Maintaining neutrality

Blogger Bilbo, an occasional visitor here, has paid a rare compliment to biochemist and creationist-witchfinder Larry Moran for his clear explanation of the difference between neutral theory and genetic drift.
Moran’s intention is to clarify a post by biologist P Z Myers, and it succeeds. Myers’ “strapline” is that near-neutral theory has “won”, over adaptationism:

The neutral theory states that most of the variation found in evolutionary lineages is a product of random genetic drift. Nearly neutral theory is an expansion of that idea that basically says that even slightly advantageous or deleterious mutations will escape selection — they’ll be overwhelmed by effects dependent on population size. This does not in any way imply that selection is unimportant, but only that most molecular differences will not be a product of adaptive, selective changes.

Note the nod to the (unspecified) importance of natural selection. Moran’s piece leaves that out, and says:

What Neutral Theory tells us is that a huge number of mutations are neutral and there are far more neutral mutations fixed by random genetic drift that there are beneficial mutations fixed by natural selection. The conclusion is inescapable. Random genetic drift is, by far, the dominant mechanism of evolution…

Replying to objectors, he goes on:

They think that random genetic drift is only important when the alleles are neutral (or nearly neutral). Then they use this false equivalency as a way of dismissing random genetic drift because it only deals with “background noise” while natural selection is the mechanism for all the interesting parts of evolution. I think we should work toward correcting this idea by separating the mechanisms of evolution (natural selection, random genetic drift, and others) from the quality of alleles being produced by mutation (beneficial, detrimental, neutral)…

…The revolution is over and strict Darwinism lost. We now know that random genetic drift is an important mechanism of evolution and there’s more to evolution than natural selection. Unfortunately, this blatantly obvious fact is not understood by the vast majority of people and teachers.There are even many scientists who don’t understand evolution.

If I had £10 for every time I’ve heard people use that last sentence as a jibe (Jerry Coyne used it of James Shapiro, for example), I would be rich! Phylogeneticist and population geneticist Joe Felsenstein (there are big hitters on this thread, as you see) protests slightly in a longish comment:

I am not sure what has been proven:

…2. That the many adaptations that we see are not the result of natural selection? Gould and Lewontin made the point in their “Spandrels of San Marco” paper that we could not assume that any adaptation we saw was itself directly brought about by natural selection for that purpose. But the high level of adaptation of living systems (a level they have to have, else they could not survive and reproduce) must have been the result of natural selection. Mutational processes alone and/or genetic drift alone just could not have made a bird that flies or a fish that swims, not ever.

…I think that it would be a tragedy if the promotion of a series of newer and newer evolutionary theories causes people to forget the one important point — that if there is no natural selection you will not get (or maintain) adaptations.

Pause to note the basis of his argument here – I’ll return to it later. Various other comments bring us to the happy conclusion that nobody is really disagreeing (perhaps after somebody mentioned that creationists might pick up on the argument!). There’s room for both selectionism and neutralism. Somehow the agreement seems superficial, and Tom Mueller’s remark on the thread bears careful reflection:

I think what needs to be understood here is the concept of “theory” as working “model” that can crank out useful answers in deliberately and precisely defined (perhaps even contrived) situations.

The whole thing needs to be seen in the context of Moran’s overall position, and that is helped by reading (a long read, I’m afraid) a series of posts he hosted in 2010, by Arlin Stoltzfus, on The Mutationist Myth. I won’t try to reiterate all his arguments, which you can read yourself, but his thesis is, in the end, that the Neo-darwinian synthesis got its view of evolution fundamentally wrong in various centrally important ways, partly by disregarding the importance of mutation for evolution (preferring to emphasize gene pools and changing frequencies), but mainly by inheriting Darwin’s view that organisms are closely adapted to their environments.

So he argues that mutationally-based theories such as the near-neutral theory are a replacement for, not a mere adjustment of, the Modern Synthesis. This would seem not to be an isolated view (at least Larry Moran concurs) – and his reasoning certainly makes a good case for it. The fact that neutral theory retains some place for natural selection, then, does nothing to detract from the fact that the long-running neutralist-adaptationist debate, despite evolution’s being an incontrovertible fact as sure as gravity, etc etc, has been a Malthusian struggle for survival between two entirely different concepts of evolution. Read the Stoltzfus series and you’ll agree, I think.

Understanding this (even if, as seems inevitable in such a climate, you don’t understand evolution) can help give a context for a paper like that of Austin Hughes (2008) , looking at an in-the-field (rather than theoretical) example, the evolution of rhodopsins in the eye, demonstrating that it best fits a pattern of non-adaptive evolution. He claims the role of positive selection is often over-emphasised (actually he claims that it is carelessly and wrongly assumed in most published research):

Contrary to a widespread impression, natural selection does not leave any unambiguous “signature” on the genome, certainly not one that is still detectable after tens or hundreds of millions of years. To biologists schooled in Neo-Darwinian thought processes, it is virtually axiomatic that any adaptive change must have been fixed as a result of natural selection. But it is important to remember that reality can be more complicated than simplistic textbook scenarios.

TOF’s recent post is applicable here: as soon as near-neutral fixation and selection are both operating together – plus alternative splicing, overlapping genes, epigenetics, cultural inheritence and so on, all mutually interacting – you have a case of “organised complexity”  that makes makes understanding specific outcomes harder than predicting the path of individual ice-blocks in Saturn’s rings. Michael Clegg writes:

It is simply not possible to incorporate the complexities of variable selection driven by temporal and spatial environmental change together with drift, migration, and demographic structure into a comprehensive model that is susceptible to analysis. Yet, evolution is actually determined by the continuous operation of these and other factors. Thus, while the conclusions of population genetic models are mathematically true, they may not always contribute to empirical knowledge.

…It is also important to realize that the limits to knowledge in population genetics, and hence also the limits to knowledge in the allied sciences of molecular evolution and conservation biology, are not obvious. Workers in these fields have only come to a partial appreciation for the limits of knowledge as they have explored the empirical content of population genetic theory over a period of more than sixty years.

It’s because of arguments like these that Eugene Koonin’s 2009 overview  (which I cited in a recent comment) echoes Myers’ obligatory hat-tip to adaptive selection, but severely downplays its actual importance:

Natural (positive) selection is an important factor of evolution but is only one of several fundamental forces and is not quantitatively dominant; neutral processes combined with purifying selection dominate evolution.

And:

The majority of the sequences in all genomes evolve under the pressure of purifying selection or, in organisms with the largest genomes, neutrally, with only a small fraction of mutations actually being beneficial and fixed by natural selection as envisioned by Darwin.

You may feel the technicalities of all this go over your head (I urge you to read the Stoltzfus series anyway, though, as the history is interesting). But let me tell you what seems to be the bottom line. Darwin’s use of natural selection was to explain, in lieu of  a creator, why he found nature to be so exquisitely crafted, seeing selection as:

…daily and hourly scrutinizing, throughout the world, every variation, even the slightest; rejecting that which is bad, preserving and adding up all that is good; silently and insensibly working, whenever and wherever opportunity offers, at the improvement of each organic being in relation to its organic and inorganic conditions of life.

Long-tailed Tits

This observational belief (from one of history’s great field naturalists) seems to have inspired Felsenstein’s comment on Moran’s blog. Felsenstein doesn’t really argue the theory – he just appeals to the eyes of the beholder of actual nature. But it is here, whatever the differences in theory, that the fundamental disagreement lies. Stoltzfus, in his last post of the series, writes of Neodarwinist adaptationism:

And this problematic view of variation is based on reasoning from the premise that organisms are exquisitely and pervasively adapted to their niches, to the conclusion that variation must play just the right role of supplying abundant raw materials to make this possible. I believe that there is something fundamentally wrong with this mode of reasoning. Perhaps it betrays a kind of subconscious Panglossian agenda.

The difference, then, is that near-neutral theorists tend to interpret what they see in nature as showing that organisms are not superbly adapted to their environments, contra Darwin’s “Panglossian” rose-tinted view. Theoretical technicalities aside, it’s a question not merely of how evolution enables survival, but whether it has produced a jerry-built bodge, or “endless forms most beautiful.”

“Understanding evolution” is one thing – but here we’re talking about the things that have struck awe into field biologists from Aristotle onwards – the giraffe’s specialisations for height, the mole’s for digging, the octopus’s camouflage, the compound eye at the very theoretical limit of optical possibility, the eagle’s camera eye spotting rabbits a mile away, the orchids matched to their many individual pollinators – those things that in the past made nature a byword for “perfection” and “wisdom.” Naturalists find that level of adaptation in any organism they study. They even see it in the lion that kills its step-children, if one finds the selfish-gene a beautiful concept. They see it in the ecosystems that organisms comprise. They see it in the totality of the interdependent biosphere.

But the neutral theorists, looking at the same things (assuming they get out into the natural world, which I suppose isn’t necessarily so) see mostly imperfections – and their theory, apparently the more correct, is bound only to deliver imperfection. They see what their theory predicts. But so do the adaptationists, so who’s right? Neutral theory’s father, Moto Kimura, hedged his bets:

Kimura argued that molecular evolution is dominated by selectively neutral evolution but at the phenotypic level, changes in characters were probably [my emphasis] dominated by natural selection rather than genetic drift. (Wikipedia)

Positive selection, then, is “rare” and a “departure from the norm” (Austin Hughes, op cit), but nevertheless manages to account for the myriads of wonderful features we actually see all around us, and yet these are in some sense independent of the genetic level of organisation responsible for them. Why would that work? “The F1 car works fine, but the components were taken from a skip and assembled by monkeys – but hey, an engineer dropped by every few days too.”

“Adaptation” is a word we all learned in school biology – but in Felsenstein’s comment it’s actually loaded in favour of his preferred explanation. “To adapt” means to change something to fit a role, which is what natural selection does by dint of killing everything that doesn’t fit – assuming positive selection is working effectively, contra neutral theory.

If forms and behaviours in fact arise by neutral mechanisms and happen to work astonishingly well, they are not “adapted” but preposterously lucky: remember, selection is not operating on them, or it would still be strict Darwinism at root. Similarly, I suppose, if these forms and behaviours were created by God, they would not be “adapted” any more than Beethoven “adapted” Eroica as a symphony: they would be designed for purpose.

But admitting “adaptation” as a descriptive term, let me summarise some propositions that seem to arise :
(1) Neutral theory appears to fit the scientific data better than adaptation theory.
(2) Neutral theory appears to account for most changes in evolution: adaptation is the exception, not the rule.
(3) Neutral theory itself has no capability whatsoever of producing any degree of adaptation, unless it allows a final controlling role to natural selection, which its proponents appears to deny.
(4) Adaptation, nevertheless, is the most pervasive feature observed in biology.
(5) We therefore appear to lack an adequate evolutionary explanation for the most pervasive feature in biology.

What did I miss here? Probably, the detailed unpacking of how the two theories (and all the others) interrelate in real life – but there was remarkably little reference to that on the Moran thread. It surely can’t be good enough to shrug and say, “A little adaptation goes a long way.”

giraffe-weevil

Jon Garvey

About Jon Garvey

Training in medicine (which was my career), social psychology and theology. Interests in most things, but especially the science-faith interface. The rest of my time, though, is spent writing, playing and recording music.
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18 Responses to Maintaining neutrality

  1. Lou Jost says:

    This is mostly a good post!

    However, some of the conflicts you highlight are not real conflicts, and some of the positions of the players in this debate are over-zealous. The debate about the relative importance of adaptation versus neutral evolution hinges entirely on what is meant by “importance”. Everyone agrees that most change, at the level of DNA, is nearly neutral. At the same time, nearly everyone who gets out of their lab and looks at nature can see that many phenotypic characters are not neutral. You insightfully said of neutral theorists: “…Assuming they get out into the natural world, which I suppose isn’t necessarily so”. Larry Moran in particular is a lab guy who has little or no exposure to nature in the wild, and his posts reflect this hole in his knowledge. He speculated, for example, that a zebra’s stripes might be a neutral character. Anyone who has spent much time hunting animals (either for sport, for photography, or for study) will be aware of the many ways that color and pattern (especially in babies) affects detectability and hence survival. He also wrote a post wondering why a jacaranda tree (which he could not identify) would have flowers shaped and colored as they are, implying that these characters might be random.
    http://sandwalk.blogspot.com/2013/06/name-this-tree.html
    There are in fact suites of very specific adaptations to pollination by a given agent, and these adaptations are very similar in most of the flowers pollinated by that agent, even when the flowers belong to completely different families.

    Even characters that might at first sight seem neutral, such as leaf margin serrations, or whether a plant has compound or simple leaves, often turn out to have selective value when careful measurements are made (and these characters cluster in particular habitat types, even across families, confirming the lab observations). I am sure that many characters really are neutral, but many of the most conspicuous ones are demonstrably adaptive. This includes many characters involved in camouflage and mimicry.

    So, my take on your final list of propositions:
    “(1) Neutral theory appears to fit the scientific data better than adaptation theory.”
    No. Neutral theory best describes the majority of changes in DNA bases, but adaptation theory best describes most macroscopic characters (though there are also many neutral characters).

    “(2) Neutral theory appears to account for most changes in evolution: adaptation is the exception, not the rule.”
    Depends entirely on the kinds of changes we are talking about, DNA changes or phenotypic ones.

    “(3) Neutral theory itself has no capability whatsoever of producing any degree of adaptation, unless it allows a final controlling role to natural selection, which its proponents appears to deny.”
    Hmm, not exactly. As you’ll remember from Gould’s spandrels, neutral variation can accidentally produce changes that later may be adaptive. Characters that are initially neutral can become fixed in the population, and these may become adaptive if the physical or genetic environment changes. This happened in Lenski’s citrate eating bacteria. (Also, and this is an important point Larry made, under certain well-defined circumstances, maladaptive genes can be fixed in a population by drift.)

    “(4) Adaptation, nevertheless, is the most pervasive feature observed in biology.”
    Most pervasive when looking at conspicuous morphological traits, yes.

    “(5) We therefore appear to lack an adequate evolutionary explanation for the most pervasive feature in biology.”
    Darn. Up to here this post was pretty good. But this last statement is malicious. Jon, you know that variation occurs across the whole genome. Most of that variation has little effect on phenotype (this is the point of the neutralists), but some of it does (no neutralist would say otherwise– the literature is piled high with proof that genetic variation sometimes affects non-neutral traits). Natural selection (+ drift in these non-neutral mutations) explains when and why mutations that are adaptive will spread. You are inventing a mystery or conflict here when there is none.

    • Jon Garvey Jon Garvey says:

      I was definitely being provocative. But I think the conflict is real, if only from seeing it expressed by its various proponents over the years, not only in the blogs but in papers I’ve read. I referenced too much external material as it was – could have done more.

      I agree that the lab v field divide seems significant – but that’s bound to awaken the suspicion that there is a genuine mismatch between the molecular and the phenotypic evidence: the very fact that experts in the field have, for many years now, failed to acquiesce in your “nothing to see here” resolution suggests either more problems than meet the eye or more professional blinkers than ought to exist. But I think it’s significant that as a field naturalist, the ubiquity of adaptation is self-evident to you: you’re that side of the divide, in other words. We lack a molecular biologist here – though a couple of geneticists lurk.

      I’m still not convinced that the overwhelming predominance of neutral changes at the micro level (at which the lab boys excel) actually leaves sufficient room for the degree of adaptation seen at the macro level (which field people study, and tend to treat via the mathematical modelling of pop. gen). It is the sum of the micro that explains the macro, after all – unless perhaps that is less the case than supposed. As far as my limited reading allows, I’ve been looking for papers that resolve that dysjunction – and so far have seen detailed papers that accentuate the problem, and general reviews (like yours, perhaps) which minimise it.

      And that’s why I still think there’s a story hiding in the detail, so far untold at least to my satisfaction – and it seems to me to folks like Moran and Koonin too. That is, how does phenotypic adaptation work so well when so heavily outweighed by neutral molecular changes? It’s compounded, again from what I’ve read, by the very real doubts about the reliability of the tools used to assess selection (eg Clegg’s and the other two papers from that book). So that’s why for a leading worker like Felsenstein to base his argument on “there must be selection – we see it all around” seems to raise a problem for research rather than to help settle a long-running dispute.

  2. Lou Jost says:

    “…You’re that [adaptationist] side of the divide, in other words.”
    I don’t think of myself as on one side of the divide or the other. Rather, I don’t see a divide. I constantly use neutral segments of DNA for my phylogenetic work, and I suspect that initially neutral variation in flower traits of my orchids (and colors in birds) eventually may have adaptive significance and may be one of the driving forces of speciation. My main mathematical paper in population genetics identifies the genetic and demographic factors controlling divergence of neutral alleles between partially-isolated populations, and is intended as a guide to conditions favorable to speciation.

    There is conflict only when someone (like Larry M.)begins to suggest that most conspicuous phenotypic features are neutral. This does not follow from the ubiquity of neutral variation in genomes (most of which appears to have little or no function–pace ENCODE!), and is held mostly by people who don’t get out much….

    But even Larry, when he is not deliberately trying to be provocative (I wish writers wouldn’t do that), is really only arguing that trait neutrality should be the default assumption unless proven otherwise. I’d still disagree and say that a naturalist’s knowledge of how organisms fit into their environment should count for something, though it should not be a substitute for actual testing of hypotheses. But that is a relatively minor quibble about burden of proof, not a fundamental rift in our understanding of evolution.

  3. Lou Jost says:

    “The majority of the sequences in all genomes evolve under the pressure of purifying selection or, in organisms with the largest genomes, neutrally, with only a small fraction of mutations actually being beneficial and fixed by natural selection as envisioned by Darwin.” –Koonin (as quoted in your post)

    “Purifying selection” is one kind of natural selection, and even the quote you give from Darwin shows that Darwin did not think of natural selection only in terms of beneficial mutations:

    “…daily and hourly scrutinizing, throughout the world, every variation, even the slightest; rejecting that which is bad, preserving and adding up all that is good..”—Darwin

    Koonin’s “purifying selection” is what Darwin describes as “…daily and hourly scrutinizing, throughout the world, every variation, even the slightest; rejecting that which is bad…”

    Of course Darwin didn’t know the math behind genetic drift so he didn’t realize that natural selection cannot always reject the bad. That is an important thing about evolution that we learned post-Darwin.

    • Jon Garvey Jon Garvey says:

      Lou

      I’ve presented my case from my sources, and I don’t want to prolong the discussion overmuch. I mentioned Darwin only to show he was impressed with adaptation: he found Paley’s watch on the Heath and concluded natural selection was the gifted designer. But I don’t think you can justly argue that he and Koonin are actually saying the same, the latter just filling a few gaps, when he lists six major tenets of Neo-darwinism as needing revision and three as falsified.

      Darwin saw selection as a vigilant livestock breeder, intent on improving the line and breeding only from the best – maybe even sending the rest to slaughter if they were cattle or racehorses. His idea of “good” and “bad” is of tiny variations about the mean which only an expert can exploit.

      For Koonin, the vast majority of variations are near-neutral and totally unseen by natural selection. They include phenotypic variations – for example, my own unconjugated hyper-bilirubinaemia is mildly deleterious but extremely unlikely to affect reproduction; at any rate it’s a dominant trait. So too is my mild astigmatism, squinting down several generations of excellent riflemen.

      On one side of that high ridge of accumulating near-neutrality are seriously deleterious mutations, which are subject to purifying selection, that is they are seriously detrimental. Purifying selection is a dog warden shooting mangy strays, not a breeder competing for prizes.

      On the opposite side of the near-neutral rockies is a comparatively tiny number of advantageous mutations subject to positive selection. It is such a small percentage compared to the rest that I’ve yet to see a paper that quantifies it in terms other than “too low to measure”. They also will accumulate, but will themselves be subject to moderately-deleterious mutations that can become fixed by drift (Moran), and these will be far, far commoner than further advantageous improvements fixed by positive selection. My question was how that disproportionately small proportion of the mass is sufficient to account for all the adaptation that Darwin saw in nature (and I won’t even get into the development of new bauplana). I don’t think your answer is persuasive.

      How do I know Darwin and Koonin are at variance? Simply because Darwin says so, in the last page of his first edition:

      “And as natural selection works solely by and for the good of each being, all corporeal and mental endowments will tend to progress towards perfection.”

      By contrast, Koonin says:

      “There is no consistent trend towards increasing complexity in evolution, and the notion of evolutionary progress is unwarranted.”

      If that isn’t chalk and cheese, then Stalin was the Pope. Incidentally, Darwin is being philosophically pretty vague in that statement. “The good of each being” could use some definition: “each being” clearly isn’t the majority of individual beings that lose out in his “struggle for existence”. Nor is it the “being” called a species, which is an evolving continuum he argues against defining in ch 2. He still seems to be thinking as a Victorian livestock breeder, “improving the line” towards an equally undefined idea of “perfection” (which maybe means winning a rosette at the local show?).

      • Lou Jost says:

        Jon, my comment addressed a much narrower point. Koonin talks about purifying selection as if it were different from natural selection. This is false. Your own quote from Darwin, just below Koonin’s quote, shows that Darwin understood natural selection to include purifying selection (“rejecting that which is bad”).

        The important point that Darwin got wrong was, as you mention, the idea that organisms constantly “improve” in any given trait. Both Darwin and his critics thought that intermediate steps in evolution must each be advantageous. Population genetics now shows that this is not true. Populations explore a much larger space than early Darwinists had imagined, so that evolution is a much more effective solution-finding process than previously thought. Small local valleys in fitness can be crossed (and we have a precise understanding of how large those crossable valleys can be, relative to population size).

        I’m not sure why this sort of thing excites people who think evolution needs a guiding hand from a god, since it reveals that the speed and power of naturalistic evolution is greater than Darwin and Wilberforce imagined.

        “My question was how that disproportionately small proportion of the mass is sufficient to account for all the adaptation that Darwin saw in nature (and I won’t even get into the development of new bauplana). I don’t think your answer is persuasive.”

        But the arguments you give here have no bearing at all on that particular question. You can see the logical flaw by imagining two almost-identical organisms, differing only in that one has no junk DNA and the other has a vast amount of junk DNA. The two have vastly different relative “masses” of neutrally-evolving DNA. Indeed, by increasing the amount of junk DNA, I can arbitrarily get the proportion of neutral variation versus functional variation as close to 100% as I want. But the actual number of traits available to natural selection are exactly the same in the two organisms. The addition of neutral variation doesn’t matter at all.

        • Jon Garvey Jon Garvey says:

          Again, the devil’s in the detail, Lou. According to that fount of wisdom, Wikipedia, in protein coding genes in Drosophila, where the best work has been done, frankly deleterious mutations amount to 70%, and “the rest” to weakly deleterious or beneficial (ie, near neutral, non-selected) mutations.

          That is, the positively selected proportion is neglible, or at least undetectable (for which I’ve heard various explanations about how what’s beneficial in one situation is deleterious in another, and so on: but lack of evidence is still lack of evidence).

          My analogy, then, was based on protein-coding genes. Adding the rest of the genome, even if all of it were junk, would simply add to the near-neutral pile and make the maths worse.

          • Lou Jost says:

            OK, that is a clearer argument, but you may be mixing up two claims. Note that your argument in this comment is NOT consistent with the argument you gave from Koonin and other “neutralists” in the main post. In this comment you say that in the Drosophila protein-coding DNA, 70% are frankly deleterious, while in your post you used Koonin and others to argue that
            “…. the vast majority of variations are near-neutral and totally unseen by natural selection.”

            I suppose the discrepancy is due to sometimes taking the whole genome as the unit of analysis, and other times taking protein-coding alleles as the unit of analysis.

            In any case, even for protein-coding genes, I would think the important number is not the proportion of neutral or deleterious mutations versus beneficial ones, but rather the absolute frequency of beneficial ones. And yes, that latter number is very very low. Lenski’s bacteria cultures are giving us some clues about that number. While low, it is not undetectable any longer. But it required a lot of work to estimate!!!

            And yes, whether a mutation is beneficial or not depends on the environmental and genetic context.

            • Jon Garvey Jon Garvey says:

              Lenski’s work seems to endorse my main point, in that there were astonishingly few minor modifications (was it 3 or something?), mostly deleterious in terms of actual biochemical function, if advantageous in the experimental setting in enhancing an existing ability to metabolise citrate.

              That experimental setting essentially simplified the selection pressure to a single simple parameter: citrate tolerance. It’s a population genetics abstraction on a petrie dish, which I suppose is a necessary constraint in that kind of experiment but, once more, is reductionist considering the multiple interactions in a wild setting.

              And to obtain them how many generations, and what population size? And what comparison does that have with advanced eukaryotes having a slow generation time, a small population, a complex environment and (in the case of chimp/man divergence) many thousands of individual new phenotypic traits, including the small matters of upright gait. advanced intelligence, language etc.

              Lenski’s work certainly has little to do with Koonin’s stuff on purifying selection, which was mostly in the context of small populations of sexually reproducing animals.

              Incidentally when Dennis Venema wrote about Lenski’s work on BioLogos he said (citing a paper, if I remember) that this work was not far from a speciation event. He seemed pretty quick to disown that when I challenged it. But if I or a creationist had said it, melanogaster would certainly have said I didn’t understand evolution, I suspect.

              • Lou Jost says:

                Your characterization of Lenski’s experiment is wrong in important ways.

                “[Lenski’s] experimental setting essentially simplified the selection pressure to a single simple parameter: citrate tolerance.”

                No, citrate was a standard chelating agent in the medium and, as far as I know, nobody thought it would play any role in the experiment. The experiment was designed to look for adaptation to a standard minimal medium. The mean fitnesses of Lenski’s clones all rose rapidly during the early generations; citrate metabolism played no role in this.

                Lenski estimates about 100 mutations were fixed in each of the 12 culture (many of these would be different in each culture, so the total number of mutations fixed in the whole population would be much greater than 100). Of these 100, about 10-20 per culture were beneficial according to Lenski (as quoted in Wikipedia). So most mutations were neutral, but a significant proportion were beneficial, and these were enough to raise fitness greatly.

                One culture developed the ability to turn on its citrate-using machinery even in the presence of oxygen (normal E coli can’t do this, and this is the basis of standard lab tests for confirming the presence of E coli in a sample). This innovation did not offer a huge advantage at first, but later mutations refined the genome and made this culture vastly more fit (in the experimental environment) than the original strain.

                Your criticism that this is an oversimplified situation is unfair; they are looking at whole, complex organisms and examining the whole genome for effects. It is holistic.

                Its relevance for complex, slowly reproducing eukaryotes is unclear, but these bacteria are evolving with an enormous handicap relative to complex eukaryotes–E coli is asexual, so all the beneficial mutations have to arise in the same lineage. This is orders of magnitude slower than in complex eukaryotes, where sex can mix novelty from different lineages.

              • Lou Jost says:

                I don’t remember the speciation discussion with Dennis. Discussions of speciation in non-sexual organisms are always going to be as much about definitions of species as about reality.

                But if these had been complex sexual eukaryotes like orchids or birds, the species concept is clearer. There would have been two speciation events if sexual eukaryotes had been involved. The first would be driven by the initial rapidly-evolving differences in fitness between habitats: the experimental organisms all became specialists on the experimental medium, and out-competed the wild strain there, but were out-competed by the wild strain in the “normal” habitat. In eukaryotes, once you have that, hybrids between the types are usually less fit than either pure type. This will strongly reduce gene flow between the types, and eventually neutral and adaptive genetic differences lead to genetic incompatibilities, causing reproductive isolation, the criterion for speciation in sexual organisms.

                The second speciation event would be between the ordinary experimental cultures and the citrate-users, only in this case the new species would take over all the habitat of the parent species, if the habitats were not completely isolated from each other.

                A fossil hunter digging at a single site would notice a sudden change as the new type took over. Unless he or she were very lucky, he wouldn’t be digging in the one little spot where the change occurred gradually.

  4. Lou Jost says:

    I had time this afternoon to look at the Austin Hughes article you cited about rhodopsin optimization. It is basically the same story as the evolution of citrate use in Lenski’s bacteria: a couple of nearly neutral mutations that spread by drift, followed by a mutation that, in the presence of these neutral ones, improves fitness. The fixation of these now-adaptive suites of genes takes place by natural selection.

    It is interesting to remember that this is exactly the mechanism biologists mentioned years ago to show why Behe was wrong about the “Edge of Evolution”. Behe claimed that three particular mutations would virtually never arise simultaneously in an organism, so a novelty that required three mutations would never evolve. Because of genetic drift, the condition of simultaneity can be relaxed. Populations store vast amounts of “silent variation” which a single mutation can convert to something useful.

  5. GD GD says:

    Another paper that challenges neo-Darwinism is a review by Jablonka and Lamb, “Soft inheritance: Challenging the Modern Synthesis”, Genetics and Molecular Biology, 31, 2, 389-395 (2008). I am not providing an analysis for this review, but point out the clear statements by these authors, summarised in their Abstract as:

    “….These discoveries are clearly incompatible with the tenets of the Modern Synthesis, which denied any significant role for Lamarckian and saltational processes. In view of the data that support soft inheritance, as well as other challenges to the Modern Synthesis, it is concluded that that synthesis no longer offers a satisfactory theoretical framework for evolutionary biology.”

    I think ideologues of Darwinism cannot hide behind claims of ‘quote mining’; I find it amazing that even though the very pillars of Darwin’s views have been either demolished, or shown to be simply incompatible with our common understanding of ‘laws of science’ (i.e. natural selection as a clear and quantifiable law of science), these ideologues will stubbornly cling to their prejudiced views (against the evidence!!!)

    This review commences with the following introductory statement, “There are winds of change in evolutionary biology, and they are blowing from many directions:…” and they list the major areas which provide ‘the winds of change’.

    Just what would this area of constant conflict and disagreement provide as a new paradigm? I am sceptical on this point, for the obvious reason that Darwin’s views have found major uses in areas outside biology, and this will continue to hamper attempts that break away from ideology and instead show the focus and discipline required for genuine scientific effort. It is more than ironic that these same people claim they are not blinkered and instead claim scientific objectivity – clearly they have deluded themselves, and instead cling to their nonsense because it fits in with their belief of a purposeless and pointless Universe and an accidental and nihilistic existence for the human race.

    • Jon Garvey Jon Garvey says:

      GD

      It seems to me the issue at the “sociology of science” level has largely to do with tribal identity. A good number of innovators, some very experienced and prestigous, present their views quite clearly as constituting dissent from, and a challenge to, Neodarwinian theory. Jablonka is one, but Shapiro has done so, as has Margulis, Noble, Kauffman and many more, all from different directions (as your Jablonka quote intimates).

      Staunch Neodarwinians react either by marginalising these people as self-promoters (or sometimes as creationists!), or by saying there is no real disagreement, and that all is compatible with the Modern Synthesis. Even the dissenters are wont to close ranks in the face of “common enemies” such as actual creationists, who might otherwise see the dissent and … say there is dissent. Which would never do.

      Forgetting that and looking at the science, it seems to me that what is emerging is not the error, but the incompleteness of the Neodarwinian synthesis. The new findings certainly don’t deny the existence of random mutations or natural selection. The problem is, though, that if the new science isn’t simply wrong itself, the modern synthesis is no longer the whole story, and much hinges on its being so.

      Hence the ploy of saying that these new mechanisms are real but rare – if that is so, they can be neglected and the simple model still works. But if they are significant, then biology in effect becomes as opaque as human history and its predictions very fallible approximations. They may still be useful, as weather forecasting or economic advice is useful, but they push biology away from “hard science” towards the “soft sciences” like psychology and sociology – or even the humanities like history.

      That’s only a major problem in a society (or sub-culture) in which science is the only true knowledge, and is in the end destined to provide all knowledge. In such a case loosening Neodarwinism’s control threatens to portend the Death of God (the god in question being materialism).

      Most important of all, in the bigger picture of your last paragraph, the apparently scientific support of biology for a materialist naturalist worldview – the very thing that made it more than an esoteric scientific theory – is blown out of the water. If the simple theory doesn’t explain everything, then one can’t any longer justify the absolute claim that evolution is undirected or purposeless.

      • GD GD says:

        Jon,

        As a scientist I cannot fault with anyone working within their discipline, and putting forward hypothesis and models that seek to address their data and outlook. Thus my main comment has been the inadequacy of Darwin’s view when we consider the enormous range of knowledge offered by the bio-world, and the ridiculous extension of this inadequate outlook to include almost any human activity, including philosophy and religion.

        My second objection is (clearly misunderstood by many) that it is unfair to burden the bio-sciences with the requirements that would be made on this (relatively so compared to the exact sciences) somewhat crude model. I have said that I am thankful that I was not drawn to the bio-sciences mainly for this reason. Discipline seems to have taken flight when people such as Dawkins and Huxley let loose with their nonsense.

        The main point to consider is the health and future of the bio-sciences. I am sufficiently optimistic to believe that scientists drawn to the bio-sciences will see through the propaganda and instead find satisfaction in doing bio-science. The rest (such as Lou) will continue to fight their imaginary windmills.

        • Lou Jost says:

          I like the expanded toolbox that biologists are discovering (though I object to the way this is sometimes over-sold). I’m continually amused by theists who think that “the enemy of my enemy must be my friend”. Just because older evolutionary theory gets criticized and acquires new tools, you get all excited. But these new tools are not any more useful to theists than the old ones. There is still no evidence of “control from above”, and with every new tool, the old argument that there wasn’t time for naturalistic evolution just keeps getting weaker and weaker.

          • GD GD says:

            You are making the mistake I have been pointing out – no scientific discipline can survive “my enemy your enemy” outlooks. It seems that every time Darwinism is shown to be lacking (by both theists and atheists) people such as you turn to the enemy syndrome. Nor is any science asked to find “control from above or below or from aliens dropping in with meteors”. Such stuff is part of your ideology, and more often perpetrated by anti-theists. Science must be better then ideology.

            • Lou Jost says:

              I just told you I embrace discovery of new mechanisms for evolution. You guys are the ones who hold ideology above empirical evidence.

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