Another philosopher proclaims a nonexistent “crisis” in evolutionary biology

As Wikipedia notes, Project Syndicate “is an international not-for-profit newspaper syndicate and association of newspapers. It distributes commentaries and analysis (‘opinion pieces’) by experts, activists, Nobel laureates, statesmen, economists, political thinkers, business leaders and academics to its member publications, and encourages networking among its members.”

I can’t remember how I came across an article featured on Project’s Syndicate‘s latest webpage, “Evolutionary theory’s welcome crisis,” but a hat-tip to the reader who gave me the link. When I saw that title, and learned that the author, John Dupré, is a professor of philosophy of science at the University of Exeter and also director of Egeneis, a genomics institute at the university, I got worried.  We often see molecular biologists (e.g., James Shapiro) and philosophers (e.g., Thomas Nagel and Jerry Fodor) proclaiming the imminent death of modern evolutionary theory, so someone who wears both hats could be especially muddled—and dangerously misleading.  And my suspicions were correct. Dupré indeed proclaims a severe crises in evolutionary biology, but he’s absolutely wrong. The theory is not in crisis, but, as usual, the author simply describes new that supplements the theory but doesn’t lead to its drastic revision.

While decrying Biblical creationism as a threat to science, Dupré nevertheless sees that the modern, or “neo-Dawinian” theory of evolution is outmoded, and is about to experience a big sea change.

The creationists are right about one thing: contrary to the impression given by much popular writing on the subject, the theory of evolution is in crisis. But this is a positive development, because it reflects the non-linear progress of scientific knowledge, characterized by what Thomas Kuhn described in his influential book The Structure of Scientific Revolutions as “paradigm shifts.”

So what’s the big crisis? The way Dupré describes it at first, things don’t look so dire:

For the last 70 years, the dominant paradigm in evolutionary science has been the so-called “new synthesis.” Widely publicized in recent years by Oxford evolutionary biologist Richard Dawkins, the new synthesis unites Darwin’s theory of natural selection with Mendelian genetics, which explains heredity.

The current crisis in evolutionary science does not imply complete rejection of this paradigm. Rather, it entails a major, progressive reorganization of existing knowledge, without undermining the fundamental tenets of evolutionary theory: organisms alive today developed from significantly different organisms in the distant past; dissimilar organisms may share common ancestors; and natural selection has played a crucial role in this process.

Other assumptions, however, are under threat.

Well, since the factors outlined in the first and second paragraph are the major parts of modern evolutionary theory, and are still valid, what assumptions are now so threatened that they’ve engendered a crisis? Dupré sees four:

  • Horizontal gene exchange.  As Dupré notes:

Other assumptions, however, are under threat. For example, in the traditional “tree of life” representation of evolution, the branches always move apart, never merging, implying that species’ ancestry follows a linear path, and that all evolutionary changes along this path occur within the lineage being traced. But examination of genomes – particularly microbes – has shown that genes moving between distantly related organisms are an important catalyst of evolutionary change.

Well, yes, we’ve known for a while that microbes can have “wide gene exchange”—movement of chunks of DNA between distantly related species of bacteria. That also can happen in eukaryotes: rotifers, for example, have genes from bacteria and plants in their own DNA, pea aphids have genes from fungi, and, more closely-related species, like butterflies, can exchange genes by hybridization that can be advantageous and used by natural selection to produce changes in pattern.  But this doesn’t constitute a crisis—it’s imply a very interesting finding that shows that variation in a genome can arise by processes other than mutation of an organism’s own DNA. The disposition of that variation still must occur via either natural selection (it can be good or bad) or genetic drift (no effect on fitness).  This hasn’t really changed the theory of evolution one iota, though it’s changed our view of where organisms can acquire new genes.

  • Evolution based on “macromutations.”  One of the assumptions of modern evolutionary theory is that complex adaptations are usually built from several to many genes of small effect.  That doesn’t mean that genes that have large effects don’t ever occur, but they’re posited on theoretical grounds to be rare.  Dupré claims that we now know that much of evolution indeed rests on macromutations:

Moreover, the new synthesis assumes that the main drivers of evolution are small mutations generated by chance within a species. But recent evidence suggests that large changes, caused by the absorption of a chunk of alien genetic material, may be just as significant. Indeed, the absorption of entire organisms – such as the two bacteria that formed the first eukaryotic cell (the more complex cell type found in multicellular animals) – can generate large and crucial evolutionary change.

This is true, but what Dupré doesn’t mention—and I hope he knows better, because he should if he’s learned anything about evolution—is that these big events of symbiosis that produced mitochondria, chloroplasts, and perhaps flagella, are extremely rare, and we’ve known that for a few decades.  This is not new information, and it hasn’t caused a “crisis,” for most adaptive change within species is, contra Lynn Margulis, not caused by symbioses or even horizontal gene exchange. When we examine the genetic basis of adaptations, we find that it is almost invariably due to mutations within an organisms’s DNA, not ingestion of another species.  Moreover, for complex adaptations, several to many genes are involved, although for simple traits, like a color change in moths (e.g., speckled to black in Biston betularia, the “peppered moths”) single mutations can be important.

  • Evolution based on epigenetic change (i.e., environmentally induced changes in DNA that aren’t coded in the genome). As Dupré notes,

Recent developments in molecular biology have put the final nail in the coffin of traditional genetic determinism. For example, epigenetics – the study of heritable modifications of the genome that do not involve alterations to the genetic code – is on the rise.

Yes, we now know that DNA can be modified in regular ways: “imprinted” in different ways by male vs. female parents, and that imprinting can have crucial evolutionary significance, for example in producing conflicts between paternal and maternal genes in fetuses.  But what Dupré doesn’t recognize is that this methylation is actually coded in the DNA itself (which tells a genome how to get modified when it finds itself in one sex or another), so yes, it does involve alterations of the genetic code. Other kinds of epigenetic change that are produced solely by the environment and not by the genome itself, such as changes in weight or flower color, are not stable because the DNA reverts to earlier forms. Hence such changes do not last more than a few generations, and so cannot be the basis of permanent evolutionary change.

  • Evolution based on miRNA (“microRNAs”).  We have learned in the last few years that tiny molecules of “microRNA” can play a crucial role in regulating gene expression since they can bind to the “messenger RNA” that produces proteins, preventing protein production.  As Dupré notes:

And the many kinds of small RNA molecules are increasingly recognized as forming a regulatory layer above the genome.

Well, no, not really, because microRNAs are made by the DNA: their production is coded in the genome!  Thus they are in no sense a “regulatory layer above the genome,” any more than regulatory proteins are “above the genome.” The evolutionary dynamics of microRNAs can be completely analyzed and understood in a normal evolutionary framework: whether or not changes in their code are adaptive will determine if they increase or decrease in frequency, or float around if they have no effect on fitness.

So what Dupré has done here is combine several interesting findings about evolution—findings that are easily incorporated into our existing framework—and cast them as somehow causing a “crisis” for modern evolutionary theory. While these findings are interesting (evolution would be boring if we didn’t find new phenomena to study), they’re not paradigm changing, as Dupré insists, nor do they undermine the gene-centered framework of modern evolutionary biology:

Beyond undermining the gene-centered theories of evolution that have dominated public consciousness for several decades, these developments call for new philosophical frameworks. Traditional reductionist views of science, with their focus on “bottom-up” mechanisms, do not suffice in the quest to understand top-down and circular causality and a world of nested processes.

Almost every word in these two sentences is either wrong or obscure.  Gene-centered theories are not undermined. We do not need a new philosophical framework for evolution, much as Dupré wants one. Traditional reductionist views are still valid and yielding valid insights (what is microRNA other than a “bottom-up” phenomenon that regulates genes?).  And what in the world is “top-down and circular causality”? I don’t think he means the environment, which is a big factor in natural selection. Absent the environment, there are no “top down” processes in evolution: everything is bottom up.  “Top down” in fact, is a phrase used by theologians to add God to the workings of science, which has always been best understood by reductionist thinking (granted, there are also epiphenomena like the wetness of water, but those must always be consistent with lower-level phenomena). Now Dupré doesn’t seem to be a goddie, but he still seems susceptible to the nebulous woo of “top down causation.”

What bothers me about Dupré is not so much his bringing to public attention new insights into how organisms work, for that’s a good thing. What bothers me is that, like so many others, he casts these new discoveries as things that throw the theory of evolution in crisis. And that plays into the hands of creationists, no matter how strongly Dupré decries creationism. As an evolutionary biologist—which Dupré is not—I think I’d know if my field was in crisis.  Yet I haven’t heard any recent lamentations from my colleagues.

And there are findings that could put modern evolutionary theory in crisis. If we found, for example, that in most species mutations weren’t random, that is, if they didn’t occur irrespective of the adaptive “needs” of the organism, that would be a major revision of evolutionary theory.  But it hasn’t happened.

As usual, rumors of the death of evolutionary biology are greatly exaggerated.

77 Comments

  1. Posted September 7, 2012 at 8:32 am | Permalink

    Yeah, I find intelligent design emotionally unappealing too. Nevertheless, I suspect it is the future.

    • Occam
      Posted September 7, 2012 at 12:27 pm | Permalink

      Before addressing the question whether ID may or may not be “the future”, however defined, there is a small practical matter of order:
      Two different posters signing under an identical pseudonym, i.e. “Occam”, are going to be definitely confusing for our fellow WEIT readers. I modestly believe I have some claims to precedence here. It’s a problem of ID. (See how confusing the slightest acronymical ambiguity can be?)

      • Posted September 7, 2012 at 12:39 pm | Permalink

        Fair enough. I should be posting under “William” now.

    • Ichthyic
      Posted September 8, 2012 at 7:08 am | Permalink

      ID is not just emotionally unappealing, it’s entirely intellectually vacuous.

      are you saying you expect our future to be a complete lack of biological science?

      • Posted September 8, 2012 at 10:36 am | Permalink

        Someone who thinks that intelligent design theory is intellectually vacuous is clearly not familiar with the work of Dr. Kent Hovind. May I suggest familiarizing yourself with that of which you speak, “sir.”

        • Elle
          Posted September 8, 2012 at 3:11 pm | Permalink

          Kent Hovind? That Kent Hovind? Now, seriously. That guy is hopeless.

          • Posted September 8, 2012 at 3:32 pm | Permalink

            Hopelessly brilliant!

            • Elle
              Posted September 8, 2012 at 4:06 pm | Permalink

              You are entitled to your opinion. But I beg to differ.

              • Christian
                Posted September 9, 2012 at 2:25 am | Permalink

                Well, I can assure you he is just joking.

                Why he tried to post the same joke here where people are not familiar with his true position, I don’t know.

              • Elle
                Posted September 9, 2012 at 6:15 am | Permalink

                That’s a relief.

              • Posted September 9, 2012 at 8:39 am | Permalink

                Oh, I would never joke about Dr. Kent Hovind. As Christian mentions, however, my posts in this thread may not be entirely, 100% serious.

                @ Christian – Is there any chance you’re the same Christian who posts on CARM? I know it’s a common name, but still.

              • Christian
                Posted September 9, 2012 at 10:15 am | Permalink

                Yep, I’m the same Christian.

              • Elle
                Posted September 9, 2012 at 2:40 pm | Permalink

                And I would never joke about him being hopeless. :-)

  2. Posted September 7, 2012 at 8:48 am | Permalink

    There is one and only one radical sea-change with respect to the science of Evolution, but it’s nothing that invalidates the New Synthesis. Indeed, it’s entirely dependent upon it.

    That revolution is the work that Venter and his colleagues are doing: we are now becoming the intelligent designers that Christians would have us believe Jesus is.

    Of course, this is no different from any other field of science. Newton and Kepler described the motion of the planets, and we’ve taken that knowledge and created artificial heavenly wanderers of our own. Pasteur figured out what causes disease, and we’ve radically changed the progression of disease. Rutherford found the holes in atoms, and today we smash them.

    Should it be any surprise that we’re now doing the same with Darwin’s great discovery?

    Cheers,

    b&

    • Marella
      Posted September 7, 2012 at 5:11 pm | Permalink

      I still don’t have my cuttle-fish skin yet dammit.

      • Posted September 7, 2012 at 5:53 pm | Permalink

        Nor I my retractable claws.

        <sigh />

        b&

  3. TJR
    Posted September 7, 2012 at 8:51 am | Permalink

    Yet another case where the whole thing is based around strange redefinitions of words. I must have missed the bit where the dictionary said

    Crisis: a situation where lots of really cool and interesting stuff has been discovered recently.

    This must mean that Curiosity has put the exploration of Mars into crisis.

    • Posted September 8, 2012 at 11:26 pm | Permalink

      It does seem like yet another example of language inflation, just as anything even pretty good is now “awesome”.

      /@

  4. Sigmund
    Posted September 7, 2012 at 8:54 am | Permalink

    I’ve worked in molecular biology for the past twenty years and have known about almost all these phenomenon the entire time. The only “new” thing he mentioned, microRNAs, are, as Jerry has said, encoded in the genome just the same as other genes. They don’t give rise to proteins (they function by regulating the translation or stability of target RNAs) but their biology is perfectly compatible with the standard evolutionary theory.

    • Tim
      Posted September 7, 2012 at 10:18 am | Permalink

      With respect to the microRNAs, Jerry, you might want to reword the sentence,

      Thus they are in no sense a “regulatory layer above the genome,” any more than any other regulatory protein is “above the genome.”

      to read,

      Thus they are in no sense a “regulatory layer above the genome,” any more than regulatory proteins are “above the genome.”

      since your current wording implies that microRNAs are proteins.

      • whyevolutionistrue
        Posted September 7, 2012 at 10:59 am | Permalink

        Indeed; I fixed it. Thanks!

  5. Posted September 7, 2012 at 8:57 am | Permalink

    Project Syndicate is, more than anything else, a political tool.
    Last week Ana Palacio, Spain’s former (right wing) minister was using it to settle scores with Baltasar Garzón and Julian Assange.
    She wrote an entirely illogical and disingenuous attack piece- while (unethically) failing to mention the government she was a member of tried to stop Pinochet’s extradition twice.

  6. CJ
    Posted September 7, 2012 at 9:25 am | Permalink

    Well said Dr. Coyne.

    I’ve actually been waiting for you to chime in on the recent misleading reports on junk DNA:

    http://sandwalk.blogspot.ca/2012/09/the-encode-data-dump-and-responsibility_6.html

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

      I knew Larry would throw a fit when he read they’ve upped the percentage of functional DNA to 80%!

      • CJ
        Posted September 7, 2012 at 9:32 am | Permalink

        to be clear, i think Larry is right that the talk by some scientists and the media has been misleading.

        • Sigmund
          Posted September 7, 2012 at 9:36 am | Permalink

          I agree (although I think Larry himself is a little too conservative in his estimation of the percentage of functional DNA.)

    • gluonspring
      Posted September 7, 2012 at 9:48 am | Permalink

      I found the press releases on this shockingly misleading, until I realized it was the scientists themselves who were being misleading. Another case of trying to make a nice contribution into something bigger than it is. In this case, also probably an attempt to make the huge expense seem worth it.

      It’s shameful, really. As Moran points out, there is no way Birney could be so stupid as not to anticipate the hype his GROSSLY misleading language would generate. As punishment, he should be made to spend 500 hours explaining to Creationists why fossil retroviruses are not God’s clever embedded program for enabling non-mutation based micro-evolution of Kinds.

      • gluonspring
        Posted September 7, 2012 at 9:50 am | Permalink

        within Kinds. Got to get my creationist nonsense straight.

      • Torbjörn Larsson, OM
        Posted September 7, 2012 at 11:07 am | Permalink

        That wasn’t Birney’s concern as “lead analysis coordinator”, at all. In his own words, after describing the 80 % figure in detail:

        Q. Ok, fair enough. But are you most comfortable with the 10% to 20% figure for the hard-core functional bases? Why emphasize the 80% figure in the abstract and press release?

        A. (Sigh.) Indeed. Originally I pushed for using an “80% overall” figure and a “20% conservative floor” figure, since the 20% was extrapolated from the sampling. But putting two percentage-based numbers in the same breath/paragraph is asking a lot of your listener/reader – they need to understand why there is such a big difference between the two numbers, and that takes perhaps more explaining than most people have the patience for. We had to decide on a percentage, because that is easier to visualize, and we choose 80% because (a) it is inclusive of all the ENCODE experiments (and we did not want to leave any of the sub-projects out) and (b) 80% best coveys the difference between a genome made mostly of dead wood and one that is alive with activity. We refer also to “4 million switches”, and that represents the bound motifs and footprints.

        We use the bigger number because it brings home the impact of this work to a much wider audience. But we are in fact using an accurate, well-defined figure when we say that 80% of the genome has specific biological activity.

        The needs of the few, or one, outweigh the needs of the many. That is because science is elitist by way of the process, not democratic.

        • Posted September 7, 2012 at 11:30 am | Permalink

          Actually, as a Brit who is surrounded by scientists all day, I suspect that Ewan Birney didn’t really think too much about Creationists and their nonsense. He was far more excited about all the data and the papers and the iPad app and the virtual machine and the science.

          When it comes to science, the needs of the few (the Creationists) should not dominate the needs of the many (the scientists). The moment we change the way we report science and shy away from perfectly valid discussions about what it means for a piece of DNA to be “functional” (which might be very different to “important” or “necessary”), we lose a part of ourselves and the Creationists win.

          I agree that he was a bit careless with that one phrase but it is counter-productive in the extreme to let that dominate the conversation. Let’s talk about the science, not the language, and what the results really mean, not what people with an agenda will twist them into. (Whatever the figure, it was going to be greater than before and the Creationists would still have jumped on it and still been wrong.)

          If you want to fight Creationists, why not concentrate on how MESSY everything is – how genes are not “neatly packaged” like we used to think (and good “design” would predict). (Sigh.)

          • Torbjörn Larsson, OM
            Posted September 7, 2012 at 12:00 pm | Permalink

            Absolutely. Epigenetics and *evolutionary differences between bacteria and eukaryotes*, which this confirms, is disastrous for creationists ideas of pre-loaded “information”.

          • gluonspring
            Posted September 7, 2012 at 12:05 pm | Permalink

            I think it is more misleading than merely as it concerns creationists. I think that in almost any ordinary or typical term of art sense of the words used in the abstract it is a misrepresentation of the results. Worse, it really does come across as conscious misrepresentation. I agree that Creationists will indeed distort any finding, so it is a bit of a waste of time try to prevent that, and scientists are already leveling appropriate criticism, so maybe it doesn’t really matter. Still, I think they did not meet the bar for objectively presenting their results.

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

              The thing is, it was one small part of a much larger press release. If you read the whole of Ed Yong’s article, or watch the whole video on Nature, the emphasis is not on this at all. It is all being blown out of proportion by a small group of being singling out that one snippet and making it the whole story.

              Personally, I agree that it was an error of judgement and also disagree with the definition (and %) of “functional” that Ewan Birney settled on but there is no need to vilify him as some kind of monster. He is a great scientist and has done some amazing things, as has the ENCODE project as a whole. It just saddens me that rather than focus on all the cool and exciting possibilities that these data and results throw up, people are so eager to criticise and write off the whole enterprise before they have even had the time to read the papers. But then it is much easier to criticise science than to do it, and much easier to spout opinion than try to really understand an incredibly complex set of experiments and data.

              I’m looking forward to trying to get to grips with the results and see what it all really means. I’m looking forward to having some of my preconceptions challenged, even if I remain highly skeptical that the amount of important functional DNA will even reach 20%. And I’m trying really hard not to let any cantankerous, bitter kill-joys spoil that.

              • gluonspring
                Posted September 7, 2012 at 1:49 pm | Permalink

                I don’t think he is a monster (he didn’t write the abstract alone in any case). I know many people who worked on the ENCODE project and they are decent people doing good science. I just think the abstract writers succumbed to the temptation to over-hype their results. While technically accurate given their definitions, they presented it in a way that one could easily anticipate would be misleading and that one could just as easily anticipate would be the headline. I don’t think they are bad people for doing that, just human. Who hasn’t succumbed to the temptation to over-hype their results? The incentive to not over-hype is the predictable howls from your peers when you do. We are just doing our part to howl.

                “The thing is, it was one small part of a much larger press release.”

                Perhaps. But this is not some obscure point that they made on page eight that was taken out of context. It is the main claim in the abstract that summarizes the whole project.

                In any case, I certainly don’t want to dampen people’s enthusiasm to read the papers. At 30 papers total, it will take a lot of enthusiasm to get through them ;-) I plan to read quite a few of them myself, and not just to criticize them, but because I expect that it is solid work and that I will learn many interesting things that will, as you say, make me rethink some of my assumptions. At least I hope so.

  7. gluonspring
    Posted September 7, 2012 at 9:34 am | Permalink

    “But what Dupré doesn’t recognize is that this methylation is actually coded in the DNA itself”

    What do they teach these guys where he was trained? Everyone knows this.

    JAC keeps mentioning molecular biologists and their odd skepticism of evolution. None of the molecular biologists I have worked with fall into this category so it seemed odd to me. Now that he’s reminded me of the kind of people he’s thinking of, Shapiro and Margulis for example, I see what he is talking about. I guess I have categorized these people into a different slot than “molecular biologists”. I have thought of them as examples of the “successful crank”. It’s a surprisingly common phenomena. It’s like after a certain level of success, certain scientists go crazy. Pauling and his Vitamin C obsession, Luc Montagnier and his descent into something like homeopathy, and so on. Examples abound of this sort of thing. I have a couple of conjectures for why this might be:

    * People who make big discoveries are more lucky than special, and this becomes apparent when they try to repeat their first act.

    * People who make big discoveries start to believe their own PR too much… think they don’t have to be careful or skeptical of their own work, and coupled with the deference others show them they quickly wander off the ranch.

    * People who make big discoveries have big egos and are not content to add decorations to Darwin’s theory, they want to be a new Darwin to replace the old Darwin, and this ambition ego-blinds them.

    The latter was John Horgan’s suggestion, that people like Gould made such an outsized point out of minor variations on evolutionary theory largely because they are not content to be Darwin’s footnoters. Darwin solved, once and for all, the biggest question in biology, and that leaves everyone else since in a position to never be able to equal that. Some people are comfortable with that, some just can’t accept it.

    • ritebrother
      Posted September 7, 2012 at 10:44 am | Permalink

      I’ve also been a bit surprised and taken aback (and I must admit a little bit offended-not that anyone should care) by recent statements of a supposed predilection among molecular biologists to doubt evolution. I’ve been in the field for 20 years and have never encountered this. In my experience through several top-tier institutions in the US, evolution, in particular molecular evolution, has always been an integral part of mainstream mol. bio. training and practice. Indeed, I had to take a molecular evolution course taught by Masatoshi Nei as a graduate student at Penn State as part of my Mol Cell Bio Ph.D. program. I’m curious what those with this opinion (including our host) think predisposes molecular biologists to doubt evolution.

      • ritebrother
        Posted September 7, 2012 at 11:00 am | Permalink

        I should add that, as a molecular biologist, I agree with every one of Jerry’s responses in this piece, as would probably 95-100% of practicing academic molecular biologists.

      • Torbjörn Larsson, OM
        Posted September 7, 2012 at 11:12 am | Permalink

        Well, it used to be blamed on engineers.

        As that was my first education, I’m glad you take up the torch of anecdote. (O.o)

      • Posted September 7, 2012 at 1:05 pm | Permalink

        I’ve worked in molecular biology and bioinformatics in Britain and Ireland for 14 years (including PhD) and never met a molecular biologist who doubted evolution. It is definitely an integral part of the education and increasingly the basis of daily activities. (BLAST searches etc. are ubiquitous these days.) In my experience, it is the engineers and computer scientists who are most likely to erroneously believe is some kind of new “paradigm shift” in evolution.

        • gluonspring
          Posted September 7, 2012 at 1:59 pm | Permalink

          I too have never met a molecular biologist who doubted evolution. It’s fundamental to most of their work. I think that engineering expatriate are possibly part of the problem in some places, pressed into data analysis without understanding enough of what is already known (that was my career path too). The people JAC singles out, though, don’t seem to fit that mould. It seems to me that JAC is pointing out more prominent people, well known people, who have a fairly traditional background in molecular biology. That makes me wonder if it’s not “successful crank” syndrome (an example of Gouldism, a handy term that Perrault used in a comment below). I don’t know, though, just guessing.

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

          “In my experience, it is the engineers and computer scientists who are most likely to erroneously believe is some kind of new “paradigm shift” in evolution.”

          I am not attempting to deride engineers or computer scientists, but this has been my experience, as well. Though, both of my alma maters are in the South.

          • Posted September 8, 2012 at 3:25 am | Permalink

            Yes, I would like to stress that of the people I have encountered who erroneously believe is some kind of new “paradigm shift” in evolution, most are engineers or computer scientists … NOT that of the engineers or computer scientists I have met, most erroneously believe is some kind of new “paradigm shift” in evolution. The vast majority that I encounter (generally in interdisciplinary projects) accept evolution just fine and neither think it is in crisis nor undergoing some kind of major revolution.

  8. couchloc
    Posted September 7, 2012 at 9:47 am | Permalink

    For those interested you can learn about Dupre’s broader views here. He is a very well-established philosopher of science who works on biology specifically.

    http://www.galilean-library.org/site/index.php/page/index.html/_/interviews/john-dupre-the-disunity-of-science-r46

  9. Nicolas Perrault
    Posted September 7, 2012 at 10:07 am | Permalink

    From a non specialist point of view Dupré seems to have caught some form of Gouldism. This is an ego induced infection that stubbornly resists Occam’s razor. Should it be called “G diff.”?

  10. jeffery
    Posted September 7, 2012 at 10:21 am | Permalink

    It makes me wonder just what his motivations are for taking these findings as a “crisis”: has he a new theory that’s going to make him famous, or wealthy? Is he a “closet-creationist”? Or is he just pissed off at some particular evolutionary biologists and is engaged in a juvenile quest for revenge? Stay tuned! The facts will out!

    • Mark Joseph
      Posted September 7, 2012 at 11:28 am | Permalink

      Might be a bit simpler explanation: It makes a better headline (from the journalist’s point of view, not the scientist’s) to trumpet a “crisis”, rather than to write responsibly of “a brief compendium of new and exciting developments in evolutionary biology.”

  11. William Stewart
    Posted September 7, 2012 at 10:42 am | Permalink

    Regarding the phrase “paradigm shift”: Read the essay titled “The Revolution That Didn’t Happen” by Steven Weinberg in the New York Review of Books.

    • Peter Beattie
      Posted September 18, 2012 at 5:03 am | Permalink

      And if you’re looking for the full text of Weinberg’s essay, here is a link</a.

  12. JonLynnHarvey
    Posted September 7, 2012 at 10:49 am | Permalink

    I have observed in academia that artists like philosophers of art, but very few scientists are that impressed with the field of philosophy of science.

    Philosophers need training in science. I recall that for years there were neo-Kantians insisting quantum physics could not be true (because it violated Kantian philosophy). The definitive rebuttal to this (circa late 1960s) was written by a philosopher whose undergraduate major was physics!!!

  13. Scott near Berkeley
    Posted September 7, 2012 at 11:11 am | Permalink

    Simple thanks to you Jerry, for expounding on a complex subject and making it understandable.

    I’m getting “crisis” fatigue, what with all the dentists, power companies, etc. “hating” the phony pictures in advertisements on the internet…”hating” some guy (local!! how about that!!) who has solved the power, foreign language, etc. “crisis” with “one weird trick.”

    Do NOT click on those!!

  14. Ben Murray
    Posted September 7, 2012 at 11:13 am | Permalink

    With regard to this:

    “Traditional reductionist views of science, with their focus on “bottom-up” mechanisms, do not suffice in the quest to understand top-down and circular causality and a world of nested processes.”

    Perhaps he is referring to the idea that systems approaches, using the vast amounts of data now available, are required to understand biological regulation, and that analysis of individual components and interactions will not be able to explain the observed phenomena. Various types of feedback loops and cross-talk will give rise to emergent phenomena that won’t be reveialed by the individual component interactions.

    I’m fairly skeptical of this view myself, but it’s certainly out there (and, in fact, has been out there for decades).

    • Ben Murray
      Posted September 7, 2012 at 11:14 am | Permalink

      And that still doesn’t add up to a transformational crisis in evolutionary biology!

  15. Posted September 7, 2012 at 11:20 am | Permalink

    As an evolutionary biologist, the only thing approaching a crisis in evolutionary biology is how hard it is to get funding in the current climate unless your work has “impact”. (Well, that and the tendency of certain “champions” of evolution to think that the fight against Creationism should be top of everyone’s priority list and then going ballistic at other scientists who have different priorities and “make their life difficult”. When did the joy of science get killed by the fight?)

  16. Mark Joseph
    Posted September 7, 2012 at 11:33 am | Permalink

    “But this (a listing of illustrations of how the genome can change other than by mutations) doesn’t constitute a crisis—it’s a very interesting finding that shows that variation in a genome can arise by processes other than mutation of an organism’s own DNA. The disposition of that variation still must occur via either natural selection (it can be good or bad) or genetic drift (no effect on fitness). This hasn’t really changed the theory of evolution one iota, though it’s changed our view of where organisms can acquire new genes.” (note that I snipped out the extraneous word “imply” in the quote)

    What a perfectly marvelous, concise, complete answer to those who might ask about the “crisis” in evolutionary biology, and who are probably vaguely remembering some discussion of these processes other than mutation. This will be used in future discussions. Thank you!

  17. Thanny
    Posted September 7, 2012 at 11:38 am | Permalink

    Eukaryotes are not the result of a merger between two bacteria.

    The merger was between an archaeon and a bacterium.

    • Torbjörn Larsson, OM
      Posted September 7, 2012 at 12:20 pm | Permalink

      I doubt that for three reasons:

      – Many phylogenies conclude a previous split and divergence of the nuclear genome between archaea and eukaryotes.

      – Many phylogenies place archaea and eukaryote viruses at the root of respectively clade. In the eukaryote case, the Megaviruses are amitochondriate in gene content. Meaning they diverged from eukaryotes before the mitochondria endosymbiosis event.

      – Metabolic analysis predicts that archaea is low energy density specialists, predicting their low permeability membrane (little ion loss) and small genome with little metabolic redundancy. Eukaryotes on the other hand are heterotroph or photosynthetic high energy density specialists. In both cases the largest energy stress would come after oxygenation, having bacteria crowd them out as medium energy density opportunists with a set of metabolic options.

      It is then likely the three domains split as oxygenation took place. Meaning that by the time the mitochondria endosymbiosis event happened, because oxygenated metabolism made it a useful acquisition, the nuclear genome was already starting to specialize between autotrophs and eukaryote heterotrophs.

      [Maybe the parasitic Megaviruses should be seen as the ultimate heterotrophs, metabolizing cellular compounds in toto in their viral factory.]

      The merger could very well be between an amitochondriate eukaryote and a bacterium.

      • Claudiu Bandea
        Posted September 12, 2012 at 9:55 am | Permalink

        I agree with your point Torbjorn that “the merger could very well be between an amitochondriate eukaryote and a bacterium”. Also, interesting note about the evolutionary origin of Megaviruses. You might want to take a look at this paper: http://precedings.nature.com/documents/3888/version/1. I would be very interested in your thoughts!

  18. Torbjörn Larsson, OM
    Posted September 7, 2012 at 11:55 am | Permalink

    Maybe it is my naiveté from my astrobiology interest, but I thought that it was clear despite early and overblown observations of phylogenetic problems, like horizontal gene transfer, lineages are consistently found.

    Whole genome methods, often complemented with matrix methods describing transfer events, robustly yields repeatable phylogenies. Protein fold families can work with lineage topologies all the way back to the RNA/protein world. [“The evolution and functional repertoire of translation proteins following the origin of life”, Goldman et al, PLOS Biol. Dir. 2010.]

    Protein fold families can’t resolve between cellular lineages and communities as such, but there are gene family models that purport to do that. And they predict that there was little transfer at the start but birth rates were high, with gene transfer and loss kicking in during the Archaean Expansion. (Gene duplication seems to be mostly a later eukaryote invention.) [“Rapid evolutionary innovation during an Archaean genetic expansion”, David et al, Nature 2010.]

    it reflects the non-linear progress of scientific knowledge, characterized by what Thomas Kuhn described

    Could we please reject Kuhn as postmodernist: “believed that scientists’ subjective experiences made science a relativized discipline.”

    I don’t know of any measure of “paradigms”, or any scientific idea of science as “linear”.

    But you know, we can measure science efficiency. For example in the numbers of publications, that seems (no statistical test, I admit) to increase exponentially in fruitful areas. Meaning efficiency growth is roughly linear on average.

    The content changes, but that is what an increase in observations and test of theory gives us. It is a very simplistic and likely very wrong model to have science pass a series of “paradigm” bottlenecks – it can’t predict the measurable steady output.

    these big events of symbiosis that produced mitochondria, chloroplasts, and perhaps flagella,

    I thought the endosymbiont theory of the flagella was pretty much gone after the discovery of how protein export mechanisms could evolve to flagella by simple steps from passive pores?

  19. Posted September 7, 2012 at 12:38 pm | Permalink

    I also find horizontal gene transfer really interesting and I do wonder if it’s perhaps overlooked in evolution. Admittedly I come from a background in molecular biology and microbiology so I think perhaps if most evolutionary biologists come from zoology and botany they might be missing out on the majority of species.

    That said I really don’t see it as any sort of challenge to evolution, it just means it’s more exciting. I’d say HGT is actually a perfect example of the selfish gene. What could be a better way to illustrate that than genes actually being able to switch hosts?

  20. MadScientist
    Posted September 7, 2012 at 2:03 pm | Permalink

    So a philosopher doesn’t need to know any biology (or any other science for that matter) to criticize it, but if you speak about philosophy you are expected to have read every philosopher known to history.

    • couchloc
      Posted September 7, 2012 at 2:25 pm | Permalink

      Tsk, tsk, MadScientist. You don’t even know this individual and are making wild assumptions about him. Actually he is a Fellow of the American Association for the Advancement of Science.

      • Peter Beattie
        Posted September 18, 2012 at 5:13 am | Permalink

        Well, MadScientist is right to the extent that holding forth on biology while lacking basic knowledge in the subject is more than embarrassing for a philosopher of biology. I’d even go so far as to say it’s professional misconduct.

  21. Gordon
    Posted September 7, 2012 at 2:35 pm | Permalink

    As a very lay person and non-scientist I found the two threads running through this interesting from the perspective of trying to keep up with what goes on. The non-crisis in evolution was not news and I was pretty aware that the developments mentioned were slotted into the standard explanation. The 80% ENCODE function figure did however mislead me and it was good to get the clarification here and in the links.

    The main point that I would make is that informed lay trust (carefully avoiding ‘faith’here) in science depends in part on accurate summaries of the science to non-specialists who I think could cope with two percentages in one sentence. A statement such as (hoping I have understood correctly) “20% of DNA has a clear(?) function and 80% is biologically active” is not that diificult to understand and can be expanded on. The two percentages bit is a response to the ENCODE spokesman who suggested this might confuse people.

  22. Leigh Jackson
    Posted September 7, 2012 at 8:05 pm | Permalink

    I’m wondering if Dupre has read Carl Woese:
    A New Biology for a New Century.

    I’m pretty sure Shapiro has. Shapiro’s book has virtually the same title as Woese’s paper.

    There’s also a book out this year by Eugene Koonin: The Logic of Chance: The Nature of and Origin of Biological Evolution.

    I have only just stated reading this but that dreaded phrase “paradigm shift” has already made an appearance. The shift according to Koonin is away from adaptationism towards contingency as the central motif of evolution. This is similar to Shapiro in as much as it de-emphasises the importance of natural selection, but in a move opposite to Shapiro, Koonin then pushes randomness into center stage.

    Woese, Shapiro and Dupre all have agendas. Behe’s was never really disguised. Woese was explicit enough too. Big anti-reductionist pro-ecological biology like Dupre. Shapiro looks to be just playing games.

    • Leigh Jackson
      Posted September 8, 2012 at 7:06 pm | Permalink

      Just discovered and now recall that Jerry gave the heads up for a free download of Koonin’s book twelve months ago. I was too late at the time and had completely forgotten about it.

  23. kelskye
    Posted September 7, 2012 at 11:57 pm | Permalink

    I remember listening to a talk he gave called The Boundaries Of Darwinism. I gave it a couple of listens and couldn’t really figure out what the fuss what about; I just attributed that to my layman understanding of “Darwinism”. One interesting result was different colonies of ants working together, though I had thought that symbiotic relationships in nature were already well understood from a Darwinian perspective.

  24. Posted September 8, 2012 at 5:28 am | Permalink

    I think what he meant by “top-down” is something like the group selection, selection pressure from above-genes environment.

    But yes, it is obscure.

  25. Posted September 8, 2012 at 6:19 am | Permalink

    If a locust has twice the genome of a human, and it is a Divine Code – intelligently designed – no gibberish or junk, then we had best be watching the locusts. Where have they hidden their complexity? What are they up to? I don’t trust them.

  26. Schenck
    Posted September 8, 2012 at 2:01 pm | Permalink

    Dupre comes off as “I’m brilliant and already know about this stuff, but laypeople, mere mortals, have a terrible understanding of science, they don’t even know what’s going on, so I’m about to shake-up their world with this normal stuff”.

    Also, Kuhn? Does anyone even really buy that anymore?

    • El Schwalmo
      Posted September 8, 2012 at 11:14 pm | Permalink

      I guess there are some problems. The first is that nobody really defines what ‘theory of evolution’ (AKA mechanismus of evolution) means for him. Not knowing this makes it a little problematic to judge if that what you understand by ‘theory of evolution’ is in a crisis or not. I guess that it’s very difficult for an active researcher to see his paradigm in crisis as long as he can work and publish his results, getting grants etc. There are more important things to do than to reflect the theoretical framework of your paradigm, as long as it works.

      Another question is who decides if a theory is in crisis. People working in that framework or philosophers of science, looking from ‘outside’? I’m tending to the second line.

      There are different lines of thougt concerning problems of theories. Coyne seems to bring to focus what’s known and tries to integrate new discoveries in an established an successful framework. But here we are close to the first problem: how to decide, that new discoveries can be integrated into a framework, if that framework isn’t clearly stated?

      E.g. Coyne is stating that events like symbiogenesis are extremely rare and adaptation is forged by small mutations and natural selection. I your theory of evolution is like that of Lamarck (‘dualistic’ in the sense of containing two mechanisms, one for adaptation, one for generation ‘true’ novelties), the center of interest should be examination of the rare processes. If your theory is ‘monistic’ (like that of Darwin, who tried to explain ‘anagenesis’ via mechanisms of adaptation), the rare events are just unimportant ‘noise’.

      So ‘crisis’ may lie in the eye of the beholder. If a concept of evolution doesn’t contain ‘big events’ as an important issue, and you find events like these, you can argue that a theory of evolution, that misses events of that kind, is wrong in the sense of ‘not complete’, aka ‘crisis’, if you postulate that a theory must integrate all observations. If these events are not important for you, there’s no crisis.

  27. John Dupre
    Posted September 10, 2012 at 5:11 pm | Permalink

    Having just read this thread, a couple of things strike me forcefully. (I’ll of course ignore the abuse.) No one discusses the main point of my column, which was that what distinguishes science from non-science (here creationism) is above all debate, argument and openness to revision of views in the light of evidence. It was ironic to find hardly more disagreement in all these posts than one would find on a creationist website. Rather, the overwhelming message is: we’re all experts, we all know the same truths.
    I’m actually a great believer in scientific expertise. It’s what I spend my life studying. And no, I’m not a biologist. In 900 words (what Project Syndicate allows) I didn’t get a chance to mention my significant reservations about Kuhn, but he has some deep insights that justify his status as the most influential theorist of science in the twentieth century. I think particularly of his account of ‘normal science’, the general condition of successful science in which it is not productive or even acceptable to think too hard or critically about what one is doing. (Cf. the dismissive references in this thread to Margulis, Shapiro, Gould, etc.) Anomalous findings are ignored, accommodated with ad hoc hypotheses, or treated as minor exceptions. (I won’t pursue the technical disagreements here; but I am amazed that everyone on this blog seems to think that epigenetics is just imprinting.)
    Kuhn’s treatment of crisis and revolution is more problematic, though he is surely right to say that science progresses in a non-linear way. “Crisis” may have been an unfortunate choice of words, something of an exaggeration. On the other hand given the strength of reaction it has produced I’m tempted to think it was well-chosen. Perhaps it’s rather a crisis of complacency.

    • Posted September 11, 2012 at 12:34 am | Permalink

      With all due respect, to say that “The creationists are right about one thing… the theory of evolution is in crisis” goes well beyond exaggeration. If I were to apply half the level of exaggeration to describe how much of an error this is, I would describe it as “brain-dead absurdity”. You are clearly not brain-dead. “The theory of evolution” (whatever you mean by that most ambiguous of terms) is most certainly not in crisis.

      Epigenetics is interesting but does not threaten evolution as a whole. It does have an impact on how we understand about adaptation and, in particular, the effect of “nature versus nurture” on phenotype (though not always in the direction people imagine). It certainly makes life complicated when you study responses to environmental change.

      It is much more than imprinting but I think Jerry was just using imprinting as an example. The point is that epigenetic markers are erased and rewritten on very short time-scales, whereas the epigenetic machinery and DNA code recognised by that machinery is not and thus, in line with other features of organismal biology, it is a system that has evolved like any other. (The environment is not reaching out and directly making a modification – it is triggering an epigenetic response, which is encoded by the genome.)

      As a “front-line” evolutionary biologist, trying to keep up with all the data coming through from projects like ENCODE, I can assure you that we are not “complacent” about any aspect of evolutionary theory. (Except, possibly, the fact that evolution happened – that is so well supported that it is seems incredibly unlikely to ever be overturned.) What we are – and rightly so – is cautious. Great claims need great evidence. New ideas also need to fit with all the existing data as well as the exciting new stuff. For this reason, Jerry is entirely and absolutely right to explain all these things within a gene-centred framework and that framework still works (as long as you understand what is meant by “gene” in that context).

      Finally, when a fantastic new discovery is tested, double-tested and validated, it is accepted and becomes part of the joyous “poetry of reality” as Dawkins put it. Even here, there is no crisis. Evolutionary theory moves on but, like all good science, it does so slowly and carefully, not in a series of knee-jerk paradigm shifts that ignore the fact that we have our current understanding for a reason – and that reason is past experiments and past data that still need explaining under any new framework.

      (I also wonder if you are making a mistake that I made once before of confusing Reductionist philosophy (still alive) with reductionist approaches (clearly limited in some circumstances)?)

    • Dan L.
      Posted September 13, 2012 at 9:08 am | Permalink

      (I won’t pursue the technical disagreements here; but I am amazed that everyone on this blog seems to think that epigenetics is just imprinting.)

      Precisely NOTHING is stopping you from arguing otherwise. Do you have an argument?

      Of course not. More strutting and posturing by another turf-obsessed philosopher.

      I don’t know if you realize this, Herr Philosopher, but debate and disagreement requires…well, debate and disagreement. So it makes precisely zero sense for you to criticize Coyne or the commenters here for having an opinion that disagrees with your own. By your own hypothesis, this disagreement is necessary for the health of scientific inquiry. How about a little consistency?

      • John Dupre
        Posted September 14, 2012 at 1:19 am | Permalink

        I said I’d ignore abuse, too–so here’s a real failure of consistency. But actually I did assume that readers of this blog would know perfectly well that epigenetics included far more than imprinting (parent of origin specific modifications). The controversial question is whether this broader category has evolutionary potential and I take it that the consensus of this blog’s readers, to which I alluded, is that they do not because of relatively low intergenerational durability. My view is that this is irrelevant given the possibility of behavioural transmission as classically illustrated by Michael Meaney’s work on maternal rearing by rats. But this is, as I said, controversial.

        I agree that debate requires debate; but one also has to make assumptions about the basic level of shared understanding, which can prove disappointingly optimistic.

    • Peter Beattie
      Posted September 18, 2012 at 6:23 am | Permalink

      » John Dupré:
      I’ll of course ignore the abuse

      Which is very brave of you, especially since there hasn’t been any.

      No one discusses the main point of my column, which was that what distinguishes science from non-science (here creationism) is above all debate, argument and openness to revision of views in the light of evidence.

      Yes, how dare people focus on the biology stuff that makes up more than half of your column, especially when that biology stuff is in urgent need of revision.

      It was ironic to find hardly more disagreement in all these posts than one would find on a creationist website.

      So you are taking comfort from the fact that professional biologists consistently criticise your understanding of biological phenomena? Because that means they are “circling the wagons”? How embarrassing for a philosopher of science to defend an attitude that is the main cause of people fooling themselves—i.e. anti-science.

      And how embarrassing not to see the distinction between openness to disagreement on the one hand and actual disagreement on a specific issue on the other.

      Cf. the dismissive references in this thread to Margulis, Shapiro, Gould, etc.

      Those references are dismissive only of certain specific ideas, and again: your implication that the mere fact that something is being dismissed is evidence of a lack of criticism towards established ideas that those dismissed ideas would challenge is ludicrous. You know as well as anybody else that only a qualitative assessment of those ideas can tell us whether their dismissal was justified or not.

      Since you’re so fond of comparisons to creationists: in those circles, the ‘argument’ is rather popular that ‘They laughed at Galileo too’. Maybe, but the also laughed at Bozo the Clown. And incidentally it is science that is the main method of making sure that you’re not being Bozo the Clown.

      I am amazed that everyone on this blog seems to think that epigenetics is just imprinting.

      Amazing indeed, if only it weren’t false. Here is what Jerry says in the very same paragraph that contains the reference to imprinting (my emphasis):

      Other kinds of epigenetic change that are produced solely by the environment and not by the genome itself, such as changes in weight or flower color, are not stable because the DNA reverts to earlier forms. Hence such changes do not last more than a few generations, and so cannot be the basis of permanent evolutionary change.

      It seems a little less amazement at your own distorted interpretations is in order, as is a little more careful reading.


3 Trackbacks/Pingbacks

  1. […] to philosophy, of sorts, Jerry Coyne has been writing some stimulating stuff, first here, on attempts to suggest that the theory of natural selection is in crisis [no, not from lightweight […]

  2. […] commentaries on evolutionary theory recently. One was by philosopher John Dupré, the other by evolutionary biologist Jerry Coyne. Actually, the latter was a commentary on the former, and it had a typical Coyne-style title […]

  3. […] commentaries on evolutionary theory recently. One was by philosopher John Dupré, the other by evolutionary biologist Jerry Coyne. Actually, the latter was a commentary on the former, and it had a typical Coyne-style title […]

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