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Reviewing James Shapiro’s book, Darwinist admits: Growing number of gene scientists unconvinced by Darwinism

Recently, we’ve been looking at James Shapiro, a non-Darwinian molecular geneticist and author of Evolution: A View from the 21st Century, currently debating ID theorists and researchers. Here’s a review of his work by Adam Wilkins is a leading UK biologist and one time editor of the journal BioEssays, in Genome Biology and Evolution (January 24, 2012).

Wilkins admits something that everyone knows but few  convinced Darwinists like himself will actually admit: A growing body of scientists, especially those from molecular biology, developmental biology or developmental genetics, and microbiology are unconvinced by the alleged power of Darwin’s natural selection to create the world of life that we see:

…the book’s contention that natural selection’s importance for evolution has been hugely overstated represents a point of view that has a growing set of adherents. (A few months ago, I was amazed to hear it expressed, in the strongest terms, from another highly eminent microbiologist.) My impression is that evolutionary biology is increasingly separating into two camps, divided over just this question. On the one hand are the population geneticists and evolutionary biologists who continue to believe that selection has a ‘creative’ and crucial role in evolution and, on the other, there is a growing body of scientists (largely those who have come into evolution from molecular biology, developmental biology or developmental genetics, and microbiology) who reject it.

He thinks that this is not quite a Thomas Kuhn-type paradigm crisis yet.

The rest is interesting, especially his defense of natural selection:

The arguments from paleontological evidence for the importance of natural selection largely concern the observed long-term trends of morphological change, which are visible in many lineages. It is hard to imagine what else but natural selection could be responsible for such trends, unless one invokes supernatural or mystical forces such as the long-popular but ultimately discredited force of “orthogenesis.”

Consider what that means: The real reason for fronting Darwin only – as opposed to any other way that evolution might occur – is that otherwise we must invoke the supernatural?

One wonders what all those scientists who reject “Darwin only” think of that.

Our old friend Larry Moran thinks genetic drift is important in evolution. (Gotcha! Closet Catholic!) Lynn Margulis, of endosymbiosis fame? (Oh, you know what they say about her …) Shapiro himself? (I heard he goes to secret meetings with … )

Finally, people who want to hear themselves think just have to say, enough. Evidence matters. Lack of evidence matters. Freedom to think matters.

And evolution is not about protecting the position of the Darwin lobby vs. God.

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36 Responses to Reviewing James Shapiro’s book, Darwinist admits: Growing number of gene scientists unconvinced by Darwinism

  1. Perhaps the various ID factions will eventually agree on whether. Shapiro is a good guy or an eviluionist.

  2. First, I don’t think you could name ANY current biologists who are “Darwin only”. That’s a figment of the IDers imagination. Darwin was wrong in many respects, even as he “hit the jackpot” on the central questions of the origin of the species. Anyone today who is “Darwin only” would get laughed at by modern scientists.

    Second, what Wilkins is defending in the paragraph you like there is “methodological naturalism”. When you ask me to consider what this means, I understand this to mean that from a paleontological perspective, natural selection is the only viable solution running. The only “runners up” are anti-knowledge, anti-science superstitions. People are free to embrace those supersitions (or to subscribe to discredited ideas about [naturalistic] orthogenesis, for that matter), but that’s just to break with science, to totally corrupt scientific epistemology, and wander into theology, or worse.

    Which means if you do value scientific knowledge and the epistemology it rests on and the fruits of scientific research and analysis, there aren’t many options. You are welcome to walk away from science toward the supernatural, as you have, but that IS walking away from science, toward the supernatural.

    Third, evidence matters. That’s precisely why “Godidit” is problematic. To go there, one must abandon model-based epistemology, the epistemic connection between our senses and experience and models of reality that perform under objective testing conditions.

    Evolution, insofar as it is a scientific endeavor, is as much about banishing God from its discourse as physics or chemistry is — natural explanations for natural phenomena. If “Zeus” is a natural god, some being that interacts in a physical way like any other part of the physical world, then science is ready and equipped to study Zeus, scientifically, and propose and vet models that perform (or not) against our natural experience of Zeus. So, science is not interested in protecting itself from God, or gods per se — natural gods are fine — but rather it must protect its epistemology if it is to have anything to produce at all.

    If it doesn’t, and it lets a “supernatural foot in the door”, it’s a total loss, and the enterprise is reduced to nothing more than theology.

    Fourth, it’s significant that Shapiro, for example, is not criticized as anti-science in the way that ID is and should be. Because while he has a critical, opposing hypothesis to advance (against some existing and popularly accepted models), his method and epistemology are scientific.

    Critical, “thinking independently” and being skeptical are all good, noble values in science. It’s nullifying scientific epistemology with appeals to the “supernatural” that are fundamentally problematic, fundamentally anti-science. There are, and will continue to be controversies within science, in and around evolutionary theory, but there’s an ontological difference between those disputes and the eschewing of ID. So long as Shapiro can work within the method, and consistent with the epistemic requirements of science, it’s all good, even and especially when the disputes become bitter.

    It’s a whole different kettle of fish when one tries to insert a supernatural agent into the explanatory framework. Science just seizes up, and can’t function when such incoherent (in terms of science) elements are introduced.

  3. I’m glad to see that some scientists “coming out of the closet” to question a fundamental aspect of Darwinian evolution. In my opinion, there’s been far too much ideological contamination of research into genetic adaptation. Terrified by the potential of religious influence or implications, many researchers have adopted a dogmatic rigidity that’s foreign to the spirit of scientific inquiry.

    As I think I’ve said before here, “God probably exists, get over it, and let’s get on with science regardless of where the data takes us.”

  4. As to this comment:

    ‘On the one hand are the population geneticists and evolutionary biologists who continue to believe that selection has a ‘creative’ and crucial role in evolution and, on the other, there is a growing body of scientists (largely those who have come into evolution from molecular biology, developmental biology or developmental genetics, and microbiology) who reject it.’

    a few notes:

    Did Natural Selection Construct Metazoan Developmental Sequences? – Paul Nelson – July 2011
    The necessary and sufficient conditions of the process of natural selection (Endler, Natural Selection in the Wild, 1986) are (1) variation, (2) selection or fitness differences, and (3) inheritance. These conditions impose evidential demands on any investigator who wishes to employ natural selection in evolutionary (i.e., historical) explanation. Data from model systems (e.g., C. elegans, Drosophila, and Danio), as well as theoretical analyses, raise challenges for the use of natural selection as the causal process responsible for the origin of developmental sequences. In particular, the conditions of (2) selection differences and (3) inheritance have not been adequately described in current theories of the evolution of the Metazoa.
    http://www.evolutionnews.org/2.....48301.html

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

    Metamorphosis Video Exclusive: Dr. Ann Gauger Discusses Limits of Natural Selection – October 2011
    http://intelligentdesign.podom.....0_42-07_00

    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/2.....55121.html

    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/2.....51281.html

    Darwinism’s Last Stand? – Jonathan Wells

    Excerpt: Despite the hype from Darwin’s followers, the evidence for his theory is underwhelming, at best. Natural selection – like artificial selection – can produce minor changes within existing species. But in the 150 years since the publication of Darwin’s Origin of Species by Means of Natural Selection, no one has ever observed the origin of a new species by natural selection – much less the origin of new organs and body plans.
    http://www.evolutionnews.org/2......html#more

    EXPELLED – Natural Selection And Genetic Mutations – video
    http://www.metacafe.com/watch/4036840

    “…but Natural Selection reduces genetic information and we know this from all the Genetic Population studies that we have…”
    Maciej Marian Giertych – Population Geneticist – member of the European Parliament – EXPELLED

    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.
    http://www.evolutionnews.org/2.....ellig.html

    Darwin proven wrong, again! Experimental Evolution Reveals Resistance to Change
    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.
    http://www.uncommondescent.com.....to-change/

  5. Natural selection is pretty central to the theory of evolution. I’m not sure I’ve seen any mainstream post-Darwinian alternatives.

    Third, evidence matters. That’s precisely why “Godidit” is problematic. To go there, one must abandon model-based epistemology, the epistemic connection between our senses and experience and models of reality that perform under objective testing conditions.

    No, it’s not problematic and it does not exclude scientific inquiry. Analogously, it is commonly said that Alexander the Great conquered the world, but such a statement does not claim that he did it single-handedly, and it certainly does not end all historical and archaeological inquiry.

  6. @Querius,

    Can you build and test models that invoke supernatural agents as predicates for the model, or supernatural forces? If you can, how would that be done?

    If not, then noting that Alex’s conquest doesn’t attach, here, even if we supposed he DID conquer the world single-handedly. The issue is not whether everything is attributed to Alexander, or God, or just some things. God as supernatural, whether “totally hands on”, or less so, defeats any attempt to build a testable model. If such a model WERE possible, then this God would not be supernatural, but natural, by definition.

  7. eigenstate:

    A policeman sees a drunk man searching for something under a streetlight and asks what the drunk has lost. He says he lost his keys and they both look under the streetlight together. After a few minutes the policeman asks if he is sure he lost them here, and the drunk replies, no, that he lost them in the park. The policeman asks whey he is searching here, and the drunk replies, “this is where the light is.”

  8. Funny, I read the review, and took away an almost completely message than News.

    I’d advise readers to take a look for themselves.

    “The matter of selection is then virtually ignored until the final section of the book. There we read, as one of nine bullet-points that summarize the core message: “The role of selection is to eliminate evolutionary novelties that prove to be non-functional and interfere with adaptive needs. Selection operates as a purifying but not creative force [emphasis added].”

    I cannot imagine many evolutionary biologists subscribing to that position. The
    objections to it come from both genetic arguments and paleontological data.”

    But please, read it, and the book for that matter. Not sure the hacked into quotemines version will please you as much as the original….

  9. Can you build and test models that invoke supernatural agents as predicates for the model, or supernatural forces? If you can, how would that be done?

    Of course not. But that’s not what I’m suggesting. As bornagain77 implies, science only deals with measurable cause and effect relationships. Obviously, there are many things that cannot be (directly or indirectly) measured quantitatively, and science makes no pretensions about them. I contend that the knowledge of the existence of God has no effect on scientific experiments.

    For example, let’s first assume that all God did was act as a first cause that initiated the inflation of the universe. While causation probably transcended Planck time after its initiation, does it bother you that you can never perform any scientific experiments or collect data during and before this increment? Is the theory of Planck time anti-science as a result?

    Now let’s assume that God does not exist and somehow all the amazing complexity of the chemical cycles, the organelles, and the incredible complexity of the DNA code within a single cell was somehow able to organize itself to a profound level of complexity over a few billion years. Wouldn’t a scientist be better off from a pragmatic standpoint by assuming an excellent Design for any new discovery rather than assuming that new discoveries are either evolutionary junk (such as “junk” DNA) or vestigial?

    Assuming that God does exist, again it’s pragmatic to assume it was all Designed. Thus, there’s no difference in scientific progress except that scientists who assumed a Design seem to have a bit of an advantage over those who assumed a lack of design.

    Finally, some people want to try to either prove or disprove (by exclusion) the existence of God, but I believe that these attempts are futile. Any competent statistician could completely hide the acts of God within probability and chaos. So you could never really be certain if “Goddidit” or not.

  10. It seems to me the reviewer, in essence, says, “There’s a big divide beginning to happen in evolutionary science – but I still find myself on the traditional side of it.”

    He sees that Shapiro attributes more to selection than some statements might indicate, but not as much as most evolutionary biologists would want. That doesn’t alter the fact that he recognises a growing body of opinion agreeing with Shapiro – and most notably that the division tends to follow along disciplinary lines.

    One’s view of evolution is likely to be profoundly affected by the type of science one pursues.

    That so many discussions deny such a division and claim there is a single, agreed, T of E is evidence in support of Wilkins’ observation that the disciplines simply ignore each other in this matter. I’ve written on that here .

  11. This is a completely straw man.

    There is no closet here. Shapiro’s ideas are controversial in biology, but he is in no closet, and he’s not the only biologist with controversial ideas.

    The “dogmatic rigidity” you see is imaginary, and Shapiro’s ideas tell us absolutely nothing (as no science can) about whether God exists or not.

  12. In fact it occurs to me that the word that terrifies IDists about evolutionary theory is the word “random”.

    It is harmless.

    Also, largely, meaningless.

  13. The quote on purifying selection needs to be put into context. Shapiro has strongly worded opinions, and he may be worng on some technical speculations, but he is firmly planted in the empirical tradition.

    • Cells are built to evolve; they have the ability to alter their hereditary characteristics rapidly through well-described natural genetic engineering and epigenetic processes as well as by cell mergers.
    • Evolutionary novelty arises from the production of new cell and multicellular structures as a result of cellular self-modification functions and cell fusions. In many cases, these new structures involve the amplification and/or rearrangement of existing functional molecular components. In addition, cells (and associated entities such as viruses) have the capacity to generate entirely new nucleic acid, protein, and other molecular components that can subsequently be integrated into functional cell or multicellular systems. As discussed previously, it remains to be thoroughly investigated to what degree cell sensing, information processing, and genome targeting can heuristically accelerate the production of useful novelties. A priori, functionally relevant guidance for natural genetic engineering would appear to enhance the probability of success in generating useful novelties. This supposition requires rigorous testing.
    • Natural genetic engineering and other evolutionarily innovative processes respond to stimuli that place the core organism objectives of survival, growth, and proliferation in peril. These dangerous challenges are most likely to occur at times of major ecological disruption.
    • Active hereditary variation and evolutionary innovation will continue as long as ecological disruptions and challenges to core vital objectives persist.
    • The role of selection is to eliminate evolutionary novelties that prove to be non-functional and interfere with adaptive needs. Selection operates as a purifying but not creative force.
    • Evolutionary inventions that survive purifying selection and prove useful are subject to microevolutionary refinement, perhaps by the kind of processes envisaged in conventional theories.
    • Successful evolutionary inventions are subject to amplification, reuse, and adaptation to new functions in response to successive ecological challenges.
    • Taxonomically specific characters become established as the functional integration of past evolutionary novelties increasingly places constraints on the kinds of additional inventions that will prove functional.

    Shapiro, James A. (2011-06-08). Evolution: A View from the 21st Century (FT Press Science) (Kindle Locations 2618-2638). FT Press. Kindle Edition.

  14. Reading through this it occurs to me that Shapiro has created some confusion as to how this self-engineering applies to multicelled organisms.

    It is one thing for microbes to respond to stress by increasing the rate of mutation, but much more problematic for it to happen the the germ cells of metazoans.

    Also, if you look up selection, you find modes of selection that are not purely negative. Shapiro is only addressing one of them.

    Balancing selection
    Directional selection
    Disruptive selection
    Negative selection (natural selection)
    Assortative mating
    Hypergamy
    Koinophilia

  15. The noun “selection” is problematic for starters, and applying “positive” or “negative” to it, potentially misleading.

    It is simply the differential reproduction of variants within the current environment. That’s not positive or negative, it’s just a biased sampling of genetic sequences, where the bias is towards sequences that tend to result in phenotypes that thrive in that environment.

    Sure, it means that highly deleterious new variants are rapidly weeded out. But it also means that existing variants that become advantageous become more prevalent, and any new variants that are advantageous become more prevalent. These aren’t two different processes.

  16. There are some useless semantic distinctions, but I think it’s fair to say that once you get beyond weeding out lethal mutations, there can be many kinds of selection. Darwin noted sexual selection and female choice. These can have many subsets and can lead to population changes that would be unexpected based purely on biochemical efficiency.

    I don’t think Shapiro even addresses this.

  17. No, I don’t think he does. I think his work is interesting, but he seems to be trying to put a more controversial spin on it that the work warrants.

    It’s a bit annoying.

    But then it also gives the lie to the idea that in science everybody dogmatically adhere’s to consensus! That could not be further from the truth. The way to get your work in high-impact journals is to challenge the consensus, not merely support it. In fact, there’s a shortage of good published replications precisely because the market for replicative studies is nothing like as good as the market for novelty.

  18. There’s a phrase, “lawyered up” for writing that is careful to to the point of being boring. I suspect that is the way laymen view most published science.

    If you want to be noticed you have to engage in purple prose. You have to be outrageous.

    I’ve seen touches of this in Gould and Mayr. But I think Shapiro’s book would be better if he had been more cautious.

  19. The only “runners up” are anti-knowledge, anti-science superstitions. People are free to embrace those supersitions …, but that’s just to break with science, to totally corrupt scientific epistemology, and wander into theology, or worse.

    Well said. Or it would be, if you were stating it about the current revelations about evolution. The entire difficulty enters in with “model based epistemology.” Now I understand that post-normal science is rather keen and all, but ditching empiricism for feigned competency with mathematical hieroglyphics doesn’t cause religious utterances to covert themselves into valid demonstrations of fact. This is just as true for Young Earth notions as it is for any adherence to Darwinist notions. And making an appeal that Darwinism has the blue-ribbon as the doxastic cult of the oligarchic stakeholders doesn’t really cut it. Though Kuhn would certainly appreciate the notion.

    Can you build and test models that invoke supernatural agents as predicates for the model, or supernatural forces?

    As somehow especially different than virtual photons and the rest of the quantum nonsense? Can’t imagine. More to the point, have we evolved bacteria into biplanes yet? Has that test been performed and passed? Or is this all just speculative nonsense to provide an Atheistic Creation Myth as salve for the Faithful?

    The sole reason that Darwinian notions are so contentious is precisely because they have not been demonstrated successfully. Indeed, the only tests thus far have been a long string of outright frauds and failures. And then there’s Monsanto…

  20. In fact it occurs to me that the word that terrifies IDists about evolutionary theory is the word “random”.

    Wrong again, as usual. It does not terrify us. The claim cannot be tested- as YOU say it is meaningless- your entire position is meaningless.

    That may terrify us- teaching nonsensical, untestable and unscientific crap to our kids.

  21. It is meaningless unless its meaning is given.

    It is perfectly possible to test a specific stochastic hypothesis.

    As has been done, over and over.

    It appears that we evolved via stochastic processes.

    There is nothing terrifying about that conclusion. It certainly doesn’t imply there is no God.

  22. We are STILL waiting on a testable hypothesis pertaining to stochastic processes. You say it has been done and I say you are spewing untruths.

    You cannot test your claim:

    It appears that we evolved via stochastic processes.

    Also if tere isn’t any difference between a god and no god, what do you think that means?

  23. No you aren’t.

    There are lots of testable hypotheses, and they have been tested. You just ignore them.

    And I didn’t say there isn’t any difference between a god and no god.

    I said that science won’t tell you the answer to the question as to whether there is a god.

  24. There are lots of testable hypotheses, and they have been tested.

    Not pertaining to stochastic processes. If there were you would just present them so we could look but you don’t because you can’t.

    So stuff a sock in it.

    Also I am the one saying there wouldn’t be a difference between god and no god is your position is true.

    And what you say about what science can and can’t do is meaningless.

  25. Strange that EVERY time Elizabeth makes claims of testable hypotheses pertaining to stochastic processes and gets called on it, she runs away.

  26. Nope.

    But I’m not going to give you any more, Joe. Google Scholar is as available to you as it is to me.

  27. Google scholar?

    What do I search for?

  28. Nothing says Elizabeth Liddle is a loser more than her refusal to support her claims.

    Google scholar? I googled and found nothing pertaining to a testable hypothesis for biological evolution pertaining to stochastic processes.

    Bluff called…

  29. Joe, every single empirical paper on evolutionary biology is a test of a hypothesis about stochastic evolutionary processes.

    Take Lenski’s e-coli experiments if you want.

    Or his AVIDA studies.

    That you don’t recognise them as such is your problem, not mine.

  30. Joe, every single empirical paper on evolutionary biology is a test of a hypothesis about stochastic evolutionary processes.

    That cannot be true as it would be assuming the very thing that needs to be tested.

    Take Lenski’s e-coli experiments if you want.

    Those experiments support baraminology. The AVIDA studies have been exposed as nonsense as they do not use realistic parameters.

    But anyway what was Lenski’s hypothesis? If E Coli mutates via stochastic processes at some time they will be able to utilize citrate?

    IOW Elizabeth you don’t have any idea what you are saying but you say it anyway.

  31. How can we test the claim that any bacterial flagellum “evolved” via stochstic processes?

    How can we test the claim that anything evolved via stochastic processes?

  32. By doing exactly what Lenski did and plotting the probability distributions from frequencies in his data.

  33. Lenski doesn’t have any idea if the mutations were caused by stochastic processes.

    Also no one knows if any flagellum could evolve from a population that never had one.

    IOW yu are proving that you don’t know what you are talking about.

    Ya see we cannot do probability distribution on something we don’t know is even possible.

  34. Excellent analogy, bornagain77. Eigenstat’s mindset was revealed to be fatuous, with the discovery of the quantum level of matter.

    The latter is replete with paradoxes, by definition, repugnant to reason, mysterious, beyond our understanding. Eigenstat would have had to accept all that, assuming he is a working scientist, or kept his mouth shut on the subject.

    And yet in an indirect manner, he is rubbishing quantum physics. He must be aware from the many posts on here on the subject, of the extraordinarily compelling, effectively incontrovertible evidence, for, not just an almighty and omniscient creator-God, but also that it is a personal God.

    Instead, his whole post is predicated on the assumption that a) there is no god, and b) if there were, consideration of it would thoroughly foul up science, which is “reggeler as clockwork”. (True, not expressly articulated by Eigenstat in that way, but the simplistic, confused implication is there)

    Only ‘clockwork’ science, as the frontier, went out as quantum phyics came in, and cosmology has developed, as has been extensively delineated in UD this past week.

  35. There’s one thing I don’t understand. You said that we could study a natural god, like Zeus. but then you say that ID is anti-science. Couldn’t a natural god design life and then be studied? If it were studied, what methodology would be used? Aren’t people like Bill Dempski and others trying to establish that methodology?

  36. eigenstate:

    Darwin was wrong in many respects, even as he “hit the jackpot” on the central questions of the origin of the species.

    Except that Darwin didn’t hit the jackpot on the origin of species. His work certainly didn’t explain the origin of species. What he provided was a series of anectdotal observations, wildly extrapolated with fertile imagination. Indeed, he was constantly prodding the reader to “imagine” this or that speculative possibility, coupled with what essentially amounted to: “God wouldn’t have done it the way we see it in nature.”

    Darwin was a skilled rhetorician. Successful in explaining the origin of species — or much else in biology for that matter — he was not.

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