Larry Moran defends Paul Nelson!

_{Vincent Torley

December 11, 2012

Intelligent Design}

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On Sunday, November 25, Dr. Paul Nelson gave a video presentation at Pastor Rick Warren’s Saddleback Church in southern California, entitled, Darwin or Design? Watching the video, I thought that he did a brilliant job in exposing the inadequacy of natural selection to account for major evolutionary changes – especially, the origin of animal body plans. I strongly recommend that Uncommon Descent readers take the time to watch Dr. Nelson’s presentation. It’s one of the best critiques of neo-Darwinian evolution that I’ve ever seen. Devastating is the only word I can use to characterize it.

How Animal Body Plans expose the inadequacy of Neo-Darwinian Evolution, in a nutshell

Dr. Nelson has kindly summarized his case, in a comment he made over on Why Evolution Is True:

Mutations that disrupt body plan formation are inevitably deleterious. (There’s only one class of exceptions; see below.) This is the main signal emerging from over 100 years of mutagenesis in Drosophila.

Text from one of my Saddleback slides:

1. Animal body plans are built in each generation by a stepwise process, from the fertilized egg to the many cells of the adult. The earliest stages in this process determine what follows.

2. Thus, to change — that is, to evolve — any body plan, mutations expressed early in development must occur, be viable, and be stably transmitted to offspring.

3. But such early-acting mutations of global effect are those least likely to be tolerated by the embryo.

Losses of structures are the only exception to this otherwise universal generalization about animal development and evolution. Many species will tolerate phenotypic losses if their local (environmental) circumstances are favorable. Hence island or cave fauna often lose (for instance) wings or eyes.

What that means is that even after 100 years of careful investigation, there’s no way known to science that unguided changes are capable of generating new, viable body plans for animals. And yet at some point in the past, these plans must have been generated: there are dozens of different phyla of animals, each with its own body plan. Dr. Nelson concludes that only a foresighted mechanism – intelligence – could have done the job.

Professor Coyne’s piqued response to Nelson

One person who hasn’t watched Dr. Nelson’s presentation (but who really should have) is Professor Jerry Coyne, who forthrightly declared in a recent post entitled, A Marshall McLuhan moment with creationist Paul Nelson: “I haven’t yet watched Nelson’s talk (some reader please do it and report back).” Among the 141 comments (as at the time of writing), I couldn’t find one which even attempted to provide a synopsis of Dr. Nelson’s talk. I found one sneering putdown which accused Nelson of mis-representing evolution, but made no attempt to refute his arguments, and another post by someone who admitted that (s)he was still “trying to at least have a general understanding of what biology is and how it works,” and who described the video as “extremely deceptive” (which it certainly wasn’t).

One thing I should mention about Dr. Nelson is that he has a Ph.D. in philosophy of biology and evolutionary theory from the University of Chicago, where Professor Coyne teaches. It is fair to assume, then, that Dr. Nelson is familiar with the views of leading thinkers in the field of evolutionary biology.

In his post, Professor Coyne quoted from an email that he’d received last week from Dr. Nelson, inviting him to comment on the presentation he gave at Saddleback Church. For Coyne’s benefit, Dr. Nelson summarized his argument as follows:

… I made a case (a) that natural selection is quite real, but (b) that the process faces genuine limits, set by the logic of selection itself, to explain macroevolution. (Emphases mine – VJT.)

Clear enough, one would have thought. In the same email, Dr. Nelson also criticized Professor Coyne for declaring, in recent posts on Why Evolution Is True, that the views of Dr. James Shapiro on natural selection are unrepresentative of biologists. Here’s the relevant excerpt:

Skepticism about the efficacy of natural selection is widespread within evolutionary biology (see below). Jim Shapiro is hardly alone in this regard. So when you tell your WEIT audience that natural selection is the only game in town for building complex adaptations, you can expect two consequences:

1. Readers who already know about the thinking of workers such as Eric Davidson, Michael Lynch, Andreas Wagner, John Gerhart & Marc Kirschner, or Scott Gilbert (all of whom, among many others, have recently expressed frank doubts about selection) must discount what you say about the centrality of natural selection to evolutionary theory — because they know that just isn’t so.

2. Readers who do not already know about Davidson, Lynch, etc. — upon coming across their ideas — must wonder why you told them that natural selection is the sine qua non of evolutionary explanation.

Either outcome is bad.

Nowhere in his email did Dr. Nelson deny the reality of natural selection, or its role in accounting for adaptations. What Nelson did deny is the proposition that all evolutionary biologists regard it as central to evolutionary theory, and view it as the only “game in town” for building complex adaptations.

Professor Moran defends Dr. Nelson

Even Intelligent Design critic Professor Larry Moran, of the University of Toronto, thought that Dr. Nelson had correctly paraphrased the views of the five scientists listed above. In a comment to Coyne’s post, he wrote:

I think this is basically correct. All of these authors question in some way or another the “centrality” of natural selection to evolutionary theory. We can quibble about the exact meaning of words and sentences but I, for one, don’t think Nelson is way off base here. Perhaps Nelson shouldn’t have said “expressed doubts about selection” because it could be taken to mean that the authors deny that positive natural selection exists. I don’t think that’s what Paul Nelson meant. He may be an IDiot but he’s not that stupid.

Sadly, however, Professor Coyne appears to have misconstrued Dr. Nelson’s email from the start, as belittling the importance of natural selection, when Dr. Nelson was really attacking its centrality in accounting for complex adaptations. In his post, he wrote:

True, I’ve had scientific disagreements with Davidson, Gerhart, and Kirschner about theories of “evolvability” and “modularity,” but I never saw them claiming that natural selection is unimportant in forging the adaptations of organisms. (Emphasis mine – VJT.)

Circling the wagons

But Coyne went further. He then emailed five of the biologists listed by Nelson (Davidson, Lynch, Wagner, Gerhart and Kirschner) and asked them to comment on Dr. Nelson’s claims. (Coyne enclosed Nelson’s email with his own.) Here is a selection from Professor Coyne’s email:

… I have read the papers of many of you, and while I know that several of you question aspects of modern evolutionary theory, I wasn’t aware that any of you denied the efficacy of selection in accounting for adaptations….

At any rate, if Nelson has accurately characterized your views, do let me know….

Professor Moran defends Dr. Nelson again!

Am I the only one who thinks that Professor Coyne was asking these scientists a loaded question? Evidently not. Professor Larry Moran was of the same opinion. In a comment to Coyne’s post, he wrote:

I don’t think Jerry’s question is fair. Paul Nelson was not accusing these authors of denying a role for natural selection in “obvious adaptations.”

The replies that Professor Coyne got back from these biologists affirmed their belief in the importance of natural selection to evolution – which Nelson had never contested in the first place! Rather, what Nelson claimed was that these scientists denied that natural selection was “the only game in town for building complex adaptations.” None of the replies Coyne received showed that Nelson was wrong on this vital point. I’ve quoted key excerpts from these scientists’ responses, so that readers can judge for themselves. Emphases are mine.

Davidson:

Of course I would not disagree for one second about the importance of adaptive selection for species specific characters of all kinds, whether on protein or regulatory sequences.

Lynch:

The ID crowd tends to misinterpret my embracing of what I call “nonadaptive” mechanisms of evolution (drift, mutation, and recombination) as implying a rejection of Darwinian processes.

You are correct that it is wrong to characterize me as someone who doesn’t believe in the efficacy of natural selection.

Wagner

I do believe that natural selection is essential for evolutionary adaptation. I also believe that we can understand the diversity of life through entirely natural causes, natural selection being an important one of them.

Gerhart

I haven’t tracked down what Dr. Nelson said we said about natural selection — presumably that we don’t think it’s important. We do think it’s important, and our writing about the means by which organisms generate phenotypic variation wouldn’t make any sense without it.

Kirschner

I really do not know why any thinking person would believe that I question natural selection or the role of genetic change in evolution as agreed upon by population biologists… Whether evolutionary biologists dismisses what we write as beside the point, I still endorse the basic idea of genetic variation and selection. It is just that to go beyond the genes to the phenotype, which after all is under selection, we may want to learn how the phenotype is created.

Coyne’s Marshall McLuhan moment

There is a famous scene in Annie Hall in which Woody Allen and Diane Keaton are waiting in line for a movie, when an academic behind them starts pontificating about Fellini and Beckett. Allen is getting more and more annoyed by the pretentious bore. Finally, when the man starts talking about Marshall McLuhan, Allen steps out of the movie frame and confronts him with the real Marshall McLuhan, who tells the academic, “You know nothing about my work.” Allen then says, “Wouldn’t it be great if life were really like this?”

Professor Coyne evidently thought he’d had a Marshall McLuhan moment, for he seized on the responses he got from the five scientists he emailed, and waved them in front of his readers, concluding his post with the following message:

Nelson can consider himself pwned, though of course he’ll take the above and somehow make it seem that they agree with him… Nelson is either an outright liar or is completely ignorant of the views of these biologists. Nelson either hasn’t read their work, hasn’t understood it, or has read it and understood it but distorted it. Regardless, it’s ignorance, willful or not. But this is what creationists must do if they want to make their ridiculous views seem respectable.

Memo to Professor Coyne: there’s a big, big difference between saying that natural selection is “important” or even “essential” for evolutionary adaptation, and saying it’s “the only game in town for building complex adaptations.” And speaking of willful ignorance, why did you make no attempt to present Dr. Nelson’s case against neo-Darwinian evolution and then refute it? If I didn’t know better, I’d say you were hiding something.

UPDATE:
When Dr. Nelson, in one of his replies to Professor Coyne’s post, adduced quotes from one of the scientists he’d cited (Michael Lynch) demonstrating that Lynch is much more of a skeptic of natural selection than most people would allow, Professor Moran began to get cold feet about his defense of Nelson. In a follow-up comment, he challenged Nelson, saying:

… I was giving you the benefit of the doubt.

Do you, or do you not, claim that Lynch and the others deny the existence of natural selection? Do you, or do you not, claim that all of these authors deny that adaptations are caused primarily by natural selection?

I will take your refusal to answer as evidence that Jerry was right and you really are ignorant (or lying) about the works of these authors.

Dr. Nelson’s reply was direct and to the point:

Seriously, Larry — nowhere did I say that any of the authors under discussion denied (a) the existence of natural selection, or that (b) natural selection produces adaptations.

Please re-read my original email to Jerry, which he quotes above. My point concerned the central role or relative strength of selection, as compared to other possible processes, in the thinking of workers such as Michael Lynch. Anyone still reading this thread should familiarize themselves with Lynch’s now-classic 2007 paper on the topic, “The frailty of adaptive hypotheses for the origins of organismal complexity,” PNAS May 15, 2007, available as open access here:

http://www.pnas.org/content/104/suppl.1/8597.full

Is Dr. Nelson misquoting Lynch? You be the judge

I’d like to close with a collection of quotes from The frailty of adaptive hypotheses for the origins of organismal complexity (PNAS 2007 104 (Suppl 1) 8597-8604; published ahead of print May 9, 2007, doi:10.1073/pnas.0702207104) by Professor Michael Lynch, one of the scientists cited by Dr. Nelson in his email. My thanks to Dr. Nelson for providing the link in the comment above. Let readers judge whether Dr. Nelson has quoted him fairly:

…It has long been known that natural selection is just one of several mechanisms of evolutionary change, but the myth that all of evolution can be explained by adaptation continues to be perpetuated by our continued homage to Darwin’s treatise (6) in the popular literature. For example, Dawkins’ (7–9) agenda to spread the word on the awesome power of natural selection has been quite successful, but it has come at the expense of reference to any other mechanisms, a view that is in some ways profoundly misleading…

What is in question is whether natural selection is a necessary or sufficient force to explain the emergence of the genomic and cellular features central to the building of complex organisms…

First, evolution is a population-genetic process governed by four fundamental forces. Darwin (6) articulated one of those forces, the process of natural selection, for which an elaborate theory in terms of genotype frequencies now exists (10, 11). The remaining three evolutionary forces are nonadaptive in the sense that they are not a function of the fitness properties of individuals: mutation is the ultimate source of variation on which natural selection acts, recombination assorts variation within and among chromosomes, and genetic drift ensures that gene frequencies will deviate a bit from generation to generation independent of other forces. Given the century of work devoted to the study of evolution, it is reasonable to conclude that these four broad classes encompass all of the fundamental forces of evolution.

Second, all four major forces play a substantial role in genomic evolution. It is impossible to understand evolution purely in terms of natural selection, and many aspects of genomic, cellular, and developmental evolution can only be understood by invoking a negligible level of adaptive involvement (12, 13).

Natural selection is just one of four primary evolutionary forces. [Quote from Table 1]

There is no evidence at any level of biological organization that natural selection is a directional force encouraging complexity. In contrast, substantial evidence exists that a reduction in the efficiency of selection drives the evolution of genomic complexity.[Quote from Table 1]

The literature is permeated with dogmatic statements that natural selection is the only guiding force of evolution, with mutation creating variation but never controlling the ultimate direction of evolutionary change (for a review, see ref. 17)…

Most biologists are so convinced that all aspects of biodiversity arise from adaptive processes that virtually no attention is given to the null hypothesis of neutral evolution, despite the availability of methods to do so (32–34)…

The hypothesis that expansions in the complexity of genomic architecture are largely driven by nonadaptive evolutionary forces is capable of explaining a wide range of previously disconnected observations (13, 40) (Table 2). This theory may be viewed as overly simplistic. However, simply making the counterclaim that natural selection is all powerful (without any direct evidence) is not much different from invoking an intelligent designer (without any direct evidence)…

Certainly, many of the above-mentioned embellishments of eukaryotic genes have adaptive functions in today’s multicellular species, but observations on current deployment may have little bearing on matters of initial origins…

Multicellularity is widely viewed as a unique attribute of eukaryotes, somehow made possible by the origin of a more complex cellular architecture and, without question, with the assistance of natural selection. However, it is difficult to defend this assertion in any formal way…

Nevertheless, King (45) states that “this historical predisposition of eukaryotes to the unicellular lifestyle begs the question of what selective advantages might have been conferred by the transition to multicellularity;” and Jacob (46) argues that “it is natural selection that gives direction to changes, orients chance, and slowly, progressively produces more complex structures, new organs, and new species.” The vast majority of biologists almost certainly agree with such statements. But where is the direct supportive evidence for the assumption that complexity is rooted in adaptive processes? No existing observations support such a claim, and given the massive global dominance of unicellular species over multicellular eukaryotes, both in terms of species richness and numbers of individuals, if there is an advantage of organismal complexity, one can only marvel at the inability of natural selection to promote it. Multicellular species experience reduced population sizes, reduced recombination rates, and increased deleterious mutation rates, all of which diminish the efficiency of selection (13). It may be no coincidence that such species also have substantially higher extinction rates than do unicellular taxa (47, 48)…

…[C]ontrary to popular belief, natural selection may not only be an insufficient mechanism for the origin of genetic modularity, but population-genetic environments that maximize the efficiency of natural selection may actually promote the opposite situation, alleles under unified transcriptional control…

Although those who promote the concept of the adaptive evolution of the above features are by no means intelligent-design advocates, the burden of evidence for invoking an all-powerful guiding hand of natural selection should be no less stringent than one would demand of a creationist…

If complexity, modularity, evolvability, and/or robustness are entirely products of adaptive processes, then where is the evidence? What are the expected patterns of evolution of such properties in the absence of selection, and what types of observations would be acceptable as a falsification of a null, nonadaptive hypothesis?

Neutral evolution to the rescue?

Lynch, it seems, is a big fan of neutral evolution as an explanation for complexity. And it looks like Professor P.Z. Myers agrees with him, for in a recent post entitled, Complexity is not usually the product of selection, which criticizes evolutionist John Wilkins, Myers writes:

…[C]omplex traits are the product of selection? Come on, John, you know better than that. Even the creationists get this one right when they argue that there may not be adaptive paths that take you step by step to complex innovations, especially not paths where fitness doesn’t increase incrementally at each step. Their problem is that they don’t understand any other mechanisms at all well (and they don’t understand selection that well, either), so they think it’s an evolution-stopper — but you should know better.

This is the trap Michael Behe falls into, too. It’s the assumption that you have to have an adaptive scenario for every step, and an inability to imagine non-adaptive solutions. I think if selection were always the rule, then we’d never have evolved beyond prokaryotes — all that fancy stuff eukaryotes added just gets in the way of the one true business of evolution, reproduction.

So let’s work through a hypothetical scenario of increasing complexity, and you try to see where selection is essential. And then I’ll give some real world examples….

The bottom line is that you cannot easily explain most increases in complexity with adaptationist rationales. You have to consider chance as far more important, and far more likely to produced elaborations…

Even in something as specific as the physiological function of a biochemical pathway, adaptation isn’t the complete answer, and evolution relies on neutral or nearly neutral precursor events to produce greater functional complexity.

Readers who want to check out Professor Michael Behe’s responses to Thornton (a critic of Behe’s work, whom Myers cites in his article) can go here and here (the latter link has a good collection of articles).

Professor Larry Moran has endorsed P.Z.Myers’ article, in a recent post of his own, entitled, On the Evolution of Complexity (11 December 2012), in which he writes:

Can you go from some simple character to a more complex feature without invoking natural selection? Yes, you can. Complex features can evolve by nonadaptive means.

Missing the point of Dr. Nelson’s argument?

While I appreciate the general point that these scientists are trying to make, that neutral or nearly neutral random events can sometimes generate functional complexity, it seems to miss the whole point of Dr. Nelson’s argument, that mutations in the genes that control animals’ body plan aren’t just neutral – they’re deleterious. Either that, or they’re mutations that reduce functionality, rather than increasing it. If Dr. Nelson is right about these points, then his argument for the necessity of Intelligent Design is a telling one, not only against neo-Darwinists but also against advocates of a greater role for random, neutral evolutionary changes, such as Lynch.

Would it be too much to hope that one of the evolutionary biologists mentioned in this post will actually take the time and trouble to address Dr. Nelson’s original argument, which he made in his video presentation, that unguided processes – whether they be natural selection, mutation, recombination or genetic drift – are incapable of explaining the origin of animal body plans? Or would that be too difficult? Time will tell. Meanwhile, I’m not holding my breath. Expect a lot more academic obfuscation in the days to come.

Comments

The typical popular presentation of Darwinian evolution — the sort you get in Carl Sagan, Bertrand Russell, etc. — is basically Epicurean. And so, aside from any biological objections to the particulars of neo-Darwinism (ID criticisms regarding irreducible complexity or other biological criticisms coming from Margulis etc.), Darwinism as an account of origins suffers from all the philosophical defects you have outlined. (And of course, as a Platonist, I reject Epicureanism as well.)
This brings me to a topic I'm keenly interested in (whether others here are as well remains to be seen!). Namely, how promising is it, do you think, to develop and promote non-Epicurean interpretations of Darwinism? Is an Aristotelian Darwinism viable? A Platonic Darwinism? How about a Hegelian Darwinism (if one can avoid Haeckel's mistakes)? In ordinary usage, I believe, "Darwinism" sometimes functions as a term for a metaphysical view and sometimes as a term for an empirical theory. How to distinguish between them? Here's a suggestion: if "Darwinism" is taken as having any implications at all for ethics or politics, then it's being used as metaphysics. On the one hand, I don't want to say that Epicurean metaphysics is the only metaphysics that makes sense of Darwinism, to the extent that Darwinism is an empirical theory at all. On the other hand, I don't want to say that it's a completely free, almost arbitrary choice as to which metaphysics makes sense of some given scientific theory. If I had to identify my own views, I would say that I'm an Aristotelian about organisms, in that I do think there's some really profound insight in his distinction between morphe and hyle. But I don't think the reality of form requires that forms be permanent, and in that regard I'm willing to strike a deal between Aristotelianism and Darwinism. That is, I read Darwinism as a theory of morphogenesis: of the origins of forms. What it's not, though, is a theory about the origin of form-as-such, which is basically what we're looking for in abiogenesis. (Maybe we can call it "the problem of amorphogenesis"?)Kantian Naturalist_{December 14, 2012
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haha. Non-Kantian Non-Naturalist!Mung_{December 13, 2012
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Timaeus, let's just say that I use a pseudonym here because I want to conceal my real identity, and that means glossing over certain parts of my biography. By "some philosophy", I mean that, of all the philosophy that there is, I studied some of it. :)Kantian Naturalist_{December 13, 2012
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Kantian: The typical popular presentation of Darwinian evolution -- the sort you get in Carl Sagan, Bertrand Russell, etc. -- is basically Epicurean. And so, aside from any biological objections to the particulars of neo-Darwinism (ID criticisms regarding irreducible complexity or other biological criticisms coming from Margulis etc.), Darwinism as an account of origins suffers from all the philosophical defects you have outlined. (And of course, as a Platonist, I reject Epicureanism as well.) When you say you studied "some philosophy" in graduate school, that is puzzling to me. Graduate school doesn't usually allow for double majors! So you would either be studying philosophy, or something else. But possibly your graduate program was in a subject that overlaps with philosophy -- political theory, or religion, or history/philosophy of science?Timaeus_{December 13, 2012
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BA 77, the information and links you provide are greatly appreciated. Thanks.bpragmatic_{December 13, 2012
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tm:
...my mind is not so blown that I am emotionally required to question basic facts, like the fact that DNA contains ALL the information necessary for biological systems to run.
No need to let logic or facts get in the way then.Mung_{December 13, 2012
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In other news, people talk big about little things to increase their academic profile. Or maybe it's the same news. Or maybe it's the fact that I didn't learn biochem in the seventies and so none of this is a surprise to me and my mind is not so blown that I am emotionally required to question basic facts, like the fact that DNA contains ALL the information necessary for biological systems to run. If it didn't, they wouldn't last longer than it takes a single protein or RNA to degrade, or a single small molecule to diffuse throughout the cell or through a membrane.tragic mishap_{December 13, 2012
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Your #6 was another perceptive comment. Indeed, metaphysics is often put forward on the authority of science by famous scientists who otherwise mock or slight metaphysics. And by popular science writers as well. It wasn’t until I got to university and starting studying philosophy and intellectual history that I realized how much metaphysics the usual presentation of evolutionary theory contained. By the time I finished grad school, I had transformed from being a rabid “molecules to man by sheer chance plus long ages” (my heroes were people like Carl Sagan), to being a Darwin skeptic on the level of science and a Darwin foe on the level of metaphysics.
Thanks. I studied biology as an undergraduate and some philosophy in graduate school. What I eventually decided is that both science and metaphysics need to stand on their own feet, and that conflating them is a recipe for confusion and disaster. With regards to empirical biology, I think that "evo-devo" and complexity theory are very promising approaches to explaining the origins of phenotypic variation, so whether that makes me a "Darwin skeptic" or depends on how one construes "Darwin"/"Darwinism". With regards to metaphysics, I'm an unrelenting critic of Epicurean materialism, so whether that makes me a "Darwin foe" depends on how those terms are being cashed out at the level of metaphysics. I'm not hostile towards Epicureanism for ethical or political reasons -- I'm hostile towards it because it lacks a compelling account of consciousness, intentionality, or normativity -- and those are all aspects of human existence that cannot be neglected by any metaphysical system. The Epicureans got away with it because at that time, the Kantian/post-Kantian emphasis on consciousness (esp. self-consciousness), intentionality, and normativity simply hadn't been thematized. It becomes thematized in Kant precisely as a way of responding to Epicurean materialism (and also, I'm convinced, responding to Spinoza is a major concern of the Critique, whether or not Kant was aware of it).Kantian Naturalist_{December 13, 2012
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Kantian Naturalist: Your #6 was another perceptive comment. Indeed, metaphysics is often put forward on the authority of science by famous scientists who otherwise mock or slight metaphysics. And by popular science writers as well. It wasn't until I got to university and starting studying philosophy and intellectual history that I realized how much metaphysics the usual presentation of evolutionary theory contained. By the time I finished grad school, I had transformed from being a rabid "molecules to man by sheer chance plus long ages" (my heroes were people like Carl Sagan), to being a Darwin skeptic on the level of science and a Darwin foe on the level of metaphysics. Coyne is past his prime as an evolutionary thinker. You can always tell. When a professor at a prestigious university (which expects intensive research and graduate teaching from its faculty) has endless hours to spend on the internet, bickering with fundamentalists etc., you know that the professor is starting to "take it easy" as he nears the home stretch to retirement. Faculty with serious research programs simply don't have time to engage in lengthy conversations with a popular audience of mostly non-scientists. Nor should they want to, any more than a Metropolitan Opera singer would want to interact with Justin Bieber fans on their opinions about what makes for a good singing voice. The limelight-seeking, and hence vulgarization, of the American professoriate has become a matter of serious cultural concern. Blog sites are popping all over the place, where university faculty take a professional holiday from rigorous argument and from the obligation to represent opposing views at their strongest rather than by straw men, and where they indulge in talking about subjects way outside of their expertise, while contriving to use their academic status to lend weight to their opinions in those areas. Can you imagine Kant running a blog site, writing weekly columns about antinomies and synthetic a priori judgments, and wrangling with people who think that Deepak Chopra and E. O. Wilson are profound thinkers? And airing his views on the Greek bailout, anthropogenic global warming, and same-sex marriage along the way? On my previous point, it would be interesting to see a graph of the publication frequencies of peer-reviewed articles and technical academic books by Coyne, Dawkins, Myers, Ken Miller, Eugenie Scott, Moran, Shallit, Rosenhouse, and other rabid pro-Darwinians, as they have become more and more involved in blogging, touring the country to make speeches against ID and creationism, working with the NCSE, appearing on television and radio, etc. My guess -- and it's more than a guess, in the case of Miller and Scott -- is that the downward line would be very pronounced.Timaeus_{December 13, 2012
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tragic mishap, when you get the chance: http://www.ncbi.nlm.nih.gov/pubmed/22010165 http://circgenetics.ahajournals.org/content/4/5/576Mung_{December 12, 2012
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tm, I am so happy to hear that when someone responds to a post of yours with something you disagree with that the information you choose to respond with is just something you found in your DNA.
Fail. Body plans =/= Free will Physical =/= spiritualtragic mishap_{December 12, 2012
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In re: djockovic @ 7
I think it’s less that they think ONLY that version can do the work, and more that they’ve been saying for so long now that it’s a done deal that they don’t want to budge an inch. I think they’re also a bit frightened by what the new theory is throwing up because it simply doesn’t look anything like the crude copying error + NS + time version they have been touting and which, due to the word “error”, does fantastic theological work for them. Put the two together and it’s a bit like asking them to turn in a winning hand, and trust that the cards will be as kind to them.
That seems highly plausible to me, and a sad commentary on the state of affairs. It also strikes me, quite frankly, as a strong indication of the unfortunate after-effects that Monod's Chance and Necessity has had on speculation about the metaphysical and cultural-political implications of evolutionary theory. Hans Jonas and John Dewey did a much better job (in The Phenomenon of Life and Experience and Nature, respectively) of showing how a healthy respect for the traditional notion of teleology could be reconciled with Darwinism. Interestingly, neither Jonas nor Dewey were theistic evolutionists, but they both thought that a philosophically interpretation of Darwinism was consistent with natural piety. (Though I wouldn't want to assimilate their views to one another; Jonas had far more respect for traditional religion than Dewey did. In fact, I take a lot of inspiration from Jonas, though my methods are quite different from his.)Kantian Naturalist_{December 12, 2012
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Here we are, almost in the year 2013, and they are still searching: In Search of the Causes of Evolution: From Field Observations to Mechanisms But it's a fact.Mung_{December 12, 2012
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As to natural selection not living up to all the exuberant hype as this great 'undirected' creative engine that knows no bounds in its inventiveness, here a few minor problems with all that hype: (repeat from other thread) Inconsistent Nature: The Enigma of Life’s Stupendous Prodigality – James Le Fanu – September 2011 Excerpt: Many species that might seem exceptionally well adapted for “the survival of the fittest” are surprisingly uncommon. The scarce African hunting dog has the highest kill rate of any predator on the savannah, while cheetahs may have no difficulty in feeding themselves thanks to their astonishing speediness — but are a hundred times less common than lions. http://www.evolutionnews.org/2011/09/inconsistent_nature051281.html Accidental origins: Where species come from – March 2010 Excerpt: If speciation results from natural selection via many small changes, you would expect the branch lengths to fit a bell-shaped curve.,,, Instead, Pagel’s team found that in 78 per cent of the trees, the best fit for the branch length distribution was another familiar curve, known as the exponential distribution. Like the bell curve, the exponential has a straightforward explanation – but it is a disquieting one for evolutionary biologists. The exponential is the pattern you get when you are waiting for some single, infrequent event to happen.,,,To Pagel, the implications for speciation are clear: “It isn’t the accumulation of events that causes a speciation, it’s single, rare events falling out of the sky, so to speak.” http://www.newscientist.com/article/mg20527511.400-accidental-origins-where-species-come-from.html?page=2 Oxford University Admits Darwinism’s Shaky Math Foundation – May 2011 Excerpt: However, mathematical population geneticists mainly deny that natural selection leads to optimization of any useful kind. This fifty-year old schism is intellectually damaging in itself, and has prevented improvements in our concept of what fitness is. – On a 2011 Job Description for a Mathematician, at Oxford, to ‘fix’ the persistent mathematical problems with neo-Darwinism within two years. http://www.evolutionnews.org/2011/05/oxford_university_admits_darwi046351.html The Strength of Phenotypic Selection in Natural Populations This review demonstrates that our information about the strength of phenotypic selection in natural populations has increased dramatically in the past 2 decades, but many important issues about selection remain unresolved. http://www.oeb.harvard.edu/faculty/hoekstra/PDFs/Kingsolver2001AmNat.pdf Darwin proven wrong, again! Experimental Evolution Reveals Resistance to Change (Fruit Flies) Excerpt: Our work provides a new perspective on the genetic basis of adaptation. Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles. https://uncommondescent.com/intelligent-design/darwin-proven-wrong-again-experimental-evolution-reveals-resistance-to-change/ Austin Hughes: Most Evolutionary Literature Showing Positive Selection in the Genome is “Worthless” – Casey Luskin – 2012 Excerpt – When University of South Carolina evolutionary biologist Austin Hughes was asked about the problem with positive Darwinian selection, he says, “The problem is there really isn’t all that much evidence that it actually happens to the extent to which it would be needed to explain all of the adaptive traits of organisms.” http://www.evolutionnews.org/2012/01/austin_hughes_m055121.html Darwin’s Legacy – Donald R. Prothero – February 2012 Excerpt: In four of the biggest climatic-vegetational events of the last 50 million years, the mammals and birds show no noticeable change in response to changing climates. No matter how many presentations I give where I show these data, no one (including myself) has a good explanation yet for such widespread stasis despite the obvious selective pressures of changing climate. http://www.skeptic.com/eskeptic/12-02-15/#feature On Enzymes and Teleology – Dr. Ann Gauger – July 19, 2012 Excerpt: “This is an interesting turn in evolutionary thinking. People have been saying for years, “Of course evolution isn’t random, it’s directed by natural selection. It’s not chance, it’s chance and necessity.” But in recent years the rhetoric has changed. Now evolution is constrained. Not all options are open, and natural selection is not the major player, it’s the happenstance of genetic drift that drives change. But somehow it all happens anyway, and evolution gets the credit.” http://www.evolutionnews.org/2012/07/on_enzymes_and062391.html Hundreds Of Natural-selection Studies Could Be Wrong, Study Demonstrates – Mar. 30, 2009 Excerpt: “Our finding means that hundreds of published studies on natural selection may have drawn incorrect conclusions,”,,, “Nei said that many scientists who examine human evolution have used faulty statistical methods in their studies and, as a result, their conclusions could be wrong. For example, in one published study the scientists used a statistical method to demonstrate pervasive natural selection during human evolution. “This group documented adaptive evolution in many genes expressed in the brain, thyroid, and placenta, which are assumed to be important for human evolution.”,,, “But if the statistical method that they used is not reliable, then their results also might not be reliable,”,,, “we are saying that these statistical methods can lead scientists to make erroneous inferences,” he said. (Hmm, 3 years later — no honest corrections!) http://www.sciencedaily.com/releases/2009/03/090330200821.htm “Although living things occupy a three-dimensional space, their internal physiology and anatomy operate as if they were four-dimensional. Quarter-power scaling laws are perhaps as universal and as uniquely biological as the biochemical pathways of metabolism, the structure and function of the genetic code and the process of natural selection.,,, The conclusion here is inescapable, that the driving force for these invariant scaling laws cannot have been natural selection.” Jerry Fodor and Massimo Piatelli-Palmarini, What Darwin Got Wrong (London: Profile Books, 2010), p. 78-79 What Darwin Got Wrong: – Stephen Meyer – Feb. 2010 Natural selection by definition only “selects” or favors functional advantage. What we have learned in biology over the last 50 years shows that at every level in the biological hierarchy — whether we are talking about novel genes, proteins, molecular machines, signal transduction circuits, organs, or body plans — functional advantage depends upon the occurrence of a series of vastly improbable and tightly coordinated mutational events. Careful quantitative analysis has shown that these events that are so improbable as to put thresholds of selectable function well beyond the reach of chance.bornagain77_{December 12, 2012
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For all of his frothing at the mouth it is very telling taht Coyne cannot produce any positive evidence for natural selection actually doing something.Joe_{December 12, 2012
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bpragmatic you ask;
Just curious, has “natural selection” been defined and demonstrated by evolutionary “scientists” to have “neo-darwinian evolutionary” causal effect at all known levels of biochemical interactions that are pertinent to the so called evolutionary history of chemicals to living systems?
Short answer, No! The slightly longer answer is,,, The ‘princess and the pea’ problem is pointed out by Dr. John Sanford, at the 8:14 minute mark, of this following video,,,
Genetic Entropy – Dr. John Sanford – Evolution vs. Reality – video http://vimeo.com/35088933
,,,In which Dr. Sanford points out ‘selection’ only acts at the coarse level of the entire organism and yet the vast majority of 'slightly detrimental' mutations are far below the power of selection to remove from genomes before they spread throughout the entire population.
"Moreover, there is strong theoretical reasons for believing there is no truly neutral nucleotide positions. By its very existence, a nucleotide position takes up space, affects spacing between other sites, and affects such things as regional nucleotide composition, DNA folding, and nucleosome building. If a nucleotide carries absolutely no (useful) information, it is, by definition, slightly deleterious, as it slows cell replication and wastes energy.,, Therefore, there is no way to change any given site without some biological effect, no matter how subtle." - John Sanford - Genetic Entropy and The Mystery of The Genome - pg. 21 - Inventor of the 'Gene Gun'
The 'princess and the pea problem' facing natural selection is further discussed here (with the illustration from Sanford's book):
Evolution Vs Genetic Entropy – Andy McIntosh – video http://www.metacafe.com/watch/4028086/
and here
The GS Principle (The Genetic Selection Principle) - Abel - 2009 Excerpt: The GS Principle, sometimes called “The 2nd Law of Biology,” states that selection must occur at the molecular/genetic level, not just at the fittest phenotypic/organismic level, to produce and explain life.,,, Natural selection cannot operate at the genetic level. http://www.bioscience.org/2009/v14/af/3426/fulltext.htm
As to Natural Selection fixing an unambiguously beneficial mutation (instead of just preventing the buildup of slightly detrimental mutations), well, to my knowledge, in metazoans (multi-cellular creatures) the fixation of a unambiguously beneficial mutation has not been observed:
Experimental Evolution in Fruit Flies (35 years of trying to force fruit flies to evolve in the laboratory fails, spectacularly) - October 2010 Excerpt: "Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles.,,, "This research really upends the dominant paradigm about how species evolve," said ecology and evolutionary biology professor Anthony Long, the primary investigator. http://www.arn.org/blogs/index.php/literature/2010/10/07/experimental_evolution_in_fruit_flies
And there is a principled reason for believing that unambiguously beneficial mutations cannot be selected to fixation:
Poly-Functional Complexity equals Poly-Constrained Complexity The primary problem that poly-functional complexity presents for neo-Darwinism, or even Theistic Evolutionists is this: To put it plainly, the finding of a severely poly-functional/polyconstrained genome by the ENCODE study, and further studies, has put the odds, of what was already astronomically impossible, to what can only be termed fantastically astronomically impossible. To illustrate the monumental brick wall any evolutionary scenario (no matter what “fitness landscape”) must face when I say genomes are poly-constrained by poly-functionality, I will use a puzzle: If we were to actually get a proper “beneficial mutation’ in a polyfunctional genome of say 500 interdependent genes, then instead of the infamous “Methinks it is like a weasel” single element of functional information that Darwinists pretend they are facing in any evolutionary search, with their falsified genetic reductionism scenario I might add, we would actually be encountering something more akin to this illustration found on page 141 of Genetic Entropy by Dr. Sanford. S A T O R A R E P O T E N E T O P E R A R O T A S Which is translated ; THE SOWER NAMED AREPO HOLDS THE WORKING OF THE WHEELS. This ancient puzzle, which dates back to 79 AD, reads the same four different ways, Thus, If we change (mutate) any letter we may get a new meaning for a single reading read any one way, as in Dawkins weasel program, but we will consistently destroy the other 3 readings of the message with the new mutation (save for the center). This is what is meant when it is said a poly-functional genome is poly-constrained to any random mutations.
a few notes to that effect:
A Serious Problem for Darwinists: Epistasis Decreases Chances of Beneficial Mutations - November 8, 2012 Excerpt: A recent paper in Nature finds that epistasis (interactions between genetic changes) is much more pervasive than previously assumed. This strongly limits the ability of beneficial mutations to confer fitness on organisms. ,,, It takes an outsider to read this paper and see how disturbing it should be to the consensus neo-Darwinian theory. All that Darwin skeptics can do is continue to point to papers like this as severe challenges to the consensus view. Perhaps a few will listen and take it seriously. http://www.evolutionnews.org/2012/11/epistasis_decr066061.html Unexpectedly small effects of mutations in bacteria bring new perspectives - November 2010 Excerpt:,,, using extremely sensitive growth measurements, doctoral candidate Peter Lind showed that most mutations reduced the rate of growth of bacteria by only 0.500 percent. No mutations completely disabled the function of the proteins, and very few had no impact at all. Even more surprising was the fact that mutations that do not change the protein sequence had negative effects similar to those of mutations that led to substitution of amino acids. A possible explanation is that most mutations may have their negative effect by altering mRNA structure, not proteins, as is commonly assumed. http://www.physorg.com/news/2010-11-unexpectedly-small-effects-mutations-bacteria.html Scientists Map All Mammalian Gene Interactions – August 2010 Excerpt: Mammals, including humans, have roughly 20,000 different genes.,,, They found a network of more than 7 million interactions encompassing essentially every one of the genes in the mammalian genome. http://www.sciencedaily.com/releases/2010/08/100809142044.htm
related notes:
The Real Barrier to Unguided Human Evolution - Ann Gauger - April 25, 2012 Excerpt:,,, they did say that since there are some 20,000 genes that could be evolving simultaneously, the problem is not impossible. But they overlooked this point. Mutations occur at random and most of the time independently, but their effects are not independent. (Random) Mutations that benefit one trait (are shown to) inhibit another (Negative Epistasis; Lenski e-coli after 50,000 generations). http://www.evolutionnews.org/2012/04/the_real_barrie058951.html More from Ann Gauger on why humans didn’t happen the way Darwin said - July 2012 Excerpt: Each of these new features probably required multiple mutations. Getting a feature that requires six neutral mutations is the limit of what bacteria can produce. For primates (e.g., monkeys, apes and humans) the limit is much more severe. Because of much smaller effective population sizes (an estimated ten thousand for humans instead of a billion for bacteria) and longer generation times (fifteen to twenty years per generation for humans vs. a thousand generations per year for bacteria), it would take a very long time for even a single beneficial mutation to appear and become fixed in a human population. You don’t have to take my word for it. In 2007, Durrett and Schmidt estimated in the journal Genetics that for a single mutation to occur in a nucleotide-binding site and be fixed in a primate lineage would require a waiting time of six million years. The same authors later estimated it would take 216 million years for the binding site to acquire two mutations, if the first mutation was neutral in its effect. Facing Facts But six million years is the entire time allotted for the transition from our last common ancestor with chimps to us according to the standard evolutionary timescale. Two hundred and sixteen million years takes us back to the Triassic, when the very first mammals appeared. One or two mutations simply aren’t sufficient to produce the necessary changes— sixteen anatomical features—in the time available. At most, a new binding site might affect the regulation of one or two genes. https://uncommondescent.com/intelligent-design/more-from-ann-gauger-on-why-humans-didnt-happen-the-way-darwin-said/
bornagain77_{December 12, 2012
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Just curious, has "natural selection" been defined and demonstrated by evolutionary "scientists" to have "neo-darwinian evolutionary" causal effect at all known levels of biochemical interactions that are pertinent to the so called evolutionary history of chemicals to living sytems?bpragmatic_{December 11, 2012
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tm, I am so happy to hear that when someone responds to a post of yours with something you disagree with that the information you choose to respond with is just something you found in your DNA.Mung_{December 11, 2012
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But I thought genetic mutations don't affect body plans because the "information" for body plans is not found in DNA! /sarcasmtragic mishap_{December 11, 2012
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The most important lesson that most ID advocates never seem to be able to learn is that they are wrestling with sociopaths or as someone once put it, "powers and principalities in high places."Mapou_{December 11, 2012
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I think it’s less that they think ONLY that version can do the work, and more that they’ve been saying for so long now that it’s a done deal that they don’t want to budge an inch.
Could be. Remember Fodor's book? 'What Darwin Got Wrong' or such? There's nothing in the book that was theistic or the like, much less denying evolution. They just questioned natural selection as a concept - and the response was furious.nullasalus_{December 11, 2012
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Of related interest to this video on ontogenetic depth (the fact that embryonic mutations are, by far, the least likely to be tolerated), Dr Nelson did another talk on ORFan genes:
Widespread ORFan Genes Challenge Common Descent – Paul Nelson – video with references in description http://www.vimeo.com/17135166 Genomes of similar species - Cornelius Hunter PhD. Excerpt: Different variants of the Escherichia coli bacteria, for instance, each have hundreds of unique genes. And some of these genes have been found to have important functions, such as helping to construct proteins. [8] Massive genetic differences were also found between different fruit fly species. The fruit fly is one of the most intensely researched organisms and in recent years a systematic study of the genomes of a dozen different species was undertaken. Evolutionists were surprised to find novel features in the genomes of each of these different fruit fly species. Thousands of genes showed up missing in many of the species, and some genes showed up in only a single species. [9] As one science writer put it, “an astonishing 12 per cent of recently evolved genes in fruit flies appear to have evolved from scratch.” [10] These so-called novel genes would have had to have evolved over a few million years—a time period previously considered to allow only for minor genetic changes. [11,12] ,,, etc.. etc… http://www.darwinspredictions.com/#_4.2_Genomes_of From Jerry Coyne, More Table-Pounding, Hand-Waving - May 2012 Excerpt: "More than 6 percent of genes found in humans simply aren't found in any form in chimpanzees. There are over fourteen hundred novel genes expressed in humans but not in chimps." Jerry Coyne - ardent and 'angry' neo-Darwinist - professor at the University of Chicago in the department of ecology and evolution for twenty years. He specializes in evolutionary genetics.
how ORFan genes relates to ontogenetic depth is that ORFan genes are found to be expressed very early in embryonic development:
New genes in Drosophila quickly become essential. - December 2010 Excerpt: The proportion of genes that are essential is similar in every evolutionary age group that we examined. Under constitutive silencing of these young essential genes, lethality was high in the pupal (later) stage and (but was) also found in the larval (early) stages. http://www.sciencemag.org/content/330/6011/1682.abstract Age doesn't matter: New genes are as essential as ancient ones - December 2010 Excerpt: "A new gene is as essential as any other gene; the importance of a gene is independent of its age," said Manyuan Long, PhD, Professor of Ecology & Evolution and senior author of the paper. "New genes are no longer just vinegar, they are now equally likely to be butter and bread. We were shocked." http://www.sciencedaily.com/releases/2010/12/101216142523.htm New Genes, New Brain - October 2011 Excerpt: “This is one of the first studies to look at the role of completely novel genes” in primate brain development,,, A bevy of genes known to be active during human fetal and infant development first appeared at the same time that the prefrontal cortex,,, Finally, 54 of the 280 genes found to be unique to humans were also highly expressed in the developing prefrontal cortex,,,, “We were very shocked that there were that many new genes that were upregulated in this part of the brain,” said Long, who added that he was also taken aback by synchronicity of the origin of the genes and the development of novel brain structures.,,, (From the PLoS article, author’s summary: We found these genes are scattered across the whole genome, demonstrating that they are generated by many independent events,,, Our data reveal that evolutionary change in the development of the human brain happened at the protein level by gene origination,,) http://the-scientist.com/2011/10/19/new-genes-new-brain/
further notes:
Understanding Ontogenetic Depth, Part II: Natural Selection Is a Harsh Mistress - Paul Nelson - April 7, 2011 http://www.evolutionnews.org/2011/04/understanding_ontogenetic_dept_1045581.html earlier video: No Evidence For Body Plan Morphogenesis From Embryonic Mutations - Paul Nelson - video http://www.metacafe.com/watch/5548184/
bornagain77_{December 11, 2012
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@Kantian Naturalist I think it's less that they think ONLY that version can do the work, and more that they've been saying for so long now that it's a done deal that they don't want to budge an inch. I think they're also a bit frightened by what the new theory is throwing up because it simply doesn't look anything like the crude copying error + NS + time version they have been touting and which, due to the word "error", does fantastic theological work for them. Put the two together and it's a bit like asking them to turn in a winning hand, and trust that the cards will be as kind to them. As for Coyne, you're spot on.djockovic_{December 11, 2012
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This, presumably, is because Coyne wants to hang on to the simple version of evolution (the one that no longer works) because it’s the only one that can do the theological work he requires of it. And this is key because Coyne is no longer really a biologist, but is, instead, a political activist with a New Atheist agenda who uses a politicised science for political gain.
It is interesting that the New Atheists think that only ultra-adaptationist, panselectionist evolution can carry out the anti-theological work they want to see carried out. I don't know Coyne's stuff. He just struck me as the kind of scientist who has nothing but contempt for philosophy, and then goes ahead and does nothing but philosophy. (Much like Krauss and Hawking.) I usually tune that out pretty quickly.Kantian Naturalist_{December 11, 2012
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When evolutionists are or can be said to be questioning the old theory in part , or a wee bit more, then surely this coupled with serious criticism by well degre-ed people means there is a unnatural problem with the theories credibility. How could a well evidenced "theory" be so under suspicion for being wrong??? Is evolution really founded on scientific evidence as opposed to a persuasive hunch and lines of reasoning and other subjects backing it up?? Is it in the odds that this scepticism could exist for actual scientific theories ? The already odds are against evolution with every new paid thinker on evolution questioning it. In our time either evolutionary biology will crash and burn or its critics will. Conclusions claiming to be based on natures evidence, scientific methodology behind even that, have a intellectual attrition problem if they are not true.Robert Byers_{December 11, 2012
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What's astonishing here though, surely, is that the issue is simple enough. Coyne is offering a version of evolution that has numerous critics in the field; he is pretending those criticisms don't exist; and when challenged he changes the issue and asks about cheetahs running faster in order to illicit, irrelevant, but seemingly supportive responses . This, presumably, is because Coyne wants to hang on to the simple version of evolution (the one that no longer works) because it's the only one that can do the theological work he requires of it. And this is key because Coyne is no longer really a biologist, but is, instead, a political activist with a New Atheist agenda who uses a politicised science for political gain.djockovic_{December 11, 2012
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By the way, Kirschner and Gerhart are the authors of The Plausibility of Life. Nelson's not making this stuff up. Their words are right there in the popular literature for everyone to see. I've quoted them before here at UD. Before they introduced their own theory evolutionary theory was incomplete because it lacked a theory of the origin of novelty. Here's one quote:
Novelty by definition is always a surprise, but when the surprise is too great, it is completely implausible. [Smacks of ID!] The plausibility of life rests on the plausibility of generating novelty, and that in turn rests on mechanisms newly uncovered in biology.
IOW, not on natural selection.Mung_{December 11, 2012
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I love Gerhart's response:
I haven’t tracked down what Dr. Nelson said we said about natural selection — presumably that we don’t think it’s important.
I don't criticize him for this comment. I think he's done well to say he hasn't checked the source and he is responding based upon an assumption according to what Coyne sent him. Seems pretty honest.Mung_{December 11, 2012
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What Nelson did deny is the proposition that all evolutionary biologists regard it as central to evolutionary theory, and view it as the only “game in town” for building complex adaptations.
Shades of Gould: I thought that view was "...effectively dead, despite its persistence as textbook orthodoxy." By the way, this view seems to still be the prevalent view over at TSZ. In support of Nelson and contra Coyne see The Evolution of the Genome Chapter 11, Macroevolution and the Genome.Mung_{December 11, 2012
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