The Anti-Synthesis

Why we don’t want another “Synthesis”

High-level debates in evolutionary biology often treat the Modern Synthesis as a framework of population genetics, or as an intellectual lineage with a changing distribution of beliefs. Unfortunately, these flexible notions, used to negotiate decades of innovations, are now thoroughly detached from their historical roots in the original Modern Synthesis (OMS), a falsifiable scientific theory.

The OMS held that evolution can be adequately understood as a process of smooth adaptive change by shifting the frequencies of small-effect alleles at many loci simultaneously, without the direct involvement of new mutations. This shifting gene frequencies theory was designed to support a Darwinian view in which the course of evolution is governed by selection, and to exclude a mutation-driven view in which the timing and character of evolutionary change may reflect the timing and character of events of mutation. The OMS is not the foundation of current thinking, but a special case of a broader conception that includes (among other things) a mutation-driven view introduced by biochemists in the 1960s, and now widely invoked. This innovation is evident in mathematical models relating the rate of evolution directly to the rate of mutation, which emerged in 1969, and now represent a major branch of theory with many applications. In evo-devo, mutationist thinking is reflected by a concern for the “arrival of the fittest”. Though evolutionary biology is not governed by any master theory, and incorporates views excluded from the OMS, the recognition of these changes has been hindered by woolly conceptions of theories, and by historical accounts, common in the evolutionary literature, that misrepresent the disputes that defined the OMS.

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347 thoughts on “The Anti-Synthesis

  1. Mung: So your students learn from you that we do not have a predictive theory of evolution?

    Or do they learn from you that we do have a predictive theory of evolution, but that it’s essentially useless? How pragmatic is that?

    The former, of course. Does that bother you?

  2. Allan:

    If control resides other than in DNA, indicate where, and how that is inherited.

    Mung:

    That’s woo. Hand-waving. Even if we do not currently know the where and the how it certainly doesn’t follow that it’s in the DNA.

    Yeah, Allan. How do you know Jebus isn’t in control? Huh? Prove it.

    When the DNA sequences that contain the instructions are actually identified then I will believe the instructions are in the DNA.

    What are you expecting those instructions to look like, Mung? An IKEA manual?

  3. keiths: What are you expecting those instructions to look like, Mung? An IKEA manual?

    More woo. This time from keiths. If I am unable to say what those instructions look like it doesn’t follow that they must exist in the DNA.

    Besides, I’m not the one that is claiming instructions must exist in the DNA. Those who claim that they must be in the DNA are the ones who need to say what they look like and identify them. Sheesh.

  4. Joe Felsenstein: Does that bother you?

    It surprises me. I thought population genetics was the savior of evolutionary biology. I mean, why define evolution as changes in allele frequencies otherwise?

    So you disagree with Stoltzfus?

    …the original Modern Synthesis (OMS), a falsifiable scientific theory…

  5. Mung: It surprises me. I thought population genetics was the savior of evolutionary biology. I mean, why define evolution as changes in allele frequencies otherwise?

    If we have enough information about fitnesses, population sizes, mutation rates, we can do reasonably well in making short-term predictions of gene frequency changes in time. We can also make predictions about what we will see when we examine multiple populations in the present, ones we have not yet looked at. We can make inferences about past events too.

    All the stuff about “savior of evolutionary biology”, well, that’s your phrase so you have to ask yourself.

  6. Mung: I mean, why define evolution as changes in allele frequencies otherwise?

    Well, because that’s what changes (more broadly, haplotype frequencies change). Or do you have some alternative? Mystic cosmic auras, maybe?

  7. phoodoo: So when you have a patchwork of theories, and they can’t be combined to give you any coherence of what is happening overall

    What does it mean to “give you any coherence of what is happening overall”?

    In what way do you think the situtation in biology is any different from the situation in other branches of science? I can tell you it isn’t.

  8. Mung: CharlieM: Please give me a specific example of a stretch of DNA instigating any activity in an organism.

    DNA is basically inert. Take a stretch of DNA and by itself it won’t do much at all.

    DNA is much more inactive compared to RNA and proteins, but it is not actually inert. DNA aptamers actively bind to certain structures and polymers and in that way can participate in gene regulation.

    And there are examples known where deoxyribozymes, that is ribozymes made of DNA instead of RNA, have been evolved with artificial selection, to catalyze chemical reactions. Though no examples of these have been found in wild organisms.

  9. Mung: Besides, I’m not the one that is claiming instructions must exist in the DNA. Those who claim that they must be in the DNA are the ones who need to say what they look like and identify them. Sheesh.

    They have, haven’t you heard of HOX genes? As with all genes, they are context-specific. You can’t put HOX-genes into a bacterium and expect it to grow limbs and digits, or a spine. But when other genes are present in the correct arrangement, the environmentally determined interaction between the HOX genes and the rest of the genome is what results in developmental processes.

    Analogous to how your hard drive can contain software, which is basically instructions for your CPU to do certain things. But as most software, it is context-specific. It will only run on certain operating systems. And it often requires you have other software installed first, like JAVA or DirectX, some .dll files or what have you.

    People like Charlie M who say DNA doesn’t determine development, or doesn’t contain instructions, are attacking a straw-man. Nobody has ever really claimed that DNA in isolation is what results in development. It is, and always was, changes in gene expression patterns. DNA does contain instructions for doing lots of things, but those instructions require all sorts of different hardware, and they only make sense in the presence of other already-present instructions etc. etc.

    One of the very first and therefore very famous gene-expression systems known is the Lac-Operon in E coli. The Lac-Operon is an environmentally regulated operon. The local concentrations in various carbohydrates regulates the genes.

  10. Mung,

    That’s woo. Hand-waving. Even if we do not currently know the where and the how it certainly doesn’t follow that it’s in the DNA.

    Of course it’s in the DNA. This has long been established. The sequence of every macromolecule made by the cell, and hence every product thererof, is in the DNA.

    When the DNA sequences that contain the instructions are actually identified then I will believe the instructions are in the DNA.

    I think you are way too seduced by your analogies.

  11. phoodoo,

    So you think one day we will find which part of the DNA tells a spider the best technique for weaving a web?

    Who knows? But it is clear that spider web weaving is encoded in DNA. That is what is inherited down the spidey-generations, not those molecules which bathe a particular copy of it (manufactured from that or a different copy).

    Mutations in DNA can result in worse webs. Or do you think that is wrong?

  12. I do feel this incessant desire to knock DNA off from its (generally) undisputed perch traces directly to Richard Dawkins. His most famous book was about gene centrism, and therefore – for no better reason – It Must Go.

    It’s about now that someone unearths a quote from Denis Noble or some other ‘third-wayer’ who is confused between evolution and development.

  13. Kantian Naturalist:
    CharlieM,

    I know that Varela and Weber article quite well. I’ve read it a few times and I’ve been following Varela’s work for a long time (over twenty years, in fact).

    This link worked for me: Life after Kant (PDF).

    Thanks for that link.

    Kantian Naturalist:
    But I’m not sure how relevant that discussion is to the question we were discussing earlier in this thread, which is whether we need a single overarching comprehensive theory of biology (an ‘extended evolutionary synthesis’) or if a patchwork of smaller partial theories (an ‘anti-synthesis’) is sufficient.

    Well I would argue that in both cases (the development of the individual and the evolution of life) many researchers have been looking for simple cause and effect solutions. But it is becoming increasingly apparent that the answers are not to be found in simplicity but in the interaction of very complex systems. I can’t count the number of times I have found in papers and articles, “it is more complex than we thought”. Why would anyone expect simplicity?

    Of course it is quite legitimate to break down and simplify as an aid to understanding. But for a full understanding things must be put back together and viewed from the workings of the whole. The whole is more than the sum of the parts and cannot be understood by studying the parts alone. Too many people focus on DNA or genes and believe they are dealing with reality when in fact they are abstracting from reality when they do this.

  14. Allan Miller:
    phoodoo,

    Who knows? But it is clear that spider web weaving is encoded in DNA. That is what is inherited down the spidey-generations, not those molecules which bathe a particular copy of it (manufactured from that or a different copy).

    Mutations in DNA can result in worse webs. Or do you think that is wrong?

    Well, then you must believe if they can just find the gene for web weaving, they can put that gene into a pig, and it will try to swing from branches and squeeze its spinneret glands.

    Should be easy for science to do soon. Should be interesting.

    Hopefully they don’t try to put it into babies in North Korea though.

  15. CharlieM,

    Too many people focus on DNA or genes and believe they are dealing with reality when in fact they are abstracting from reality when they do this.

    Only genes are inherited down the generations, not the molecules produced from them. So, although gene expression patterns are complex when it comes to development, it remains the fact that what is being extracted during development is the information in DNA, passed down the generations.

    I don’t know how helpful it is to confuse these two arenas, but it’s what you are doing in every post.

  16. phoodoo,

    Well, then you must believe if they can just find the gene for web weaving, they can put that gene into a pig, and it will try to swing from branches and squeeze its spinneret glands.

    No. What kind of a moron would expect to be able to do that? If we find the code that makes planes fly, we should just be able to put it in an iPhone and make it fly too. It’s that dumb.

  17. Allan Miller:
    CharlieM,

    Yes – that! You express it one way – that there is an interplay of system components – that, I agree with. But then you say something else – that there is a ‘superior control’. That, I disagree with. It is that latter notion that I have no idea what would disabuse you of.

    When you wrote the answer above what was the controlling factor? Was it you and your thoughts, or was it your DNA, or your genes or what? Do you feel that you are responsible for your own actions?

  18. CharlieM,

    When you wrote the answer above what was the controlling factor? Was it you and your thoughts, or was it your DNA, or your genes or what? Do you feel that you are responsible for your own actions?

    Actions of developed nervous systems are not a good analogy for the genotype-phenotype system.

  19. CharlieM,

    No, whole functional cells are inherited down the generations.

    Wrong. If you radioactively label all the atoms, all the radioactivity will disappear a few cellular generations down the line – from DNA as well as protein and RNA. But, like a Cheshire-Cat grin, the DNA sequence will magically remain, surrounded by its latest secretions. That is what is inherited.

  20. CharlieM:

    Well I would argue that in both cases (the development of the individual and the evolution of life) many researchers have been looking for simple cause and effect solutions. But it is becoming increasingly apparent that the answers are not to be found in simplicity but in the interaction of very complex systems. I can’t count the number of times I have found in papers and articles, “it is more complex than we thought”. Why would anyone expect simplicity?

    Perhaps that used to be the case, when we only knew how to build simple models (because building complex models takes much more time!). These days we can build very complex models using powerful computers. So I think that the preference for simplicity over complexity was pretty much just a technological constraint that we’ve overcome.

    Of course it is quite legitimate to break down and simplify as an aid to understanding. But for a full understanding things must be put back together and viewed from the workings of the whole. The whole is more than the sum of the parts and cannot be understood by studying the parts alone. Too many people focus on DNA or genes and believe they are dealing with reality when in fact they are abstracting from reality when they do this.

    I don’t know how much biology today is really genocentric. I do think there was a trend in popular reporting on science when every few months there would be a “scientists discover gene for ____!” article. But I wouldn’t cast any blame on scientific researchers for the shallow and simplistic way that their discoveries are reported to the lay public.

    For that matter, Talbott is not saying anything that wasn’t said years earlier by well-known biologists, such as Susan Oyama and Brian Goodwin. He’s just able to write for a broader public than they could.

  21. keiths: So Charlie is comfortable with the idea that this combination is the “master controller”, but uncomfortable with the idea that DNA by itself is. Yet the proteins trace back to the DNA.

    Maybe you could answer the questions I asked Allan?

  22. If you transplant DNA from one cell to another, what develops is the ‘DNA organism’, not the ‘cell organism’. One can break the phenotypic continuity, the so-called extra-DNA control, indicating that it is not inherited as such. But one cannot break genetic continuity.

  23. Allan Miller:
    CharlieM,

    Actions of developed nervous systems are not a good analogy for the genotype-phenotype system.

    Actions of developed nervous systems are not an analogy for anything, they are what we observe in reality.

  24. Kantian Naturalist,

    I don’t know how much biology today is really genocentric. […]

    This hints at the confusion I allude to again and again between evolution and development. Gene-centricity properly refers to evolutionary phenomena, not developmental ones. Although it’s pretty clear that mutations in DNA indicate a primary role there too. But, no-one is forcing any particular stance on researchers.

  25. CharlieM,

    Actions of developed nervous systems are not an analogy for anything, they are what we observe in reality.

    So are bananas. I only assumed that you imported them to form some kind of analogy for the kind of thing you wanted to assume at the lower level. If you didn’t even mean that, your comment makes even less sense.

  26. Allan Miller:
    CharlieM,

    Wrong. If you radioactively label all the atoms, all the radioactivity will disappear a few cellular generations down the line – from DNA as well as protein and RNA. But, like a Cheshire-Cat grin, the DNA sequence will magically remain, surrounded by its latest secretions. That is what is inherited.

    A totipotent cell is passed down from mother to offspring. From this various forms differentiate while DNA sequence remains basically unchanged.

    In sexual reproduction the change in DNA that occurs between generations due to the construction of the gametes is achieved through the activity of the whole cells being transformed, not just the DNA.

    The way you attempt to isolate DNA is a good example of the abstraction I mentioned.

  27. Allan Miller: I think you are way too seduced by your analogies.

    But I am not the one claiming that DNA must contain “instructions.” 🙂

    Nor am I the one appealing to instructions in a computer, a machine, by way of comparison.

  28. Again, instructions in DNA only make sense in the broader genomic context. Yes, there probably are instructions for how to build webs, but you can’t just pick a set of genes out and put it in to a completely different organism and expect the same result, because the context is missing.

  29. CharlieM: A totipotent cell is passed down from mother to offspring. From this various forms differentiate while DNA sequence remains basically unchanged.

    Because of changes in gene expression caused by interaction between the DNA and the environment.

  30. CharlieM,

    A totipotent cell is passed down from mother to offspring. From this various forms differentiate while DNA sequence remains basically unchanged.

    In sexual reproduction the change in DNA that occurs between generations due to the construction of the gametes is achieved through the activity of the whole cells being transformed, not just the DNA.

    The way you attempt to isolate DNA is a good example of the abstraction I mentioned.

    You have described 1 generation. And, you are far too obsessed with animals. Evolution has a much wider application. I was talking about ‘over the generations’, not the trivial case of a cell and its recent complement of synthesis.

    It is trivial that a cell will be stocked with recently-transcribed RNAs and proteins. The ‘molecular chattels’ in a cell obviously come from a short time ago – from the ‘parent cell’. But what survives over the generations is the DNA sequence – not even the physical DNA, but its sequence. None of the other molecular sequences survive; they are generated afresh from DNA. That includes the sequences that do the generation.

    I can only repeat the exercise I mentioned earlier – if you transplant DNA from one cell to that of another species, what arises (if anything) is determined by the DNA, not by the stock of proteins and small molecules. DNA determines the species that emerges, not ‘the cell’. Your higher control does not reside anywhere. You Are Wrong.

  31. Mung,

    But I am not the one claiming that DNA must contain “instructions.” 🙂

    Nor am I. Nonetheless, it determines all that follows.

  32. Allan Miller:

    Mung,
    But I am not the one claiming that DNA must contain “instructions.”

    Nor am I. Nonetheless, it determines all that follows.

    Endless word lawyering. as if terms like “instructions” are Harry Potter spells.

  33. phoodoo:

    Well, then you must believe if they can just find the gene for web weaving, they can put that gene into a pig, and it will try to swing from branches and squeeze its spinneret glands.

    Allan:

    No. What kind of a moron would expect to be able to do that?

    The question pretty much answers itself.

  34. CharlieM:

    Maybe you could answer the questions I asked Allan?

    Which were:

    When you wrote the answer above what was the controlling factor? Was it you and your thoughts, or was it your DNA, or your genes or what? Do you feel that you are responsible for your own actions?

    My actions originate with my own choices, so in that sense I am responsible for them. Did I ultimately determine the kind of person I would be, and the choices I would make? No, of course not. I didn’t pre-exist myself, so I wasn’t there to determine (or even influence) the factors that gave rise to me. And any influence I’ve actually had over the course of my own development ultimately rests in factors outside of my control.

    Putting that in terms of DNA, I didn’t determine my genetic makeup, nor did I determine the environment in which I would develop, which influenced how my DNA was expressed.

    I know it disappoints you, but there is no woo there.

  35. Allan Miller:
    phoodoo,

    Yup

    So THAT’S how DNA works! The plane has to have a code, And that code wouldn’t work on an Iphone, you can’t tell an Iphone to fly a plane. A plane can’t fly without a code, just like a spider can’t weave a web without the code.

    Now I think I get it.

    Is the code called the Wright Brothers code, named after the inventors of the code?

  36. phoodoo,

    I think you too are getting carried away with an analogy. That’s the trouble with analogies. I knew I was taking a chance in using one.

  37. Kantian Naturalist: I don’t know how much biology today is really genocentric. I do think there was a trend in popular reporting on science when every few months there would be a “scientists discover gene for ____!” article. But I wouldn’t cast any blame on scientific researchers for the shallow and simplistic way that their discoveries are reported to the lay public.

    Yes, facts do indeed get distorted by the media. But whether there is one overarching theory of evolution or there is a multitude of interweaving theories, they virtually all begin from a common assumption. And that assumption is that the direction evolution takes is in no way whatsoever predetermined. It began with one or a few fortuitous events and since then has blindly made its own set of paths.

    Well I think that the evolution of life does have a predetermined path. And the movement towards autonomy that we witness within the various classes and phyla of life is evidence of this path. We see a direction in which various types of organism take control away from the environment that they inhabit.

    For that matter, Talbott is not saying anything that wasn’t said years earlier by well-known biologists, such as Susan Oyama and Brian Goodwin. He’s just able to write for a broader public than they could.

    And Talbott is not saying anything that wasn’t said decades ago by himself. It is just that now he has much more evidence to work with.

    I would say that Goodwins, How the Leopard Changed Its Spots, was written for, and did reach the broader public.

  38. Allan Miller:
    If you transplant DNA from one cell to another, what develops is the ‘DNA organism’, not the ‘cell organism’. One can break the phenotypic continuity, the so-called extra-DNA control, indicating that it is not inherited as such. But one cannot break genetic continuity.

    You are trying to persuade me that DNA is in control by giving me an example of genetic manipulation and control by humans.

  39. Allan Miller:
    CharlieM,

    So are bananas. I only assumed that you imported them to form some kind of analogy for the kind of thing you wanted to assume at the lower level. If you didn’t even mean that, your comment makes even less sense.

    I’d like to make it clear that I never have and never expect to be involved in the importation of bananas. (Not that I have anything against this, I love bananas.) 🙂

  40. CharlieM: Well I think that the evolution of life does have a predetermined path. And the movement towards autonomy that we witness within the various classes and phyla of life is evidence of this path. We see a direction in which various types of organism take control away from the environment that they inhabit.

    Whereas I think that this claim requires either conflating evolution and development or looking at the history of life on Earth with such a strong anthropocentric bias that one prunes away everything that doesn’t lead to us.

  41. CharlieM: You are trying to persuade me that DNA is in control by giving me an example of genetic manipulation and control by humans.

    That’s a nonsensical response. The DNA is transplanted. Just because a human transplanted that DNA doesn’t mean that human is in control of how that DNA interacts with the cell.

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