Jim Shapiro continues his misguided attack on neo-Darwinism

The science editor of HuffPo keeps asking me to come aboard and contribute a column, and I keep saying that I’m not going to write for free for a profit-making venture (their columnists are all wage slaves, or rather no-wage slaves, since they’re never paid). And I always take the opportunity to offer some “constructive” criticism about the page.  One of my complaints is that they give a venue for James Shapiro, a colleague in biology at the University of Chicago, to attack neo-Darwinian evolution for completely bogus reasons.  There is no scientific vetting of whether what Shapiro (or anyone else) says is correct.  And in his case, his criticisms of modern evolutionary theory are dead wrong. So HuffPo perpetuates the idea that something is wrong with evolutionary theory.

Shaprio has four beefs about neo-Darwinism (the modern theory of evolution)

1.  It’s not “gradual,” but can happen nearly instantaneously due to things like horizontal gene transfer, gene duplication, and other “self-engineering” features of the genome. In my post linked to above, I explain why this is fallacious.  Some evolution can happen quickly due to horizontal gene transfer, but that’s not the main engine of adaptive evolution, and even gene duplication takes a long time for the duplicated genes to evolve new function.  Also, groups of genes transferred “horizontally,” between very unrelated organisms, will persist only if they have a salutary effect on the fitness of the recipient.

2. Conventional evolutionary mechanisms (presumably natural selection and genetic drift) aren’t efficacious in creating big organismal changes. In this respect Shapiro comes very close to creationism. In fact, in one of his posts he explicitly uses a creationist trope:

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.

Given the fossil evidence of transitional forms—showing that fish became amphibians, amphibians became reptiles, reptiles became mammals as well as birds, even-toed terrestrial mammals became whales, and early primates became humans (please, cladists, keep your objections to yourself!)—such a statement is simply embarrassing, and is identical to ones you’ll see in the creationist literature.  Shapiro should know better.

3. Mutations aren’t “random” as neo-Darwinians contend. (By “random,” evolutionists mean “mutations occur regardless of whether they’d enhance the fitness of the organism.”)  In fact, we know of no evidence for mutations occurring nonrandomly or “adaptively”, i.e., that the occurrence of mutations is somehow biased in a direction that makes them more likely to be favorable when they arise, particularly when the environment changes in a way that requires favorable mutations to fuel adaptive evolution.  There has been some controversy about the occurrence of “adaptive mutation” in bacteria, but that’s died out because there’s simply no evidence that the phenomenon occurs.

4. Increasing “fitness” (average reproductive output of a gene or genotype) is not the key to adaptive evolution. In the same link as the “no-cats-from-dogs” statement, Shapiro basically dismisses the importance of natural selection:

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.

What he’s saying, of course, is that natural selection (“optimizing fitness”) had nothing to do with the diversity of life.

This is all deeply misguided, and I suspect that Shapiro simply doesn’t understand natural selection. He certainly hasn’t proposed an alternative theory that explains all the adaptations we see in nature, and merely ascribes them in some nebulous way to the self-tinkering of the genome.  But none of the mechanisms he adduces (save horizontal gene transfer, which is really just a big mutation, since that sort of transfer need not automatically be adaptive) can replace natural selection.

In his latest columns at HuffPo, (Part 1 and Part 2), Shapiro makes the same mistake, assuming that some features of the genome—the vertebrate immune system in this case—shows that natural selection is ineffective in molding adaptive traits of organisms, and that the innate nature of the genome has really replaced the conventional view of adaptive evolution.  He assumes here that something as complex and “directed” as the vertebrate immune system could not have evolved by random mutation. What Shapiro fails to realize here is that these “innate features of the genome” that produce the appearance of “directed change” are themselves molded by a combination of random mutation and natural selection, creating a genome that operates in an adaptive way.

Let’s take a look at the way the immune system adaptively responds to challenges: in this case the presence of foreign proteins (“antigens”), such as those found on the surface of parasites or microbes, that must be neutralized.  At the risk of doing short shrift to what is a breathtakingly impressive (and evolved) mechanism for fighting off disease and parasites, the vertebrate immune system operates like this:

  • A foreign substance (or protein) invades the body. These substances are called antigens. (The coat proteins of bacteria and viruses are examples of such antigens).  They pose a danger to the host.
  • The body recognizes the antigen as foreign and swings into action to neutralize it.  It does so by allowing a group of specialized cells (“B cells”) to generate a huge variety of different molecules, called antibodies, to neutralize the antigens. Antibodies are glycoproteins (large proteins with an attached carbohydrate) whose sequence is determined by the host’s DNA.
  • The amazing thing is how the body uses a small number of genes in the B cells to generate a huge variety of protective antibodies, for we never know what foreign molecule is going to enter our bodies. (Antibodies are specific to antigens: not just any antibody molecule will neutralize an antigen.) What happens is that there are two processes, called somatic hypermutation and VJ recombination, that take the DNA sequence of the antibody-producing genes and mutate it, either creating “errors” in the DNA sequence or swapping bits within and among genes by physical recombination.  This generates a large number of variable antibody proteins.  Most of these won’t be useful for neutralizing the invading antigens, but some will.
  • The “useful” antibodies, produced by random mutation and recombination, bind to the invading antigens; this alerts yet another cell type to migrate to the bound antigen-antibody complex and destroy the invading cell/protein.
  • In another amazing part of this process, those cells that have undergone the “right” mutations and recombination (i.e., those whose DNA has changed in a way that produces antibodies useful to the invader) are induced by feedback from the antigen-antibody complexes to differentially proliferate in the body. Cells having the “right” mutations are stimulated to divide more often. This allows them to produce more of the useful antibody.  Thus the population of the “good” immune cells is enriched, through differential replication, when they have a useful effect. I haven’t followed the literature on this, but I’m not sure we know exactly how the production of a successful antibody feeds back to the cells to induce them to divide more often.
  • The reader will have recognized, as does Shapiro, that this differential proliferation of cells with the “right” mutations is a form of natural selection: the replicators (cells) that produce the most adaptive protein are those that proliferate, enriching the body in those cells and helping fight off the invader.  Moreover, those cells remain in our body, which is why we can fight off infections more easily when we’re reinfected with the same antigen a second time. This is in fact the way vaccinations work: by giving us a mild form of the invader (or disease), which allows our bodies to produce more of the cells that can later swing into action when a real invader comes on the scene.  Vaccinations involve “priming” the immune system with a small amount of antigen (i.e,  the cowpox virus in the case of our first vaccination—Jenner’s vaccination for smallpox), allowing us to be prepared with extra antibody when the genuine infection comes.  This use of our body’s evolved defenses by medical research is one of the great triumphs of the human mind.

This is all well and good, and Shapiro describes the process clearly in his first post (the second is way, way too complicated for the general reader).  But his mistake comes when he assumes that the “adaptive” process of the immune response itself did not arise by the normal process of natural selection (random mutation followed by selection among genetic variants), but is somehow an inherent adaptive feature of the genome that renders “normal” natural selection unimportant.

Note that there are two levels of selection going on here.  The first is the immune response itself:  mutations (random ones, Dr. Shapiro!) occur in B cells, and those cells with the “right” mutations are caused to differentially proliferate. This is “somatic” natural selection; that is, selection within one generation and within one body to produce an adaptive result.  But the appearance of the system itself requires a second form of selection: “regular” natural selection among ancestral vertebrates. In this process, those individuals having rudimentary immune systems better able to generate adaptive variants leave more offspring than other individuals whose immune systems can’t produce the variety of molecules needed to fight off a diversity of invaders.

The key point is that there is no evidence that the evolution of the immune system in this way (by differential reproduction of individuals instead of cells) involved anything other than natural selection among individuals having randomly produced mutant variants of an ancestral immune system.  In other words, the whole system of hypermutability within B cells, and the feedback mechanism that allows cells with the “right” mutations to divide more often, arose by selection among individuals having slightly different forms of the immune system.  In the end, the whole system appears “designed” to fight off invaders—even “designed” to produce the right mutations for the right invader, even though that’s not the way it works—but yet that whole system evolved by the usual step-by-step Darwinian process within ancestors.  What is the alternative, Dr. Shapiro? Did God bequeath us a fully-functioning immune system de novo? I think not.

Evidence that such a system can indeed evolve comes from parallels within bacteria.  Bacteria that are invaders themselves have their own process of producing antigens that avoid detection by the invader’s antibodies.  In this process, bacteria have “hypermutable” genes called contingency loci that can produce new coat proteins that aren’t recognized by the somatically evolving vertebrate immune system.  (This is the result of an “arms race” between the bacteria and the host’s immune system.) The evolution of contingency loci comes from pretty much the same mutational process responsibile for the evolution of hypermutability of B cells—both are evolved phenomena. Note especially that in both the contingency loci of bacteria and the hypermutability loci of vertebrates, the mutations that occur are random: variants are produced regardless of whether they’d help the beleaguered vertebrate trying to destroy the antigens or the besieged bacterium trying to avoid antibodies.  But in both cases the cells producing “adaptive” responses (in the case of bacteria, the coat proteins that evade the host’s antibodies) undergo differential reproduction.

That is natural selection, pure and simple: randomly produced genetic variants followed by sorting out of those variants based on their ability to render their carriers more likely to survive. But somehow Shapiro manages to convey to the public that something else is going on here—some non-Darwinian process that can’t be explained by natural selection. And that’s bunk.

In fact, Shapiro sees my natural-selection scenario above, which is accepted by virtually every biologist who works on the immune system or on contingency loci, as a “philosophical” difference between him and me:

For instance, Jerry Coyne criticized another of my recent blogs on evolutionary theory with the following comment:

“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.” We will return to the importance of this philosophical difference later in the blog.

It’s not a philosophical difference, it’s a scientific difference, and all the facts are on my side.  There’s no evidence that the immune system resulted from anything other than garden-variety natural selection—the same sort of selection that helps bacteria evade the defenses of their hosts.  Yet Shapiro claims that the immune system is “excluded from the prevailing philosophy of genetic change” (i.e., natural selection):

Three remarkable things about somatic hypermutation and CSR are explicitly excluded from the prevailing philosophy of genetic change. First, they are adaptive and purposeful genome changes. Second, they are functionally targeted. Third, for CSR, targeting involves intercellular signals that depend on how other cells in the immune system perceive a particular infection.

Yes, the changes are adaptive, and if you want to be metaphorically teleological about it, yes, they’re “purposeful”: the “purpose” of the changes is to fight off invaders. (I never use the word “purpose” when I lecture to students, as it implies a designer.)  But equally “purposeful” are the adaptations of our ability to tan, or the ability of our cats to grow longer fur in winter.

The functional targeting and intercellular signals are simply part of the system that evolved.  There’s nothing about this system that can’t be explained by natural selection, just as the “hypermutability” of bacterial contingency loci fall within the ambit of natural selection.  If selection is strong enough, you can indeed evolve a system in which most of the products (e.g., the mutant B cells) produce useless proteins, for that hypermutable system still pays off often enough (i.e., generates the right molecule) that on the whole it increases the organism’s fitness.  If you have a gene that produces five bad mutations for every good one, that gene can still be positively selected if the advantage of the rarer good mutation is strong enough to outweigh the detriments of the more numerous bad ones.

In the end, Shapiro pulls a scientific boner by saying that if the immune system evolved in such a complicated way, other cells should have too. But this is a red herring:

If immune cells can do all the above, is there any scientific reason we would assume that other cells cannot do the same? Coupling DNA restructuring to transcription is of major significance. All cells can target transcription to functionally relevant sites in the genome. Given that the immune system is how evolution evolved rapid protein evolution, should we not look to it for clues about basic evolutionary processes?

The burden of explaining what other cells lack that lymphocytes possess lays [sic] with those who wish to adopt the position that the immune response is unique and does not reflect a more general capacity to target genome change. Evolution has obviously refined antibody-producing cells for their immune system functions. But do immune cells have unique capacities for natural genetic engineering missing in other cells? If the answer is no, as I believe, then we need to incorporate adaptive genome restructuring into our most fundamental thinking about biology.

Well, we’ve seen that the immune system is not unique in its ability to “target” genome change: contingency loci in bacteria operate in the same way. But just because a complicated feedback system has evolved in one group does not mean that exactly the same mechanism will evolve in all cells, or in all groups of organisms. Indeed, we know that’s not the case.  Insects’ resistance to organophosphate insecticides, for instance, has evolved by the simple modification of an enzyme that renders the insecticides ineffective.  Surprisingly, it’s often the very same single mutation in different groups of insects. There’s no hypermutability here, no complex organic feedback, no “adaptive genome restructuring” or “natural genetic engineering.”  It’s just a random mutation that happens to render the insect impervious to pesticides.

I am not sure why Shapiro is so obtuse about this, for he’s been trumpeting these same misconceptions for decades.  My own theory is that the man simply doesn’t understand the kind of population thinking in which “natural genetic engineering” can result from garden-variety natural selection.  (I often find that molecular biologists fail to grasp natural selection, even though it seems conceptually simple.)  At any rate, Shapiro’s claims in HuffPo are damaging to the public understanding of science, for they make people think, unjustifiably, that there’s something very wrong with modern evolutionary theory.  Well, his arguments aren’t convincing to biologists, although they could perhaps snow the layperson with complex terminology, just as Michael Behe snows the public with the idea of “irreducible complexity.”

The onus is on Shapiro to show exactly how the systems of “adaptive genome restructuring” he so admires require us to abandon our notion of adaptation via natural selection.  He hasn’t convinced me, nor, as I’ll show in a subsequent post, one reviewer of his new book on this topic.

119 Comments

  1. stevehayes13
    Posted April 7, 2012 at 6:30 am | Permalink

    ‘I am not sure why Shapiro is so obtuse about this…’ I suspect it is because he thinks it is a philosophical matter.

  2. newenglandbob
    Posted April 7, 2012 at 6:34 am | Permalink

    Thank you for this. This clears up a lot of confusion for me, having read Shapiro’s book and having doubts about his claims.

  3. Justicar
    Posted April 7, 2012 at 6:52 am | Permalink

    Excellent write-up, Jerry. With respect to how the cells ‘know’ to ramp up their numbers when a ‘correct’ solution to an invasion is happened upon is now something I’m very much interested to know, too. Hopefully, a virologist we all know and love either knows the answer, or knows someone who does who she can pester into detailing for everyone else’s edification.

  4. Posted April 7, 2012 at 7:17 am | Permalink

    At any rate, Shapiro’s claims in HuffPo are damaging to the public understanding of science, for they make people think, unjustifiably, that there’s something very wrong with modern evolutionary theory.

    If you ever wanted a reason to write an unpaid article for a profit making entity, this is it. Those reading Shapiro on Huffpost, likely do not visit your blog (yes I said it) for the rebuttal.

    • Justicar
      Posted April 7, 2012 at 7:27 am | Permalink

      Jerry could just look at his stats to see what the traffic is like when he’s linked to in an article there. And if it’s low, he can conclude one of three things: nobody read the piece, or a lot of people read the piece but know off-hand what the rebuttal already is, or that people read the piece and swallowed it hook, line and sinker and thus needn’t be encumbered with so tedious a task as knowing what Jerry actually has to say.

      That last part is heresy!

    • onkelbob
      Posted April 7, 2012 at 7:50 am | Permalink

      And if there is a reason never to visit PoHuff this is it too. As a dyed in the wool cynic, I contend that the crank magnetism at PoHuff is too strong to overcome. PoHuff deliberately finds a self-selected population of writers who will immediately resonate with the readership; a group that exhibits an insurmountable Dunning-Kruger confirmation bias. Dr. Coyne’s presence there would not influence the thinking of the vast majority. To the contrary I propose it would provide intellectual cover for the crank theories that are rampant. It is apparent that most of the readers there do not read to understand, they read to refute. As such, I contend the result will be that the readers will point to some crank in the comments section as pwning him, and by doing so reinforce their collective preconceptions.
      To me, it is tilting at windmills, you cannot win, nor can you hope for a draw. The only outcome is a loss, the loss of your time and effort, and a further bolstering the crank’s reputation.

      • Scott near Berkeley
        Posted April 7, 2012 at 1:39 pm | Permalink

        “resonate”??! …more like “naturally select” the readership.

        Re Huffing Po, I’ve given up on that execrable assemblage of electrons on the internet. Dizzy rabbis, unscience, like science, and they never give up on the supernatural, in one guise or another.

    • Gluon
      Posted April 7, 2012 at 11:22 am | Permalink

      I think the better argument for not publishing an article on HuffPo is just not to lend a good name to a bad publication. It gives them too much credibility.

      On the other hand, the complaint that HuffPo allows Shapiro a column seems like an unrealistic complaint. So far as I can tell from a cursory search, he’s a legitimate scientist with a long and ongoing publication history in legitimate journals. It is perfectly reasonable to expect a publication like HuffPo to filter out the legitimate scientists from the mere pretenders and not give space to pretenders, but it seems a bit much to expect them to arbitrate among legitimate scientists and decide who is right, even when one of them is an outlier who seems so obviously wrong to so many scientists. It’s clear that Shapiro is at the least over-selling the role of cooperation and genome-self-innovation, probably to try to make a name for himself in a world where the biggest mystery was solved 150 years ago, much as Stephen Jay Gould overemphasized the suddenness of speciation to try to make his own name. At worst, he is actively trying to find a biological justification for a prior religious or philosophical position. Either way, it is far from obvious that HuffPo should be able to decide as an editorial matter that he is so wrong and illegitimate that he shouldn’t be considered fit for a science column.

      • Posted May 12, 2012 at 7:44 am | Permalink

        When I tried to re-find the Shapiro piece through a search engine last week the first thing that came up related to “evolution” and whatever other keyword(s) I’d used was a column on the topic by Deepak Chopra.

        This is clearly not a site with any interest nor with the ability to determine science vs hooey. I assume they think of Shapiro’s credentials as a nice bonus. Prior to stumbling across this exchange I’d largely ignored the site; recently poking around through it it appears that a general New Age “there’s more going on in the world than we can understand” editorial line is the order of the day. Yuck.

        • Posted May 12, 2012 at 8:30 am | Permalink

          Just to be clear – when I tried to find a HuffPo piece on evolution, Chopra blathering on pseudo-scientifically was the top suggested link.

  5. Posted April 7, 2012 at 7:36 am | Permalink

    That was terrific. I loved your explanation of the antibody process. It was downright beautiful. Thanks.

  6. David Leech
    Posted April 7, 2012 at 7:46 am | Permalink

    (I often find that molecular biologists fail to grasp natural selection, even though it seems conceptually simple.)

    and some biochemists I know, it’s infuriating.

    • Posted May 12, 2012 at 7:48 am | Permalink

      I’m a layman who had a really great basic science education (in fact my first couple of college yrs I was a bio major) and that’s stunning to me that a few of you note this. How does this happen?!

      Shapiro repeatedly states that also that two organisms classified as different species can’t breed. I should think the average farmer could refute that let alone science faculty…

  7. phosphoros99
    Posted April 7, 2012 at 7:55 am | Permalink

    I would argue that the real “problem” with evolution is the standard interpretation of what the phenomenon represents.

    I submit that the nineteen century concept, still articulated by Professor Richard Dawkins for example, that “descent with modification by natural processes” represents “design without a designer” is fallacious and is adhered to either because of ignorance of the role that information technology plays in the design of living organisms or because of commitment to a particular worldview .

    tp://www.ncbi.nlm.nih.gov/pubmed/15353802

    Science. 2004 Sep 3;305(5689):1462-5.
    Bmp4 and morphological variation of beaks in Darwin’s finches.
    Abzhanov A, Protas M, Grant BR, Grant PR, Tabin CJ.
    Source

    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
    Abstract

    Darwin’s finches are a classic example of species diversification by natural selection. Their impressive variation in beak morphology is associated with the exploitation of a variety of ecological niches, but its developmental basis is unknown. We performed a comparative analysis of expression patterns of various growth factors in species comprising the genus Geospiza. We found that expression of Bmp4 in the mesenchyme of the upper beaks strongly correlated with deep and broad beak morphology. When misexpressed in chicken embryos, Bmp4 caused morphological transformations paralleling the beak morphology of the large ground finch G. magnirostris.

    • Posted April 7, 2012 at 8:16 am | Permalink

      I’m sorry but I don’t see how the article you cite relates to your opening assertion.

      • stevehayes13
        Posted April 7, 2012 at 8:23 am | Permalink

        Neither do I.

        • phosphoros99
          Posted April 7, 2012 at 9:28 am | Permalink

          http://plato.stanford.edu/entries/information-biological/

          “If we take this second route, our task then is to identify the similarities between the cases of semantic phenomena used as models and the biological systems we seek to understand, and to show how those similarities are informative. If we think of genes or cells as literally carrying semantic information, our problem changes. Paradigm cases of structures with semantic information — pictures, sentences, programs — are built by the thought and action of intelligent agents”.

          The Encylopedia cites two possible interpretations of biological information.

          Our experiences to date suggests that the latter should be preferred.

          At any rate since two plausible considerations are still available to us the concept of “design without a designer” has not been scientifically demonstrated but is a worldview imposition on the data.

      • phosphoros99
        Posted April 7, 2012 at 8:30 am | Permalink

        We now know that the essential feature of living organisms is semantic (prescriptive) information.
        The variation in the shape of the finches beak is due to gene regulation all done within an information based platform.
        The article on Biological Information in the Standford Encylopedia of Philosophy at the following website may be of assistance

        http://plato.stanford.edu/entries/information-biological/

        • Posted April 7, 2012 at 9:15 am | Permalink

          I still don’t see it, even after skimming that article. What exactly do you see as “fallacious” in the statement that you criticize?

          • Gluon
            Posted April 7, 2012 at 12:04 pm | Permalink

            I don’t see it either. And that webpage is a poorly written entry in a philosophy encyclopedia. It is not a science article, but an article *about* science. It invokes concepts like “information” without showing much understanding and even less teeth. Contrast that mush with, say, coalescent theory.

            • phosphoros99
              Posted April 7, 2012 at 12:23 pm | Permalink

              Professor Freeman Dyson gives a definition of life at :

              http://www.edge.org/3rd_culture/dyson_ad/dyson_ad_index.html

              “For the purposes of this discussion, life is defined as a material system that can acquire, store, process, and use information to organize its activities. In this broad view, the essence of life is information, but information is not synonymous with life. To be alive, a system must not only hold information but process and use it. It is the active use of information, and not the passive storage, that constitutes life”.

              would you agree with the above statement ?

              • Torbjörn Larsson, OM
                Posted April 7, 2012 at 3:01 pm | Permalink

                To paraphrase Johst: “when I hear the word information, I reach for my gun”.

                Information is always relative a physical system which is why we have many measures of it, it has no independent existence. Which, it seems, your own references are confirming.

                But there is decidedly no measures of “biological” or “semantic” information. Genomic variation can be measured by Kolomogorov complexity: random variation increases KC. Genomic learning of the environment through adaptation can be measured by Shannon channel information theory: information is channeled into the genome, decreasing its KC information content by fixating useful genes. But that is it. No information theory exists on cellular content or semantic information, whatever that is.

                This is what Dyson refer to btw, the essence of life is evolution (variation and selection). That he chooses to unnecessarily clothe biology in information theory is because Dyson is reificating information. He is a Templeton religionist.

        • Posted April 7, 2012 at 12:09 pm | Permalink

          My reading of that section is that it’s a mistake to look at genes as *informational* rather than purely materialistic (“We think that the reification of “the informational gene” is problematic”…). What are you referring to?

          • phosphoros99
            Posted April 7, 2012 at 1:57 pm | Permalink

            What is the difficulty with looking at genes as information ?

            • newenglandbob
              Posted April 7, 2012 at 2:00 pm | Permalink

              The same as looking at genes as chopped liver. It has no meaning, as pointed out to you earlier and you still have given no definition of the word.

              • phosphoros99
                Posted April 7, 2012 at 4:26 pm | Permalink

                The following is a good working definition.

                Does DNA convey meaning by the arrangement of its bases?

                what is conveyed or represented by a particular arrangement or sequence of things : genetically transmitted information.
                • Computing data as processed, stored, or transmitted by a computer.
                • (in information theory) a mathematical quantity expressing the probability of occurrence of a particular sequence of symbols, impulses, etc., as contrasted with that of alternative sequences.

              • newenglandbob
                Posted April 7, 2012 at 5:02 pm | Permalink

                Yes, that is a good definition of information. That is a good basis for how natural selection changes an organism by having the “particular arrangement or sequence of things” changed, which changes the outcome. So how is that not valid?

            • Posted April 7, 2012 at 4:27 pm | Permalink

              Well, I don’t know; I’m not an expert on information or genes, but presumably you are, and can answer my question? I’m asking *you*, what is it about quotes in the link you cited like, “We think that the reification of “the informational gene” is problematic…”, that supports *your* comments?

              • phosphoros99
                Posted April 7, 2012 at 5:46 pm | Permalink

                “Yes, that is a good definition of information. That is a good basis for how natural selection changes an organism by having the “particular arrangement or sequence of things” changed, which changes the outcome. So how is that not valid?”

                I did not say that the basis for the changes was not valid – it is valid.

                My position is that there is no scientific basis for the claim that what we are observing is “design without a designer” as the phenomenon we are observing is based on information.

                Can you cite a single instance in which it has been demonstrated (not assumed) that information which instructs , such as we see in DNA, arose solely from the laws of physics and chemistry ?

              • newenglandbob
                Posted April 7, 2012 at 6:38 pm | Permalink

                Because physics and chemistry is all there is. Can you show evidence that there is another mechanism?

              • phosphoros99
                Posted April 7, 2012 at 8:11 pm | Permalink

                “Because physics and chemistry is all there is”.

                The question remains to be answered even though you believe physics and chemistry is all there is.

                Can you cite a single instance in which it has been demonstrated (not assumed) that information which instructs , such as we see in DNA,arose solely from the laws of physics and chemistry ?

              • newenglandbob
                Posted April 8, 2012 at 2:26 am | Permalink

                Can you show a single instance that proves it does not? No, you cannot. You show no other means whatsoever. The burden of proof in on you.

              • J.J.E.
                Posted April 7, 2012 at 8:18 pm | Permalink

                Phosphorus99, you’re assuming your conclusion. Such question begging is tedious. Your argument depends on the assumptions that “information that instructs” both requires a designer and is what we see in genetics. I reject your definition of “information that instructs”. Not only that, your discourse doesn’t even clear the most basic bar that one discussing evolution and genetics needs to clear: you don’t communicate a clear understanding of what natural selection means. Until you have demonstrated that you have assimilated the logic of natural selection, it isn’t worth discussing your tendentious misconceptions.

              • phosphoros99
                Posted April 8, 2012 at 4:26 am | Permalink

                “Phosphorus99, you’re assuming your conclusion”.

                I am assuming nothing.
                I am asking a question which should be very
                simple to answer.

                Can you cite a single instance in which it has been demonstrated (not assumed) that information which instructs , such as we see in DNA, arose solely from the laws of physics and chemistry ?

              • newenglandbob
                Posted April 8, 2012 at 4:44 am | Permalink

                When do you answer the questions put to you? You put stuff out there with nothing to back it up and then ask specious questions. Your word salads are inane.

              • phosphoros99
                Posted April 8, 2012 at 6:47 am | Permalink

                You may find the following easier to answer.

                Can you cite any instance of the production of information which instructs what to do and if you can what was the source of that information ?

              • newenglandbob
                Posted April 8, 2012 at 7:03 am | Permalink

                Same old inane question from you. Where is your evidence of the designer? You have none. Around here we expect people to put up evidence of shut up.

                By the way, “production of information” is NOT a noun.

              • Posted April 8, 2012 at 7:07 am | Permalink

                I’m a little confused.

                I don’t think “information that instructs” is a good definition of genes at all. The way I understand it genes do not “instruct” at all. By virtue of their construction, they are simply copied into molecules that cause things to happen in organisms.

                The things that are caused to happen and the copying process are driven simply by chemical processes (which are driven by physical processes). I don’t see any “instructing” going on.

              • phosphoros99
                Posted April 8, 2012 at 7:33 am | Permalink

                I’ll take my leave with a paraphrase of George Orwell’s words:

                “Sometimes one’s role is simply to point out the obvious”.

              • newenglandbob
                Posted April 8, 2012 at 7:34 am | Permalink

                You misspelled oblivious.

              • Posted April 8, 2012 at 7:49 am | Permalink

                Are you running away P99?
                Didn’t answer questions or provide evidence.
                Typical.

              • Posted April 8, 2012 at 7:52 am | Permalink

                Sorry, didn’t mean to embed that.

              • J.J.E.
                Posted April 8, 2012 at 2:23 pm | Permalink

                Again, P99, I reject your use of the term “information that instructs”. It is a poor analogy that isn’t applicable to any system without demonstrated teleology. Again, I was careful with the words I chose. You are question begging, in particular by using the language of “instruction”. Instruction is inherently teleological, ergo your question is circular. Think about your question more carefully, ditch the pretentious and self-aggrandizing allusions to those more original to yourself, and when your thoughts have clarified a bit, return here and re-ask a different question.

                I will take your failure to reply as acquiescence to my calling your question erroneous.

              • phosphoros99
                Posted April 8, 2012 at 4:50 pm | Permalink

                Thanks for the cordial response.
                I’ll rephrase the question.

                The following is a definition of teleology.

                teleology |ˌtelēˈäləjē; ˌtēlē-|
                noun ( pl. -gies) Philosophy
                the explanation of phenomena by the purpose they serve rather than by postulated causes.

                • Theology the doctrine of design and purpose in the material world.

                Within the context of the philosophical definition of teleology.

                Can you cite a single instance in which it has been demonstrated (not assumed) that function such as that observe with DNA arose solely from the laws of physics and chemistry ?

              • newenglandbob
                Posted April 8, 2012 at 4:55 pm | Permalink

                No, we can not cite a SINGLE instance, just trillions upon trillions of them. Can you cite even ONE of your designer causes? Can you show even ONE example of a designer’s purpose? I guess not because you have been asked a half dozen times and failed to answer.

                Oh yes, you STILL didn’t answer mkJones’ question.

              • phosphoros99
                Posted April 9, 2012 at 10:13 am | Permalink

                “But it is a mistake of reification to treat this abstraction as an extra entity, with mysterious relations to the physical domain. The result is to obscure the ontological side of evolutionary theory, which can and should remain straightforwardly materialistic”.

                No need to answer, the statement is a worldview commitment

              • Posted April 9, 2012 at 10:43 am | Permalink

                So you disagree with the article *you* cited? I’m not sure how it helps you to cite a widely respected resource with which you *disagree*.

              • phosphoros99
                Posted April 9, 2012 at 2:16 pm | Permalink

                I do not disagree with the article. I believe that it achieves its purpose – a discussion on biological information.

                It is well written and presents different points of view on how the function that DNA serves is interpreted.

                Some of those points of view – as in the sentence quoted – represent commitment to a particular worldview.

                I see no value in engaging such an approach. Truth can only be determined when all options are entertained , assessed , accepted or rejected on their merit rather than on worldview commitment.

              • Posted April 9, 2012 at 3:55 pm | Permalink

                Well, you’re not making your case well to a layman audience, but perhaps you’re aware of this failing from past efforts.

                You have a point you’re trying to make to do with information and genes, but you’ve been unable to make it without using teleological language, which obviously begs the question, I’m sure you’ll agree. And a professional article you cite in support actually *disagrees* with your view, so we’ve only seen expert opinion *contra* your view. You have just dismissed those expert sentiments as a ‘commitment to a particular world view’ without any argument. That’s not charitable, to say the least, is it? For example, should I dismiss whatever it is you’re trying to communicate as a ‘commitment to a particular world view’? How should I distinguish between the indistinct ideas presented by *you*, an anonymous commentator on t’internet, and the reasonably well-articulated thoughts of the award winning, well-bearded philosophers who wrote the SEP article, do you think?

              • phosphoros99
                Posted April 9, 2012 at 5:07 pm | Permalink

                The following is from the same article in the Stanford Encylopedia.

                “If we think of genes or cells as literally carrying semantic information, our problem changes. Paradigm cases of structures with semantic information — pictures, sentences, programs — are built by the thought and action of intelligent agents. So we need to show how genes and cells — neither intelligent systems themselves nor the products of intelligence — can carry semantic information, and how the information they carry explains their biological role”.

                How do the authors know that genes and cells are not “the products of intelligence” ?

              • Posted April 9, 2012 at 5:36 pm | Permalink

                “How do the authors know that genes and cells are not “the products of intelligence” ?”

                You would have to ask them; are you seriously suggesting that two philosophers of biology would have no reason or evidence for this position, but are simply *presupposing* it? That’s a serious allegation, and you would need to demonstrate their lack of thought and consideration, in that case. I’m beginning to see why you’re anonymous now! I’m open to the evidence you have which justifies casting aspersions on their expertise, however, so bring it on.

                My point is that you are not challenging what they consider knowledge with *reason and evidence*, but simply dismissing their ‘knowledge’ summarily. That is not charitable, nor persuasive to a layman audience, since, as I’ve already pointed out and you’ve ignored, I would then be at liberty to dismiss *your* objections summarily too. Wouldn’t I?

                Incidentally, why would they ‘need to show how genes and cells…can carry semantic information, and how the information they carry explains their biological role’? What conclusion can you draw, do you think, that they’re concerned about the source of the semantic information?

              • Posted April 9, 2012 at 5:58 pm | Permalink

                Semantic information?!
                Come on, who on earth considers genetic information “semantic”? You just keep making things up.

                Well, maybe you do P99.

              • phosphoros99
                Posted April 9, 2012 at 7:51 pm | Permalink

                “You would have to ask them; are you seriously suggesting that two philosophers of biology would have no reason or evidence for this position, but are simply *presupposing* it”?

                They no doubt have reason but I deduce from your response that neither you nor they have evidence.

                When you find it kindly share it with me.

              • Posted April 10, 2012 at 1:52 am | Permalink

                Your position is to assert that respected academics have no evidence for their positions? Nice. It’s clear to all what *your* presuppositions are.

              • phosphoros99
                Posted April 10, 2012 at 3:49 am | Permalink

                I don’t think that appeal to authority is an adequate tool in scientific or philosophical considerations.

                The authors presented no evidence to support their position. Maybe someone else could seek to correct that failing.

              • Posted April 10, 2012 at 4:39 am | Permalink

                Well, then you are wrong. What you perhaps mean is that *fallacious* appeals to authority are inadequate in scientific or philosophical considerations, and then you would be correct. Sadly, that is not what you said; so you’ve shown some faulty reasoning, which obviously casts a little doubt on your other comments.

                To establish this as a fallacious appeal to authority, you would have to demonstrate that either philosophers as an academic whole are unsafe to treat as authorities (and some do argue that), which invalidates your original citing, or that the award-winning Godfrey-Smith and Sterelny are peculiarly unrepresentative or incompetent, and therefore unsafe to treat as authorities. Which also invalidates your original citing.

                So, we return once again to my original query, which wasn’t anything to do with your initial assertion, but was prompted by this thought; why did you cite an article that doesn’t support your comments? And now we have this further problem: why did you cite the article anyway, when you don’t think an “appeal to authority is an adequate tool in scientific or philosophical considerations”, so you presumably didn’t expect it to be treated as authoritative?

                Do you see how puzzling that citing is?

              • phosphoros99
                Posted April 10, 2012 at 5:41 am | Permalink

                Thank you for both your courtesy and input. It has been very useful.

              • J.J.E.
                Posted April 10, 2012 at 10:00 am | Permalink

                “Can you cite a single instance in which it has been demonstrated (not assumed) that information which instructs , such as we see in DNA, arose solely from the laws of physics and chemistry?”

                Again, you refuse to shelve the circular language. I can’t agree with the question begging, tendentious phrase: “information which instructs”.

                If I actually accept the term and its implications without tedious qualification, I’ve already conceded the point. So, no, I won’t answer such a malformed question.

                Let me ask you a less tendentious one: can you cite a system of information analogous to biological DNA even among demonstrated examples of teleological systems? It is my contention that the type of information carried by hereditary molecules is uniquely haphazard, degenerate, kludgy, contingent, etc. It makes Windows ME seem well-designed by comparison. If you propose that genomes manifest the mind of a designer, then your designer is a lazy fuck with poor design skills and a very short-sighted vision.

              • phosphoros99
                Posted April 10, 2012 at 11:41 am | Permalink

                I changed the question – see above.

                Would you prefer to have a program of similar sophistication to Windows ME as your operating system ?

                I couldn’t help that last question, it was begging to be asked but I’m definitely over with this one. I think that it has been exhausted both in terms of what has and has not been said.

                Thank you

  8. Brian
    Posted April 7, 2012 at 8:12 am | Permalink

    Jerry, don’t ever write for HuffPo. Never mind that they are a profit-making venture asking you to write for free, the real problem is if HuffPo is pure rubbish and no self respecting atheist and scientist should ever write for them. There are some exceptions of good stuff on HuffPo when it comes to science and religion, Victor Stenger and Sam Harris and a few others have written some good things (why they wrote them there is beyond me, but they did write them and their stuff is good). But for the most part HuffPo writes pure pseudo-scientific and anti-atheist rubbish. How often do you wind up blogging about the nonsense they put online now?! Do you really want your blog appearing aside the craziness of Rabbi Lurie or nonsense of Jim Shapiro, to name just two of many others? Dude, don’t contribute to a rubbish website like that. The big thing is you don’t give them your credibility, they can’t claim to be a website Jerry Coyne writes for. Keep unaffiliated with them! You doing just fine here.

    Why Evolution Is True is an excellent blog! Keep doing what you are doing!

    • Posted April 7, 2012 at 8:25 am | Permalink

      Sorry, I have to disagree. If Jerry wants to reach out and change some minds instead of primarily “preaching to the choir”, he should jump at the chance to address a big audience of people who are inclined to think differently. This is the discussion with the biggest payoff. Such an article will have a greater impact per hour of writing than anything Jerry might write here (because most of us are already converts, and even if that were not the case, Huffpo has a much bigger audience).
      I bet there are lots of people who read stuff like Shapiro’s in Huffpo, and who suspect something is amiss, but because there is no rebuttal by scientists, they assume the articles represent scientific consensus. I think scientists should address this group, in the same forums that print the pieces we object to.

      • Posted April 7, 2012 at 9:00 am | Permalink

        I agree with you Lou. Since HuffPo doesn’t have a comment section (as far as I can tell), I think articles like this deserve a rebuttal. And that rebuttal needs to come from an expert.

        Jerry, I think you should write something for them but make it clear that it is a direct rebuttal to Shapiro’s article and insist on being able to see exactly what they are going to publish.

        • onkelbob
          Posted April 7, 2012 at 9:33 am | Permalink

          “Since HuffPo doesn’t have a comment section…” The site has an active comment section, with an equally responsive original poster. Of course the comment section is a veritable amen corner, and the OP’s responses consist of arguments from authority.

          • Posted April 7, 2012 at 9:45 am | Permalink

            Somehow I missed the comments before. You have to scroll way down for them.
            Has anyone here posted a link to this post in a comment? I don’t have time yet but it might help people who look at the comments there. Later I’ll try to read what people have said.
            Gotta go now.

            • Posted May 12, 2012 at 7:55 am | Permalink

              I have posted on there (I’m new here as well). Thus far Shapiro’s counterargument to one of my points is that I’d don’t understand things because I haven’t read his book.

              Uh-huh…

      • onkelbob
        Posted April 7, 2012 at 9:25 am | Permalink

        … “he should jump at the chance to address a big audience of people who are inclined to think differently.” “I bet there are lots of people who read stuff like Shapiro’s in Huffpo, and who suspect something is amiss…”
        You make two assertions here with which I obviously disagree. There is an obvious difficulty in falsifying either hypothesis. However, I submit to the readers, that the sheer amount of crank present on the site in question, (e.g., its well known anti-vaccine stance) clearly demonstrate the sisyphean nature of the task. That “big audience” is more prone to invoke the heckler’s veto than to listen to valid argumentation. Jerry is correct in avoiding lending them any credibility, they are a hopeless case of faex populi.

        • Scott near Berkeley
          Posted April 7, 2012 at 1:43 pm | Permalink

          Agree 100% with this line of thinking. A huge shot of conformation bias exists at nearly every internet site, but esp. the “we cover the realm and its people” -types of sites.

          Avoid.

      • Brian
        Posted April 8, 2012 at 10:07 am | Permalink

        I agree with the notion of reaching out to a bigger audience. Of course Jerry should seek out a big audience that is more than just the choir. Let’s assume for the sake of argument that Jerry is just preaching to the choir and needs a bigger audience (that might be true or that might be false, I’m not saying either way). Assume that is so…

        Why must the forum in which Jerry reaches out to a large audience be Huff Po?

        I think Jerry can find better opportunities for reaching a bigger audience than Huff Po. Jerry using Huff Po to reach a large audience gives Huff Po more credibility. Given all the psuedo-science (anti-science?) and anti-atheist nonsense posted on Huff Po, Huff Po doesn’t deserve any credibility. Jerry shouldn’t give it to them.

        To my mind this is a bit like Dawkins debating a creationist. Sure, Dawkins might reach more people, but sharing the stage with the creationist also gives creationism credibility. In particular by making it look like there is a evolution vs creationism controversy worth Dawkins debating. Also by sharing the stage with someone as reputable as Dawkins and looking equally reputable. Jerry doesn’t need to share the stage with Huff Po to reach more people nor should he.

        “I bet there are lots of people who read stuff like Shapiro’s in Huffpo, and who suspect something is amiss, but because there is no rebuttal by scientists, they assume the articles represent scientific consensus.”

        Yea, but then by Jerry Coyne blogging at Huff Po, Jerry gives the impression that there is a genuine scientific debate in which the Huff Po nonsense like Shapiro’s stuff is a credible view that scientists are considering. We neither want to give the impression that Huff Po represents genuine scientific consensus or genuine scientific debate. The stuff on Huff Po is mostly just nonsense (with some news items and Stenger articles). What should happen here is not Jerry Coyne writing for Huff Po but rather people should stop reading Huff Po. Perhaps Jerry needs a better forum than this blog to say so, I regard that as open to discussion, but then Jerry should find a good forum other than Huff Po to say so.

      • Brian
        Posted April 8, 2012 at 10:10 am | Permalink

        I should remark to both you, Lou Jost, and Lynn Wilhelm that Jerry’s blog is referred to by people like Shapiro responding to Jerry all time. Jerry’s blog already has the Huff Po audience when it comes to responding to Shapiro and company without Jerry being associated with Huff Po. If he already has the Huff Po audience to the extent it is relevant, how would blogging for Huff Po get a bigger audience?!

        • Posted April 8, 2012 at 2:10 pm | Permalink

          But surely only a small fraction of Shapiro’s readers will follow the link to this website. A larger fraction would probably read a post by Jerry in Huffpo.

    • Screechy Monkey
      Posted April 7, 2012 at 9:01 am | Permalink

      As the saying goes, Jerry Coyne writing for the HuffPo would look good on the HuffPo’s resume; not so much on his.

      • Posted April 7, 2012 at 9:07 am | Permalink

        So what? This isn’t about resumes, this is about reaching people and changing minds.

        • Posted April 7, 2012 at 9:30 am | Permalink

          I go back and forth on this. I know I’d reach a big audience, and some of them must have open minds. But I don’t want to duplicate stuff there that I write here (I think that would be unfair to the readers here), and I resent HuffPo exploiting authors’ desire for a big audience by paying them bupkes.

          • Posted April 7, 2012 at 10:14 am | Permalink

            I can see that, but I am pretty sure no one here would feel slighted if you duplicated some of this elsewhere. This blog is a good place to discuss real scientific issues, and it is a good place to get well- informed comments, while that place is a good one for breaking some barriers among less-knowledgeable readers.

            As for the dollars they earn off your work, it is kind of like the scientific journal publishing business. Scientists contribute articles for free, and referees screen the articles, also for free, while the publishers make gigantic profits…at least HuffPo isn’t charging you page fees.

          • Gluon
            Posted April 7, 2012 at 12:07 pm | Permalink

            The only way it’d bother me is if the HuffPo version of an article brought lots of HuffPo readers back to this website and into the comments here. Yikes!

          • Tim
            Posted April 7, 2012 at 12:48 pm | Permalink

            I agree with Gluon. A flood of Dunning-Krugerites here would deal a severe blow to this website. Your excellent posts have attracted a high-quality readership whose comments add a lot to the quality of the site. That may be becaue you are heavily moderating to comments. Whether or not that’s the case, when I go to even ‘lefty’ sources (e.g., Mother Jones) and see the flood of moronic commentary that accompanies anything that conflicts with wingnut canon, it is deeply depressing.

            • Marella
              Posted April 7, 2012 at 5:31 pm | Permalink

              Indeed, the high quality of the comments on this site raise it far above the norm.

          • Tim
            Posted April 7, 2012 at 12:54 pm | Permalink

            I should have mentioned: an outstanding post. Your students are fortunate indeed.

            • Torbjörn Larsson, OM
              Posted April 7, 2012 at 3:17 pm | Permalink

              I knew I forgot something! Yes, I agree, a good trouncing and an excellent source. (Of course these often go together, as a trouncing need some heft.)

              As for the HuffHuffPooPoo stuff I go with denialism blog at the moment: denialists can only productively be ridiculed, a mighty weapon for rationality during the last millenniums. And effectively these sites are denialist, provocation (everywhere) and specialist take down (US) sells well and they attract a paying crowd.

          • Heintje
            Posted April 8, 2012 at 8:08 pm | Permalink

            Not only that. If I were the management of PuffHo, and I realized that by giving platform to crackpot ideas I can lure legitimate academics into writing for PuffHo for free in attempts to refute them, what would be the rational course of action in the future? Publish more crackpot ideas, of course!

            Besides, I agree with Onkelbob’s comment above on the sisyphean nature of the task.

        • Brian
          Posted April 8, 2012 at 10:24 am | Permalink

          In a sense it is about resumes. But not so much Jerry’s resume as much as Huff Po’s and the more silly bloggers there.

          There’s a bit of strategy to consider here. Part of that is reaching a big audience. But that isn’t the only part. It also includes framing the discussion and your position and your opponent’s position in the mind of your audience. Framing as in who is making credible arguments and who isn’t. If you share the stage with someone and boost their resume by doing so, the good resume suggests to the audience that this is a person who makes credible arguments, enough to earn the credibility on their resume. It’s about image.

          If Huff Po gains more credibility than it deserves, that might get more people reading Jerry’s stuff but that won’t necessarily mean changing their mind. The primary objective is to change minds (and not letting Huff Po treat their bloggers poorly).

          Note that part of the strategy is indeed making sure Huff Po treats their bloggers well. This is a different goal than the one I am raising, but Jerry is entitled to that goal and there is merit to it.

      • Brian
        Posted April 8, 2012 at 10:13 am | Permalink

        Agreed :-) My sentiments exactly. I allude to this below in a response, but I like how you said it!

  9. gillt
    Posted April 7, 2012 at 8:47 am | Permalink

    Some evolution can happen quickly due to horizontal gene transfer, but that’s not the main engine of adaptive evolution.

    HGT, as an engine of variation, is biologically significant in microorganisms to the extent that the experts say it presents a huge conceptual challenge (some same impossible) when inferring phylogenies in microorganisms.

    • Torbjörn Larsson, OM
      Posted April 7, 2012 at 3:23 pm | Permalink

      But I thought that has been solved by diverse synthetic methods like megamatrixes et cetera!? (I’m sorry, I have a good reference somewhere but I can’t get hold of it. Pretty sure there was something better than megamatrixes.

      It was my understanding that they converged on phylogenies, often trees with a modicum of HGT, without any statistical problems.

  10. Posted April 7, 2012 at 8:52 am | Permalink

    Thanks for the science post.
    And the new word–“ambit”.

    Now I thought “adaotuve” (in #3) might be a new word but it seems to be a typo. I rarely assume typos here anymore, you are always surprising me.

    • whyevolutionistrue
      Posted April 7, 2012 at 9:29 am | Permalink

      I fixed it, thanks.

  11. Desnes Diev
    Posted April 7, 2012 at 8:54 am | Permalink

    Shappiro: “If immune cells can do all the above, is there any scientific reason we would assume that other cells cannot do the same?”

    Embryological data, perhaps. If hypermutability such a common phenomenon, complex Metazoa would produce much more cells and show much more apoptosis during development than what is observed. In fact, it is hard to see how they would develop coherently at first.

    This being says I may be wrong as I am really not sure to understand Shapiro’s “philosophical” thoughts.

    Desnes Diev

  12. Ken Pidcock
    Posted April 7, 2012 at 9:00 am | Permalink

    There has been some controversy about the occurrence of “adaptive mutation” in bacteria, but that’s died out because there’s simply no evidence that the phenomenon occurs.

    Meh. If by “adaptive mutation” you mean specific mutational events in response to specific environmental changes, there may be no evidence. Nevertheless, there’s little question that stress-induced mutagenesis can accelerate bacterial evolution in particular environments.

    • Posted May 12, 2012 at 8:17 am | Permalink

      I have a problem with the framing of this that Shapiro has done. Mutations are at root errors (most of them with negative consequences to my understanding.)

      Why would we be surprised that environmental stresses would increase the rate of error in a biological process? Given that random mutations that are severe enough to make individuals non-viable take them out of the population, why would we be surprised that in some cases the viable organisms end up with a mutation that assists them in some way?

      We’re basically increasing the rate of the dice rolls, and then attributing the fact that the set of players who don’t lose all their money & go home are having success because they somehow control the dice. And not, y’know, because they are by definition the ones left at the table.

      Shapiro gathers page after page of studies in which people got a grant to – in my mind – prove little more than confirmation bias.

      As I commented on HuffPo, Shapiro’s stance fails for me because it fails to explain the fact that most mutations don’t help any organism do anything, most species go extinct and therefore his Invisible Hand of Nature guiding mutations seems to be really, really terrible at what he claims it’s doing on purpose.

  13. s.k.graham
    Posted April 7, 2012 at 9:43 am | Permalink

    Way back in _The Selfish Gene_I, recall Richard Dawkins touching briefly and positively on the possibility of genes influencing the probability of mutations in other genes (including germ-line genes, as opposed to dead-end immune cell genes). One simple and obvious mechanism would be to increase/decrease the activity of the error-correction machinery on different parts of the genome (and this could further vary by cell type, developmental stage, etc. — as in the immune system). In the replicator-centric, selfish-gene view, it makes perfect Darwinian sense that such “natural genetic engineering” (not Dawkin’s phrase, of course) would arise sometimes by chance, and then be favored by natural selection if it actually helped the gene(s) responsible to thrive. But I also recall that Dawkins indicated there was a lot of push-back against this idea among biologists (but that was back in the 70’s).

    If Shapiro restricted his point to claiming that biologists fail to recognize how much “natural genetic engineering” goes on, or how important such mechanisms might be in evolution, he might have a point. I don’t know the status of this question among biologists. It may well be that biologists reject the idea too quickly and are not looking for it. But that is a discussion for biologists, not a lay-audience.

    Darwinism as a whole, particular in light of the “selfish gene”, does not conflict with the idea of “natural genetic engineering” and in fact embraces it. Random mutation and natural selection would have given rise to the very genes that influence the mutation (or duplication, or horizontal transfer) of other genes (or even themselves).

    Shapiro is just giving fodder for religious folks, who do not even understand the argument, to say “see, see, Darwin was wrong!”

  14. Pray Hard
    Posted April 7, 2012 at 9:49 am | Permalink

    Attack Darwin = sell more books.

  15. Ougaseon
    Posted April 7, 2012 at 9:51 am | Permalink

    I can’t remember where I read it, but someone proposed that natural selection is a meat-space implementation of Bayesian inference. I like that analogy, and it has helped me clarify natural selection to several people who were having difficulty understanding it (Note, however, that they were not already hostile to the idea, they just didn’t quite see how it worked…)

    Perhaps Shapiro or others having a hard time with natural selection could benefit from working through that analogy, especially if it seems like the population-level thinking is the sticking point.

    • Torbjörn Larsson, OM
      Posted April 7, 2012 at 3:36 pm | Permalink

      As I understand it, it is not an analogy but a genetic population is a bayesian inference mechanism learning from the environment.

      It is easy to see in asexual populations, where you can put a new generation’s alleles as the prior and their reproduced alleles as the posterior. For the actual learning part you have to integrate to fixation and many generations.

      Agreed on the necessity to see that we are talking the genome of a whole population (so fixation), or the idea of teleology raises its ugly warty religious head…

    • Gluon
      Posted April 7, 2012 at 4:22 pm | Permalink

      This is funny, given how few people seem to understand Bayesian inference. It strikes me a bit like saying, “He doesn’t understand Newton’s laws? Well, try explaining it to him in terms of General Relativity.”

      • Marella
        Posted April 7, 2012 at 5:34 pm | Permalink

        I wonder if I can learn about Bayesian Inference if someone explains it to me in terms of Natural Selection?

  16. Pray Hard
    Posted April 7, 2012 at 9:59 am | Permalink

    Very informative article for us not-actually-scientists guys.

    Closet creationism does seem to sell these days, though.

    Maybe Mr./Dr. Shapiro should read Darwin’s Dangerous Idea by Dan Dennett. It opened my eyes as I struggled through it a number of times.

  17. Posted April 7, 2012 at 10:11 am | Permalink

    A bit old, but stuff on the evolution of the immune system here http://www.talkdesign.org/faqs/Evolving_Immunity.html

    The Transib family of transposons also provide evidence for the origin og RAG genes

  18. Posted April 7, 2012 at 11:55 am | Permalink

    Coyne and Shapiro in the faculty lounge:

  19. MAUCH
    Posted April 7, 2012 at 12:49 pm | Permalink

    I can see what’s going on here in this adaptation or creation debate. In all honesty laymen like myself can barely scratch the surface of how the immune system works. By Shapiro unloading on us a Gish gallop of impressive sounding obfuscation it leaves us confused and very possibly in doubt. The easy way out of this conundrum is to conclude that god unloaded a miracle or two. Isn’t this a much more parsimonious solution?

  20. Tulse
    Posted April 7, 2012 at 2:46 pm | Permalink

    Jerry, thanks for the brief introduction to immune mechanisms. It is amazing to me that the body actually mutates a part of itself to respond to infection. Is this the only example of “intentional” mutation in a healthy human? Are there cases of other organisms that use mutation within themselves for other purposes?

    I’m also curious as to how hypermutability gets restricted to the appropriate genes. What prevents the entire genome from undergoing mutation? Is there a simple explanation you can share?

  21. Gluon
    Posted April 7, 2012 at 4:36 pm | Permalink

    “I am not sure why Shapiro is so obtuse about this, for he’s been trumpeting these same misconceptions for decades.”

    John Horgan had a point in The End of Science (*) about this, a point I think Dawkins also made in The Selfish Gene (it’s been 20 years, so I don’t recall). In a very real sense, Darwin solved the one Big Question of biology. It’s done, and we can’t ever solve it again, just as we can’t ever discover Newton’s Laws or Relativity again. Everyone since Darwin has been filling in details. Important details, but not conceptual revolutions. Ambitious people are sometimes not satisfied with that detail filling role, or with the merely practical working out of mechanisms. They want to shake the foundations of knowledge, to be a giant like Darwin. What’s an ambitious person to do in an age when the Big Questions are answered? In many cases, SJ Gould is a good case in point, this leads them to overreach and to try to paint the details they are working on, often important details, often very useful details that will change our lives, as something intellectually deeper than they really are.

    This phenomena is actually quite common, it seems to me. Physics seems to be overrun with it, which should not be surprising given the thirst for recognition coupled with how much of physics is actually solved (cf Lederman’s coining of the term The God Particle for something considerably more mundane).

    • BillyJoe
      Posted April 7, 2012 at 7:22 pm | Permalink

      Yet Richard Dawkins has not done so and he is the probably the best known evolutionists in existence today.

    • Heintje
      Posted April 8, 2012 at 8:13 pm | Permalink

      Hasn’t Leon Lederman been quoted saying that he wanted to call Higgs Boson the goddamn particle, but the publisher didn’t allow it.

      Not sure about the authenticity of the quote though.

    • IntelligentAnimation
      Posted December 29, 2012 at 9:38 pm | Permalink

      Darwin was a disgrace to science and everything he added to our knowledge of evolution was wrong. He spelled his name right but I can’t give him much else.

      Gradualism? Wrong.

      Random changes? Wrong.

      Selection as a cause? Wrong!

      Nice statue of him at his shrine, though.

  22. Hempenstein
    Posted April 7, 2012 at 5:38 pm | Permalink

    I see on Amazon that Lynn Margulis liked his book.

    • BillyJoe
      Posted April 7, 2012 at 7:27 pm | Permalink

      Not content with showing that symbiosis can occur and did occur, she then wanted to make the mechanism she discovered the basis of all evolutionary change.

      At least Shapiro has the excuse that he is supremely knowledgable about microbiology but abyssmally ignorant about evolution.

  23. Marella
    Posted April 7, 2012 at 5:44 pm | Permalink

    I have often been surprised when reading a book on some aspect of biology to realise that the author has misunderstood natural selection in some way. It may be a simple concept, but it is obviously a difficult one for human brains to come to grips with. Many fail, even those who you would expect to have a clear understanding of it.

    • IntelligentAnimation
      Posted December 29, 2012 at 9:48 pm | Permalink

      Marella, I think Shapiro understands selection quite well, although he gives it a shade too much credit. He says it is a “purifying force” not a “creative” one.

      In many ways he is correct in this, because selection can’t bring forth novel traits. Selection creates nothing, but what Shapiro is saying is that it winnows out the less favored, leaving in the remainder more prevalently favorable traits.

      I see his point, from the standpoint of discussing selection with a Darwinist in a way they may understand, but technically, selection is not a force. All of the force of change (evolving) is within the organism.

      • whyevolutionistrue
        Posted December 30, 2012 at 4:37 am | Permalink

        I’m sorry but you’re spouting garden-variety creationism. You obviously haven’t read all the refutations of the “selection-can’t-create-novel-traits” arguments, beginning with Rich Lenski’s experiment on citrate metabolism.

        I think you need to go post your ignorant criticisms at the Discovery Institute.

  24. superatheist
    Posted April 7, 2012 at 9:02 pm | Permalink

    I am disappointed in this criticism of neo-Darwinism, even though I agree that we have to add to it – not reject it. For example, the thing about diversity of living organisms on earth, purely natural selection and random mutation can’t account for all of it. As Gould had explained that contingency and accidents are very important to understand this diversity. Not all phenotypic evolution is just a product of Natural selection, Gould’s “Tires to sandals” – pre-adaptations – are also very important. This is the kind of discussion that I would like to learn some more about.

    • newenglandbob
      Posted April 8, 2012 at 4:40 am | Permalink

      Not all phenotypic evolution is just a product of Natural selection

      No one claims that. That is a strawman issue.

      • superatheist
        Posted April 8, 2012 at 6:15 am | Permalink

        If you read the Evolutionary Biology textbooks at the undergraduate level that I am reading, there is hardly any mention of sprandels or developmental reprogramming. Of course, I know that the field of evolutionary biology, is not just textbooks and lectures given in a university. Some people like Piglucci and Gould – if I remember correctly – think that the synthesis gives Natural selection too much weight. I am not interested in the argument over which mechanism is more important, all of them work and we have to view evolution from a pluralistic point of view. Prof.Lewontin’s full review of WEIT, gives you a better idea of what I am talking about.

  25. Posted April 8, 2012 at 4:43 pm | Permalink

    Reblogged this on urbanperegrines.

  26. Posted April 8, 2012 at 8:27 pm | Permalink

    It would take me *weeks* of blogging to correct Shapiro. Great job, Jerry, especially for a non-immunologist. Great job, man!

  27. Michael Syvanen
    Posted April 9, 2012 at 2:14 pm | Permalink

    I found Shapiro’s objections to natural selection incoherrant when I first heard them over 30 years ago. I just can’t see what his problem is.

    In any case I am responding here because of this quote by Jerry:

    “What Shapiro fails to realize here is that these “innate features of the genome” that produce the appearance of “directed change” are themselves molded by a combination of random mutation and natural selection, creating a genome that operates in an adaptive way.”

    This is I believe a very straightforward and common sense explanation for many of the mutational mechanisms that we see operating in nature. However, this is not a view that was easily accepted by modern evolutionary thinkers especially those trained in the discipline of population genetic theory. I made the arguement in a 1984 Ann Rev Genet that transposable elements evolved under natural selection via the beneficial mutations they induced over time. This argument was bitterly opposed by traditional population geneticists at that time. They considered such an argument as teleological.

  28. IntelligentAnimation
    Posted December 29, 2012 at 10:11 pm | Permalink

    I have read Shapiro’s book and have now read Coyne’s rejection of it. I think Shapiro built up an excellent case to support his claims, yet Coyne simply inserts the words “random” and/or “selection” where he sees fit without actually showing any evidence of randomness.

    It should be exceedingly easy to determine random from intelligent genetics. The two could not be more different and we get dozens of mutations with each generation.

    Try letting your 2-year old randomly slap at buttons on the keyboard on your next message rather than intelligently editing it and see the results. Basically it is chaotic, useless mess versus functional order.

    Well over 99% of mutations fit the form, function and context of the individual. The VERY rare dysfunctional (harmful) genetic changes are easily explained by radiation or mutagenic chemical interferfence.

    Genetic changes are not random. They are as intelligently controlled as all other aspects of all life. Why would they have been any different than all other molecules in living organsims?

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4 Trackbacks/Pingbacks

  1. [...] the disagreement between, say, Jerry Coyne and Jim Shapiro — see Jerry Coyne’s “Jim Shapiro continues his misguided attack on neo-Darwinism – can continue on indefinitely without resolution. It seems clear that Shapiro’s claim [...]

  2. [...] a recent posting on his Why Evolution Is True website, “Jim Shapiro continues his misguided attack on neo-Darwinism,” Jerry Coyne attacks me again. Let us examine some of his [...]

  3. [...] a tentative work in progress, conventional evolutionists make absolutist statements like “all the facts are on my side.” Making obviously inflated and unrealistic assertions is hardly likely to convince anyone who has [...]

  4. [...] [...]

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