Intelligent Design

When I’m wrong

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In a recent post in which I questioned the claim that over 100 mutations get fixed in the human population in every generation, I remarked, “I’m happy to be proved wrong.” Guess what? I meant it. After weighing the evidence presented on both sides, I’ve decided that there are no good mathematical arguments showing that 130 mutations couldn’t have been fixed in each generation of the human lineage, over the past five million years. Although the equations of population genetics are based on assumptions, these assumptions have been tested – and validated – for bacteria. And while the mutation rate per individual per generation is five orders of magnitude greater for human beings than for bacteria, the fact that the human genome is about 1,000 times larger than that of a bacterium, coupled with the fact that there are multiple cell divisions per generation in animals, explains why humans would have a much higher mutation rate. Of course, arguments from extrapolation aren’t always valid, and for all I know, there might be any number of reasons why fixation rates of 100 per generation for human beings (as predicted by the equations of population genetics) are biologically implausible. But the onus is clearly on the skeptic to explain why we shouldn’t believe the claim that 100 mutations are fixed in the human population in every generation. Dr. Kozulic (who is a well-published biochemist) is a prominent skeptic; and in my last post, Branko Kozulic responds to Professor Moran, I gave him the opportunity to state his case. Since Dr. Kozulic is from Croatia, I also assisted him in presenting his argument as clearly as possible, in English. After sifting through the replies by wd400 and Nick Matzke, I have come to the conclusion that the arguments that Dr. Kozulic and I presented in our post failed to establish that a fixation rate of 100 per generation for human beings, even during the Paleolithic era, would be infeasible. To uninitiated laypeople like myself, such a high rate of fixation for a very thinly scattered Stone Age population sounds highly counter-intuitive at first sight, but that does not make it untrue. After weighing the arguments, I now think that the neutral theory of evolution can account for the number of mutations fixed in the human population over the last five million years (roughly 22.4 million).

My concession on this point does not mean that I think the neutral theory of evolution can account for the pattern of fixation events observed in the human lineage, let alone the existence of orphan genes. Those are separate issues, and should be addressed as such.

After reading Professor Moran’s recent post, On being “outed” as a closet Darwinist, I would like to make it clear that I am fully aware that Moran publicly disagrees with many of Darwin’s ideas. In our previous post, Dr. Kozulic and I characterized Professor Moran as a “Darwinist” in one important respect only, as we expressly stated. To illustrate what I mean, I’d like to quote from his 2006 essay, Macroevolution:

The Creationists would have us believe there is some magical barrier separating selection and drift within a species from the evolution of new species and new characteristics. Not only is this imagined barrier invisible to most scientists but, in addition, there is abundant evidence that no such barrier exists. We have numerous examples that show how diverse species are connected by a long series of genetic changes.

If Professor Moran can think of a handy label to describe someone who holds such a view, then I shall gladly use it in future, when referring to him. “Gradualist” is a term that comes to mind, but I don’t think Professor Moran would appreciate that label, either. Moran also rejects the view that microevolution is sufficient to account for macroevolution, as his essay makes clear.

Professor Moran and I disagree on many things, and I’m sure we’ll have many lively exchanges in the future, but it would be downright churlish of me not to acknowledge that my attempts to show that the neutral theory could not account for 22.4 million mutations arising in the human lineage over the last five million years have failed. I also wish to state that I had no intention of giving any offense to Professor Moran in our exchange of views, and that I have always striven to remain as polite as possible, while publicly disagreeing with him. The next time I’m dining out, I shall order a glass of red wine and silently toast him.

Before I finish this post, I’d like to quote a passage from Dr. Kozulic’s 2011 paper, Proteins and Genes, Singletons and Species – a paper which I have cited on numerous occasions, on Uncommon Descent:

If just 200 unique proteins are present in each species, the probability of their simultaneous appearance is one against at least 104,000. [The] Probabilistic resources of our universe are much, much smaller; they allow for a maximum of 10149 events [158] and thus could account for a one-time simultaneous appearance of at most 7 unique proteins. The alternative, a sequential appearance of singletons, would require that the descendants of one family live through hundreds of “macromolecular miracles” to become a new species – again a scenario of exceedingly low probability. Therefore, now one can say that each species is a result of a Biological Big Bang; to reserve that term just for the first living organism [21] is not justified anymore.

The fallacy in the logic here should now be apparent. There is no reason to suppose that one singleton has to be fixed in the population before another one can be. The paper has therefore failed to demonstrate that speciation is an event that lies beyond the reach of chance.

An excellent case can be made that not only the emergence of life, but also key events in the history of life such as the Cambrian explosion, in which 30 novel body types emerged over a relatively short span of 20 million years, were events whose occurrence lies far beyond the reach of chance. Intelligent Design is on very strong ground here. However, I now believe that the argument that speciation itself is equivalent to a Biological Big Bang is a much weaker one. The origin of orphan genes remains an ongoing scientific mystery, but we should be wary of making a mountain out of a molehill. The imputation of design in this case would require much stronger supporting calculations than we have seen to date, and the mathematics contained in these calculations also needs to be very carefully scrutinized. During this time of scrutiny, we must be our own harshest critics. In a 2013 post on Uncommon Descent, I suggested that the “edge of evolution” may lie at the species level, using the definition of “species” employed in Dr. Kozulic’s paper. It appears that I spoke too soon. I think it is fair to say that the question of where the edge of evolution lies has now been thrown open again.

78 Replies to “When I’m wrong

  1. 1
    Moose Dr says:

    I have been pondering this discussion of fixation due to drift. I find it very troubling to my darwinian brain to consider that “slightly beneficial” or “slightly deleterious” mutations are fixed not because of their advantage/disadvantage but due to drift alone.

    This is a problem for darwinism! We can be sure that slightly deleterious mutations outnumber slightly beneficial mutations 1000 to 1 at least. If slightly deleterious mutations are getting fixed at nearly the same rate as slightly beneficial, then we are evolving down hill, folks.

  2. 2
    Barry Arrington says:

    Dr. Torley,
    Over the years you have posted some of UD’s greatest hits, including its (by far) all time best seller. Your contributions here are priceless, and we look forward to many more flashes of Torley brilliance in the years to come.

    Your post here shows that not only do you have a penetrating mind, but also you are a man of integrity and strong character. Admitting a mistake can be one of the most difficult things we can do. This is especially the case when your interlocutors have been as boorish as Dr. Matzke.

  3. 3
    JLAfan2001 says:

    Wow, this is a bad time for UD and ID in general.

    First, Eric Anderson gets refuted on a self-replicating molecule with function.

    Then, VJTorley gets refuted on the neutral theory.

    And Barb posts a link that we have mathematical proof that the universe came from nothing validating Krauss after all the mocking he took.

    SHHHH….Hear that? It’s the sound of the gaps tightening.

    Torley, you said:

    “The paper has therefore failed to demonstrate that speciation is an event that lies beyond the reach of chance.”

    “I think it is fair to say that the question of where the edge of evolution lies has now been thrown open again.”

    Will you now admit that Neo-Darwinism is a valid, proven science and that there is no need for an intelligent designer or will you continue to fool the naive into thinking the opposite?

  4. 4
    JLAfan2001 says:

    Another thing. If the neutral theory has been validated, wouldn’t that be proof that most of the human genome is in fact just as WD400 and Moran has been saying? If that is the case, that would be another nail in ID’s coffin.

  5. 5
    JLAfan2001 says:

    Meant to say that the human genome would in fact be junk.

  6. 6
    gpuccio says:

    VJ:

    I believe you have expressed your ideas very well, and in the end you have been convinced by the arguments of your interlocutors, and have clearly stated that. That is very good.

    I remain of the idea I have already expressed. Neutral mutations happen, and their number and fixation is of no real interest to ID theory, because neutral mutations, either fixed or not, are only a variation of random variation. They have no effect on the probabilistic evaluation of the emergence of functional outcomes, which is the only pertinent issue in ID theory.

    I think that the main reason why some in ID are hostile to the concept of neutral mutations is that they are a strong argument for common descent. So, I understand that those who don’t accept CD have some difficulties to accept the neutral interpretation of much of the variation we observe in natural history.

    On the contrary, I accept CD (and I believe that you do, too), and I see in neutral mutation exactly one of the strongest arguments in favor if ID. The interpretation of the sequence diversity of similar proteins in various species is, at the same time, a strong argument for CD and a strong argument for ID. That’s what is sometimes called the “big bang theory” of protein evolution. It means that new protein appear at the beginning of their history, at some definite time, and then, in the course of evolution, they traverse their own functional space: they change in sequence without changing much in structure and function. IOWs, they undergo neutral mutations.

    That is a strong argument for CD. But it is also a strong argument for ID. Indeed, it shows that translated genes cannot leave their own functional island, because negative selection acts against that. Only neutral variation is allowed. That’s probably also the reason why synonymous mutations are more abundant than they should be: the simple fact is that many non synonymous mutations are really deleterious, and are selected against.

    So, we are back to the total failure of the neo darwinian algorithm.

    a) Functional, translated genes can only remain what they are, or change slightly.

    b) Non functional, non translated genes (such as pseudogenes or non coding DNA segments) can undergo any kind of variation, because variation is by definition neutral here. As the sequence is not functional and is not translated, it cannot be “seen” by NS, neither positively nor negatively.

    So, these non functional sequences can go anywhere in the search space, and they can be fixed at any time. Any sequence has the same probabilities of being fixed as any other sequence. Genetic drift is totally irrelevant.

    Therefore, arguing that a new complex functional sequence can be derived from a non functional sequence without a design intervention is like saying that new complex functional sequences can be found by a purely random walk.

    Which, as we know, is not true.

    That’s why, when darwinists argue that functional proteins derive from non coding sequences by mutation and variation, they are really arguing for design, without knowing it.

  7. 7
    gpuccio says:

    VJ:

    I had not read this last statement of yours:

    The fallacy in the logic here should now be apparent. There is no reason to suppose that one singleton has to be fixed in the population before another one can be. The paper has therefore failed to demonstrate that speciation is an event that lies beyond the reach of chance.

    I don’t agree, and I don’t understand why you say that. IMO, the paraghraph you quote from Dr. Kozulic’s 2011 paper is perfectly correct. Please, see also my post #6.

    Could you please clarify the reasons for that statement? I can’t see any connection between that conclusion and the discussion about neutral fixation. Please, explain.

  8. 8
    gpuccio says:

    JLAfan2001:

    Please, look at my post #6. Your comments are welcome.

  9. 9
    tragic mishap says:

    I will have to agree with gpuccio here. Neutral evolution doesn’t help in the evolution of novel protein folds because there is no relation between which mutations get fixed and which are steps on the road to novel folds. This means ID theorists are completely justified in probability arguments based on protein folds, and that has virtually nothing to do with the current issue. ID has never denied that proteins can evolve neutrally. The probability barrier is erected by novel folds/function. In response, we have always been told that selection allows fixation of incrementally beneficial mutations, but those mutations are never made explicit and meanwhile evolutionary theory is abandoning selection altogether!

  10. 10
    gpuccio says:

    tragic mishap:

    Exactly! You have stated it very well 🙂

  11. 11
    scordova says:

    Dr. Torley,

    You are indeed an individual of great integrity and courage.

    I wish I had been more forthright in asserting that the Mendel team by and large accepts for the sake of argument the tenets of neutral theory on mathematical grounds but not on functional grounds. I guess my mention of the Mendel team in the links I referred you to was buried in the long discussions.

    The team showed that the working assumption of neutral theory leads to functional disasters where abundant damage is “fixed” (made permanent) in the genomes of species. I feel guilty that if I been clearer and more articulate, I might have spared you having to make a retraction.

    ID isn’t supported just by IC and CSI and critical analysis of OOL, it is supported by population genetics. And this has been unfortunately too obscure a topic, but evidence of ID is there in the study of the details.

    One evidence for ID is that huge amounts of damaged genes are “fixed” (Darwinian double-speak for ‘made permanent’, not really repaired, lol). Sharks and fish without stomachs, beetles without wings, snakes without legs, troglobites without eyes, maybe even one fish without hemoglobin, huge numbers of paralogous reduntdant genes gone.

    Though Darwinists would never concede it, when a species line goes completely extinct, it’s genome is permanently “fixed” in the sense that the damage is made permanent.

    Maybe to appreciate why the Mendel team was pushing some elements of neutral theory, consider Darwin’s statement:

    natural selection is daily and hourly scrutinising, throughout the world, the slightest variations; rejecting those that are bad, preserving and adding up all that are good; silently and insensibly working, whenever and wherever opportunity offers

    Charles Darwin

    What neutral theory unwittingly demonstrated was not only does natural selection fail to preserve the good, it fails to keep the bad from becoming a permanent feature of the population (aka “fixed”).

    If the bad trait is almost neutral to selection, it can be treated as neutral, and thus the bad are guaranteed to be made permanent in the population. It essentially destroyed Darwinism as a mechanism of preserving design, and hence it becomes dubious that it can even make design in the first place.

    PS
    1. You bailed me out of bad situation by posting this thread. I’ve unfortunately been getting a reputation as an ID turncoat because I don’t refrain from being critical of claims by other ID proponents. I speak my conscience, even if I’m wrong. Thanks for helping me out.

    2. You were faster than me, my penance was offered about 8 years after I first put forward my ideas:
    Admitting significant errors in my understanding of physics.

  12. 12
    wd400 says:

    Well, I’m glad you’ve at least been able to admit your errors.

    JLAFAn,

    Indeed – that most of the genome diverges at near to the netural rate is one of the good arguments for the fact most of our genome is junk. If randomly swapping out these bases doesn’t change anything then those bases can hardly be doing any sequence-specific functions.

  13. 13
    mahuna says:

    Is there some reason someone picked 5 million years? Ann Gauger suggests in her book that humans (homo sapiens) might be 1 million years old. The more common guess is that humans are perhaps 100,000 years old. And we have no direct ancestors. So exactly whose DNA has been randomly mutating for 5 million years?

  14. 14
    tjguy says:

    JLA says:

    And Barb posts a link that we have mathematical proof that the universe came from nothing validating Krauss after all the mocking he took.

    Whoa! Mathematical proof of Krauss’s tomfoolery?

    How in the world do you come up with that?

    My bet is that the equation has been rigged. How do we know their starting point accurately reflects reality?

    Me thinks you are far too easily persuaded, but I’m sure the math is over our heads. At least I know it is over mine.

  15. 15
    Mung says:

    During this time of scrutiny, we must be our own harshest critics.

    ^^^^^
    |||||

  16. 16
    bornagain77 says:

    wd400 states,,,

    “one of the good arguments for the fact (ahem belief) most of our genome is junk.”

    I wonder if the following would be a good argument, in wd400’s mind, that our genome is not mostly junk?

    Do you believe Richard Dawkins exists?
    Excerpt: DNA is the best information storage mechanism known to man. A single pinhead of DNA contains as much information as could be stored on 2 million two-terabyte hard drives.
    http://creation.com/does-dawkins-exist

    Information Storage in DNA by Wyss Institute – video
    https://vimeo.com/47615970

    Quote from preceding video:
    “The theoretical (information) density of DNA is you could store the total world information, which is 1.8 zetabytes, at least in 2011, in about 4 grams of DNA.”
    Sriram Kosuri PhD. – Wyss Institute

    Storing information in DNA – Test-tube data – Jan 26th 2013
    Excerpt: Dr Goldman’s new scheme is significant in several ways. He and his team have managed to set a record (739.3 kilobytes) for the amount of unique information encoded. But it has been designed to do far more than that. It should, think the researchers, be easily capable of swallowing the roughly 3 zettabytes (a zettabyte is one billion trillion or 10^²¹ bytes) of digital data thought presently to exist in the world and still have room for plenty more.
    http://www.economist.com/news/.....d-magnetic

    I just can’t seem to muster the blind faith that atheists have to believe that staggering complexity is an accident! 🙂

    Perhaps wd400 can help me become a true believer in Darwinian evolution by showing me a violation of the following null hypothesis so as to give me at least a small hint towards the feasibility of the unguided processes of Darwinian evolution to produce such an astonishing systems architecture?

    The Capabilities of Chaos and Complexity: David L. Abel – Null Hypothesis For Information Generation – 2009
    Excerpt of conclusion pg. 42: “To focus the scientific community’s attention on its own tendencies toward overzealous metaphysical imagination bordering on “wish-fulfillment,” we propose the following readily falsifiable null hypothesis, and invite rigorous experimental attempts to falsify it: “Physicodynamics cannot spontaneously traverse The Cybernetic Cut: physicodynamics alone cannot organize itself into formally functional systems requiring algorithmic optimization, computational halting, and circuit integration.” A single exception of non trivial, unaided spontaneous optimization of formal function by truly natural process would falsify this null hypothesis.”
    http://www.ncbi.nlm.nih.gov/pm.....MC2662469/
    Can We Falsify Any Of The Following Null Hypothesis (For Information Generation)
    1) Mathematical Logic
    2) Algorithmic Optimization
    3) Cybernetic Programming
    4) Computational Halting
    5) Integrated Circuits
    6) Organization (e.g. homeostatic optimization far from equilibrium)
    7) Material Symbol Systems (e.g. genetics)
    8) Any Goal Oriented bona fide system
    9) Language
    10) Formal function of any kind
    11) Utilitarian work
    http://mdpi.com/1422-0067/10/1/247/ag

    Three subsets of sequence complexity and their relevance to biopolymeric information – Abel, Trevors
    Excerpt: Three qualitative kinds of sequence complexity exist: random (RSC), ordered (OSC), and functional (FSC).,,, Shannon information theory measures the relative degrees of RSC and OSC. Shannon information theory cannot measure FSC. FSC is invariably associated with all forms of complex biofunction, including biochemical pathways, cycles, positive and negative feedback regulation, and homeostatic metabolism. The algorithmic programming of FSC, not merely its aperiodicity, accounts for biological organization. No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization. Organization invariably manifests FSC rather than successive random events (RSC) or low-informational self-ordering phenomena (OSC).,,,

    Testable hypotheses about FSC

    What testable empirical hypotheses can we make about FSC that might allow us to identify when FSC exists? In any of the following null hypotheses [137], demonstrating a single exception would allow falsification. We invite assistance in the falsification of any of the following null hypotheses:

    Null hypothesis #1
    Stochastic ensembles of physical units cannot program algorithmic/cybernetic function.

    Null hypothesis #2
    Dynamically-ordered sequences of individual physical units (physicality patterned by natural law causation) cannot program algorithmic/cybernetic function.

    Null hypothesis #3
    Statistically weighted means (e.g., increased availability of certain units in the polymerization environment) giving rise to patterned (compressible) sequences of units cannot program algorithmic/cybernetic function.

    Null hypothesis #4
    Computationally successful configurable switches cannot be set by chance, necessity, or any combination of the two, even over large periods of time.

    We repeat that a single incident of nontrivial algorithmic programming success achieved without selection for fitness at the decision-node programming level would falsify any of these null hypotheses. This renders each of these hypotheses scientifically testable. We offer the prediction that none of these four hypotheses will be falsified.
    http://www.tbiomed.com/content/2/1/29

    The Law of Physicodynamic Insufficiency – Dr David L. Abel – November 2010
    Excerpt: “If decision-node programming selections are made randomly or by law rather than with purposeful intent, no non-trivial (sophisticated) function will spontaneously arise.”,,, After ten years of continual republication of the null hypothesis with appeals for falsification, no falsification has been provided. The time has come to extend this null hypothesis into a formal scientific prediction: “No non trivial algorithmic/computational utility will ever arise from chance and/or necessity alone.”
    http://www-qa.scitopics.com/Th.....iency.html

    Is Life Unique? David L. Abel – January 2012
    Concluding Statement: The scientific method itself cannot be reduced to mass and energy. Neither can language, translation, coding and decoding, mathematics, logic theory, programming, symbol systems, the integration of circuits, computation, categorizations, results tabulation, the drawing and discussion of conclusions. The prevailing Kuhnian paradigm rut of philosophic physicalism is obstructing scientific progress, biology in particular. There is more to life than chemistry. All known life is cybernetic. Control is choice-contingent and formal, not physicodynamic.
    http://www.mdpi.com/2075-1729/2/1/106/

  17. 17
    Mung says:

    wd400, given the definition of “junk” you are using, most of the segments on my new hard drive probably qualify as junk too. So what.

  18. 18
  19. 19
    StephenB says:

    JLAfan2001

    Barb posts a link that we have mathematical proof that the universe came from nothing validating Krauss after all the mocking he took.

    Could you point me in the right direction so that I can evaluate your claim? Are you saying that Barb agrees with Krauss? Are you saying that mathematics can disprove causality? Are you saying that a universe can come from nothing? Please clarify.

  20. 20
    JLAfan2001 says:

    StephenB

    Follow BA77 link which will lead you to the link that Barb has posted. I would say that she doesn’t agree with it since she is a theist.

  21. 21
    lpadron says:

    Scordova,
    Turncoat? Hardly. I greatly appreciate your holding the ID camp to the same standards we hold those on the other side of the debate to.

  22. 22
    Barb says:

    JLAfan2001, “And Barb posts a link that we have mathematical proof that the universe came from nothing validating Krauss after all the mocking he took.”

    Hold up a second. I posted a link to a blog which had an article that I found interesting. I DID NOT state that I believed it. The scientists believe that they have mathematical proof of a spontaneously appearing universe, which they get from a particular theorem.

    There aren’t enough Holiday Inn Express hotels in the universe for me to begin to understand the math involved. As near as I can tell from a cursory reading, the universe didn’t so much “come into being from nothing”, but, due to quantum fluctuations, some previously existing energy or matter state(s), multiple branes, or whatever subsequently evolved or merged into the universe that we observe today.

    Going back for another reading I note that it says that the two branes were also created from nothing. In the universe, even in a vacuum, particles pop in and out of being in pairs of particle/antiparticle. They don’t exist for very long and don’t generally impact the larger scope of things.

    However, it is theorectically possible–at least as far as this article is concerned–that such particle/antiparticle creation at some point in the distant past appeared in just the right place to begin a chain reaction with other particle/antiparticle pairs and create ‘space’.

    This theory expands upon vacuum fluctuations and explains the ‘how’, or the hypotheses on ‘how’ at least.

  23. 23
    fossil says:

    I think admitting we are wrong when we are is not only healthy for us mentally but also builds trust that we are not a bunch of deceivers out to get the gullible. Everyone makes mistakes we are not always right – we are fallible humans not machines.

    That being said I think we need to look at the big picture. One might show me an interpretation of a plausible lineage in one small part of the fossil record but overall I believe in what Dr. Gould called “punctuated equilibrium” and with the idea of many explosions within the fossil record where things come into existence suddenly and then basically goes into stasis. I also think what ID has to say about those explosions that they occur very rapidly with no precursors is also valid. Along that line to me the whole understanding of human origins seems to be still up in the air and very confused with very little precious evidence connecting man with apes.

    Even Dr. Lenski’s experiments after some 60000 generations only changed bacterial diet which humans have also done (Lactose intolerance) within far less number of generations. No one has noticed that those bacteria have changed into anything else than what they were originally nor has anyone ever seen a dog pop out a cat or vice versa. Besides breeders know very well that a dog or a cat can be altered on so much then either the process stops or difficulties set in (there is nothing more heartier than the Heinz variety mutt) If something is mutated almost without exception it usually has difficulty surviving rather than thriving.

    Furthermore as a YEC with the exception of the age of the earth as a mass I find a lot of evidence for life being rather young on this planet. Such things as the presence of soft tissue and segments of intact DNA in fossils dated by radiometric means to more than one hundred million years to me testify that life is not millions of years old after all nor do I think many arguments for preservation are that strong.

    If what these kind of things show are true than the whole discussion of neutral theory, in my opinion, goes up in smoke. If man has not been in existence as long as science says he has there is no way he could have evolved from something pre-ape to what we are now and to me there is no theory in existence that can show how that could possibly have happened within a much shorter time frame than theorized. Just ask Dr. Meyer concerning the Cambrian explosion.

  24. 24
    Mung says:

    In this thread Sal apologizes for not clearly telling VJT he was wrong when Salvador apparently knew that VJT was wrong, while on another thread Sal whines about being castigated for having the temerity to tell VJT that he was wrong.

  25. 25
    JLAfan2001 says:

    Barb

    See post # 20. I know that you don’t accept a universe formed from the quantum vacuum because your god won’t allow it.

  26. 26
    scordova says:

    What I would have done different over the course of these discussions when I provided a link my essay on Rupe and Sanford, was to have specifically highlighted this discovery of the Mendel team:

    We first confirm that our numerical simulations correctly tallying the fixation of neutral mutations. We show that neutral mutations go to fixation just as predicted by conventional theory (i.e., over deep time the fixation rate approached the gametic mutation rate).

    Johns Sanford, Christopher Rupe, the rest of the Mendel Team

    But some qualification. They obviously were setting this up as a Proof by Contradiction. If things fix as easily as Kimura asserted, we should all be dead 100 times over.

    Their simulation wasn’t based on equations, but was built to validate or refute equations! All they did was have a population, added mutations to it, tracked the mutations over millions of years of simulated time, and saw if the mutations fixed.

    The model was simply: mom has X number of mutations and so did Dad. The put an identifier on the mutation, and see if at the end of millions of years some of the mutations got fixed, and then they counted them up. Thus they proved Kimura’s 1st result:

    We first confirm that our numerical simulations correctly tallying the fixation of neutral mutations. We show that neutral mutations go to fixation just as predicted by conventional theory (i.e., over deep time the fixation rate approached the gametic mutation rate).

    Johns Sanford, Christopher Rupe, the rest of the Mendel Team

    Kimura’s second result was that if the mutation is slightly deleterious according to

    S less than 4ne

    Then 50% of these deleterious mutations would fix in the population. Kondrashov tried to say there might be cleaning out mechanism to save the day, but the simulation didn’t bear that out. The fact we have now many studies saying huge amounts of genomes have had dysfunction made permanent in the species (loss of stomachs, eyes, legs, wings, proteins, DNA, who knows what else), the result of the Mendel simulation is believable.

    Some have criticized Mendel’s accountant as being unrealistic, but that is just a charade. Why aren’t Darwinists publishing their simulations with the RIGHT parameters?

    I pointed out the rather humorous fact that it is the creationists that were most eager to make computational population genetic simulations and publish the results:
    ICC 2013, Calling All Darwinsts, Where is Your Best PopGen Simulation. The Mendel program has all sorts of features. The depth that the 10 or so geneticists and engineers put to the program is incredible. I believe in some cases some of the sims had to be run on super computers.

    Kimura’s 2nd result (fixation of deleterious mutations) unwittingly destroyed Darwin’s claims that NS will purge the bad and just keep adding the good. NO! Real evolution in the wild keeps losing the good, and just keeps adding the bad!

    The only way out of this is for Darwinists to say, loss of stomachs, eyes, legs, wings, blood, proteins, etc. is “beneficial” and so to is acquisition of inherited diseases like tay-sachs, juvenile diabetes, cystic fibrosis, sickle cell anemia, etc. “Beneficial” indeed 🙄 Saving the Darwinian paradigm through constant equivocation of what “beneficial” really means.

    My apologies to Dr. Torley if I gave the impression I that I didn’t think fixation rates were equal to mutation rates. It was not my intention, but I hope these discussions have shown that ID has rich treasures to find in population genetics.

  27. 27
    bornagain77 says:

    I’m certainly not sold that mathematics has lent any rigid support to the modern synthesis of neo-Darwinism so as to demarcate is as a genuine scientific theory instead of the pseudo-science that it really is.

    “For many years I thought that it is a mathematical scandal that we do not have a proof that Darwinian evolution works.”
    Gregory Chaitin – Proving Darwin 2012 – Highly Respected Mathematician

    Active Information in Metabiology – Winston Ewert, William A. Dembski, Robert J. Marks II – 2013
    Except page 9: Chaitin states [3], “For many years I have thought that it is a mathematical scandal that we do not have proof that Darwinian evolution works.” In fact, mathematics has consistently demonstrated that undirected Darwinian evolution does not work.
    http://bio-complexity.org/ojs/.....O-C.2013.4

    Oxford University Seeks Mathemagician — May 5th, 2011 by Douglas Axe
    Excerpt: “Grand theories in physics are usually expressed in mathematics. Newton’s mechanics and Einstein’s theory of special relativity are essentially equations. Words are needed only to interpret the terms. Darwin’s theory of evolution by natural selection has obstinately remained in words since 1859.” …
    http://biologicinstitute.org/2.....emagician/

    “On the other hand, I disagree that Darwin’s theory is as `solid as any explanation in science.; Disagree? I regard the claim as preposterous. Quantum electrodynamics is accurate to thirteen or so decimal places; so, too, general relativity. A leaf trembling in the wrong way would suffice to shatter either theory. What can Darwinian theory offer in comparison?”
    (Berlinski, D., “A Scientific Scandal?: David Berlinski & Critics,” Commentary, July 8, 2003)

    WHAT SCIENTIFIC IDEA IS READY FOR RETIREMENT? Evolution is True – Roger Highfield – January 2014
    Excerpt: If evolutionary biologists are really Seekers of the Truth, they need to focus more on finding the mathematical regularities of biology, following in the giant footsteps of Sewall Wright, JBS Haldane, Ronald Fisher and so on.
    The messiness of biology has made it relatively hard to discern the mathematical fundamentals of evolution. Perhaps the laws of biology are deductive consequences of the laws of physics and chemistry. Perhaps natural selection is not a statistical consequence of physics, but a new and fundamental physical law. Whatever the case, those universal truths—’laws’—that physicists and chemists all rely upon appear relatively absent from biology.
    Little seems to have changed from a decade ago when the late and great John Maynard Smith wrote a chapter on evolutionary game theory for a book on the most powerful equations of science: his contribution did not include a single equation.
    http://www.edge.org/response-detail/25468

    Nobel Prize-Winning Physicist Wolfgang Pauli on the Empirical Problems with Neo-Darwinism – Casey Luskin – February 27, 2012
    Excerpt: “In discussions with biologists I met large difficulties when they apply the concept of ‘natural selection’ in a rather wide field, without being able to estimate the probability of the occurrence in a empirically given time of just those events, which have been important for the biological evolution. Treating the empirical time scale of the evolution theoretically as infinity they have then an easy game, apparently to avoid the concept of purposesiveness. While they pretend to stay in this way completely ‘scientific’ and ‘rational,’ they become actually very irrational, particularly because they use the word ‘chance’, not any longer combined with estimations of a mathematically defined probability, in its application to very rare single events more or less synonymous with the old word ‘miracle.'” Wolfgang Pauli (pp. 27-28) –
    http://www.evolutionnews.org/2.....56771.html

    Murray Eden, as reported in “Heresy in the Halls of Biology: Mathematicians Question Darwinism,” Scientific Research, November 1967, p. 64.
    “It is our contention that if ‘random’ is given a serious and crucial interpretation from a probabilistic point of view, the randomness postulate is highly implausible and that an adequate scientific theory of evolution must await the discovery and elucidation of new natural laws—physical, physico-chemical, and biological.”
    Murray Eden, “Inadequacies of Neo-Darwinian Evolution as a Scientific Theory,” Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution, editors Paul S. Moorhead and Martin M. Kaplan, June 1967, p. 109.
    http://www.creationscience.com.....tes32.html

    Oxford University Admits Darwinism’s Shaky Math Foundation – May 2011
    Excerpt: However, mathematical population geneticists mainly deny that natural selection leads to optimization of any useful kind. This fifty-year old schism is intellectually damaging in itself, and has prevented improvements in our concept of what fitness is. – On a 2011 Job Description for a Mathematician, at Oxford, to ‘fix’ the persistent mathematical problems with neo-Darwinism.
    http://www.evolutionnews.org/2.....46351.html

    HISTORY OF EVOLUTIONARY THEORY – WISTAR DESTROYS EVOLUTION
    Excerpt: A number of mathematicians, familiar with the biological problems, spoke at that 1966 Wistar Institute,, For example, Murray Eden showed that it would be impossible for even a single ordered pair of genes to be produced by DNA mutations in the bacteria, E. coli,—with 5 billion years in which to produce it! His estimate was based on 5 trillion tons of the bacteria covering the planet to a depth of nearly an inch during that 5 billion years. He then explained that the genes of E. coli contain over a trillion (10^12) bits of data. That is the number 10 followed by 12 zeros. *Eden then showed the mathematical impossibility of protein forming by chance.
    http://www.pathlights.com/ce_e.....hist12.htm

    And all this is besides the fact that the modern synthesis itself is falsified empirically:

    http://www.uncommondescent.com.....ent-495996

    Moreover, even if Darwinists were able to come up with a mathematical demarcation criteria down to the level of physics (which they won’t), so as to designate Darwinism as a real scientific theory instead of a pseudo-science, they still would not prove that Darwinism was unguided (i.e. atheistic) since mathematics itself testifies to God’s handiwork:

    Mathematics and Physics – A Happy Coincidence? – William Lane Craig – video
    http://www.metacafe.com/w/9826382

    1. If God did not exist the applicability of mathematics would be a happy coincidence.
    2. The applicability of mathematics is not a happy coincidence.
    3. Therefore, God exists.

    Of humorous note:

    “Darwin’s theory is easily the dumbest idea ever taken seriously by science.”
    Granville Sewell – Professor Of Mathematics – University Of Texas – El Paso

    “You might think that a theory so profound would be laden with intimidating mathematical formulas and at least as difficult to master as Newton’s Mechanics or Einsteins Relativity. But such is not the case. Darwinism is the most accessible “scientific” theory ever proposed. It needs no math, no mastery of biology, no depth of understanding on any level. The dullest person can understand the basic story line: “Some mistakes are good. When enough good mistakes accumulate you get a new species. If you let the mistakes run long enough, you get every complicated living thing descending from one simple living thing in the beginning. There is no need for God in this process. In fact there is no need for God at all. So the Bible, which claims that God is important, is wrong.” You can be drunk, addled, or stupid and still understand this. And the real beauty of it is that when you first glimpse this revelation with its “aha!” moment, you feel like an Einstein yourself. You feel superior, far superior, to those religious nuts who still believe in God. Without having paid any dues whatsoever, you breathe the same rarified air as the smartest people who have ever lived.”
    – Laszlo Bencze

  28. 28
    nullasalus says:

    Just to explain – as has been explained to Krauss, and others, over and over again (and which Krauss has understood, but he’s responded by punting rather than making a big deal out of it.)

    There is no scientific proof of a universe coming from “nothing”, nor mathematical. When scientists, including the ones in the paper being referenced, talk about ‘nothing’ it’s utterly distinct from the ‘nothing’ that’s relevant to the philosophical question: it’s a something, a set of physical laws and states. Which leads us to ask, where that came from, and if it came from something else, etc. On and on until we get to the necessarily existent, or claims of ‘it’s just magic, sometimes things just are and have no explanation’, etc.

    Sorry to derail VJT’s thread, but this was being discussed and it’s worth a mention. See: http://edwardfeser.blogspot.co.....thing.html

  29. 29
    Eric Anderson says:

    JLAfan2001 @3:

    First, Eric Anderson gets refuted on a self-replicating molecule with function.

    Nope. But we do have JLAfan2001 coming here to make misrepresentations. 🙂

    So far, I’ve been supremely vindicated and no-one has offered a single example of a self-replicating molecule. That, notwithstanding that I explicitly granted that such a thing might be possible in principle. But, unfortunately, it appears the nuances may escape some.

    I don’t want to take vjtorley’s thread OT, so if you have some refutation to make or something of substance to contribute, you’re invited over to the other threads to try and make it. Or just let us know what self-replicating molecule you’ve discovered, and I’ll be the first to nominate you to the Nobel Committee to great fanfare.

    http://www.uncommondescent.com.....iogenesis/

    http://www.uncommondescent.com.....ent-495959

  30. 30
    Eric Anderson says:

    Sal @26:

    Great comments worth chewing on. Your takeaway in particular:

    Kimura’s 2nd result (fixation of deleterious mutations) unwittingly destroyed Darwin’s claims that NS will purge the bad and just keep adding the good. NO! Real evolution in the wild keeps losing the good, and just keeps adding the bad!

    This is of course precisely what any sane engineer would expect if we started introducing random changes into a highly-functional, highly-specified, sophisticated system. But of course, we mustn’t listen to the engineers, because . . . well, they’re engineers. And biology is . . . you know . . . biology.

  31. 31
    StephenB says:

    JLAfan2001

    Follow BA77 link which will lead you to the link that Barb has posted. I would say that she doesn’t agree with it since she is a theist.

    I don’t understand. Krauss thinks that a universe can come from out of nothing. You think that Barb disagrees with him, as well she should. Any rational person would know that nothing can begin to exist without a cause. Mathematics has nothing to do with it.

    With whom do you agree? Barb or Krauss? Presumably, you agree with Krauss since you imply that he should not have been mocked for his position and since you opined that “this is a bad time for UD and ID in general.”

  32. 32
    Mung says:

    RE: Mendel’s Accountant

    Gibson, Baumgardner, Brewer and Sanford provide the following link in their paper:

    http://www.MendelsAccountant.info

    My question is, where’s the source code? Apparently it’s written in Fortran?

  33. 33
    wallstreeter43 says:

    JLAFAN , ksince krauss himself has constantly backpeddled when he is confronted by people of common sense about the universe coming from nothing the weasel krauss then admits that he isn’t talking about a literal nothing, and David Albert destroys him on this fact.

    http://www.nytimes.com/2012/03......html?_r=0

    Krauss seems to be thinking that these vacuum states amount to the relativistic-­quantum-field-theoretical version of there not being any physical stuff at all. And he has an argument — or thinks he does — that the laws of relativistic quantum field theories entail that vacuum states are unstable. And that, in a nutshell, is the account he proposes of why there should be something rather than nothing.

    But that’s just not right. Relativistic-quantum-field-theoretical vacuum states — no less than giraffes or refrigerators or solar systems — are particular arrangements of elementary physical stuff. The true relativistic-quantum-field-­theoretical equivalent to there not being any physical stuff at all isn’t this or that particular arrangement of the fields — what it is (obviously, and ineluctably, and on the contrary) is the simple absence of the fields! The fact that some arrangements of fields happen to correspond to the existence of particles and some don’t is not a whit more mysterious than the fact that some of the possible arrangements of my fingers happen to correspond to the existence of a fist and some don’t. And the fact that particles can pop in and out of existence, over time, as those fields rearrange themselves, is not a whit more mysterious than the fact that fists can pop in and out of existence, over time, as my fingers rearrange themselves. And none of these poppings — if you look at them aright — amount to anything even remotely in the neighborhood of a creation from nothing.

    Krauss, mind you, has heard this kind of talk before, and it makes him crazy. A century ago, it seems to him, nobody would have made so much as a peep about referring to a stretch of space without any material particles in it as “nothing.” And now that he and his colleagues think they have a way of showing how everything there is could imaginably have emerged from a stretch of space like that, the nut cases are moving the goal posts. He complains that “some philosophers and many theologians define and redefine ‘nothing’ as not being any of the versions of nothing that scientists currently describe,” and that “now, I am told by religious critics that I cannot refer to empty space as ‘nothing,’ but rather as a ‘quantum vacuum,’ to distinguish it from the philosopher’s or theologian’s idealized ‘nothing,’ ” and he does a good deal of railing about “the intellectual bankruptcy of much of theology and some of modern philosophy.” But all there is to say about this, as far as I can see, is that Krauss is dead wrong and his religious and philosophical critics are absolutely right. Who cares what we would or would not have made a peep about a hundred years ago? We were wrong a hundred years ago. We know more now. And if what we formerly took for nothing turns out, on closer examination, to have the makings of protons and neutrons and tables and chairs and planets and solar systems and galaxies and universes in it, then it wasn’t nothing, and it couldn’t have been nothing, in the first place. And the history of science — if we understand it correctly — gives us no hint of how it might be possible to imagine otherwise.

    JLAFAN , now I know that instead of admitting that lawrence krauss was 100% completely wrong !my our gonna let him slide! not because you are following the evidence in an unbiased manner but because you are totally biased in favor of the secular view.

    I have also showed you in our conversation a on veridical Nde’s and the shroud of turin in that you are willing to follow non peer reviewed evidence in favor of someone as ignorant and biased as Collin berry ..

    JLAFAN I think you really need to take a good hard look at how yoir approaching these subjects. We have been friends for a whileand as a friend I have to point these things out to you.

    You know that I know the shroud of turin well and I have constantly called you out on your bias against the shroud and anything that favors theism .

    It’s almost like you want atheism to be true.

  34. 34
    Mung says:

    Salvador Cardoza:

    What I would have done different over the course of these discussions when I provided a link my essay on Rupe and Sanford, was to have specifically highlighted this discovery of the Mendel team:

    In this thread where did you provided a link to that essay?

    I can’t find it.

  35. 35
    Mung says:

    Salvador Cardoza:

    Hats off to VJTorley for vindicating claims I’ve made about neutral theory (non-Darwinian evolution) for almost the last eight years at UD.

    http://www.uncommondescent.com.....king-rate/

    Vincent, do you think that you’ve vindicated Salvador’s claims about neutral theory?

    Salvador, what claims have you made about neutral theory for the last 8 years here at UD that were vindicated by Vincent’s post?

  36. 36
    Querius says:

    Nicely stated, wallstreeter43.

    The “nothing” that we need to consider is the “doesn’t exist” variety of nothing. A nothing that has no time, thus no probability.

    An example of a “doesn’t exist” kind of nothing is

    *** the Easter Bunny ***.

    To speculate of about quantum states that result in Something from the Nothing, is equivalent of crediting the Easter Bunny as the source for our existence.

    I’m not completely convinced that even Darwinists could swallow that. 😉

    -Q

  37. 37
    Mung says:

    Salvador Cordova, March 31, 2014:

    Hats off to VJTorley for vindicating claims I’ve made about neutral theory (non-Darwinian evolution) for almost the last eight years at UD.

    Vincent Torley, March 30, 2014:
    http://www.uncommondescent.com.....lles-heel/

  38. 38
    gpuccio says:

    VJ:

    I would sum up how I see the situation as follows:

    a) You were probably wrong in your argument about the number of mutations from chinps to humans, and its relation to neutral theory. You did well admitting that.

    b) You were not wrong about speciation and the edge of evolution and all the rest. That has nothing to do with the first problem. Therefore, you were wrong in saying that you were wrong about those things!

  39. 39
    wallstreeter43 says:

    Correct quierius
    It’s actually worse then magic , and people like JLAFAN swallowed the lie up without actually thinking about what it said.

    Dawkins was heckled in Australia during his debate with cardinal pell.
    Out of non being comes non being. To believe otherwise is to believe in magic, but at least with the magician we have the magician, the hat and the rabbit.

  40. 40
    tjguy says:

    OT:

    Fossil says:

    Furthermore as a YEC with the exception of the age of the earth as a mass I find a lot of evidence for life being rather young on this planet. Such things as the presence of soft tissue and segments of intact DNA in fossils dated by radiometric means to more than one hundred million years to me testify that life is not millions of years old after all nor do I think many arguments for preservation are that strong.

    Fossil, I’m just curious about one thing. You seem to believe that life is young as are the fossils, especially those with intact DNA in them. Wouldn’t that mean also that the rocks within which these fossils are buried are also young? So most of the Grand Canyon would have been laid down in the recent past according to this thinking, right?

    So your reason for believing in an old earth is what? Distant starlight? Other old rocks that don’t have fossils in them? Just curious.

    Thanks.

  41. 41
    bornagain77 says:

    Of related note to Barb’s ‘universe from nothing’ paper. I think the present paper Barb cited suffers the same fatal flaw as Krauss and Hawking’s previous attempts to get around the beginning of the universe did.

    The Universe Is Not Eternal – Johanan Raatz – March 1, 2014
    Excerpt: One thing known for certain about quantum gravity is something called the holographic principle. Precisely put, the holographic principle tells us that the entropy of a region of space (measured in terms of information) is directly proportional to a quarter of its surface area. The volume of this region is then actually a hologram of this information on its surface.
    Except this tells us something interesting about the universe as well. Entropy, or the amount of disorder present, always increases with time. In fact not only is this law inviolate, it is also how the flow of time is defined. Without entropy, there is no way to discern forwards and backwards in time.
    But if the holographic principle links the universe’s entropy and its horizon area then going back in time, all of space-time eventually vanishes to nothing at zero entropy. Thus Carroll’s argument is unsound. We already have enough knowledge about what happens beyond the BVG theorem that Craig cites. The universe is not eternal but created.
    It is interesting to note that this also undermines claims made by atheists like Hawking and Krauss that the universe could have fluctuated into existence from nothing. Their argument rests on the assumption that there was a pre-existent zero-point field or ZPF. The only trouble is that the physics of a ZPF requires a space-time to exist in. No space-time means no zero-point field, and without a zero-point field, the universe can not spontaneously fluctuate into existence.
    http://blog.proofdirectory.org.....t-eternal/

    And remember, atheists have been fighting tooth and nail against the evidence for a beginning of the universe ever since Einstein added his ‘fudge factor’ to his equation:

    “Much later, when I was discussing cosmological problems with Einstein, he remarked that the introduction of the cosmological term was the biggest blunder of his life.”
    — George Gamow, My World Line, 1970

    Evidence For The Big Bang – Michael Strauss – video
    https://vimeo.com/91775973
    Entire Video
    Scientific Evidence for the Existence of God – Michael Strauss – video
    https://vimeo.com/9195703

    Big Bang Exterminator Wanted, Will Train – Denyse O’Leary – October 20, 2013
    Excerpt: “Perhaps the best argument in favor of the thesis that the Big Bang supports theism is the obvious unease with which it is greeted by some atheist physicists. At times this has led to scientific ideas, such as continuous creation or an oscillating universe, being advanced with a tenacity which so exceeds their intrinsic worth that one can only suspect the operation of psychological forces lying very much deeper than the usual academic desire of a theorist to support his/her theory.”
    Cosmologist Christopher Isham
    http://www.evolutionnews.org/2.....77961.html

    It is also interesting to point out that a ‘hypothetical’ geometry is postulated in the ‘universe from nothing’ paper, but when considering our present geometry that we currently live in, the ‘real’ geometry that we currently live in and that we can actually test empirically and thus remain ‘scientific’ in our conclusions, then our present geometry reveals something very special to us. Namely, that consciousness is central to the universe:

    The Galileo Affair and Life/Consciousness as the true “Center of the Universe”
    Excerpt: 1. Consciousness either preceded all of material reality or is a ‘epi-phenomena’ of material reality.
    2. If consciousness is a ‘epi-phenomena’ of material reality then consciousness will be found to have no special position within material reality. Whereas conversely, if consciousness precedes material reality then consciousness will be found to have a special position within material reality.
    3. Consciousness is found to have a special, even a central, position within material reality. [14]
    4. Therefore, consciousness is found to precede material reality.

    I find it extremely interesting, and strange, that quantum mechanics tells us that instantaneous quantum wave collapse to its ‘uncertain’ 3D state is centered on each individual conscious observer in the universe, whereas, 4D space-time cosmology (General Relativity) tells us each 3D point in the universe is central to the expansion of the universe. These findings of modern science are pretty much exactly what we would expect to see if this universe were indeed created, and sustained, from a higher dimension by a omniscient, omnipotent, omnipresent, eternal Being who knows everything that is happening everywhere in the universe at the same time. These findings certainly seem to go to the very heart of the age old question asked of many parents by their children, “How can God hear everybody’s prayers at the same time?”,,, i.e. Why should the expansion of the universe, or the quantum wave collapse of the entire universe, even care that you or I, or anyone else, should exist? Only Theism, Christian Theism in particular, offers a rational explanation as to why you or I, or anyone else, should have such undeserved significance in such a vast universe. [15]

    Psalm 33:13-15
    The LORD looks from heaven; He sees all the sons of men. From the place of His dwelling He looks on all the inhabitants of the earth; He fashions their hearts individually; He considers all their works.
    https://docs.google.com/document/d/1BHAcvrc913SgnPcDohwkPnN4kMJ9EDX-JJSkjc4AXmA/edit

    Also of note:

    The Scale of The Universe – Part 2 – interactive graph (recently updated in 2012 with cool features)
    http://htwins.net/scale2/scale.....olor=white

    The preceding interactive graph points out that the smallest scale visible to the human eye (as well as a human egg) is at 10^-4 meters, which ‘just so happens’ to be directly in the exponential center of all possible sizes of our physical reality (not just ‘nearly’ in the exponential center!). i.e. 10^-4 is, exponentially, right in the middle of 10^-35 meters, which is the smallest possible unit of length, which is Planck length, and 10^27 meters, which is the largest possible unit of ‘observable’ length since space-time was created in the Big Bang, which is the diameter of the universe. This is very interesting for, as far as I can tell, the limits to human vision (as well as the size of the human egg) could have, theoretically, been at very different positions than directly in the exponential middle.

    Verse:

    Job 38:19-20
    “What is the way to the abode of light? And where does darkness reside? Can you take them to their places? Do you know the paths to their dwellings?”

  42. 42
    Timaeus says:

    wallstreeter (33):

    jlafan2001 DOES want atheism to be true.

    Why else would he refuse to investigate, not only the technical scientific literature that counts against his current position, but the more reflective writings produced by philosophically and theologically acute scientists? And why else would he refuse to investigate the profound religious literature of the ages?

    By artificially limiting the possible alternatives to shallow scientific materialism and shallow fundamentalism, he rules out the deepest reflections of truly thoughtful scientists (scientists such as Newton and Kepler and Heisenberg and Polanyi, as opposed to one-dimensional “skeptics” like Krauss and Moran and Dawkins), and he rules out the deepest thoughts of truly great religious writers (thinkers such as Plato, Plotinus, Augustine, Aquinas, Sankara, Ramanuja, Kierkegaard, Buber, etc., as opposed to Gish, Morris, and Ham). He clearly does not want the deepest thoughts about either nature or God to gain access to his soul.

    He wants to set up a simple default position: if fundamentalism isn’t true, then atheism is true. And since he believes he can prove that fundamentalism isn’t true, he’s got his warrant for atheism, regardless of how bad his scientific arguments for Darwinism are. So he has no motive to improve his scientific understanding, and no motive for investigating the case for God that doesn’t come from literalist-inerrantist exegesis.

    Why would he set up such a false dichotomy (between narrow fundamentalism and atheism), unless he was rigging the argument so that it would be easy to show that God did not exist?

    Is jlafan2001 conscious of any intellectual or personal dishonesty here? He might not have been, at the beginning, when he was first revolting against fundamentalism. But it is now a year or two since his break with fundamentalism, and he has had plenty of time to investigate more sophisticated understandings of science, and deeper forms of religion. He hasn’t availed himself of that time. The only reasonable conclusion is that he doesn’t any longer want to be talked out of atheism. He is now comfortable there.

    This makes sense; fundamentalists tend not to be seekers. They tend to want black-and-white answers. Then, when their religion collapses, that same tendency persists, and they go for atheism, because it also is a black-and-white answer. Jlafan2001 liked simple answers when he was a fundamentalist, and he likes simple answers now. He doesn’t want to be a seeker, reading, and learning, and wrestling all his life with what is true. He wants to take a clear side, as he did as a young fundamentalist. He’s chosen to take the side of Panda’s Thumb, Pharyngula, Dawkins, Coyne, Krauss, Tyson, etc., for the same reason that he once chose to take the side of Ham, Gish, Morris, etc. The existential stretching of the life of a seeker is not for him. He wants a religious formula.

    And I could live with this, if atheism were merely his private choice. It is his sanctimoniousness about his atheism, his triumphalism over having rejected his fundamentalist past, his glee at attacking the Bible, his image of himself as a crusader for science, his self-induced delusion that he has reached his conclusions by considering all the evidence impartially, etc., that I find offensive.

    We have had people here, such as Kantian Naturalist, who have made intelligent arguments for religious unbelief. Jlafan2001 makes unintelligent arguments for religious unbelief. And that’s because he doesn’t really want to wrestle any longer with the big issues; he just wants atheism to be true.

  43. 43
    Barb says:

    JLAfan writes, “Barb, See post # 20. I know that you don’t accept a universe formed from the quantum vacuum because your god won’t allow it.”

    A universe formed from a quantum vacuum is not nothing. Where did the quantum vacuum come from? A universe that simply appeared from “nothing” goes against all rational thought and experimental science.

    The ZPF mentioned above by BA77 doesn’t appear in the blog post I linked. However, they do mention the cosmological constant, which they take to be non-zero. The post goes on to show what the cosmological constant is in their new(ish) theory:

    What plays the role of the cosmological constant in Dongshan and co’s new theory? Interestingly, these guys say a quantity known as the quantum potential plays the role of cosmological constant in the new solutions.

    This potential comes from an idea called pilot-wave theory developed in the mid-20th century by the physicist David Bohm. This theory reproduces all of the conventional predictions of quantum mechanics but at the price of accepting an additional term known as the quantum potential.

    The theory has the effect of making quantum mechanics entirely deterministic since the quantum potential can be used to work out things like the actual position of the particle.

    However, mainstream physicists have never taken to Bohm’s idea because its predictions are identical to the conventional version of the theory so there is no experimental way of telling them apart. However, it forces physicists to accept a probabilistic explanation for the nature of reality, something they are generally happy to accept.

  44. 44
    jerry says:

    I have some questions that maybe someone who is following this in detail can answer. It would be helpful in trying to understand just what is being agreed to.

    Just what is being postulated by the neutral theory of evolution?

    Does it say that novel proteins are being developed? Or is it saying that proteins are just being modified over time and there is no leaving the island of functionality. Or is it better to say that new coding regions are being modified by mutations a little bit at a time and consequently the proteins expressed will be slightly different over time?

    And if this is true are the new proteins not substantially different from the previous proteins in function? Aren’t we just talking about different alleles of the same coding region?

    My reading on this which might be very wrong is that there is species X about 5-7 million years ago and somehow this species becomes divided in some way, probably geographically, so that the two or more populations are unable to inner breed. Let’s call these populations, X1 and X2. And over time the neutral theory is modifying each population so that there will be a time when they will not be able to breed with each other even if they found each other again and if they wanted to. So X1 becomes species Y and X2 becomes species Z.

    Is the neutral theory saying that the only difference between Y and Z is that there will be similar coding regions in each genome that will code for different proteins. These different proteins will explain the different characteristics of Y and Z.

    Does genetic drift say that there might have been 2 or more alleles at a specific coding region in species X but that only one variation will now appear in species Y and a different variation will appear in species Z. And if that is true what does the two different alleles do in terms of explaining behavioral characteristics between Y and Z. Or is what is being postulated is that a new allele will appear in one of the two species through a mutation and that this new allele may become fixed through genetic drift?

    I assume the neutral theory will not explain completely unrelated coding regions in Y and Z but only those coding regions differences that could feasibly arise by small changes in a specific region over time.

    Also what type of mutations are we talking about? Are we talking about SNP’s or are we talking about the whole gamut of Allen MacNeill’s engines of variation?

    I always thought the neutral theory discussions were a red herring and said so on another thread about this topic. From what I am reading it sounds like the neutral theory is a whole lot about nothing. The real issues lie somewhere else.

    Could someone explain why I am wrong on this?

  45. 45
    jerry says:

    Timaeus,

    He wants to set up a simple default position: if fundamentalism isn’t true, then atheism is true.

    Last Saturday night I went to a play which celebrated the life of a famous American author. It was basically a reading of the author’s thoughts during the author’s life as interpreted by the playwright. The playwright took the published works and letters of the author and then wrote the play.

    I left the play with the following two thoughts, the author was a fantastic wordsmith and often wrote very entertaining prose and poetry and second the author’s thinking was essentially vacuous. Nearly all that the author said was based on taking the opposite side of the conventional wisdom of the time.

    One of the expressed viewpoints was that 19th century restrictive religious dogma that was repressive obviously meant that there was no God at all. Another was that repressive doctrines on sex meant that there should be no restrictions on sex at all. There were a couple others in the same vein, namely, I find this sort of activity repressive, so the complete opposite must be the best way.

    We find similar thinking everywhere in our society. One common one is that, someone will point out the problem with some aspect of capitalism and the solutions is to get rid of capitalism and establish some sort of socialism. I am sure others here can point to other ideas which have similar origins.

  46. 46
    bornagain77 says:

    Barb, I’m going to run that paper by Johanan Raatz and see if I can get any additional information for you.

  47. 47
    vjtorley says:

    Hi gpuccio,

    Thank you for your very thoughtful comments.

    I’d like to make it clear that I remain extremely skeptical of the idea that a protein can acquire a new function as a result of an unguided natural process.

    Dr. Kozulic stated in his 2011 paper: “If just 200 unique proteins are present in each species, the probability of their simultaneous appearance is one against at least 10^4,000.” He then went on to say that the idea of them appearing sequentially wouldn’t work either. It is the latter statement that I am querying. If Dr. Kozulic is mistaken on this point, then the odds of the 200-odd proteins that characterize a new species appearing in a lineage over a period of a few million years can no longer be calculated. Hence we don’t know enough to say it’s impossible. Hence we cannot show mathematically that speciation marks the edge of evolution.

    I should add that in his 2011 paper, Dr. Kozulic uses a very conservative figure of 1 in 10^20 for the odds of a single protein suddenly appearing as a result of an unguided process. Dr. Axe uses a different figure of about 1 in 10^77. The two figures are strikingly different in their implications: it’s likely that there have been far more than 10^20 “trial events” on the primordial Earth, but there could not have been anywhere near 10^77 events. This obviously affects the mathematics of speciation, too.

    I should say that I believe speciation may well mark the edge of evolution, and I’d be quite happy if the evidence showed it did. I’d just like to see a good mathematical demonstration of that point. I hope that clears up matters.

  48. 48
    NickMatzke_UD says:

    Well, now you have some idea why scientists get annoyed with IDists. Before, we were being told that we should take this bogusness seriously because the allegedly esteemed Dr. Kozulic was leveling the criticism. Turns out he had no idea what he was talking out. This sort of thing goes on with almost every ID claim, what’s almost unique here is that the IDist backed off — after several days of epic confusion, aspersions being cast at the evolutionists trying to point out the errors, and even at Sal Cordova!

    The main problem scientists have with ID isn’t about atheism/theism or whatever. It’s about the general incompetence of the biology arguments of IDists.

  49. 49
    bornagain77 says:

    I hold that JLAfan’s preferred Nihilistic worldview is false because it is unable to be lived out in any realistic sense:

    Atheism and Nihilism – Dr. Craig – video
    https://www.youtube.com/watch?v=2cWLvp_6wq0

    Existential Argument against Atheism – November 1, 2013 by Jason Petersen
    1. If a worldview is true then you should be able to live consistently with that worldview.
    2. Atheists are unable to live consistently with their worldview.
    3. If you can’t live consistently with an atheist worldview then the worldview does not reflect reality.
    4. If a worldview does not reflect reality then that worldview is a delusion.
    5. If atheism is a delusion then atheism cannot be true.
    Conclusion: Atheism is false.
    http://answersforhope.com/exis.....t-atheism/

    The Heretic – Who is Thomas Nagel and why are so many of his fellow academics condemning him? – March 25, 2013
    Excerpt: Nobody thinks his daughter is just molecules in motion and nothing but; nobody thinks the Holocaust was evil, but only in a relative, provisional sense. A materialist who lived his life according to his professed convictions—understanding himself to have no moral agency at all, seeing his friends and enemies and family as genetically determined robots—wouldn’t just be a materialist: He’d be a psychopath.
    http://www.weeklystandard.com/.....tml?page=3

    Moreover, this psychopathic characteristic inherent to the atheistic philosophy is born out empirically, in that people who do not believe in a soul tend to be more psychopathic than the majority of normal people in America who do believe in a soul. You can pick that psychopathic study of atheists around the 14:30 minute mark of this following video:

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

    Of related interest:

    Does the Causal Principle Apply to the Universe? – Dr. Craig – video
    https://www.youtube.com/watch?v=dxU4ND8HdYg

  50. 50
    jerry says:

    The main problem scientists have with ID isn’t about atheism/theism or whatever. It’s about the general incompetence of the biology arguments of IDists.

    This is a rather stupid comment. Apparently some people here have wrestled with one aspect of evolution, originally came to a wrong conclusion, and then retracted. This sounds like honest debate. Also it is not reflective of ID in general since most of the major players in ID rarely if ever comment here. Also the topic itself has not been shown to amount to much by anyone.

    Maybe you could address why the neutral theory explains a large percentage of the evolution debate. From what I gather it is just a minor side issue. But I would like to be proven otherwise. That would be very helpful.

  51. 51
    bornagain77 says:

    NickMatzke_UD, I find it strange that you would think it a victory for Darwinian thought when no empirical evidence whatsoever was presented to prove unguided material processes can produce functional information. In fact the only admission on Dr. Torley’s part that I can see is that he finds Darwinian conjectures for the generation of functional information to be somewhat less impossible than he thought so before. But an argument for a theory based on the premise of ‘you have not proved my theory absolutely impossible therefore it must be true’ is not a scientific argument in the first place! If fact such an argument is an completely absurd form of argument as far as science is concerned:

    Darwinism Not Proved (Absolutely) Impossible Therefore Its True – Alvin Plantinga
    http://www.metacafe.com/watch/10285716/

    Of related note, Matzke has been shown to use the dishonest practice of ‘literature bluffing’ here:

    Calling Nick Matzke’s literature bluff on molecular machines – DonaldM UD blogger – April 2013
    Excerpt: So now, 10 years later in 2006 Matzke and Pallen come along with this review article. The interesting thing about this article is that, despite all the hand waving claims about all these dozens if not hundreds of peer reviewed research studies showing how evolution built a flagellum, Matzke and Pallen didn’t have a single such reference in their bibliography. Nor did they reference any such study in the article. Rather, the article went into great lengths to explain how a researcher might go about conducting a study to show how evolution could have produced the system. Well, if all those articles and studies were already there, why not just point them all out? In shorty, the entire article was a tacit admission that Behe had been right all along.
    Fast forward to now and Andre’s question directed to Matzke. We’re now some 17 years after Behe’s book came out where he made that famous claim. And, no surprise, there still is not a single peer reviewed research study that provides the Darwinian explanation for a bacterial flagellum (or any of the other irreducibly complex biological systems Behe mentioned in the book). We’re almost 7 years after the Matzke & Pallen article. So where are all these research studies? There’s been ample time for someone to do something in this regard.
    Matzke will not answer the question because there is no answer he can give…no peer reviewed research study he can reference, other than the usual literature bluffing he’s done in the past.
    http://www.uncommondescent.com.....ent-453291

    And he was also exposed here:

    Hopeless Matzke -David Berlinski & Tyler Hampton August 18, 2013
    http://www.evolutionnews.org/2.....75631.html

    Matzke was also heavily involved in the theatrical literature bluff(s) at the Dover Trail as well he was recently involved in a concerted effort to censor publication of ID friendly material (details upon request). Thus Matzke, IMHO, (from what little I know of the man) has repeatedly shown himself to be a dogmatist who is willing to distort anything and everything in order to keep his preferred Darwinian worldview from being threatened. i.e. He could could care less about investigating whether Darwinian evolution is actually true or not.

  52. 52
    vjtorley says:

    Hi Sal,

    Thank you for your posts. I’m very interested in your models of the neutral theory. I can’t claim to be able to comment on them in any detail, as I haven’t studied the theory in the same depth as you have, but the overall approach you’re taking, of showing that too may harmful mutations would eventually build up over the course of time, sounds very promising. By the way, what do you recommend in the way of good online resources for studying the neutral theory, for laypeople like myself?

  53. 53
    vjtorley says:

    Hi Nick,

    I have previously thanked you for making the effort to educate people on this thread about population genetics. That is commendable.

    I do feel, however, that you’re over-generalizing when you complain about “the general incompetence of the biology arguments of IDists.” I don’t think anyone could credibly describe Dr. Douglas Axe as an incompetent biologist. If you’d care to debate him, go ahead. Personally, I think you’d come off second best.

    Dr. Kozulic can speak for himself, and I’m quite sure he’d be very happy to debate you in a public forum on the topic of fixation. May I remind you also that whatever the merits of his views on population genetics, he is a well-published biochemist. Give credit where credit’s due, I say.

  54. 54
    wd400 says:

    I don’t think anyone could credibly describe Dr. Douglas Axe as an incompetent biologist.

    You mean Douglas “protein corc-oduck” Axe – i think it’s probably possible. As to credit where it’s due – given these posts, Kozulic wouldn’t be due credits for an undergrad genetics course. He might be good at what he does, but he’s demonstrated himself to be all at sea (and extraordinarily arrogant) when it comes to pop. gen.

  55. 55
    scordova says:

    Nick,

    after several days of epic confusion, aspersions being cast at the evolutionists trying to point out the errors, and even at Sal Cordova!

    No kidding! If VJ didn’t step in, I’d be in the dog house again as the ID turncoat. Now I know what it’s like to be as “loved” as Nick at UD. 🙂

    Much as I hated taking on your side of the question, Nick, and being against the claims of one of my own beloved associates here at UD, I felt I would be doing VJ a disservice by not saying something.

    Well, we’re all on the same page now pretty much at least about the rate of fixation relative to the rate of mutation, at least in terms of an abstract mathematical theory.

    However, I take VJ’s side that Kimura’s theory fails as functional theory for the evolution of complexity.

    To the rest of the readers:

    Perhaps to alleviate confusion, I’ll use Kimura/Nei to emphasize the mindless variety of neutral theory that attempts to explain the deep past vs. ReMine/Sanford neutral theory that merely asserts the general absence of selection in the wild. ReMine/Sanford agrees with Kimura/Nei that selection is generally not working on most of the genome, but it would be wrong to say ReMine/Sanford are really neutral evolutionists since they are clearly creationists.

    The fact that neutral and nearly neutrals get fixed at a high rate is devastating to anti-teleological versions of evolutionary theory. It shows the opposite of what Darwin claimed. Real evolution keeps losing the good, and adding up the bad.

    It is as simple as this: if the ratio of dysfunctional to functional mutations is 10 to 1 (or whatever, just as long as dysfunctional is higher), and most fixation (what is made permanent) has little to do with selection but just random chance, where does this lead? Not to more coordinated and integrated IC systems. There is abundant evidence evolution destroys IC in the wild.

    A consequence of Kimura/Nei is we should all be dead 100 times over (to quote Kondrashov), but we obviously are not dead, so I don’t think whatever “fixed” our genes was due to random mutations getting fixed by random events. Kimura’s claim, though mathematically feasible as affirmed also by Mendel’s accountant, utterly fails in terms of being functionally feasible. Mendel’s accountant affirmed Kimura’s results, but connected the dots in ways Kimura himself didn’t see coming.

    Kimura’s “2nd result” pretty much demolished the implicit hypothesis of increasing complexity claimed by Darwin and Dawkins.

    The complexity of organisms today indicates the mode of evolution that created complexity was not according to chance mechanisms of Kimura/Nei neutral theory. And we know if something is not by law and chance, it likely to be designed.

  56. 56
    scordova says:

    Hi Sal,

    Thank you for your posts. I’m very interested in your models of the neutral theory.

    And thank you again. I’d have been in the doghouse with other IDists again if it weren’t for you posting this discussion and supporting some of my claims.

    I can’t claim to be able to comment on them in any detail, as I haven’t studied the theory in the same depth as you have, but the overall approach you’re taking, of showing that too may harmful mutations would eventually build up over the course of time, sounds very promising. By the way, what do you recommend in the way of good online resources for studying the neutral theory, for laypeople like myself?

    Actually there are no really good resources for the layman, and my posts at UD have been an attempt to help develop such material for consumption in the public domain for free.

    Nick, WD400, Gordon Davisson, Joe Felsenstein, Larry Moran, Allen MacNeill and so many others have helped me get some of my educational ideas “peer reviewed” over the net. I’m now at the point of writing the ideas up, and you’ll get to see them publicly peer reviewed, and if there are errors we all can work at cleaning them up.

    For example, I just threw out a trial balloon here to see if any one would pounce on it:

    Kimura’s second result was that if the mutation is slightly deleterious according to

    S less than 4ne

    Then 50% of these deleterious mutations would fix in the population.

    Our “peers” didn’t object, so I suppose the claim is good enough to move forward with for now. They know of course if they complain, I’ll simply ask, “then what proportion of bad will get fixed, tell me the percentage?” Of course, I think they realize there isn’t much way of getting out of it, it’s like me asking, “so how badly did Darwin beat the puppy?” Whatever figure they give won’t be a figure that is supportive of mindless evolution.

    I’ll post some of the discussions at UD and CEU. The CEU forum is a more formal forum for scholarly discussion rather than advocacy (which blogs tend to be).

    So to answer your question, I’ll be writing some posts with you as the primary audience in mind and maybe college level students as well. I hope we can dialogue in the comment section so as to help me articulate the case with as much clarity and simplicity as possible.

  57. 57
    wallstreeter43 says:

    Timeus (42) . I have noticed that myself with JLAFAN1

    He has said on numerous occasions that he won’t accept something unless it is with a certain brand of Christian belief.
    You hit the nail, right on the head .

    He ignores all the great evidences for God’s existence and when a tiny breadcrumb is brought up by atheists against Christianity , no matter how bad the odds for it being true automatically registers in his mind as all Christianity not being true .

    We have discussed the shroud of turin for many months and despite the massive evidence for authenticity one article comes out by an amateur scientist claiming that he can replicate the shroud and JLAFAN automatically blows up and enters the “this proves Christianity wrong ”
    Despite the fact that this scientist has been challenged to do it and chickens out saying he doesn’t feel like it lolololololololo.

    JLAFAN’s mind has been conditioned as you said to get clear black and white answers.
    This also flies against the face of what Christ tells us in the bible , that there has to be some faith involved here in order for anyone to follow him.

    He didn’t tell us to through our brains out the window, but he also didn’t tell us to throigh our faith out the window like Jlafan has done.
    What he doesn’t understand is that the fundamentalism he used to practice
    Was never true Christianity in the first place.

  58. 58
    gpuccio says:

    VJ at #47:

    There is no problem about the simultaneous or sequential appearance of new proteins.

    Just follow me a little bit.

    a) “Simultaneous” obviously does not mean “in one attempt”. What we have to consider is the whole system, which is made of:

    a1) a population size (a number of replicators)

    a2) a mean replication time

    a3) a time span (the time available for the new “species”, or whatever, to appear), IOWs for the transition from A (the precursor) to B (the new thing)

    a4) a mutation rate

    a5) the number of new proteins that characterizes the new state (B) versus A

    a6) the probability for each new protein to arise in a random system, in one attempt

    b) Given those numbers, we can make a few easy computations

    c) I will assume an extremely generous model.

    c1) Out population is the whole prokaryotic population on our planet. I will estimate it at 5*10^30 individuals (I have found that on the internet)

    c2) I assume a mean replication time of one division every 30 minutes

    c3) I assume a time span of 4 billion years (2.1*10^15 minutes)

    c4) I assume a mutation rate of 0.003 mutations per genome per generation (from internet, again)

    c5) I assume that B is characterized, versus A, by 3 new proteins, completely unrelated at sequence level with all the proteins in A, and unrelated one with the others

    c6) I assume the same functional complexity for each of the 3 proteins, of 357 bits (Fits), which is the median value for the 35 protein families evaluated in Durston’s paper.

    Multiplying c1 by c2 by c3 by c4, we get the total number of possible mutations in our system in the time span of 4 billion years. The result, with those numbers, is 1.0512*10^42. That is a higher threshold for the total number of individual new states that can be reached in our system in the time span (if each mutation gives a new state).

    OK?

    Now, each of our 3 functional proteins has a probability of 1:2^357 of being found in one attempt (one new state tested). That is 1:(3.4*10^108).

    Now, using the binomial distribution, it is easy to compute the probability of having 3 successful results in 1.0512*10^42 attempts, when the probability of success in one attempt is 1:(3.4*10^108).

    The result is: 5.568067e-264

    That is the probability of finding our 3 new functional proteins in our system, in all the time span, with all the reproductions and mutations possible in that system.

    Obviously, I am considering the system as random, with uniform probability distribution. I am not considering any intervention of NS, in any sense, so this is a computation for the powers of neutral variation.

    As already said, genetic drift is irrelevant in that reasoning, because we are already considering all the possible states that can be reached in the system.

    I am fully available to discuss any aspect of this model.

  59. 59
    bornagain77 says:

    Barb, here is his response:

    What exists prior to space-time, even if describable by physics, is not what the materialists assume it to be:

    And the Spirit of God was hovering over the waters/wavefunctions (of chaos/probability).” 🙂

    They don’t realize the implications of Hempel’s Dilemma here on the blurring of the line between physics and metaphysics.

    “The question is: does the Wheeler-DeWitt equation allow this?

    “We prove that once a small true vacuum bubble is created, it has the chance to expand exponentially,” say Dongshan and co.”

    Hempel’s dilemma is very much relevant here! The Wheeler-DeWitt equation specifies a wave-function of the universe, BUT on a materialist paradigm there is something they do not know about the wave-function of the universe that becomes apparent on an idealist understanding:

    https://www.youtube.com/watch?v=sTnnZNNbrUc

    This applies Orch-OR to the WDW Equ, which I think needs upgrading, but the same metaphysical implications are valid on digital physics.

  60. 60
    Axel says:

    Is it the same foreign-language school you’ve been going to as Cornelius Hunter, GP and BA77?

    They don’t look like Cyrillic script to me, so I’d take a stab at Croation. Bit puzzled by the occasional monosyllabic, Anglo-Saxon word somebody’s mischievously interpolated, though.

    The penalty of understanding zilch about the nitty-gritty of the empirical nub of science, I suppose. Still, it tickles the heck out of me when I see such densely esoteric disquisitions. Keep up the good work, both of you (and CH). Just the sight of it, I find beautiful to look at.

  61. 61
    Querius says:

    IMHO, the mathematics of fixation includes a significant flaw. It assumes that everyone on Earth is equally likely to produce offspring from anyone else on Earth. This is demonstrably false.

    Isolation of populations is one requirement for speciation. Even imperfect isolation will protect variations and mutations from fixation over time.

    -Q

  62. 62
    scordova says:

    Here you go VJ, especially for you:

    Neutral theory and non-Darwinian for newbies, Part 1.

  63. 63
    vjtorley says:

    Hi Sal,

    Much appreciated. Thank you.

  64. 64
    vjtorley says:

    Hi gpuccio,

    I greatly appreciate the work you’ve put into your model. I’m a little busy at the moment, but I’ll get back to you with some comments in a few hours. Thanks again.

  65. 65
    bornagain77 says:

    Barb, if you are interested, Johanan Raatz has just loaded a new video in response to an atheistic physicist who challenged him:

    Martymer81, Quantum Non-Realism, AND Magic Powers!! 😀 – video
    https://www.youtube.com/watch?v=cpw8PieSSg8

  66. 66
    scordova says:

    Salvador Cardoza:

    What I would have done different over the course of these discussions when I provided a link my essay on Rupe and Sanford, was to have specifically highlighted this discovery of the Mendel team:

    In this thread where did you provided a link to that essay?

    I can’t find it.

    ROTFL! That’s not the only thread involved in this discussion. My mention of NEUTRAL theory to Dr. Torley in a comment on March 4, 2014 probably had some influence, and it was in that comment that I linked to Rupe and Sanford’s work. Of course you didn’t find mention of it, you’re looking in the wrong thread (the one dated March 30, 2014).

    Mung makes an innuendo that I never mentioned Rupe and Sanford to VJTorley. This whole discussion began possibly because of a comment that mentioned Rupe and Sanford

    Haldane’s Dilemma comment

    March 4, 2014 at 4:04 pm

    VJTorley,

    Something very important, Larry Moran isn’t using natural selection as the mechanism of the fixation rate for evolution, he is using NEUTRAL EVOLUTION.

    See:
    IF not rupe or Sanford would you believe Wiki

    Compare what I said with what Moran said

    says the rate of new mutations is the rate at which new mutations become features of every member of the population (a process called fixation).

    and that agrees with Moran

    This corresponds to a substitution rate (fixation) of 121 mutations per generation and that’s very close to the mutation rate as predicted by evolutionary theory.

    Mung fails yet again to discredit me despite his creepy stalking vendetta behaviors. What’s the matter Mung, having to grasp at straws since you have nothing substantive? 🙂

    You’re right down there with Upright Biped, casting insults as if I had orchestrated something against my friend VJ Torley. Baloney on both you guys.

    Find something better to do Mung than pursuing your vendetta against me. It makes you say stupid things.

  67. 67
    Mung says:

    Salvador, you can’t debate either myself or Upright Biped.

    You delete my posts from your threads.

    Pat yourself your backs.

  68. 68
    Upright BiPed says:

    Sal,

    Refrain from invoking my name in your arguments with Mung.

  69. 69
    Mung says:

    Upright BiPed, Salvador refuses to argue with me.

  70. 70
    Mung says:

    Salvador:

    Mung makes an innuendo that I never mentioned Rupe and Sanford to VJTorley.

    Liar. Repent.

  71. 71
    vjtorley says:

    Hi gpuccio,

    I’d just like to ask a couple of questions about your model.

    I note that your bacterial mutation rate of 0.003 mutations per genome per generation agrees with the figure given in Wikipedia and in Nature magazine (see http://www.nature.com/nrmicro/.....3_BX1.html ). So far so good.

    Your next critical assumption is that the new species of bacterium is characterized by three new proteins which are completely unrelated to existing proteins, chemically speaking. That might be a bit strong. What if we relaxed the assumption a little, and assumed that the three new proteins each had a 50% similarity to some existing protein?

    Finally, your proof correctly calculates the odds of Nature hitting upon three particular proteins within the time available. But it doesn’t have to be those three particular proteins, if we want to get a new species of bacterium. It can be any three new proteins, so long as they’re biologically compatible with the existing ones. (Not being a biologist, I’d have no idea how you’d calculate the proportion of new proteins that are biologically compatible with the existing set. Kirk Durston might have some good ideas on that point.)

    What does your model look like if you incorporate these more relaxed assumptions?

  72. 72
    gpuccio says:

    VJ:

    Here are the answers:

    We must start with the functional units that are completely and certainly unrelated, at all levels, sequence, structure and function.

    The best option for that is to consider protein superfamilies, and that is the model I have always defended here.

    Now, I am not particularly interested in how many new basic protein domains (superfamilies) a particular species exhibits. I usually refer to the appearance of a new superfamily as a moment of certain design intervention.

    At present, there are a little more than 2000 superfamilies listed in SCOP.

    The existing literature tells us that about half of them were already present in LUCA. All the others appeared at various times, in various phyla and species, at a slowing rate, up to mammals (included).

    I refer to superfamilies to be sure, completely sure, that the whole functional complexity has to be explained, and that no related precursor is known at the time of first appearance of a new superfamily.

    The evolution of proteins inside a superfamily or a family is less extreme, because some homology to similar precursors can be found. I am sure that in most cases design can be inferred even in those cases, but why should we start with the more difficult scenario, when even one new protein superfamily is completely unexplainable in darwinian terms?

    You mentioned 200 proteins in a new species. I reduced that to 3 unrelated new proteins. If the new proteins can be matched to some homologue already existing in the precursor, then we have to compute the functional information of the transition from one protein to the new one. Durston’s method can do that. However, it is more simple to reason in terms of even one new superfamily, and relate to the list of 35 protein families for which Durston has already computed functional complexity, as an example.

    The second argument you give is very popular among darwinists. It’s what I call the argument of “any possible function”. It goes more or less this way:

    Evolution is not looking for a specific target. Indeed, any possible function that emerges from a random walk can be used.

    That is completely wrong, for many reasons:

    a) In a complex system, like a prokaryote, new functions can be useful only if well integrated with what already exists. The more complex a system, the less likely it is that generic functions can have a role in it. Indeed, I believe that it is extremely unlikely that one single new functional protein may be of any help even in a prokaryote, except in very selected cases. In the general case, a certain number of new proteins will be needed, and adjustements will be necessary to what is already there. IOWs, the concept of irreducible complexity comes in. So, when I compute only the functional complexity of one or a few isolated proteins, I am really being generous with the enemy.

    b) The new function, however complex it is, must not only do something in the cell. It must give a reproductive advantage to the cell. Otherwise, it has no hope to be fixed.

    You will say: but your model was about neutral evolution, not about NS. That’s true. My model is about neutral evolution of a new function, but it assumes that the new function, however unlikely it is, will be recognized, expanded and fixed by ND once it has been achieved by neutral mutations. Otherwise, it will be only a transitory state like any other, designed to remain confined to the cellular clone where it originated, and to be quickly degraded by new mutations.

    IOWs, even if neutral mutations were able to generate a new functional protein (and they are not), that protein should be functional enough to give a reproductive advantage to the existing cell, otherwise it could never emerge. OK, it could be fixed by drift, but that would add huge new improbabilities to the original computation of how likely it is to simply reach that sequence.

    Now, can you imagine how many new proteins, however functional, can give a reproductive advantage to an existing cell? IOWs, if we introduced in an existing bacterium, one at a time, one gene for one protein of the 2000 existing superfamilies, in how many cases would that immediately confer a reproductive advantage to the cell?

    c) Finally, even we we ignored the two above objections, and if we admitted that any of the existing 2000 superfamilies could give a reproductive advantage, if found, that would not really change much the computation. Our global target space would just be the sum of the functional spaces of the existing 2000 superfamilies. That would give an advantage of a few orders of magnitude. Do you think that would count? No. We are talking about improbabilities of hundreds of orders of magnitude here, just for 3 medium proteins.

    Of course, it would be a little bit easier to find those superfamilies which are simpler, let’s say with domains definitely shorter than 100 AAs, but even for them the improbabilities are huge. And what about the others? What about proteins of 300, 500 or 1000 AAs? All unrelated?

    Let’s talk a minute of the edge of evolution. IOWs, about how much functional variation RV + NS can really do in the real world.

    Behe has put it above two AAs, in his very good book, and considering very good arguments from observable scenarios. Axe, with different experimental consideration, puts it at about 5 AAs. I believe that is probably very true.

    Dembski, with very general considerations, proposes 500 bits (about 116 AAs) as universal probability bound. I have proposed 150 bits (about 35 AAs) starting from a model like the one I posted here.

    You mention 1:10^70 as the number of folding proteins, from Axe again, I believe. That is probably true. But remember, folding is not all. A protein must not only fold to be visible to NS. It must confer a reproductive advantage in a definite environment.

    I often quote the following paper:

    “Experimental Rugged Fitness Landscape in Protein Sequence Space”

    http://www.plosone.org/article.....ne.0000096

    which experiments with a mutated protein in a phage, trying to find the original wild type sequence which confers full infectivity. Well, here RV and NS are acting at their most, starting from a random library of peptide sequences, in a very favorable context (the function is maintained, even if at low levels, so NS can act just from the beginning).

    I always quote the final conclusion of the authors:

    “The question remains regarding how large a population is required to reach the fitness of the wild-type phage. The relative fitness of the wild-type phage, or rather the native D2 domain, is almost equivalent to the global peak of the fitness landscape. By extrapolation, we estimated that adaptive walking requires a library size of 10^70 with 35 substitutions to reach comparable fitness.”

    Well, 10^70 is the order of magnitude proposed by Axe for folding proteins, and 35 AAs is my “universal biological bound”.

    Coincidences? Probably, but what it means is that we are on the right way, and that our intuitions about the functional space of proteins are quite right.

    Durston has computed functional information for 35 different protein families. Only six of them have functional complexity below 150 bits (my biological bound). All of them are very short peptides (33 -55 AAs). Insulin (65 AAs) already has a functional complexity of 156 bits.

    The biggest protein in the list, Paramyx RNA Pol, has a functional complexity of 1886 bits.

    In my simple model, even if only one new unrelated protein of the median functional complexity of 357 bits, were to be found to confer some definite advantage to a new species, the probability of that single event in 4 billion years, in the whole planet, would still be 5.78e-132.

    IOWs, not a single new protein superfamily of median complexity could ever be generated on our planet by neutral mutations alone. And no functional precursors to superfamilies have ever been shown to exist, so the role of NS in that scenario is nil.

  73. 73
    gpuccio says:

    VJ:

    I have to make a correction in the computations I gave. That’s because I considered the higher tail, but I made a mistake in introducing the data in the program.

    The probability for 3 proteins is 6.550667e-198, and not 5.568067e-264 as I had given. That’s the probability for 4 proteins.

    The probability for one protein is 3.4e-66, and not 5.78e-132, which is the probability for 2 proteins.

    The consclusions do not change at all, but I apologize for the error.

  74. 74
    gpuccio says:

    VJ:

    Please, look also at this post of mine (#56) in the thread:

    http://www.uncommondescent.com.....ent-496408

    And please, consider the important article I mention there:

    http://genome.cshlp.org/conten.....2.full.pdf

  75. 75
    vjtorley says:

    Hi gpuccio,

    Thanks very much for the clarifications. I think we can agree that the de novo appearance of new proteins in bacteria would have been an event beyond the reach of chance, and thus achievable only as a result of Intelligent Design.

    The question I’m currently wrestling with is how to apply these calculations to the human case. I’d be interested to hear your opinions of the following paper:

    http://www.plosgenetics.org/ar.....02379-g002

    “De Novo Origin of Human Protein-Coding Genes” by Dong-Dong Wu, David M. Irwin, Ya-Ping Zhang, in PLoS Genetics. Published: November 10, 2011. DOI: 10.1371/journal.pgen.1002379.

    Thoughts?

  76. 76
    gpuccio says:

    VJ:

    Let’s say that mammals originated about 300 million years ago.

    Let’s say that in humans there are 130 mutations per genome per replication. Let’s take that number for all mammals, just as an approximation.

    I have no idea what the mean generation time for mammals could be. Let’s take 1 year.

    I am not sure how many mammals there could be on the earth. From some internet gross evaluations, let’s say 10^12.

    So, let’s compute the higher threshold for new states reach since mammals appeared on earth:

    3*10^8 (number of years) * 1 (mean generation time) * 130 (mutations per generation per genome) * 10^12 (population size) = 3.9e22

    That is about 20 orders of magnitude smaller than the states tested in my bacterial model.

    So, if the appearance of one new functional protein of average functional complexity was utterly unlikely in the bacterial model (10e-66), here, in the whole span of mamal evolution, we are at about 10e-89 for one protein.

    Does this give some idea of “how to apply these calculations to the human case”?

    Regarding the paper, it is just another example in favor of my scenario:

    a) New genes appear at a greater rate than suspected, even in humans.

    b) Many of them are both transcribed and translated

    c) Many of them are probably functional, and their function could be very refined (see preferential expression of some of them in the testis and in the brain)

    d) Many of them seem to derive from non coding DNA in precursor species, where they are not translated and almost certainly they are not functional.

    e) Nothing of that can be explained by a traditional darwinian scenario, neither by neutral mutations nor by NS.

    f) These are clear examples of design. The design starts in advance, and is completed if and when the desired effector is necessary.

    However, I still believe that new protein coding genes, even if relatively abundant, cannot explain the huge phenotypic differences between chimps and humans. The explanation must certainly reside in the elusive regulatory components.

  77. 77
    Paul Giem says:

    There is an important philosophical point here. Remember that the function of natural selection is to explain the appearance of design in living organisms. That appearance of design is strong enough to inspire Richard Dawkins to say, “Biology is the study of complicated things that give the appearance of having been designed for a purpose.” So any system that does not invoke a designer has to explain away that appearance of design. Neutral mutations cannot do that, as is commonly recognized. So we have to have positive selection if the BW thesis is to be supported.

    But as P. Z. Meyers points out, the scientific evidence strongly supports the idea that evolution is overwhelmingly neutral (And Sanford points out that it is actually slightly deleterious). So there is no good explanation for the appearance of design. The only way to make a case for evolution is to say that we have the mutations necessary because of neutral mutations, and that they are also selected so as to design new ORFan genes, or to deny that such genes exist. I’m glad I don’t have to argue on that side. 🙂

  78. 78
    gpuccio says:

    Paul:

    I am very glad too 🙂

    Sometimes I feel real compassion for our “adversaries”. It must be really bad to have to defend something which cannot be defended. I say that seriously, I am not joking.

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