Should there be a “Third Way” of evolution? I think not.

January 30, 2015 • 9:45 am

Someone just called a fairly new “Evolution-Needs-a-New-Paradigm” website to my attention, and I wish they hadn’t. The site, “The Third Way of Evolution,” has been going for some time and, according to the its notes, was created last May by two biologists, James Shapiro (here at the University of Chicago) and Dennis Noble, a renowed physiologist who was formerly a professor at Oxford, as well as by Raju Pookottil, an engineer credited with creating the site. Pookottil, showing the distressingly common trait of many engineers to question evolution while at the same time showing profound ignorance of the data supporting it, has allowed this to appear in his profile:

While [Pookotti]  was always unconvinced about the idea that a supreme intelligence could have created all life on earth, life unquestionably carries the hallmarks of design. As a weeding out instrument, natural selection has a certain role to play in evolution. But it cannot be the fundamental mechanism and the creative force driving evolution.  Even after 150 years, there are only a handful of examples of selection in action; and they are not very convincing ones either.

Evolution, he believes, is more of a Lamarckian process. In his book, Pookottil proposes a mechanism that could potentially explain how the whole thing might be working. Organisms do not need to depend on accidental mutations and selection. They have built in capabilities that allow them to interact with the environment and devise clever solutions. If a panda is in the process of generating a new thumb, it has worked out exactly where it needs one and how to build it. The emerging field of epigenetics is spearheading a comeback for Lamarckian evolution. There is now a rapidly growing list of examples that demonstrate that acquired characteristics can be transmitted for many generations. If Lamarckism is the future, here is how it could be working; right from forming the very first cells, to generating novel proteins, all the way to building whole complex organisms.

Here we have both the misguided criticism of evolution that characterizes the  wholesite (really, few and “not very convincing” examples of selection in action?), as well as the invocation of “revolutionary” new processes for which there’s virtually no evidence—or at least no evidence that the processes had an important role in evolution and adaptation. (In Pookottil’s case, it’s a nebulous form of Lamarckian inheritance.) The scenario of a panda somehow working out where it needs a new thumb and then building it is laughable, even if it doesn’t involve a quizzical panda pondering what it might do to strip leaves from bamboo.

But what is “The Third Way of Evolution”? The site explains:

 The vast majority of people believe that there are only two alternative ways to explain the origins of biological diversity. One way is Creationism that depends upon intervention by a divine Creator. That is clearly unscientific because it brings an arbitrary supernatural force into the evolution process. The commonly accepted alternative is Neo-Darwinism, which is clearly naturalistic science but ignores much contemporary molecular evidence and invokes a set of unsupported assumptions about the accidental nature of hereditary variation. Neo-Darwinism ignores important rapid evolutionary processes such as symbiogenesis, horizontal DNA transfer, action of mobile DNA and epigenetic modifications. Moreover, some Neo-Darwinists have elevated Natural Selection into a unique creative force that solves all the difficult evolutionary problems without a real empirical basis. Many scientists today see the need for a deeper and more complete exploration of all aspects of the evolutionary process.

As for the last sentence, who would deny that we need to explore more deeply how evolution works? After all, we don’t know everything about it. But what we do know is that the outlines of modern evolutionary theory, and the importance of natural selection, seem indisputably correct for now, and that there’s no pressing need for an overturning of that theory.

Given the site’s explicit denial of creationism, it’s a bit surprising that it has been touted by Denyse O’Leary, the reliably vacuous “reporter” on ingelligent design for the ID website Uncommon Descent. But of course ID advocates try to hide their creationism under a bushel, changing their tactics to assert simply that the modern theory of is fatally flawed. Once the theory is demolished, they hope, Jesus will then rush in to fill the gap.

But I digress. What is distressing about the “Third Way” site is that about 50 biologists, physicians, physicists, mathematicians, historians of science, and even an expert in semiotics have joined this anti-Darwinian chorus. As I read over the list, I recognized quite a few names, especially those in my field, and I’m pretty familiar with their views. Here are a few of them (all gave permission to be included on the “Third Way” site); and I’ll add links to critiques that I or others have written about their “revolutionary” ideas. At the end I’ll give my brief take on this “Third Way.


Shapiro has long been an advocate of “adaptive mutation”: the view that mutations are not “random” in the sense that evolutionists think (that is, that the relative probability of a mutation occurring is independent of how much it would boost an individual’s reproductive success, an idea that could also be called “indifferent” mutation). Rather, says Shapiro, adaptive mutations occur relatively more often than maladaptive ones when the environment changes. I’ve written about the lack of evidence for Shaprio’s view, and about Shapiro’s misunderstandings of evolution, several times before: go here to see the list of posts.
Noble has made many unevidenced claims that, he says, call for an overturning of neo-Darwinism. These include the idea that mutations aren’t random (Shapiro’s view), that adaptive traits in evolution can be acquired from the environment rather than produced by gene mutations, that the gene-centered view of evolution is wrong, and that important evolutionary change is not gradual but instantaneous.  I’ve criticized all of these claims hereJablonka
Jablonka, along with her colleague Marion Lamb, are perhaps the most vociferous promoters of the idea that adaptive evolution does not come from random mutations winnowed by the environment, but from “epigenetic changes”—modifications of the DNA, like methylation, that are produced by the environment itself and then inherited across generations. Suffice it to say that despite all the noise emitted by the epigenetics boosters, we have not a single case of evolution operating in that way. At most, DNA modifications induced by the environment are inherited for only one or a few generations, and are almost never adaptive. There is not a single adaptation we can point to that has evolved in the way these people propose. Yet that hasn’t stopped them from repeatedly telling us that their theory has been unduly neglected and that when we finally recognize how great it is, it will completely overturn our view of evolution.  My criticisms of the “epigenetics-is-important” view of evolution can be found here, and of Jablonka’s in particular here.
Newman believes that natural selection is insufficient to explain “macroevolution” (big changes between groups that are, for instance, involved in the creation of new phyla), and that evolution of that type involves “saltations” (big instantaneous leaps) involving not natural selection on genes, but changes in the “self-organization” of the matter and biochemical pathways that make up organisms. I have criticized his views at length here and showed that none of them, since they’re supported by no evidence, call for a radical revision of modern evolutionary theory.
Keller isn’t really a practicing physicist; she’s a historian and philosopher of science. But never mind; everyone is welcome to criticize evolution—so long as their criticisms are sound.  I haven’t followed Keller extensively but I did review one of her books—a book arguing that evolution was not only not centered on the gene, but that the gene itself was a virtually useless concept. My review is largely behind a paywall, so I’ll send a pdf to anyone who wants it. But here’s a short excerpt from it (Nature; 2004):

Unfortunately, the book is long on complaint and short on substance, and ultimately fails to make its case against the primacy of the gene. Despite her repeated claims that the recent history of genetics is replete with “major reversals”, “serious provocations” and “radical modifications”, the gene emerges unscathed. Many of the alleged problems highlighted by Keller turn out to be semantic issues likely to be of little interest to either working biologists or serious philosophers of science. Moreover, the level of analysis is disturbingly superficial: Keller seems more interested in forcing genetics into the Procrustean bed of her thesis.

 I’m not well acquainted with Bejan’s work, since he doesn’t publish in evolution journals, but Joe Felsenstein has taken apart some of his and his collaborators’ evolutionary ideas (most notably a “constructural law”) over at Panda’s Thumb.

Odling-Smee is an exponent (along with my former Ph.D advisor Dick Lewontin) of the idea of “niche construction.” That’s the notion that the behavior of organisms themselves, since it affects their environments (“niches”), must affect their subsequent evolution. The classic example is the beaver: by evolving to adopt a lifestyle that creates a new habitat (the construction of ponds by felling trees that dam streams, as well as by building “lodges” as their homes), the beaver creates new selective pressures that can affect its evolution.

Now this idea is intriguing and sound in principle, and the process must have operated during the evolution of some species. But does it require our rethinking standard evolutionary theory (SET)? In this post (point #4), I argue “no”.  As I wrote last November:

While this idea is getting new attention, and deservedly so, it doesn’t call for a revolution in SET. First of all, it’s not particularly new. The idea of “gene-culture” coevolution has been around a long time. One example is pastoralism, in which humans changed their environment by keeping domestic animals that give milk.  And that has changed our evolution, for cultures that are pastoral have undergone evolution involving the use of lactose. Genes that break lactose down into digestible components are usually inactivated after weaning in humans, who, over most of our history, didn’t have a source of milk after they stopped suckling. That’s why many of us are “lactose intolerant.” When we suddenly got a rich source of nutrition from our sheep and cows, pastoral cultures evolved so that the genes metabolizing lactose weren’t inactivated,but were turned on for life. (Individuals with genes allowing them to digest milk had up to 10% more offspring on average than intolerant individuals!) Thus, our own culture affected our subsequent evolution. This did not cause us to dismantle SET; rather, it was an interesting sidelight on how culture itself caused genetic change.

Second, we don’t know how pervasive this process is. That is, while many organisms do affect their environments, we don’t know how often that environmental change feeds back to the organism to cause additional evolution. In some cases it probably doesn’t: fish adapt to an unchanging fluid medium, the coat color of polar bears cannot affect their environment of ice or snow, and the hooves of the chamois don’t affect the granitic structure of the Swiss Alps. So how often “niche construction” is important is an open question, albeit an interesting one. But I don’t see it overthrowing SET, for it’s simply a novel way that the environment can change and affect organismal evolution.

So what is the “Third Way” of evolution? As far as I can see, it’s basically a grab-bag of criticisms of evolution that are unfounded, as well as proposals of new mechanisms whose importance is yet to be established (or, in the case of adaptive mutation, has been shown to be unlikely by experiments), and of processes, like niche construction, that fit comfortably within modern evolutionary theory. The common theme of nearly every “Third Wave” member whose work I know is this: “Modern evolutionary theory is deficient because it has ignored my own view of what is important.” In other words, the whole site is solipsistic.  The “Third Way” of evolution boils down to what one colleague said to me: “All these views are wildly and incommensurably different, and some are in the category of ‘not even wrong’.”

The colleague added:

What many of [the adherents to “The Third Way”] do agree on is one thing: “Nobody’s paying enough attention to me!”

Too right!

108 thoughts on “Should there be a “Third Way” of evolution? I think not.

    1. Eh? Unlike vision, there’s nothing gradual about circumcision. Having a bit of a bell-end peeping out is not acceptable.

    2. Funnily enough, my brother was born without a foreskin, and he comes from a long line of catholics – which, by the way, stopped in our generation 🙂

    1. The big, mainstream theories which scientists find sexy to attack seems to run in fads. A few decades ago it seemed to me that all the scientists who styled themselves edgy tried to topple relativity. Now they try and topple RM+NS. In 2035, no doubt the “[theory] is wrong” de jour will be something else.

      1. I’m not sure what you are referring to but one of the critics of General Relativity was Prof. Robert Dicke of Princeton, Un. who developed what is referred to as the Brans/Dicke theory. Unfortunately, Dicke’s claim that the interior of the Sun rotated 10 times as fast as its atmosphere, which was one of his proposed evidences, was never found by other researchers. This in addition to a prediction of the travel time of radio waves sent to a Mars probe and back not agreeing with the experimental result.

        1. Well, we really do need to go beyond General Relativity with its singularities and infinities. I haven’t heard mention of Brans/Dicke for a while, but MOND still seems to have its adherents. Still, GR has passed every empirical test thrown at it, which is inconvenient, as it gives no hints as to what the next step might be. Nature is stubborn.

  1. Damn, I guess I need to get working on figuring out how to make my body dissolve those useless vestigels or give me wheels on my feel since I travel on roads a lot.

    I wonder if these folks jump on the bandwagon of bad ideas in the hopes that they’ll get lucky and become famous.

      1. I love that “accountant” was one of the desirable professions. It made me think of the Monty Python skit.

  2. It has been my experience that, only with great reluctance and close supervision, should engineers be encouraged to do science. And then only while wearing protective head gear.

        1. I should have been a little less terse. My point was that education and experience as an engineer does not automatically preclude a wider view of science.

          1. Occasionally one of my sisters will remind me that I taught them to knit when we were very young children. However, I can assure you that in my subsequent career, essentially as an engineer, albeit based on a degree in physics, I have never indulged in any knitting. 🙂

          2. 😀

            Whereas I, an erstwhile biologist, can engineer a one-stitch muffler–any length!– with the best of ’em.

            Sounds as if you did notice my tongue, hidden though it was within my cheek. 😉

          3. Well, in contrast to scientists, engineers can’t go on theorising for ever. They have to get it right first time or the plane crashes, bridge falls down, usw.

    1. Another anti-evolution engineer is Walter James Remine. He knows so little about biology that in his book The Biotic Message he claimed that humans and apes differ in 48 million genes. Yep, he thinks we have millions of genes (“Since humans and apes differ in 4.8 x 107 genes, there has not been enough time for difference to accumulate.”)

      1. I’m guessing that should be “4.8 x 10^7”
        (That’s 10[up-sign]7 if it hasn’t appeared again. Does anyone/everyone else call it – a raised inverted v – an “up-sign”?)

  3. Fortunately these ideas are not being presented by Dr. Mohamed Noor in his on-line course Intro to Genetics and Evolution, now starting its fifth week.

      1. I noticed you in the discussion forum there and immediately thought I am way at the other end of the spectrum, because I am such a beginner. But I am learning a lot, and love the course. Now I need to go study…

      2. Thought I had been banned for a while, but I guess that was just the site messing up.

        I really need to get around to starting the week 4 problem set and taking the midterm.

  4. Understanding why there are some in Science who do not seem to believe in the scientific method is puzzling. But that person who said – Nobody is paying enough attention to me, could be the answer. Maybe to them the third way is kind of like the highway. My way or the highway.

  5. Dear Prof. Coyne

    if you have not yet (which is quite improbable, after all) taken notice of Andreas Wagner’s first popular science book “The Arrival of the Fittest. Solving Evolution’s Greatest Puzzle” )2014) – I herewith want to highly recommend it to you. A more complex scientific elaboration of his theory of “transformative change in living systems” is given in his Oxford University Press book “The Origins of Evolutionary Innovations” from 2011.
    As for my biological understanding he consistently and convincingly provides what was missing from neo-Darwinism and what has always troubled me about it (like many of the “Third Way”.

    Rosmarie Maran

    1. “transformative change” is a good example of something I mentioned on your pet linguistic hate column a few days ago – the (American) academic tautology, an adjective derived from an abstract noun, in this case “transformation” qualifying a noun of exactly the same meaning.

  6. Every time I see mention of a “third way” or “middle path” or “best of both worlds” scenario coupled with some reference to fundamentalist religion, a little red flag pops up in my neural networks: SPIRITUALITY ALERT. Someone is about to open the crypt and drag out the old, tired, crumbling, overworked Cutting-Edge. Again.

    Man-made religion is man-made and sexist and shallow and extreme and wrong and tied to the politics of control and domination — but hey, what if we did something daring and original and just focused on a vaguer, purer vision of the supernatural like a Creative Drive or Higher Force? Like every religious leader ever in the history of humanity? It would be fresh. It would be unexpected. It would be a replay of the theology of the last several millennium … before they all got into the details.

    It seems to me that scientists would want to present a serious idea by framing it between 2 other valid and respectable ideas. They would look for “extremes” well within the field of legitimate expertise. For example, if they’ve got a new theory regarding Egyptian history they won’t want to compare and contrast it with Ancient Astronauts. If they’ve got some interesting idea in cosmology they won’t start out reassuring people that they don’t go as far as Velikovsky. And if they’re bringing up something in evolution, they won’t mention “creationists” being one of the sides they’re carefully avoiding, so don’t get confused.

    1. It shows an awareness that most criticisms of Neo-Darwinism of which the public is aware are based on some form of crackpottery like creationism. Unfortunately their disavowal of creationism is not on the face of it evidence of non-crackpottery.

      No theory of anything as complicated as evolution is ever quite complete. There will always be outstanding issues, and new additions to the edifice should be welcome. Niche construction certainly sounds intriguing to this layman. I reserve the right to be suspicious of approaches that, instead of adding a new wing to the edifice, want to dynamite it.

      1. So we need a new poster, like the one from the 70s: “Just Because You’re Paranoid Doesn’t Mean They’re Not Out To Get You”.

        This one says “Just Because You’re Not A Creationist Doesn’t Mean You’re Not A Crackpot”

    2. JAC: Here’s a comment I got from an ignoramus who is now banned. I’ve added a sentence at the end.

      Everytime someone is bringing up the Darwinian theory which has more holes than SpongeBob a red flag pops up in my neural network: ATHEIST ALERT!
      Atheism is the most illogical position in my view, thank god I don’t have enough faith to be a atheist.

      p.s. I like to eat chalk.

  7. Ouch! Bejan’s unsupported ad hoc “law” rubbed me the wrong way, and seeing how short shrift Felsenstein did with it maybe it did the same for him.

    The vast majority of people believe that there are only two alternative ways to explain the origins of biological diversity.

    Two alternatives? One of those ways was (more or less) alone 2 centuries ago, now the other lives alone. This site is not describing the science.

    Neo-Darwinism ignores important rapid evolutionary processes such as symbiogenesis, horizontal DNA transfer, action of mobile DNA and epigenetic modifications.

    I would like to have references to where these mechanisms are ignored instead of observed. That the mitochoncrial endosymbiosis happened (symbiogenesis) is a crucial part of the generic phylogenetic topology what I know of [ ]. So is horisontal gene transfer, et cetera.

  8. I recently read one of Jablonka’s books. (_Evolution in Four Dimensions_.) The stuff about epigenetics was all “could be”.

    EFK is a curious case – sometimes what she writes is reasonable, and sometimes she goes completely off. For example, she has a book _Refiguring Life_, where the middle chapter is an attempt to apply (lay, which makes it even worse) psychoanalysis on Schroedinger, trying to understand why he wrote _What Is Life?_. I also remember her mentioning in seminar (visiting when I was at UBC) that she was convinced that computer hardware had something like “the sign of militarism” because computing had been created by the DoD. I didn’t have time to ask what she meant.

    1. Huh? Early transistor computers weren’t exclusively DOD. Universities and for-profit corporations contributed significantly to their development. One of the earliest ones wasn’t even American, it was British.

      I don’t think you should ask what she meant. I suspect you’d get a very tinfoil hat answer and thus be disappointed.

      1. I don’t think you should ask what she meant. I suspect you’d get a very tinfoil hat answer and thus be disappointed.

        when I question someone and the tinfoil hat comes out of their pocket and onto their head, I usually find that to fairly well mark the point at which I can safely cease worrying about anything further that is said.

  9. “The commonly accepted alternative is Neo-Darwinism, which is clearly naturalistic science (1)but ignores much contemporary molecular evidence and (2)invokes a set of unsupported assumptions about the accidental nature of hereditary variation.

    1)This should be one of the first items on everyone’s Bullshit Detection Check List, when directed at a well established scientific theory.

    2) This statement pretty much leaves no room for doubt. This statement should not be possible from someone well learned in biology. The only other option, besides ignorance, is lying. Blatantly.

    1. There has to be a term for defining a false conflict by lying, then stepping in with a bogus solution while announcing “Mission Accomplished”.

    2. “The only other option, besides ignorance, is lying.”

      That’s not true. There’s also delusion. They may want their own pet theory to be true so badly that they come to actually believe they are right and everyone else is wrong. They *should* know better. They are not really ignorant; but they are not lying either. They actually believe it.

      Again, I recommend the book “Mistakes Were Made (But Not By Me)” for an in-depth analysis of this type of thinking.

      1. I new I should have explained further, but damn, my comments are always too long and torturous. I had thought to expand on the word “lying” in the original comment.

        I’ll try to keep it short. What you describe involves lying to one’s self. Either the delusional person never even looks or acknowledges the evidence, in which case ignorance, or they are aware of it and lie to themselves about it. If you keep lying to yourself about something, over time you feel less guilty and defensive about the lie, and some time later you begin having trouble remembering if you are lying to yourself about it or not, and eventually you forget you were ever lying to yourself about it.

        Also, you can substitute other words for lie, for example mislead, but if you are aware that you are distorting things it is still lying. If you eventually lose your awareness of having distorted things, it was still lying that got you there.

        1. I think pac is talking about something else, something more like unconscious bias.

          Personally I think one of the things most of us struggle with (including me) is a bias against bias. 🙂 What I mean by that is: it is extremely hard for most of us to understand how someone of about the same intel and education, viewing the same evidence, can come to a radically different conclusion honestly. Our own cognitive processes feel so right and obvious that anyone who disagrees with us about something important must either not be seeing the problem the right way (they lack our data), or they are not thinking right (insane/delusional), or they must be lying about it for some reason. For most of us, there is no rational conclusion from our data + reasoning other than the one we hold. We have a hard time putting ourselves in someone else’s emotional shoes, but we have an incredibly hard time putting ourselves in the intellectual shoes of someone we strongly disagree with. So hard, we often simply can’t do it.

          You see this with political discussions (example: dems thinking tea pariers are insane or greedy), with religious ones, and yes, sometimes with scientific ones too.

          Of course, we humans are also notoriously bad at detection our own reasoning mistakes. 🙂 That should be a warning bell that “insane or lying” is not the conclusion we should leap to, but it typically isn’t.

          These folks are smart. Educated. Probably not lying for the money or fame. Not delusional in any medical sense. They are simply humans that have reached different conclusions from the same data, as difficult as that may be for us to grok.

          1. I think there is much to the points that you raise. I may be exhibiting some of the flaws that you describe, and which I think you describe accurately, but I think in this specific case, which is not unique, that the various paths taken by the people who have endorsed that website, to arrive at their actions / statements regarding the TOE, are indeed flaws and that they need to be criticized. I think they have arrived where they did due to flaws that, though they are normal (pretty much all humans exhibit them), it is in the best interests of us all to try and correct.

            I agree that they are simply humans that have reached different conclusions from the same data. They are likely all decent, interesting people that have / do contribute usefully to society. It has been my experience that just about, literally, anybody I have come to know something about to some degree beyond the superficial persona we typically see of each other in our day to day lives, no matter how stereo-typically incompatible with me they might seem, I can’t help but empathize with them and to care about them.

            But nevertheless. In this specific case these people are exhibiting all too human flaws and they should be called on it. I don’t feel good about it when it happens to me (getting called on it), but when I am able to think clearly on it I can say that I am all in favor of somebody doing me the favor of showing me that I am wrong. But, being human, I can’t promise I’ll be gracious, or easy, about it.

  10. I really appreciate threads like this. I am interested in the intrusion of woo into evolutionary theory, and clear precise thinking on the topic. Speaking of which, are you going to review that (apparently) over-hyped “group selection” paper about spiders?

      1. JAC said he’d write a review of the paper and I don’t think that has appeared yet. I looked at every page on the site matching Pruit.

  11. I just finished Wagner’s “Arrival of the Fittest.” It came highly recommended by the likes of Jerry Coyne and Larry Moran, so I suspect it isn’t a crank book or an error ridden book.

    So it is all the more remarkable by presenting a rational basis for all the things about evolution that Behe and Axe and Shapiro find puzzling.

    Mainly it explains how mutation always seems to find viable variations. It seems obvious that evolution requires variations to be continuously reachable and chainable, but nothing written for the layman has ever satisfied me as conclusive.

      1. Evolution generally explores variations that are just one nucleotide different from what is current.

        If you randomize the “characters” in a gene, the odds of getting anything useful or even viable approach zero.

        So the question becomes, how can evolution replace many, if not most of the elements of a coding sequence over time. If functional sequences were not connectable by point mutations, evolution might not work at all.

        I really think Wagner is on to something. I don’t suppose his ideas are entirely original, but his presentation is.

        1. how can evolution replace many, if not most of the elements of a coding sequence over time. If functional sequences were not connectable by point mutations, evolution might not work at all.

          Many functional sequences have duplicates. When one duplicate mutates, the other works fine and the organism works fine. This feature allows mutation in the other sequence to proceed through many generations until it haphazardly ‘finds’ some beneficial multi-change mutation. In most cases, the benefit may not even be to the original sequence function, but might contribute to some other entirely different function. This is termed co-option or exaptation.

          One reason Behe finds mutation to be so improbable (IMO) is that he constructs models that don’t allow the above processes to occur: his models assume mutation only occurs in the “working” sequence and that exaptation never happens.

    1. That is on my list of books to read. One item of relevance is that large populations contain a vast reserve of genetic variation, such that every gene can be mutated somewhere. On really big populations like in the bacteria in your colon every gene will be mutated multiple times.

      1. The question Wagner attempts to answer is why are alleles even possible. Why are they commonplace. How is it that in bacteria, the same gene function can be represented by coding sequences that are almost entirely different?

        And can mere mutation replace much or most of a coding sequence one step at a time. How could that be possible.

        1. To your first question, I think one reason is b/c most genes code for proteins, and proteins are made from combinations of 20 or so different amino acids. Each amino acid will be water soluble or not, and the water soluble ones will be positive or negative in charge to different degrees. For each amino acid with its properties, there are several other amino acids with similar properties.
          So a given gene codes for a specific series of amino acids in a protein, but there are many many other proteins possible with completely different amino acids, but these proteins could still be functionally similar to our given protein b/c they use chemically similar amino acids. These would of course be coded for by completely different genes unrelated to each other.

          I hope I am being clear. I can’t always tell.

          Now, what is also interesting is that although this is certainly possible, and there are examples of it, these examples are in fact not the ‘norm’. Most functionally similar proteins are similar in amino acid sequence, coded for by similar genes. This is actually one of those overwhelmingly strong arguments for common evolutionary ancestry of genes in ‘gene families, rather than independent ‘creation’ of genes.

          To your second question: Yes. It can gradually erase a gene. I do not think it would likely convert a gene to a completely different gene b/c there are faster ways to make a novel gene. But once a gene is ‘killed’ by a mutation it is gradually erased by mutations. An example I know of are the hemoglobin genes of the Ice Fish. This fish completely lacks red blood cells and has no need for hemoglobin. One of its hemoglobin genes seems to be completely erased (related, normal fish still have it), and its other hemoglobin gene is almost completely erased. Only a fragment remains.

  12. Why do people disparage evolution so? It’s simple and elegant, true, and we know more about how it works than Darwin did (he had no idea what transmitted the biological information to each generation until genetics came along). Perhaps all you need to say to such people is: “Occam’s Razor!”.

    1. God.
      Whatever piffle you hear about magisteria, Darwin refutes all revealed religion. That’s why I have respect for William Jennings Bryan: he was honest. He said “if this is true then my religion is false.” He picked the wrong side but I prefer honest error to weaseling about compatibility.

    1. Yes. As young adults they may run into the bad ideas before being fully grounded in the good ones, and at best delay, at worst derail, their future careers.

      1. That’s why I wanted to ask EFK about the comment I mentioned – *I* understand computing, but my fellow students might not have (certainly graduate students in the humanities with undergraduate CS minors, etc. are unusual – though increasingly common), so …

  13. What is it about evolution that so attracts the wibbly wobbly kinds of scientists? There are other science fields that attract this sort, like research in human behavior, etc., but c’mon. I do agree that the Modern Synthesis does not explicitly mention things like horizontal gene transfer or evo devo because those were found after the Synthesis was defined, but so what? That does not mean the ‘Original Syn’ is wrong, just incomplete. Just roll the new things into it and move on.

    1. I agree–that seems so blindingly obvious.

      Even if some of their unsupported avenues of variation-generation were true, how does that change the fact that selection acts on variation? Isn’t that basically the core of the new synthesis? (In addition to random variation, which none of the above seem concerned about anyway.) And do any of them address common descent?

      This is about how I felt when punctuated equilibrium burst onto the scene. Perhaps it would be shown to be true in some instances, but how would that not be just an additional phenomenon to incorporate under the umbrella of the new synthesis?

    2. Yes, fields such as Evo-Devo are concerned with examining the specifics of evolution not upturning it. As for horizontal gene transfer, it’s not a very common mechanism and seems more important to asexually reproducing organisms. But even if it were so (say viruses’ implanting DNA into its animal hosts) that wouldn’t disprove SET (as the inserted DNA is still being acted upon by selection if it is not silenced). To argue that it’s a completely novel mechanism would be like cell biologists saying to anatomists: “Aha! Those squiggly things under the microscope are a much better explanation of locomotion than muscles.”

  14. Also, they show some serious misunderstanding of epigenetics (“Lamarckian”? – how could it closely resemble Lamarck’s ideas? In order for it to truly resemble his views new genes would have to spring up, old genes would be killed off, etc so that a “new” trait could be produced – they probably wouldn’t stretch that far as it sounds completely bonkers so they’re left with epigenetics instead). On a side note, epigenetics is anything which is outside of the genome; that includes histone and protein modifications, anything that effects mRNA, not only DNA methylation. That goes on all the time (as genes have to be regulated to not turn organisms into useless piles of goo). The methods of regulation has evolved, as is the case in plants which use RNA interference more than animals, but the DNA sequence’s effect as a regulating factor is selected; for example, miRNA’s evolved through a duplication and then an inverted duplication events which produced a molecule which could target the original gene’s mRNA. There might be something similar going on with DNA methylation, but it would certainly not “disprove” SET and might only be a unique effect rather than standard operation.

    1. Besides inheritance of acquired characters, Lamarck had another interesting idea that does not get mentioned too often. He considered that the history of life on earth (seen then as ‘progression’ in the fossil record) was because microbes spontaneously generate, and make lineages that become more advanced by a ‘complexifying force’. So things like mammals and birds are descended from lineages started long ago. Things like worms are from lineages started not too long ago, and of course the microbes today were recently spontaneously generated.
      It was really a neat idea, since it explained the diversity of life today and the progression seen in the fossil record.
      I hope the Third Way’ers do not hear about it!

        1. Exactly. First, there is no evidence for a complexifying force. Second, this view of evolution can not predict nor explain the observed nested homologies of anatomy between different lineages.

  15. Is it me or does this new ‘Third Wave of Evolution’ seem like the Theory of Evolution meets the Law of Attraction as promulgated by Marianne Williamson, Wayne Dyer and Oprah and other New Age Gurus and Snake Oil Salesmen!

  16. I just loved reading this Jerry!
    Maybe all these specialized people are suffering from what Dan Kahneman calls The Focusing Illusion:
    “Nothing In Life Is As Important As You Think It Is, While You Are Thinking About It”.

  17. I suppose we’ll see where these ideas are in 10-20 years time. With that “third way” along with the “extended synthesis” both pushing the boundaries, perhaps something will come of some of it.

    It is interesting that ID proponents will jump on anything that criticises “Darwinism” as if they are still operating on the dichotomy that it’s Darwinism that stands in their way of ID being legitimate science…

  18. While I think many of them sincerely think they’ve found some revolutionary science, there is going to be a minority who sees this not as a third way of evolution, but as a third way of funding.

  19. That Odling-Smee (Lewontin) idea sounds close to the topic of “The Extended Phenotype”. Dawkins covered the area pretty completely as far as I can tell. I don’t think he would agree that it changes the paradigm , just makes it more interesting.

  20. This is Darwin envy coupled with niche construction.. got to make a name, got to get their attention, listen to me, damn you!

  21. I have a professor of palaeontology, who told us there was a whole new concept of evolution, where groups not only branch off each other, but also re-unite so that the tree of life becomes more like a network.

    I can accept this on the species level – two closely related species forming a fertile hybrid one – but she made it appear that it works on higher levels too, like genera and families.

    I can’t imagine that, and if I did, it must be restricted to some unusual cases and is hardly a threat to the whole tree-of-life paradigm.

    The concept was called reticulate evolution, apparently first introduced by John Veron. Does anyone here know more about his work and if he himself claimed that, or if my professor just got confused?

    1. Vernon thought that many species and higher taxa of corals arose and were continuously maintained by frequency hybridizations between members of other different. Much of his book is devoted to that idea. There are claims in the literature of genetic evidence consistent with that kind of fusion of lineages. The evidence is poor.
      Veron, J. E. N. 1995. Corals in space and time. Comstock/Cornell, Ithaca and London.

    2. There was an appreciable amount of comment a few years back – 2000~2003, perhaps? – about the apparent large extent of horizontal gene transfer between different groups of Archaea and Bacteria. How much of that was by conjugation and how much by Margulis-like symbiosis is a bit more unclear. That work seems to lead to unresolvable patterns of relationships at the root of the tree of life, which some people interpret as a network (“reticulate” – net-like) and others as a “ring” of inter-related species at the root.
      There’s valid science in there, but how exactly to convert standard cladistics to handle horizontal gene transfer isn’t TTBOMK resolved yet.

  22. I think you are quite right in that most these ‘Revolutionary New Ways’ is attention seeking (and hence fund finding).
    There are a few things (some of them already mentioned above) that I noted many non-biologists fail to understand, such as:

    – Random mutation does not really need to be random, just random to its effects on selection.
    – NS is better described not as ‘survival of the fittest’, but ‘reproduction of the fit enough’.
    – Point mutations are not the only mutations, and probably not the most important ones with regard to evolution at that.
    – Epigenetic effects over a few -or even many- generations does *not* amount to adaptation. The true interest of epigenetics is that it studies how the environment (= mostly other genes and their products) influence gene expression and thus cell differentiation and phenotype.
    – Many of these ‘new’ concepts, such as ‘niche construction’ or ‘symbiosis’ are not at all in contradiction with ET.

    If these, and a few more, concepts would be known a bit more widely, much of this could be prevented, immo.

    1. “– Many of these ‘new’ concepts, such as ‘niche construction’ or ‘symbiosis’ are not at all in contradiction with ET.”

      Nor do they sound all that “new” to me. (But then, you’ve already implied that. 😀 )

  23. So much I could say here. It does indeed sound like a group case of “people aren’t paying enough attention to my pet theory.” The thing that I find astounding is not that people would push their pet theory as holding some relevant place within the structure of a well-established theory (like SET or gene theory), but that they would actually suggest that said pet theory should supersede the well-established one. An action like that would require, first and foremost, evidence that the well-established theory is incorrect, and secondly that the individual’s pet theory has some empirical backing in reality. There are many ways to theoretically cook up ad hoc explanations for observable phenomena, but that’s called speculation, not science.

    What are those “unsupported assumptions about the accidental nature of hereditary variation” that Darwinism relies upon? Where is even a single example that important evolutionary change has been “not gradual but instantaneous”? Of course, such a statement begs the question of how one delineates between “gradual” and “instantaneous”. Similarly, how does one differentiate between “macroevolution” events and more “micro” ones? Who is the arbiter of these relative terms?

    I am not a trained biologist, but I do think that many people’s qualms with SET are at least partially attributable to their poor grasp of what randomness is and what it is capable of, stochastically. As a statistician, I certainly have seen evidence for this lack of understanding almost uniformly across disciplines.

  24. It has occurred to me that Lamarckism would be a very much more effective and efficient form of evolution. Natural selection is such an indirect and horribly inefficient process that it takes millennia (in most cases) for it to make any improvement. If I were a benevolent creator I would certainly make evolution Lamarckist.

    Unfortunately evolution doesn’t seem to be Lamarckist and there’s no mechanism for it to work.

  25. Big bang and natural selection bad science. Homeopathy and acupuncture good science.

    According to the Institute of Science in Society. Directors Mae-Wan Ho and Peter Saunders.

    Ho hum.

  26. “While this idea [niche construction] is getting new attention, and deservedly so, it doesn’t call for a revolution in SET. First of all, it’s not particularly new.”

    Spot on. You’ll be interested in a paper I wrote with Kevin Laland, where we argue over exactly this point. I and others say there’s nothing new here. He argues there is. It was published last year, in Evolution. Here:

  27. Thanks, but I wish you cleared up this claim: “clearly naturalistic science but ignores much contemporary molecular evidence” instead of attacking.

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