Saturday, May 31, 2014

The Third Fourth? Way

Back in 1997, James Shapiro wrote an article for the Boston Review entitled "A Third Way." It was a very confusing article. His main point seemed to be that conventional neo-Darwinism wasn't a complete picture of modern evolutionary theory.

That part wasn't news since by 1997 the ideas of Neutral Theory and random genetic drift had been around for thirty years. Apparently, Shapiro was three decades behind in his understanding of evolution.

Shapiro doesn't demonstrate that he understands population genetics and random genetic drift. This just one (of many) criticisms that I mentioned in my review of Shapiro's book Evolution: A View from the 21st Century in NCSE Reports [Evolution: A View from the 21st Century]. Shapiro responded to my review at: Reply to Laurence A Moran’s review of Evolution: A View from the 21st Century] and I discussed his response on my blog [James Shapiro Responds to My Review of His Book].

The "third" way, according to Shapiro's 1997 article, is not classic Darwinism and it's not creationism. Instead, it's a new way of looking at evolution.
What significance does an emerging interface between biology and information science hold for thinking about evolution? It opens up the possibility of addressing scientifically rather than ideologically the central issue so hotly contested by fundamentalists on both sides of the Creationist-Darwinist debate: Is there any guiding intelligence at work in the origin of species displaying exquisite adaptations that range from lambda prophage repression and the Krebs cycle through the mitotic apparatus and the eye to the immune system, mimicry, and social organization? Borrowing concepts from information science, new schools of evolutionists can begin to rephrase virtually intractable global questions in terms amenable to computer modelling and experimentation. We can speculate what some of these more manageable questions might be: How can molecular control circuits be combined to direct the expression of novel traits? Do genomes display characteristic system architectures that allow us to predict phenotypic consequences when we rearrange DNA sequence components? Do signal transduction networks contribute functional information as they regulate the action of natural genetic engineering hardware?

Questions like those above will certainly prove to be naive because we are just on the threshold of a new way of thinking about living organisms and their variations. Nonetheless, these questions serve to illustrate the potential for addressing the deep issues of evolution from a radically different scientific perspective. Novel ways of looking at longstanding problems have historically been the chief motors of scientific progress. However, the potential for new science is hard to find in the Creationist-Darwinist debate. Both sides appear to have a common interest in presenting a static view of the scientific enterprise. This is to be expected from the Creationists, who naturally refuse to recognize science's remarkable record of making more and more seemingly miraculous aspects of our world comprehensible to our understanding and accessible to our technology. But the neo-Darwinian advocates claim to be scientists, and we can legitimately expect of them a more open spirit of inquiry. Instead, they assume a defensive posture of outraged orthodoxy and assert an unassailable claim to truth, which only serves to validate the Creationists' criticism that Darwinism has become more of a faith than a science.
Now Shapiro has joined forces with some other "revolutionaries" and started a new website called "The Third Way." It has grandiose goals ....
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 supernatural intervention by a divine Creator. The other way is Neo-Darwinism, which has elevated Natural Selection into a unique creative force that solves all the difficult evolutionary problems. Both views are inconsistent with significant bodies of empirical evidence and have evolved into hard-line ideologies. There is a need for a more open “third way” of discussing evolutionary change based on empirical observations.
There's only one problem. I'm familiar with Shapiro's ideas and with the ideas of most of the other people listed on the website and I don't think any of them (except Eugene Koonin) have anything significant to say about evolutionary theory. Futhermore, most of them don't seem to understand that there's already been a revolution and population genetics, Neutral Theory, etc. won the day. They seem to have completely missed that revolution.

They are advocating a fourth way that skips right from adaptationism to something else.

They are like a group of would-be revolutionaries marching up Rue de Lyon in Paris only to discover that the Bastille has been replaced by an open square and an opera house.

Note: There aren't many biologists that are interested in this "Third Way" but the creationists are lapping it up [A Group of Darwin-Skeptical Scientists Seeking a "Third Way" in Biology Have Launched a New Website; Welcome to Them!].


45 comments:

  1. The "Third Way." Superior to both? Right.

    I'll be the first to link to the classic Xkcd cartoon.

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    1. "Dead meat" can come back to life just like dead meat became life.... It looks like Dinogenes is changing the history... we just don't know which one...

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    2. More primordial soup nonsense

      Are you sure "The Bandwagon" by Claude Shannon is primordial soup nonsense? ;)

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  3. Larry, is the neutral theory in this article the same neutral theory that you refer to?

    http://www.sciencedaily.com/releases/2014/05/140527101346.htm

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    1. The Neutral Theory used in ecology uses some of the same equations as the neutral mutation theory of population genetics. But the entities that are "neutral" are species, not alleles, and instead of mutation the new species arrive by migration.

      So it's not the same thing, so I agree with anthrosciguy and Larry: no.

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  4. The problem with views like Shapiro's is twofold: if there is all this "natural genetic engineering"

    1. ... what keeps it there in the face of mutation. Adaptations for long-term advantage tend to decay away because the mutation rate of deleterious alleles (those that eliminate the "engineering") is greater than the selection coefficient favoring them, if they are only used very infrequently.

    2. ... what guarantees that all these natural genetic engineering manipulations are adaptive? If I take my car and dramatically re-engineer it by disconnecting the engine and putting it in the trunk, that might not help it run. What super-intelligence is embodied in the natural genetic engineering to guarantee that the dramatic major changes it makes in the genome are adaptive? That issue is not faced by Shapiro as far as I know.

    Once these two questions are faced, we find ourselves right back in the boring old Modern Synthesis. We need natural selection and the natural genetic engineering is just one more category of mutation.

    I believe that these, particularly #2, have been raised by Jerry Coyne in his rebuttal of Shapiro.

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    1. Shapiro, in the comments section of a website one or two years ago (sadly I don't know which one anymore) was asqued to answer how did cells actually perform said "natural genetic engineering". His answer was a honest "I don't know". Basically, the whole thing amounts to making endless lists of genetic "entities", and stating that cells use all those to auto-engineer themselves. There's nothing in the book that even hints at how this could possibly be done. He also falls into the whole BS of probabilities, etc, that have been debunked ad nauseam.

      I still cry over the money I spent on his book.

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    2. I believe I recall looking through a bunch of "directed mutation" papers by Shapiro and others, and finding the following: The others started off by being possibly more enthusiastic than Shapiro about the abilities of microorganisms to band together as a sort of "overmind" to both increase mutation rates and increase the proportion of favorable mutations. These papers focused on particular favorable mutations that could be achieved in one or two steps. Gradually, as the other scientists found increasing numbers of favorable mutations that did *not* happen in greater proportion (compare Lenski), their papers began to retract the claim that mutations were being directed. Shapiro seemed to me to be the only one who continued to adhere to the view that microorganisms in groups were self-directing mutations.

      I do not think Shapiro is at all a god-botherer. Rather, I think he feels past work regarding somewhat surprising behaviors/capabilities of microorganisms in groups sets the table for discovery of genetic engineering as being among those capabilities.

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    3. Judmarc, are you referring to Cairnsian mutation, aka "Fred"?

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    4. Diogenes, my apologies - I truly don't remember the names of the folks who started out as coauthors with Shapiro of the "directed mutation" papers, who've since retracted.

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    5. BTW, just a bit more detail about something I referred to in passing above:

      past work regarding somewhat surprising behaviors/capabilities of microorganisms in groups

      IIRC, the past work had to do with signaling and concerted activity among bacterial colony members.

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    6. Judmarc, are you referring to Cairnsian mutation, aka "Fred"?

      After some Googling - looks like the same thing I'm thinking of, or at least very similar. A name came up while Googling that I do recall being on some papers I read, Barry Hall.

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    7. Joe Felsenstein says: “…the natural genetic engineering is just one more category of mutation”

      Indeed, just like Masatoshi Nei (see the excerpt below from Nei’s recent book “Mutation-Driven Evolution”), Shapiro considers natural mutational events the primary force of evolution. I’m rather surprised that Lawrence Moran, a great admirer of Masatoshi Nei, does not embrace Shapiro’s work:

      “…many evolutionists including Motoo Kimura and Jack King believed that phenotypic evolution [in contrast to molecular evolution; this parenthesis mine] is caused primarily by natural selection. By contrast, Nei (1975, 1987, 2007) proposed that since phenotypic evolution is ultimately controlled by DNA and RNA molecules, both molecular and phenotypic evolution must be primarily caused by mutation. Nei’s view has been based on the new findings in the study of molecular evolution and developmental biology. He considered all kinds of DNA changes (nucleotide substitution, gene duplication, polyploidization, epigenetics, etc.) as mutations and tried to explain all phenotypic evolution by mutation. Previously I called this view neomutationism (Nei 1983, 1984), neoclassic theory (Nei 1987), and the new mutation theory (Nei 2007), but in this book I have decided to call it the theory of mutation-driven evolution or neomutationism depending on convenience”
      .

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    8. Nei and other recent mutationists, by declaring mutation to be the "driving force" of evolution, have given an unfortunate impression. They want their view to replace the Modern Synthesis, but in doing so, have they discarded natural selection? Do they really believe that a nonrandom high degree of adaptation can be achieved by mutation alone?

      I think that, if pressed, they would acknowledge that structures such as the elephant's trunk, or the ability of the hemoglobin molecule to carry oxygen, are able to exist because natural selection acted on the variation that mutation caused. Mutational processes my constrain the directions and speeds of evolution, but by themselves they do not create the high levels of adaptation that we see.

      I wish that, in their zeal to declare a replacement of the Modern Synthesis by their view, they had not given this impression.

      Shapiro, on the other hand, really seems to believe it. He omits natural selection as an actor in his new 21st century theory. He seems to really think that natural genetic engineering will somehow produce high degrees of adaptation. This is like turning the repair of your car over to me. Not expected to result in a good outcome.

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    9. Joe Felsenstein: ”Do they really believe that a nonrandom high degree of adaptation can be achieved by mutation alone?” And, should I add, by neutral evolution and genetic drift?

      Interestingly, as pointed out by Nei, even the “fathers” of neutral evolution theory, Motoo Kimura and Jack King believed that phenotypic evolution is caused primarily by natural selection (see Nei's text above).

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  5. It seems like you would like to muzzle any thinking not married to your own. What can a place for discussion harm? These aren't creationists yet you still wave your hand at them. What are you afraid of?

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    1. IOW, you're OK with Shapiro writing a book explaining his views, but not with Larry Moran writing a blog post criticizing those views.

      So, sorry, who is it who is trying to "muzzle" discussion?

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    2. I'm afraid of people who scream "censorship" in the face of criticism. I'm afraid of people with bad arguments who taunt "what are you afraid of." I'm not keen on spiders, either.

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    3. Beau, have you ever wondered why real scientists like Larry Moran never bleat on about be muzzled or censored ?

      And who are you to say Shapiro isn't a creationist ? I've read a fair amount of his blatherings and he comes across to me as a creationist that is just to gutless to say that it's baby jebus all the way down and instead drones on and on about information science, control circuits, hardware, networks and other really bad analogies that just scream "I've got an invisible friend that explains everything and nothing".

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    4. sea beau stoddard: "It seems like you would like to muzzle any thinking not married to your own. What can a place for discussion harm? These aren't creationists yet you still wave your hand at them. What are you afraid of?"
      It seems like you would like to muzzle any criticism of ideas you agree with. What can a place for discussion harm? What are you afraid of?

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    5. steve oberski, it's not clear to me that Shapiro is actually a Creationist. While he does seem to display some characteristics of the breed, he also lacks others. For instance, one of the defining characteristics or Creationists is that no matter how they veil their religious presuppositions to begin with, sooner or later they do get around to their true praise-Jesus-and-fight-the-devil-Darwin agenda. When's the last time Shapiro made any noise about God or the Bible?

      Myself, I'm inclined to put Shapiro in the same unshakably committed to a dubious idea category as Christian "Genomic Potential Hypothesis" Schwabe, Periannan "Independent Birth of Organisms" Senapathy, and Alan "Birds Are Not Dinosaurs" Feduccia, none of whom are, themselves, Creationists.

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    6. Cubist, Shapiro may not have an invisible friend, although I personally doubt this.

      What he does have in common with creationists in general and IDiots specifically is a most likely deliberate misrepresentation of what evolutionary theory actually is, a pseudoscientific explanation of how evolutionary change works that makes no testable claims and is couched in language that is so vague that it impossible to even establish a basis for discussion.

      He uses the same metaphors and analogies that IDiots do, likening biological processes to human designed systems.

      He lies down with creationists dogs and is infested with IDiot fleas.

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    7. Re Steve Oberski

      I was not able to find anything about Shapiro's ethnic background but, from his name, it would appear that his invisible friend, if any, is not Yeshua bin Yusef of Nazareth.

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    8. Enough. There is no evidence Shapiro is a creationist. Accusing someone of being creationist is a serious accusation and should not be made without evidence.

      I'll admit that his logic is shabby, and it's crackpot logic, and his logic is shabby in the same way that creationism is shabby: he employs exclusively negative argumentation. Whereas the creationists say "evolution can't explain it, therefore God of the Gaps", Shapiro says, "Neo-Darwinism can't explain it, therefore Natural Genetic Engineering of the Gaps."

      The sad fact is that Gap Thinking does appeal to small subset of scientists, even ones who are not necessarily religious.

      Some of you may recall I have a history with James Shapiro. After ENCODE's shit "80% functional" abstract was published I argued with him at HuffPost. Then my comments started disappearing, which I interpreted as him banning me. He denied banning me, and I was accused of having lied about him banning me. However, a few months back I again tried commenting at his blog, on a neutral subject, and again my comment disappeared. So I assume I was banned.

      At any rate, I'm no fan of Shapiro's, but "creationist" is a serious accusation, and should not be bandied about to score points. Some people are just addicted to "X of the Gaps" argument; for him X = "Natural Genetic Engineering."

      The bacteria is his all-knowing, invisible God that works in mysterious ways.

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  6. As an innocent bystander, I find Joe Felsenstein's arguments very relevant.

    Engineering, no matter how well done could hardly be a suitable mechanism. For optimal opportunities to exploit the conditions for survival in the ever changing conditions for life all over the planet, life needs to have it's own way. To be bound to whatever modifications any kind of engineering would allow would mean that life no longer would be free to grab any opportunity that offered itself.

    Life is adaptive. It's capability of adapting to changing conditions and use of the available gene pool is what does the trick. Where would the smarts responsible for prediciting the future needs of life be located?

    Life takes it's chances, sometimes it leads to a dead end.

    I have read Shapiro's book...

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  7. I first encountered Shapiro at a conference in Exeter where he tried to argue that bacteria are intelligent because populations find adaptive peaks. I asked what was added by calling this clearly population-level adaptation "intelligence". I got nastily slapped down, but several attendees said to me later that they wondered the same thing.

    Here's ,y review of his book: http://evolvingthoughts.net/2011/08/yet-another-post-darwinism/

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    1. I enjoyed your review. Do you know of any biologist or philosopher who gave Shapiro's book a positive review?

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    2. I have read Shapiro's book. But I had forgotten the quotation that John gives in his interesting review. In particular the part where Shapiro's "natural genetic engineering" is characterized as:

      a highly targeted and well-regulated series of changes with a clear adaptive benefit.

      Thanks, John, for that quote, and for pointing out the connection of Shapiro's views to teleology.

      I wonder how the natural genetic engineering system guarantees the outcome to have a "clear adaptive benefit"? And what guarantees that it will continue to have this benefit? And what maintains the natural genetic engineering in the face of mutation, if it is only used once in a long while?

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    3. Do you know of any biologist or philosopher who gave Shapiro's book a positive review?

      I believe VJ Torley likes it quite a bit. :)

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    4. This is a beautiful quote;

      "Shapiro’s book is not, despite its subtitle, evolution for the 21st century. It is instead evolution for the 16th century, before Francis Bacon had written:

      For the inquisition of Final Causes is barren, and like a virgin consecrated to God produces nothing. [The Advancement of Learning. iii. 5]"


      Very nice!

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  8. Is it frowned upon for an academic to use a Wikipedia page as a reference? I remember Shapiro citing the wiki article on the Modern Synthesis in his "Mobile DNA and evolution in the 21st century" review.

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  9. I am just wondering how Shapiro would interpret outcomes of Ames tests. If bacteria are so intelligent why don't they back-mutate more often in the absense of a mutagen?

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    1. Interesting point. Do you have a reference?

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  10. There is a revolution and its from YEC/ID .
    This other group of card carrying evolutionists is just MORE PROOF that everyone is smelling something wrong with old man Darwin.
    Its just another example of more critics jumping up and saying mE TOO. I think there is room for improvement and correction.
    Thats the equation in this. Not their new conclusions but that another heap of "scientists" thinking THERE MUST BE another way/option to explain biological complexity and diversity without jettisoning evolutionism completly. A last gasp perhaps?!
    YEC is the right side but iD helps us and maybe this NEW WAYer's will help too.
    Although i wonder about the Israeli(third world nation on the Yankee dole if i may say so) endorsement.
    They should have a readers forum. Some of us could help direct them.
    Remember YEC was here first everybody!!

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    1. "more critics jumping up and saying mE TOO."

      Not to stir the old Bob Byers crackpot but Shapiro has long been seeding the grounds of creationism with his off-target criticisms of evolutionary biology. He is not "more critics jumping up and saying mE TOO", he is old news struggling to stay relevant by appealing to whatever crowd will buy his books.

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    2. Sean Boyle
      He has mustered a big gang there on this web thing. And it seems to me constantly Pro evolutionists are seriously questioning this or that about evolution under the influence of modern creationists etc.
      Its saying something about evolutionisms status these days.

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    3. ...because the anti-vaccine and homeopathy crowds conclusively prove that "a big gang there on this web thing" is an excellent proxy for measuring the scientific validity of a given viewpoint.

      /sarcasm off.

      We are actually just sick of people who don't know what they are talking about making grand proclamations.

      again to quote Jacques Monod; "Another curious aspect of the theory of evolution is that everybody thinks he understands it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually, as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology. "

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  11. Robert Byers said: Some of us could help direct them.
    Remember YEC was here first everybody!!

    You (who are 'us', beside yourself?) never direct us. Why don't you?
    "YEC was here first" is poor directing, we have not forgotten your other "firsts" - flat earth, geocentricism, epicycles and much more. All your firsts are false and you are a joke.

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  12. Hey, Larry. You're missing the Carnival of Evolution again. But perhaps you're boycotting it because of this:

    "So-called “junk” DNA. Carl Zimmer assesses a recent controversy in which none other than EE&O’s Editor-in-Chief, T. Ryan Gregory, features prominently. Only a small fraction of our DNA codes for proteins; when this was initially discovered, the non-coding DNA was termed “junk.” Reporting on results suggesting that the overwhelming majority of DNA in our genome has a function, Science announced, “ENCODE Project writes eulogy for junk DNA.” This is too hasty, Zimmer explains, judging by Gregory and his colleagues’ arguments that much non-coding DNA lacks any function."

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    1. I don't know what to do about the Carnival of Evolution. Lately, I haven't been very impressed with the articles that are highlighted and this month is no exception.

      Carl's article covered the paper by my friends and colleagues, Alex Palazzo and Ryan Gregory [see The Case for Junk DNA: The onion test]. He (Carl Zimmer) did a pretty good job of covering the main points of the paper but there were some flaws that the authors weren't happy about.

      I agree with you that the blog author (Adam Goldstein) who published this month's Carnival of Evolution misspoke.

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