires an explanation. That “[it] is the net result of a plethora of dynamic reactions and interactions among chemical molecules” could be said of just about anything, and is not therefore an explanation.

    It’s no different from “woo did it.”

    Since chemistry can operate by itself there’s no need to assign this to any intelligence. By drawing crude analogies, you’re only providing ad hoc explanations for the problem at hand instead of trying to determine how such a system may have arisen.

    The point is not how it arose but how it functions. Does the process require a code, and if so why?

  598. 598
    Mung says:

    Carpathian, since you consider everything above the physical later to be immaterial, what would convince you that the link layer exists?

  599. 599
    Mung says:

    Evolve, whether or not there once was a “stereochemical era” does not help you in the least. Your position is that we are still in that era. Silly person.

  600. 600
    kairosfocus says:

    Ev, in short, there is a principle of demonstrating adequacy of claimed causes before projecting to the remote past; vera causa — traces back to Newton. You are at the threshold of seeing the massively patent: the only empirically observed, needle in haystack plausible cause of the FSCO/I required for OOL, for starters, is design. If you cannot credibly show blind chance and mechanical necessity under reasonable circumstances doing what is needed, that is a clue. Secondly, a reasonable estimate for additional FSCO/I to get a body plan is 10 – 100mn bases. If you cannot address irreducible complexity [ie multiple mutually necessary parts to get core function] and pop generation time and size issues to reach something of that order, you are again staring at the same issue. Many of us who are here standing up on this question against the tide of the times do so because we have thought long and hard on those challenges. Just for fun, consider the difficulties to get realistic kinematic self replication of an entity that does significant other things going. KF

    PS: If you think a descriptive phrase abbreviation for functionally specific complex organisation and associated information is a synonym for “complexity” you do not begin to grasp what is on the table.As a clue, I came to ID through thermodynamics reasoning, as my always linked note will document. I suggest you start from Orgel and Wicken. Here: http://www.uncommondescent.com.....am-with-a/

  601. 601
    Evolve says:

    Mung,

    ///the requirements for the transfer of recorded information (recorded in a physical medium) and it’s conversion into a physical effect…///

    The single molecule called RNA can carry recorded information and convert it into physical effects, accomplishing both roles on its own without the need for translation. How does your creation model account for such a possibility? How does creation help explain the transition from such an RNA World to the current DNA World? These are molecules and chemistry at play. Only chemical and physical principles can make sense of them, not ad hoc analogies to design.

    ///it just happens, that’s all///

    Of course if earthquakes, hurricanes and supernova explosions can just happen, then so can another natural phenomenon called life. What’s the alternative you have? It was designed on purpose but don’t ask who, what or when. Case closed! No further examination required.

    ///Are you saying something non-physical (immaterial) is going on in these man-made physical systems?///

    No, what I meant is clear unless you want to be defiant. First of all man-made objects don’t exist naturally, but life’s molecules and their constituents are present naturally everywhere, even in space. These molecules react to produce other molecules SPONTANEOUSLY – and the net effect of these reactions is what we call life. Man-made stuff only act at the behest of their designers and not spontaneously. This is an important distinction which you guys fail to acknowledge without fail because if you do, your entire premise will collapse. The whole ID movement rests on drawing analogies with human designs. That’s your only “positive evidence”!

    ///That “[it] is the net result of a plethora of dynamic reactions and interactions among chemical molecules” could be said of just about anything, and is not therefore an explanation.///

    C’mon, I was trying to keep the message short and simple. One can go on and on about the explicit chemistry involved.
    For eg: KF compared the ribosome to a tape reader in his post. He has this simple Lego-block like picture in his mind where a static mRNA string threads through a static ribosome much like how a tape moves through the tape reader.

    But the ribosome isn’t doing the same thing really. The ribosome is not even in one piece. It’s the 30S subunit in complex with initiation factors IF1 and IF3 that attaches first to the 5′-UTR of the mRNA by means of hydrogen bonding between the Shine-Dalgarno sequence on the mRNA and 16S rRNA of the 30S subunit in bacteria. This recruits the IF2 initiation factor which carries tRNA-formylated methionine towards the start codon. Codon-anticodon base pairing occurs and the initiation complex forms. The complex then binds to the 50S ribosomal subunit. During elongation, multiple tRNAs enter the A-site of the ribosome, but only the one that base pairs with the codon binds. This binding places two amino acids adjacent to each other. The amino group of one amino acid attacks the carboxyl group of the adjacent one to form a peptide bond which is catalyzed by an rRNA called peptidyl transferase utilizing one GTP. This covalent bond formation causes deacylation the tRNA in the P-site.

    This is just a start, actually! From this alone you can see the chemistry at work, one reaction paves the way for a subsequent one, multiple reactions occur at the same time, bonds form and break, structures and conformations change and products get generated. Textbooks would simply say that the ribosome has 3 sites – A, P and E through which tRNAs move. But see what this technical paper has to say:

    http://www.ncbi.nlm.nih.gov/pubmed/9598294
    …Structural studies do not support the three operationally defined sites in a simple fashion as three topographically fixed entities, thus leading to new concepts of tRNA binding and movement: (1) the hybrid-site model describes the tRNAs’ movement through the ribosome in terms of changing binding sites on the 30S and 50S subunits in an alternating fashion. The tRNAs thereby pass through hybrid binding states. (2) The alpha-epsilon model introduces the concept of a movable tRNA-binding domain comprising two binding sites, termed alpha and epsilon. The translocation movement is seen as a result of a conformational change of the ribosome rather than as a diffusion process between fixed binding sites. The alpha-epsilon model reconciles most of the experimental data currently available.

    It is this dynamic chaos that’s being underappreciated in your simple comparisons to man-made objects. All this chemistry happens on their own under the right environmental conditions with no external intervention. You got to acknowledge the fact that nature can produce its own designs.

  602. 602
    kairosfocus says:

    Ev, please show us an organism that is a living cell and operates on RNA and ribozymes, rather that predominantly DNA-RNA- ribosome- protein and protein based enzymes, etc. Or, something substantially at that level. KF

    PS: Don’t confuse simplified presentation with lack of awareness of just how horrendously complex and functionally specific, carefully organised the full protein synthesis story is. I am focussing on a simple readily grasped aspect, just as, I am not giving the full wall sized chart of cellular metabolism, which would not fit in a blog post image anyway. And BTW, more FSCO/I raises the complexity-specificity functional barrier to blind watchmaker mechanisms even higher. BTW, here is a first level overview: http://en.wikibooks.org/wiki/A....._synthesis

  603. 603
    Evolve says:

    KF,

    All present-day life have DNA-based chemistry because they are thought to have descended from a common ancestor with the same sort of chemistry. However, an RNA World is thought to have existed prior to that, relics of which still linger on. For instance, there are RNA viruses whose genome is either a single-stranded or double-stranded RNA. There are RNA enzymes in modern-day cells too. The Ribosome is arguably the most important cellular component today and at its heart is an RNA enzyme called peptidyl transferase which catalyzes the crucial peptide bond formation between amino acids to produce proteins. Other examples of ribozymes include self-splicing introns, hammerhead ribozymes etc.

  604. 604
    EugeneS says:

    Evolve #601,

    “The single molecule called RNA can carry recorded information and convert it.”

    This does not solve the problem of coordinated coding/decoding and therefore that of a protocol. In this light, it does not matter how many molecules there are, one or many. So you can’t get away with it. As soon as memory is required, we are dealing with a sign and its processing. And, BTW, the RNA world is just a hypothesis. Its sole purpose is to do away with obvious complexity issues. It fails.

  605. 605
    Evolve says:

    ///functionally specific…///

    Functions are unintended consequences of molecular interactions. Shed your teleology and follow the chemistry. One reaction makes another possible, which makes another possible and you get a cascade of reactions generating life.

  606. 606
    Mung says:

    Evolve:

    First of all man-made objects don’t exist naturally, but life’s molecules and their constituents are present naturally everywhere, even in space. These molecules react to produce other molecules SPONTANEOUSLY – and the net effect of these reactions is what we call life.

    Proteins in the cell do not arise SPONTANEOUSLY. They are manufactured, by machines. They are no less artifacts than man-made objects.

    Man made objects are as natural as anything else in the cosmos, unless you’re going to go all question-begging on us.

    …but life’s molecules and their constituents are present naturally everywhere, even in space.

    Not true. And can you please show us the spontaneous generation of codes and coding? Please.

  607. 607
    Evolve says:

    Eugene,
    No, in an RNA World you don’t need any decoding since the same molecule that carries the information can also produce the physical effect. RNA world is indeed a hypothesis, but one with supporting evidence.

    ///Its sole purpose is to do away with obvious complexity issues. It fails.///

    That’s silly. The hypothesis strives to explain the data in front of us.

  608. 608
    Evolve says:

    ///Proteins in the cell do not arise SPONTANEOUSLY. They are manu