A neo-neo-Darwinian Synthesis?

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Mike Lynch has a new sweeping paper titled The Origins of Eukaryotic Gene Structure over at Molecular Biology and Evolution. In it he attempts to marry population genetic theory with a broad evolutionary view of genomic architecture. I won’t really attempt to summarize Lynch’s paper, but if you have a biological background I highly recommend it. For those of you who aren’t as fluent in the language of biology the last 2/3 of the paper which focuses on molecular genetics might seem a bit of an alphabet soup (TATA, UTR, mRNA, etc.). But I don’t think the material is fundamentally difficult, and I believe that attempting to digest the details of genuine evolutionary biology which grapples with the microevolutionary dynamics that lay at the root of macroevolutionary diversity can impart to one a better sense of what the science of evolution is all about. For those without access I have uploaded the file as “lynch2005″ in the gnxp forum. Don’t be daunted when the Adobe tells you that it is “38 pages,” as only 18 of them are text (the rest being citations and figures). I will quote a portion of the conclusion though that communicates the thrust of his argument:

Because evolution is a population-level process, any theory for the origins of the genetic machinery must ultimately be consistent with basic population-genetic mechanisms. However, because natural selection is just one of several forces contributing to the evolutionary process, an uncritical reliance on adaptive Darwinian mechanisms to explain all aspects of organismal diversity is not greatly different than invoking an intelligent designer.

This paper represents a first step towards the formal development of the general theory for the evolution of the gene that incorporates the universal properties of random genetic drift and mutation pressure…A significant area of future research will be take these observations on gene and genome complexity to the next level, to evaluate whether natural selection is a necessary and/or sufficient force to explain the evolution of the celluar and developmental complexities of eukaryotes

A few points on this conclusion. Molecular Biology and Evolution is not a popular press publication, so Lynch’s jab at adaptationists is not meant to give comfort to Intelligent Design. Rather, much of his work over the past few decades has been to emphasize that random genetic drift is a very powerful force. The mutational meltdown theory is a case in point. It is interesting to me that Lynch is echoing some of the sentiments expressed in Why Men Don’t Ask for Directions, making an analogy between strong adaptationism and Intelligent Design (The Blind Watchmaker is a lucid and accessible exposition of the adaptationist paradigm). I think the important point about Lynch’s paper is tha it is reflective of the same mentality which suffuses Armand Leroi’s The scale independence of evolution, that macroevolution and microevolution are operational categories which exist for sake of verbal convenience, not fundamentally distinct processes. In discussions with many lay persons who have some familiarity with the “evolution controversies” we almost always stumble over the problem that I do not assume anything of the kind, and I need to go back to ground zero and rework their perception of the models which are genuinely assumed in evolutionary biology. Even if an individual does not subscribe to a Creationist or Intelligent Design theory, they usually accept the terminology, distinctions and arguments put forward by Creationists and ID theorists as coherent and relevant. In reality these talking points emerge out of a parallel intellectual and theoretical culture from that of mainstream evolutionary biology, which, unfortunately, is much more intuitively comprehensible (see my argument in Endless forms most continuous?). In any case, though Intelligent Design proponents argue that evolution is on its last legs it seems to me that the rise of the post-genomic era, bioinformatics and evo-devo all point to a future where evolutionary biology becomes even more robust, with tendrils of consiliated unity arising from the common substrate of molecular biology and the formal language of population genetics.

12 Comments

  1. interesting!

  2. Razib: 
     
    This is a very interesting paper. 
     
    On Dr. Lynch, you write that “…much of his work over the past few decades has been to emphasize that random genetic drift is a very powerful force…” 
     
    Part of his work, yes. But he’s also done quite fundamental work on the evolution of novel gene function (i.e., involving selective forces, among others), and stressing the importance of taking population genetics into account.  
     
    Kumar

  3. Razib, 
     
    Is it really worth your time to joust with the Intelligent Design folks so much? Shaq doesn’t take on the WNBA. 
     
    Steve

  4.  
    Is it really worth your time to joust with the Intelligent Design folks so much?
     
     
    probably not. but alas, since the derb interview a non-trivial # seem to be trickling into the message boards. and unlike ID vs. evolution, the WNBA is not more popular than the NBA…. 
     
    Part of his work, yes. But he’s also done quite fundamental work on the evolution of novel gene function (i.e., involving selective forces, among others), and stressing the importance of taking population genetics into account. 
     
    are you talking about the force et al. paper (i.e., subfunctionalization)? i might comment on more of lynch’s work in the next few months…though some of it is probably too obscure to interst most GNXP readers.

  5. razib: 
     
    No it is not too obscure. it is fascinating.

  6. I find it interesting no connection between this post and Cochran’s Moyziz post was made. If a sizable number of genes have been undergoing selective sweeps, then is natural selection not just one of several forces contributing to the evolutionary process or the major force? And how do you quantify the various ‘forces’ contributing to the evolutionary process? Is there a way to actually measure evolutionary forces in a similar way physical forces are measured? Or is the statement ‘random genetic drift is a very powerful force’ no more rigorous than an adaptationist argument. 
     
    I recall Pinker making the comment that gentetic drift occurs, but at some point it’s likely that selection will act on the genes. It doesn’t seem likely that we can determine whether or not certain genes were under strong selective forces at some point in the past without resorting to adaptationist argument. Did humans start walking upright due to genetic drift or selection acting on genes that contributed to an upright gait? 
     
    I’m also curious as to the accuracy of the statement the microevolution and macroevolution are “not fundamentally distinct processes.” Is that an assumption, a proven fact, a philosophical bias-like saying quantum mechanics and general relativity HAVE to be reconcilable, though in reality they are not reconciled? Are the processes similar, but the details differ. And what makes one process ‘fundamentally’ distinct from another? 
     
    For example, much has been written, mostly by David B, about how cultural evolution is not like biological evolution. But are the differences in the details or the process itself. In other words, can you use the same model with both processes, but change the details and parameters, or is an entirely process required? 
     
    Since cultural evolution is at root a biological phenomenon, should the processes really be viewed as distinct? And if they are distinct, can a similar argument be made to make a distinction between micro and macro evolution.

  7. selection vs. drift: one common assertion is that if s, the selection coefficient, is > than 1/(2Ne), where Ne is effective population, than selection is stronger. as Ne drops, than drift becomes stronger. remember, in a population of large size the probability of fixation is 2s, where s is the selection coefficient, and the power of sampling variance between generations is weak and so can be ignored. in a small population sampling variance is powerful, i.e., probability of fixation becomes 1/(2Ne) as s is usually small enough to be discarded. 
     
    Did humans start walking upright due to genetic drift or selection acting on genes that contributed to an upright gait? 
     
    not to be trite, but check to see the Ks vs. Ka ratios on those genes! :) check our RPM’s detecting natural selection for details. 
     
    ike saying quantum mechanics and general relativity HAVE to be reconcilable 
     
    the analogy is weak becauase ‘macroevolution’ (to my knowledge) has little theory. much of what is macroevolution that is decoupled from microevolution is simply (from what i know) description, rather than a general model. in other words, macroevolutionary phenomenon are simply the gross large scale manifestations of microevolutionary processes. some thinkers, like s.j. gould and niles eldridge, have tried to argue that macro processes are different and exhibit emergent properties. they are a minority view from what i can glean.

  8. Razib, thanks for the equation, but how do you determine s and wouldn’t you need to know something about historical population sizes? 
     
    And thanks for the link, but do we know what genes code for a trait like walking upright? And if a gene becomes prevalent in a subpopulation thru drift and that subpopulation remixes with the larger population where selection then acts on the gene, would Ks vs Ka ratio test to determine selection still work? 
     
    Finally, I think my analogy is more apt than you give it credit for. With the QM/GR dichotomy, the mathematics at one level is not reconcilable at the other. My question then involves the modeling at one level scaling up to another. The question is does it? You seem to be pretty confident it does. I feel uncomfortable siding with Gould on anything, but I may have to on this one. 
     
    Now, I don’t know much about biology and even less about molecular biology, but I do know something about modeling. It’s trivial to be reminded that modeling by nature is only an approximation of real world processes and if the same model is used to model two different processes, it doesn’t mean the processes are fundamentally the same. It could be we’re trying to stretch one model that works well with one process to another process regardless of how well it actually models that process or phenomenon. 
     
    P.S. Here’s what I hope to be an amusing anecdote regarding intuitiveness of evolutionary biology and specifically speciation. I was talking to a friend who grew up in a very fundamentalist home and had rebelled against that upbringing and turned into a staunch atheist and fully accepted evolution. He is reasonably intelligent, but not especially well educated. One day we were discussing evolution when he said that the founder of a species had to be an hermaphrodite!

  9. Razib, thanks for the equation, but how do you determine s and wouldn’t you need to know something about historical population sizes? 
     
    re: s, easier to calculate in laboratory than in the field. basically it is the difference between the fitness of those carrying allele x vs. mean population fitness.  
     
    re: population sizes, again, easy to control in laboratories. this is why drosphila is so big. harder to calculate in the context of populations in the wild, but not impossible to calculate long term effective population via assays of neutral markers (signatures of population bottlenecks and as well as lack of functional constraint, etc.). 
     
    but do we know what genes code for a trait like walking upright? And if a gene becomes prevalent in a subpopulation thru drift and that subpopulation remixes with the larger population where selection then acts on the gene, would Ks vs Ka ratio test to determine selection still work? 
     
     
    in the long term, yes. 
     
    With the QM/GR dichotomy, the mathematics at one level is not reconcilable at the other. My question then involves the modeling at one level scaling up to another. The question is does it? You seem to be pretty confident it does. I feel uncomfortable siding with Gould on anything, but I may have to on this one. 
     
    i am aware that QM is probabilistic while GR is classlica/deterministic, that there is a fundamental paradigm dichotomy. the short of it is this: there is no math in macroevolutionary “models” which are fundamentally different from microevolutionary ones. i have seen work on mathematical expositions of speciation and panspecies evolutionary dynamics, but they are always extrapolations of ‘microevolutionary’ processes (drift, selection, etc.).  
     
    let me give you an illustration. in macroevolutionary systematics, where you compare across many taxa (consider the chordates), you often use ribosomal RNA because they are functionally constrained and so the “molecular clock” on these regions of the genome tick VERY slowly. on the other hand, if you want to compare across a singular species, something like mtDNA is far better because the clock for this ticks MUCH farther. finally, if you want to make distinctions within a subpopulation (i.e., molecular confirmation of pedigrees) you would want something like variable number tandem repeats (VNTRs) which are highly differentiated between individuals, even closely related ones. the point is that the general concept/process is the same, the generation of a ‘constant’ rate of genetic variation as a proxy for geneological distance. eldridge and gould would have you accept things like taxon level selection and stuff from what i can remember. i’ve read anthologies where eldridge contributes, and i notice no mathematics. the models are purely verbal.

  10. This is an interesting paper. I wonder how the following article relates? 
     
    Earliest Animals Had Human-like Genes 
     
    http://hum-molgen.org/NewsGen/11-2005/msg60.html 
     
    ?The genes of animals usually contain extra bits of DNA sequence, called introns ? information which has to be removed as cells create new molecules. The number of introns in genes, however, varies greatly among animals. While humans have many introns in their genes, common animal models such as flies have fewer. From an evolutionary perspective, it was long assumed that the simpler fly genes would be more ancient. The current study reveals the opposite: early animals already had a lot of introns, and quickly-evolving species like insects have lost most of them.?

  11. Sperm filtering adds significant selection to a subset of the human genome. Does that subset show significant differences compared to the non-sperm-filtered genome? Do sperm-filtered genes have fewer introns?

  12. I would summarize this paper as explaining the evolution of ?gene-architectural complexity? as a biological example of the ?simulated annealing? algorithm with the inverse of ?effective population size? playing the role of ?heat?.

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