James Shapiro goes after natural selection again (twice) on HuffPo

August 22, 2012 • 11:13 am

I hate to give attention to my Chicago colleague James Shapiro’s bizarre ideas about evolution, which he publishes weekly on HuffPo rather than in peer-reviewed journals. His Big Idea is that natural selection has not only been overemphasized in evolution, but appears to play very little role at all.  Even though he’s spreading nonsense in a widely-read place, I don’t go after him very often, for he just uses my criticisms as the basis of yet another abstruse and incoherent post. Like the creationists whose ideas he appropriates, he resembles those toy rubber clowns that are impossible to knock down.  But once again, and for the last time, I wade into the fray. . .

In his post of August 12, “Does natural selection really explain what makes evolution succeed?” (his answer, of course, is “no”), Shapiro simply recycles some discredited arguments used by creationists against evolution. The upshot, which we’ve heard for decades, is the discredited idea that natural selection is not a creative process. I quote:

  • “Darwin modeled natural selection on artificial selection by humans. He ignored the inconvenient fact that human selection for altered traits has never generated a truly new organismal feature (e.g., a limb or an organ) or formed a new species. Selection only modifies existing characters. When humans wish to create new species, they use other means.”

This is the old canard that artificial selection doesn’t create “new features.”  His definition of a “new organismal feature” is, of course, one that hasn’t been generated by artificial selection, so it’s all tautological.  Of course we haven’t seen whole new organs or limbs arise in the short term, for people have been doing serious selection for only a few thousand years, and have not even tried to create new organs or limbs. But we can create a strain of flies with four wings, breeds of dogs that would be regarded as new genera if they were found in the fossil record, and whole new biochemical systems in bacteria.  Both Barry Hall and Rich Lenski, for example, have demonstrated the evolution of brand new biochemical pathways that have evolved to deal with new metabolic challenges. Now that is a “new organismal feature”!

Often new species are created by hybridization, but Shapiro forgets that that hybridization is often followed by either natural or artificial selection for increased interfertility of the new hybrid form, so it truly becomes an interbreeding population that characterizes a species.  And that, of course, gives a crucial role to selection, as it did in the experiments of Loren Rieseberg and his colleagues on hybrid sunflowers.

Finally, we have selected for increased reproductive isolation in the laboratory, showing that full speciation is possible via artificial selection. My own student Daniel did this, as did Bill Rice and William Salt in lab experiments on Drosophila, which in effect created—by artificial selection—new species from a single original species.

What Shapiro fails to offer is an alternative mechanism for the origin of those features of organism that appear “designed”?  Was it God?  What turned an artiodactyl like Indohyus into a whale—a transition that is fully documented in the fossil record?  Was it simply the “self-organization of the genome” that somehow fortuitously moved the nostrils atop the head, turned the front limbs into flippers, got rid of the hair and external ears, and wrought many other morphological and internal changes? How exactly did this happen, Dr. Shapiro? Might natural selection have played a role? Or was it “spontaneous genome organization,” whatever that means?

  • “Unlike most followers, Darwin acknowledged later that significant, sudden changes could occur in a fundamentally different way. He wrote about ‘… variations which seem to us in our ignorance to arise spontaneously. It appears that I formerly underrated the frequency and value of these latter forms of variation, as leading to permanent modifications of structure independently of natural selection’ (Origin of Species, 6th edition, Chapter XV, p. 395, emphasis added). So a way to rephrase my question is to ask: Have we learned since 1859 about processes that can lead to organism change “independently of natural selection?” The answer is overwhelmingly positive.Two fields principally illuminated the basic mechanisms of heredity and variation:
    • cytogenetics (the study of chromosome behavior in heredity using both genetic and microscopic methods) and
    • molecular genetics (using DNA analysis to identify the nature of genome change).”

Neither of these_though they can lead to organism change (i.e. “mutation”)—can also produce adaptation.  As always, Shapiro is ducking the whole question of how organisms acquire those features that make them thrive in their environments.

If he’s going to respond to this post at HuffPo, which he will, here’s a challenge for him: what role, precisely, do you think natural selection plays in evolution—especially the kind of evolution that produces the “adaptive” features that so excite our wonder? How on earth do cytogenetics or molecular genetics alone explain the transformation of fish into tetrapods, deerlike animals into whales, or account for cryptic coloration, mimicry, and adaptive behaviors? They can’t, for there has to be some process that winnows out the variation that arises.  That process is natural selection. How did the ancestral marsupial produce descendants like marsupial “flying squirrels” and “moles” in Australia that look very much like placental mammals? Did that have anything to do with natural selection? If not, explain how you think it happened.

Shapiro’s latest post, “Cell mergers and the evolution of new life forms: symbiogenesis rather than selection,” is just about as bad.  Here he merely reprises Lynn Margulis’s argument that symbiosis was important in evolution: both mitochondria and chloroplasts (which respectively produce energy and photosynthesis), were the result of ancestral cells taking up and using symbiotic bacteria.  And yes, that’s correct, and was a huge contribution of Margulis.

The problem for Shapiro, as it was for Margulis, is that they went on to suggest think that symbiosis is a replacement for natural selection.  It isn’t.  In fact, symbiosis occurs hand-in-hand with natural selection, because following the origin of an organism like a lichen or a chloroplast-containing cell via symbiosis, one finds natural selection acting on the “combination” organism, modifying both components. In fact, neither chloroplasts nor mitochondria can survive on their own outside of cells: both have been modified by natural selection to become part of an integrated and adapted cell. It is the whole vehicle—the symbiotic combination organism—that undergoes selection, with the best combinations leaving more offspring.  In fact, Shapiro unwittingly alludes to this when he says this:

In all these cases, there is active DNA transfer between genome compartments. Typically, DNA sequences travel from the organelle genomes to the nuclear genome. Thus, the nucleus actually encodes most of the proteins in each of its organelles, even though they have their own genomes and protein synthesis machinery.

Restructuring of both nuclear and organelle genomes is an important aspect of evolution. Some groups of organisms are actually identified by the organization of their mitochondrial DNA.

Yes, and how does that “active DNA transfer” happen? It’s because those cells that best reapportion the genomes between “host” and “symbiont” DNA leave more offspring.  And that’s natural selection.

I wouldn’t go after Shapiro except that he spews this anti-evolutionary nonsense at HuffPo, and naive readers might get the impression that biologists are beginning to doubt that natural selection is important.  Well, as far as evolutionary biologists regard adaptations, it is: natural selection is the only game in town.

Yes, we now know of a whole host of new mechanisms to generate genetic variation, including symbiosis and the ingestion of DNA from distantly related species. But to produce adaptation, something has to winnow out the wheat from the chaff: those variants that reduce reproduction from those that enhance it.  And that’s natural selection.  There is no alternative, and Shapiro, despite his endless series of “blogs,” has never suggested one.  His never-ending attacks on natural selection and neo-Darwinian evolution should be an embarrassment to HuffPo, which will apparently publish anything since they don’t have to pay for it; but they’re also an embarrassment to me, for Shapiro works at my university and, in my view, his writings impugn our reputation for excellence in evolutionary biology.

So again, I tender my challenge: tell us, Dr. Shapiro: you’re always banging on about new sources of genetic variation, but you never seem quite able to tell us how that variation is translated into adaptive evolution. If it’s not natural selection, what is it?

51 thoughts on “James Shapiro goes after natural selection again (twice) on HuffPo

  1. Thanks for this. As someone who peruses and often comments in the HuffPO science section, I’ve wondered from time to time if there was anything to Dr. Shapiro’s posts. They’re often overloaded with jargon and, not being a biologist, I usually can’t make heads or tails of it. Although the intelligent design like phrases he started dropping a few weeks ago gave me a good clue.

  2. I wouldn’t go after Shapiro except that he spews this anti-evolutionary nonsense at HuffPo, and naive readers might get the impression that biologists are beginning to doubt that natural selection isn’t important.

    I’m inclined to think that a bit unfair. I don’t see Shapiro as anti-evolutionist, though I do see him as anti-Darwinist.

    Yes, the creationists sometimes cite Shapiro, just as they have cited Gould. But Gould was no help to the creationist case, nor will Shapiro help them.

    Those who say the dog wags its tail, and those who say that the tail wags the dog, pretty much agree on factual observations. There difference is philosophical. Likewise, Shapiro’s disagreement with Darwinism is mostly philosophical. He seems to want to change the emphasis, and has a different view of what is important.

    My big problem with Shapiro (and previously with Gould), is that their criticism comes with a lot of handwaving but no clear alternative to what they criticize. On the other hand, I don’t think it hurts to have a diversity of views about this.

    1. As I note in my book, an important part of the modern theory of evolution is that adaptation is produced by natural selection. So I don’t see this as being unfair. And it’s not a philosophical difference at all: it’s about the mechanism of adaptive evolution. That is a scientific question, not a philosophical one. It’s not just a change in “emphasis”.

      And yes, it does hurt to have a diversity of views if some of them are wrong. Creationism is a different view of evolution: should we teach that to the kids? To get to the truth, we have to weed away the false, so diversity in itself is not necessarily good.

      And yes, Shapiro has helped the creationist cause as far as I can see, for they quote him in support of their critiques of Darwinism. How do you know that doesn’t help them?

  3. “His Big Idea is that natural selection has not only been overemphasized in evolution, but appears to play very little role at all.”

    He should run that past the farmers whose crops are being swallowed up by pigweed which is now Roundup resistant.

    “Glyphosate-resistant pigweed not only dominates in cotton fields, but it has wide ranging effects on other crops and productions, as well.”

    And no one could see that happening?

    1. Glad to see that you beat me to that excellent current example. Search [Roundup Palmer Pigweed] to get all the info you might want on this. I first heard about it on CBS Sunday Morning this past Sunday, and right now it’s also front & center on their website .

      Cotton and soybean farmers of a fundamentalist strip will rightfully blame Monsanto, but will they grasp that this is natural selection/evolution in action?

  4. This is the old canard that artificial selection doesn’t create “new features.”…

    I dispute that! This is not an old canard, its an old crococanard. 🙂

    Seriously, Shapiro complains about the lack of extra-limbed domestic species, Cameron complains about the lack of toothy ducks. Maybe they can get together and ask the burning question on everyone’s mind: ‘if evolution is true, why haven’t we bred any four-winged crocoducks?’

  5. Of course, the early Mendelians, right after the rediscovery of Mendel’s work, got excited about mutation and decided that it, not natural selection, was the explanation for evolution. So there is nothing very new about Shapiro’s argument. But people may not realize this when it appears in the HuffPo.

    1. Having neither read Shapiro’s book nor his HuffPo posts, I cannot tell wherther he’s just another Gould or Goldschmid or Margulis or hwat have you, or really closet creationist. But I defineitely had an exchange on the bolg Homologous Legs, a long time ago, with a creationist constantly citing Shapiro as evidence for his weird views.

  6. ffs Darwin himself edited the Origin in order to address and resolve this criticism. That it’s still being used is appalling.

    1. “He ignored the inconvenient fact that human selection for altered traits has never generated a truly new organismal feature (e.g., a limb or an organ) or formed a new species. Selection only modifies existing characters.”

      This is factually false. He should check the last edition of the Origin and look for the name George Mivart.

  7. Honestly, how often does evolution produce new limbs or organs? Mammals, reptiles, fish, etc. still all have four limbs. Insects still all have six limbs, and almost all of them have wings or remnants of wings.

    1. New appendages and body plans happen quite often in the modular arthropods. See the figure illustrating “the arthropod head problem”, trying to keep tabs on the head and its appendages as the original trilobite segmentation looses segments (Chelicerata, Myriapoda, Crustacea/Hexapoda), and transforms legs (I assume) to chelicera and pedipalps (Chelicerata) and antenna and mandibles et cetera (Myriapoda, Crustacea/Hexapoda).

      Wings should be an excellent example of new limb, seeing how they likely started out as gills as I understand it.

      Snakes and other legless animals uses new forms of tractions. Maybe we should call that function “phantom limbs”. =D

      Same goes for spiders, when they use webs threads for flying during wind dispersal.

      How about the varying number of stomachs in animals, why wouldn’t they qualify as organs?

      Lungs, independently evolved in tetrapods and lungfishes. Et cetera.

    2. Actually, extra legs, arms heads etc do get thrown up fairly frequently as mutations, however if they do not confer an evolutionary advantage to the organism in question, they do not progress past the random mutation stage.

  8. “symbiosis occurs hand-in-hand with natural selection”

    I think this response to the symbiogenesis article is a little weak.

    Preferable: Symbiosis, indeed symbiogenesis, is driven by natural selection.

    In the quote, just replace ‘symbiosis’ with any other characteristic, say, ‘the ability to fly’, and perhaps you see my point.

    Natural selection was operating on archaea and bacteria prior to the merger, during the merge (which undoubtedly was a very long gradual process) and after the merger. The merger happened because of natural selection.

    I’m not arguing with you so much as trying to make the counter-argument to Shapiro’s baloney more concise.

  9. “Like the creationists whose ideas he appropriates, he resembles those toy rubber clowns that are impossible to knock down.”


    Ha ha! I had one of those as a kid. Bozo the clown. I thought it was kind of creepy. As an adult I never found clowns funny. Boring, and a little creepy.

    “When humans wish to create new species, they use other means.”


    We do? Well, for god’s sake man, do tell how that could be equivalent to a natural process! Are you invoking a god? Aliens?

    “But to produce adaptation, something has to winnow out the wheat from the chaff: those variants that reduce reproduction from those that enhance it. And that’s natural selection.”


    I have trouble understanding how this could be denied. In any case, arguing about the various processes that can result in genetic changes has no bearing on the question of the process by which those changes survive or not.

    1. And peanut butter goes well with that other ‘Atheist’s Nightmare’, the banana. Coincidence? I think not.

      1. Actually, peanut butter does not go with banana. But it does go with Miracle Whip and potato chips. Cheap port, madeira or sherry to wash it down with, is optional.

    2. Well, apart from the fact that biopoiesis is not evolution, you could be eating a pbj (or pbb) sandwich with new life in it every day, and never know.


    3. I think Einstein would be very saddened to hear that our inability to describe all mechanisms whereby mass is acquired would invalidate general relativity describing how mass behaves.

      Unfortunately I don’t think it bothers creationists that they ‘invalidate’ all of science, and all of knowledge, by such an analysis. They see it as an added bonus.

  10. Shapiro does have a mechanism.
    He thinks organisms – and his pet example is bacteria – direct their own evolution towards their own goals. It’s a form of directed mutation and introduces “purpose” into the equation. That’s right, bacteria direct their own evolution purposefully towards desired ends
    The idea is breath-taking in its stupidity.

    1. Thanks for that comment. I found his article very difficult to read but I was getting that impression as well and you’ve confirmed it. For example, he says things like “natural selection can’t be creative”

      It actually fits in with the general woo outlook at the Huffington Post. Ms. Huffington is very much into New Age BS, stuff like “The Secret”, etc.

  11. “‘Does natural selection really explain what makes evolution succeed?’ (the answer, of course, is ‘no’)” — Surely, “his answer”?

    “naive readers might get the impression that biologists are beginning to doubt that natural selection isn’t important” — “… is important”?


  12. Shapiro’s endosymbiosis theory falls apart spontaneously. Not only can’t he predict coordinated DNA transfer to the nucleus, but he can’t predict why it happens in that direction and not the other as it should be equally probable for his mutational mechanisms.

    There are several hypotheses on why that is as I remember it, but the result is fortuitous. According to Lane’s energy theory on eukaryotes it predicts the increased energy density that small-genome mitochondrion energy “plants” produce in comparison with prokaryotes that can at best use copies of their whole genome.

    Hence there is by now a specific selective pressure that keeps the gene flow going in the exclusive direction. (Modulo the genes that are still necessary for local metabolic enzyme production, I believe.)

  13. It seems to me, like most great scientific ideas, once one thinks about it, it becomes difficult to see how Darwin could be wrong. How could natural selection possibly not be what makes evolution “succeed”? (Calling it “success” is very strange in and of itself.) Does Shapiro really think (a la Billy Joe’s comment) that organisms somehow direct their own evolution? If so, Billy Joe is right – it is breaktakingly stupid.

  14. Natural selection is the default – it takes some extreme circumstances for selection not to happen.

  15. Here are a couple of clues to James Shapiro’s thinking:

    ” Darwin’s model of human selection is an intentional, goal-directed process with a desired outcome. It is precisely the opposite of a blind force.”

    “natural genetic engineering (the ability of all cells to cut, splice, copy, and modify their DNA in non-random ways)”

    What he calls “natural genetic engineering” is defined by him as “an intentional, goal-directed process with a desired outcome”. And, as I said, he bases this on his study of bacteria. Bacteria have intentions, and goals, and goal directed processes!

    In fact, all the processes that he mentions were produced by random mutation and natural selection. There is nothing non-random, intentional, or goal-directed about them.

  16. I think part of the problem is that Shapiro confounds novelties arising in an organism with novel changes in the population over evolutionary time. Evolution is a population-level phenomenon.

    I think replacing “organisms” with “populations” can help readers avoid Shapiro’s trap:
    “As always, Shapiro is ducking the whole question of how POPULATIONS acquire those features that make them thrive in their environments”.

        1. I can’t speak for BillyJoe, but I think he means that the adaptive features of organisms arise via selective sweeps in populations.

  17. Just out of curiosity, has Shapiro ever answered your challenges directly or via any legitimate peer-reviewed publication?

    1. Yes, he does it all the time on his HuffPo blog; needless to say, I haven’t been convinced by them. It would take a LOT to convince me that natural selection isn’t very important!
      He wrote a HUGE response today to me and told me to put it on this website, since it was too long for HuffPo (where he was going to publish a condensed version). I told him that our exchanges should be limited to posts, and I will call attention to his response at HuffPo when it’s up.

  18. Someone in HR at UChicago should have been fired over the hiring of Shapiro. He strikes me as more Liberty Baptist University material.

  19. I found Dr. Shapiro’s article disappointing in an unusual way after reading your book. I hadn’t done a lot of reading about evolution since I read your book and your blog, and I was surprised that a biology professor from your university doubted something like natural selection (especially after reading your book). I was a little uncomfortable with what I might find, so I went to read Shapiro’s article ready to learn some facts that would make me uncomfortable.

    Instead of make me uncomfortable with facts, I was annoyed by the excessive use of soft, philosophical points such as such as natural selection is a short answer (so people like it), or people who question evolution are abused, and there is a scientific crusade for Darwinian evolution, etc. If you want to challenge the professional consensus, you should start with brutal facts, not give me all this talk about being open-minded. UFO conspiracy theorists give me a lot of similar soft talk too, but they take a long time to get to the facts.

    Dr. Shapiro then lists some causes of genetic variation (some of which I remember your book or blog addresses in depth, such as gene transfer, hybridization, genetic duplication, etc.) but doesn’t explain how natural selection does not act on them. For example, I do not see how natural selection would not act on hybrids… or for that matter, any genetic change.

    I’ll be following what Dr. Shapiro says closely, and I hope his answer gets right to the point without any philosophical talk or comments on the battle for education or atheist crusades, etc. If he actually makes some good factual points, then I’ll read a book he recommends.

  20. The question of whether or not Shapiro’s arguments are being helpful to creationism is answered affirmitively just by noting that the Discovery Institute is so happy with them. They are promoting Shapiro as evidence that there is “dissent” among biologists, as in the Disco’tute “Dissent from Darwin” list. And, in many people’s minds, if not Darwin then creationism.

    Actually, Darwin could have happily signed the “Dissent from Darwin” statement;

  21. In a letter today in an Afrikaans newspaper in South Africa a well-known creationists quotes Jerry Coyne as follows:

    “Virtually all of the non-creationist opposition to the modern theory of evolution… ­come from molecular biologists. I’m not sure whether there’s something about that discipline (the complexity of molecular mechanisms) that makes people doubt the efficacy of natural selection, or whether it’s simply that many molecular biologists don’t get a good grounding in evolutionary biology.”

    Is this a correct quote and if so could you refer me to the full item so that I can see whether it was taken out of context or was not elaborated on – as I suspect.

    The quote is being used to “prove” that it is not only creationists who oppose evolution but also scientists. I would like to have ammo to kick his… well, to kick his arguments out of the park!


    1. Yep, I said this, and I think it’s in one of my posts on Shapiro (just enter “Shapiro” into the search engine and then do a “find” for the quote. I don’t have it at hand and don’t have time to hunt for it right now. However, just because all of the opposition to evolution from scientists comes from molecular biologists doesn’t meant that there is a LOT of opposition to evolutionary biology from molecular biologists! That’s the mistake the newspaper made. In fact, very, very few molecular biologists don’t accept the modern theory of evolution: James Shapiro happens to be one, and one of the rare exceptions. It’s like saying that because virtually all serial killers are men, that serial killing is widespread among men.

      And you can quote me on this to that newspaper.

      1. Thanks, especially for finding the time to reply to my query. I can use this quite well.

        Your book WEIT remains one of the best. Using it daily in debates. TH Pretoria

  22. Great post and thanks for your effort! I have been getting Shapiro followers on my website bugging me that the way I describe evolution isn’t true. However once you aks them how it does work, you just get nonsense back. No normal discussion is possible with them. He has even send emails to my supervisor complaining that my visions on evolution are wrong and that he should do something about it. It is very frustrating..

  23. I am not a biologist or a creationist just an interested layman. What I understood from my reading of Shapiro is that he doesn’t deny a role to natural selection in weeding out wrong’ns – that presumably is why it’s called natural selection. What he disputes is the source of the variation that is subsequently weeded out. The argument is more between random mutation v ‘natural genetic engineering’. Shapiro holds that the issue of natural selection remains the case irrespective. It is his idea that organisms can adapt, or mutate, purposefully in a way that is not just down to blind chance that needs to be addressed. I personally don’t see that this invokes any idea of a divine creator. No more so than any other purposeful activity in nature – such as a rabbit running away from a fox. These abilities can evolve as everyone agrees, but Shapiro argues that this kind of purposeful activity has evolved at a much more fundamental level than assumed by the idea of random mutation in life-forms.

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