Darwinism Evolution Genetics Natural selection speciation

Real Time Evolution “Happening Under Our Nose”

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A couple of weeks ago a friend forwarded me a link to this recent article about “ongoing research to record the interaction of environment and evolution” by University of California, Riverside biologist David Reznick. Reznick’s team has been studying adaptive changes in guppies. Reznick’s work focuses on tracking what happens in real-world situations in the wild, rather than the somewhat artificial environments in the lab. As a result, Reznick has gathered some of the more trustworthy and definitive data about changes over time in a real-world environment, largely free from the intervention and interference of the coated lab worker.

The article states:

The new work is part of research that Reznick has been doing since 1978. It involved transplanting guppies from a river with a diverse community of predators into a river with no predators – except for one other fish species, an occasional predator – to record how the guppies would evolve and how they might impact their environment.

In the recent follow-up research, Reznick’s team studied “how male color pattern affected” their differential survival in the environment. Significantly, the team even gathered DNA from the guppies over time to track who their parents were and reconstruct a guppie pedigree to help determine the reproductive success. Without going into all the details, which are interesting in their own right, the key point for my purposes today is that this adaptive change occurred extremely quickly.

Graduate student, Swanne Gordon, noted,

Our research shows that these fish adapted to their new habitats in less than one year, or three to four generations, which is even faster than we previously thought.

Reznick adds,

People think of evolution as historical. They don’t think of it as something that’s happening under our nose. It is a contemporary process. People are skeptical; they don’t believe in evolution because they can’t see it. Here, we see it. We can see if something makes you better able to make babies and live longer.

What Really Happened?

Now normally when my friend forwards a link, I will just review the article, realize it is making claims beyond the data, and move on. But coincidentally, just days earlier I had been reading Chapter 7 of Lee Spetner’s 1998 book, Not by Chance!

Part of Spetner’s argument is that many adaptive changes we see in nature are in fact not examples of a Darwinian process of chance changes + natural selection, but instead the result of specific programming capabilities in the organism to allow it to respond to changes in the environment. Indeed, what caught my eye about the article my friend forwarded is that Spetner had discussed Reznick’s earlier experiments in that very context.

After describing two different predators of the guppies: (i) the cichlid, which prey on large mature guppies; and (ii) the killfish, which prey on small immature guppies, Spetner continues:

Reznick and his team took 200 guppies from the Aripo [river in Trinidad] and put them in a tributary of the river that is home to the killfish but has no cichlids and had no guppies. Changes soon appeared in the newly introduced guppies. The fish population soon changed to what would normally be found in the presence of the killfish, and Reznick found the changes to be heritable.

The full change in the guppy population was observed as soon as the first samples were drawn, which was after only two years. One trait studied, the age of males at maturity, achieved its terminal value in only four years. The evolutionary rate calculated from this observation is some ten million times the rate of evolution induced from observations of the fossil record [Reznick et al. 1997].

Reznick interpreted these changes as the result of natural selection acting on variation already in the population. Could natural selection have acted so fast as to change the entire population in only two years?

Spetner goes on to argue that the adaptive change observed in the guppies is more likely the result of a programmed response to environmental change, and provides several examples of such changes in other species.

Where is the Darwinian Evolution?

Darwinian evolution, as we know, is supposed to work by natural selection weeding out random variation. The Neo-Darwinian model has traditionally gone a step further, suggesting that those random variations are genetic in nature — taking place in the DNA as a copying error here, a misplaced sequence there, an accidental cut-and-paste elsewhere . . .

So the question arises: do the kinds of rapid, adaptive, reversible changes Reznick observed owe their existence to this kind of Darwinian process, or are they the result of a pre-programmed genetic response to environmental changes?

Spetner makes a good argument that we are observing the latter. He goes on to show that even many of the classical examples of Darwinian evolution — you know, the examples of random mutation + natural selection that even most evolutionary skeptics have tended to accept: convergent “evolution” of plants in similar environments, the “evolution” of bacteria to live on lactose or salicin — are not good examples of Darwinian evolution at all. Even that icon of icons, finch beaks in the Galapagos, is likely not a good example of the alleged Neo-Darwinian mechanism of random mutation + natural selection.

All of this prompts me to ask a simple, but pointed, question:

How many good examples are there of Darwinian evolution?

The more research I do the more I come to the same conclusion Spetner did, namely that most adaptive changes are not the result of the random, purposeless changes Darwinian evolution posits as the engine of biological novelty.

Even skeptics of the grand evolutionary claims tend to accept, either specifically or implicitly, that Darwinian evolution can produce all kinds of minor adaptive changes, the so-called microevolutionary changes: variations in finch beaks, insect resistance to insecticides, coloration of peppered moths, and so on. And indeed, the “selection” side of the formula seems to work well, which is simply the somewhat pedestrian observation that if an organism is poorly adapted to its environment it has a poor chance of surviving.

Yet the engine of the novelty, the alleged random variation that is supposed to provide all this adaptive variability on which selection can work its magic, seems stubbornly absent. Even these most common of examples, on closer inspection, do not support the Darwinian claim. Thus the doubts multiply. If Darwinian evolution cannot even claim explanatory credit for things like bacteria being able to metabolize lactose, what can it explain? The more closely we look, the more anemic the Darwinian claim becomes.

Now we could be intellectually lazy and call every adaptive change we observe an example of “evolution.” But the problem with observing a change and claiming that we have observed “evolution” is that (i) we rob the word of explanatory value if it is applied indiscriminately, and (ii) we trick ourselves into thinking we have an explanation for what occurred, when in fact we have have no idea what is happening at the molecular level or the organismal level to produce the change. Claiming that we are witnessing “evolution” in such circumstances becomes then not so much an explanation as a confession of ignorance.

Real Darwinian Evolution

There are no doubt quite a number of legitimate, confirmed examples of random mutation + natural selection producing an important biological effect. For example, I think Behe’s review of malaria/sickle cell trait is a legitimate example of Darwinian evolution in action. And the circumstances of that example are rather telling: (a) large population size, (b) meaningful amount of time, (c) very strong selection pressure, (d) and change that can be caused by one or two single-point mutations.

If we see adaptive change outside of these parameters — small population, short timeframe, an adaptation that requires significant genetic change — we might be better served to suspect that we are witnessing a programmed adaptive response, rather than Darwinian evolution. And rather than being naively impressed with the great power of Darwinian evolution to act more rapidly than anticipated, we should be prompted to look deeper to find what is actually taking place.

Your Turn

In addition to the malaria/sickle cell example, what other examples of legitimate, confirmed Darwinian evolution can you think of?

378 Replies to “Real Time Evolution “Happening Under Our Nose”

  1. 1
    Barry Arrington says:

    EA:

    In addition to the malaria/sickle cell example, what other examples of legitimate, confirmed Darwinian evolution can you think of?

    Yes, the malaria/sickle cell example is adaptive. OTOH, it is not necessarily a general improvement. Same with the development of antibiotic resistance. Behe’s description (“trench warfare”) is apt. In a sense, we are witnessing “devolution” that happens to be under the particular selection pressures present, adaptive.

    I am unaware of any genuinely novel molecular information that has been created by these forces (I mean observed to be created; not inferred to have been created). The +2 point barrier seems to be insurmountable.

  2. 2
    Bob O'H says:

    You shifted from discussing adaptive change to discussing novelty. Is there any evidence that the evolution of the guppies was the evolution of novelty? In other words, is there evidence that there wasn’t enough standing genetic variation in the introduced populations?

  3. 3
    Andre says:

    If sickle cell is the evolutionists best example then they are in trouble. How exactly is a mutation that kills you beneficial? Has anybody ever considered the reason these sufferers are not getting maleria is because the mozzies have a mechanism that recognize the food source is suspect? All animals including humans have sensory input about the food we are to not eat. Why would insects be any different when it comes to food sources?

  4. 4
    mahuna says:

    Is anyone suggesting that the new guppies are a new specie?

    If not, then all we’re talking about is a new breed like orchids or dogs. And we already know that isolated populations tend to produce odd colors, etc. But as soon as you break the isolation, the critters snap back to standard characteristics.

    So I’m not sure why setting up a test miles from the lab, and therefore more expensive to monitor, was expected to produce anything new. Did anyone believe that tests in the lab could NOT have produced a set of guppies that looked any way the guys running the experiments wanted?

  5. 5
    Virgil Cain says:

    And more evidence for Lee Spetner’s hypothesis- he discusses these guppies in his latest book.

  6. 6
    Eric Anderson says:

    Barry @1:

    Behe’s First Rule of Adaptive Evolution is applicable in the case of malaria/sickle cell. And in nearly all other examples of Darwinian evolution.

    For other readers who may not be familiar, Behe’s rule is “Break or blunt any functional coded element whose loss would yield a net fitness gain.” Two additional ways to think about this same concept:

    1. It is quite easy to break something. Indeed, experimentally, what we see when we start introducing mutations and the like is breakdown of function, not formation of new function. Evolution — at least insofar as the Neo-Darwinian paradigm is concerned — by random mutations and similar chance changes will tend to break things.

    and as a corollary:

    2. If a particular adaptive advantage can be obtained by either breaking an existing function or building a new function, evolution will break the existing function to achieve the adaptation. (And, I might add, without regard to whether the temporary advantage is net harmful in the long run.)

    In the few cases of legitimate Darwinian evolution (like malaria/sickle cell), we find that the adaptation resulted from a loss of function or a loss of information, not from an introduction of new information or new functional specificity.

    —-

    Barry, thanks for reminding me of this point.

    So I should add to my question and make it a two-part inquiry:

    1. How many examples are there of legitimate, confirmed Darwinian evolution?

    and

    2. How many of these examples consist of new information or an increase of functional specificity, rather than loss of function/information?

  7. 7
    Eric Anderson says:

    Bob O’H @2:

    Is there any evidence that the evolution of the guppies was the evolution of novelty? In other words, is there evidence that there wasn’t enough standing genetic variation in the introduced populations?

    There was clearly phenotypic change in the population. Reznick’s work shows that and demonstrates with significant confidence that the change happened rapidly. That aspect is not in question.

    What is less clear from the article and from Reznick’s prior work, is whether (a) the change was genetic in nature, and (b) how the change came about.

    The first point is more nuanced, and I did not really discuss it in the OP. Briefly, it is possible to have phenotypic variation without any genetic change whatsoever. This is rather common and has been observed in both plants and animals. In other words, a particular genetic profile can play out in slightly different ways, depending on the environment, resources, food availability, opportunity for growth, feedbacks from the environment, etc.

    I am not aware of whether Reznick’s DNA sampling actually isolated a genetic change responsible for the different coloration of the guppies. It does seem likely that a genetic change occurred, because they state that the change was heritable. (Again, that is not completely clear from the article and there are some interesting nuances we could pursue, but perhaps another time.)

    So let’s assume that the change Reznick observed in just a couple of years was in fact a genetic change — a bona fide reordering of certain nucleotides in the genome. Then we still have the question of how that could come about.

    Reznick seems to implicitly recognize that such a genetic change could not have occurred by random mutations or other known evolutionary mechanisms within just a couple of years, because the article says that he believes the change was the result of natural selection acting on pre-existing variation in the population.

    Yet if the variation was genetic and the variation was already in the population, then (i) his team should be able to identify it in the original population (which doesn’t seem to have happened), and (ii) it is simply an example of selection (which no-one disputes happens anyway and which is not the source of any evolutionary development and which, therefore, does not teach us anything about how such development could have come about).

    What appears to be happening is that Reznick is confused, as are so many evolutionary biologists, about the ramifications of his research. He says that “evolution” is happening right “under our nose” and that this is the kind of evidence that should convince people who “don’t believe in evolution.”

    Yet, if he means “evolution” in the simple sense of some change in a population, then (a) no-one would dispute that anyway, and (b) it doesn’t tell us anything about how the changes came about, which is precisely the matter at issue.

    On the other hand, if he means “evolution” in the sense of generating new biological information and new biological function as the result of random mutations and other evolutionary mechanisms, then his research certainly has not shown any such thing. Indeed, he seems to admit that such could not have occurred.

    It is the classic confusion and conflation that so many Darwinists fall into: they have a preconception that all of nature came about through things like random mutations and natural selection, so when they see any change in nature they naively, and without solid evidence, jump to the conclusion that “Gee, we must be seeing evolution in action.” This cognitive dissonance between what the data actually say and what Darwinists think the data should say under their theory causes no shortage of sloppy thinking and muddled conclusions.

    —–

    Now let me be very clear. I think Reznick’s work is commendable. He has tackled a legitimate situation in the real world and has gathered some very tantalizing and useful data.

    Unfortunately, his knee-jerk “isn’t-evolution-amazing” reaction is blinding him to other possibilities. Indeed, I think his research is incredibly interesting and points to the fascinating possibility that the guppies likely have programmed into their very organism a way to quickly adapt (clearly morphologically, and possibly even genetically) to environmental change. That is not the kind of thing that has anything to do with the Darwinian mechanism. It is not the kind of thing that confirms traditional evolutionary theory. The data is far more interesting than just another pedestrian confirmation of selection in action or some such.

    The data is pointing, even shouting, in another direction.

    Hopefully Reznick will take off the Darwinian blinders long enough to realize what a fascinating result he has actually uncovered.

  8. 8
    Mapou says:

    People think of evolution as historical. They don’t think of it as something that’s happening under our nose. It is a contemporary process. People are skeptical; they don’t believe in evolution because they can’t see it. Here, we see it. We can see if something makes you better able to make babies and live longer.

    Still the same condescending and lying propaganda. I can’t stand it when scientists think they can talk to the public as they would to children. Any field of science that feels free to blatantly lie to the public is not science but ideology covering a hidden agenda.

  9. 9
    Eric Anderson says:

    Andre @3:

    If sickle cell is the evolutionists best example then they are in trouble. How exactly is a mutation that kills you beneficial?

    Good point, and something I didn’t really discuss in the OP. Barry’s comment @1 and my reply @6 focus a bit more on this.

    —–

    Not a big deal, but just by way of clarification, it isn’t that mosquitoes don’t bite prey with sickle cell, but rather that the defective haemoglobin molecules in the red blood cell of a sickle cell carrier interfere with the malaria parasite’s impact, leading to a selective advantage. It is, however, a loss of function mutation that is disadvantageous outside of the malaria context.

  10. 10
    Virgil Cain says:

    What sickle-cell anemia indicates is that “beneficial mutation” is relative as a genetic disease could be beneficial and evolution seems to be nothing more than contingent serendipity. And evolution via breaking things isn’t exactly a mechanism to bet the house on.

  11. 11
    buffalo says:

    <blockquote cite="Part of Spetner’s argument is that many adaptive changes we see in nature are in fact not examples of a Darwinian process of chance changes + natural selection, but instead the result of specific programming capabilities in the organism to allow it to respond to changes in the environment."

    Yes. This is what IDvolution posits.

    IDvolution – God “breathed” the super language of DNA into the “kinds” in the creative act.

    This accounts for the diversity of life we see. The core makeup shared by all living things have the necessary complex information built in that facilitates rapid and responsive adaptation of features and variation while being able to preserve the “kind” that they began as. Life has been created with the creativity built in ready to respond to triggering events.
    Since it has been demonstrated that all living organisms on Earth have the same core, it is virtually certain that living organisms have been thought of AT ONCE by the One and the same Creator endowed with the super language we know as DNA that switched on the formation of the various kinds, the cattle, the swimming creatures, the flying creatures, etc.. in a pristine harmonious state and superb adaptability and responsiveness to their environment for the purpose of populating the earth that became subject to the ravages of corruption by the sin of one man (deleterious mutations).
    IDvolution considers the latest science and is consistent with the continuous teaching of the Church.

  12. 12
    Eric Anderson says:

    Thanks, Virgil @5. I’ll have to check it out.

    —–

    Incidentally, I’m not necessarily suggesting that I am completely on board with Spetner’s approach — or at least with his particular characterization of it. Nevertheless, I think he makes some excellent points about the limitations of alleged evolutionary mechanisms, as well as the possibility of more pre-programming than has been previously thought.

  13. 13
    Mung says:

    I think we should stop referring to changes in gene frequencies as Darwinian evolution. In fact, I think we should stop calling it evolution.

  14. 14
    jerry says:

    How much of what is happening to the guppies, the result of epigenetics?

  15. 15
    Zachriel says:

    Eric Anderson: I think Reznick’s work is commendable. He has tackled a legitimate situation in the real world and has gathered some very tantalizing and useful data.

    What’s interesting is that all these sorts of studies are nearly always done by biologists based on evolutionary principles.

    Reznick clearly distinguishes between phenotypic plasticity and adaptive plasticity, and even finds a relationship between them. See Ghalambor et al., Non-adaptive plasticity potentiates rapid adaptive evolution of gene expression in nature, Nature 2015.

  16. 16
    Mapou says:

    The guppies were obviously programmed to adapt. Natural selection and random mutations had nothing to do with it. No stochastic search mechanism (e.g., Darwinian evolution) or any kind of optimizing system can solve the combinatorial explosion problem. Anybody who has played with genetic algorithms knows that they’re only good for toy applications.

    The combinatorial explosion kills Darwinian evolution dead. It’s simple math, folks. Evolution is not science. It’s superstition.

  17. 17
    tjguy says:

    And then you have the problem of stasis – no evolution occurring for hundreds of millions of years – or so the claim goes. How credible is that really?

    Here we have evolution in fast forward and there, we have no evolution – at least none that is visible. I guess this type of guppy evolution would not show up in the fossil record anyway.

    But when your theory explains high speed changes as well as no changes over millions and millions of years, in other words if it is so flexible as to explain anything and everything thrown at it, how can it be falsified?

    I guess I agree with most others here – this is not an example of the type of change that is necessary for common descent type of evolution to take place. It is just another example of natural selection choosing among the current genetic information the best genes available for their new environment. The information already existed. Nothing new was created.

  18. 18
    Mapou says:

    tjguy, there was no natural selection involved in these guppy adaptations, IMO. It is a complex genetic program responding to environmental cues precisely as it was programmed to do by the original genetic designers. That is all.

  19. 19
    tjguy says:

    Is that how they are explaining it?

    Hasn’t that same type of change been explained by natural selection in the past?

    In other words, does this then take away some of the claimed abilities of natural selection to cause change?

    At any rate, the conclusion remains the same – no new genetic information which means it is not the type of change Darwin needs to support his hypothesis.

  20. 20
    Eric Anderson says:

    Mung @13:

    I think we should stop referring to changes in gene frequencies as Darwinian evolution. In fact, I think we should stop calling it evolution.

    Yes. One of the great rhetorical tools of the evolutionary proponent is to use the same exact word to refer to wildly different phenomena. That way if the little tiny, uncontroversial phenomena can be proven, then the whole grand theory is proven. At least that is the thinking used to convince the uninitiated.

    It isn’t even necessarily intentional. It is often due just to sloppy thinking. In the present case, for example, I don’t have any reason to think Reznick is anything other than genuinely sincere in thinking that he has seen evolution occur right “under our nose.” Indeed, as he suggests, how could anyone doubt evolution with such evidence.

    All very sincere.

    And completely confused.

    Would that the term “evolution” referred to a specific, well-defined, agreed-upon phenomenon, rather than a hodge-podge of semi-related phenomena, ranging from the obvious and the well-supported at one end of the spectrum to the outrageous and the wildly-speculative at the other.

  21. 21
    Virgil Cain says:

    Eric- Hopefully Dr Spetner will say something here.. In the book he just notes what happened and says if the variation already existed in the guppies and the different predators were the difference then it isn’t evidence for random mutations doing anything. If the change was brought on by the guppies themselves or some built-in response to the predatory selection then it isn’t evidence for random mutation. The change happened in two years so it would have had to be some very lucky mutations that caused the change.

  22. 22
    Mapou says:

    EA:

    Yes. One of the great rhetorical tools of the evolutionary proponent is to use the same exact word to refer to wildly different phenomena. That way if the little tiny, uncontroversial phenomena can be proven, then the whole grand theory is proven. At least that is the thinking used to convince the uninitiated.

    I would not call it a “rhetorical tool” or a “thinking”. It’s an outright condescending and insulting lie. It insults the public’s intelligence, the same public who pays their salaries. We should not put up with this behavior and be polite in our criticism. They don’t deserve it.

  23. 23
    Eric Anderson says:

    Jerry @14:

    How much of what is happening to the guppies, the result of epigenetics?

    Good question. I’m not sure we know at this point, but we can make some educated guesses.

    If by “epigenetics” we mean the broad concept of everything that occurs in the organism other than changes to the genetic code itself (changes to gene expression, for example), then likely we are dealing almost exclusively with epigenetics in this case. There is no evidence, and no rational expectation, that the changes in the guppy population in only 4 generations and in the short span of one year resulted from random mutations or similar chance changes to the genome. It seems to be a very clear case of a switching mechanism — definitely not random.

    The only caveat I would add is that some organisms have the remarkable ability to proactively make changes to their genome in response to environmental cues (some bacteria for example have this ability) — an epigenetic mechanism that makes a genetic change. Whether we call the result epigenetics or genetics, it is clearly a controlled process and has nothing whatever to do with the alleged Neo-Darwinian evolutionary mechanisms such as random mutations. Whether guppies have this kind of ability is, as far as I know, not yet demonstrated and thus still an open question.

  24. 24
    Mapou says:

    EA:

    It isn’t even necessarily intentional. It is often due just to sloppy thinking. In the present case, for example, I don’t have any reason to think Reznick is anything other than genuinely sincere in thinking that he has seen evolution occur right “under our nose.” Indeed, as he suggests, how could anyone doubt evolution with such evidence.

    All very sincere.

    I hope you’re joking. The man is not a scientist. He’s a professional liar.

  25. 25
    Eric Anderson says:

    Zachriel @15:

    What’s interesting is that all these sorts of studies are nearly always done by biologists based on evolutionary principles.

    Not really. It is simply an observation of what happens with a species in the wild. Evolutionary theory wasn’t necessary to perform the study and hasn’t been particularly helpful in understanding the data. Indeed, it has been an impediment. It would be more accurate to say that many good studies are done by biologists in spite of evolutionary principles.

    Reznick clearly distinguishes between phenotypic plasticity and adaptive plasticity, and even finds a relationship between them. See Ghalambor et al., Non-adaptive plasticity potentiates rapid adaptive evolution of gene expression in nature, Nature 2015.

    Sounds all very impressive. That is, until you unpackage it. After all, what is meant by “rapid adaptive evolution of gene expression”? What is the word “evolution” doing in that phrase?

    What is evolving in a case like this? Again, we are right back to the basic point.

    If by “evolution” all we mean is any change in an organism or a population, then we have fallen into a rhetorical trap and have put forward an illusory explanation. In contrast, if we are claiming something more — for example, that this “evolution” occurred through purely natural processes without any pre-programming or designed mechanism — then we are adding an unwarranted gloss and grossly misinterpreting the data.

    Finally, if what we mean is that organisms in the past “evolved” the ability to later “evolve” more rapidly, then we are not drawing any supportable conclusions from the data, we are just making up stories about some hypothetical evolutionary past to salvage our ever more tenuous naturalistic paradigm.

    Again, no-one doubts that adaptation can occur quickly. There are many examples, and Reznick’s guppies are an excellent example, with good, solid data. The question is not whether adaptation occurs, or even whether selection occurs following that adaptation. The question on the table is the source of the adaptive mechanism and the adaptive capability. And the more we learn the more the traditional Neo-Darwinian mechanisms are being pushed to the fringes of relevance.

  26. 26
    Eric Anderson says:

    tjguy @19:

    Is that how they are explaining it?

    Hasn’t that same type of change been explained by natural selection in the past?

    That has always been the traditional explanation for this kind of thing — finch beaks, insects and insecticide, peppered moth, etc. Also, Reznick seems to think the change in the guppy population is an example of natural selection.

    Indeed, it is possible that it is an example of natural selection. As Mapou @18 points out, it may well not be, but let’s assume for purposes of discussion that the guppies show a marvelous example of natural selection in action. Great. What was being selected and where did it come from? Certainly not from random mutations or some similar chance process.

    In other words, does this then take away some of the claimed abilities of natural selection to cause change?

    Natural selection doesn’t have any abilities. It isn’t a force of any kind. It is just a label applied after the fact to describe the stochastic results of differential reproduction.

    But, taking your question a bit broadly, yes. That is one of the big takeaways of the guppy experiment and other experiments with bacteria and finches. The traditional RM+NS mechanism becomes more and more marginalized as we learn what is actually going on in the biology. Neo-Darwinian evolution (RM+NS) seems to be limited to the relatively rare scenarios that have the characteristics we see in, say, the malaria/sickle cell situation.

    That is why I am interested to know of other good, solid, confirmed examples of Darwinian evolution in action. I’m struggling to think of many — which should be surprising, because even evolution skeptics have long granted that Darwinian evolution can produce all kinds of microevolutionary changes. For my part, I’m not so sure anymore and I’m not just asking a rhetorical question in the OP. I genuinely want to know whether RM+NS is really such an anemic and marginalized driving force in biology as I am starting to suspect.

    At any rate, the conclusion remains the same – no new genetic information which means it is not the type of change Darwin needs to support his hypothesis.

    Absolutely correct.* And this is the key point that Reznick and other proponents of the grander claims of evolutionary theory seem to have a hard time grasping.

    —–

    * Even if there were arguably some “new information” produced by an adaptive mechanism actually altering the genome (questionable, but let’s go with it for purposes of discussion), it still would not be an example of the kind of thing that traditional evolutionary theory can rely on for proof of the theory.

    It certainly would not be Neo-Darwinian evolution, or even Darwinian evolution understood more broadly. We might be tempted to call it “pre-programmed evolution” or “adaptive evolution” or something like that. But why even use the loaded and easily-misunderstood word “evolution” in that case? It doesn’t help us understand anything that is going on in the actual biology and in fact just confuses things. Better to call it a “pre-programmed adaptative response” or something like that. Much more accurate and useful terminology than “evolution.”

  27. 27
    Upright BiPed says:

    Glad to see you back Eric.

  28. 28
    Mapou says:

    IMO, to accept intelligent design is to accept that advanced designers must have programmed the ability of living organisms to adapt to various environments. There is no way that a random optimizing process can anticipate future challenges. Knowing this, we are free to speculate and even make predictions about how such an adaptive mechanism might work.

    I hypothesize that the nervous systems or brains of the more complex species likely contain a gene modification module that responds to environmental cues by selecting or suppressing relevant genes. This happens, not only during the various stages of development to adulthood but also as a result of environmental stimuli. Careful research should reveal this, IMO.

    It’s about time the ID community starts making some serious scientific predictions based on intelligence and design. We, too, are intelligent designers. We know a lot more about it than we think. Many among us are handicapped by various philosophical and religious traditions. This is why ID has been stuck in rut, IMO. But it does not matter in the end. Evolution does not have a prayer. Sooner of later, the hammer comes down. Hard.

  29. 29
    Box says:

    Eric Anderson: Natural selection doesn’t have any abilities. It isn’t a force of any kind. It is just a label applied after the fact to describe the stochastic results of differential reproduction.

    Why do you not add “and survival” to your last sentence? I know you have given this subject a lot of thought, so I suspect there must be a good reason.

    My understanding is that natural selection is a destructive force which acts on an abundance of viable creatures that chance *magically* produces. If an organism continues to exist it can be said that it is “untouched” by natural selection — the grim reaper. For one thing natural selection is the direct result of limited resources. Natural selection, by killing off viable creatures, removes precious information. In other words natural selection is a hindrance to evolution, assuming that “the goal” of evolution is finding all viable creatures.
    Would you care to comment on my view?

  30. 30
    Zachriel says:

    Mapou: Anybody who has played with genetic algorithms knows that they’re only good for toy applications.

    Actually, genetic algorithms can be quite adept at solving complex problems or navigating complex spaces.

    tjguy: And then you have the problem of stasis – no evolution occurring for hundreds of millions of years – or so the claim goes.

    That’s not correct. Evolution proceeds even in cases of living fossils.

    Eric Anderson: It is often due just to sloppy thinking. In the present case, for example, I don’t have any reason to think Reznick is anything other than genuinely sincere in thinking that he has seen evolution occur right “under our nose.”

    Reznick’s research papers don’t seem confused. See Ghalambor et al., Non-adaptive plasticity potentiates rapid adaptive evolution of gene expression in nature, Nature 2015. Can you be specific?

    Eric Anderson: It is simply an observation of what happens with a species in the wild.

    And it happens to be an evolutionary biologist who devised the experiment and made the observations. Quite prolific those evolutionary biologists.

    Eric Anderson: It would be more accurate to say that many good studies are done by biologists in spite of evolutionary principles.

    Nearly all good studies are done by biologists holding evolutionary views. On the other hand, Intelligent Design appears to be scientifically sterile.

    Eric Anderson: After all, what is meant by “rapid adaptive evolution of gene expression”?

    Changes in heritable gene expression, as opposed to changes in gene expression due to phenotypic plasticity. What did you think it meant?

    Eric Anderson: Finally, if what we mean is that organisms in the past “evolved” the ability to later “evolve” more rapidly, then we are not drawing any supportable conclusions from the data, we are just making up stories about some hypothetical evolutionary past to salvage our ever more tenuous naturalistic paradigm.

    You’re conflating phenotypic plasticity with evolution. You seem to be the one confused, not Reznick.

    Box: natural selection is a hindrance to evolution, assuming that “the goal” of evolution is finding all viable creatures.

    No. Mere viability is not “the goal” of natural selection, but selection of the most prolific.

  31. 31
    kairosfocus says:

    Box, he probably implies across time as in multiple generations yielding a cumulative result. KF

  32. 32
    Bob O'H says:

    Eric Anderson @ 7 –

    I am not aware of whether Reznick’s DNA sampling actually isolated a genetic change responsible for the different coloration of the guppies.

    see here for changes at the DNA level, although they don’t link it to function.

    What appears to be happening is that Reznick is confused, as are so many evolutionary biologists, about the ramifications of his research. He says that “evolution” is happening right “under our nose” and that this is the kind of evidence that should convince people who “don’t believe in evolution.”

    Yet, if he means “evolution” in the simple sense of some change in a population, then (a) no-one would dispute that anyway, and (b) it doesn’t tell us anything about how the changes came about, which is precisely the matter at issue.

    On the other hand, if he means “evolution” in the sense of generating new biological information and new biological function as the result of random mutations and other evolutionary mechanisms, then his research certainly has not shown any such thing. Indeed, he seems to admit that such could not have occurred.

    I don’t think it’s Reznick who’s confused – it’s you. I think it’s clear that he’s talking about heritable phenotypic change, so yes, we all agree that that’s happened and there’s nothing controversial. So why do you then criticise him and call him confused because his work doesn’t look at evolutionary novelty? Does he claim to do that? Or are you creating confusion by mis-interpreting what he meant by ‘evolution’?

  33. 33
    Virgil Cain says:

    Zachriel:

    Actually, genetic algorithms can be quite adept at solving complex problems or navigating complex spaces.

    They are intelligently designed to do so.

    Nearly all good studies are done by biologists holding evolutionary views.

    Name ONE study that relied on undirected evolution.

  34. 34
    Virgil Cain says:

    If genetic change arose within two years and caused the phenotypic change then we can easily rule out natural selection as NS requires random mutations and this happened too rapidly for that.

  35. 35
    Bob O'H says:

    Virgil – The assumption is that the genetic variation was in the founder population.

  36. 36
    Virgil Cain says:

    Bob O’H- That still means no one can say natural selection didit as they have no idea how that genetic variation arose. They also need a way to test that assumption.

  37. 37
    Mapou says:

    Zachriel, the resident prevaricator:

    Mapou: Anybody who has played with genetic algorithms knows that they’re only good for toy applications.

    Actually, genetic algorithms can be quite adept at solving complex problems or navigating complex spaces.

    This is a lie. I am an AI researcher and I know about GAs. Complex problems kill them dead because they cannot get past the combinatorial explosion. To get good results from GAs, one must severely restrict the problem space.

    Besides, nobody needs GAs to solve any problem on a computer because they can already be easily solved by a regular randomizing optimizer.

  38. 38
    Mapou says:

    Guppies prove one thing: Nobody needs that RM+NS crap. Organisms are programmed to modify their genes in direct response to environmental cues. Some trees are so good at this, they can do it during their lifetimes. They can adapt to their environments by having a different genetic signature at the top than at the bottom.

  39. 39
    Eric Anderson says:

    Mapou @22 and @27:

    Let’s be careful to not go a bridge too far. A lie is an intentional act meant to deceive. There are many ways to be wrong and to draw a wrong conclusion. That someone does so does not mean that they are a liar. Neither you nor I know Reznick personally and I don’t believe we have any reason to accuse him of lying.

    As a general matter I have found that behavior can more often be explained as a result of incompetence than conspiracy. We can vigorously disagree with someone’s position and defend our own. We can be frustrated and annoyed with their obstinance, and I share your frustration at some level. But with few exceptions (including perhaps a couple of occasional posters on this forum), we should be very hesitant to attribute intentional deception and call someone a liar.

    I stick by my assessment that Reznick is doing good work and is sincere in his belief that he is watching “evolution” happen right “under his nose.” I strongly disagree with his representation of the implications of his data. But he is not a liar.

  40. 40
    Eric Anderson says:

    Mapou @28:

    I hypothesize that the nervous systems or brains of the more complex species likely contain a gene modification module that responds to environmental cues by selecting or suppressing relevant genes. This happens, not only during the various stages of development to adulthood but also as a result of environmental stimuli. Careful research should reveal this, IMO.

    Good thought. My understanding is that some examples have already been discovered, and more will no doubt be uncovered. Not just in more complex species either.

  41. 41
    Mapou says:

    EA @39,

    Sorry but I completely disagree with your perspective. Any scientist worth his/her mantle knows that the way to serve science is to conduct experiments to try to falsify a theory, not to corroborate it. All evolutionary biologists use exactly the same approach to science: let’s find ways to buttress Darwinian evolution. It should be the other around, for crying out loud.

    Evolutionary “scientists”, IMO, are all dishonest, gutless, butt-kissing opportunists. They work for the grant money and the accolades, not for science. This is my opinion and I stand by it.

  42. 42
    Mapou says:

    And by the way, as far as conspiracy is concerned, let me say this. Of course, there is a conspiracy. Whoever controls the grant money is part and parcel of the conspiracy. It is a conspiracy that uses the veneer of science to attack traditional religions. Science be damned.

  43. 43
    Dr JDD says:

    This is primarily down to the indoctrination of a false definition of the word “evolution”.

    Those pesky committed atheistic materialists have certainly been very successful at engraining that into most scientists.

  44. 44
    Zachriel says:

    Mapou: I am an AI researcher and I know about GAs. Complex problems kill them dead because they cannot get past the combinatorial explosion.

    Then you’re doing it wrong.

    Mapou: To get good results from GAs, one must severely restrict the problem space.

    Computers generally don’t have the resources of nature, so they can’t solve problems of the same scope; however, they can solve complex problems far faster than random search.

  45. 45
    Virgil Cain says:

    It is very telling that Zachriel cannot post any examples of GA’s solving complex problems.

  46. 46
    Eric Anderson says:

    Box @29:

    Good catch. I was writing quickly and reverted to the old common terminology that is sometimes used. You are right, even reproduction itself is not the whole story — unless of course we talk about reproduction that eventually leads to offspring who develop to the point of being able to in turn reproduce. Which is another way of saying they “survive” long enough to reproduce. 🙂

    My understanding is that natural selection is a destructive force which acts on an abundance of viable creatures that chance *magically* produces. If an organism continues to exist it can be said that it is “untouched” by natural selection — the grim reaper. For one thing natural selection is the direct result of limited resources. Natural selection, by killing off viable creatures, removes precious information.

    Thanks, interesting thoughts.

    Yes, chance is at the heart of innovation in the evolutionary viewpoint. (A few individuals like to imagine that there are some as-yet-undiscovered natural laws that will produce organisms, but that is wishful thinking.) Regardless, yes, natural selection simply means that some organisms get caught by the grim reaper, as you say, before reproducing.

    In reality, it is chance all the way down. Natural selection does not have any discernable directionality, which is a point often missed by evolutionary proponents. So the theory proposes organisms created by chance which then survive by chance. That is really the sum and substance of the whole theory: “Stuff Happens.”

    In other words natural selection is a hindrance to evolution, assuming that “the goal” of evolution is finding all viable creatures.
    Would you care to comment on my view?

    I’m not sure it is correct to suggest that the goal of evolution is finding all viable creatures. If it has any goal (borrowing words as we must from intentionality), evolution’s goal is simply ongoing existence — survival. Whether that means innumerable creatures filling all available niches or a single creature filling just one niche on the entire earth, evolution doesn’t care. There is no directionality one way or another.

    Finally, I think an evolutionist might quibble with your suggestion that natural selection kills off “viable creatures.” I understand what you mean by “viable,” but they might prefer to define viable as “suited to the environment” or “suited for survival,” in which case natural selection’s job is to kill off those that aren’t viable.*

    At another level, though, if we think of “viable” in a broader sense or if we simply acknowledge that some creatures were produced that didn’t end up surviving, then you are quite right: to that extent natural selection is a hindrance to evolution. It removes, it culls, it eliminates, it lessens possibilities. If anything, natural selection helps to keep a population within a stable norm, rather than veering off in new and uncharted directions.

    On an interesting related note, there are a cellular processes that actively pursue and destroy misshapen, broken or non-working parts — the “unfit” proteins, cellular mechanisms, and even entire cells. This may look like “natural selection” at the molecular and cellular level and we could apply such a label, but in reality it is a very carefully controlled and engineered process that helps keep the organism functioning within designed parameters. Though not identical in means, natural selection fills something of a similar role at the organismal and population level — keeping the population in check and functioning within normal parameters.

    —–

    * Of course natural selection doesn’t do anything. Some creatures just happen to survive — again, by chance — and then we come along later and attach a label to the results.

  47. 47
    Eric Anderson says:

    Bob O’H @32:

    So why do you then criticise him and call him confused because his work doesn’t look at evolutionary novelty? Does he claim to do that? Or are you creating confusion by mis-interpreting what he meant by ‘evolution’?

    I haven’t called him confused because his work doesn’t look at evolutionary novelty. I think the work he has done is great.

    He is confused because he thinks he has witnessed “evolution” right under his nose, and at the same time laments that lots of people don’t believe in evolution, when he has the data right there, under his nose.

    Yet the guppy experience is nothing that an evolutionary skeptic would object to. Further, what evolutionary skeptics object to is not resolved by Reznick’s data.

    So he complains that people don’t believe in evolution and that he has data that proves evolution. Yet the guppy experiment does not demonstrate anything relevant to what the skeptics object to, and ironically, it may not even stand as an example of meaningful Neo-Darwinian evolution at the micro level.

    The problem, as so often, is that evolutionists are very sloppy and flexible with the way they use the word “evolution.” As Philip Johnson has pointed out (paraphrasing), evolution “means both the tiny changes and the grand creative process; we can prove the tiny changes so we think we’ve proved the whole grand creative process.” You have to escape from that intellectual trap to understand that the latter does not follow from the former, and it is surprisingly difficult for people who have been indoctrinated in materialistic evolutionary theory for years to make that logical breakthrough.

  48. 48
    Eric Anderson says:

    Zachriel @30:

    And it happens to be an evolutionary biologist who devised the experiment and made the observations. Quite prolific those evolutionary biologists.

    You seem quite adamant to point out that most biological experiments are performed by biologists with evolutionary views. What is your point — that that most biologists have been indoctrinated with an evolutionary viewpoint throughout their schooling and careers, rather than a non-traditional viewpoint? Sure. I agree with that.

    You’re conflating phenotypic plasticity with evolution. You seem to be the one confused, not Reznick.

    Where did I do that? I certainly did not intend to equate anything with “evolution.” I have been repeatedly pointing out that the word is as plastic as the theory itself. It morphs and changes in different directions depending on the rhetorical needs of the proponent. Thus, Reznick laments that skeptics don’t believe in “evolution,” and claims that his experiment proves “evolution,” all the while not realizing that what skeptics object to has nothing to do with what his experiment shows.

  49. 49
    Eric Anderson says:

    Actually, genetic algorithms can be quite adept at solving complex problems or navigating complex spaces.

    It is true that advances can be made using a trial-and-error process. It is a legitimate tool in any designer’s toolbelt. Computers are helpful because they speed up the process exponentially.

    Yet any genetic algorithm or other trial-and-error process (the famous NASA antenna that evolutionary proponents like to point to, for example) has to be carefully and closely parameterized or it will not produce anything of value and will be useless as a tool. The only way genetic algorithms do better than random search is if they are parameterized on the front end and/or subject to intelligent selection on the back end.

    Not an impressive thing to rely on if one hopes to produce a functioning organism.

  50. 50
    Mapou says:

    Zachriel:

    Mapou: I am an AI researcher and I know about GAs. Complex problems kill them dead because they cannot get past the combinatorial explosion.

    Then you’re doing it wrong.

    You must be a magician.

    Mapou: To get good results from GAs, one must severely restrict the problem space.

    Computers generally don’t have the resources of nature, so they can’t solve problems of the same scope; however, they can solve complex problems far faster than random search.

    This is about as stupid an answer as you can get. You either don’t understand what the combinatorial explosion means or you’re just lying as usual. Which is typical of all Darwinists and atheists. No big surprise there.

    The combinatorial explosion increases the search space exponentially. The problem is especially intractable when working with DNA sequences. It does not matter if you have a computer the size of the earth or the size of the entire universe. Heck, a computer the size of trillions upon trillions of universes would be no better than a Commodore 64.

    PS. Get some education.

  51. 51
    Virgil Cain says:

    Mapou:

    This is about as stupid an answer as you can get.

    Welcome to the world of Zachriel. 😎

  52. 52

    The most parsimonious explanation is that inteligent design is happening under our noses.

  53. 53
    Bob O'H says:

    Eric Andweson @ 47 –

    Yet the guppy experience is nothing that an evolutionary skeptic would object to.

    Really? How is it different in that regard from the peppered moth or Darwin’s Finches? They are both also just examples of adaptation, but evolutionary skeptics have objected to them.

  54. 54
    Virgil Cain says:

    Bob O’H- the objection is due to evolutionists using them to support Common Descent. “We see this over very little time so more time means more change.” We also object to them being used as examples of natural selection because no one knows what caused the variation.

  55. 55
    Dr JDD says:

    And to add to Virgil Cain and much of the point of this thread: none of these examples provide evidence of addition of novel information.

    Again, as Eric has already demonstrated there is a complete failure to understand what is objected to by those that deny evolution’s explanatory power of common descent.

  56. 56
    Dr JDD says:

    My car has automatic air conditioning. Therefore I when it is hot the ac comes on. Therefore it has adapted or evolved.

    My car also has automatic windshield wipers. When it starts raining they come on. Therefore it has adapted hence evolved.

    To say these things is as dumb as to say because an organism already contains information allowing them to adapt or change to a different environment that this is proof of evolution.

    And again, it comes down to sloppy labelling if ALL AND ANY adaptation as termed evolution, then the failure to separate this form of adaptation (utilisation of existing information) from the type claimed to evolve the proteosome, the splicing machinery, ATP syntheses, etc etc from dirt.

  57. 57
    Mapou says:

    Dr JDD:

    And again, it comes down to sloppy labelling if ALL AND ANY adaptation as termed evolution

    It’s not sloppy at all. It’s calculated mischief. It’s an outright lie and deception hoping that the public is too stupid to notice.

    PS. All evolutionary scientists should be fired and their alma mater vilified.

  58. 58
    Zachriel says:

    Eric Anderson: Natural selection does not have any discernable directionality, which is a point often missed by evolutionary proponents. So the theory proposes organisms created by chance which then survive by chance.

    That is incorrect. Natural selection is due to heritable differences that lead to differences in reproductive potential.

    Eric Anderson: natural selection simply means that some organisms get caught by the grim reaper, as you say, before reproducing.

    That is also incorrect. Most natural selection just means a small difference in the number of viable offspring.

    Eric Anderson: You seem quite adamant to point out that most biological experiments are performed by biologists with evolutionary views. What is your point

    That ID is scientifically sterile, and evolutionary biologists are clearly on the right track due to their long history of success.

    Eric Anderson: Yet any genetic algorithm or other trial-and-error process (the famous NASA antenna that evolutionary proponents like to point to, for example) has to be carefully and closely parameterized or it will not produce anything of value and will be useless as a tool.

    Genetic algorithms can be very general. Whether they are successful then depends on whether the landscape exhibits positive structure.

    Mapou: You either don’t understand what the combinatorial explosion means

    The limitation of genetic algorithms isn’t primarily the size of the search space, but the structure.

  59. 59
    Mapou says:

    Zachriel:

    Mapou: You either don’t understand what the combinatorial explosion means

    The limitation of genetic algorithms isn’t primarily the size of the search space, but the structure.

    Man, why don’t you pack it? Why do you insist on always talking from the wrong extremity? Must be a genetic thing, eh? Like kleptomania or Tourette’s syndrome or something?

    Your time is coming, you hear me, Zacky-o? Soon, the hammer comes down. Hard. And sooner than you think. I’ll be watching you people squirm with a beer in one hand, a bag of cheetos in the other and a smirk on my face. LOL.

  60. 60
    Virgil Cain says:

    Zachriel:

    Natural selection is due to heritable differences that lead to differences in reproductive potential.

    That is incorrect. Natural selection is due to random/ happenstance heritable differences that lead to differences in reproductive potential. And that is whatever it is.

    That ID is scientifically sterile,

    Only to the scientifically illiterate. And who cares what they say about science?

    and evolutionary biologists are clearly on the right track due to their long history of success.

    Of what? Procuring grants? They haven’t had any success supporting undirected evolution. Most don’t even try.

  61. 61
    wd400 says:

    How many of you guys read the paper? Because they demonstrate pretty clearly the change in orange colouration in the experimental population had an genetic basis…

  62. 62
    Virgil Cain says:

    Note to Eric: In Dr Spetner’s new book his discussion on guppies pertains to their ability to adapt their morphology and behavior to the type of predator in the area. Cichlid fish prey on the larger mature guppies whereas killfish prey on the smaller immature guppy-puppies :). Under cichlid pressure guppies adapt by maturing early and having many small offspring, which can evade the predator. Under killfish pressure they mature late and have fewer albeit larger offspring, which can evade the killfish. (Spetner “the Evolution Revolution , 2014, pg 71-2)

  63. 63
    Mapou says:

    wd400, give us break. They claim it shows Darwinian evolution in action. It does not. It’s a damn lie.

  64. 64
    Box says:

    Eric,

    Eric Anderson:

    Yes, chance is at the heart of innovation in the evolutionary viewpoint. (A few individuals like to imagine that there are some as-yet-undiscovered natural laws that will produce organisms, but that is wishful thinking.)

    Chance produces an abundance of viable creatures — “viable” as in suited for existence — for natural selection to act on. This brings me to the idea that prior to natural selection there is a more fundamental selection: one may call it “existential selection”. Under materialism organisms are bags of chemicals “who” are performing a (very) dynamic balancing act — homeostasis — until they don’t and die. Is there a reason for this balancing act? Well there is no reason stemming from within the organism, since not one single part, atom or molecule, of the organism is interested in the organism; let alone in its continued existence. The only reason that the organisms that we see today don’t fall apart is because the ones that did didn’t pass the filter of existential selection and are not longer among the “living”. So, organisms don’t fall apart because, well …. they are there (?)

    Barham: How can living systems be so robust (dynamically stable), when they consist of thousands of chemical interactions that must all be coordinated precisely in time and space? From the point of view of physics, cells (not to speak of more complex organisms) should not exist, and yet they do. How is that possible?
    The only suggestion Darwinism has to offer is chance: those systems that just happened to be stable are the ones that we see today.

  65. 65
    wd400 says:

    wd400, give us break. They claim it shows Darwinian evolution in action. It does not. It’s a damn lie.

    They show a phenotype changing as the result of selection a heritable trait. That’s certainly Darwinian evolution.

  66. 66
    Virgil Cain says:

    Darwinian evolution requires the changes to be accidental/ happenstance. That’s certainly not apparent in this case.

  67. 67
    Mapou says:

    wd400:

    They show a phenotype changing as the result of selection a heritable trait. That’s certainly Darwinian evolution.

    You must be a relative of Zachriel, the resident prevaricator. Where the RM+NS evidence? None to be found anywhere. This is just another example of lying Darwinists insulting the public’s intelligence with their condescending crap.

  68. 68
    wd400 says:

    This experiment is far too short for mutation to be important. The evidence is for selection on standing genetic variation. If you imagine this variation is not random with respect to fitness then it’s really up to you to explain how that’s possible — it’s a very speculative claim that lacks evidence or indeed a plausible mechanism.

  69. 69
    Andre says:

    WD400

    You have it all wrong. It is you that have to explain how happenstance just got lucky again for the fish. If you actually apply your mind to the history of life then you would have to say happenstance is very lucky. All these creatures all adaptation by some luck process… You are welcome to believe it I’ll pass….

  70. 70
    wd400 says:

    Have you read the paper? Or the press release? It’s not clear that this comment relates to that paper at all…

  71. 71
    Eric Anderson says:

    Bob O’H @53:

    Really? How is it different in that regard from the peppered moth or Darwin’s Finches? They are both also just examples of adaptation, but evolutionary skeptics have objected to them.

    What do you think the guppy observations tell us, and why do you think an evolutionary skeptic would object to those observations? Skeptics have no problem with the data. It is the beyond-the-data speculations and naive power-of-evolution proclamations that skeptics object to. Skeptics have no issue with the idea of organisms adapting to their environment.

    Same with peppered moths and finch beaks. Indeed, most evolutionary skeptics (certainly nearly all prominent ID proponents) have long accepted that these could be examples of natural selection. There are many issues with Kettlewell’s particular observations (topic for another day) and some with the finch beak observations. But most skeptics have said, in essence, “Sure. So the percentage of light and dark moths in the population changed. So what? It doesn’t tell us anything at all about how we got a moth in the first place.”

    What peppered moths, Galapagos finches, bacterial resistance, insecticide resistance and guppies all demonstrate very clearly is the following fundamental principle:

    Organisms have the ability to adapt to temporary environmental change while ultimately resisting long-term fundamental change. None of these observations demonstrate progression toward a new and different type of organism. All they demonstrate is temporary oscillation around a norm. And as far as changes in organisms, that is all that has ever been empirically observed in nature.

  72. 72
    Eric Anderson says:

    UB @27:

    Thanks. Lots of other stuff going on, but I still check in occasionally. Regularly see things I would like to write on, but this one caught my eye (and I happened to have a bit of time that day). 🙂

  73. 73
    Eric Anderson says:

    Dr JDD @56:

    Excellent examples. Well said.

  74. 74
    Mapou says:

    wd400:

    This experiment is far too short for mutation to be important.

    So why claim it supports Darwinian evolution then? Never mind. I know. It’s the usual damn lies. All Darwinists are habitual liars.

    The evidence is for selection on standing genetic variation. If you imagine this variation is not random with respect to fitness then it’s really up to you to explain how that’s possible

    No. it is up to the experimenter to show that it happened that way. Again, no evidence. Why no evidence? Because it did not happen that way. That’s why.

    But since, obviously out of desperation, you are placing the onus on the reader to prove the Darwinist interpretation of the experimental results to be just a bunch of crap, I will oblige. The reason that none of it could have happened via any kind of blind random process is that the combinatorial explosion forbids it. As simple as that. The search space is too huge for a stochastic solution. It would take trillions upon trillions of years. I’ll leave as an exercise to you to figure out why.

    — it’s a very speculative claim that lacks evidence or indeed a plausible mechanism.

    This is nonsense, of course. The refutation of the Darwinist stochastic prediction is straightforward and unassailable. The only alternative is a nonrandom process. Read and weep.

  75. 75
    wd400 says:

    No. it is up to the experimenter to show that it happened that way

    To be clear: you want the experimenters to go to a natrual population and assess whether genetic variants in that population were produced randomly with respect to fitness or by some unknown non-random process? How could you even start to do this?

    (there are plenty of lab experiments that demonstrate mutations are random with respect to fitness, btw)

  76. 76
    Mapou says:

    wd400,

    I don’t want the experimenters to do anything other than retract the paper and their interpretation. It’s obviously crap. I already know for a fact that they cannot prove that the variants occurred randomly. I know for a fact that guppies are programmed genetically to adapt to their environments in a non-random way.

    Regarding your allusion to labs experiment that demonstrate whatever, the hell with that. I don’t trust anything coming from evolutionary biologists. The fact that they are “evolutionary” anything makes them liars in my book.

  77. 77
    wd400 says:

    Who needs science when Mapou just knows stuff…

  78. 78
    Mapou says:

    wd400 @77,

    Man, I’m not your dog. So you can pack it you know where. I explained in simple terms why a random search would be impossible. If you reject my argument, then you too are a gutless liar in my book.

  79. 79
    Eric Anderson says:

    Zachriel @58:

    Natural selection is due to heritable differences that lead to differences in reproductive potential.

    Sounds very impressive. That is, until we unpackage it. The point is about directionality. Where is the directionality in saying that there are “heritable differences that lead to differences in reproductive potential”? If all you are saying is that the organisms that inherit characteristics allowing them to reproduce are more likely to reproduce, then fine. We are all in agreement about that useless tautology. On the other hand, if you are claiming some kind of directionality, then let’s hear it.

    What traits does natural selection favor, in what direction does it lead? Larger organisms or smaller organisms? Faster organisms or slower organisms? Light-colored organisms or dark-colored organisms? Feathered organisms or scaly organisms? Tall organisms or short organisms?

    Please elucidate for us the directionality you think is brought to bear by the power of natural selection. This will be of immense interest not just to me but to the scientific community at large.

  80. 80
    Eric Anderson says:

    wd400 @61:

    Thanks for your comment.

    So is it your understanding that the genetic variation was present in the guppy population at the outset, rather than arising through some kind of mutation event during the short timeframe of the study?

    And would the adaptation the researchers observed in the population be due then not to generation of new genetic information during that timeframe, but rather due to differential survival (that is to say, differential predation in this case which culled some of the individuals, and therefore, some of the genetic pool), thus leaving a more uniform population better adapted for the new environment?

    Thanks,

  81. 81
    wd400 says:

    I take it you didn’t read the paper (or the press release?)

    The change by both differential survival and differential reproductive success, as is made pretty clear in the intro of the PR.

    There doesn’t appear to e a significant decrease in the variance of the orange colouration, so it’s not clear that the population is more uniform after the experiment. It’s certainly better adapted to the environment of the experiment.

  82. 82
    Zachriel says:

    Eric Anderson: Where is the directionality in saying that there are “heritable differences that lead to differences in reproductive potential”?

    It depends on the environment, of course. In bacteria, the presence of antibiotics leads to the prevalence of the antibiotic resistance trait. In the Galápagos ground finch, beak size can be shown to change with climate patterns which cause changes in food sources. In guppies, predation causes a change in coloration. These are all directional, and certainly not tautological. Notably, these causative patterns were found by biologists based on evolutionary principles.

    Eric Anderson: And would the adaptation the researchers observed in the population be due then not to generation of new genetic information during that timeframe, but rather due to differential survival (that is to say, differential predation in this case which culled some of the individuals, and therefore, some of the genetic pool), thus leaving a more uniform population better adapted for the new environment?

    The distribution of genetic variation (distinct from phenotypic plasticity), like many random variables, tends to form a normal distribution around the mean. With directional selection, the mean is pushed to one side, and the distribution becomes narrower and somewhat skewed. Over time, as new variations are introduced, the curve returns to a normal distribution around the higher mean.

  83. 83
    Virgil Cain says:

    Zachriel:

    Notably, these causative patterns were found by biologists based on evolutionary principles.

    They could have easily been based on baraminology.

  84. 84
    Eric Anderson says:

    Box @64:

    Thanks, good thoughts. We’ve had some discussions in the past here about the issue of far-from-equilibrium systems and how such things could arise and persist.

    After considering the implications of some of his own research Craig Venter changed his views about how life works and concluded, “Life is basically the result of an information process, a software process.”

  85. 85
    Eric Anderson says:

    wd400 @81:

    The change by both differential survival and differential reproductive success, as is made pretty clear in the intro of the PR.

    You didn’t answer the question. Was the variation in the population at the outset, or are you suggesting that some new trait, some new information, some new characteristic showed up during the timeframe of the experiment?

    . . . so it’s not clear that the population is more uniform after the experiment. It’s certainly better adapted to the environment of the experiment.

    The authors conclude, in part: “Second, we detected only very few regions across the genome with signatures of selection common to all populations. In contrast, the two experimental populations shared many such regions. Together our results suggest convergent genetic evolution in introduced populations but not natural populations.”

    I’m curious how a population that becomes more specifically adapted to its new environment can be anything other than more uniform with respect to the adaptive trait, as compared to the pre-transplanted population.

  86. 86
    wd400 says:

    I don’t how much more explicit I can be that the results came about via selection on standing variation.

    For the second question — the most likely way to maintain variance in a phenotype over rounds of selection is for that trait to be effected by multiple genes. As previously rare alleles become more frequent the variety of multiple-allele haplotypes in the population becomes greater and (if those lead to phenotypic differences) you end with plenty of phenotypic variance as a result, even as the mean of the distribution shifts.

    Now, answer my question: did you read the paper before you launched into all of this?

  87. 87
    wd400 says:

    Although I guess I can answer my own question, since the quote you provided above is not actually for that paper in the press release…

  88. 88
    Andre says:

    WD400

    Selection is impotent how many times do we have to highlight this?

  89. 89
    EugeneS says:

    Zahriel

    Actually, genetic algorithms can be quite adept at solving complex problems or navigating complex spaces.

    Have you programmed a single move operator for a real industrial problem yourself?

    In practice, the algorithm designer invariably has to handle a lot of exceptions, tweak a lot of parameters. And that already may destroy the original nice looking concept.

    Parameter setting for GAs, if they are to really work in practice, is a combinatorial problem in its own right.

    Darwinism is no good for practical applications. It is no good for anything really. Natural selection is prohibitively weak in comparison with actual GAs because GAs model intelligent artificial selection, not natural selection.

    In practice, the domain knowledge of the expert is crucial to problem solving. An expert is one who knows about exceptions and how to deal with them.

  90. 90
    wd400 says:

    You can talk you want Andre, but in science you have to provide evidence if you want to be taken seriously.

  91. 91
    Virgil Cain says:

    wd400:

    You can talk you want Andre, but in science you have to provide evidence if you want to be taken seriously.

    And what evidence supports undirected evolution?

  92. 92
    Andre says:

    WD400

    You have frequented this site for a long time paper after paper showing NS as impotent and here you are disputing it. I can’t help but wonder what is your agenda?

  93. 93
    wd400 says:

    I don’t have an “agenda”, but am interested in how anti-mainstream science ideas propagate and insulate themselves from the mainstream.

    Threads like this are a pretty great source of information on that…

  94. 94
    Andre says:

    WD400

    I will say it again NS is impotent. You keep telling us how it is responsible for everything. The bedrock of your worldview and yet in the last 10 years paper after paper showing it as inadequate. What gives? I thought you are a science guy that follows the evidence…

  95. 95
    wd400 says:

    So, I don’t think selection is responsible for everything. Most of our genome, for instance, is junk and that’s certainly not the result of selection. But selection is an important part of evolutionary biology, I dont agree that “paper after paper” has shown that it’s “inadequate”.

  96. 96
    ppolish says:

    Inanimate is fine tuned & animate is guided and purposeful. Evidence is overwhelming. Evidence One-Two Punch. Many Scientists are reeling. Wobbling. No mas no mas.

  97. 97
    Andre says:

    WD400

    If a person handwave all the evidence like that you can be sure it’s an agenda. So again WD400 what is your agenda?

  98. 98
    Andre says:

    WD400

    Since the 60’s we’ve known about selection as inadequate the tempo of its impotence has increased are you denying it? Are you handwaving the evidence? What is your agenda?

  99. 99
    wd400 says:

    I find it very odd to be accused of “hand waving” by someone who literally refers to “paper after paper” without providing a single example. I’ve discussed why I post here, that’s as close as I have to an agenda.

  100. 100
    Zachriel says:

    EugeneS: the algorithm designer invariably has to handle a lot of exceptions, tweak a lot of parameters.

    1. Computers generally have much lower computational resources than nature.
    2. The amount of fiddling required to make computation plausible depends on the problem landscape.

    Andre: You have frequented this site for a long time paper after paper showing NS as impotent and here you are disputing it.

    Can you cite a few such papers published in the peer literature?

  101. 101
    Andre says:

    Do I have to post them? Are you saying in all the years commenting here you have never seen one? What is your agenda?

  102. 102
    Mapou says:

    wd400:

    I don’t have an “agenda”, but am interested in how anti-mainstream science ideas propagate and insulate themselves from the mainstream.

    That sounds exactly like an agenda to me. You are a con artist. That’s what you are. A master weaver of lies and deception, just like all the others.

  103. 103
    Virgil Cain says:

    1. Computers generally have much lower computational resources than nature.

    Cuz you say so? Computers are not constrained by reality whereas nature is.

  104. 104
    Zachriel says:

    Andre: Do I have to post them?

    You only have to pay taxes. Meanwhile, if you can’t support your claim, then readers will reasonably disregard it.

  105. 105
    Virgil Cain says:

    Zachriel:

    Meanwhile, if you can’t support your claim, then readers will reasonably disregard it.

    Exactly why most readers reasonably disregard Zachriel’s comments.

  106. 106
    Mapou says:

    Why is wd400 still preaching the lie that the genome is mostly junk? I thought this was already shown to be a lie.

  107. 107
    Mapou says:

    No random mutations = no Darwinist evolution.

    When will evolutionary biologists grow a pair and act like real scientists? When will they design experiments to try to falsify Darwinian evolution instead of trying to support it?

  108. 108
    Andre says:

    WD400

    Are you denying that there are studies that show NS as impotent. Do you deny they exist? What is your agenda?

  109. 109
    Carpathian says:

    Andre:

    If a person handwave all the evidence like that you can be sure it’s an agenda.

    For every “ID” scientist there are thousands of “Darwinist” scientists.

    What then is the agenda of ID proponents?

  110. 110
    Andre says:

    Zachriel

    Are you denying that there is evidence that NS is impotent?

  111. 111
    Andre says:

    Carpathian

    Who said anything about ID? Are you also denying the evidence that NS is impotent? Are you handwaving bona fide findings?

  112. 112
    Zachriel says:

    Andre: Are you denying that there is evidence that NS is impotent?

    Natural selection can be directly observed.

  113. 113
    Carpathian says:

    Andre:

    Who said anything about ID?

    You stated that those people who hand-wave away evidence, must have an agenda.

    If this is true, then IDists must have an agenda since they hand-wave away evidence.

    So again, what is the point of ID?

    Why is it necessary for biological ID to be accepted by the majority of people who instead accept the findings of a majority of scientists?

  114. 114
    Andre says:

    Zachriel

    Arteficial selection is observed natural selection not at all.

  115. 115
    Andre says:

    Carpathian

    Why are you deflecting? I’ll ask again. Are you denying the evidence that NS is impotent?

  116. 116
    EugeneS says:

    Zachriel,

    1. A computer has nothing by and in itself. It is the algorithm and its implementation that has a potential for problem solving. And even then an algorithm without a processor for it is really nothing.

    2. The amount of fiddling required to make computation plausible depends on the problem landscape.

    What do you mean? The fitness landscape is determined by the fitness function, that is key to GAs functioning well. Nature has no fitness function at all. It has very weak means of selecting. Artificial selection is active and it is orders of magnitude more powerful. Humans can make decisions to select an individual showing the faintest signs of a desired trait. Nature can’t do it because it cannot make decisions. Selection in the case of nature is rather a metaphor because it is passive. Nature selects only from among existing functions, not for a future function. It has zero potential for novelty. Nature can only produce ordered or disordered states. It is inert to function.

    First, function should come about, and only then does selection pressure apply. The first step can only be a result of intelligent actions, i.e. actions as part of planning, decision making and forethought.

  117. 117
    Zachriel says:

    Andre: Arteficial selection is observed natural selection not at all.

    Natural selection is observed, such as in guppies, finches, bacteria. For instance, see Grant & Grant, Natural selection in a population of Darwin’s Finches, The American Naturalist 1989: “we combine functional and ecological aspects of trait variation in a population of Darwin’s finches to demonstrate an interpretable fitness advantage in terms of survival to individuals with certain beak shapes.”

  118. 118
    Andre says:

    Zachriel

    Honestly what is your agenda? The latest research on the Galapagos finches falsify Darwin’s theory.

    http://www.jstor.org/stable/10.....b_contents

    There was no Natural selection involved in the creation or collapse of the Galapagos finches, it was good old adaptation nothing more nothing less.

    Why is this so hard to accept? Even Michael Lynch who is no friend of ID has this to say;

    “As it turns out, Lynch’s approach to explaining genome complexity might be just what evolution needs to withstand criticisms leveled by the ID community. The popular misconception about evolution is that it proceeds entirely by natural selection and that it always benefits species, Lynch explains. The problem with this understanding is that it makes evolution via natural selection sound to some like evolution with a purpose. “Explaining everything in the natural world with natural selection is not that different from intelligent design,” he says. “An intelligent design person just says well, here’s something complex, let’s just invoke an intelligent designer. If you’re willing to invoke natural selection to explain everything, that’s not science. It doesn’t explain anything to simply say, ‘natural selection did it.’ Mutations don’t arise de novo [anew] at the whim of natural selection.”

    Numerous random changes accumulate in the genome. Some of those changes work, but most don’t. What we see in organisms today isn’t necessarily the most ideally adapted form, but instead what’s simply good enough. Indeed, many experts in evolution share this view, but it’s a view that has not made it into the popular understanding.”

    Then in August 2015 the latest in a long line of papers proving that NS is impotent……

    http://www.sciencedaily.com/re.....091206.htm

    The topic was discussed right here;

    http://www.uncommondescent.com.....w-species/

    I see WD400, Zachriel and Carpathian all ignored commenting on it…..

    So again gentlemen are you denying than NS is impotent even with the latest evidence you have been exposed to?

  119. 119
    Andre says:

    Now let me ask you guys, lets see who can spot what the problem is with Michael Lynch’s view?

    Can WD400, Carpathian and Zachriel spot the problem?

  120. 120
    Zachriel says:

    Zachriel: 1. Computers generally have much lower computational resources than nature.

    EugeneS: A computer has nothing by and in itself.

    We’re discussing evolutionary algorithms, as implemented on a computer. In any case, the point stands.

    Zachriel: 2. The amount of fiddling required to make computation plausible depends on the problem landscape.

    EugeneS: The fitness landscape is determined by the fitness function, that is key to GAs functioning well.

    As we said. Some landscapes are not amenable to evolutionary search. In nature, the fitness function is the relationship between the genome, phenotype, and the environment.

    EugeneS: Nature has no fitness function at all.

    The fitness function in biology is an abstraction referring to the relationship between the genome, phenotype, and the environment.

    EugeneS: Artificial selection is orders of magnitude stronger.

    Often true, but not necessarily. For instance, bacteria in contact with an antibiotic will be under strong selection.

    EugeneS: Humans can make decisions to select an individual showing the faintest signs of a desired trait. Nature can’t do it because it cannot make decisions.

    Actually, natural selection can be very sensitive with larger populations. With sexual selection, this is further magnified.

    EugeneS: Nature selects only from among existing functions, not for a future function.

    While not precisely true — phenotypic plasticity and protein mutation give a bit of a look ahead —, it’s close enough for our purposes.

    EugeneS: t has zero potential for novelty.

    Novelty is a result of sources of variation, and also from the perspective of time where small changes accumulate into something new.

  121. 121
    Andre says:

    Zachriel

    If I had any hope for you it is now gone and will never return

    Actually, natural selection can be very sensitive with larger populations. With sexual selection, this is further magnified.,

    Nothing can be very sensitive?

    Whahahahahahahahahahahahahahaha!!!!!!!!!!!!!!!!!!!!

    Whahahahahahahahahahahahahahahahahahahahahahahaha!!!!!!!!!!!!!

    Whahahahahahahahahahahahahahahahahahahahahahahahahahahahahahahahahahaha!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

  122. 122
    Andre says:

    Whahahahahahahahahahahahahahahahaha!!!!!!!!

    It is proven that Natural selection is impotent and then Zachriel drops this gem!

    It is sensitive!

    Whahahahahahahahahahahahahahaha!!!!!

    Help me I can’t stop laughing!

    Whahhahahahahahahahahahahahahahahaha!

  123. 123
    Zachriel says:

    Andre: There was no Natural selection involved in the creation or collapse of the Galapagos finches

    Um, that paper is all about the effects of natural selection on hybridization; so no, it doesn’t undermine Grant & Grant.

    Andre: Then in August 2015 the latest in a long line of papers proving that NS is impotent……
    http://www.sciencedaily.com/re.....091206.htm

    The study concerns a case where selection constrains speciation. That doesn’t mean selection always constrains speciation. As the paper states, “The interplay between selection and aspects of the genetic architecture of traits (such as linkage, dominance, and epistasis) can either drive or constrain speciation.”

  124. 124
  125. 125
    Andre says:

    Zachriel

    Like I said you are foobar…. You can’t even spot the problem… Don’t you see it? Are you so blinded by your hatred for truth that anything can fool you?

  126. 126
    Carpathian says:

    Andre:

    Why are you deflecting? I’ll ask again. Are you denying the evidence that NS is impotent?

    I have assumed your statement to be true.

    You….
    ….stated that those people
    ….who hand-wave away evidence,
    … must have an agenda.

    If this is true,
    …. then IDists must have an agenda
    …. since they hand-wave away evidence.

    For every ID scientist, there are thousands in opposition .

    Since you ignore this evidence, according to you, you must have an agenda.

    What is the point of ID?

  127. 127
    Carpathian says:

    Andre:

    Whahahahahahahahahahahahahahaha!!!!!!!!!!!!!!!!!!!!

    You and Virgil Cain should publish a paper.

    It could be called, “Proving Your Point With Disrespect And Exclamation Marks”.

    This would be required reading for students in science class.

  128. 128
    Andre says:

    Carpathian

    You are defelecting again, can we ask? Is there such a thing as an honest Darwinist?

    My question to you again and I hope by the power of evolution not Grayskull that you will answer.

    Are you denying the evidence that Natural selection is impotent?

  129. 129
    Andre says:

    Carpathian

    How can I not laugh at such comedy? Its impossible to keep a straight face when someone says……

    “Natural selection is sensitive”….. think about what that means….

  130. 130
    Virgil Cain says:

    Carpathian:

    For every “ID” scientist there are thousands of “Darwinist” scientists.

    And yet not one of those alleged ” thousands of “Darwinist” scientists” can support evolutionism. Not one of them can model it. And not one of them uses it as a research heuristic.

  131. 131
    Carpathian says:

    Andre:

    You are defelecting again, can we ask? Is there such a thing as an honest Darwinist?

    Is there such a thing as an honest IDist?

    When Bill Dembski was asked who the designer was, he said God.

    That was an honest response.

    So I’ll ask you to back up the statement you made.

    Since you and other IDists hand-wave away evidence of “Darwinism”, according to you , you must have an agenda.

    So, what is the agenda of ID?

    Why does it exist?

  132. 132
    Virgil Cain says:

    Zachriel:

    Natural selection can be directly observed.

    That is incorrect. It can only be natural selection if the genetic change was accidental/ happenstance. and we don’t have a methodology for making that determination.

    Zachriel is an insipid troll and an equivocator.

  133. 133
    Virgil Cain says:

    Carpathian:

    Since you and other IDists hand-wave away evidence of “Darwinism”…

    There isn’t any evidence for darwinism, well beyond disease and deformities.

  134. 134
    Andre says:

    Carpathian

    I guess you still haven’t figured it out yet so let me help. What you guys talk about natural selection is no different that saying God did it. A creature is big it was natural selection. A creature is small natural selection. A creature is optimal it’s natural selection. A creature is not optimal it’s natural selection. If it happens it’s natural selection, if it does not happen it’s natural selection. If a creature benefits it’s natural selection if a creature is impeded it is natural selection.

    Since natural selection is responsible for everything it means it is impotent and is actually responsible for nothing.

    Get it? (Won’t hold my breath)

  135. 135
    Andre says:

    Carpathian

    Please answer my question first. Are you denying the evidence that natural selection is impotent?

  136. 136
    Andre says:

    Virgil Cain

    Please be gentle with natural selection it is very sensitive, I heard it is so sensitive it cries when it farts.

  137. 137
    Carpathian says:

    Virgil Cain:

    And yet not one of those alleged ” thousands of “Darwinist” scientists” can support evolutionism. Not one of them can model it. And not one of them uses it as a research heuristic.

    Of course they can and of course they do.

    Not one IDist however, has ever attempted to model biological ID.

    If they ever tried they would fail.

    Knowing this, all methodology questions are off the table, unlike “Darwinism” which welcomes them.

  138. 138
    Carpathian says:

    Virgil Cain:

    Zachriel is an insipid troll and an equivocator.

    Everyone who disagrees with you is a troll.

    Questioning ID is not allowed.

    That’s what makes ID unscientific.

  139. 139
    Carpathian says:

    Andre:

    Please be gentle with natural selection it is very sensitive, I heard it is so sensitive it cries when it farts.

    Is that an example of what you’ll teach in a fifth grade science class?

    Keep up the toilet humor.

    The fact that you behave like children is a major difference between our two sides.

  140. 140
    Virgil Cain says:

    Carpathian:

    Of course they can and of course they do.

    Nope, not one of those alleged ” thousands of “Darwinist” scientists” can support evolutionism. Not one of them can model it. If they could they would tell someone about it.

    Not one IDist however, has ever attempted to model biological ID.

    We have modeled directed evolution.

    Everyone who disagrees with you is a troll.

    That is incorrect. Both you and Zachriel have proven to be trolls.

    Questioning ID is not allowed.

    Relevant questions are allowed. Scientifically relevant questions are allowed. You are just to stupid to post any relevant questions.

  141. 141
    Virgil Cain says:

    Carpathian:

    The fact that you behave like children is a major difference between our two sides.

    Children vs pathological liars. At least children are honest and open.

  142. 142
    Andre says:

    Carpathian

    Do you agree that natural selection is sensitive?

  143. 143
    Eric Anderson says:

    wd400 @86:

    I don’t how much more explicit I can be that the results came about via selection on standing variation.

    Excellent. So what we have is nothing more than a simple, run-of-the-mill case of a population being impacted by a new environment, resulting in differential reproduction/survival — in other words, natural selection. All well and good.

    So, now we can get back to the key points in the OP:

    1. The guppy observations do not demonstrate anything particularly relevant to the questions evolution skeptics have raised. Nobody doubts that if certain members of a population are less adapted to an environment then they will be less likely to survive and contribute to the ongoing gene pool of that population.

    For Reznick to lament that people don’t “believe in evolution” and to suggest that his observations show evolution happening under our nose demonstrates that either (a) he is reading more into his observations than they merit, (b) he doesn’t understand the points raised by most evolution skeptics, and/or (c) he is conflating very different concepts under a single word “evolution.” Most likely all three of the foregoing.

    2. No-one doubts that less fit organisms are less likely to survive in their particular environment. This is a completely pedestrian observation, is something that was known long before Darwin, and we don’t need any evolutionary theory to point this out.

    The key claim of Neo-Darwinism is not that poorly adapted organisms are less likely to survive. Rather, that the organisms and the biological machinery came about in the first place through some kind of purely natural process — under classical Neo-Darwinism, primarily due to random mutations in DNA.

    Such a claim has never been demonstrated at any significant level. It certainly has not been demonstrated by the guppy observations, as Reznick and you yourself acknowledge. The only place it seems to have ever been demonstrated is in cases like malaria/sickle cell. I am interested in learning about other confirmed cases of Neo-Darwinian evolution in action.

    Observing that natural selection has taken place and triumphantly pronouncing that we are witnessing “evolution” is but an exercise in equivocation. We can’t just ignore the critical first part of the RM+NS equation.

    —–

    In answer to your other question, I read the press release and the abstract, but was unable to access the full paper. It is quite clear from what I was able to read that Reznick is confused about skeptics’ arguments and is conflating very different concepts when he talks about “evolution”. That is my primary point. I have already indicated, right up front, that I think Reznick did some good work and obtained some interesting results. I have never argued with a single aspect of his work or the paper, so you don’t need to indignantly defend his work or his paper.

    However, if for some reason you believe there are additional details or nuances in the paper that either (i) demonstrate the RM part of the Neo-Darwinian claim, (ii) refute the key issues raised by evolutionary skeptics, or (iii) demonstrate that Reznick clearly differentiates between natural selection acting on pre-existing biological systems and the ability of blind-natural processes to generate those biological systems in the first place, then please, by all means, provide me a copy and highlight those aspects and I will be more than happy to retract the points I have made.

  144. 144
    mike1962 says:

    Andre @136

    😀

  145. 145
    Eric Anderson says:

    All, some good points made and an interesting discussion.

    I know it can be frustrating debating with other strongly held viewpoints — I get just as annoyed as the next person when someone can’t see my well-articulated and well-thought-out point — but let’s try to keep the vitriol down just a bit.

    Thanks,

  146. 146
    Mapou says:

    EA responding to wd400:

    The key claim of Neo-Darwinism is not that poorly adapted organisms are less likely to survive. Rather, that the organisms and the biological machinery came about in the first place through some kind of purely natural process — under classical Neo-Darwinism, primarily due to random mutations in DNA.

    Well said. But you’re not going to win this debate because you’re debating with psychopaths and jackasses.

  147. 147
    wd400 says:

    Darwinian evolution is selection acting on heritable variants. This is an example of that, as are Darwin’s finches, peppered moths, sticklebacks and papers in your average issue of American Naturalist, Evolution or Behavioural Ecology. So we certainly have witnessed evolution in action. If you want to also test that mutations are random with respect to fitness you have to do more controlled experiments (why do you think the sickle cell mutations are random, but the guppies could be inducing some unknown / untestable power of adaptive mutation?), but Luria and Delbrück started that work in the 1940s and it goes on to today.

    This study doesn’t simply demonstrate that less fit creatures are less likely to survive and reproduce. It also shows this process can generate substantial phenotypic change in a short time. It is unlikely that any of the fish in the ancestral population had as much colouration as the average fish in the evolved population.

    So we are left with the “problem” that Reznick said that one reason people are skeptical of evolution is because they can’t see evolutionary changes over short time scales. I don’t think you can reasonably claim that skeptics are OK with the results Reznick describes in a thread where IDist after IDist has stood up to make ignorant proclamations about a paper they never read. And I do think one reason people don’t “get” evolution is that don’t know about nice clean examples of rapid evolutionary change of the sort Reznick describes. So I guess I fail to see the “problem” here.

  148. 148
    wd400 says:

    Andre,

    Do you agree that natural selection is sensitive?

    Sensitive means, roughly, “able to detect small differences”. In the context (large population size) selection is indeed sensitive, even an allele with a very small fitness benefit is quite likely to be fixed.

  149. 149
    Box says:

    WD400: Darwinian evolution is selection acting on heritable variants.

    Translation: some organisms don’t survive an inhospitable environment while others do and this simple fact somehow amounts to “evolution”.

    Eric Anderson: No-one doubts that less fit organisms are less likely to survive in their particular environment. This is a completely pedestrian observation, is something that was known long before Darwin, and we don’t need any evolutionary theory to point this out.

  150. 150
    Mapou says:

    Darwinian evolution is selection acting on heritable variants.

    So it’s no longer random mutations anymore? It’s heritable variants now? Please use the word random when you speak about Darwinian evolution. Otherwise you are lying and being deceptive again. I say this because the random part, the part that you are trying to hide, is precisely why Darwinian evolution is nothing but chicken feather voodoo science.

    Any random search mechanism used to explain evolution is falsified by the combinatorial explosion.

    Can you read this? Read it over and over 20 times. Can you really read it? Or are you going to keep babbling about your nonsense?

  151. 151
    Zachriel says:

    Andre: Darwin Sexual selection falsified!
    http://phys.org/news/2012-06-u.....fatal.html
    https://www.newscientist.com/article/dn13535-have-peacock-tails-lost-their-sexual-allure/

    The first link explores Bateman’s Principle, not sexual selection in general. It’s been known for some time that Bateman’s Principle is overly broad, however, it is largely supported by a number of studies, males having a higher variance in reproductive success in a great number of species.

    Your second link notes that the result is contradicted by other studies.

  152. 152
    ppolish says:

    WD400: Darwinian evolution is selection acting on heritable variants.

    Guided purposeful evolution as selection acting on heritable variants makes sense. But believing unguided purposeless evolution is acting on heritable variants is nonsense.

  153. 153
    wd400 says:

    Here’s an idea Box, read the rest of my post.

  154. 154
    Virgil Cain says:

    Natural selection eliminates the less fit. That is all it does. And the less fit changes. And to be qualified as natural selection the genetic changes have to be accidents, errors or mistakes. Natural selection does not apply to directed evolution

  155. 155
    Box says:

    WD400,
    I almost always read your posts — #147 included. If I missed something essential kindly point it out.

  156. 156
    wd400 says:

    The bit starting “This study doesn’t simply demonstrate that less fit creatures…” shows that your “translation” is wrong (because it ignores heritability)

  157. 157
    Andre says:

    WD400

    Natural selection can detect?

    Whahahahahaha!!!!!

    Are you serious?

  158. 158
    Mapou says:

    Andre:

    Whahahahahaha!!!!!

    I like that bone chilling laugh. You should copyright it. 😀

    I got one that I use quite often but I admit I borrowed it from someone else.

    ahahaha…AHAHAHA…ahahaha…

  159. 159
    Andre says:

    Mapou.

    How can one not laugh? We have heard that NS is sensitive, NS can detect…… Now how is it that our interlocutors can give attributes that belong exclusively to a conscious being to a process that is actually immaterial? But then deny that any such conscious immaterial being can ever exist?

    It cracks me up!

  160. 160
    Dionisio says:

    Evolution does happen these days.
    Here’s a strong convincing proof:

    https://blog.xamarin.com/xamarin-evolve-2016-call-for-participation/

    🙂

  161. 161
    Dionisio says:

    Andre @157

    Yes, it can! Of course! Why not?

    🙂

  162. 162
    Box says:

    WD400: This study doesn’t simply demonstrate that less fit creatures are less likely to survive and reproduce. It also shows this process can generate substantial phenotypic change in a short time. It is unlikely that any of the fish in the ancestral population had as much colouration as the average fish in the evolved population.

    WD400, what is your claim exactly?
    1) phenotypic change is caused by natural selection.
    2) phenotypic change is caused by random mutation.
    3) phenotypic change of the overall fish population is caused by natural selection.
    4) something else.

  163. 163
    EugeneS says:

    Zachriel,

    “Computers generally don’t have the resources of nature, so they can’t solve problems of the same scope.”

    Your comments lack specificity. That gives away deficit of real knowledge. Knowledge is always concrete.

    You seem to appeal to the first principles but even then you systematically fail. Why is that? Why is there such a contrast between what you say and how things really are?

    Computers do not solve problems. Humans do. In particular by writing code.

    The functional complexity of the simplest organism is prohibitively large for blind search to build it from scratch. Nature only had 10^17 seconds at its disposal. But even that is not the biggest problem.

    Life is logic-based, prescription-based with symbolic control being in the center of its organization. Life is not exclusively physicality-based. Life cannot be without intelligent decision making and foresight at the foundation of it.

    Evolutionists either lie or don’t even understand the challenge.

  164. 164
    Zachriel says:

    EugeneS: Computers do not solve problems. Humans do. In particular by writing code.

    Or computers can be used to model phenomena, such as genetic evolution.

    EugeneS: The functional complexity of the simplest organism is prohibitively large for blind search to build it from scratch.

    The simplest extant organisms are the result of billions of years of evolution, not blind search.

    EugeneS: Nature only had 10^17 seconds at its disposal.

    Don’t worry! Bacteria don’t replicate nearly so fast. Assuming replication a hundred times a year over a billion years, that’s about 10^11 generations. There are approximately 10^30 bacteria on Earth. Each has a genome of about 10^6 bases. Altogether, we have in the ballpark of 10^47 base replications. Now, which computer were you using that can hold 10^36 bases, and then manipulate them 10^11 times? Can you get it done before lunch?

  165. 165
    Virgil Cain says:

    Zachriel:

    Or computers can be used to model phenomena, such as genetic evolution.

    ID is OK with genetic evolution. Computers do not model undirected evolution.

    There are approximately 10^30 bacteria on Earth.

    And they have always been bacteria. They will never be anything else besides bacteria or dead.

  166. 166
    EugeneS says:

    Zachriel,

    “Don’t worry!”

    You of course can choose to stay ignorant.

    “10^47 replications.”

    And yet, an average protein domain has a space of size 20^150. A unicellular organism has to have some 300+ substantially different proteins all functioning in accord, in order to sustain life. There are experimental studies showing that even billions of years are not enough for blind search to produce anything of that complexity. These studies show that solutions corresponding to functioning proteins may be sparsely located in the state space. A solution is typically a point in the state space surrounded by chaos. There can be clusters of solutions but I think that it all depends.

    These solutions are severely constrained to be functional. Anyone who works in AI will tell you that constraints are harmful to local search, esp. to blind evolutionary search.

    But that is not the main problem. Stay focused and face the main challenge: life is prescription-based, controlled and organized. In order to even start evolution needs a cell functioning as a heterogeneous whole.

    The {data+processor} complex that is key to life, is irreducible. It is absolutely causally dependent on intelligence making decisions in the context of planning with foresight.
    How can a naturally produced system use symbolic representations?

    There is no other alternative to intelligence. You don’t understand the real challenge.

    Why are things you say so far from reality?

  167. 167
    Zachriel says:

    EugeneS: And yet, an average protein domain has a space of size 20^150.

    The question was whether a computer could represent the computational resources of nature. The answer, then, is no. Hence, to solve even basic problems, programmers often have to take shortcuts. Even protein folding is largely out of reach of computation. Glad we have that settled then.

    EugeneS: These studies show that solutions corresponding to functioning proteins may be sparsely located in the state space.

    As for searching protein space, we know that evolution can reduce the search time dramatically, but that it depends on the structure of the search space. As functional proteins can be found by purely random search, that implies that the space is rather dense in proteins. See Keefe & Szostak, Functional proteins from a random-sequence library, Nature 2001.

  168. 168
    bornagain says:

    as to:

    “As functional proteins can be found by purely random search

    actually the ATP binding protein is regarded as a ‘man-made’ protein that was evolved independent of nature.

    Moreover, Dr. Hunter comments here on the ‘fudged’ lower end estimates for functional proteins:

    Why Greta Christina’s critique of God-guided evolution misses the mark – August 18, 2014
    Excerpt: Keefe and Szostak managed to isolate four ATP binding proteins from a library of 6×10^12 proteins, and concluded that the proportion of all possible protein sequences that are actually functional might be as high as 1 in 10^11, or 1 in 100,000,000,000, and that functional proteins could therefore have arisen by an unguided, stochastic (i.e. random) process. (Their 2001 paper in Nature 410:715-718 can be accessed here.) Another team of scientists (Taylor et al., 98:10596-10601, 2001, doi:10.1073/pnas.191159298) estimated that a random protein library of about 10^24 members would be sufficient for finding one chorismate mutase molecule, making the problem of unguided natural processes hitting upon a functional sequence difficult but by no means impossible (see here for their article). Dr. Cornelius G. Hunter is a graduate of the University of Illinois where he earned a Ph.D. in Biophysics and Computational Biology. In a recent personal communication, Dr. Cornelius Hunter explained to me why these estimates of the probability of finding a functional protein sequence by chance are wildly over-optimistic, and pointed out that a more realistic estimate would be 1 in 10^60, or 1 in 1 million million million million million million million million million million:
    “First, Keefe and Szostak is not relevant as they were not seeking functional proteins, but merely mild ATP binding. Second, Taylor, et. al. deals with a simple, helix only, protein (homodimeric AroQ), biased the sequence toward helix forming amino acids and sequence patterns, did not fully randomize the sequence but only randomized regions, and is vague about how they arrive at their 10^24 tries required. Even if their calculation of 10^24 is reasonable, you’re dealing with a pretty simple protein… AroQ is toward the simple end of the spectrum… And finally there are several studies on slightly more complex, challenging proteins, all of which come in at around 10^60 – 10^80 attempts required.”
    Dr. Hunter also poured scorn on the suggestion, voiced by some experts, that the first proteins may have been relatively short, making their emergence by random processes far more likely. He wrote:
    “Proteins are by no means created equal. They occupy a wide spectrum of size and complexity… Nor is there reason to think that evolution could live with the shorter, simpler ones at first, and then later somehow the larger, more complex ones would evolve. The larger ones appear to be needed, and there are not obvious gradual pathways to forming them.… We’re still not close to the more complex proteins.”
    http://www.uncommondescent.com.....-the-mark/

    How Proteins Evolved – Cornelius Hunter – December 2010
    Excerpt: Comparing ATP binding with the incredible feats of hemoglobin, for example, is like comparing a tricycle with a jet airplane. And even the one in 10^12 shot, though it pales in comparison to the odds of constructing a more useful protein machine, is no small barrier. If that is what is required to even achieve simple ATP binding, then evolution would need to be incessantly running unsuccessful trials. The machinery to construct, use and benefit from a potential protein product would have to be in place, while failure after failure results. Evolution would make Thomas Edison appear lazy, running millions of trials after millions of trials before finding even the tiniest of function.
    http://darwins-god.blogspot.co.....olved.html

    Of related note, it is good to realize just how big 10^12 (a trillion) actually is:

    “The largest dump truck in the world would have to carry more than nine full loads to move a trillion grains of sand. A regular dump truck will have to make 150 trips.”
    http://www.bobkrumm.com/blog/2.....-trillion/

    Moreover, it is found that Szostak’s 1 in a trillion man-made protein, (i.e. ATP binding), is disruptive when expressed in a cell:

    A Man-Made ATP-Binding Protein Evolved Independent of Nature Causes Abnormal Growth in Bacterial Cells – 2009
    Excerpt: “Recent advances in de novo protein evolution have made it possible to create synthetic proteins from unbiased libraries that fold into stable tertiary structures with predefined functions. However, it is not known whether such proteins will be functional when expressed inside living cells or how a host organism would respond to an encounter with a non-biological protein. Here, we examine the physiology and morphology of Escherichia coli cells engineered to express a synthetic ATP-binding protein evolved entirely from non-biological origins. We show that this man-made protein disrupts the normal energetic balance of the cell by altering the levels of intracellular ATP. This disruption cascades into a series of events that ultimately limit reproductive competency by inhibiting cell division.”
    http://www.plosone.org/article.....ne.0007385

    Strange Behavior: New Study Exposes Living Cells to Synthetic Protein – Dec. 27, 2012
    Excerpt: ,,,”ATP is the energy currency of life,” Chaput says. The phosphodiester bonds of ATP contain the energy necessary to drive reactions in living systems, giving up their stored energy when these bonds are chemically cleaved. The depletion of available intracellular ATP by DX binding disrupts normal metabolic activity in the cells, preventing them from dividing, (though they continue to grow).,,,
    In the current study, E. coli cells exposed to DX transitioned into a filamentous form, which can occur naturally when such cells are subject to conditions of stress. The cells display low metabolic activity and limited cell division, presumably owing to their ATP-starved condition.
    The study also examined the ability of E. coli to recover following DX exposure. The cells were found to enter a quiescent state known as viable but non-culturable (VBNC), meaning that they survived ATP sequestration and returned to their non-filamentous state after 48 hours, but lost their reproductive capacity.
    Further, this condition was difficult to reverse and seems to involve a fundamental reprogramming of the cell.
    http://www.sciencedaily.com/re.....143001.htm

    More realistic estimates for functional proteins were recently gone over here by Dr. Hunter:

    Yockey and a Calculator Versus Evolutionists – Cornelius Hunter PhD – September 25, 2015
    Excerpt: In a 1977 paper published in the Journal of Theoretical Biology, Hubert Yockey used information theory to evaluate the likelihood of the evolution of a relatively simple protein.,,,
    Yockey found that the probability of evolution finding the cytochrome c protein sequence is about one in 10^64. That is a one followed by 64 zeros—an astronomically large number. He concluded in the peer-reviewed paper that the belief that proteins appeared spontaneously “is based on faith.”
    Indeed, Yockey’s early findings are in line with, though a bit more conservative than, later findings. A 1990 study of a small, simple protein found that 10^63 attempts would be required for evolution to find the protein.
    A 2004 study found that 10^64 to 10^77 attempts are required, and a 2006 study concluded that 10^70 attempts would be required.
    These requirements dwarf the resources evolution has at its disposal. Even evolutionists have had to admit that evolution could only have a maximum of 10^43 such experiments. It is important to understand how tiny this number is compared to 10^70. 10^43 is not more than half of 10^70. It is not even close to half. 10^43 is an astronomically tiny sliver of 10^70.
    Furthermore, the estimate of 10^43 is, itself, entirely unrealistic. For instance, it assumes the entire history of the Earth is available, rather than the limited time window that evolution actually would have had.,,,
    http://darwins-god.blogspot.co.....ersus.html

    of related note as to just how incredibly ‘fine-tuned’ proteins are intelligently designed to be:

    Quantum criticality in a wide range of important biomolecules
    Excerpt: “Most of the molecules taking part actively in biochemical processes are tuned exactly to the transition point and are critical conductors,” they say.
    That’s a discovery that is as important as it is unexpected. “These findings suggest an entirely new and universal mechanism of conductance in biology very different from the one used in electrical circuits.”
    The permutations of possible energy levels of biomolecules is huge so the possibility of finding even one that is in the quantum critical state by accident is mind-bogglingly small and, to all intents and purposes, impossible.,, of the order of 10^-50 of possible small biomolecules and even less for proteins,”,,,
    “what exactly is the advantage that criticality confers?”
    https://medium.com/the-physics-arxiv-blog/the-origin-of-life-and-the-hidden-role-of-quantum-criticality-ca4707924552

    Quantum coherent-like state observed in a biological protein for the first time – October 13, 2015
    Excerpt: If you take certain atoms and make them almost as cold as they possibly can be, the atoms will fuse into a collective low-energy quantum state called a Bose-Einstein condensate. In 1968 physicist Herbert Fröhlich predicted that a similar process at a much higher temperature could concentrate all of the vibrational energy in a biological protein into its lowest-frequency vibrational mode. Now scientists in Sweden and Germany have the first experimental evidence of such so-called Fröhlich condensation (in proteins).,,,
    The real-world support for Fröhlich’s theory (for proteins) took so long to obtain because of the technical challenges of the experiment, Katona said.
    http://phys.org/news/2015-10-q.....otein.html

    Proteins ‘ring like bells’ – June 2014
    As far back as 1948, Erwin Schrödinger—the inventor of modern quantum mechanics—published the book “What is life?”
    In it, he suggested that quantum mechanics and coherent ringing might be at the basis of all biochemical reactions. At the time, this idea never found wide acceptance because it was generally assumed that vibrations in protein molecules would be too rapidly damped.
    Now, scientists at the University of Glasgow have proven he was on the right track after all.
    Using modern laser spectroscopy, the scientists have been able to measure the vibrational spectrum of the enzyme lysozyme, a protein that fights off bacteria. They discovered that this enzyme rings like a bell with a frequency of a few terahertz or a million-million hertz. Most remarkably, the ringing involves the entire protein, meaning the ringing motion could be responsible for the transfer of energy across proteins.
    The experiments show that the ringing motion lasts for only a picosecond or one millionth of a millionth of a second. Biochemical reactions take place on a picosecond timescale and,,, (are) optimised enzymes to ring for just the right amount of time. Any shorter, and biochemical reactions would become inefficient as energy is drained from the system too quickly. Any longer and the enzyme would simple oscillate forever: react, unreact, react, unreact, etc. The picosecond ringing time is just perfect for the most efficient reaction.
    These tiny motions enable proteins to morph quickly so they can readily bind with other molecules, a process that is necessary for life to perform critical biological functions like absorbing oxygen and repairing cells.
    The findings have been published in Nature Communications.
    Klaas Wynne, Chair in Chemical Physics at the University of Glasgow said: “This research shows us that proteins have mechanical properties that are highly unexpected and geared towards maximising efficiency. Future work will show whether these mechanical properties can be used to understand the function of complex living systems.”
    http://www.gla.ac.uk/news/headline_334344_en.html

  169. 169
    Zachriel says:

    bornagain: actually the ATP binding protein is regarded as a ‘man-made’ protein that was evolved independent of nature.

    Nonetheless, it shows that functional proteins are rather dense in protein space.

    bornagain: “First, Keefe and Szostak is not relevant as they were not seeking functional proteins, but merely mild ATP binding.”

    ATP is the function.

    bornagain: Of related note, it is good to realize just how big 10^12 (a trillion) actually is

    Yes, it’s about one trillionth of a mole.

    bornagain: Moreover, it is found that Szostak’s 1 in a trillion man-made protein, (i.e. ATP binding), is disruptive when expressed in a cell

    Which demonstrates that it exhibits ATP binding in a living cell.

  170. 170
    EugeneS says:

    Zachriel,

    Yes, one of the capabilities of intelligence is to use shortcuts. I’d like to have a look at the paper but I don’t have access to full text. Without seeing the full text it is difficult to make a judgement. I suspect the authors make some assumptions that make life easy as it were. Many Thanks, anyway.

    However, I repeat from my previous comment.

    In order for evolution to even start, there must be an already functioning heterogeneous cell.

    The {data+processor} complex that is key to life, is irreducible. It is absolutely causally dependent on intelligence making decisions in the context of planning with foresight.

    How can a naturally produced system use symbolic representations?

  171. 171
    wd400 says:

    Box,

    I really can’t see how it could be any plainer — selection in this case (any many others) lead to a substantial change in phenotype. As I said, it is unlikely any fish the ancestral populations had as much colouration in the evolved populations. So it’s not just “unfit creatures die”, as you claimed in in you translation.

  172. 172
    Zachriel says:

    EugeneS: one of the capabilities of intelligence is to use shortcuts.

    And because of the limitations of computation, many complex spaces can’t be explored without help. The inability to completely simulate evolutionary dynamics with a computer doesn’t imply that evolution doesn’t work. Generally, computer simulations can only replicate simplified models of biological evolution, but this still allows the exploration of simple cases.

    EugeneS: In order for evolution to even start, there must be an already functioning heterogeneous cell.

    For evolution to occur, there has to be replication. This probably does entail a cell membrane of sorts to provide segregation, but it may not require the vast complexity of modern cells.

    EugeneS: The {data+processor} complex that is key to life, is irreducible.

    Irreducible structures can evolve. The mammalian middle ear is a canonical example.

    EugeneS: How can a naturally produced system use symbolic representations?

    “Symbolic representations” can evolve from simpler relationships.

  173. 173
    bornagain says:

    Zach, your pathetic excuse making for the gross empirical shortcomings of neo-Darwinian claims reminds me of a little boy denying that he ate the chocolate cake all while he has the chocolate icing all over his face and mouth.

    If only a good spanking would cure you of your blatant, over the top, dishonesty as it would the child.

  174. 174
    Box says:

    WD400: I really can’t see how it could be any plainer — selection in this case (any many others) lead to a substantial change in phenotype.

    So, the average phenotype of the fish population changed, because unfit creatures die?

    WD400: As I said, it is unlikely any fish the ancestral populations had as much colouration in the evolved populations. So it’s not just “unfit creatures die”, as you claimed in in you translation.

    Okay, so you claim that something else is going on. What exactly? And how do you explain it?
    Stop building up the suspense.

  175. 175
    Virgil Cain says:

    Zachriel:

    Irreducible structures can evolve. The mammalian middle ear is a canonical example.

    Except the mammalian middle ear A) does not fit the definition of irreducible complexity and B) did not evolve from a simpler system.

    “Symbolic representations” can evolve from simpler relationships.

    Of course there isn’t any evidence for such a thing.

  176. 176
    bornagain says:

    Of related note:

    African cichlid fish: a model system in adaptive radiation research:
    “The African cichlid fish radiations are the most diverse extant animal radiations and provide a unique system to test predictions of speciation and adaptive radiation theory(of evolution).—-(surprising implication of the study?)—- the propensity to radiate was significantly higher in lineages whose precursors emerged from more ancient adaptive radiations than in other lineages”
    http://www.pubmedcentral.nih.g.....d=16846905

    Multiple Genes Permit Closely Related Fish Species To Mix And Match Their Color Vision – Oct. 2005
    Excerpt: In the new work, the researchers performed physiological and molecular genetic analyses of color vision in cichlid fish from Lake Malawi and demonstrated that differences in color vision between closely related species arise from individual species’ using different subsets of distinct visual pigments.
    http://www.sciencedaily.com/re.....072648.htm

    Is the outcome of evolution predictable? – Oct 28, 2014
    Excerpt: There are only very few circumstances in which one can investigate the repeatability of evolution, because spatially independent environments that are populated by the same species are extremely rare in nature. “The young and completely isolated crater lakes along the Central American Volcanic Arc in Nicaragua provide an ideal setting to study parallel evolution. Several crater lakes house populations of Midas cichlid fish that have developed independently from the ancestral population in the nearby great lakes of Nicaragua. This setting is like a natural experiment”, explains Axel Meyer.
    In two of these crater lakes, Apoyo and Xiloá, new types of Midas cichlids evolved, independently from each other, in less than 10,000 years. These new species show identical morphological adaptations that are not found in the ancestral population: from the shallow, murky water to the new habitat of the deep, clear water of the crater lakes. “In each of the two crater lakes new species of the Midas cichlid evolved with an elongated body – a phenotype that does not exist in ancestral lakes from which the colonisers of crater lakes came from”, explains Meyer,,,
    “Our study shows that complex parallel phenotypes in similar environments can evolve very rapidly, repeatedly and yet via different evolutionary routes. This is a microevolutionary example of rewinding Gould’s tape and resulting in the evolution of two very similar species, albeit by non-parallel evolutionary routes”, sums up Axel Meyer.
    http://phys.org/news/2014-10-o.....ution.html

    Dr. Arthur Jones, who did his Ph.D. thesis in biology on cichlids, (fish), comments

    “For all the diversity of species, I found the cichlids to be an unmistakably natural group, a created kind. The more I worked with these fish the clearer my recognition of “cichlidness” became and the more distinct they seemed from all the “similar” fishes I studied. Conversations at conferences and literature searches confirmed that this was the common experience of experts in every area of systematic biology. Distinct kinds really are there and the experts know it to be so. – On a wider canvas, fossils provided no comfort to evolutionists. All fish, living and fossil, belong to distinct kinds; “links” are decidedly missing.”
    Dr. Arthur Jones – did his Ph.D. thesis in biology on cichlids – Fish, Fossils and Evolution – Cichlids at 29:00 minute mark (many examples of repeated morphology in cichlids) – video
    http://edinburghcreationgroup.org/video/14

  177. 177
    Virgil Cain says:

    Zachriel:

    Nonetheless, it shows that functional proteins are rather dense in protein space.

    Small proteins that undirected evolution cannot account for, maybe.

    I should stop picking on poor Zachriel. It’s a “taking candy from a baby” sort of thing. Besides Zachriel is incapable of learning.

  178. 178
    EugeneS says:

    Zachriel,

    Irreducible structures can evolve

    That is a side issue. Irreducible structures are called irreducible because they cannot be reduced to physicalistic causation. This is so because in practice they invariably require insight, foresight and decision making.

    I repeat. For evolution to even start you need an irreducible structure requiring a symbolic representation.

    “Symbolic representations” can evolve from simpler relationships.

    And that capability is evidenced by?

  179. 179
    wd400 says:

    Box,

    Okay, so you claim that something else is going on

    Nope. Why would you think this result required anything other than natural selection? You have picked up that these are heritable changes? And the experiment ran over successive generations?

  180. 180
    ppolish says:

    Guppies with a certain coloring, that were already in the population – were not eaten. They survived and flourished.

    All the other colors were eaten. This is extermination. Guppy genocide. Oh heck, let’s call it Natural Selection lol.

  181. 181
    Mapou says:

    Zachriel:

    The question was whether a computer could represent the computational resources of nature. The answer, then, is no.

    That is a lie. The question was whether the so-called computational resources of nature make a difference in the face of the dreaded combinatorial explosion. They don’t. Again, get some education.

  182. 182
    Box says:

    WD400,

    Box:
    Okay, so you claim that something else is going on.

    WD400: Nope. Why would you think this result required anything other than natural selection?

    Great. So, I was right, all you claim is the tautological “unfit organisms die”.

  183. 183
    Zachriel says:

    EugeneS: Irreducible structures are called irreducible because they cannot be reduced to physicalistic causation.

    They’re called irreducible because they are not able to be reduced, that is, “the removal of any one of the parts causes the system to effectively cease functioning.”

    EugeneS: This is so because in practice they invariably require insight, foresight and decision making.

    Actually, there are plausible pathways to irreducibility. We offered to discuss one, the mammalian middle ear.

    EugeneS: For evolution to even start you need an irreducible structure requiring a symbolic representation.

    No, you just need replication, which can be as simple as a replicating molecule. See Robertson & Joyce, Highly Efficient Self-Replicating RNA Enzymes, Chemistry & Biology 2014.

    EugeneS: And that capability is evidenced by?

    Crick proposed, on evolutionary principles, that RNA formed the core of protein synthesis. This has since been confirmed. RNA can act as messenger and enzyme, including their own replication. RNA can also coopt peptides to enlarge their enzymatic capabilities, and as chaperones to aid in binding and stabilization. This provides a simple start to protein synthesis.

  184. 184
    wd400 says:

    Box, I’m fast beginning to think you are an idiot. Is it really that hard to read a plain sentence? My “claim” is not simply that unfit creatures die, but that differential survival of heritable variants can lead to substantially phenotypic change in a population, making it well-adapted to its environment.

  185. 185
    Zachriel says:

    Mapou: The question was whether the so-called computational resources of nature make a difference in the face of the dreaded combinatorial explosion.

    And the evidence was based on limitations of modern computational methods applied to various non-biological problems.

    Box: So, I was right, all you claim is the tautological “unfit organisms die”.

    All organisms die. Some leave many or fewer descendants. A heritable trait that provides a reproductive advantage results in natural selection. The definition is a tautology, as are all definitions. That coloration in a guppy can provide a reproductive advantage in a given environment, that is, the link of causation between color and reproductive success, is not tautological, but empirical.

  186. 186
    Mapou says:

    Liar for Darwin, Zachriel:

    Mapou: The question was whether the so-called computational resources of nature make a difference in the face of the dreaded combinatorial explosion.

    And the evidence was based on limitations of modern computational methods applied to various non-biological problems.

    The limitations of computers are irrelevant to the fact that the combinatorial explosion fully falsifies Darwinian evolution. It’s dead, Jim. LOL.

  187. 187
    Box says:

    WD400: My “claim” is not simply that unfit creatures die, but that differential survival of heritable variants can lead to substantially phenotypic change in a population, making it well-adapted to its environment.

    How is that different from “unfit creatures die”, as in: the blue ones die en the orange ones don’t?
    So, for the last time: ‘is there something else going on or not?’

  188. 188
    Zachriel says:

    Mapou: The limitations of computers are irrelevant to the fact that the combinatorial explosion fully falsifies Darwinian evolution.

    Nope. It depends on the structure of the landscape.

  189. 189
    Mapou says:

    Let me see Zachriel, wd400 and the other Darwinist liars on this discussion board refute my simple claim that the combinatorial explosion (CE) fully falsifies Darwinian evolution. No stochastic search mechanism (e.g., RM+NS) has a prayer against the mighty hammer of CE. It kills them dead before they are even born.

  190. 190
    wd400 says:

    I really don’t think it can be explained more simply Box. So I guess we are done.

  191. 191
    Zachriel says:

    Mapou: refute my simple claim that the combinatorial explosion (CE) fully falsifies Darwinian evolution. No stochastic search mechanism (e.g., RM+NS) has a prayer against the mighty hammer of CE.

    Please be specific. How do you calculate the number of combinations? Do you mean bases ^ number of bases? If so, then it obviously depends on the landscape.

  192. 192
    Mapou says:

    Liar for Darwin, Zachriel:

    Mapou: The limitations of computers are irrelevant to the fact that the combinatorial explosion fully falsifies Darwinian evolution.

    Nope. It depends on the structure of the landscape.

    That is a lie. It depends on no structure whatsoever. Either the search is random or it is not. If it is random, the CE kills it. If it’s not random, then it is not Darwinian evolution.

  193. 193
    Box says:

    WD400: I really don’t think it can be explained more simply Box. So I guess we are done.

    There is nothing left to explain WD400. Your position is an empty shell.

  194. 194
    Mapou says:

    Zachriel is a lying psychopath. Why is the jackass even allowed on this board?

  195. 195
    Zachriel says:

    Mapou: If it’s not random, then it is not Darwinian evolution.

    Evolution isn’t random, and its trajectory depends on the landscape. Consider a crawler on a simple two-dimensional landscape. It moves in a random direction. If the direction is down, then it stays where it is. If the direction is up, then it moves to the new location. If the direction is level ground, then it splits, so now there are two crawlers. It’s a very simple model, but shows why it depends on the landscape.

    A trivially simple counterexample to the “combinatorial explosion” is a Mount Fiji landscape.

  196. 196
    Zachriel says:

    Box: How is that different from “unfit creatures die”, as in: the blue ones die en the orange ones don’t?

    The hereditarily blue ones tend to leave fewer progeny *because* they are blue, and the hereditarily orange ones tend to leave more progeny *because* they are orange.

    In other words, it’s not random happenstance, but a *result* of the environmental conditions and their hereditary character. The claim isn’t tautological because it depends on the observed facts.

  197. 197
    Box says:

    Z: The hereditarily blue ones tend to leave fewer progeny *because* they are blue, and the hereditarily orange ones tend to leave more progeny *because* they are orange.

    What the *hell* are you trying to tell me??

    Z: The claim isn’t tautological because it depends on the observed facts.

    Idiotic argument. Many tautological statements depend on observed facts, one example is “red barns are red” and here is another “what survives survives”.

  198. 198
    Mapou says:

    Zachriel:

    Mapou: refute my simple claim that the combinatorial explosion (CE) fully falsifies Darwinian evolution. No stochastic search mechanism (e.g., RM+NS) has a prayer against the mighty hammer of CE.

    Please be specific. How do you calculate the number of combinations? Do you mean bases ^ number of bases? If so, then it obviously depends on the landscape.

    No it does not and it never does. It’s only about whether or not the search is random. It could be as simple as bases ^ number of bases since this alone kills Darwinian evolution. But it’s worse than that, much worse. Evolution has no way of knowing how many bases needs to be searched. Heck, it has no idea what it is searching for. The search space of evolution is infinite.

    Evolution is dead.

  199. 199
    Zachriel says:

    Box: What the *hell* are you trying to tell me??

    You asked a question, How is that different from “unfit creatures die”, as in: the blue ones die en the orange ones don’t? The difference is a showing of causation. It’s not merely that the hereditarily blue ones died and the hereditarily orange ones lived, but that the blue ones died because they were blue, and the orange ones lived because they were orange.

    Box: Many tautological statements depend on observed facts, one example is “red is red” and here is another “what survives survives”.

    If the truth of the statement “depends”, then it’s not a tautology, by definition.

  200. 200
    Mapou says:

    Zachriel:

    Evolution isn’t random, and its trajectory depends on the landscape.

    RM+NS is not random? That is news to me. The “landscape” is just another deception you are inserting into the discussion. It’s obviously bullshit. Random mutations must work randomly on all bases. Otherwise, it’s intelligent design which calls for non-random processes.

  201. 201
    Zachriel says:

    Mapou: RM+NS is not random? That is news to me.

    Variation is random with respect to fitness, but natural selection is not random.

  202. 202
    Zachriel says:

    Mapou: It could be as simple as bases ^ number of bases since this alone kills Darwinian evolution.

    A trivially simple counterexample is a Mount Fiji landscape.
    http://www.uncommondescent.com.....ent-583265

  203. 203
    Mapou says:

    Zachriel:

    Mapou: RM+NS is not random? That is news to me.

    Variation is random with respect to fitness, but natural selection is not random.

    Whether or not the fitness function is random (a stupid idea since it is not random by definition) is irrelevant since it does not conduct the search. Random mutations, by contrast, are random by definition. They cannot possibly search through the combinatorial explosion unless your name is Zachriel, the liar for Darwin.

    All Darwinists are pathetic gutless liars. You should all be tarred and feathered and paraded down the street as an example for the other liars in the scientific community.

  204. 204
    Mapou says:

    All Darwinists are traitors to their own species. It’s one thing to lie to your neighbor but it’s another to lie to the whole world. Jackasses, all of them.

  205. 205
    Andre says:

    So natural selection is sensitive and it’s directed and it can decide?

    Wow this is special stupid.

  206. 206
    Mapou says:

    You’re pissing me off, Zachriel. I’m out of this discussion. I got better things to do. May you throw a clot or something, jackass.

  207. 207
    Box says:

    Z: You asked a question, How is that different from “unfit creatures die”, as in: the blue ones die en the orange ones don’t? The difference is a showing of causation. It’s not merely that the hereditarily blue ones died and the hereditarily orange ones lived, but that the blue ones died because they were blue, and the orange ones lived because they were orange.

    So you are telling me that blue is unfit and orange isn’t. A question for you: what led you to believe that I, or anyone else, didn’t get that already?

    Z: If the truth of the statement “depends”, then it’s not a tautology, by definition.

    Nope, “red barns are red” and “what survives survives” are tautologies.

  208. 208
    Virgil Cain says:

    Zachriel:

    Variation is random with respect to fitness,…

    Actually the word “random” with respect to mutations means they are accidents, errors and mistakes.

    but natural selection is not random.

    Natural selection is only non-random in the sense that not all individuals have the same probability of being eliminated (Mayr, “What Evolution Is”). In that sense mutations are non-random as some loci have a higher mutation rate than others.

    Natural selection is non-random in a very trivial way.

  209. 209
    Virgil Cain says:

    wd400:

    but that differential survival of heritable variants can lead to substantially phenotypic change in a population, making it well-adapted to its environment.

    And yet whatever is good enough gets to survive and reproduce. In a changing environment that is the best you can hope for.

  210. 210
    Zachriel says:

    Mapou: Whether or not the fitness function is random (a stupid idea since it is not random by definition) is irrelevant since it does not conduct the search.

    The fitness function is an abstraction, and represents the relationship of the hereditary reproductive potential of the organism to the environment. We provided a simple counterexample to your claim.

    Box: So you are telling me that blue is unfit and orange isn’t.

    You asked a question. How is that different from “unfit creatures die”, as in: the blue ones die en the orange ones don’t? The difference is the causal link between the hereditary characteristics of the organism and its reproductive potential in a given environment.

    Box: Nope, “red barns are red” and “what survives survives” are tautologies.

    Yes, those are tautologies, and neither depend on anything outside the statements themselves.

  211. 211
    Mapou says:

    By the way, has anybody ever figured out who the hell that anonymous jackass who calls himself Zachriel really is? Everybody knows who I am. A click on Mapou above takes you to my blog.

  212. 212
    EugeneS says:

    Zachriel,

    “Crick proposed, on evolutionary principles, that RNA formed the core of protein synthesis. This has since been confirmed.”

    Nothing of the sort! The more research is done, the more clear it becomes that the RNA-world hypothesis is bluff. It just begs the question of what is necessary for life to kick-start. RNAs that are of any use even potentially are chemically unstable and require intelligent control in order to stay around.

    RNA translation in living organisms absolutely requires adapters that determine what the effect of translation should be. Until such time as evolutionists face the challenge of explaining in detail how this could have formed without planning and foresight, no hand-waving about mammalian middle ears will be taken seriously.

    The major challenge still remains: how can symbolic representation come about in a system that is produced merely as a result of physical interactions? Symbolic representations cannot be reduced to the motion of the particles of matter but are a special type of constraint on the motion of the particles of matter.

    Why is it that things you say are in stark contrast with reality? Do you even understand that this is the case?

    Mindless processes never could and will never be able to explain intelligence. Attempts to make believe they can are ideologically motivated.

    The RNA-world hypothesis raises more questions than purports to resolve. It is actually more complex to have a single structure providing metabolic function while serving as a memory.

    Do you understand that for replicating a heterogeneous system there must be provided a description of the system and stored in memory? This brings the issue of being able to write/read and interpret a symbolic representation from memory and execute instructions in the process of replication. Replication of the heterogeneous cell is not the same as replication of a crystal.

    Evolutionism cannot even get anywhere close to facing the challenge. This is because it fails to acknowledge the simple undeniable truth: life as a programmatically controlled prescription-based functional whole can only be explained in terms of decision making, control, planning and foresight.

  213. 213
    Mapou says:

    Why does UD give jackasses like Zachriel a free pulpit to spread their virulent disease? The jackasses already conquered the schools and the media. They are like some nasty avian flu or something. Why help them at all?

    Ban them all. That’s what I would do.

  214. 214
    Andre says:

    Mapou

    I think it’s good that they post here onlookers can see what they say stuff like natural selection makes choices, is sensitive and is directed. Lay it open for all the world to see their utter stupidity. I personally encourage it. Sure when they blatantly lie it’s unpleasant bit it is just another viewing of their character for all to see.

  215. 215
    EugeneS says:

    Zachriel,

    ““Crick proposed, on evolutionary principles, that RNA formed the core of protein synthesis. This has since been confirmed.”

    Sorry, I did not properly read this sentence. My fault. That in itself is right. However, that does not mean the RNA-world hypothesis has been confirmed, which is how I read your sentence the first time.

    All the other things I mentioned in 212 remain relevant to the discussion.

  216. 216
    Mapou says:

    Andre @214,

    You do have a point.

  217. 217
    Phinehas says:

    WD400: Darwinian evolution is selection acting on heritable variants.

    Artificial selection is selection acting on heritable variants. Is artificial selection Darwinian?

    WD400: but that differential survival of heritable variants can lead to substantially phenotypic change in a population, making it well-adapted to its environment.

    And how do we know it is well-adapted? Because unfit stuff dies. What have you said above that isn’t simply unfit stuff dies and fit stuff doesn’t, where “unfit” and “fit” mean nothing other than that it did or didn’t die?

    Stuff dies. Stuff happens. I feel so intellectually fulfilled now.

  218. 218
    Box says:

    Phinehas #217,

    LOL!

  219. 219
    Zachriel says:

    Zachriel: Crick proposed, on evolutionary principles, that RNA formed the core of protein synthesis. This has since been confirmed.

    EugeneS: Nothing of the sort!

    That is incorrect. See Nissen et al., The structural basis of ribosome activity in peptide bond synthesis, Science 2000: “we establish that the ribosome is a ribozyme and address the catalytic properties of its all-RNA active site.”

    EugeneS: The more research is done, the more clear it becomes that the RNA-world hypothesis is bluff.

    It apparently led to a successful prediction regarding protein synthesis, tending to confirm the hypothesis. While the hypothesis may not be correct, it is hardly a “bluff”.

    EugeneS: RNAs that are of any use even potentially are chemically unstable and require intelligent control in order to stay around.

    They probably do require segregation, but simple lipid bilayers can form membranes.

    EugeneS: Until such time as evolutionists face the challenge of explaining in detail how this could have formed without planning and foresight, no hand-waving about mammalian middle ears will be taken seriously.

    While no one knows how translation originally arose, the argument from irreducibility is not a valid argument.

    EugeneS: The major challenge still remains: how can symbolic representation come about in a system that is produced merely as a result of physical interactions?

    Sure it’s a challenge, but there’s no a priori reason it couldn’t have evolved from a simpler relationship. Only an investigation of specifics can answer that question.

    EugeneS: The RNA-world hypothesis raises more questions than purports to resolve.

    That’s the sign of a good hypothesis; it leads to all sorts of new investigations. This is contrary to ID, which is scientifically sterile.

    EugeneS: That in itself is right.

    Okay. The points raised above address your larger point. Successful predictions tend to confirm, but do not prove a hypothesis.

    Phinehas: And how do we know it is well-adapted?

    In some cases, we can determine the cause involved. With guppies, it has been shown that coloration depends on predation.

  220. 220
    Phinehas says:

    Z:

    In some cases, we can determine the cause involved.

    The cause of what? Unfit stuff dies because it is unfit. Stuff is unfit because it dies.

    Stuff dies. Stuff happens. What a remarkable theory!

  221. 221
    Zachriel says:

    Phinehas: Unfit stuff dies because it is unfit.

    Fitness is specific to the characteristics of the organism and the environment. An organism may be perfectly viable, but leave fewer offspring on average due to differences in traits. When we connect the differences in traits to differences in reproductive success, then that is called natural selection. The result is a change in the mixture of traits that make up the population, and that is called adaptive evolution.

  222. 222
    Phinehas says:

    We keep asking for someone to point us to the “theory of evolution.” No one seems to be able to do that. So, I propose the following, provisionally of course.

    The Theory of Evolution: Stuff happens. Stuff dies. More stuff happens. More stuff dies. Voila! The human brain.

    It is the above that allows someone like Dawkins to attain intellectual fulfillment.

    Mix in a little “God doesn’t exist” and you might be able to stretch that into intellectual superiority.

  223. 223
    Zachriel says:

    Phinehas: We keep asking for someone to point us to the “theory of evolution.”

    You could start with Darwin’s Origin of Species, but it is a bit dated.
    http://darwin-online.org.uk/Fr....._1859.html

    You could check out an encyclopedia.
    https://en.wikipedia.org/wiki/Evolution

    Or you could take a class at your local university.
    http://evolution-textbook.org/

  224. 224
    Phinehas says:

    Z:

    Fitness is specific to the characteristics of the organism and the environment.

    Stuff not dying is connected to the stuff that didn’t die and the stuff that happens around it. Got it.

    An organism may be perfectly viable, but leave fewer offspring on average due to differences in traits.

    Stuff that didn’t die may not have died, but might leave behind fewer things that die or don’t die due to differences in them either being killed or not killed by the stuff that happens. Okay, I think I am tracking so far.

    When we connect the differences in traits to differences in reproductive success, then that is called natural selection.

    When we connect the differences in things that did or didn’t die either by being killed or not killed by the stuff that happens to the difference in how many died or didn’t die, we like to use an anthropomorphized term implying intelligent involvement prepended with an adjective that denies intelligent involvement to refer to the fact that stuff dies. Aaaaall righty then.

    The result is a change in the mixture of traits that make up the population, and that is called adaptive evolution.

    The result is that stuff changes in the differences in things that did or didn’t die either by being killed or not killed by the stuff that does or doesn’t happen, and that is called adaptive evolution, allowing someone like Dawkins to be an intellectually fulfilled atheist. Oooookay.

  225. 225
    Zachriel says:

    Phinehas: Stuff not dying is connected to the stuff that didn’t die and the stuff that happens around it. Got it.

    Natural selection concerns differences in reproductive success. Organisms may or may not be reproductively successful for a variety of reasons, not all of them representing natural selection. It’s when heritable traits result in differential reproductive potential that we have natural selection.

  226. 226
    Phinehas says:

    Z:

    Natural selection concerns differences in reproductive success.

    As does artificial selection, which has the remarkable advantage of actually involving selection.

    Organisms may or may not be reproductively successful for a variety of reasons, not all of them representing natural selection.

    Sure. There could be actual selection involved, making it artificial instead of natural.

    It’s when heritable traits result in differential reproductive potential that we have natural selection.

    Or artificial selection, which has the remarkable advantage of actually involving selection.

    I get the feeling I’m missing the point somehow.

  227. 227
    Phinehas says:

    Here’s the thing, Z: Natural selection doesn’t really involve any selection, so you’re just left with “natural.” Naturally, stuff happens. Naturally, stuff dies. Naturally, things change. ObeeKaybee.

  228. 228
    Zachriel says:

    Phinehas: As does artificial selection

    Sure. Artificial selection was discussed by Darwin to show the range of available variation over time. However, artificial selection doesn’t explain the observed results with guppies or finches not under artificial selection.

    Phinehas: Natural selection doesn’t really involve any selection

    Darwin coined the term based on a parallel with artificial selection, but it’s an inexact phrase. Natural selection refers to differential reproductive success due heritable traits.

  229. 229
    Virgil Cain says:

    However, artificial selection doesn’t explain the observed results with guppies or finches not under artificial selection.

    And natural selection doesn’t explain the observed results with guppies or finches not under artificial selection.

    Darwin coined the term based on a parallel with artificial selection,

    Except there isn’t any parallel.

    Natural selection refers to differential reproductive success due heritable traits.

    That is incorrect. Natural selection refers to differential reproductive success due heritable traits that are due to happenstance variation.

  230. 230
    Virgil Cain says:

    You could start with Darwin’s Origin of Species, but it is a bit dated.
    http://darwin-online.org.uk/Fr….._1859.html

    You could check out an encyclopedia.
    https://en.wikipedia.org/wiki/Evolution

    Or you could take a class at your local university.
    http://evolution-textbook.org/

    Darwin’s wasn’t a scientific theory. Wikipedia doesn’t reference a scientific theory of evolution and neither does the textbook.

    Evos have to be the most dishonest people ever.

  231. 231
    Virgil Cain says:

    While no one knows how translation originally arose, the argument from irreducibility is not a valid argument.

    Not an argument. The argument from irreducible complexity is no different than the argument from signs of work. Both have only one known source.

  232. 232
    mike1962 says:

    Mapou: Ban them all. That’s what I would do.

    Having them here allows thinking people to access their flawed arguments and see them for what they are.

  233. 233
    Steve says:

    This is all just trivialities, Zachriel.

    The elephant in the room is that differential reproduction only succeeds because organism reproduce in excess.

    Excess reproduction is a designed object that ensures life’s continuation. Meaning evolution is subsumed under a designed system and is impotent absent design.

    Not only that, we can see that not only does excess reproduction guarantee an organism’s survival, it by the way of contributing to the food chain, ensures the survival of other organisms as well.

    The random nature of inherited traits is built into the system to ensure than the organism leaves viable progeny no matter what the environment throws its way.

    Nothing is left to chance.

    That is design in action; a much clearer, easy to grasp, succinct explanation that is far and away superior to the disconbobulated blob that is the modern synthesis.

    Zachrie said: Fitness is specific to the characteristics of the organism and the environment. An organism may be perfectly viable, but leave fewer offspring on average due to differences in traits. When we connect the differences in traits to differences in reproductive success, then that is called natural selection. The result is a change in the mixture of traits that make up the population, and that is called adaptive evolution.

  234. 234
    Andre says:

    Now natural selection is not only directed, sensitive and make choices but Zachriel says natural selection is also concerned.

    Is Zachriel talking about a loving God here?

  235. 235
    ppolish says:

    Holy crud what a great post Steve. But could you change “Nothing is left to chance” to “Not anything is left to chance”. “Nothing” is part of the Design, as is chance. Awesome Design!

  236. 236
    EugeneS says:

    Zachriel:

    “However, artificial selection doesn’t explain the observed results with guppies or finches not under artificial selection.”

    Exactly the opposite is true. Adaptability can only be explained by intelligent tuning. The guppies had already been preprogrammed to execute adaptation routines under certain conditions. The changed conditions serve as a trigger for those built-in routines.

    Have you ever solved a real industrial engineering problem in the field? It is all about tweaking and making stuff work. Because things are discrete in the real world, it is a combinatorial problem. The problem of parameter tuning is not amenable to blind search. It may be amenable to heuristically guided search, but that IS a different story. Heuristics encode intelligence. Heuristics are rules stemming from practice of solving similar problems. That is why GAs work and Darwinian evolution does not.

    However the main problem is not even that. You know what it is. I have repeated it many times now: how to explain naturalistically the existence of {program+processor} in life?

    That alone ruins all evolutionist thought. It is evolutionism that is scientifically sterile, not the intelligent design hypothesis. Unfortunately, the level of indoctrination in the evo-camp does not allow people to see the real picture.

    You know what is really disturbing about all this? It is that everybody uses the right hypothesis in practice: that everything is rational, everything should work from first principles up to implementation. Everybody knows this. However, having done what is rational = i.e. assuming intelligence behind all things, evolutionists wrap it up as ‘proof of evolution’ or ‘confirmation of evolution’ if you like the latter better than the first.

    I am amazed by how indoctrinated people like you are. Why is this? I think this is because you have never solved a single real problem in anger. Once you have done it, illusions start disappearing. So far, in your case, there is no sign of it, unfortunately.

    What membranes are you talking about?! As soon as you are dealing with heterogeneity, you have to start with a program and its processor, memory and symbolic representation, reading and writing.

    The main problem is this and there is absolutely no way out except recognize intelligent causation. There is no chemical evolution at all: nothing to select from, no autonomous self-sustaining entities. It is all bluff. Take {program+processor} apart and you break it. Full stop. Nothing works.

    You are wrong in assessing RNA-world as a fruitful hypothesis. It is okay for a hypothesis to pose new questions, but it must help answer at least one. The RNA-world does not. Why? Because it does not stand the test of reality. The reality is, you need control, i.e. intelligence guiding the synthesis to get to decent size RNAs. Plus you need an irreducibly complex translation system.

    Irreducibility is one of the strongest arguments against evolutionism. And it is a very good argument because it reflects reality. No wonder you don’t want to recognize the fact.

    The challenge for evolutionism remains: how to ‘explain away’ the need for intelligence in the presence of instructions and their processing at the heart of life.

    No make believe will help evolutionists until they radically change the approach from sterile hypotheses to something that reflect how things are in the real world.

  237. 237
    Box says:

    Eric Anderson: At another level, though, if we think of “viable” in a broader sense or if we simply acknowledge that some creatures were produced that didn’t end up surviving, then you are quite right: to that extent natural selection is a hindrance to evolution. It removes, it culls, it eliminates, it lessens possibilities.

    Andreas Wagner proposes a view of life as a universal library (in a 5000-dimensional cube no less) stuffed with all the innovations that chance has come up with. This is his abstract attempt to explain how evolution can find all those improbable things like proteins.
    Now what is the role of natural selection in all of this? A purely negative one I would say; it constantly removes stuff from Wagner’s imaginary library.
    The crazy thing is that when natural selection (read: natural elimination) doesn’t do its destructive work it receives praise, even by Wagner, who says that “natural selection can preserve innovations”. What’s seems more important here is that natural elimination can destroy innovations.
    Some things are left untouched by natural elimination, since when is that “preserving”?

    Eric Anderson: If anything, natural selection helps to keep a population within a stable norm, rather than veering off in new and uncharted directions.

    If there is something like an evolutionary search for improbable things then NS doesn’t help at all. For the evolutionist it’s nothing to be cheerful about and certainly no reason to feel intellectually fulfilled.

  238. 238
    Zachriel says:

    Steve: differential reproduction only succeeds because organism reproduce in excess.

    Correct!

    Steve: we can see that not only does excess reproduction guarantee an organism’s survival

    As the vast majority of species that have ever existed are extinct, it’s hardly a guarantee. However, if there is no excess reproduction, then extinction is guaranteed through attrition. With single-celled organisms reproducing through fission, fecundity is intrinsic.

    Andre: Now natural selection is not only directed, sensitive and make choices but Zachriel says natural selection is also concerned.

    Well, let us know when you are ready to be serious.

    EugeneS: you have to start with a program and its processor, memory and symbolic representation

    No, a simple replicator and membrane may be sufficient. Certainly, it can’t be rejected in principle as you attempt to do.

    EugeneS: It is okay for a hypothesis to pose new questions, but it must help answer at least one. The RNA-world does not.

    It explains why the ribosome is a ribozyme, indeed, a prediction made a generation before its confirmation.

    EugeneS: Irreducibility is one of the strongest arguments against evolutionism.

    We offered to discuss a canonical example of the evolution of irreducibility, the mammalian middle ear, but everyone avoided the topic.

  239. 239
    Zachriel says:

    Box: Now what is the role of natural selection in all of this? A purely negative one I would say; it constantly removes stuff from Wagner’s imaginary library.

    Assuming the landscape has positive structure, natural selection makes the exploration tractable. If evolution had to explore every nook and cranny of sequence space, then, indeed, it would be impotent. However, it only has to explore regions near to the ‘best so far’.

    Consider a toy landscape, where the vast majority of the space is death, there are a few distant regions of habitability, but those regions are connected by tendrils. Evolution would quickly travel those tendrils to find those regions.

    Everything depends on the fitness landscape. We have the history of life on Earth, and many examples of how small changes lead to advantages, such as fins to legs to arms to wings, pathways between regions of fitness.

  240. 240
    EugeneS says:

    Zachriel:

    “No, a simple replicator and membrane may be sufficient. Certainly, it can’t be rejected in principle as you attempt to do.”

    It may not be enough as you attempt to convince us. It is never enough in principle as for a {program + processor} you need to have intelligence.

    Even so, I am glad you now recognize reality at least partially because you are now using an “and” in your sentences. So even for you it is already not that simple, because an “and” really means complexity, not incrementality. Ok, Zachriel, you are on the right track. Keep it up. Maybe conversing with people here on this blog is starting to do you good 🙂

    Mind you, membranes must be used in a functional metabolizing whole which is programmed to function in a coherent way. But anyway, not too bad as a beginning!

    Ok, so membranes AND replication. That’s a start.

    The next bit for you, Zachriel, is realize that replicating heterogeneous functional structures is not the same as replicating crystals.

    I think that you are still avoid addressing the real issue.

    Before discussing mammalian ears you need to address the hard core issue: the reliance of life on programming and executing instructions.

    Mammalian ear is a red herring. Until such time as you tackle the real issue, your arguments will not be taken seriously. But anyway, I am glad you started changing your argumentation. Keep it up!

  241. 241
    Zachriel says:

    EugeneS: It is never enough in principle as for a {program + processor} you need to have intelligence.

    Molecular replicators act as messenger and enzyme. That provides all you need to start the process of evolution.

    EugeneS: Before discussing mammalian ears you need to address the hard core issue: the reliance of life on programming and executing instructions.

    Already have. ‘Programming and executing instructions’ can possibly evolve from simpler relationships.

    EugeneS: Mammalian ear is a red herring.

    No. It shows how irreducible complexity can evolve through incremental selectable steps.

  242. 242
    bornagain says:

    OT: LOL, finally proof that atheists are mentally impaired:

    “Shutting down part of the brain that’s responsible for problem solving” causes atheism.

    Shutting down part of brain changes views on God, immigrants: study – October 14, 2015
    Excerpt: Temporarily shutting down part of the brain that’s responsible for problem solving can supress your religious views and prejudices toward immigrants, a new study has found.
    Researchers out of the University of York, in England, and the University of California, Los Angeles, used magnetic energy to safely and temporarily shut down specific regions of the brain of some study participants.
    When the posterior medial frontal cortex — a part of the brain located near the surface and roughly a few inches up from the forehead — was shut down, participants reported a decrease in their religious convictions and were more positive toward new immigrants critical of their country.
    http://www.ctvnews.ca/health/s.....-1.2609612

    Mental impairment would explain Zachriel’s inability to follow even the simplest of arguments quite well wouldn’t it? 🙂

  243. 243
    EugeneS says:

    Zachriel,

    I thought you were beginning to understand. Was I wrong?!

    The great question for you is not whether evolution occurs but whether you can convincingly explain to us that for life to kick-start you can do away with intelligence.

    Do not change your focus. Address the real issue. I repeat it for you:

    Can you explain how the complex {program+processor} can come about without intelligence.

    I claim that it is irreducibly complex and infeasible without intelligence. Whether irreducibly complex systems can evolve is a red herring here for this discussion.

    How can they come into existence without intelligence, is the real issue.

    Stop your funny claims about mammalian ears. It is really funny because in order to understand what happens at the level of tissue and organs one first needs to have a clear picture about the nano-machines responsible for biological function at the molecular level.

    There is absolutely no way you can get your head round tissular or organismal functions without first addressing the simplest, i.e. molecular level functions simply because basic molecular functions underpinning life are horrendously complex.

  244. 244
    EugeneS says:

    Zachriel,

    “That provides all you need to start the process of evolution.”

    No matter how many times you repeat a false claim, it remains a false claim.

    [I] “already have” [addressed].

    You have addressed nothing. Hand-waving and interspersing your sentences with ‘maybe’ and ‘possibly’ are not an argument.

    You know what… I don’t know how many people there are under you nick, but for some reason, after talking to you lot, I realize I am really close to laughing. I don’t mean to be rude.

  245. 245
    Zachriel says:

    EugeneS: The great question for you is not whether evolution occurs but whether you can convincingly explain to us that for life to kick-start you can do away with intelligence.

    It’s still an open question, but the evidence indicates a natural cause, and there’s no scientific evidence of a designer.

    EugeneS: Can you explain how the complex {program+processor} can come about without intelligence.

    It’s still an open question, but there’e no a priori reason to exclude a natural cause.

    EugeneS: I claim that it is irreducibly complex and infeasible without intelligence.

    Irreducible structures can evolve naturally in incremental selectable steps.

    EugeneS: Whether irreducibly complex systems can evolve is a red herring here for this discussion.

    It’s not a red herring when you introduce it as an intrinsic barrier, as you did just now — right now, as in your previous sentence.

    EugeneS: No matter how many times you repeat a false claim, it remains a false claim.

    True, however, the claim is not false. When you have replication with variation, you have evolution. Whether adaptation occurs depends on the fitness landscape.

    EugeneS: I realize I am really close to laughing.

    We try to be entertaining as well as informative.

  246. 246
    Andre says:

    Zachriel

    It’s still an open question, but the evidence indicates a natural cause, and there’s no scientific evidence of a designer.

    What evidence? Please I’m very curious give us this evidence and I will concede!

  247. 247
    EugeneS says:

    Zachriel,

    It is funny really. Biological evolution is a property of living systems by definition. The limits of evolution are debatable but this is a red herring for this discussion, namely in relation to how life started.

    Life is more than replication as it also includes metabolism, reaction to stimuli and nobody knows what else. Replication and autonomy are among the properties of living systems. Replication of homogeneous structures is not the same as replication of heterogeneous structures. There is a colossal difference.

    Irrespective of other functions of life that must all be present and interacting, even taken in isolation, replication of living systems is necessarily irreducibly complex and crucially depends on read/write operations and instruction processing.

    Reducing life to chemistry is therefore a huge category error.

    Referring to the start of life as an open question is not a way out because there is already enough scientific knowledge about it to absolutely rule out chance and necessity as key factors behind it.

  248. 248
    ppolish says:

    Now that we’ve seen guppies evolve ie change markings, let’s try the experiment on
    Coelacanth. Bet they evolve ie change markings too.

    Although color change survival of the fittest evolution can’t be confused with arrival of the fittest evolution. The latter is founded on design. Teleological Design or Theistic Design, take a side:)

  249. 249
    PaV says:

    wd400:

    Here’s how the abstract to the paper ends:

    The lack of genetic convergence in the natural populations suggests that convergent evolution is lacking in these populations or that the effects of selection become difficult to detect after a long-time period.

    How is this anything other than pure rubbish?

    The “lack of genetic convergence” is explained by “convergent evolution [being] lacking in these populations.”

    IOW: something is lacking because the cause of the ‘something’ is lacking. But, if the cause of ‘something’ is lacking, then, of course, the ‘something will be lacking. Pure tautology!!

    And, then:

    “[O]r, that the effects of selection become difficult to detect after a long-time period.”

    IOW, it’s either not there, or, we can’t detect it.
    But, of course, either Santa Claus is not at the North Pole, or, we can’t detect him.

    How is this a statement with any kind of substance to it?

  250. 250
    wd400 says:

    I see you are also reading the wrong paper, PaV.

    FWIW, in this other paper they demonstrate convergent evolution in experimental pools but can’t find the same signal in natural populations. The discussion has a long section about why that might be, the implications about that result and which suggests means by which those explanations might be tested. That’s pretty typical of any scientific paper. It’s also pretty typical that an abstract only briefly mentions results that are discussed more thoroughly in the body on the paper.

  251. 251
    Eric Anderson says:

    wd400 @147:

    Darwinian evolution is selection acting on heritable variants. This is an example of that, as are Darwin’s finches, peppered moths, sticklebacks and papers in your average issue of American Naturalist, Evolution orBehavioural Ecology.

    Box has already made some effort to clarify what you are saying, so I apologize for beating a dead horse, but let’s press just a bit:

    First of all, let’s be very clear: natural selection is not a force. It is a label. But even accepting that for convenience purposes we were to apply a generalized short-hand label to the results of our observations, the real points we started with remain:

    1. Observing that natural selection occurred doesn’t tell us anything about how the variation came about in the first place. That is the part of the theory that needs to be supported. If someone loudly proclaims support for their theory when only half of the equation is supported by the evidence, then they can, and should, expect some healthy skepticism.

    2. Even in clear cases where the Neo-Darwinian RM+NS mechanism is at play (malaria/sickle cell trait), it doesn’t address the concerns that evolution skeptics have raised. Indeed, it confirms them. No prominent evolution critic or ID proponent disputes examples like the malaria/sickle cell trait situation. Yes, congratulations, Neo-Darwinian theory can explain some things. Minor things. Uncontroversial things. Things that, ironically, demonstrate just how anemic the RM+NS mechanism is.

    3. That Reznick thinks an example of natural selection on guppies should help convince people of the truth of evolution demonstrates that that either (a) he is reading more into his observations than they merit, (b) he doesn’t understand the points raised by most evolution skeptics, and/or (c) he is conflating very different concepts under a single word “evolution.” Most likely all three of the foregoing.

    This study doesn’t simply demonstrate that less fit creatures are less likely to survive and reproduce. It also shows this process can generate substantial phenotypic change in a short time. It is unlikely that any of the fish in the ancestral population had as much colouration as the average fish in the evolved population.

    What process? The process of the less fit surviving? Or, again as Box has been trying to clarify, are you proposing that some other genetic or epigenetic effect was at work? If so, what was it? Reznick appears to dismiss the idea that we are dealing with the Neo-Darwinian random mutation process (and I believe you also feel the same way, based on earlier comments above). So what “process” are you referring to? No vague labels please. What do you think was actually going on in individual guppies — what was occurring at the genetic or the epigenetic level?

    And I do think one reason people don’t “get” evolution is that don’t know about nice clean examples of rapid evolutionary change of the sort Reznick describes.

    If it is a “nice clean” example, then it is certainly the kind of thing evolution skeptics have no issue with. And it is also the kind of thing that has no bearing on — and therefore no ability to address — the issues skeptics have raised. No-one claims nature is forever static. No-one disputes that populations can change. The issue is how and to what extent the minor observed changes can be extrapolated to explain the existence of all of biology. If someone fails to see the difference, they are simply failing at logic.

  252. 252
    Eric Anderson says:

    Box @149:

    Exactly. Well said.

  253. 253
    Eric Anderson says:

    Zachriel @195:

    Evolution isn’t random, and its trajectory depends on the landscape.

    @201:

    Variation is random with respect to fitness, but natural selection is not random.

    And what, pray tell, produced the landscape? Or, to put it in less theoretical, more concrete, real-world terms: What produced the particular environment in which the creature finds itself? Are you proposing that there is some force that creates a particular environment so that creatures can develop toward a concrete direction? Or can we acknowledge, as we should, that the environment itself is essentially a random result.

    And what “trajectory” should that organism take once in that environment? Larger/smaller, faster/slower, feathers/scales, and and on. There is no directionality anyone can point to.

    So we have random variation that is then subjected to random environmental situations. And proponents like to pretend natural selection (again not a force, just a label), somehow “filters” the randomness and provides meaningful direction?

    Nonsense. It is randomness all the way down.

  254. 254
    Eric Anderson says:

    Box @237:

    Yes, the literature (starting with Charles himself) is replete with people describing natural selection as though it were some kind of natural force. Every rational person doubts that random changes by themselves are up to the task? Not to worry — tada! Natural Selection to the rescue!

    Coincidentally, I was talking to my son this afternoon about this issue and he wondered whether it was worth the effort to get people to understand natural selection isn’t a force or whether we should just let them keep talking that way. Now I fully realize that most people aren’t interested in the nuances, but I think it is important for two reasons: (i) so often the claim of natural selection’s power descends into a circular argument (i.e., it becomes logically fatal); and (ii) perhaps even worse, at least in practice, it gives people the false impression that they have an explanation in hand for this or that particular phenomenon — Natural Selection did it! That is not only useless, it is actually corrosive to discovery and understanding. It impedes knowledge. And, unfortunately, it is pervasive.

    Thanks for your other thoughts and comments that help clarify these issues.

  255. 255
    Mung says:

    Yes, the literature (starting with Charles himself) is replete with people describing natural selection as though it were some kind of natural force.

    Well if you’re going to offer a designer substitute it darned well better be capable of at least creating the appearance of design!

    Coincidentally, I was talking to my son this afternoon about this issue and he wondered whether it was worth the effort to get people to understand natural selection isn’t a force or whether we should just let them keep talking that way.

    Is natural selection the cause or the effect? Evolutionists equivocate over this all the time.

    It’s the cause, one says.

    It’s the effect, says another.

    It both cause and effect, says a third.

    They all claim to understand evolution though. You can bet on that.

  256. 256
    wd400 says:

    Well, EA, very briefly.

    First-year philosophy discussion about what “force” means are about the least interesting thing I can imagine. We call selection, recombination, drift and the rest of them evolutionary forces because they change the trajectories of populations through time. If we want to argue about usage then I’m not interested.

    If you are interested in experiments about the randomness of mutation then wild populations of animals is not hte place to look. Start at Luria-Delbruk and move on. I still don’t know why you think sickle cell is definately a random mutation but think perhaps these fish and see guess what’s coming(?) and use some unknown biological process to create adaptive mutation.

    Of course the the process I’m talking about in that post evolution by natural selection — multiple generations of selection acting on heritable variants to create a change such that the most members of the population have a phenotype that no member of the ancestral is likely to have had. I you really think Box’s infantile “translation” is a a useful contribution then I see now point in carrying on .

  257. 257
    Box says:

    WD400: post evolution by natural selection — multiple generations of selection acting on heritable variants to create a change such that the most members of the population have a phenotype that no member of the ancestral is likely to have had.

    Are you saying that it is likely that this changed phenotype — “that no member of the ancestral is likely to have had” — is due to new genetic or epigenetic information?
    Or is there no new information at the molecular level?
    Stop building the suspense already.

  258. 258
    Steve says:

    Zachriel,

    Again, this statement is meaningless without excess reproduction, which is NOT the result of evolution.

    Excess reproduction precedes evolution.

    Therefore, evolution is a sub-component of design.

    The random nature of variation is a designed object, that allows organisms to meet any challenge from the environment.

    The environment puts a pitcher on the mound that throws a mean curve. Organisms respond by changing the lineup with a slew different batters, each using a different batting strategy, at least one of which will hit the ball out of the park BEFORE their 3 outs have been used.

    Design is the team (and strategy), evolution the scorekeeper (and batboy).

    True, however, the claim is not false. When you have replication with variation, you have evolution. Whether adaptation occurs depends on the fitness landscape.

  259. 259
    wd400 says:

    Again, this statement is meaningless without excess reproduction, which is NOT the result of evolution.

    Why do you think this? What prevents non-designed systems from reproducing at above the replacement rate?

    What do you think would happen in to an allele for increased reproduction in a population where all individuals not carrying that allele where simply replacing themselves?

    Apart from this particular hang up you seem to be OK with evolution as explained by mainstream evolutionary biology?

  260. 260
    Eric Anderson says:

    wd400 @256:

    First-year philosophy discussion about what “force” means are about the least interesting thing I can imagine. We call selection, recombination, drift and the rest of them evolutionary forces because they change the trajectories of populations through time. If we want to argue about usage then I’m not interested.

    This is not a philosophical discussion. The usage of terms goes to the heart of what is being claimed, particularly when a term is regularly thrown out as some kind of explanation for this or that observation. Recombination and drift are real processes. We can observe them, even calculate and map them to some extent. The other one you threw in there — “selection” — is not a process. I would be happy to avoid a usage discussion if people would stop using the term as though it is a force, as though it is a cause, as though it imparts some directionality to what would otherwise be a random process.

    If you are interested in experiments about the randomness of mutation then wild populations of animals is not hte place to look. Start at Luria-Delbruk and move on.

    What makes you think I disagree with the randomness of mutations? I am more than happy to assume that mutations are random (largely, speaking). There is a lot of interesting research pointing to non-random genetic change, but I’m happy to treat “mutations” as essentially random.

    I still don’t know why you think sickle cell is definately a random mutation but think perhaps these fish and see guess what’s coming(?) and use some unknown biological process to create adaptive mutation.

    Two things.

    First, with sickle cell we can point to a couple of single point mutations, coupled with the other characteristics I have outlined above. I am willing to agree, willing to stipulate, that Neo-Darwinian evolution can produce an effect like the malaria/sickle cell situation. But by all means, if it turns out not to be a case of random mutation, then we have even fewer cases of the already shrinking examples of legitimate Neo-Darwinian evolution. (I’ve been asking for other clear examples, but haven’t had any takers yet.)

    Second, if there was a functional change in the guppies at the genetic level in the course of a year or two, we are likely not talking about random genetic change, and therefore not Neo-Darwinian evolution. Furthermore, if there was no genetic change, but there was an epigenetic change, then, again, this does not reflect Neo-Darwinian evolution, but rather an epigenetic response to the environment. Finally, if the genetics were there all along and all we had was some “natural selection” going on, then it isn’t anything particularly controversial nor interesting.

    I take it, although you seem to be avoiding Box’s question, that you think the latter, namely that the genetic variation was already there in the population at the outset. Fine. Then what Reznick has is a case of run-of-the-mill differential survival in a new environment. Interesting observations to be sure. But nothing that confirms the RM part of the evolutionary claim, nothing that evolution skeptics would object to in the first place, nothing that demonstrates the broad truth of “evolution” as Reznick thinks.

    —–

    (BTW, you seem to be very skeptical about non-random genetic change. Are you saying that no organisms are known to make non-random genetic changes in response to environmental change?)

  261. 261
    Mung says:

    Mutations are magically random.

  262. 262
    Mung says:

    wd400:

    Apart from this particular hang up you seem to be OK with evolution as explained by mainstream evolutionary biology?

    If “mainstream” means “Darwinian” then no.

    Is Darwinism no longer mainstream?

  263. 263
    Mung says:

    wd400:

    What prevents non-designed systems from reproducing at above the replacement rate?

    The fact that non-designed systems capable of reproduction don’t actually exist might pose a barrier.

    Do you have some evidence for these non-designed reproductive systems?

  264. 264
    wd400 says:

    I can’t imagine a definition of force that includes drift by excludes selection. Selection very obviously imparts directionality too.

    You’re own comment sure make it sounds like you are interesting in the randomness of mutation

    serving that natural selection has taken place and triumphantly pronouncing that we are witnessing “evolution” is but an exercise in equivocation. We can’t just ignore the critical first part of the RM+NS equation.

    You’ve already been told that the guppies example has been shown to be a genetic change. That you and the rest of the choir above keep going on about this paper (that you haven’t read) is pretty clear evidence that skeptics do have a problem with this sort of result, I would have thought.

  265. 265
    Mung says:

    wd400:

    Selection very obviously imparts directionality too.

    No, it doesn’t.

    Direction is direction towards something or some outcome. It is end directed. It is teleological.

    Darwinian selection is non-teleological. Therefore it does not and cannot impart directionality.

  266. 266
    wd400 says:

    I forgot to reply to the question about randomness of mutations. There is no evidence that mutations are anything other than random with respect to fitness, despite many experiments on this topic.

  267. 267
    bornagain says:

    DNA sun protection: Researchers observe one of the world’s fastest chemical reactions for the first time – October 16, 2015
    Excerpt: Our DNA contains the bases adenine, guanine, cytosine and thymine. The chemists used ultra short blasts of light to shoot base pairs guanine and cytosine which were stimulated with UV light. They were only able to reveal the protective molecular mechanism using this method of femtosecond spectroscopy, because the process happened within a few quadrillionths of a second.
    During the so-called electron-driven proton transfer process (EDPT), a hydrogen atom is displaced within the molecular compound. The base pair, however, immediately returns to its original starting structure from the same procedure. “Nature uses the reaction to strengthen the DNA’s resistance to light by orders of magnitude — it is sort of a sun protection for DNA,”,,
    “The DNA building blocks themselves thereby relieve, (the work load on), the cells’ hugely complex and very slowly active repair mechanisms using enzymes. The discovery of these enzymes this year was awarded the Nobel Prize for Chemistry. Without the passive processes we observed, the cells’ active repair mechanisms would be completely overloaded,”
    http://www.sciencedaily.com/re.....084856.htm

  268. 268
    Mung says:

    wd400:

    There is no evidence that mutations are anything other than random with respect to fitness, despite many experiments on this topic.

    So?

  269. 269
    Andre says:

    Amazing Natural selection has all the attributes we would assign to a concious being. Direction, sensitivity, desicion making… Are you guys confusing nothing with something?

  270. 270
    Popperian says:

    @Eric Anderson#260

    This is not a philosophical discussion. The usage of terms goes to the heart of what is being claimed, particularly when a term is regularly thrown out as some kind of explanation for this or that observation. Recombination and drift are real processes. We can observe them, even calculate and map them to some extent. The other one you threw in there — “selection” — is not a process. I would be happy to avoid a usage discussion if people would stop using the term as though it is a force, as though it is a cause, as though it imparts some directionality to what would otherwise be a random process.

    Actually, it a philosophical discussion. Popper’s theory of the universal growth of knowledge is Darwinian in nature. Specifically, knowledge is variation controlled by criticism. And it’s universal in that it refers to the growth of knowledge in books, brains and even genomes. Nor is it limited to knowing subjects.

    In the case of biology, natural selection plays the role of criticism.

    One thing that Paley clarified was what it means for something to have the appearance of design. Specially, the rock can serve many purposes, but is not well adapted to do so. It can be a paper weight, building material, a weapon, store heat, etc. And it could still serve those purposes just as well even if it was modified significantly. However the watch is a rare configuration of matter. If its key parts are modified even a little it would perform the purpose of keeping time significantly less well. It is not a raw material. Nor could have it have always been lying there in its current state. It is well adapted to serve a purpose. As such, it requires a different kind of explanation than the rock.

    But how does it get well adapted? From a comment in another thread…

    the features of organisms are the result of a set of instructions which describe what transformations of raw materials should occur to bring them about when a copy is made. We might not understand exactly how those instructions interact with each other due the complex way they are mediated by other instructions, but it’s those instructions that bring about those particular features none the less.

    IOW, the concrete biological features of organisms are the result of the kind of transformations that occur when the requisite knowledge is present there. So the origin of those features is the origin of those instructions. Right? That’s what needs to be explained.

    The appearance of design can be explained because the growth of human knowledge, which human beings use to solve design problems, can be explained. This is in contrast to assuming design is an immutable primitive that cannot be explained, or the philosophical idea that knowledge comes from authoritative sources, which we’ve already rejected in the vast majority of spheres. For example, we have discarded the idea of the divine right of kings to rule. What we are really concerned with ideas people hold, not their sources.

    I can exhibit the intent to create a drug for the purpose of curing cancer, but unless the requisite knowledge of how to actually kill just cancer cells without killing the patient is actually present, the problem will remain unsolved. “That’s just what some designer must have wanted” is insufficient because it doesn’t explain the origin of that knowledge.

  271. 271
    Popperian says:

    @EugeneS

    The first primitive replicators do not need to exhibit highly accurate replication when starting out because they only have to compete with other low accuracy replicators.

    Furthermore, while Pailey’s solution ruled itself out, he did clarify what it means for something to exhibit the appearance of design. Low accuracy replicators are not well adapted for the purpose of replication. They are like Pailey’s rock, which does not exhibit the appearance of design. As such, they do not need the same kind of explanation as the the watch.

  272. 272
    Andre says:

    Popperian

    What primitive replicators? Care to show us these primitive ones or are you just speculating?

  273. 273
    Andre says:

    Popperian

    What other low accuracy replicators? Care to show them or are you again speculating?

  274. 274
    Box says:

    WD400: You’ve already been told that the guppies example has been shown to be a genetic change.

    By “genetic change” do you mean:

    1) a genetic change in the fish population as a whole, in the sense that, due to natural selection, there has been a numerical change towards more individual orange guppies. However there is no new DNA code produced.

    2) a genetic change in the sense that we find (or expect to find) new code in the guppy DNA. New code that was not present in any of the members of the ancestral population.

  275. 275
    Box says:

    Popperian: The first primitive replicators do not need to exhibit highly accurate replication when starting out because they only have to compete with other low accuracy replicators.

    What Popperian assumes here is robustness of all sorts of “primitive replicators”. What the materialist routinely fails to take in account is that a robust organism — an organism that doesn’t fall apart — is something that their position cannot explain at all.
    I already addressed this point in #64, but it is very important IMO. Allow me to quote Barham again.

    How can living systems be so robust (dynamically stable), when they consist of thousands of chemical interactions that must all be coordinated precisely in time and space? From the point of view of physics, cells (not to speak of more complex organisms) should not exist, and yet they do. How is that possible?
    The only suggestion Darwinism has to offer is chance: those systems that just happened to be stable are the ones that we see today.

    A bag of chemicals with countless chemical interactions, which remains dynamically robust (stable) is incomprehensible from the point of view of physics. Why doesn’t it fall apart, while it does not contain one single part which, of itself, is interested in the continued existence of the bag of chemicals?
    Only occasionally materialists give some indication that they are aware of the problem.

    Dawkins: But, however many ways there may be of being alive, it is certain that there are vastly more ways of being dead, or rather not alive. You may throw cells together at random, over and over again for a billion years, and not once will you get a conglomeration that flies or swims or burrows or runs, or does anything, even badly, that could remotely be construed as working to keep itself alive.

    [my emphasis]

    It’s not entirely clear, but Dawkins seems to be (also) talking about the basic ability of “not falling apart”, which is far more miraculous than being able to fly, swim and so forth.
    Out of the enormous collection of bags of chemicals that do fall apart chance has to find ones that don’t. By definition, chance does so unaided by natural selection, since natural selection only acts on bags of chemicals that don’t fall apart; before they replicate.
    Only after chance has found a few of these improbable bags of chemicals that don’t fall apart, natural selection extends a “helping hand” by eliminating most of them.

    (…) it has been estimated that 99.9% of all species that have ever lived on Earth are now extinct.

    The assumption of an easy to find sheer endless variety of robust forms is critical to the Darwinian concept of a constructive natural selection. If one takes into account that robustness is a miracle and extremely hard to find, then one must conclude that natural selection is a tremendous hindrance to evolution.

  276. 276
    Virgil Cain says:

    wd400:

    I forgot to reply to the question about randomness of mutations. There is no evidence that mutations are anything other than random with respect to fitness, despite many experiments on this topic.

    Random with respect to fitness is a nonsense phrase. With evolutionism all mutations are HAPPENSTANCE, ie accidents, errors and mistakes.

    Also James Shapiro has produced evidence that organisms initiate the mutations. Work that was started by Barbara McClintock.

    The SOS response is such and initiated response. Transposition is also initiated by the organism to repair damaged DNA.

    The bottom line is people who say “random with respect to fitness” are either ignorant or dishonest.

  277. 277
    Virgil Cain says:

    Poperian:

    The first primitive replicators do not need to exhibit highly accurate replication when starting out because they only have to compete with other low accuracy replicators.

    What “first primitive replicators”? Please be specific and show your work.

  278. 278
    Zachriel says:

    Andre: What evidence?

    You could start here:
    http://molbio.mgh.harvard.edu/szostakweb/

    EugeneS: Biological evolution is a property of living systems by definition.

    Sure. The scientific endeavor is to unify theories of biology and chemistry.

    EugeneS: Life is more than replication as it also includes metabolism, reaction to stimuli and nobody knows what else.

    Extant life includes many features that may have emerged after life began.

    Eric Anderson: First of all, let’s be very clear: natural selection is not a force. It is a label.

    ‘Air pressure is not a force. It’s a label for the effect of stochastic motion of gas molecules.’

    Eric Anderson: Observing that natural selection occurred doesn’t tell us anything about how the variation came about in the first place. That is the part of the theory that needs to be supported.

    That’s right. Darwin pointed to artificial selection to show the amount of novel variation that is possible.

    Eric Anderson: Neo-Darwinian theory can explain some things. Minor things.

    Epidemiology is hardly a minor thing, at least to humans.

    Eric Anderson: What do you think was actually going on in individual guppies — what was occurring at the genetic or the epigenetic level?

    See Ghalambor et al., Non-adaptive plasticity potentiates rapid adaptive evolution of gene expression in nature, Nature 2015.

    Eric Anderson: And what, pray tell, produced the landscape?

    At least part of that landscape is due to basic physics; fusion on the Sun, rotation and revolution of the Earth, the collection of water in basins, rain, snow, ice, the formation of land, etc. Other aspects of the environment are biological organisms themselves, including competitors.

    Eric Anderson: Are you proposing that there is some force that creates a particular environment so that creatures can develop toward a concrete direction?

    Light comes from above.

    Eric Anderson: Or can we acknowledge, as we should, that the environment itself is essentially a random result.

    The environment is hardly random. While chaotic, it’s highly structured. Light comes from above.

    Eric Anderson: And what “trajectory” should that organism take once in that environment? Larger/smaller, faster/slower, feathers/scales, and and on. There is no directionality anyone can point to.

    Grow upwards little tracheophyte, grow upwards!

    Eric Anderson: Every rational person doubts that random changes by themselves are up to the task? Not to worry — tada! Natural Selection to the rescue!

    ‘Every rational person doubts that random molecular motions by themselves are up to the task of filling the corners of a vacuum chamber. Not to worry — tada! Gas pressure to the rescue!’

    Eric Anderson: Is natural selection the cause or the effect?

    Something can be both cause and effect. Natural selection is the effect of fecundity and differential reproductive potential. Natural selection causes changes in the distribution of traits in a population.

    Steve: Again, this statement is meaningless without excess reproduction, which is NOT the result of evolution.

    Excess reproduction is a natural consequence of binary fission.

    Eric Anderson: Recombination and drift are real processes.

    We can also observe natural selection and adaptation.

    Box: A bag of chemicals with countless chemical interactions, which remains dynamically robust (stable) is incomprehensible from the point of view of physics.

    There is nothing known about a living organism which is contrary to physical theory.

  279. 279
    Virgil Cain says:

    Zachriel:

    We can also observe natural selection and adaptation.

    Evidence please.

    There is nothing known about a living organism which is contrary to physical theory.

    The genetic code is contrary to physical theory as there aren’t any physical processes that can produce a code. Also life is not reducible to physical processes.

  280. 280
    Zachriel says:

    Oops. Wrong attribution above.

    Mung: Is natural selection the cause or the effect?

    Something can be both cause and effect. Natural selection is the effect of fecundity and differential reproductive potential. Natural selection causes changes in the distribution of traits in a population.

  281. 281
    Virgil Cain says:

    Natural selection is a result. And as a result of natural selection allele frequencies change.

  282. 282
    Eric Anderson says:

    wd400 @266:

    I forgot to reply to the question about randomness of mutations. There is no evidence that mutations are anything other than random with respect to fitness, despite many experiments on this topic.

    Thanks.

    I will do a brief post on this (hopefully within a week or two). Just so that we are clear and you don’t later try to squirm out of what you wrote above, let me remind you what the question was. It was not about “mutations” it was about “genetic change.”

    We can easily define a “mutation” as something non-purposeful, unexpected, random by definition. As I said, I don’t have a problem with that viewpoint of a “mutation” and am happy to agree that mutations are random with respect to fitness.

    The question is: “Are you saying that no organisms are known to make non-random genetic changes in response to environmental change?”

  283. 283
    Eric Anderson says:

    wd400 @264:

    Let’s cut to the chase. This is very simple. There are only three possibilities:

    (i) a novel genetic change arose within 1-2 years, in which case we are not dealing with random, Neo-Darwinian evolution;

    (ii) there was an epigenetic change that arose within 1-2 years, in which case we are not dealing with Neo-Darwinian evolution;

    (iii) there was no novel genetic change that arose and no epigenetic change that arose,* and so all we are dealing with is a shift in the population due to “natural selection.” In this case (a) the first part (the important part) of the evolutionary story is missing and unsupported, (b) no prominent evolution skeptics have an issue with the idea of differential survival anyway, and (c) even if we give away the store and assume a Neo-Darwinian origin for the genetics in the first place, the observations still do not demonstrate the larger claims of “evolution,” which are the real issue.

    Please tell us, which is it — (i), (ii) or (iii)?

    —–

    * For the love of clarity and to help put this to rest, please do not refer to a shift in gene frequencies in the population as a novel genetic change. We’re talking about actual novel change arising within an organism or organisms here, not some fluctuation in a statistical measure across a population. If you think the genetics existed in at least one organism in the original pool in the first place, then you are in (iii).

    Update: I see that Box already tried pinning this down multiple times. Please do read his question @274 carefully. Thanks,

  284. 284
    PaV says:

    wd400:

    A tautology is a tautology. It doesn’t matter what the paper is, or what they propose to do next. It is an error in logical thought.

  285. 285
    PaV says:

    wd400:

    What’s this “other paper”? Do you have a link?

  286. 286
    wd400 says:

    How many times to I have to say that this is an example of evolution by natural selection, acing on standing variation. If you want direct tests of the randomness of mutation there are plenty of studies for that. If you accept mutation is random then if follows the standind variation is the result of a random process. If you think these are not random mutations then you are left to explain how these fish are inducing mutations that will be adaptive in a future environment they don’t know they are being transported to.

    You seem to be confused about what mutations are in the other comment — instead of playing games do you want to say what non-random genetic changes (that aren’t mutations?) do you have in mind?

  287. 287
    Popperian says:

    What Popperian assumes here is robustness of all sorts of “primitive replicators”. What the materialist routinely fails to take in account is that a robust organism — an organism that doesn’t fall apart — is something that their position cannot explain at all.

    Again, low fidelity replicators would not be well adapted for the purpose of replication. They are like the rock Paley finds in a field, which serves a purpose but does not need the same sort of explanation as the watch.

    They do not exhibit the appearance of design as clarified William Paley.

    From the paper The constructor theory of life

    The second point is that natural selection, to get started, does not require accurate self-reproducers with high-fidelity replicators. Indeed, the minimal requirement for natural selection is that each kind of replicator produce at least one viable offspring, on average, per lifetime – so that the different kinds of replicators last long enough to be “selected” by the environment. In challenging environments, a vehicle with many functionalities is needed to meet this requirement. But in unchallenging ones (i.e. sufficiently unchanging and resource-rich), the requirement is easily met by highly inaccurate self-reproducers that not only have no appearance of design, but are so inaccurate that they can have arisen spontaneously from generic resources under no-design laws – as proposed, for instance, by the current theories of the origin of life [11, 31]. For example, template replicators, such as short RNA strands [32], or similar “naked” replicators (replicating with poor copying fidelity without a vehicle) would suffice to get natural selection started. Since they bear no design, they require no further explanation – any more than simple inorganic catalysts do.(11)

  288. 288
    Box says:

    WD400: How many times to I have to say that this is an example of evolution by natural selection, acing on standing variation.

    I take it then, that by “standing variation”, you simply mean to say that the ‘selected’ gene variant was already present in the ancestral population. In other words, there is no novelty at the genetic level.

    Why don’t you admit that? When asked, why don’t you simply answer: “I’m talking about option (iii), mr. Anderson”?

    Eric Anderson:

    (iii) there was no novel genetic change that arose and no epigenetic change that arose,* and so all we are dealing with is a shift in the population due to “natural selection.” In this case (a) the first part (the important part) of the evolutionary story is missing and unsupported, (b) no prominent evolution skeptics have an issue with the idea of differential survival anyway, (…)

    * For the love of clarity and to help put this to rest, please do not refer to a shift in gene frequencies in the population as a novel genetic change. We’re talking about actual novel change arising within an organism or organisms here, not some fluctuation in a statistical measure across a population. If you think the genetics existed in at least one organism in the original pool in the first place, then you are in (iii).

  289. 289
    wd400 says:

    For one because all the extra stuff actually clouds the point. For instance, there are almost certainly combinations of alleles (“genetics”) that did not exist in “at least one organism in the original pool” that are present in the evolved population. That’s one result of selection on heritable variants over generations that isn’t included in your infantile “translations” of natural selection.

  290. 290
    Mung says:

    wd400:

    You seem to be confused about what mutations are in the other comment — instead of playing games do you want to say what non-random genetic changes (that aren’t mutations?) do you have in mind?

    Let’s start with DNA repair. DNA repair isn’t mutations. It is non-random. And it affects the genome.

    Why in your mind does DNA repair not meet the definition?

  291. 291
    wd400 says:

    What’s with all these spammy posts Mung? DNA repair doesn’t lead to a change in genetics from one generation to the next, which is the relevant point for evolution. It’s also random with respect to fitness — if it wasn’t then mutations would not be either.

    But surely you know this? So why all these silly comments?

  292. 292
    Box says:

    Popperian #287,

    Your non-response illustrates clearly the point I was making: the blindness of materialists for the unlikelihood that bags of chemicals (or any dynamic conglomeration of chemicals) are dynamically stable.
    The writers of the paper you cite obviously suffer from the same blind spot.
    Materialist simply assume the continued existence of replicators in all sizes and shapes — although that doesn’t make sense from the perspective of physics.

    I understand that this baseless assumption is foundational to your absurd belief. Probably foundational to the extend that reflecting on it is no longer possible.

    In the imagination of Darwinians, life-forms are easy to find and come in extreme abundance and variety. In that context, there is constructive “natural selection” for the pruning of all that excessive stuff.

  293. 293
    Andre says:

    WD400

    Please do tell hoe did a random process create a non random process to prevent random processes from happening?

  294. 294
    Virgil Cain says:

    The whole argument is whether or not all mutations/ genetic change are accidents, errors and mistakes. That is why the OoL is KEY. If the OoL = Intelligent Design it would be a given that the genetic changes are NOT accidents, errors and mistakes.

    And Intelligent Design OoL means that evolution is directed, for the most part. Directed evolution is exemplified by evolutionary and genetic algorithms.

    The point of DNA repair is it is obvious it is a directed process. Transposition is also a directed process with the transposon containing the coding for two of the enzymes it requires to move around.

  295. 295
    ppolish says:

    Physicists meet to discuss the discovery of “highly organized information systems in nature”. The conference “intends to address the “in vivo” (role of information in nature)”,
    http://www.informationuniverse.rug.nl

    Physics joining ID in taking the lead in Evo Bio. Good on them.

  296. 296
    Popperian says:

    @box#292

    Materialist simply assume the continued existence of replicators in all sizes and shapes — although that doesn’t make sense from the perspective of physics.

    Can you kindly point out what part of the quote or the paper “doesn’t make sense from the perspective of physics”?

    Thanks.

  297. 297
    Popperian says:

    The whole argument is whether or not all mutations/ genetic change are accidents, errors and mistakes. That is why the OoL is KEY. If the OoL = Intelligent Design it would be a given that the genetic changes are NOT accidents, errors and mistakes.

    I’m suggesting the fundamental issue is between the idea that designers create the knowledge they use to solve problems and the idea that knowledge doesn’t genuinely grow at all. It just gets moved from one place to another or is mechanically extrapolated though observations. But the latter does not withstand rational criticism.

    The contents of theories do not come from observations. They start out as conjectures (guess) that we then criticize and discard error we discover. There is no guarantee that our conjectured theories about how the world works will solve the problems we want to solve. Nor is it guaranteed that it will not solve some other problem we didn’t intend to solve, either.

    If the contents of theories did come from observations then we should be much father along because all you’d have to do is observe something and you would be guaranteed to get the right theory from those observations every time. Nor should there be significant gaps in how we make progress. Rather it should be very linear and continuous. Yet, this doesn’t describe progress in science.

    IOW, human intelligent designers create knowledge though a process of trial and error, which is darwinian in nature. It’s part of a universal explanation of the growth of knowledge.

    In the case of biological Darwinism, the process isn’t just random, but random to any particular problem to solve. Unlike people, bacteria or individual cells do not conceive of problems like we do. But that isn’t a insurmountable problem because we start out with variation on existing knowledge that we do not know will solve the problem we want to solve, either. In both cases, variation is not guarantee to solve problems. Both represent variation controlled by criticism.

    Human knowledge is explanatory in nature, while biological knowledge is non-explanatory. It reprints useful rules of thumb. While people can create both explanatory and non-explanotry knowledge, only people can create explanatory knowledge because only people are universal explainers. People can conjecture explanations about how the world works to solve problems. However, bacteria are not universal explainers because they cannot conceive of problems, let alone conceive of theories of how to solve them.

    So, what’s key is that there are diffident kinds of knowledge. Explanatory and non-explanatory.

    For example, imagine I’ve been shipwrecked on a deserted island and I have partial amnesia due to the wreck. I remember that coconuts are edible so climb a tree to pick them. While attempting to pick a coconut, one falls, lands of a rock and splits open. Note that I did not intend for the coconut to fall, let alone plan for it to fall because I guessed coconuts that fall on rocks might crack open. The coconut falling was random in respect to the problem I hadn’t yet even tried to solve. Furthermore, due to my amnesia, I’ve hypothetically forgotten what I know about physics, including mass, inertia, etc. Specifically, I lack an explanation as to why the coconut landing on the rock causes it to open. As such, my knowledge of how to open coconuts is merely a useful rule of thumb, which is limited in reach. For example, in the absence of an explanation, I might collect coconuts picked from other trees, carry them to this same tree, climb it, then drop them on the rocks to open them.

    However, explanatory knowledge has significant reach. Specifically, if my explanatory knowledge of physics, including inertia, mass, etc. returned, I could use that explanation to strike coconut with any similar sized rock, rather than vice versa. Furthermore, I could exchange the rock with another object with Significant mass, such as an anchor and open objects other than coconuts, such as shells, use this knowledge to protect myself from attacking wildlife, etc.

    So, explanatory knowledge comes from intentional conjectures made by people and have significant reach. Non-explanatory knowledge (useful rules of thumb) represent unintentional conjectures and have limited reach. Knowledge can be created without intent in the form of useful rules of thumb. The knowledge of how to build biological adaptations isn’t explanatory in nature but non-explanatory and occasionally results in useful rule of thumb that improves biological adaptions.

  298. 298
    Virgil Cain says:

    Biological Darwinism is real if and only if living organisms arose from non-living matter and energy via stochastic processes.

  299. 299
    Eric Anderson says:

    Zachriel @245:

    I hereby offer you a guest post opportunity to support the following claim you made with respect to the origin of life:

    “the evidence indicates a natural cause”

    Let me know if you want to take up the opportunity and we’ll get your guest post up for discussion.

  300. 300
    Eric Anderson says:

    wd400 @286:

    Well, we’ve finally pinned down the source of your misunderstanding.

    If you accept mutation is random then if follows the standin[g] variation is the result of a random process.

    No, it does not follow at all. It only follows if we assume that mutation is the source of the variation. If something else is the source of the variation, something other than mutation, then it doesn’t follow at all.

    Again, the question at stake is not whether organisms poorly adapted to their environment are less likely to survive than those that are better adapted. That is obvious and we don’t need evolutionary theory to tell us that. Nor do we need a convenience label.

    What evolutionary theory has to bring to the table — in the context of the present discussion, what the Neo-Darwinian random-mutations-in-DNA mechanism has to bring to the table is an explanation of how the organisms in all of their varieties came on the scene in the first place. We can’t just assume it happened by mutation. It has never been demonstrated that mutations have that creative ability; indeed the evidence points strongly to the contrary.

  301. 301
    Eric Anderson says:

    Virgil Cain @276:

    Thanks for your comments. Just one clarification on terminology:

    By the term “random with respect to fitness” wd400 uses, it is meant that the mutation is indeed “happenstance,” as you suggest. As far as we know, most mutations appear to be random, without regard to whether they will help the organism survive or not. And the overwhelming majority do not help the organism survive or are outright harmful — which is precisely the problem for Neo-Darwinian theory.

    In contrast to these “mutations,” there are examples of controlled genetic changes that some organisms initiate, among other things, in response to environmental cues.

    For clarity of discussion, we should distinguish these from “mutations.” They are not random, they are not errors, they are purposeful and controlled. “Genetic changes” yes, but not “mutations.”

  302. 302
    EugeneS says:

    Popperian,

    This is how I see this whole business.

    Zachriel seem to have recognized the problem of initial complexity as they stated that for evolution to even start, one needs membranes and replication.

    I read this ‘and‘ as a tacit recognition of initial complexity necessary in order for life to even start.

    The next step they need to take is recognize the huge difference between replicating homogeneous structures and replicating heterogeneous structures. This difference is not a difference of degree but a difference of kind.

    There is absolutely no way out of the reductionist conundrum. Either reductionists honestly accept the need for starting complexity or they will never get the correct picture. The start of life could not be simple in principle.

    The start of life is absolutely dependent on there being a starting irreducibly complex structure including data, a program to read this data in and do something meaningful about it, and the processor which will translate the program and execute it.

  303. 303
    wd400 says:

    You appear to be confused about what mutations are – do you want to describe one of these non-mutational genetic changes?

  304. 304
    Virgil Cain says:

    Hi Eric Anderson:

    By the term “random with respect to fitness” wd400 uses, it is meant that the mutation is indeed “happenstance,” as you suggest.

    And yet directed mutations can be random wrt the current fitness.

    For clarity of discussion, we should distinguish these from “mutations.” They are not random, they are not errors, they are purposeful and controlled. “Genetic changes” yes, but not “mutations.”

    Yes, “mutation” seems to imply “accident, error and mistake”.

  305. 305
    EugeneS says:

    Virgil Cain,

    I mostly agree with you. However, I have problems with ‘directed evolution’. I think that this is an oxymoron. I believe there is hardly any evolution at all, where by evolution I mean undirected oscillations around attractors in the parameter space. Darwinian evolution is dwarfish and cannot account for novelty. Perhaps all behavioural intelligence of an organism is built-in as a template. It manifests itself as meaningful genetic responses to external stimuli.

  306. 306
    Zachriel says:

    Eric Anderson: I hereby offer you a guest post opportunity to support the following claim you made with respect to the origin of life: “the evidence indicates a natural cause”

    The offer is appreciated. However, such a discussion presupposes the validity of evidence for evolution, and the history of common descent. Not sure how to engage such a discussion without those already being established.

  307. 307
    Zachriel says:

    Eric Anderson: What evolutionary theory has to bring to the table — in the context of the present discussion, what the Neo-Darwinian random-mutations-in-DNA mechanism has to bring to the table is an explanation of how the organisms in all of their varieties came on the scene in the first place. We can’t just assume it happened by mutation.

    Case in point. The evidence for divergence from common ancestors is an important clue as to the origin of life. But if you reject this billions year history of divergence, then you will find assertions concerning the trunk of that tree to be unfounded.

  308. 308
    Zachriel says:

    EugeneS: Zachriel seem to have recognized the problem of initial complexity as they stated that for evolution to even start, one needs membranes and replication.

    Some sort of segregation may be required. A lipid membrane is a reasonable and available mechanism.

    EugeneS: I read this ‘and‘ as a tacit recognition of initial complexity necessary in order for life to even start.

    Of course there is complexity involved.

    EugeneS: The next step they need to take is recognize the huge difference between replicating homogeneous structures and replicating heterogeneous structures.

    A dividing membrane is among the simplest of problems. A molecular replicator is the hard problem.

  309. 309
    EugeneS says:

    Zachriel,

    How complex a constituent sub-problem is does not matter. The point is the resultant structure must cater for replication and autonomy. This is complexity in principle.

    Heterogeneous systems to replicate require the existence of:

    1. memory;
    2. a symbolic representation of the system being able to be stored and retrieved from memory;
    3. a reader/writer of these symbolic representations to/from memory;
    4. a processor which actually executes instructions in order to rebuild the system using the representation.

  310. 310
    Zachriel says:

    EugeneS: This is complexity in principle.

    Z: Of course there is complexity involved.

    EugeneS: Heterogeneous systems to replicate require the existence of:
    1. memory;
    2. a symbolic representation of the system being able to be stored and retrieved from memory;
    3. a reader/writer of these symbolic representations to/from memory;
    4. a processor which actually executes instructions in order to rebuild the system using the representation.

    What Crick conjectured, based on evolutionary principles half a century ago, is now known to be possible, a molecule which can act as

    1. memory;
    2. a symbolic representation of the system being able to be stored and retrieved from memory;
    3. a reader/writer of these symbolic representations to/from memory;
    4. a processor which actually executes instructions in order to rebuild the system using the representation.

  311. 311
    wd400 says:

    Again, the question at stake is not whether organisms poorly adapted to their environment are less likely to survive than those that are better adapted. That is obvious and we don’t need evolutionary theory to tell us that. Nor do we need a convenience label.

    You keep saying stuff like this as if it’s related anything I’ve said. Which leads me to a question:

    what do you think happens to a population where the degree to which individuals are adapted to their environment is not heritable?

  312. 312
    Virgil Cain says:

    Zachriel:

    The offer is appreciated. However, such a discussion presupposes the validity of evidence for evolution, and the history of common descent. Not sure how to engage such a discussion without those already being established.

    Translation: Zachriel is too chicken to make a claim it has to actually support.

  313. 313
    Virgil Cain says:

    The evidence for divergence from common ancestors is an important clue as to the origin of life.

    There isn’t any such evidence so that would be a problem.

  314. 314
    Eric Anderson says:

    What makes you think I am confused about mutations? I have already agreed with your statement that mutations appear to be essentially random with respect to fitness. That is not the question.

    The question is whether there are other genetic changes besides mutations. There is growing evidence that such changes can and do exist. As I said earlier, I’ll hopefully get to that in another post. Briefly, however, Spetner describes a couple of examples in his book, including experiments with Salmonella bacteria and E. coli.

    Regardless, independent of the above, the real issue of the OP is how some people seem to jump from meager observational evidence to larger unwarranted conclusions about the power of the evolutionary mechanism.

  315. 315
    Eric Anderson says:

    Zachriel @278:

    At least part of that landscape is due to basic physics; fusion on the Sun, rotation and revolution of the Earth, the collection of water in basins, rain, snow, ice, the formation of land, etc. Other aspects of the environment are biological organisms themselves, including competitors.

    Of course. So are you arguing that the landscape is the result of deterministic forces? Or the result of chance?

    See Ghalambor et al., Non-adaptive plasticity potentiates rapid adaptive evolution of gene expression in nature, Nature 2015.

    Phenotypic plasticity is indeed an interesting phenomenon. And what do you suppose drives that plasticity? Epigenetic activity in most cases. Regardless, it certainly isn’t the Neo-Darwinian mechanism of DNA mutations that is driving the situation in this case. Which is precisely the point.

  316. 316
    Eric Anderson says:

    Zachriel @306:

    That specific offer related to your claim about abiogenesis. No subsequent details about evolution, common descent or otherwise need be provided. We can limit the guest post to the question of abiogenesis.

  317. 317
    wd400 says:

    What makes you think I am confused about mutations?

    You say things like

    The question is whether there are other genetic changes besides mutations

    What is a non-mutational genetic change?

  318. 318
    Zachriel says:

    Eric Anderson: So are you arguing that the landscape is the result of deterministic forces?

    Certainly many aspects of the environment are the result of deterministic forces, such as sunshine.

    Eric Anderson: Regardless, it certainly isn’t the Neo-Darwinian mechanism of DNA mutations that is driving the situation in this case.

    Ghalambor links plasticity with adaptive evolution.

    Eric Anderson: No subsequent details about evolution, common descent or otherwise need be provided. We can limit the guest post to the question of abiogenesis.

    They can’t be unlinked. If someone denies evolutionary adaptation, for instance, then talk about early replicators wouldn’t have a connection to extant life.

  319. 319
    Carpathian says:

    Mapou:

    You’re pissing me off, Zachriel. I’m out of this discussion. I got better things to do. May you throw a clot or something, jackass.

    If being a theist allows one to make statements like this, I hope I never become one.

  320. 320
    Mapou says:

    Carpie @319,

    I don’t care.

  321. 321
    Virgil Cain says:

    Theists do not want Carpathian.

  322. 322
    Carpathian says:

    Mapou:

    I don’t care.

    Of course you don’t.

    If you cared about what others, such as children and young students think, you wouldn’t set such a bad example.

    The irony is that you aren’t a moral-compass-lacking atheist, but one of the “good” guys.

  323. 323
    Mapou says:

    Pack it, Carpie. Children would cheer if they saw David cut that jackass Goliath’s head off.

  324. 324
    Carpathian says:

    Virgil Cain:

    Theists do not want Carpathian.

    True.

    The last thing a theology needs is people who ask questions, especially questions a theology is not equipped to answer.

  325. 325
    Carpathian says:

    Mapou:

    Pack it, Carpie. Children would cheer if they saw David cut that jackass Goliath’s head off.

    Are you actually saying that you think children would benefit from watching a beheading?

    If this is supposed to be funny, it’s not.

  326. 326
    Andre says:

    So Carpathian just don’t like Christians….. I’m sure he thanks God everyday that he is not like those Christians.

  327. 327
    Mapou says:

    Carpie, if there is bully beating up a kid with a baseball bat and a good Samaritan comes along and kills the bully, the kid would cheer. I know I would. All atheists are lying bullies who are hellbent on imposing their crap religion on the entire world. It is not going to happen. Ever.

    Now get your head our of your atheist rear end and say something truly intelligent for a change. And get off that white horse. It does not belong to you, goddammit.

  328. 328
    Virgil Cain says:

    Yes, Carpathian, theology doesn’t need morons asking irrelevant questions and getting all belligerent like a little child.

  329. 329
    Carpathian says:

    Mapou:

    Now get your head our of your atheist rear end and say something truly intelligent for a change. And get off that white horse. It does not belong to you, goddammit.

    Another comment from you that kids could look up to.

  330. 330
    Eric Anderson says:

    wd400:

    Seriously, so you are now defining every genetic change in an organism as a “mutation”? Good grief.

    I can’t tell whether you are hung up on a definition or whether you are actually making a substantive claim that no genetic changes occur in organisms that are not random mutations.

    Do you think it is true that there are no genetic changes in organisms that are not random mutations?

  331. 331
    Eric Anderson says:

    Zachriel @318:

    They can’t be unlinked.

    This, despite the numerous attempts by evolutionists to uncouple the two? We keep hearing over and over that evolutionary theory doesn’t have to address origin of life because it is a separate issue. In addition one might just as easily argue that the evidence should run the opposite direction from what you are requiring. Namely, if a materialistic origin of life cannot get off the ground then the materialistic origins story is in serious trouble. Requiring someone to believe a materialistic evolutionary post-origins history of life before you are willing to discuss how the initial organisms could have come about in the first place is certainly a strange approach. Oh, well. I tried. The offer stands if you ever change your mind.

  332. 332
    Eric Anderson says:

    Mapou, I hope you’ve moved on, but if not, please desist. It isn’t helpful to the discussion.

  333. 333
    EugeneS says:

    Zachriel,

    What Crick conjectured and was experimentally proven is very far from your characterization.

    In fact, what happens is critically different from what you think: the effect of RNA translation (=polypeptides) is not physically determined by the trigger (=RNA codons) evoking the effect. Rather it is determined by the properties of the tRNA charged with the ‘right’ amino acid, where the right amino acid is the one that logically corresponds to the codon via what is universally known as genetic code. The word ‘code’ is not a metaphor but reflects reality whereby a configuration of matter acts as a representation, token, sign of another configuration of matter. This is the adapter hypothesis experimentally verified.

    Now, you have to explain how on earth it is possible for logical relationships to arise solely based on the dynamics of the particles of matter. Explain semiosis in terms of physics alone.

    The RNA-world is very far from what you need to show because it does not solve the original problem while raising additional problems. RNAs to be of any useful size require control i.e. intelligent guidance of their chemical synthesis. Inanimate nature (bare physics or chemistry) does not care about control. Control is about logic. Therefore the RNA-world hypothesis is self-referential. It assumes what it purports to demonstrate.

    Good luck!

  334. 334
    Zachriel says:

    Eric Anderson: We keep hearing over and over that evolutionary theory doesn’t have to address origin of life because it is a separate issue.

    It simply doesn’t purport to do so. The Theory of Evolution is a scientific theory, and like all scientific theories is of limited domain. The Theory of Evolution constitutes what we do know, while abiogenesis is still obscure. It will take new insights to explain the origin of life and how it connects to evolutionary divergence.

    As for evidence concerning abiogenesis, it depends on all sorts of evidence, from chemistry to geology to biology, and understanding much of that requires the Theory of Evolution. For instance, you can’t have a rational discussion about abiogenesis if you are arguing whether the Earth is 6000 years old or not. Acceptance of standard geology is essential for the discussion, and that includes the fossil succession. Furthermore, lines of descent appear to join together, and this can’t be ignored as it points to a single origin.

    EugeneS: What Crick conjectured and was experimentally proven is very far from your characterization.

    Based on the hypothesis that RNA World preceded DNA World, Crick hypothesized that RNA comprised the primordial ribosome, and that the primary mechanism of modern ribosomes would also be based on RNA. This has been confirmed.

    EugeneS: RNAs to be of any useful size require control i.e. intelligent guidance of their chemical synthesis.

    RNA can act as memory and enzyme, including the capability of self-replication. Whatever barrier you are proposing simply doesn’t exist.

  335. 335
    EugeneS says:

    “Simply does not exist”

    Ignorance or lack of understanding of a real problem is hardly a justification for a simplistic model. The problem is an objective one, it is not my caprice and it is being recognised as an objective issue by a school of researchers.

    I think your paradigm needs a major shift, Zachriel. It is not the 20th century any more.

  336. 336
    Zachriel says:

    EugeneS: Ignorance or lack of understanding of a real problem is hardly a justification for a simplistic model.

    You are the one proposing some sort of barrier.

    Meanwhile, Crick makes a prediction based on a bold hypothesis, and the prediction is verified. That doesn’t ‘prove’ the hypothesis, but certainly provides support. Nor can it be explained away as merely a lucky guess.

  337. 337
    Virgil Cain says:

    Zachriel:

    RNA can act as memory and enzyme, including the capability of self-replication.

    The self-sustained replication required two RNAs. There wasn’t any “self-replication”.

    RNA has minimal catalytic properties and unguided processes can’t even explain those. “They just emerged, by golly”

  338. 338
    Virgil Cain says:

    As for evidence concerning abiogenesis, it depends on all sorts of evidence, from chemistry to geology to biology, and understanding much of that requires the Theory of Evolution. For instance,

    Well then please link to this alleged “Theory of Evolution” so we can get caught up on that requirement. 😛

  339. 339
    wd400 says:

    Seriously, so you are now defining every genetic change in an organism as a “mutation”? Good grief.

    Just me and, like, every biology textbook. And yes, there is no good evidence that organisms can produce mutations that are anything other than random with respect to fitness.

  340. 340
    Virgil Cain says:

    wd400 is correct as mutation refers to all genetic change. The reason, Eric, is because blind watchmaker evolution is the over-riding framework.

    And there is plenty of evidence of organisms producing mutations in response to stimuli. Our immune system is a good example. “Random with respect to fitness” is meaningless when discussing if mutations are happenstance events, ie accidents, errors and mistakes or are they guided, planned and intentional.

    Do you really think that some Intelligent Designer designed living organisms, with all that they require, including a just-so planet, and not design them with the ability to adapt? Really?

  341. 341
    EugeneS says:

    Zachriel:

    “You are the one proposing some sort of barrier.”

    Not just me and not proposing but pointing to its existence.

    Von Neumann, Wiener, Polaniy, Hoffmayer, Pattee, Abel.

    There is a whole number of researchers suggesting that matter-symbol complementarity is objective; that Information is objective, not subjective; that information is more than just mere combinatorialism and surprisal; that it primarily is a sequence of prescriptions for their complementary processor. No {data+prescription+processor} = no information.

    Wiener: Information is just information, not matter or energy.

    In fact, not all of those researchers are or were ready to go as far as systematically questioning their naturalistic stand. Nonetheless, they all have worked towards a whole new paradigm, a new school of thought, a new insight into life as symbolically controlled matter.

    An increasing number of biologists are now acknowledging that reductionism has exhausted itself and is no longer able to provide an adequate understanding of what life is.

  342. 342
  343. 343
    Zachriel says:

    EugeneS: Not just me and not proposing but pointing to its existence. Von Neumann …

    Well, apparently Von Neumann was unaware of such a barrier.

    Von Neumann: Today’s organisms are phylogenetically descended from others which were vastly simpler than they are, so much simpler, in fact, that it’s inconceivable how any kind of description of the later, complex organisms could have existed in the earlier one. It’s not easy to imagine in what sense a gene, which is probably a low order affair, can contain a description of the human being which will come from it. But in this case you can say that since the gene has its effect only within another human organism, it probably need not contain a complete description of what is to happen, but only a few cues for a few alternatives. However, this is not so in phylogenetic evolution. That starts from simple entities, surrounded by an unliving amorphous milieu, and produces something more complicated. Evidently, these organisms have the ability to produce something more complicated than themselves.

    While we have attempted to respond to your points, you have ignored our own, such as the success of Crick’s hypothesis. Lucky guess?

  344. 344
    EugeneS says:

    Zachriel,

    I think the problem is there are too many of you, guys, hiding behind the nick. I did say that what Crick proposed was the adapter hypothesis, which was what was actually verified. It could not and did not verify evolution. And that was irrespective of his motivations or justifications or whatever. That’s the beauty of science for you: people do something and the result is objective (supposing it is real science and not mere grant-spending). How they themselves or anyone else may interpret it, is a different matter. The current overarching interpretation is evolutionary, I accept it as reality. But it is an interpretation and this has very little to do with what actual researchers actually do in science.

    Don’t forget that what people actually propose in science and how even they themselves interpret it, are different things. As I say, not all of them would describe themselves as anything other than naturalists. But there you go, what they do is provide a foundation for an entirely different paradigm. Anyway, that is now my interpretation for you )

    Nonetheless, it only shows that the issue of semiosis in biology is an objective one. No less and no more than that.

    Interpretations are not the same as facts.

    “von Neumann was unaware…”

    Even Pattee is unaware ) as he, as a naturalist probably would do, hypothesizes that symbol-matter complimentarity despite being objective is not a consequence of some ontological dualism but an emergent property of matter.

    Well, I am personally not happy with having the concept of emergence on the table. What is it really? What does emergence mean and how can I measure it? Can a phenomenon be half-emerged?

    To me, emergence is a consequence of materialistic naturalism, nothing else. Naturalists are left with this misty concept void of real meaning as the only option in a (futile) attempt to explain nature naturalistically. Information does not fit into this picture (except in some reduced form of probability, entropy and surprisal).

  345. 345
    Zachriel says:

    EugeneS: I did say that what Crick proposed was the adapter hypothesis.

    We were referring to Crick’s 1968 hypothesis, based on RNA World, that ribosomes are ribozymes. This was only confirmed by Cech & Altman in the 1980s.
    http://www.nobelprize.org/nobe.....ticle.html

    While this doesn’t ‘prove’ the hypothesis, it is strong support, and can’t be written off as just a lucky guess.

  346. 346
    Virgil Cain says:

    We were referring to Crick’s 1968 hypothesis, based on RNA World, that ribosomes are ribozymes.

    LoL! So ribosomes wouldn’t be ribozymes absent the RNA world? Really?

    That has to be the most impotent correlation evah.

  347. 347
    EugeneS says:

    “While this doesn’t ‘prove’ the hypothesis, it is strong support, and can’t be written off as just a lucky guess.”

    Ok. Maybe. I can’t say anything here really because my background is totally different. But even with the RNA world, as little as I know about it, one has to confront the same issue of symbol-matter complimentarity, in addition to the issues of RNA world itself.

  348. 348
    Zachriel says:

    EugeneS: But even with the RNA world, one has to confront the same issue of symbol=matter complimentarity, in addition to the issues of RNA world itself.

    As RNA can act as both memory and processor, that resolves the issue.

  349. 349
    EugeneS says:

    No, unfortunately, it does not. Before one can say “can act” there must be a protocol establishing the relation between the symbol and what it denotes! That is the whole issue.

  350. 350
    Zachriel says:

    EugeneS: Before one can say “can act” there must be a protocol establishing the relation between the symbol and what it denotes!

    We know that RNA can act as both memory and processor, and that such a molecule can evolve. See Robertson & Joyce, Highly Efficient Self-Replicating RNA Enzymes, Chemistry & Biology 2014.

  351. 351
    Virgil Cain says:

    We know that RNA can act as both memory and processor, and that such a molecule can evolve.

    LoL! Intelligently designed RNAs can perform a self-sustained replication only in the presence of other intelligently designed, shorter RNAs. And nothing new evolved.

  352. 352
    Eric Anderson says:

    Virgil Cain @340:

    Do you really think that some Intelligent Designer designed living organisms, with all that they require, including a just-so planet, and not design them with the ability to adapt? Really?

    I hope you weren’t directing that comment at me. It should be clear from both the OP, where I brought up the point you are making in the first place, and my comments to wd400 throughout, that I think there is evidence for non-random genetic changes.

    I was just trying to make sure wd400 disagreed and that we weren’t dealing with a definitional issue. It is silly — one more piece of Darwinian baggage hampering the understanding of biology — that every genetic change would be called a “mutation.” But when that is all the anemic Darwinian paradigm has to bring to the table, then unfortunately every square peg gets pounded into a round hole. Fine. We can deal with the poor terminology and correct the past shortsightedness of evolutionary terminology by just talking about different categories of “mutations”: those that are random with respect to fitness and those that aren’t. Whatever. We can deal with the nonsensical terminology.

    What I was trying to pin down, and what we have confirmed, is that wd400 denies the existence of anything other than random-with-respect-to-fitness genetic changes. As I mentioned to him, I was hoping to get a chance later to do a post on that.

    You have been active in the discussion and seem to have access to Spetner’s latest book. Would you be willing to do a guest post on the evidence for non-random genetic changes? Doesn’t have to be a long essay. Just a couple of the examples he cites with some references. Let me know.

    Thanks,

  353. 353
    EugeneS says:

    Zachriel,

    No reference to any paper makes sense if you assume what you purport to prove. You still need a logical non-physical formal protocol before your molecule “can act like” something.

    Ignorance of this fact or lack of understanding of this fact is no justification.

  354. 354
    Virgil Cain says:

    Eric Anderson- That was for wd400 and it pertained to the definitional issue. My apologies for any confusion.

    I have access to both of Spetner’s books, as well as Shapiro’s, which he cites, and “Evolution in Four Dimensions”, which he also cites.

    But yes, I could write something and present it. Give me a week or so to put something together.

  355. 355
    Upright BiPed says:

    Hi Eugene,

    Zachriel is not going to acknowledge the distinction in the physics of the system. People do what profits them; it’s so much easier to just say “RNA can be both a memory and a catalyst” and be done with the details. He’ll not tell you what property of a representation he thinks makes it a representation. He has no reason to.

  356. 356
    EugeneS says:

    Hi UB,

    Yes, I guess that’s true, understandably.

  357. 357
    Zachriel says:

    EugeneS: No reference to any paper makes sense if you assume what you purport to prove.

    A hypothesis is a tentative assumption used to deduce empirical implications. The hypothesis was RNA World. The implication was that ribosomes would be ribozymes. Confirmation of this supports, but does not ‘prove’ the hypothesis. However, it is far from a trivial result.

    EugeneS: You still need a logical non-physical formal protocol before your molecule “can act like” something.

    Air molecules act to fill the available space. Are you hung up on semantics?

    Upright BiPed: it’s so much easier to just say “RNA can be both a memory and a catalyst” and be done with the details. He’ll not tell you what property of a representation he thinks makes it a representation.

    In the case of a replicating molecule, the memory is of the evolved sequence that is capable of replication, which is passed to new generations, with variation.

  358. 358
    Upright BiPed says:

    Eugene, for all your efforts, you’ll be comforted to know in Zachriel’s world, oxygen represernts rust in the presence of iron.

    🙂

    cheers…

  359. 359
    EugeneS says:

    UB,

    Zachriel has not got a clue.

    Clouds are talking to rivers, rivers talking to stones. The pansemiotic world of Zachriel 🙂

    ES

  360. 360
    Zachriel says:

    Upright BiPed: oxygen represernts rust in the presence of iron.

    Good example. Oxygen acts on iron to create rust. What is the “logical non-physical formal protocol”?

  361. 361
    Virgil Cain says:

    Oxygen acts on iron to create rust.

    Oxygen alone is not sufficient to cause rust.

  362. 362
    Upright BiPed says:

    Eugene,

    Zachriel has not got a clue.

    One would not need to look any further than #360 to see that.

  363. 363
    Upright BiPed says:

    Good example. Oxygen acts on iron to create rust. What is the “logical non-physical formal protocol”?

    Zach, there’s not one; that’s the whole point. In a genuine translation system (like protein synthesis) the product of the system is not determined by the physical properties of the representation being translated.

    Welcome to 1958.

  364. 364
    Mung says:

    OT: I wonder who sent in the questions that led to this episode of ID the Future.

    ID Inquiry: Jonathan Wells on Codes in Biology

  365. 365
    Zachriel says:

    Upright BiPed: there’s not one; That’s the whole point.

    The claim was “You still need a logical, non-physical formal protocol before your molecule can act like something.” So water molecules can’t act “wet” unless there’s a logical, non-physical formal protocol.

    Upright BiPed: In a genuine translation system (like protein synthesis) the product of the system is not determined by the physical properties of the representation being translated.

    Such a system can evolve from simpler relationships.

  366. 366
    Upright BiPed says:

    The claim was “You still need a logical, non-physical formal protocol before your molecule can act like something.” So water molecules can’t act “wet” unless there’s a logical, non-physical formal protocol.

    You’ve lost your place. Let me help:

    UB: Eugene, for all your efforts, you’ll be comforted to know in Zachriel’s world, oxygen represents rust in the presence of iron.

    Zachriel: Good example. Oxygen acts on iron to create rust. What is the “logical non-physical formal protocol”?

    First Off, I was having a little fun with you repeatedly saying RNA can act as memory and catalyst and always pushing research that involves an entirely different physical event than the translation of DNA into protein. In their key physical features, these two processes have absolutely nothing in common, and one has no means to produce the kinds of effects that the other produces. Your favored scenario has neither representations nor the translation of representations. Hence, the little comment about oxygen representing rust to iron.

    But then you asked me to tell you where there’s a protocol in the formation of rust.

    So I answered you: “there’s not one; that’s the whole point. In a genuine translation system (like protein synthesis) the product of the system is not determined by the physical properties of the representation being translated.”

    And then you avoided that answer in your last response.

    You left out this entire point: In a genuine translation system (like protein synthesis) the product of the system is not determined by the physical properties of the representation being translated. That was the clarification that you asked for, but I supposed you’ve read Joyce, as I have, and you’re already aware that the product of that system is entirely determined by the properties of the RNA you are calling “memory”, and this is most likely why you made that silly comment about water being wet.

    Either that, or you actually don’t have any idea what the issues are. Either way, it doesn’t really matter. This is particularly true if all you can do is repeat the mantra “RNA can act as a memory and a catalyst”. It’s irrelevant to the process – in fact, it’s the very limitation that translation does away with. You can’t prescribe a protein from the dynamic properties of nucleotides. That’s why the cell doesn’t do it that way.

  367. 367
    Upright BiPed says:

    Such a system can evolve from simpler relationships.

    yawn

  368. 368
    EugeneS says:

    Zachriel,

    Good example. Oxygen acts on iron to create rust. What is the “logical non-physical formal protocol”?

    I am sure UB is right. You have not got a clue what the problem is. That is the whole difference!

    In chemical reactions or physical interactions, there is no protocol in the same sense as there is one in the RNA translation system. The whole point is that there is physical discontituity between RNA codons coming in and the polypeptide coming out.

    If there was a single deterministic law-like necessary physical link between the RNA and the polypeptide, there could only be produced at best a single identical regular low-information polypeptide sequence every time regardless. In reality, a single cell produces of the order of 400 different proteins.

    It is this discontinuity between the trigger (data) and the effect (the processor processing the data) that enables information processing in any physical system not necessarily RNA translation. Without it, there would be produced only redundant low-informational regular structures like crystal lattice that are entirely due to the laws of nature (minimum potential energy).

    The rules of translation are categorically not the same as the laws of nature.

    The fact that there is no single physical link between RNA and polypeptide is one of the key enablers of life. The physical discontinuity makes it possible to front-load a protocol into the physical system and make it a physical system executing rules. Rules are logical relations between the trigger(s) and the effect(s) of the trigger. It is only in this type of material systems that information transfer becomes at all possible.

    The rules of RNA translation are irreducible to the laws of nature in exactly the same way as the phonemes of a human language are irreducible to sound waves the vocal chords produce. Likewise the rules of chess are irreducible to the laws of the motion of chessmen.

    I think you have a gap in understanding here you need to close yourself.

  369. 369
    Zachriel says:

    Upright BiPed: First Off, I was having a little fun

    That’s fine. We took the discussion back to the original claim.

    Upright BiPed: So I answered you: “there’s not one; that’s the whole point. In a genuine translation system (like protein synthesis) the product of the system is not determined by the physical properties of the representation being translated.”

    That wasn’t the claim, but that “You still need a logical, non-physical formal protocol before your molecule can act like something.” Molecules act like something all the time.

    Upright BiPed: You left out this entire point: In a genuine translation system (like protein synthesis) the product of the system is not determined by the physical properties of the representation being translated.

    Indeed, we directly answered by saying it could evolve from simpler relationships, which you ignored.

    Upright BiPed: yawn

    EugeneS: The fact that there is no single physical link between RNA and polypeptide is one of the key enablers of life.

    It’s a key feature of extant life, but most researchers believe the translation system evolved from a simpler system. You are attempting to rule out such an evolutionary history a priori, but invoking woo is not an argument.

  370. 370
    Virgil Cain says:

    It’s a key feature of extant life, but most researchers believe the translation system evolved from a simpler system.

    1- There isn’t any evidence for a simpler system

    2- There isn’t any evidence that today’s system could evolve via drift and natural selection from a primitive system

    3- There isn’t any evidence that drift and natural selection can produce a simpler system.

  371. 371
    EugeneS says:

    Zachriel,

    “Molecules act like something all the time.”

    You deliberately conflate the different meanings. I have reason to believe you are doing it knowingly.

    “It’s a key feature of extant life, but most researchers believe the translation system evolved from a simpler system. You are attempting to rule out such an evolutionary history a priori, but invoking woo is not an argument.”

    I don’t care what somebody believes. The world is full of strange people. If there were stupid researchers who would wish to experimentally disprove the validity of the 2nd law, why should I care even if they were in a majority?!

    You still don’t get the issue: physicality cannot be responsible for the logic of rules. Indeed, physicality itself is logical, due to the laws of nature. It is here that you want to deliberately conflate the definitions.

    Nonetheless, physicality cannot be responsible for the appearance of logic that is incapsulated in material systems in the form of rules of behaviour on top of the laws of nature. The only thing physicality can do as regards rules, is allow them to be loaded into material systems, which it does.

    The inability to understand the issue is not an argument. Calling it strange names such as ’emergence’ is not an argument either.

    If you want to consider it a claim, you are free to do so. This claim is based on evidence. And it is as strong as the 2nd law. The logic present in material systems in the form of rules is not an emergent property of matter simply because physicality is indifferent to it. I stand by it.

    You have no evidence to the contrary. You can choose to remain ignorant. I cannot help, it is your choice. But from your responses I can see you have a lack of understanding. The real problem is that you prevaricate. It blocks you from being able to understand it.

  372. 372
    Zachriel says:

    EugeneS: You still don’t get the issue: physicality cannot be responsible for the logic of rules.

    Fundamental logic can be expressed mechanically with a few simple processes.

    EugeneS: The inability to understand the issue is not an argument.

    It’s not an argument, but a claim. It seems obvious to you, so you think merely stating the claim is sufficient, but it’s not. It’s just rewording of your belief.

  373. 373
    EugeneS says:

    Yes, it is my belief. Yes, it seems obvious to me. And I explained why many times: because inanimate nature does not care about rules of behavior.

    For a snooker ball on a horizontal plane, nature cannot distinguish between different points on the plane: any point is a point of equilibrium for the ball. These equilibrium states are called indifferent, Zachriel. Welcome to secondary school physics. When you integrate the equations of motion, a constant enters the equation. The presence of this constant is another manifestation of the same indifference.

    However, human intelligence can distinguish between the indifferent equilibrium states. Exactly by imposing rules. E.g. by drawing cells on the snooker table and assigning different utility values to different cells.

    The consumer unit switch is acted upon by the same physical forces regardless of whether it is ON or OFF. Nature does not care whether electric current flows through the wire. It takes intelligence to build rule-based material systems generating utility.

    “Fundamental logic can be expressed mechanically with a few simple processes.”

    You always appeal to simplicity. A = A, Zachriel, so what?

    What processes? How many exactly? How simple? What is ‘simple’? What is ‘mechanical’? What is ‘expressed’? What is ‘fundamental’?

  374. 374
    Zachriel says:

    EugeneS: And I explained why many times: because inanimate nature does not care about rules of behavior.

    And yet nature forms stars and planets and galaxies and rivers and clouds and storms and crystals, conforming to all sorts of rules.

    EugeneS: For a snooker ball on a horizontal plane, nature cannot distinguish between different points on the plane: any point is a point of equilibrium for the ball.

    Sure, and planes and equilibriums and and rolling objects exist in nature. So? You still haven’t made an argument. You just reword your claim.

  375. 375
    EugeneS says:

    Zachriel #374,

    Pathetic. A 6-th year school child can distinguish between the rules of a game and the laws of nature.

  376. 376
    Zachriel says:

    EugeneS: A 6-th year school child can distinguish between the rules of a game and the laws of nature.

    Rules of a game are a group of principles governing conduct when playing, especially competitively.

    Laws of nature are observed regularities in the physical world.

  377. 377
    Virgil Cain says:

    And yet nature forms stars and planets and galaxies and rivers and clouds and storms and crystals, conforming to all sorts of rules.

    And yet nature couldn’t have formed nature.

  378. 378
    Virgil Cain says:

    Eric Anderson @ 352- Here it is:

    In 1997 “Not By Chance” by Lee Spetner was published. In it he argued for a “non-random evolutionary hypothesis” which had a mechanism of “built-in responses to environmental cues” at its heart. Some mutations happened just when they were needed. And some happened at just the right place to be effective. And even others, called transposons aka jumping genes, carried within its DNA coding sequence the coding for two of the enzymes required for it to be able to move around.

    A transposon has in it sections of DNA that encode two of the enzymes it needs to carry out its job. The cell itself contributes the other necessary enzymes. The motion of these genetic elements about to produce the above mutations has been found to be a complex process and we probably haven’t yet discovered all the complexity. But because no one knows why they occur, many geneticists have assumed they occur only by chance. I find it hard to believe that a process as precise and as well controlled as the transposition of genetic elements happens only by chance. Some scientists tend to call a mechanism random before we learn what it really does. If the source of variation for evolution were point mutations, we could say the variation is random. But if the source of variation is the complex process of transposition, then there is no justification for saying that evolution is based on random events. Dr Lee Spetner “Not By Chance” page 44

    Barbara McClintock was laughed at when she elucidated her discovery of jumping genes for the simple reason they have the characteristics of being under some control.

    The “non-random evolutionary hypothesis” applies to individuals- individuals do evolve, ie change at the genetic level.

    Enter 2006 and the publication of “Evolution in Four Dimensions” by Eva Jablonka and Marion J. Lamb and the elucidation of epigenetics, ie “built-in responses to environmental cues”. I couldn’t stop thinking about “Not By Chance” wondering if Lee Spetner had read it and if he felt vindicated by it. Organisms are designed with different levels of possible variation. For example there is a possible variation with how the existing genes get expressed and another is changing the actual genes such that it changes the proteins. Change the regulation of the gene or change the gene itself. Lenski’s E. coli changed the regulation of a gene by duplicating it and putting it under control of a promoter that allowed for it to be expressed in an aerobic environment. It was an environmental factor, the presence of O2, which repressed the gene. It was another environmental factor, the presence of citrate, which made getting that gene expressed beneficial.

    “Evolution in Four Dimensions” is a good book to have around. They describe experiments of microsurgery on Paramecium. A piece of the cortex was cut out, rotated 180 degrees and reinserted. The offspring inherited the change. Lamarck 101.

    Then came 2011 and the publication of “Evolution: A View from the 21st Century” by James A. Shapiro (a colleague of Dr. McClintock) and even more support for the “non-random evolutionary hypothesis” and “built-in responses to environmental cues”. Again I wondered about Dr Spetner and if he was reading this book too. The book starts out talking about “Sensing, Signaling, and Decision Making in Cell Reproduction” and has a table of “Examples of Targeted Genetic Engineering”. Of course he thinks it all evolved because obviously that is what evolution does or maybe due to coercion from fellow U Chicago Professor Jerry Coyne that is what he had to say to prevent being attacked. But I digress, the book is well worth the read and there is evidence that some mutations happen just when they are needed. They are not random with respect to fitness; it is the organism doing some rearranging to stay fit.

    In 2014 Lee Spetner’s “the Evolution Revolution”- Why Thinking People are Rethinking the Theory of Evolution” was publisged and although he doesn’t cite “Evolution in Four Dimensions” he does cite Jablonka’s work on epigentics. He does cite both Shapiro’s work and the book “Evolution: A View from the 21st Century”.

    Moving along Lee Spetner cites several cases in which evolution happened much too rapidly to be accountable for genetic accidents and have all the appearances to have been triggered by the environment:

    1- Studies on daisy and daisy-like plants and their seed dispersal mechanisms. On the mainland the seeds are packaged such that the wind can carry them great distances- little white fluff-balls floating endlessly on a warm summer’s breeze. But on a small island that isn’t a good strategy. Once transplanted from mainland to small island they lose that seed-dispersal ability in just a few years – Cody & Overton (1996) “Short Term Evolution of reduced dispersal in Island Plant Populations” Journal of Ecology 84(1): 53-61

    2- Rhagoletis pomonella– went from feeding solely on hawthorn, to apples and onto cherries, roses and pears. Studies show the hawthorn and apple flies differ genetically

    3- Guppies- Cichlid fish prey on large mature guppies and killifish prey on small immature guppies. When cichlids are their main predator in the environment the guppies mature earlier and have many small offspring which evade the cichlids. When killifish are their main predator the guppies mature late and have fewer but larger offspring which can evade the killifish. He cites several papers that have Reznick as one of or the main contributor

    4- Lizards and rapid evolution- Losos (2001) “Evolution: A Lizard’s Tale” Scientific American 284(3): 64-69; Losos and Schoener (1997) “Adaptive differentiation following experimental island colonization in Anolis lizard” Nature 387: 70-73; and other articles by Losos and/ or Schoener

    5- Finches- Lee Spetner was here on UD and posted this one See here

    He reiterates his hypothesis is different in that with his individuals do evolve

    —–

    EA: Posted as a new head post here:

    http://www.uncommondescent.com.....ypothesis/

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