A colleague wrongfully disses modern evolutionary theory

February 18, 2012 • 7:16 am

UPDATE:  Dr. Shapiro sent me a response to my critique below and asked me to post it; I have done so in the comments (here), and have written a brief response directly below it.


Jim Shapiro is a professor in Biochemistry and Molecular Biology here at the University of Chicago, so I suppose he could be considered a colleague, though I’ve had almost no interaction with him.  I have, however, followed his activities in the literature—and with some dismay.  Shapiro, it seems, has devoted much of his writing to pointing out that the modern theory of evolution (“neo-Darwinism”) is deeply flawed and needs a new paradigm.

That, I think, is the thesis of his book, Evolution:  A View from the 21st Century, which was published in June of last year. I haven’t read it, but Shapiro presents a summary of its thesis in a piece at the HuffPo science page, “What is the key to a realistic theory of evolution?” His thesis is that, contrary to Darwin’s views, and those of modern evolutionary biologists, evolution is not as “gradual” as we think:

Darwin put it this way in Chapter 6: “If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find no such case.”

There has always been controversy about whether random variation and natural selection for improved fitness can truly explain biological evolution over time. Today we can apply genome sequence data to test Darwin’s theory. It answers clearly about gradualism.

Many genome changes at key stages of evolution have been neither small nor gradual.

Now what one means by “gradual” is a matter of taste.  Nearly all of us agree that large changes in phenotype—the complex of traits that distinguish, say, genera or families, don’t occur instantaneously but take thousands to millions of years to accomplish.  Sometimes these changes are faster than others (this is the basis of the “pattern” part of punctuated equilibrium theory), but they never happen overnight.  And we know from the fossil record that gradualism is often the case: the transformation of land-dwelling artiodactyls into whales, for example, took about ten million years, and the transformation of reptiles into modern mammals took three or four times that span.  We know this because we see the gradual transformation of fossils.  Theory also tells us that such profound evolution can’t happen instantly: it’s unlikely to see a single mutation that would, for example, transform a theropod dinosaur into a bird (many traits must change before that happens), and the coordinated change in many traits that differentiate these groups takes time, as we must await the buildup of many mutations. There’s also a limit to how fast selection can transform populations.

I’m comfortable with saying, then, that big changes in form in evolution are—and must be—gradual, with “gradual” meaning tens of thousands to millions of years.

Shapiro, however, points out that there are instances of more rapid evolution:

  • Polyploidy and other forms of speciation involving hybridization.  Sometimes different species in nature can hybridize, and, though the hybrids may be sterile, they can undergo doubling of the hybrid set of chromosomes to produce a fertile “allotetraploid” species that is fertile because each species’ chromosomes can pair during gamete formation.  This has happened many times in nature (we estimate that 2-7% of all flowering plants arose this way), and it’s very quick: about 2 generations.  We have actually seen this occur in a human lifetime in nature: this is described in WEIT. New species can also arise in this way by doubling of the chromosomes of a single species, forming an “autotetraploid”. Or, sometimes, interspecies hybrids can form new species without doubling their chromosomes; their genes sort out in a way that makes them reproductively isolated (and morphologically different) from the two parental species.  This process, called “diploid hybrid speciation,” occurs relatively quickly as well: I believe that some diploid hybrid sunflowers arose in about 50 generations.  Darwin, of course, didn’t know about this because the genetics wasn’t worked out till much later.   Polyploidy is a rapid form of evolution and speciation, one that is fairly common in plants, but very rare in animals. (The reason for its rarity in animals isn’t understood, but we discuss the theories in the book I wrote with Allen Orr, Speciation.

Many domesticated species arose by either deliberate hybridization by humans or selection on naturally-occurring hybrids.  Wheat, for example, cited by Shapiro as an example of near-instantaneous evolution, did arise by humans picking out a naturally-occurring hybrid; this probably happened twice, so that modern wheat contains the genomes from three wild species of grass. But much of the selection that makes for modern wheat was also artificial: humans picked out the variants with bigger heads that remained on the plant. So the differences between wild and cultivated wheat don’t completely exemplify near-instantaneous evolution in nature.

  • Symbiosis.  We all know, thanks to Lynn Margulis, that the evolution of the eukaryotic cell involved two rapid evolutionary events: the acquisition of mitochondria via the ingestion of one bacterium by another cell, and, in plants, the origin of chloroplasts via a similar route. Centrioles (a group of microtubules involved in cell division) may have originated via symbiosis.  And some species, like lichens, are actually a mixture of two distinct species—in the case of lichens, an alga (or cyanobacterium) and a fungus. That fusion probably happened quickly as well.

Margulis theorized that symbiosis was not only important in evolution, but ubiquitous, involved in nearly all cases of speciation and macroevolution. She was wrong. We know now that the rapid origin of new taxa by symbiosis, while critical for some evolutionary transformations, is rare.  It can hardly be used to discount the notion that “Darwinian” evolution is usually gradual.

  • Acquisition of DNA from other species.  This uptake of DNA between species, also called “horizontal gene transfer” (HGT) happens sometimes, and although rare (especially in animals), may be more common than we think.  I regard it as a form of mutation, since the acquired gene is, after acquisition, subject to evolution via natural selection.  Given its rarity (if it were common we wouldn’t be able to make good DNA-based trees of various species) and the subsequent modification of the acquired DNA by natural selection, it’s doubtful whether HGT qualifies as “instantaneous evolution.”
  • Genomic changes other than slight changes in DNA sequence.  Shapiro cites several of these which have been involved in the evolution of new genes, including gene duplication (a whole gene gets copied in its entirety, which can lead to the origin of “gene families”) and the formation of new genes by pasting together bits of old ones (this is the topic of research by my Chicago colleague Manyuan Long).  But while these pheomena are “rapid” on the DNA level, they’re not necessarily a cause of rapid evolution on the organismal, biochemical, or even genomic level.  After all, those new genes, particularly the duplicated ones, must undergo their own gradual divergence via natural selection: that’s how the different opsins in our eyes, the divergent genes in our immune system, and the different types of human hemoglobin arose.  That differentiation took a long time, because the new genes have to await mutations.

So yes, evolution can be almost instantaneous in the case of symbiosis and polyploidy, and there are mechanisms of mutation not dreamt of in the genetics of Watson and Crick. But does this invalidate the paradigm of neo-Darwinism? Shapiro thinks it does:

Was Darwin simply mistaken about the gradual nature of hereditary variation? Such ignorance would be unavoidable before we knew about Mendelian genetics and DNA. Or was there a deeper flaw in the theory that he (and Alfred Russell Wallace) propounded? The answer may well be that it was a basic mistake to think that optimizing fitness is the source of biological diversity.

Here he’s completely wrong.  Yes, evolution can sometimes be rapid, though most of the time it’s gradual, but in all cases—all cases—adaptive evolution occurs by natural selection, and that means “optimizing fitness.”  Shapiro is getting Darwinism wrong here, for he’s conflating the materials of evolutionary diversity (mutations and new genes that arise randomly) with their disposition by natural selection, a nonrandom process that does involve “optimizing fitness.” Given that adaptive differentiation between species involves natural selection, you simply cannot say that “optimizing fitness’ is not a part of biological diversity.  That attack on neo-Darwinism is misguided, and it’s wrong to suggest it to lay readers.

Shapiro’s piece then rapidly goes downhill as he starts repeating creationist arguments. Here’s one:

The first problem with selection as the source of diversity is that selection by humans, the subject of Darwin’s opening chapter, modifies existing traits but does not produce new traits or new species. Dogs may vary widely as a result of selective breeding, but they always remain dogs.

You’ll recognize this as the old creationist canard.  Yes, of course we can’t turn a dog into a cat by artificial selection, because that would take millions of years, and we’ve only been selecting on dogs for a couple of thousand years.  But the true refutation of this idea is in the fossil record: we can see land-living artiodactyls (resembling small deer) turning into whales, we can see fish turning into amphibians, we can see early reptiles turning into mammals, we can see theropod dinosaurs turning into birds, and we can see our apelike ancestors turning into more modern humans. In other words, we find in fossils precisely those transformations that Shapiro says are impossible.  I deplore that a colleague of mine makes this misguided argument, and in the Science section of HuffPo, which I’m increasingly beginning to deplore as well.

Shapiro also goes after the neo-Darwinian idea that mutations are random:

The second problem is that Darwin understood only “numerous, successive, slight modifications” as the sources of inherited change. His neo-Darwinian followers have modified this position to assert that all mutations occur randomly. They insist there is no biological input into the change process. For them, the genome determines organism characteristics. They think of it as a read-only memory (ROM), which only changes by accident.

Well, he’s wrong again here.  What we mean when we say that mutations are “random” is not that there’s no biological input into the mutation process (that would be a truly stupid assertion), but that the biological inputs into diversity occur irrespective of whether they would be useful to the organism. Mutational change occurs by accident, or as a byproduct of something else (like a gene being accidentally duplicated, or the ingestion of DNA from another species), but those changes occur whether or not they’d be “good” (i.e., increase the reproductive output of)  individuals in the species that has mutated.  Gene shuffling, gene duplication, horizontal gene transfer: all of these are biological accidents that are just the precursors of adaptive differentiation—the fuel of evolutionary change.  They’re the gas that fills the tank of the car, which moves by natural selection.  Adaptive differentiation still requires the process of natural selection: the nonrandom differential reproduction of genes (and individuals), usually involving greater success in the environment.

While Shapiro rightfully points out that there are more sources of genetic variation than were dreamt of in your genetics, Watson and Crick, he is misguided in thinking that these new sources of variation completely destroy the Darwinian idea of gradualism and natural selection.  We see many examples of gradual evolutionary change in the fossil record, and natural selection is still the only game in town when in comes to explaining adaptations.  If Shapiro knows any other way that adaptation can occur, let him tell us.

Neo-Darwinism has certainly expanded since it began to form in the 1930s, and it should: evolution is a vibrant science with new discoveries occurring weekly. But it’s simply wrong to think that those new discoveries have invalidated (or even caused a serious reassessment of) the major tenets of neo-Darwinism.  That theory is regularly pronounced dead—as it is here by Shapiro—but it refuses to lie down.

146 thoughts on “A colleague wrongfully disses modern evolutionary theory

  1. I have read Shapiro’s book and was also taken aback by his statement that natural selection per se never produced a new species. I have been waiting for reviews, and I hope that Coyne will write a full review after his has read the book. The book is a useful source of information even if you don’t go along with the main thesis.

    1. It’s is absolutely correct that selection alone has never produced a new species. Selection does not produce variation. Mutation does (and recombination leads to novel combinations of alleles, produced themselves by mutation).

      Selection (largely purifying/negative, rather than something being better than its neighbours) does generally play a role in speciation, but it acts upon standing variation in populations and subpopulations ultimately produced by mutation. It is not alone.

      My current pet species complex (Paramecium “aurelia”) has likely diverged due to differential loss of duplicated genes following the whole genome duplication event immediately preceding their divergence. It wasn’t that one species-to-be was particularly better at at something than another (initially anyway), but rather a case of mating incompatibilities arising from losses of differing duplicated genes — even just for two loci, given lowercase letters are loss-of-function mutations and you need *either* A or B to function, if you cross AAbb x aaBB, you end up with 1/4 of the offspring having aabb, a lethal variant. Do this at a few more loci (CCdd x ccDD; need either C or D to live) and now your offspring have a 1/4 + 1/4 chance of being aabb or ccdd — this itself makes interbreeding less and less frequent and your populations ultimately diverge permanently — and speciate. Natural selection in the popular sense (positive selection, “survival of the fittest” stuff) was not involved at all in this example; only negative selection removing the inviable individuals was in play. And yet speciation happened quite happily, and lead to 14 species in a fairly quick burst, evolutionarily speaking.

      (this is also a clear example of sympatric speciation, which some manage to argue is non-existant/impossible, for some reason)

      1. Natural selection in the popular sense (positive selection, “survival of the fittest” stuff) was not involved at all in this example; only negative selection removing the inviable individuals was in play. And yet speciation happened quite happily, and lead to 14 species in a fairly quick burst, evolutionarily speaking.

        How is this different from natural selection? In natural selection you have both what you call “positive” and “negative” selection — though in the wild this is really a false dichotomy — some organisms will die (negative), some will reproduce at below the rate required for stasis (negative), some will reproduce the right amount for stasis or a little more (positive), and some will reproduce at much greater than the rate of replacement (positive). And everywhere in between. All of these scenarios describe “survival of the fittest.”

        You’re making a distinction without a difference.

  2. It seems as if Shapiro has fallen prey to the allure of reductionism. Just because there is rapid change at the sequence level (macromutation) there is no guarantee it will be detected at the organismal level. Which, again, stresses the need for holistic approaches in biology. (Good grief, that sounds like woo; but I’m serious.) It’s easy to see a skewed view of evolution at the molecular level. It’s always good to step back every once in a while and see the whole picture.

    Jerry, when you say lateral gene transfer isn’t common, are you referring to the metazoa? Because when you consider it in the prokaryote context you realise genes are too mobile for meaningful phylogenies (although it is controversial). It is true we can draw trees, but only using a small, small subset of the genome. Is such a tree accurate, even if it can be drawn? (I like the paper on a 32 gene tree by Ciccarelli et al in Nature, and the comment by Dagan et al calling it a “tree of one per cent”.)

    1. I suspect he’s fallen prey to the allure of coining yet another revisionist term, something that seems to tempt an ever increasing number of academics particularly in the biological realm. So what might that be? Neo-neo-Darwinsism? I have plenty of problems with Neo Darwinism to begin with.

      I wonder if the guy’s ever read WEIT?

    2. Dagan and Martin are a little overenthusiastic with the LGT in prokes issue, IMO — almost more so than the original proponents. First of all, there clearly is a bifurcating tree of cells (since they don’t fuse in prokaryotes), and therefore there is a tree of life. I do think it is ultimately possible to recover it, but that may require some advances in phylogenetic technique (beyond just identifying core genes). I think a bigger issue with proke phylogenies might actually be the depth — bacteria have been around much longer and also have really short generations, meaning they’ve evolved much more by present day. There might just not be enough reliable phylogenetic signal to properly resolve the trees at that depth.

      Does this conflict with what Darwin said/Neo-Darwinism/Modern Synthesis? Who the fuck cares, none of them are relevant for the past few decades! 😉

    1. Yes.

      I suspect that he’ll be horrified at the suggestion.

      But I may be wrong.

      What started out as a scientific disagreement over the pace of evolutionary processes went right off the rails with the overtly creationist claim that no species can give rise to a different species.

      Even in dogs, speciation has occurred. There are breeds of dogs that cannot interbreed with others — which is one of the most-classic definitions of “species”. And several breeds of dog cannot interbreed with the basal species, the wolf.

      So, even his example was wrong in the main.

    2. It already has, in a sense.

      Shapiro is on the radar of ID adherents:


      I attended that presentation. Unsurprisingly, the title has been quote-mined. What Shapiro said, to many a gasp in the audience, refers to Dawkins’ gene-centric view developed in The Selfish Gene, the idea of organisms being essentially DNA replication machines.

  3. So where does Shapiro get his ideas from?
    Since he uses many analogies in his HuffPo paper, let me use one too: how did he get the bugs into his software?

  4. selection by humans, the subject of Darwin’s opening chapter, modifies existing traits but does not produce new traits or new species. Dogs may vary widely as a result of selective breeding, but they always remain dogs.

    This claim is just absurd. If one encountered Pomeranians and Great Danes in the wild, one would not think they are the same species, and indeed they would be reproductively isolated.

    In a real sense, dog breeds are a ring species — you may be able to breed a smaller breed to a slightly larger one and so on, but the extremes in size cannot interbreed except artificially.

        1. The quoted part about them always remaining dogs. According to cladistics, they’d have to remain dogs for the same reason that they remained mammals and chordates: a species can never evolve to stop being a member of a group that one of its ancestors was part of.

  5. I have his book (which has a very pretty cover, I must admit) sitting on my “waiting to be read” pile. I skimmed it, and the meat of the book seems to be his discussions of the many ways that genomes can be modified, above and beyond the usual point mutations.

    If he stopped there, it would be an interesting book. Generating variation turns out to be easier than we used to think. This is actually another nail in the coffin of ID or creationism, since one of the standard arguments against Darwinian evolution is the perceived improbability of some of the adaptations we observe.

    But he seems to want to push his arguments into the ID camp by hinting that these changes may not always be “blind”. If he tries to back this claim up somewhere in his book, I have not found it yet.

    However, as Larry Moran is likely to chime in here any minute to point out, Shapiro’s statement that “it was a basic mistake to think that optimizing fitness is the source of biological diversity” is in fact correct, though not for the reasons Shapiro thinks. Much variation (at least if measured at the molecular level) is apparently neutral or nearly neutral, and arises by blind genetic drift, not natural selection. Of course, this does nothing to support Shapiro’s argument.

    1. I don’t understand Larry Moran. Maybe i’m ignorant and biased by first impressions of reading his posts on this and other sites, but he seems to have a bit of a chip on his shoulder when it comes to recognizing the significance of the adaptationist program. I commend him for challenging just-so stories, but (and again, this might just be me) he seems a little overcompensating at times. Maybe he gives due credit to adaptation, but i can’t recall reading much of that in his posts.

        1. I look forward to the day when everyone will understand the role of random genetic drift in evolution and stop using “evolution” and “natural selection” as synonyms. Until that day, I will continue to do my best to inform the ignorant.

          I’m encouraged that some of you recognized the problem before I had a chance to comment. That’s progress!

          1. Larry — “the day when everyone will … stop using ‘evolution’ and ‘natural selection’ as synonyms” — Is this really what people do?

            Who says, “evolution by evolution” or “natural selection by natural selection”? 😉


              1. Providing some actual citations would go a long way in demonstrating that you’re doing something other than attacking a straw man.

              2. Speaks volumes about what? And what error is it that you did describe?

                Yes, many people see no other engine for evolution than natural selection, but that is not the same as using the terms as synonyms… 


              3. Ant, when you said “many people see no other engine for evolution than natural selection”, you are leaving out purely stochastic processes (drift), which are actually the main driving force for evolution, if evolution is defined as “change in gene frequencies over time”. (Most mutations are apparently selectively neutral or nearly so, and their fate is determined mainly by drift.) Leaving out stochastic processes is the error Larry is speaking of. And to avoid that error, Jerry specified “adaptive evolution” in his post, so he could exclude random drift.

              4. Larry, Lou & Psi (below) — I think I wrong footed you all with my sense of humour. I was facetiously criticising Larry’s use of “synonym”. If that wasn’t clear from the first comment, I would’ve thought it was clear from the second.

                Even the people who make the error that so irritates Larry (and thank you for providing the links) are not conflating evolution (“the process by which different kinds of living organisms are thought to have developed and diversified from earlier forms during the history of the earth”) and natural selection (“the process whereby organisms better adapted to their environment tend to survive and produce more offspring”), any more than a person who ignores the existence of diesel fuel would conflate internal combustion engine with petrol (gas).

                Perhaps I could have been clearer by saying:

                Yes, many people erroneously see no other engine for evolution than natural selection, but that is not the same as using the terms as synonyms


                PS. In “Dawkins on Chance”, you say, Larry, “[Adaptationists] frequently use the word ‘evolution’ as if it were a synonym for ‘evolution by natural selection.’” And that’s fine. (The English usage, if not the evolutionary biology.) But that’s not what you said here! 😀

            1. Yes. It is. Or do things like this: “The mechanism of evolution is natural selection” — (direct quote) Trevor Price, a prominent evolutionary ecologist, at a symposium at UChicago this past fall.

              Hell, we have a display case in our department titled “Natural Selection: The mechanism of evolution”. In a department with several prominent non-adaptationist non-Darwinian faculty.

              It’s fucking pervasive, even among professional biologists, and like Larry, I too will not shut up until people learn better. It’s not a case of nuanced semantic pedantry — it’s a fundamental misunderstanding of evolution, and very much flawed.

              1. I can’t help noting that even population geneticists have badly misunderstood how drift generates genetic differentiation between demes. They make a math error that causes them to misidentify the factors involved.

    2. I recognize the importance of drift on the molecular level; that’s why I discussed “adaptation” rather than “evolution” in this piece.

      1. Yes, I know you have always been careful about that. Shapiro statement doesn’t restrict itself to adaptive changes, though that is probably what he meant, based on the context.

      2. Jerry, I understand why you converted Shapiro’s statement from one that was only about diversity to one that was only about adaptation and speciation.

        Shapiro said, ” … it was a basic mistake to think that optimizing fitness is the source of biological diversity.”

        What if Shaprio had said that it is wrong to think that optimizing fitness is the ONLY source of biological diversity? Would you have a problem with that? I seem to remember a man called “Lewontin” who showed us over forty years ago that a lot of diversity was due to the segregation of nearly neutral alleles in a population. Perhaps you’ve heard of him? 🙂

        BTW, I have read Shapiro’s book and my review will be coming out soon. His book is not worth reading.

          1. He might be of the Dawkinsian camp, where neutral mutations just silently lurk about as background noise, “of interest only to molecular biologists” (Dawkins in The Greatest Tale on Earth, IIRC).

            Hopefully in a few years I can contribute yet another paper showing that’s not true 😉

            1. Yes! ALL alleles, neutral or not, experience these stochastic processes. Natural selection is superimposed on these stochastic processes and limited by them. Stochastic processes are more effective than weak differential selective pressure in causing genetic differentiation between small partially isolated populations.

  6. “And we know from the fossil record that gradualism is often the case: the transformation of land-dwelling artiodactyls into whales, for example, took about ten million years, and the transformation of reptiles into modern mammals took three or four times that span.”

    I thought Mammals transitioned from Synapsids and that Synapsids are no longer considered to be true reptiles or even mammal-like reptiles? Or is there disagreement in the field?

    Nice post Dr. Coyne

    1. There’s no disagreement about the animals or their phylogenetic relationships. Any disagreement is semantics–the use of the word ‘reptile’. If it has scientific meaning (as Reptilia, though most people call the same clade Sauropsida instead) then it includes birds and excludes all ancestors of mammals.
      In the vernacular sense, ‘reptile’ still means any amniote that’s not a mammal or a bird.

  7. I just looked at the review on Amazon for his book. One reviewer writes, “He describes living cells as cognitive, interacting with purpose to insure survival.”

    (jaw drops)

  8. “a basic mistake to think that optimizing fitness is the source of biological diversity”

    Man, this is fodder for creationists! I wonder what Shapiro thinks is the alternative then – some kind of directed evolution??

    1. Yes, but technically, I think Shapiro’s statement is correct. See my comment above. Lots of variation is neutral, or so nearly neutral as to be invisible to natural selection. Natural selection is not THE source of biodiversity, though it is an important source.

        1. DV, I am saying that GENETIC variation is largely neutral. For example, much of the variation between individuals and species is in the parts of the DNA usually classified as junk.

          Phenotypic variation can also be virtually immune to natural selection if a character’s selective advantage or disadvantage is small and the population is also small. Drift outweighs selection under those circumstances, and non-adaptive genes can become fixed in the population. This is quantified by Ohta’s “nearly neutral theory”.

          1. “Drift outweighs selection under those circumstances”

            Where is the consensus on whether “those circumstances” are involved in the majority or minority of speciation events? And I assumed by “biological diversity” Shapiro was talking about species diversity.

            I think the confusing part of Shapiro’s claim is the word “source”. I think strictly speaking natural selection “works” on genetic variation – however those variations came about. It would be non-controversial to say that natural selection doesn’t produce mutations because nobody thinks that it does. But then he actually goes on to say that selection does not produce new species! I think this is the clarification of his earlier statement (about optimizing fitness not the source of biological diversity). Do you agree?

            1. That’s a fair criticism of what I said. If biodiversity = species richness, then natural selection certainly played a leading role (though not the only role). If biodiversity = genetic diversity between individuals or species, then purely stochastic processes take the leading role.

              Even if we say biodiversity = species richness, population genetics shows that purely stochastic processes form the backdrop against which natural selection must work. Speciation is facilitated when these stochastic processes favor evolution of genetic differentiation between populations, and impeded otherwise. So in this sense, stochastic processes play a fundamental role even in the generation of species richness. If two identical islands were colonized by an organism, and there were little or no subsequent migration between islands, the two forms would diverge through drift until they became distinct species, without any involvement of natural selection (see the work of Sergey Gavrilets for the mathematical analyses backing this up.)

              Optimization of fitness is therefore not the ONLY process that generates biodiversity. Perhaps Shapiro meant his sentence in a stronger sense: Optimation of fitness is NEVER the process that generates biodiversity. If that is what he meant, he must be ignorant. (I also strongly disagree with most of his other conclusions.) I hope Jerrygoes and talks to him.

          2. I guess I (or you) don’t understand genetic drift. Isn’t it a general shift in average genome sequence between populations? How can the average genome sequence drift on its own? Isn’t the fact that it has drifted evidence that it has been selected – and that it is not neutral? Don’t genes drift when populations are exposed to different environments with different survival challenges?

            What does the statement: “optimizing fitness is the source of biological diversity” even mean? That the effect is the cause?

              1. GBJames, Genetic drift also occurs between populations. The effect is greatest when the populations are nearly isolated. The neutral alleles that drift towards high frequencies will often be different in each deme, by pure chance. This process can be modeled and the expected value of genetic differentiation between populations at equilibrium can even be calculated exactly under simple population models. If differentiation is defined to be 0 when the allele frequencies are identical in the n populations, and unity when all alleles are completely different in each of the n populations, and common alleles are weighed more heavily than rare alleles (as heterozygosity weighs them), then at equilibrium, differentiation due to drift+mutation+migration equals approximately 1/[1+P/u] where P is the pairwise migration rate and u is the mutation rate. Differentiation between populations can be large even for neutral alleles, due to purely stochastic effects.

                This formula applies to Wright’s finite island model. A nearly identical formula applies to the stepping stone model.

              2. But Lou… having sufficiently waken up to type… doesn’t this come down to the definition of “population”?

              3. GBJames, I don’t understand your question. Whether the groups in question are members of the same species or different species, and whether migration between them was high or low, they would still diverge by drift+mutation, unless they were panmictic.

              4. Lou: If we are talking about two species, then you can’t have drift between them because there is no way for genetic material from one group to influence the genetics of the other (leaving aside competition or symbiotic relations between them… which wouldn’t be drift anyway). So that means we are talking about changes gene frequencies within a single species (which early in the morning, coffee-deprived, I swapped for the word “population”).

                So.. two islands with critters of the same species on them. Is this one population or two? Doesn’t it depend on things like how close the islands are to one another, what kind of migration might occur between the islands, and other factors like that? Isn’t the idea of drift between two populations contingent on relatively infrequent contact between the two?

                I’m not arguing with you… just asking for clarification.

              5. GBJames, in your first example, with two reproductively isolated groups (e.g. two different species), both groups experience independent random drift in their allele frequencies at a given locus. If the locus is nearly neutral, Allele A might become common in one group, while purely by chance, Allele B might become very common in the other group. After a very long time, mutation will have generated unique new alleles in each group, and eventually they will not share any alleles at all at this locus. The equilibrium genetic divergence between the groups is therefore 100%, as predicted by the formula I gave you (P=0). You get complete genetic differentiation between the groups at neutral loci.

                In your second example, you are right that the amount of drift between the groups depends on their connectivity (but also on the mutation rate). With nonzero migration between the groups, the expected amount of differentiation between groups at a neutral locus is controlled by the migration rate between pairs of islands, divided by the mutation rate, as given in my formula.

                It is not an either/or situation; your first example (P=0) and your second example (P>0) are governed by exactly the same law, just with different values of P (pairwise migration rate).

            1. Curt, see my answer to GBJames below. Shifts in allele frequencies between populations will occur by chance alone, with no natural selection. Stochastic processes like these can either favor or negate weak natural selection. In small populations, stochastic processes will often dominate natural selection.

              1. Yes, and a variable portion of “genetic drift” is a signal of adaptive reaction to the changing environment.

        2. Yes.
          For starters, I recommend this: http://www.indiana.edu/~lynchlab/PDF/Lynch155.pdf

          Selection is not an all-or-nothing process, and in finite populations over a finite period of time, there is a certain window of “effectively neutral” mutations (not only on a molecular level) that are ignored by selection as drift is likely to fix (or lose) them before selection gets around to pushing the allele frequencies one way or another. In things with smaller populations (eg. big things like us and elephants; metazoa in general, eukaryotes compared to prokaryotes), this effective neutrality range gets quite big, and lots of unintelligent design gets tolerated and allowed to reach fixation. In fact, I’m willing to argue that the only reason clunky multicellular mammals are allowed to exist is that their small effective population sizes tolerate the complexity bloating to accumulate (while being worse overall at the job of producing lots of offspring).

          Not everything is adaptive, and quite a few things are effectively neutral. This is something that is tested both experimentally and by observing natural populations, so it’s not just theory or mere speculation — unlike much adaptationist storytelling.

          1. “Genetic drift” looks neutral because we’re unable to detect the diffuse probability of an adaptive component in the signal; our dogma exclusdes it so we don’t try.

            1. Mounthell, it is easy to show mathematically how drift affects alleles that are completely neutral, and how it can dominate over natural selection for alleles that are nearly neutral. Look up Ohta’s nearly neutral theory in any population genetics book. The flip side of this is that you are right, we can never be sure that a locus is neutral just by observing its allele frequencies. We can only say that the magnitude of the selection coefficients for these alleles is less than some very small number.

            2. Can you elaborate? That didn’t make sense to me…

              Do you suggest neutral mutations don’t exist? Because I kinda make my living right now off the fact that they do, via minimal selection mutation accumulation experiments.

              Fundamental theory predicts the existence of neutrality just from the simple fact that natural populations are finite, and evolution occurs over finite stretches of time. Infinite populations over infinite time models are sooo early-20th-century…

              1. Do you suggest neutral mutations don’t exist? Because I kinda make my living right now off the fact that they do, via minimal selection mutation accumulation experiments.

                Is this supposed to be an argument? If Mouthnell turned out to be right (big “if” I understand) you would hardly be the first scientist to devote his life’s work to an incorrect model. Actually, that would probably put you in the vast majority of scientists who have ever lived.

      1. That’s the whole problem with things – what sort of idiot would think that there is One Source of diversity? Shapiro is attacking a straw man, and in a very muddleheaded way.

  9. Jim Shapiro is not alone (among current evolutionary biologists) in doubting the efficacy of natural selection as the main cause of adaptive change. Andreas Wagner of the University of Zurich, for instance, has stressed in his recent work that natural selection fails to explain the origin of evolutionary innovations. Wagner argues that

    “…we know few of the principles that explain the ability of living things to innovate through a combination of natural selection and random genetic change. Random change by itself is not sufficient, because it does not necessarily bring forth beneficial phenotypes. For example, random change might not be suitable to improve most man-made, technological systems. Similarly, natural selection alone is not sufficient: As the geneticist Hugo de Vries already noted in 1905, ‘natural selection may explain the survival of the fittest, but it cannot explain the arrival of the fittest’. Any principle of innovation needs to explain how novel, beneficial phenotypes can originate.”

    (A. Wagner, “The molecular origins of evolutionary innovations,” Trends in Genetics 27 [Oct 2011]:397-410; note numbers omitted)

    1. “Random change by itself is not sufficient…” and “Similarly, natural selection alone is not sufficient…”

      I’m confused. Who has proposed that either of these is by itself sufficient?

    2. Yes,and of course there’s Paul’s hypothesis: it’s due to the Hand of God.

      Shapiro may not be alone, but he’s in a pretty small and pathetic company. None of them have proposed a credible alternative to natural selection.

        1. And your response is to insinuate that it’s a poor argument without offering your own. Thank you for the demonstration of how to simultaneously lose an argument and look like an fool doing so.

    3. “natural selection may explain the survival of the fittest, but it cannot explain the arrival of the fittest”

      What am I missing here? Does this really say anything novel or insightful?


    4. ‘natural selection may explain the survival of the fittest, but it cannot explain the arrival of the fittest’

      That bunkum is right up there with creationism. The answer is the same – it is random mutation and natural selection. Sometimes an adaptive trait isn’t even obvious until some environmental factor gives the individuals with that trait an advantage, as in the case of the Peppered Moth. In the case of humans we have the more recent example of adaptation to pathogens; folks in Europe had a very long time to adapt to various pathogens which were alien to the New World and the introduction of various pathogens to various groups in the Americas decimated the native populations and left, to a large extent, a group which was better adapted to the new pathogens. The ‘fittest’ were already there – all that was lacking was the environmental stress that would give them a reproductive advantage over the rest of the population.

      1. My, aren’t we the twitted dogmatist! The post containing Hugo de Vries’ quote remains a legitimate question; it obviously is not creationism. The question of the origins of new features — there are several sources, the question is the apportionment — is THE biology question and remains unanswered. (The moth example is prominent only because nitwits can grasp it; it is not the only innovation source/scenario.)

        Much of what is written here is not about a principle proven by data, it is instead editorializing or parroting (mis)interpretations, blank-eyed opinion, of data. Get real.

        1. Throwing the word “dogmatist” around is the surest way to convince everyone else that you’re only objecting to the “dogma” of others because it competes with your own. MadScientist actually nailed it: “the fittest” is a verbal handle to help limited human beings grasp an incredibly complex process. But “the fittest” can only be defined with respect to particular selection pressures; apply a different sort of pressure (predation versus food shortage, for example) and your estimation of “the fittest” is going to be completely different.

          You can’t make sense of “the fittest” and “selection” in isolation, they are complementary in this context.

          You can talk about the origin of new features all you want, but they don’t magically pop into existence. Selection works on the genes already in a population, there isn’t a magical drift genie poofing the right mutations into being at just the right moment. Get real indeed.

  10. I’ve often thought that phrase like ‘optimising fitness’ is misleading. ‘Penalising unfitness’ is more of a nod in the direction of the tremendous amount of death involved in evolution.

    1. Yeah, the prize for being the “fittest” is not dieing before reproducing. Emphasizing that selection works by weeding out poorly adapted individuals would be a good idea.

        1. Yeah, I guess you’re right.

          For one thing, I’m having trouble thinking of ways for They Might Be Giants to work that into a song title.

    2. Sure, purifying selection is the dominant mode of selection. However, it would be wrong to discount the role of selection for beneficial functions.

    3. Yes, yes.
      I think that Shapiro is making the mistake of thinking that the instructions that provide the function came before the function itself. Form really does follow function.

      The function that “fits” the circumstances is always available in the large pile of functions that don’t fit. Natural selection find those that fit by eliminating those that don’t….it takes time.

      As a engineer, designer I suggest that even and maybe especially “designed” things that work are revealed from the elimination of all the things that don’t work. The more talented designers both build on what’s been done and eliminate large numbers of bad designs quickly.

      IOW, even our so called top down design is very much a matter of natural selection. It’s just a matter of perspective.

  11. I hope he reads the comments and is suitably horrified:

    “James–How does this relate to Sheldrake’­s idea of morphic resonance if at all? Could archetypes transmitte­d by morphic fields influence the process of “natural genetic engineerin­g?” Also how does phenotypic plasticity relate to this if at all? Are these naturally engineered changes examples of phenotypic plasticity­?”


  12. I am only a dilettante “scientist”. I could nevertheless quite easily program a computer to gradually evolve any arbitrary stepwise function to closely resemble any other arbitrary stepwise function. A stepwise function in turn can closely approximate any continuous function. (This can be done irrespective of the number of independent variables.) The algorithm used was strictly and purely a Darwinian one. I suspect that those who criticize neo Darwinism fail to comprehend its impressive mathematical power.

  13. Even when a new species is produced via polyploidy it doesn’t mean it will succeed in the environment. Spartina anglica is a superweed but it could just have easily been the same as it’s progenitors. It is so effective as a species it’s considered to be invassive in it’s country of it’s origin and wherever it turns up.

  14. A colleague wrongfully disses modern evolutionary theory

    A few hundred years ago, they were saying that Galileo was wrongfully dissing Ptolemaic astronomy.

    I’m not saying that Shapiro is another Galileo. But I am suggesting that we should not just write off dissenting views merely on the basis that they are dissenting.

    Shapiro, it seems, has devoted much of his writing to pointing out that the modern theory of evolution (“neo-Darwinism”) is deeply flawed and needs a new paradigm.

    I am inclined to agree with him about that, but to disagree about his ideas for that new paradigm.

    (from Shapiro’s PuffHo article) Since 1859, Darwin’s followers have focused on optimizing reproductive success, now called “fitness.”

    I agree with Shapiro in disliking that focus.

    If life started out as photo-synthesizing algae (as some suggest), and then proceeded by optimizing, then humans should be highly optimal photosynthesizing algae.

    My preference is to look at evolution as a program of exploring the unknown, and finding new niches to occupy within that unknown. “Optimization” is a poor way of describing that program of exploration.

    1. Oh for crying out loud. I didn’t write off his views because they were dissenting.I criticized them because the evidence is against them. Didn’t you read my arguments at all? And I didn’t even mention all the experimental evidence in favor of the view that mutations are truly random. Or the multifarious evidence for the existence of selection in nature. If you agree with Shapiro that fitness increase isn’t important, please explain to me your own interpretation of the change in beak shape of the medium ground Finch on Daphne Major in the Galapagos in 1976-1978. I await your answer.

      As far as we know way new niches are occupied is through natural selection, which is a process of gene sorting based on differential fitness. We have plenty of evidence for that, while your idea of “finding new niches” has no mechanistic explanation of how organisms adapt to those new niches.

    2. Life didn’t start out as photosynthesizing algae (nor as photosynthesizing bacteria). Who suggests that it did?

    3. A few hundred years ago, they were saying that Galileo was wrongfully dissing Ptolemaic astronomy.

      First of all, who is it that you think “they” were? Copernicus and Kepler were already working on the heliocentric model by the time Galileo got in trouble. Galileo got in trouble for insisting the heliocentric model was true, not for being insufficiently respectful of Ptolemaic astronomy which was already being criticized by people working on heliocentric models.

      For that matter, “they” are currently saying that Deepak Chopra is “wrongfully dissing” quantum mechanics and neurophysiology. Do you disagree with “them” on that score?

      1. “they” are currently saying that Deepak Chopra is “wrongfully dissing” quantum mechanics and neurophysiology. Do you disagree with “them” on that score?

        As Carl Sagan said, “They laughed at Galileo, and they laughed at Newton, but they also laughed at Bozo the Clown.”

  15. WOW! This debate is long overdue and deserves more discussion. It seems likely to me that there are several factors that influence evolution. Scientists must consider and debate them all as is being done right now. Let’s keep an open mind and research all sides of the issue. I am fascinated with the possibility that evolution might occasionally shift into top gear. Keep the discussion alive.

  16. I did read this book. Most books take me about a week to read, but this one took me almost three months.

    It was very difficult for a lay person like me to read this book because his writing is extremely dull and boring. This is how to NOT write a book. In comparison, I would give this book a 1 and WEIT would rate 150000.

    There are tons and tons of technical jargon in this book and the references to other material actually exceeds half of the book!

    Being a lay person, I could not evaluate much of what he proposed and a lot of it sounds very plausible and he seems to make a case for many of his ideas, although, as noted here by others, he does go off the deep end now and then making living cells all sound like they have purposes and free will of their own!

    I do hope you read this book, JC, and let us know your opinion after reading it. As far as other lay people – don’t bother reading it – instead go get your gums scraped at the periodontist, since it will be less painful.

  17. Even with “sudden” changes like polyploidy and symbiosis, selection (and drift) will operate as with any other mutation to determine the long term fate of that innovation. Moreover, there almost certainly will be an extended period of fine tuning via conventional neo-Darwinian processes to stabilize the relationship, exploit new opportunities (e.g., diversification of duplicate genes), etc. Certainly with symbiosis, there have been enormous (but gradual) changes in the genomes of both partners.

  18. How strange that a professor at U.Chicago would have the wrongheaded view that because we now know more, everything people knew in the past must somehow be wrong. Obviously Euclid and Pythagoras must have been wrong about everything and Euclidian geometry is insignificant because it was Leibniz and Newton who invented the Calculus.

  19. Thanks for writing this Dr. Coyne. I had read the article on the PuffHo first. I’ve been enamored of what seemed like potential in evolution for horizontal gene transfer.

    Your article set this straight for me. It’s putting the cart before the horse.

  20. Yikes, this post became long. Here’s a quick TL;DR –

    – “HGT is rare”: not in prokaryotes and viruses, and they are the 99%.
    – “adaptive evolution”: Shapiro didn’t say “adaptive”, and neutral, unselected changes can cause speciation if there is no gene flow. You seem to be arguing a word you put into his mouth.
    – Darwin was wrong. He insisted on infinitesimal change, and any macromutation automatically refutes this insistence. However, this being wrong is not a big deal.
    – Koonin’s book “The Logic of Chance” is another book about the direction of evolution studies in light of genomics, and is FAR better than Shapiro’s.


    Re: “HGT is rare”

    I’m not sure how you can say (type) this with a straight face when it seems to be the dominant form of genomic change in 2 of the 3 domains of life on the planet, and especially a key part of the movement of genes in the viral “empire” (to use Koonin’s wording). Whether or not one thinks of viruses as “alive”, they are biologically important and are the most numerous biological entities in any ecosystem. You don’t seem to be giving HGT or the prokaryotes their due. If one doubts how common and powerful HGT is, one need only look at the evolution of antibiotic resistance for a clear example.

    Given that prokaryotes continue to be the dominant life forms on the planet and play huge roles in every aspect of the biosphere, it is disappointing to continue to see them so casually dismissed.

    And the roots of the tree of life (as well as the roots of many main branches, including the root of our very own beloved metazoa) are indeed very difficult to resolve, and HGT is one of the big reasons for that difficulty. Yes, HGT is rare in the Eukaryotes, especially the complex multicellular ones, and there is even speculation that some aspects of Eukarya (nuclear compartmentalization, introns, etc) may have come about partly to defend against HGT. But that certainly doesn’t make it biologically rare.

    *tongue in cheek* Just more elitism from the Metazoan 1%. Viruses and Prokaryotes are the 99% and will not be ignored! 😉


    Re:”Yes, evolution can sometimes be rapid, though most of the time it’s gradual, but in all cases—all cases—adaptive evolution occurs by natural selection, and that means “optimizing fitness.” Shapiro is getting Darwinism wrong here, for he’s conflating the materials of evolutionary diversity (mutations and new genes that arise randomly) with their disposition by natural selection, a nonrandom process that does involve “optimizing fitness.””

    I don’t mean to defend Shapiro, because, while his book was interesting and his examples were informative, I didn’t buy his overall argument. He seems to want to throw gradualism out the window and takes Darwin’s wrongness too far (yes, Darwin was wrong about gradualism, but is much less important than anyone thinks; more below). However, this paragraph is putting words into his mouth. He did not specify *adaptive* evolution. You added that word. I don’t think any biologist doubts that adaptation comes from natural selection.

    But when looking at the population geneticists’ definition of evolution (the change in allele frequencies in a population), then depending on the situation, selection may very well not be the most powerful cause of evolution, at least of the genome. Neutral Theory suggests the majority of evolution in that sense (i.e. of genomic change) is due to neutral changes, both the direct genetic sense of silent and neutral mutation, and in the phenotypic sense of traits which have little or no effect on survival. Of course, what is neutral doesn’t have to remain neutral, and the variation caused by all of these neutral changes can end up having huge and different effects if/when something happens that causes selection to come to bear (e.g. imagine a frameshift in a duplicated gene, which has undergone some silent/neutral changes already, causing a vastly different outcome than if those changes hadn’t occurred. But I digress.

    It is very possible for speciation to occur by neutral drift alone so long as there is no geneflow between populations. And, even without speciation, it is certainly very possible for allele frequencies in populations to change without those changes being solely due to selection. “Optimizing fitness” is certainly A source of biological diversity, but it is not necessarily THE source, and the latter is the word that Shapiro used.


    While I think Shapiro takes it way too far and makes too big a deal out of it, it is still a simple fact that Darwin was wrong about gradualism. I don’t know why people think this is such a big deal, because it’s not. It doesn’t change his brilliance and his insight. It just means he made a not unreasonable mistake, and the mistake doesn’t actually threaten the structure of his overall idea.

    He was wrong, because he demanded gradual change. He insisted on it. He insisted on infinitesimally small changes over long periods of time. That this happens is not questioned. His insistence that it is the only thing that happened is what he was wrong about. And, all it takes is one single large scale change, be it HGT, gene duplication, chromosome duplication, or even whole genome duplication (all of which are either observed or strongly implied by the evidence) to disprove his insistence that change must be gradual.

    Gradual change has its place, and it may even be dominant over long periods of time. But it is not the only game in town, and Darwin was wrong about that. Apparently, this is a big deal to some people, though I don’t really understand why.


    Anyway, to make a long post slightly longer, I can’t say I was impressed with Shaprio’s book, though some of his examples of natural genetic engineering were interesting. If anyone wants a better read along similar lines, but for the most part much more coherent and interesting and much less … what can I say… over-reaching? something like that… I’d instead recommend Eugene Koonin’s “The Logic of Chance”. Koonin is much better organized and his examples are top-notch. And, while I disagree almost vehemently with his final overall point, he presents it in such a way that you really do have to consider it, and even if it’s completely wrong, it doesn’t invalidate all of the excellent information he presents leading up to it. Good read. Amazon link: http://www.amazon.com/Logic-Chance-Biological-Evolution-Science/dp/0132542498/

    At least, these are the apparently not so humble views of this mere high school biology teacher. I welcome correction from any experts around, including the author of this blog. 🙂

    1. Yikes! Also also…

      By being nitpicky on those few points, I’m not meaning to tear apart or disagree with your entire post. For the most part, you are spot on, I think.

      You are right that he (and others I’ve read) seem to go too far in dismissing neo-Darwinism. However, it is important to remember (and I’m not claiming that you are forgetting) that Natural Selection and gradual change are not the end-all-be-all of evolution. There is a lot going on and it is very interactive and even perhaps interdependent.

      I don’t get why some people, such as Shapiro in this case, jump on one or only a few aspects of that web of interactions and basically say “This is the one that is important” and while not saying to ignore the others, seeming to imply it.

      All of the mechanisms of evolution need to be taken together as a whole, because none are wholly independent. IMHO.

  21. Are the evolutionary changes in single-celled organisms not going to be different in many ways from those in multicellular co-operatives like us? I am thinking things like the mitochondria becoming part of cells – I can see it happening at single celled creature levels when they can multiply rapidly without sex, but when sex gets involved doesn’t that change things? Are microbiologists different in their views because their world is sexless?

  22. Jim Shapiro has written a response to my piece and asked me to post it, which I do herewith:

    I appreciate the substantive tone of your comments (http://whyevolutionistrue.wordpress.com/2012/02/18/a-colleague-wrongfully-disses-modern-evolutionary-theory/ ) criticizing my HuffPost blog “What is the key to a realistic theory of evolution?” (http://www.huffingtonpost.com/james-a-shapiro/what-is-the-key-to-a-real_b_1280685.html ). However, I think you missed my main point, did not accurately represent my position, and unconsciously corroborated a number of my assertions about neo-Darwinian thinking. Let me elaborate.

    The key issue, from my perspective, is: Where do functional adaptive innovations come from in evolution? Do they come from cellular activities that restructure the genome (natural genetic engineering), or do novelties arise as a consequence of natural selection optimizing fitness over time? While you clearly believe that natural selection is the creative agent, you do not acknowledge that a controlled, signal-responsive process of genome change is the alternative innovative process that I suggest. “Perhaps natural genetic engineering plays a more important role than natural selection” is what I wrote in the blog.

    The creative roles of natural selection and natural genetic engineering are alternatives that have to be discriminated by empirical research, not by appeal to pre-existing theory. That was exactly what you did when you wrote, “Theory also tells us that such profound evolution can’t happen instantly.” This statement also mischaracterizes my argument. Did I ever claim that significant change occurred “instantly”? What I said was, “Many genome changes at key stages of evolution have been neither small nor gradual.”  Is it not true that symbiogenetic fusions and interspecific hybridizations leading to whole genome fusions are both extensive in phenotypic impact and brief in time? Certainly, the two whole genome duplications involved in the appearance of vertebrates qualify as major rapid steps in evolution.

    In response to my statement on genomic evidence for rapid changes you wrote, “we find in fossils precisely those transformations that Shapiro says are impossible.” That again is terribly misleading. I never use the word “impossible” in the way you claimed because I have seen too many previously “impossible” processes become established science. The recent discovery of cell systems for integrating DNA sequences from infecting viruses and other invaders to generate an acquired (some would say Lamarckian) RNAi-based resistance mechanism is only one example. Moreover, I never asserted that some changes did not take long times to accomplish. The pace of the fossil record really has little bearing on whether selection or genome change is responsible for innovation.

    Finally, your statements about the meaning of random mutation only underscored the accuracy of my description of the current neo-Darwinian position on genome change. You said mutations “arise randomly” and “by accident.” According to you, they are rare, infrequent, independent events. You claim, “the biological inputs into diversity occur irrespective of whether they would be useful to the organism.” This is just plain wrong, as we have known ever since Barbara McClintock’s pioneering work on maize in the 1940s demonstrated that reproductive challenges activate genome change operators (http://www.nobelprize.org/nobel_prizes/medicine/laureates/1983/mcclintock-lecture.html ). If you actually take the time to read my book (only 147 pages of text), you will find abundant evidence for non-random (i.e., regulated, targeted, reproducible) changes to the genome. Many references from the extensive literature on the mechanisms, regulation, targeting and functional integration of natural genetic engineering can also be found on my web site (http://shapiro.bsd.uchicago.edu/evolution21.shtml ).

    It is the wealth of cytogenetic and molecular observations on the controlled, adaptively responsive nature of genome change in combination with genome sequence data that oblige a deep re-evaluation of evolutionary theory on 21st Century biologists. That was my point, and I think it survives the arguments you have made.

    Jim Shapiro

    1. I will respond only briefly to Jim’s comments. First, he hasn’t produced evidence in either his rebuttal here or his original HuffPo piece that his mechanism is a viable alternative to natural selection. All variants have to be fixed somehow, and that is perforce through the increase in frequency of those variants. When Shapiro produces a theory that supplants natural selection in explaining mimicry, the beaks of finches, industrial melanism, and all the adaptations of plants and animals to their environment, then I’ll start thinking about whether natural selection is misguided.

      I think I sufficiently addressed the problem of gradualism: yes, there are very rapid changes in evolution, often caused by genome doubling or symbiosis, but those changes still must be fixed in populations, and I see no way other than natural selection, as several commenters have pointed out.

      McClintock’s work does not overturn the idea that mutations are “random” in the sense of occurring irrespective whether they’d be useful to the organism. Yes, the environment can increase mutation rate, but those mutations are more likely to be deleterious than beneficial.

      I will have a look at Jim’s book, and Larry Moran promises to publish a review soon (he says he didn’t like it).

      One clarification: yes, horizontal gene transfer is a very common evolutionary process in prokaryotes, but is not nearly as frequent in eukaryotes. It can be seen as non-gradualistic, but remember that natural selection still has to operate to fix those horizontally transferred genes in the species they invade.

      1. I am prepared to be attacked for this but here goes. Coyne suggests that until Shapiro can explain mimicry (among other phenomena) by genetic engineering, he cannot displace the neoDarwinist argument. Mimicry, far from being the best example of the power of random mutation + NS, may be the Achilles Heel of neoDarwinists. Let me explain by contrasting mimicry with camouflage. Whereas with camouflage, NS can select ANY butterfly wing pattern with approx the same degree of busy-ness as the bark pattern the insect rests on, with mimicry NS would have to make selection toward a pre-specified and specific goal, a model which itself must be undergoing random mutation. How does the mimic catch up? NS is not goal-directed. Statistically, mimicry is much more difficult to achieve via NS than camouflage is. (I’m not saying it’s impossible.) NeoDarwinist defending their interpretation of mimicry routinely say that it is very “unlikely” that similar patterns could arise by chance; therefore NS must occur, CREATING the likeness. I think genetic engineering might tend to create functionally neutral likenesses within interacting species, and then once they are in existence NS could see and select them. I intend to look into this further. So far I’ve only gathered evidence relating to the existence of constraints that tend to create likenesses between different species. Research has shown that wing patterns are controlled by relatively few genes, which may be inherited as a unit, and variants may be reproductively isolated by sexual selection such that a few similar looking “hopeful monsters” (very different yet quite viable offspring) might proliferate rapidly. The business about not-so-very-like mimics being selected until gradually you have a very-like mimics is too contrived, I think. Also when neoDarwinists say perfect mimicry is unlikely to occur “by chance” they are comparing the chance that one specific butterfly species will randomly mutate such that it looks just like another specific species. The correct way to do the math here would be to estimate how likely that ANY species might by chance look like ANY other species. The difference is like the difference between the assertion that I am going to win the lottery today versus someone will win the lottery today. Ah, but mimicry is the sacred cow of neoDarwinists, so many here will respond telling me how excellent are the powers of observation of prey and etc. Every attempt to improve upon Darwin’s theory of evolution should not be seen as an attack on it.

        1. There’s a very simple response to your objection to mimicry: selection can occur at different rates. The organism being imitated might be in a relative state of status with respect to its outward appearance — its appearance may change much more slowly than the organism “attempting” to mimic it.

          Since Shapiro is fundamentally arguing that evolution can proceed at different rates (and note no one is disagreeing with this), even Shapiro agrees that the prerequisites for mimicry due to natural selection occur frequently in the natural world.

          1. Constraints that tend to stabilize a particular wing pattern (e.g. patterns are the result of reaction diffusion processes with threshold levels) would be available to “mimic” as well, potentially pushing it toward the model, without assistance from predators. The point is this: When we see a pattern or structure in nature, our task is to explain its origin as best we can. Maybe that explanation is random mutation + NS; maybe it’s some other natural mechanism. Our task is not to explain how random mutation and NS worked together to create the pattern. Recently it was discovered that homologous genomic regions are responsible for the different mimic forms in Heliconius mimicry ring, and neoDarwinists quickly asked, How did predators achieve this? Previously it had been supposed that predators would have been necessary to eliminate the gradations between forms. Why not look into how super genes come to be without the help of predators?

      2. It is a basic category error to lump natural selection with mechanisms that generate novelty. That’s like saying Apple’s well-engineered products are the result of Compaq and DEC going out of business, or that we have Starbucks because someone evicted all the lame coffee joints and boarded them up.

        In business and technology, sources of novelty are far more important and interesting than failures. So it is in biology.

        Dr. Shapiro is not proposing an alternative to natural selection. He’s proposing multiple alternatives to gradual adaptations by random mutation: “Cellular activities that restructure the genome” – namely Transposition, Horizontal Gene Transfer, Hybridization and Symbiogenesis.

        Dr. Coyne, you said: “What one means by “gradual” is a matter of taste.” We know that hybridization can produce a new species in a couple of generations; your own words were “almost instantaneous.” We know that through HGT a bug can become a superbug immune to antibiotics in days or weeks, even minutes.

        If “gradual” means millions of years, and if it also means a handful of generations, then the word gradual is meaningless indeed.

        I also wish to challenge your statements: “The biological inputs into diversity occur irrespective of whether they would be useful to the organism” and “Gene shuffling, gene duplication, horizontal gene transfer: all of these are biological accidents.”

        Transposition and Horizontal Gene Transfer events follow specific protocols. Insertions occur at specific sites in the genome. This is why various elements are named transposons, introns, exons etc — because each type of mobile element obeys different rules, rules which we are now only beginning to understand.

        To say that these are biological accidents, when we finally have the opportunity to understand the exact procedures they follow, is to abdicate the responsibility of the scientist.

        When you say, “[Shapiro] is misguided in thinking that these new sources of variation completely destroy the Darwinian idea of gradualism and natural selection,” you are erecting a straw man. Nobody ever said that natural selection doesn’t successfully eliminate; he’s just saying that’s all it can do. As reader Psi Wavefunction said, “Selection does not produce variation. Mutation does.”

        As Shapiro said in his letter to you: “If you actually take the time to read my book (only 147 pages of text), you will find abundant evidence for non-random (i.e., regulated, targeted, reproducible) changes to the genome.”

        Random accidents are by definition not regulated, targeted or reproducible. Any assertion that a particular sequence is random is not mathematically provable (Gregory Chaitin, Information, Randomness and Incompleteness, 1990).

        This is why Neo Darwinism’s insistence that mutations are random has never been conclusively demonstrated to be true, and furthermore is not scientifically or mathematically provable in the first place. Thus a theory of random accident is at best pseudoscience.

        Note that theories of regulated, targeted and reproducible phenomena ARE science. Horizontal Gene Transfer, Transposition, Symbiogenesis, Epigenetics and Hybridization are fully scientific models of evolution. (Natural Selection’s ability to eliminate the unfit of course is science.)

        It’s time we replaced Neo Darwinism and its dogmatic insistence on gradual random accidents with what we now know from the last 50 years of genome research: Novelty can be generated quickly, through non-random, systematic, repeatable processes.

        1. “Random” has several meanings. PMarshall is using the wrong one with reference to “random” mutations. As Coyne quote clearly said, “What we mean when we say that mutations are “random” is … the biological inputs into diversity occur irrespective of whether they would be useful to the organism.” (Italics original.) PMarshall is tilting madly at a straw windmill.

          1. RBH,

            A pleasure it is to meet you again, it’s been a long time since Infidels, hasn’t it?

            Cells use transposition to repair damage. When Barbara McClintock damaged chromosomes, the plant would repair the damage with code copied or spliced from another part of the genome. It made this change because it would be useful to its survival.

            When bacteria are under stress or attack, they search for code from other genomes, inserting it into their DNA and gaining new mechanisms through Horizontal Gene Transfer. In so doing they may gain, for example, the ability to pump toxins out of their cell walls.

            Note that in both cases, only the *threat* is necessary; the organism heeds it and responds accordingly. Shapiro documents these activities scrupulously in his book, which I suggest you pick up and read.

            See “Proofreading DNA replication” page 12; DNA damage repair and mutagenesis, page 14; targeting of natural genetic engineering within the genome, page 82; antibiotic resistance and HGT, page 90 (Shapiro 2011).

            The sensing of the organism’s environment, and situational genome reorganization in response, has been well documented since McClintock discovered transposition in the 1940’s. It is a grave mistake to ignore this, as Coyne has done, and make the repeated and unprovable assertion that these changes are accidental. That’s not science, RBH, it’s pseudoscience.

            1. Umm. . . .and those mechanisms of adaptive response were given by God? Might you not entertain the possibility that they themselves evolved by natural selection acting on mutations?

    2. “The key issue, from my perspective, is: Where do functional adaptive innovations come from in evolution? Do they come from cellular activities that restructure the genome (natural genetic engineering), or do novelties arise as a consequence of natural selection optimizing fitness over time?”

      This statement doesn’t make much sense to me. “Functional adaptive innovations” flow from heritable changes. Heritable changes may be due to “small” effects (point mutation) or “large” ones. (“Natural genetic engineering” is a poor euphemism for the mechanisms in addition to point mutation/indel that generate heritable variability.)

      I don’t think it is helpful to confuse the processes that generate heritable variability with those that fix heritable changes in evolving populations. Shapiro’s “natural genetic engineering” is nothing more that a suite of mechanisms that, when added to point mutation/indel and the like, generate heritable variation. There is nothing at all non-Darwinian about these processes, since Darwinism doesn’t really care about how heritable variation comes about. Just that variation occurs and that it is heritable.

      1. @Arthur Hunt. You say Shapiro’s statement doesn’t make sense to you. “Where do functional adaptive innovations come from in evolution? Do they come from cellular activities that restructure the genome (natural genetic engineering), or do novelties arise as a consequence of natural selection optimizing fitness over time?” It seems clear to me that he is talking about the source of novelty. NS is not a source of novelty/innovation. It fixes heritable changes. It does not create them. I don’t know why this is seen as a difficult point. If genetic engineering tends to produce beneficial change, not just change that is random with respect to the needs of the organism, then genetic engineering might better explain evolution than the much slower process of gradual fitness optimization by NS. Of course NS still acts on genetically engineered forms as it would on random single-point mutations, but in the former case the role of creativity is clearly assigned to genetic engineering. There is a quasi-creativity assigned to NS acts on random change that, frankly, is problematic and the source of confusion among ID folks. I think we are much better off not assigning any creative power to NS. It selects only.

        1. Tori, about your denying NS as a creative process, see my “mural maker” analogy at the bottom of the replies to #31.

          Here you seem to also say that natural genetic engineering is somehow directed towards producing a beneficial change. What is Shapiro’s (or your) evidence for that?

        2. Hi Tori,

          What is confusing is that Shapiro seems to be setting up a dichotomy as far as the source of heritable variation. No molecular biologist I know of (except, perhaps, Shapiro?) would argue that natural selection produces heritable variation – this just makes no sense (which is why Shapiro’s sentence also makes no sense). As I see it, Shapiro’s statement here is a false dichotomy. (It may be that he is being a bit frugal with words, and is assuming that readers will equate “natural selection” with small-scale genetic changes. If so, then he should try to be a bit less obscure.)

          This is besides the fact that he also seems to be arguing that “natural genetic engineering” is in some way anti-Darwinian. This is just not so.

  23. For what it’s worth, I think your comments make sense. But gradualism is in the eye of the beholder, and maybe what Darwin called gradualism (from his macroscopic, phenotypic perspective) would still include HGT and other non-point-mutation genetic changes. Remember Darwin studied pigeons and other organisms in which he did see occasional changes that were not literally “infinitesimal” (at least, not as a physicist would use the word). His theory was based largely on these examples. So it could be said that Darwin was not wrong about gradualism, WE are wrong about our redefinition of his term in light of new genetic theory.

  24. “Perhaps natural genetic engineering plays a more important role than natural selection”

    This sentence annoys me. Perhaps Shapiro doesn’t mean it the way it sounds (I have no idea of his ideas about theism), but what could “natural genetic engineering” be but the arm of The Deity swooping down to make the giraffe’s neck just a little longer?

    1. You are way off base on this. I read his book and he defines it all in detail. He does not use magical thinking.

      1. Well, like I said, I have no idea if he meant it the way it sounds. But unless he’s got some special definition of “engineering” he should word it differently. Because that phrasing sure is loaded with intentionality and god-meddling.

          1. Maybe. But careless(?) wording like this is like handing ID quote-miners a shovel and pointing to the seam of coal.

  25. I’ve said it before, as soon as some ‘renegade’ scientist start with ‘what modern biology/physics/medicine/&c. needs is…’, you can stop reading.

    If anybody would KNOW what the relevant field of science NEEDS – if anything – it is the scientists working in the field itself, getting their hands dirty. Not some outsider.

    And “the Science section of HuffPo, which I’m increasingly beginning to deplore as well”

    ‘increasingly beginning’, I think you are being extraordinarily charitable here.

    I never liked HuffPo, the layout made my eyes bleed from the start, it’s layout done by the 14-year old nephew of the subeditor, on a sugar high, and sorely lacking in content. Went there less than a handful of times and never went back (never will). At the risk of insutling people, I find it too American, too.

  26. I don’t think Dr Shapiro’s letter helps him. Like Jerry and others said, natural selection doesn’t care where the variation comes from. Whether “natural genetic engineering” or classical random point mutations, it is all the same to evolutionary processes. Since Fisher’s and Wright’s time, we have known that the mutation rate was under biological control. It certainly is neat to know that this control might be dynamic, so that mutation rate might be higher under stress. And it is exciting to know just how many ways there are to get variation. But this is not a “revolution”, it is something that fits squarely into Darwin’s framework (and Darwin of course never restricted his source of variation to point mutations, since DNA itself was unknown).

    Natural selection could even have produced a directed “natural genetic engineering” system that creates variation in appropriate parts of the genome in response to certain environmental stresses. (Perhaps exposure to novel diseases might cause an organism to relax its control of mutation rate in regions of the DNA involved in immune response, or might make it easier to insert foreign DNA in that part of the genome, for example.) If that is what Shapiro means and if there is evidence for it, that is exciting and novel, but this kind of engineering system, if it exists, would have arisen through natural selection. It cannot be used to argue against natural selection. Shapiro would have to show on population genetic grounds that such an adaptation could not evolve by natural selection (plus drift). I have not seen Shapiro or anyone else make such an argument.

    1. @Lou Jost It sounds like you’ve already reached Haldane’s third stage of acceptance, well on your way to number four: “Theories have four stages of acceptance. i) this is worthless nonsense; ii) this is an interesting, but perverse, point of view, iii) this is true, but quite unimportant; iv) I always said so.”

      1. I do agree with 3/4 of his statements (or at least have no reason or expertise to disagree with them). But take me out in the back yard and shoot me if I ever agree with his apparent claim that under the standard view of evolution, “dogs… always remain dogs.”

        1. @ Lou Jost. I’ve read Shapiro’s book, but I don’t recall where he might have said “under the standard view of evolution, ‘dogs… always remain dogs.'” I would guess that he probably said something like _under the view of evolution by random mutation and natural selection_ because (as you note) Shapiro isn’t saying that evolution isn’t true. If “dogs remain dogs” under a neoDarwinist view, it would be because natural selection tends to stabilize species by getting rid of non-beneficial or costly mutations. Random mutation is not a good source of helpful novelty. We all agree, I think. Natural selection has to wait a very long time for one good beneficial single-point mutation and then another random mutation in that same direction! HGT, symbiosis, repetitive differentiation, duplication, and etc are more likely sources of beneficial genetic change, which natural selection can then happily select. Shapiro isn’t arguing “against natural selection.” He just thinks the best source of beneficial novelty is not the combination of random mutation and natural selection. The sort of genetic change Shapiro describes would accumulate faster than random single point mutations would. This is my humble opinion, any way, as a layperson. I actually found the book fairly uncontroversial. Don’t know what the fuss is about.

          1. Tori, the “dogs” quote from Shapiro is in Jerry’s post, and I was only going from that. We all agree that mutation is a slow source of useful variation, and the additional sources of genetic variation discovered in recent years provides more fodder for natural selection and drift. If that is all Shapiro is saying or implying, I agree with you: this is interesting, but not controversial.

            But the quote Jerry gave is really bothersome. Selection and drift work on variation, however that variation arises. But Shapiro seems to claim that selection is somehow limited to working with a fixed palette. “The first problem with selection as the source of diversity is that selection by humans, the subject of Darwin’s opening chapter, modifies existing traits but does not produce new traits or new species.” This sentence just does not make sense, unless I misunderstand him somehow. New variations continually arise in populations, whether by point mutations or by other processes. Natural selection and drift determine whether these novelties spread in the population or disappear. If the population is subdivided by barriers (geographic or otherwise), then drift + natural selection will eventually cause the subpopulations to diverge and turn into new species. So natural selection + drift is generating diversity. I don’t understand how Shapiro can deny that, but his statement seems to do so.

            Natural selection is not necessarily stabilizing, especially in subdivided populations. Drift destabilizes subdivided populations even more.

            1. @Lou Jost. Far be it from me to speak for Shapiro, but I have my own interest in the critique of natural selection as a source of novelty. Yes, after variation, drift can occur by selection. With separation, population can diverge and you have more diversity. But NS is never really a “creative force” even in populations. It can make some forms more numerous than others, but it never creates those new forms. I don’t think anyone on this forum will disagree with me when I put it this way. However, I do see some falling into language that does attribute some creative power to NS. The idea that NS can fine tune a new form, select for better and better variants of that form makes it seem as if NS is actually creating the new forms. It’s a very subtle error in logic, but a serious one. The idea that NS can gradually select in a specific direction is bothersome to me. Yes, it’s possible, but if there are better saltational mechanisms which can serve as explanations, then I prefer those.

              Now switching to look at Shapiro’s thesis, when genetic change occurs as a result of HGT, it would most likely occur, it seems to me, where they is a beneficial relationship between host and bacteria, giving the symbiont opportunity to invade the host cell. If the host does benefit from that symbiont then its genetic material may code for, say, an enzyme that might be beneficial. In this case, the genetic change would tend to be beneficial rather than not. It would not be so random with respect to the organism’s needs. It would make the change seem to be the result of foreknowledge. I’m a little out of my territory with this example, but I hope it makes sense even if the details are wrong.

              I, like everybody else on this forum probably, get uncomfortable with Shapiro’s saying cells have “cognitive” abilities. However, I think we need to redefine what we mean by “cognitive” brain processes. They may be more complex but they can’t be categorically different from the kinds of “intelligent” activities elsewhere in the body, e.g. cell signaling and so forth. Shapiro makes a quick nod to biosemiotics in his book (that’s the field I work in) which I think better explains the appearance of “cognition,” i.e. purposeful change, in cells.

              1. Tori, I think no evolutionary biologist imagines that natural selection creates a new allele. It works with the novelties that appear in individuals due to mutation and “natural genetic engineering”.

                But there is a sense in which natural selection does have creative power at the level of populations. Imagine a favorable allele arises in one individual at a certain locus, and a favorable allele arises in a different individual at a different locus. Initially no individual in the population has both favorable alleles. Natural selection (working against drift) will tend to “create” a population with both those alleles. Multiply this by 20000 loci and you have a creative force capable of making dramatic changes in population characteristics.

                Drift is also “creative” at the level of populations. It can create large differences in neighboring semi-isolated populations, especially when it acts on characters like female sexual preferences (maybe by drift, one group likes blue feathers and another likes green feathers).

              2. Lou, I think we understand each other, and I only want to point out your cautious language when you say “there is a sense in which” natural selection has creative power. And when you say drift is “creative” you use scare quotes. I believe such use of “creative” is more metaphoric than not. NS is kind of creative, in a way; it produces results that can be compared to creative activity. Drift is sort of like something that is creative insofar as things change. The tendency to entropy is “creative” in that sense too. But “creative” starts to lose its meaning.
                When I use the word “creative” I’m more interested in the actual creation of beneficial new forms, not so much their increased frequencies in a population or the neutral differences between populations due to drift. For me, in the end NS is a proof reader, not a writer. Also since drift isn’t natural selection, and sexual selection is not natural selection, I prefer to leave them out of the discussion of NS per se. Otherwise it gets too complicated (tho more interesting).

              3. Let me just add that in my example, natural selection really did create a new form in the population, one that has combined all the different beneficial novelties that arose in the separate individuals.

                The new individuals can be more well-adapted than each of the individuals which originated the beneficial novelties. This goes beyond proofreading.

              4. Okay Lou, I understand, and sometimes editors (if not proof readers) are so good they actually help the writer in significant ways. Still your example is one of accumulation and concentration of different characters created by other processes. As an emergentist, I wouldn’t accept that as truly “novel,” unless there is a synergistic effect of the aggregation….maybe a spandrel that’s beneficial. Then, yes, I concede to your point, which is more like Gould than Dawkins.

              5. Tori, think of a mural artist creating a work from colored tiles. The artist doesn’t have a clear picture of the final piece, but starts picking up colored tiles and rearranging them. The tilemaker back in his shop, meanwhile, also keeps inventing new colors for the tiles and sending them to the artist. The artist keeps rearranging the tiles, adding the new colors if they improve the picture, discarding others, until gradually the mural looks really great. That is what natural selection does. Both the tilemaker and the artist were truly creative here. The tilemaker is the source of the varied and novel raw material on which natural selection works, and the artist is natural selection. (Drift is a blindfolded artist, but natural selection is always there to veto or guide the changes made by drift. If the blindfolded artists rearranges faster than the unblindfolded artist can, then we have nearly neutral evolution….)

  27. We might ask, Is there an evolutionary dynamics lesson offered by cancer due to chronic irritation, say, of the esophagus? Irritation causes an immune reaction leading to a focal energy increase. That’s a resource that nature is quick to utilize:
    (1.) The local environment changes causing cells to modify their behavior and produce new molecular varieties, often from so-called oncogenes.

    (2.)An herbivore browsing the upper foliage of a shrub chronically irritates its musculo-skeletal system. Knock-on effects of the induced immune reaction carry epigenetically modified DNA to the lymph system. Unknown vector epigenetically modifies the germ line, causing undetectable to moderate predisposition in the new generation. Such an effect would likely become more pronounced if alloyed through both parents.

    (3.) How long would it take to measurably stretch a proto-giraffe’s neck, Mr. Lamarck? 10 generations.

  28. Dr Shapiro, it seems to me you are mixing up levels. At the level of individuals, random mutation + the more complex processes you mention = generate novel individuals. At the level of populations, natural selection + drift determine how those innovations spread (or disappear ). No one says that natural selection is a creative force at the level of the individual; it changes populations.

    So I can’t see how your “natural genetic engineering” is somehow a threat to the importance of population processes like natural selection and drift.

    The only way I can see a real conflict would be if you thought that natural genetic engineering acted with foreknowledge of what sequences would be successful, so that the gametic DNA of individuals changed in concert into a given more favorable sequence. If that happens, then yes, natural selection would take a back seat. This would be truly revolutionary (and also amazingly improbable). Is that what you are saying?

    Hope you stop by to comment.


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