Wednesday, April 01, 2015

Physiologists fall for the Third Way


I looked forward to this "conversation" because I was already familiar with Denis Noble and his strange views of evolution [A physiologist thinks about evolution]. Noble reiterated his view of modern evolutionary theory at the meeting. He thinks that modern evolutionary theory (The Modern Synthesis or Neo-Darwinism) is all about random mutation and natural selection. He thinks it is based on the views of Richard Dawkins in The Selfish Gene. Neither he nor Michael Joyner (an anaethesiologist at the Mayo Clinic) have learned about random genetic drift or Neutral Theory and neither of them have much knowledge of population genetics. In other words, they are pretty ignorant about evolution even though they feel entitled to attack it.

The photo shows Denis Noble of the left and Michael Joyner on the right. The man in the middle is David J. Paterson. He is the Editor-in-Chief of The Journal of Physiology and he's holding up a special issue of the journal. That issue is devoted to "The integration of evolutionary biology with physiological science."

It contains a number of papers from the usual suspects like James Shapiro and Eva Joyner as well as some others that are unfamiliar to me. None of the papers have anything to do with modern evolutionary theory as far as I can tell.

Don't be fooled. This is not about integrating modern evolutionary biology with physiology. The mood at the meeting was very antagonistic toward evolution. All the participants seem to be convinced that evolutionary biologists are gene-centered adaptationists who don't understand the importance of phenotype. They are certain that physiologists1 do understand phenotype and the connection between genes and phenotype—or rather the lack of connection.

They are convinced that epigenetics signals a return of Lamarck where the acquired physiological characteristics of an individual can be passed on to it's offspring and that this affects the evolution of the species in some unspecified way. They are convinced that plasticity means that evolutionary biologists are wrong. They claim that the discovery of variation between individual cells (e.g. the amounts of particular proteins) means that evolutionary biologists were wrong about the power of genes.

They believe that the failure of the human genome project to uncover the genetic basis of disease means that the core assumptions of gene-centered evolutionary biologists were wrong. The real basis of disease is much more complicated and physiologists are the only ones who known this. That's why they are primed to take over biology and lead scientists to a new understanding of evolution.

This is all in line with the ideas of The Third Way. Several of the "revolutionaries" listed on the site published papers in the special issue of The Journal of Physiology. Here's what the Third Way stands for ...
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 far as I could tell, every physiologist at the session (about 100) fell hook-line-and-sinker for this nonsense.

Here's the last paragraph of the essay by Michael Joyner and Franklyn Prendergast in the journal.
We close this essay by postulating that there has been a pervasive influence of the gene centrism inherent in the Modern Synthesis in conjunction with the Central Dogma of Molecular Biology on biomedical thinking. We believe that this influence has now become counterproductive. Thus, it is critical for new ideas stemming from evolutionary biology highlighted in this special issue of The Journal of Physiology and elsewhere to more fully inform biomedical thinking about the complex relationship between DNA and phenotype. The time has come to stop chasing Mendel.
The discipline should be embarrassed at this behavior. The journal should be embarrassed.


1. "Physiology" now means "human physiology." I don't think there were any plant physiologists or bacterial physiologists at the meeting.

35 comments :

  1. I'll just put that in the storeroom with all the other revolutionary transformations of evolutionary biology that have happened over the past few years. Hmmm...not a lot of room left.

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  2. It's OK, John, there's room at the Third Way website.

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  3. Laurence A. Moran says: “This is all in line with the ideas of The Third Way. Several of the "revolutionaries" listed on the site published papers in the special issue of The Journal of Physiology”

    In addition to the scientists you mentioned in the post, The Third Way group includes Eviatar Nevo, Eugene Koonin, Gustavo Caetano-Anollés, Frank P. Ryan, Jan Sapp, Denis M. Walsh (a colleague of yours at University of Toronto) and many other distinguished scientists.

    Do you think that these and the other scientists at The Third Way are ignorant about evolution?

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    1. "Do you think that these and the other scientists at The Third Way are ignorant about evolution?"

      I don't know what Larry thinks, but any scientists who adheres to a "movement" that starts by mentioning creationism before talking about a "third way" must have some mental problem.

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    2. @Claudia Bandea

      Yes, I think that most of those scientists are ignorant of modern (post Modern Synthesis) evolutionary theory and the proof is in their writing. The exception is Eugene Koonin. I don't know why he associates with that group.

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    3. The exception is Eugene Koonin. I don't know why he associates with that group.

      I imagine he shares some interests, e.g., statistical methods, horizontal gene transfer, incorporation of viral DNA....

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    4. Koonin's not dumb. He can be quote mined but I think we agree he's not dumb.

      Shapiro is such a classic, Newton doing alchemy, crackpot that you have to question the judgment of anyone who gets within a half mile of him.

      Has Noble ever produced a single valid criticism of modern evolutionary theory?

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    5. I see how you exited about personalities of Noble and Shapiro as well as how you cannot avoid them without performing exorcism ritual against that poor ID's things

      But I'd like to see your non-alchemic comment on the paper with the title «Transgenerational Inheritance of an Acquired Small RNA-Based Antiviral Response in C. elegans»
      Thank you.

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    6. Diogenes,

      I think you missed some of Noble's points.
      1. Noble produced experimental evidence that so called jDNA is compensated by the genome when removed.

      2.most mutations are not random due to hot spots in the genome.

      3.epigenetics and jDNA play a significant role in the early development of an organism.

      How's this not valid criticism of evolutionary theory?

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    7. But I'd like to see your non-alchemic comment on the paper with the title «Transgenerational Inheritance of an Acquired Small RNA-Based Antiviral Response in C. elegans»

      http://www.sciencedirect.com/science/article/pii/S0092867414002864

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    8. I think you missed some of Noble's points.
      1. Noble produced experimental evidence that so called jDNA is compensated by the genome when removed.

      2.most mutations are not random due to hot spots in the genome.

      3.epigenetics and jDNA play a significant role in the early development of an organism.

      How's this not valid criticism of evolutionary theory?


      Essentially, because none of those have much to do with evolution. Mutations don't have to be equiprobable across the genome, and development is not evolution.

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    9. Allan Miller,

      I'm not sure I understand you correctly. Are you saying that only random mutations are part of evolution and the equiprobable ones are not?

      If development is not evolution, if understand you correctly, how does evolution achieve "drastic changes" or macroevolutionary jumps, so to say, (new body plans)that in most species can't be accounted for in the fossil record?

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    10. Pest, You have misunderstood. Allan Miller is not saying that "only random mutations are part of evolution and the equiprobable ones are not."

      Perhaps you're confused by different uses of the word "random."

      When we're talking about evolution and call mutations "random" we're saying that the mutations a population gets have nothing to do with the population's needs. It would be better to say that mutations are indifferent to the population's needs, but traditionally we've said the mutations are random with respect to the population's needs.

      Mutations happen at higher rates at some parts of the genome than others, but that has nothing to do with their "randomness" or indifference with regards to the population's needs.

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    11. Evolution happens to populations. Development, in the technical sense used here, happens to individuals. They are not the same.

      Development is one of the many traits that can be affected by mutations. Therefore, evolution can shape changes in development.

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    12. Pest, I thought I'd posted a response, but it's disappeared (if I actually pressed 'publish' ... ). bwilson covered it, but I'll reiterate my post:

      To set hotspots in opposition to 'random' mutation implied that your sense of 'random' viewed random mutations as equally probable across the genome. It is not a requirement of evolutionary theory that mutations be distributed in any particular way. If you actually meant that hotspots indicate mutations aren't aimless, there is no evidence that regions of elevated mutation are better correlated with need than mutations elsewhere.

      As to development, any involvement of epigenetics and jDNA in the unrolling of a developmental program in an individual does not have any bearing on whether such developmental programs can change (evolve). So these things are not a challenge to evolution.

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    13. there is no evidence that regions of elevated mutation are better correlated with need than mutations elsewhere.

      And in fact there is experimental evidence contradicting the idea that mutations are directed toward the needs of an organism or population.

      There was a notion that microorganisms might be able to engage in directed mutation in response to environmental stress, and some early experiments made some researchers, including James Shapiro, quite optimistic they'd be able to prove this. However, further experiments eventually found that in fact mutations were not directed toward relief of any specific environmental stress but were random in that regard. This led all the researchers other than Shapiro to publicly abandon the directed mutation hypothesis. Shapiro alone of the original researchers continues to insist, even in the presence of a wealth of experimental data contradicting his view, that microorganisms are capable of directing their own mutations.

      If microorganisms are capable of directing mutation to relieve stress imposed by the environment, then Richard Lenski must have got hold of a load of prize dunce E. coli.

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  4. Why are so many people opposed to any innovation to the current Neo-Darwinian theory of evolution? It is still a theory isn't it? It's not written in the stone that ND way is the only way is it? The Third Way people must have some evidence to support their theory or they would be roasted chickens wouldn't they not?

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    1. Try inverting that last argument of yours. "The NDT people must have some evidence to support their theory of they would be roasted chickens wouldn't they not?"

      Try harder Pest.

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    2. Why are so many people opposed to any innovation to the current Neo-Darwinian theory of evolution?

      I am very much opposed to the Modern Synthesis (Neo-Darwian) version of evolutionary theory that people like Denis Noble and the Third Way are attacking. I support the more recent versions that are presented and described in the all latest versions of evolutionary biology textbooks.

      My main beef with the Third Way movement is that it's proponents have not kept up with the changes in evolutionary theory that have taken place in the past 40 years. They attack a strawman version of evolutionary theory while revealing that they do not understand any of the more modern concepts.

      The Third Way people must have some evidence to support their theory...

      I have yet to see a single bit of evidence from Third Way proponents that compels me to re-think or revise the evolutionary theory described in Futuyma's book or in the writings of Michael Lynch. Their "evidence" has very little to do with evolution.

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    3. I hear your frustration at the amount of work and discussion devoted to constant re-discovery that the (no longer so) Modern Synthesis cannot explain all, and that we ought to get on the very large number of really interesting questions that await.

      Were there presentations at the conference that touched on the latter (the really interesting questions)? This is a sort of roundabout way of asking why you went, since I can't believe it would be exclusively to hear the talks you've reported on so far.

      And beyond the conference, besides Richard Lenski, T. R. Gregory/Alex Palazzo, and Arlin Stoltzfus, what are some of the topics (and who are some of the researchers associated with those topics) you'd consider to be "interesting questions" currently?

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    4. This is a sort of roundabout way of asking why you went, since I can't believe it would be exclusively to hear the talks you've reported on so far.


      The main reason for attending Experimental Biology is because this is the place where biochemistry educators hang out. There are many sessions on how to teach science and dozens and dozens of posters. Not only do I learn from the sessions and posters but, more importantly, I talk to people who share my interests in improving science education.

      "Networking" may be overrated at times but in this case it's not. Many of us don't get to talk about science education with our colleagues because they aren't interested.

      The other reason for attending a general meeting is to get an overview of what's important in biochemistry & molecular biology. This is really valuable for when I write a new edition of my textbook or prepare for next year's courses.

      I get some new inspirations almost every year. This year I learned that I need to re-write the sections on lipid metabolism and I need to expand the section on intrinsic disorder in proteins.

      I also go to an editorial board meeting for Biochemistry and Molecular Biology Education and enjoy free drinks and dinner paid for by the publisher. But, of course, that's just a minor bonus! :-)

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  5. Most times Larry I think you're a closet creationist. You are constantly pointing to the ID blogs. If you're not doing that you're writing blogs like this were you quote volumously critics of evolution, and respond with an almost halfhearted btw they never heard of this or that. Or maybe you're just to fair minded and think your readers understand what you do, even if you don't quite explain your pov.

    If you were a journalist I would say you were deliberately enlightening your followers as to the errors of evolution. Imagine, physiologists think scientists should prove their claims with solid experimentation, Does that mean evolutionists are only story telling? However, as you're not a journalist I can only guess as to your intent. Maybe you just don't like showing the strengths of evolution.

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    1. My intent is to convince readers that the scientific basis of evolution and modern evolutionary theory is sound and correct.

      Unfortunately, the way people think about evolution is coming under attack from three directions and its difficult to sort them out unless you pay close attention.

      1. Creationist of all sorts attack evolution because it conflicts with their religion. Pointing out the flaws in their reasoning is like shooting fish in a barrel. It's fun, but not terribly challenging. Somebody has to do it.

      2. Some scientists are kooks and others are just misguided (but verging on kookdom). They attack strawman versions of evolution and try to promote their particular hobby horse as a paradigm-shifting revision of evolutionary theory. The Third Way groups and the Altenberg 16 group fall into this category. Sometimes I critique their proposals directly and sometimes I just point out that their credibility is suspect if they don't even understand evolution.

      3. There are some scientists who make a genuine contribution to thinking about evolution. In the past, these were the scientists who promoted Neutral Theory and the important role of random genetic drift. In more recent times it's the scientists like Michael Lynch who promote deeper understanding of population genetics and evolution by accident. I include scientists like Masatoshi Nei and Arlin Stoltzfus who are getting us to think seriously about mutationism and mutation-driven evolution. They understand evolution but insist that evolutionary theory needs to be expanded.

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  6. The important point here is that , AGAIN, evolutionism, is seen as not being accurate in many/most points. these researchers are intelligent enough and their criticisms would be seen by the publoic as scientific criticisms of old evolutionism.
    They want correction without going to creationism. Yet they smell there is a seriopus intellectual problem with old Darwin.
    The inclusion of other mechanisms within the spectrum of evolution is needed but is not enough as many think.
    If they don't know anything about evolution then when does the public know who knows? How many know? Whats the number of sciency types?
    If they are incompetent then why can't creationists question any scientist on the chance they are incompetent in these matters?!
    I still think 15 years will not pass before evolutionism, as is, has passed.
    In fact it seems creationists will be sharing the carcass.

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  7. I somewhat agree with Peter. As I've stated I'm far from a scientist but I like to learn. Professor Moran is always pointing out others shortcomings but never really explains why. To be fair I probably wouldn't understand the explanation if he offered it. When I go to a doctor I check his background, so naturally I do the same when following these debates. As far as I know Nobel is no friend to creationism yet you still paint a picture of his ignorance. When I check the backgrounds of Nobel and Moran it's obvious Nobel has made contributions that dwarf those of Professor Moran. It seems, and I hate to use this language, real scientists don't have time to entertain the blog tetherball match. At this point it seems the PZ Myers and LM's of the world are busy arguing with creationists while neither party is doing science. I will keep my comments to myself from here on out.

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    1. I just want to point out the obvious that a lot of people appreciate that Larry takes the time to run this blog. If it interferes with his job is not for me to judge, but it seems to me that he stays on top of things.

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    2. t this point it seems the PZ Myers and LM's of the world are busy arguing with creationists while neither party is doing science.

      I've heard this criticism many times. It's valid if you want to define "doing science" as playing with pipettes and publishing in scientific journals.

      If that's the way you want to define "doing science" then Denis Noble is doing science and I'm not. The ENCODE researchers are "doing science" and I'm not. Even some Intelligent Design Creationists are "doing science."

      I still think Denis Nioble is ignorant about evolutionary theory and I still think that the ENCODE researchers were wrong about junk DNA. The Intelligent Design Creationists who are "doing science" are also ignorant.

      There are times when you can check a person's credibility by counting publications and there are times when you have to examine the arguments.

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    3. If it interferes with his job ...

      It's part of my job. I'm fortunate that I have colleagues who appreciate the importance of communicating science and teaching science.

      It's called science outreach and it's supposed to be part of what professors do. Some of us do it more than others. I happen to think it's more important than publishing articles in the Journal of Biological Chemistry but most of my colleagues prefer to put their emphasis on doing experiments in a laboratory.

      I respect their decision and they (mostly) respect mine.

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    4. "When I check the backgrounds of Nobel and Moran it's obvious Nobel has made contributions that dwarf those of Professor Moran."

      Since Beau is into checking backgrounds, perhaps he can cite one, just one (1) experimental result from Noble's lab showing that somewhere, anywhere, in any of the anatomical or molecular structures in any species anywhere, there is a complex adaptation that looks like it couldn't be produced by mutation, natural selection and neutral or near-neutral drift.

      Just one?

      Failing that, perhaps one quote from Noble that was NOT misrepresented by creationists as to its meaning in context, as supporting their position when it did not?

      Just one?

      Failing that, it's argument by authority all the way down.

      Is argument by authority a valid argument? If so, who has more authority, creationists or evolutionists?

      Maybe you wanna rethink that whole argument by authority thing.

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    5. I'm sorry, I have noticed no scientific points in your arguments. There is no need to cite even Noble about random mutation (though it's not to hard to find such citations — see knock out experiment and think about it) — it's you who has no evidence for random mutation alone explaining the evolution. You even cannot prove that random mutations are enough _in terms of their quantity_ to produce inheritable immune responce in bacteria in very next generation.
      Just try to think out of dogma and you feel better.

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    6. "You even cannot prove that random mutations are enough _in terms of their quantity_ to produce inheritable immune responce in bacteria in very next generation."

      Yes you can. Empirically, beyond all reasonable doubt. And it is trivially easy to do so.

      By denying this clear and unambigous fact that almost all creationists accept, that random mutations and natural selection in fact explains and proves microevolution, you are the one who is proving you can't think out of your dogmatic viewpoints.

      In your emotional desperation to deny anything related to evolution you've gone so far as to deny direct empirical observations. You're like the flat-Earther placed in front of a telescope watching the tallest mast of a sailship be the first to emerge over the horizon, yet if asked if you can see this you just say "nope, I don't see it".

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  8. Having little to offer by way of original input, may I direct everybody's attention to possibly one of Larry Moran's best blog posts ever.

    http://sandwalk.blogspot.ca/2014/02/on-difference-between-neutral-theory.html

    Participation on this site has dramatically changed delivery of curriculum in my Biology classroom.

    I remain forever grateful!

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  9. Could the IDcreationists on this site please make a positive contribution and cite Denis Noble's #1 best killer argument that somewhere, anywhere in any species, there's an anatomical or molecular structure with an adaptation too complex to be produced by observed processes of mutation, natural selection, neutral or near neutral drift, and HGT. Just one.

    Not argument by authority. "He's a professor!" If he's so smart, and if his ideas really overlap creationist claims in any way, then he must have evidence that an adaptation exists that's too complex to be made by mutation, NS, etc. etc.

    Present that argument please. If you cannot, ask #attackgerbil at the DI.

    Someone? Anyone?

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