Friday, August 03, 2012

The Paradox of Stasis?

The word "stasis" entered our consciousness when Gould and Eldredge promoted the concept of punctuated equilibria (see Darwin on Gradualism ). Their observations of the fossil record showed that the morphology of many species remains unchanged for millions of years. Change occurs during speciation by cladogenesis when the new daughter species fixes morphological change, thereby allowing us to recognize it as a different species.

Stasis is an important observation. Here's how Gould describes it in The Structure of Evolutionary Theory (p. 759).
Abrupt appearance may record an absence of information but stasis is data. Eldredge and I became so frustrated by the failure of may colleagues to grasp this evident point—though a quarter century of subsequent debate has finally propelled our claim to general acceptance (while much about punctuated equilibrium remains controversial)—that we ureged the incorporation of this little phrase as a mantra or motto. Say it ten times before breakfast every day for a week, and the argument will surely seep in by osmosis: "stasis is data; stasis is data ..."
Okay, we get it.

What causes stasis? There are many possible explanations. One of the most common is stabilizing selection or the idea that a species is so well-adapted to its environment that any change will be detrimental. According to this view, evolution only occurs when the environment changes.

There are many problems with this explanation. For one thing, the new species that arises during the "punctuation" event coexists with the parental species in the same environment. It doesn't seem likely that the cladogenesis was driven by environmental change. Another problem, as emphasized by Gould, is that we often see stasis during major environmental changes, such as ice ages. Finally, there don't seem to be many modern species that are perfectly adapted so why should there have been so many of them in the past?

Developmental constraint was another explanation for stasis. The idea here is that morphological change is difficult because there aren't many ways of achieving it. This was the explanation preferred originally by Eldredge and Gould but they have now abandoned it as the chief mechanism of stasis.

The third explanation has nothing to do with adaptation. There's no evidence that the new morphological change is adaptive—maybe its just due to neutral alleles. If much of the morphological variation in a population is neutral then it will take a long time to become fixed in a population, especially one with a large effective population size. By chance, a small segment of the population may split off from the main body and become reproductively isolated. Due to the founder effect, this small population may accidentally contain morphological variants that rapidly become fixed in the new population by random genetic drift. When the daughter population comes back in contact with the parent population it looks different.

This explanation of stasis suggests that most morphological variation, of the sort that distinguishes closely related species, is neutral and stasis simply represent the slowness of change by drift.

I favor the last explanation as most Sandwalk readers would have guessed. I don't expect that every evolutionary biologist will prefer this explanation but I do expect most of them to be aware of all the various explanations. That's why I was surprised when I went to a recent talk at Evolutin Ottawa 2012.

The talk was by Benjamin C. Haller and the title was Solving the paradox of stasis: Stabilizing selection and the limits of detection. The author admitted that it is very difficult to demonstrate stabilizing selection and this is the "paradox" of stasis. But rather than explore other possible explanations, Haller outlined half a dozen reasons why stabilizing selection could still be true even though we can't detect it.

The next day I heard a plenary session talk by Stevan Arnold, the incoming President of the the American Society of naturalists. He claimed that stasis was due to "bounded evolution" which I think is similar to some form of balancing selection—an idea that I thought had died in the 1960s (Uyeda et al., 2011). Jerry Coyne blogged about it last year: Want evolutionary change? Wait a million years.

Here's what I think Arnold and his colleagues are saying. Morphological change is under selective pressure but only small subsets of the population are experiencing adaptation at any one time. Those small populations are constantly exchanging alleles with the main population and that tends to dampen out the short-term selection that was occurring. Over time, the local adaptations tend to revert back to the standing variation in the main population. Thus, large scale deviations in morphology only happen within strict bounds giving rise to the appearance of stasis.

I don't see that this is any different than the idea of "brownian motion" involving neutral alleles and drift but the authors claim to have ruled this out using their mathematical models.

Here's the problem. Many evolutionary biologists are convinced that morphological change has to be due to selection. According to this view, the most likely way for new species to adapt is by gradual selection for new traits over time. This makes it difficult to explain millions of years of stasis where different traits (alleles) coexist without obvious selection.

That's the "paradox" of stasis. It's not consistent with adaptive evolution of morphological traits. Balancing selection of some sort is a way out of the problem but there aren't many examples of balancing selection (sickle cell alleles in countries with malaria is one).

I didn't realize until last month that stasis was such a problem for most evolutionary biologists.
With natural selection operating in a changing environment as an agent of adaptation, we expect to see changes at the organismal, ultimately physiological and morphological level. How, though, can we explain the paradoxical situation in which environments change, even dramatically, but organisms do not? (Wake et al., 1883, quoted in Gould, 2002, p. 857).
Maybe the premise is wrong?


Uyeda JC, Hansen TF, Arnold SJ, Pienaar J. (2011) The million-year wait for macroevolutionary bursts. Proc. Natl. Acad. Sci. (USA) 108:15908-15913. [PubMed] [doi: 10.1073/pnas.1014503108]

53 comments :

  1. You may know that Gould's mantra was misappropriated by our infamous Don McLeroy, chair of the Texas Board of Education and creationist extraordinaire.
    You can see him using this mantra to advance his creationist view that species do not evolve in
    http://youtu.be/7FID0E5T3I8

    Jump to 3:35 if you cannot stomach it all

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  2. I don't understand the phrase "stasis is data" - it makes no sense semantically. Stasis is a phenomenon; data are observations - what on earth does it mean to equate a phenomenon to data? Is he trying to say something about the nature of stasis? Or is he merely saying that stasis is an observed phenomenon (in which case, why not just "stasis is observed" or "stasis is fact")? With a nonsensical mantra like that, no wonder no-one understood!

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  3. You're carrying a lot of Gouldian baggage that I don't think you should here. You're assuming that most speciation is peripatric, even accompanied by founder effect, which is almost certainly not true. You're assuming that observed morphological change seen in the fossil record is cladogenesis -- i.e. what neontologists mean by speciation, which I also think is dubious. And you're assuming that stasis is the rule despite the relative paucity of published cases, which may well be true, but I would like to see the evidence.

    On your mechanism, it seems to me that drift wouldn't result in stasis at all, but in an unconstrained random walk, i.e. the classic caricature of phyletic gradualism. I suppose that's why you need the founder effect, but I don't see even that helping all that much.

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    1. John,we've been over this before. I DO NOT assume that the pattern of punctuated equilibria is ubiquitous.

      On the other hand, I DO think that your view of evolution is biased in that you tend to see everything through the filter of vertebrate evolution.

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    2. So just how widespread do you think the pattern of punctuated equilibria is? And do you mean anything by that other than stasis, or are you talking about the whole idea, in which speciation and morphological change are coincident?

      Just how, exactly, does my filter of vertebrate evolution affect the current question? Most documentation of stasis has been in invertebrates, but there's not a huge amount even of that. Are you saying that you think stasis is rare in vertebrates?

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    3. I don't know if the pattern is as widespread as Gould would like to have thought. It's not my field. I'm simply responding to the explanations of stasis that I have heard from leading evolutionary biologists. You should have asked them why they think stasis is a problem.

      Your filter of vertebrate evolution affects the question because the fossil record isn't nearly good enough to look at local speciation events and the possibility of stasis.

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    4. My filter would affect the question if indeed I had such a filter. But the little evidence for stasis we do have comes almost entirely from invertebrates and protists, and I think I'm about as well acquainted with that as you are.

      Stasis, however, is much more easily investigated than local speciation events. All you need is two horizons in which the fossils look the same in order to show stasis. As for local speciation, the geographic sampling isn't all that much better for invertebrates as for vertebrates, at least not enough to preclude events from happening out of sight.

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  4. If you're holding Gould's book in your lap, stasis is very real: you couldn't possibly stand up under the weight of all that verbiage.

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    1. I can't read Gould. Example, I read that crap about spandrels and got both bored and perplexed. Perplexed that so many glorify(ied) this guy.

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    2. I understand. There seem to be quite a few people who are put off by Gould's style and language. Problem is, they get confused about the difference between style and substance.

      I love Gould's style. I find it much easier to understand than some of Joe's equations. :-)

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    3. (I won't rise to the remark about my equations, which are wonderful).

      In 1974 I attended a meeting where I ran a session, which had Steve Gould speaking in it (he talked about the simulations of fossil data which he did with David Raup). Afterwards I was given a tape recording of the discussion in the session and asked to arrange that it be typed out so as to appear in the symposium volume, after the papers that the participants submitted. There was no money to hire anyone so I got a little tape recorder and started typing.

      What amused me was that we all started our sentences with "and": "And I'm going to talk about X. And what I'm going to say is Y." We needed a lot of cleaning-up. Except Stephen Jay Gould. He spoke in well-formed literary English, to my astonishment. So the secret of his prolific writing was that he just talked to the bathroom mirror and then wrote it all down (or maybe he recorded it and passed it to his publisher's people).

      I think later in life he made a deal with his publishers to basically not be subject to their editing -- which led to the self-indulgent excessive wordiness. I think that was a mistake on his part.

      By the way, I do not agree that the spandrela paper was "crap". It had a big effect on work on adaptive explanations; it was a central event in discrediting pure adaptational story-telling and pushing people toward more experimental work on adaptiveness of features.

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    4. Steve Gould was usually in the audience of seminars I attended at Harvard's Museum of Comparative Zoology in the late 1980's. His questions to the speakers came out as fully formed paragraphs, which supports your hypothesis that he thought in literary English. (I, on the other hand, have to wrestle long and hard with my brain just to get a noun and a verb.)

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    5. Yeah, when I said "crap" I meant the style rather than the substance. Though the substance in the spandrels did not require that much verbiage. I don't think of verbiage as a virtue (I did not say that I am virtuous either).

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  5. I have some time ago heard a talk that stressed how much fossil/ancient areas of distribution of many species differ from contemporary ones. So while I do not have any data here that demonstrates the prevalence of stabilizing selection, it could simply be that many species track habitats in a changing climate instead of staying put and having to adapt to a new environment.

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  6. We infer that exons are subject to selection because their sequences are constrained, constrained by stabilizing selection, punctuated by rapid change in specific lineages adapting to particular problems. Not sure why this explanation is found wanting by some in the case of morphology. Ice ages are environmental changes, but the weather is the least of my worries if I'm say a deer. Intraspecific rivals, other competitors, and predators are all more likely to be the environmental influences that matter. If the weather does become intolerable, there's always migration. Coordinated community stasis alternating with bursts of anagenesis and cladogenesis make perfect sense if morphology is subject to natural selection.

    -Anaxyrus

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  7. @konrad,

    By "stasis is data," Gould was implying that paleontologists would historically publish data that implied gradual change, but would not publish data indicative of stasis as it was a "negative" or "failed" result.

    -Anaxyrus

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    1. Ah! That interpretation didn't occur to me _at all_! It's a really bad mantra - e.g. see the way Denny misinterprets (as meaning what I also guessed it to mean) it below.

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  8. I remarked in, “Advice to New Creationist Students”, that evolution theory often does not make successful predictions, or predictions at all. Meaning they simply observe data and interpret through an evolutionary lens. The idea that stasis occurs is one example of a reality (stasis is data, as Steven J. Gould put it) that was not predicted, and did not previously fit an evolution theory model. - Larry said, “There are many possible explanations (for stasis). One of the most common is stabilizing selection or the idea that a species is so well-adapted to its environment that any change will be detrimental. According to this view, evolution only occurs when the environment changes.”

    Gould and Eldredge’s proposition on this matter was arrived at outside an evolutionary paradigm in order to explain something that was contrary to evolutionary predictions. Historical biblical accounts, however, predicted what evolutionists call stasis and punctuated equilibria. The RTB (Old-earth creation) model (I referred to in “Advice to New Creationist Students”) on the other hand, explains the protracted periods of stasis followed by bursts of change. Paraphrased, God supernaturally created organisms with optimal designs. This would explain,
    1) The sudden appearances (punctuated equilibria, or possibly even micro evolutionary changes) in the fossil record. Because they are optimal, these organisms undergo limited change for the duration of their existence, accounting for stasis.
    2) The clear and notable absence of evolutionary transitional forms.

    Note: Microevolution and speciation are considered ‘design’ features in the RTB Creation model.

    While patterns in the fossil record often do not match the predictions made by the evolutionary paradigm, they are accommodated within RTB’s creation model.

    I know you Sandwalk fans won’t buy this argument, but it exemplifies how evolution theory is often inadequate, when it comes to predictive qualities.

    A study illustrating my points is: Josef C. Uyeda et al., “The Million-Year Wait for Macroevolutionary Bursts,” Proceedings of the National Academy of Sciences, USA, early edition, doi: 10.1073/pnas.1014503108. http://www.pnas.org/content/108/38/15908.full

    I’m wondering if Larry would offer this kind of stuff to help his new students “think.”

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    1. Denny,

      While anaxyrus already answered by offering you a quote by Darwin himself, the confusion among creationists about punctuated equilibrium comes from scuh kinds of misinformation as that found in RTB.

      I was trying to explain to you before, evolution is no longer in dispute. It is clear that it is real. Check carefully whatever you have available in that PNAS paper. It is not about whether evolution is true or false, but about its tempo, just like punctuated equilibrium is about tempo. Some scientists, real ones, mistook the word "gradual" to mean "in even and continuous steps. But it is an exaggeration that Eldredge and Gould "changed" our view about whether evolution would have a rhythm. As Anaryxus told you, Darwin already talked about such lack of rhythm to be expected. What these guys contributed was a name for the phenomenon, thus helping clarify something about evolutionary change, and tons of fossils showing such thing with clarify. Yes, the periods of stasis, and the periods of rapid change with transitional forms and all.

      Your "creation model" is mere wishful thinking. Just like reading horoscopes. Add to the wishful thinking the misrepresentation of scientific results by using quotes, most often from abstracts, rather than looking at the data.

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    2. Denny,

      Before buying into the RTB bullshit maybe you should first learn what evolution is. For example, how Darwin came with those ideas, and try and see if after understanding you would expect evolution to be a phenomenon were no stasis would ever occur, where species would change continuously and in even steps, if you should expect such constant rhythms. Make a little effort to walk out of the misinformation. See for yourself. Quoting from creationist propaganda does not count. Quoting from actual scientists does not count either (no matter if the quotes work for my position, I am not asking you to think like I do, I am asking you to understand the phenomenon). You have to actually understand before coming to conclusions. Can you do that or you rather let those propagandists do the thinking for you?

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    3. Evolution cannot explain everything yet, therefore it is untrue. You'll need to tell the quantum physicists and general relativists, Denny - in fact every last scientist, since by general agreement no one knows or can explain every last thing yet.

      Except the Bible. The answer there is simple: Goddidit. Must be right then. No need (or even desire) for questioning and examination of premises or conclusions. What a perfect, boring, utterly horrible sort of world.

      I'll take the continual self-questioning of the scientific way any day, thank you.

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    4. Denny says,

      Gould and Eldredge’s proposition on this matter was arrived at outside an evolutionary paradigm in order to explain something that was contrary to evolutionary predictions.

      This is absolutely wrong. Eldredge & Gould came up with punctuated equilibrium in order to reconcile the fossil record with the work of biologists such as Ernst Mayr.

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  9. Denny the creationist says: Stasis was not predicted.

    Darwin, 1859, On the Origin of Species: "the period during which each species underwent modification, though long as measured by years, was probably short in comparison with that during which it remained without undergoing any change."

    Darwin knew that positive selection would yield to stabilizing selection most of the time.

    -Anaxyrus

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  10. Stasis in the fossil record is morphological. There is no evidence that this represents genetic statis --- in fact, everything we know about population genetics would suggest that this is not the case.

    CMJ

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    1. This is true. It's too bad we can't look at the genetics of extinct species that lived millions of year ago.

      However, much of what we know about population genetics is consistent with the founder effect and the fixation of neutral alleles in small populations so it's not as far-fetched as you make out.

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    2. That would accelerate genetic change, which is the opposite of stasis. As a big fan of neutral evolution and random genetic drift, I would have thought you would have strongly opposed any suggestion of stasis at the genetic level?

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    3. Well, if it's any consolation I don't think that stasis occurs also at the genetic level. But I think that the periods of morphological stasis, if not too long, might look somewhat genetically static too just because the accumulated mutations could be few.

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  11. Larry I think your dismissal of the major impact of paleoclimate change on evolution is somewhat premature. It has proved important to the analysis of mammalian and particularly hominin evolution at the critical plio-Pleistocene boundary. The work of Elizabeth Vrba in proposing and developing the tunover-pulse hypothesis (in "Paleoclimate and Evolution, with Emphasis on Human Origins" 1996) together with Jared Diamond's popularization of it in "The Third Chimpanzee" is well known. It is still an area of active research, a recent example of the serious an quantitative work in the area is:
    "Nonlinear detection of paleoclimate-variability transitions possibly related to human evolution" Jonathan F. Donges et al, 2011
    available at http://www.pnas.org/content/early/2011/11/28/1117052108

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    1. Nobody is denying that the external environment plays a role in adaptation.

      What we're dealing with here is speciation—those small changes that distinguish one species from it's closest cousin.

      Some people—I am one—are also challenging the widespread belief that (almost) all adaptive change is driven by environmental change.

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  12. This comment has been removed by the author.

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  13. I would just like to summarize. Climate change can promote species migration and the emergence of new geographical reproductive barriers between populations of the same species. This can promote rapid cladogenesis through allopatric speciation under the new selective pressures imposed by climate change. It is how we got here.

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    1. It is how we got here.

      What you meant to say, I hope, is that your view is one of many views on how humans evolved. You just happen to prefer a traditional adaptationist explanation. But it's still pretty much a just-so story.

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    2. It is how we got here.

      Yes it is just one view among others

      You just happen to prefer a traditional adaptationist explanation

      Punctuated equilibrium, rapid speciation and a strong role for species sorting in evolutionary are I don't think the views of a traditional Dawkinesque adaptationist. Furthemore I accept Gould and Lewontin's arguments about the spandrels of San Marco. I remember as a grad. student back in England over 30 years ago, my prof. a physicist and protein crystallographer was horrified by Kimura's neutral theory of molecular evolution. He was an extreme adaptationist regarded every residue in a protein as being adaptively selected. I didn't buy that then and I most certainly don't buy it now. I agree that neutral drift is very important for evolution, but I think ultimately that selection is the only evolutionary process that can generate or at least fix innovation in organisms.

      I also hold the heterodox view that evolution occurs in Hilbert space and as a result the weak anthropic principle, which is itself a selection principle, applies to evolution. This has a relevance for the previous post on enzyme evolution. The IDiot's very large number is small compared to the extent of Hilbert space and all possible proteins exist in it.

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    3. For the adaptationist, rapid speciation and punk eek are fine.
      A significant role for species sorting in the history of life is fine as well. But species sorting is not the source of adaptation.

      -Anaxyrus

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  14. I am not a palaeontologist but when I go to museums and look through fossil collections, I do not see stasis as a widespread phenomenon - it is one end of a spectrum. Some morphological types are short-lived, others appear to remain relatively unchanged for very long periods of time. (Obviously, there is actually a slight ascertainment bias here - the longer something persists, the more likely it is to be preserved and observed.)

    As an evolutionary biologist, I still don't see the problem with stasis even if morphological change is primarily driven by selection. If something sits in a niche and that niche essentially does not change - even if it moves - why should they?

    It's interesting and it certainly destroys gradualism but gradualism was born before we knew anything about the genetic basis for evolutionary change. Mutations occur along a spectrum of scales, the phenotypic effects of mutations likewise range from none to massive, competition, environmental change, niche availability - EVERYTHING that effects long-term morphological change - occurs as a spectrum. It would seem incredibly surprising if, by chance, some species were not able to plot a stable path through all of this. It would be surprising if ALL species did this but, as far as I can tell, they do not.

    The other thing to note is that these species are showing stasis in once sense only - their fossilised morphological traits. They could be adapting their biochemistry and colour (e.g. different levels of pigments) in response to environmental change, or their behaviour (including spatial or temporal patterns of behaviour) or even some some tissue morphology, without having any change to their gross skeletal structure. Fossils are interesting but they only give a very limited - and often subjective - view on evolution.

    When it comes to evolutionary history, it is fascinating to speculate but I fail to see how we can really ever count a lack of a thoroughly documented and comprehensive explanation for specific observations as a "problem". The data is always likely to be incomplete and poorly resolved.

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    1. (Obviously, there is actually a slight ascertainment bias here - the longer something persists, the more likely it is to be preserved and observed.)

      That's not a problem with most of the species that Gould & Eldredge (and others) worked with. They were mostly small marine fossils with thousands of individuals in each layer of sediment spread out over tens of millions of years. The pattern of stasis and cladogenesis is quite obvious with these species.

      I think most of you are thinking of much bigger species were the fossil record isn't nearly as complete.

      The other thing to note is that these species are showing stasis in once sense only - their fossilised morphological traits. They could be adapting their biochemistry and colour (e.g. different levels of pigments) in response to environmental change, or their behaviour (including spatial or temporal patterns of behaviour) or even some some tissue morphology, without having any change to their gross skeletal structure.

      That's all very true but it doesn't mean what you think it means. The fact remains that the only changes that are seen (morphological) are associated with cladogenesis and they occur quite rapidly relative to the age of the species. It's possible that there are many more punctuations, or even gradual change, in the lineage that can't be detected but you still have to account for the change that you do see.

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    2. The fact remains that the only changes that are seen (morphological) are associated with cladogenesis and they occur quite rapidly relative to the age of the species.

      How do you know that? In the fossil record, cladogenesis is inferred from morphological change. All you appear to be saying is that morphological change is associated with morphological change. Even in those rare cases in which we first see one morphotype and then two morphotypes in a locality, there are other simple explanations for the phenomenon that can't be rejected: cryptic species pairs gaining visible differences or migration of a similar species from an unsampled locality.

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  15. What we see in nature now is that most species either move or go extinct when their environment changes. It seems that we should apply a principle of biological uniformitarianism analogous to geological uniformitarianism, which I think then puts stasis in a different light.

    Doesn't natural selection act to maintain the original overal morphology in spite of the slow changes in genome? Most species would then appear in the fossil record as more or less the same, because they are more or less well adapted. Certainly natural selection cannot continue adaptation in search of a hypothetical perfect adaptation.

    When a new adaptation begins to form, because of founder effects or the slower drift due to random change, wouldn't natural selection only then act as an agent of morphological change, perfecting the adaptation? Because of back breeding of temporarily separated populations or random environmental changes reversing trends toward adaptations and the physiological constraints on adaptation, this kind of speciation driven by natural selection would be relatively uncommon. But, because of the power of natural selection, the process on a geological scale would be relatively rapid. Due to the more or less random sampling in the fossil record, the transitional forms would mostly be lost (particularly in speciation events triggered by genetic drift in founder populations,) and the appearances by a new species as it spreads would appear to be geologically sudden.

    Possibly, a different situation would be radiative adaptation into a relatively empty ecosystem. Because of the lack of competition the intensity of natural selection would be minimized, resulting in a wider range of morphologies. Wouldn't the more rapid emergence of variants that could serve as new adaptations then lead natural selection to propel speciation more rapidly and more often than in the ordinary course of events? Another way of phrasing it is to say that after a mass extinction, all the environments are new, because other species are a part of the environment. And adaptation to new environments changes natural selection from a stabilizing force to a speciating force.

    Also, it seems to me that a relatively unpressured population that exhibits a wide range of individual traits would have increased incidence of incompatibility between widely variant members of the species, not just in gross morphology but in more subtle changes unreflected in the fossil record. In this situation, the accidental emergence of any kind of sexual marker or isolator would be selected for, leading to more offspring between more compatible variants. Sexual selection then would also be a force for speciation.

    At any rate, it seems that gross morphological changes are far commoner after mass extinctions, leading to whole new orders of species.

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    1. When a new adaptation begins to form, because of founder effects or the slower drift due to random change, wouldn't natural selection only then act as an agent of morphological change, perfecting the adaptation?

      Why are you assuming that the change has to be an adaptation?

      At any rate, it seems that gross morphological changes are far commoner after mass extinctions, leading to whole new orders of species.

      That's evolution at an entirely different level than the speciations we're talking about.

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    2. "Why are you assuming that the change has to be an adaptation?"

      I thought I was assuming that natural selection conserves morphology to such an extent that I was speculating about relaxation of natural selection and/or sexual selection (sexual markers or isolators arising more or less randomly) as major drivers of speciation. I think the implication is that I think natural selection's primary importance in speciation is as the maintenance of species morphology.

      "That's evolution at an entirely different level than the speciations we're talking about."

      How could the mechanisms involved in speciation within genera be excluded from formation of the more radical morphological changes? What evidence suggests that other mechanisms not at work now were involved then?

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    3. "Why are you assuming that the change has to be an adaptation?"

      "I thought I was assuming that natural selection conserves morphology to such an extent that I was speculating about relaxation of natural selection and/or sexual selection (sexual markers or isolators arising more or less randomly) as major drivers of speciation. I think the implication is that I think natural selection's primary importance in speciation is as the maintenance of species morphology."

      That is a subtle idea that deserves a lot of careful thought and discussion.

      The reason there is room for disagreement about this topic is that we are largely arguing in the absence of evidence. We have a few unconnected facts and we argue about what they mean.

      So go back to first principles. The Fundamental Theorem of Natural Selection says that the rate of natural selection is directly proportional to the variance in fitness. So if there are long periods when there is no morphological change, that means there are long periods when there is no variance in morphological fitness.

      Why do individuals all have the same fitness for morphological traits? Maybe they are at a local optimum and they do not have enough variation in fitness or opportunity for speciation events etc to bridge the gap to a better local optimum. Or maybe they have just run out of variation in those genes, and can't adapt until they acquire more variation. Or something else I have not thought of. If it is a local optimum then you, S Johnson, are right. Selection is acting to keep the species at that local optimum and selection against variation away from that optimum is reducing the available variance in fitness. If the population has already lost its variation (due to previous selection, perhaps in an environment which no longer selects) then maybe there's nothing left but the slow arrival and departure of neutral genes.

      During times of adaptive radiation, the same species which previously adapted slowly or not at all do fast morphological change. How can they do that? Maybe most of the original population is gone, leaving only small isolated populations which had already gotten to be different. Then it's predictable that they will quickly run out of variation and stop adapting, also. But they don't.

      What I'm left with is the idea that maybe genomes have a way to hide a lot of their variation from selection. They "learn" to preferentially expose to selection the genes which have worked best in the past, keeping the others in reserve. So long as that works, they only occasionally expose other genes to selection. But when that approach stops working, they "learn" to express more genes and "choose" the ones that work better now.

      I will repeat the reasoning:

      1. Populations spend much of their time showing no morphological change.
      2. But sometimes they change fast.
      3. To change fast they must have alternate genes present and ready to be expressed.
      4. But much of the time those genes are suffering from selection. The population would not maintain low variability while building up many neutral variants. High populations that go a long time with low variability maintain that only by selection.
      5. So populations have an unknown molecular mechanism that lets them keep high genetic variability even while usually not exposing the variant forms to selection.

      Simpler models do not work. In the absence of selection, neutral mutations will increase linearly, along with increasing variance in morphology. This is not observed. On the other hand, simple selection for a particular morphology will reduce the population variance and reduce the rate of adaptation. But sometimes adaptation is faster than the fossil record can record it.

      We must have our genetic variance and eat it too. There must be some mechanism that lets us have it and eat it too.

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  16. I was all set to talk about this and then cabbagesofdoom did it first.

    s johnson, you propose adaptive radiation into an empty ecosystem where there would be less natural selection. I say that on a fossil scale that would likely be over too fast to observe. Populations would quickly adapt to fit empty niches, and in a relatively few generations survival would be down to normal. Consider, say, australian rabbits. Their population went way up fast, but in just a few human generations it has stabilized. Now they mostly aren't filling new ecological niches, they are competing to see who can be the best australian rabbit.

    This may not be a question about genetics but about ecology. Species that fill brand new niches in established ecologies might tend to be disruptive. And disrupting an established ecosystem may not get them much in the long run. Species tend to do well in the long run by filling a nich that doesn't disrupt things, and continuing that for a long time. Or maybe not.

    I see the same sort of analogy in business. US Steel owns a tremendous amount of land in various places, and not just mineral rights. They might make more money if they went mostly into the realty business and gave up making steel, but they don't consider it. Steel is what they know.

    In general I like what you say and agree with it, but my natural tendency is to pick out the minor thing I would change and focus on that.

    Yes, of course we see more gross morphological changes after mass extinctions. When the biome changes and the old niches are gone, things adapt quickly. But then they must adapt to the adaptations, and adapt to *those* adaptations, until some stability arises. When there's a whole lot of adaptation to do, some of it is likely to be slow enough to notice in the fossil record.

    And consider the galapagos finches. They have active variation in beak size and shape, because they have not managed speciation events and the islands may be too small to support more species. They do not have much variation in wing shape, foot shape, or that much else. The other traits are maybe not optimized, but "satisficed". Without a lot of genetic variation to work with in those areas, how would they get a lot of selection? Presumably selection has already cut the expressed variation in genes that lead to those traits. Maybe later....

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  17. The error in all this is about drawing biological conclusions from non biological investigation.
    Fossils are not relevant to biological investigation for conclusions or corrections on biological processes.
    they are just snapshots of biological points of data.
    Any connection between them is entirely the subject of geology and speculation upon acceptance of geological timelines.

    its fine to use fossils as evidence but not biological evidence for biological processes of any history at all.
    Its been a logical error to figure out the past in biology by looking at casts of biological data.
    If the geology was wrong for sequence and time then the biology would be wrong.
    if so it would mean the biological investigation was wrong. Yet it isn't wrong but rather doesn't exist .
    there is no biology going on but only geology and conclusions about biology.
    Whoops. A error in investigation structure.

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    1. Robert Byers,

      Many fossils, including nearly all of those used to make strong inferences about the past history of life, are not casts but rather original skeletal material. Fossils provide biological as well as geological data. Why would you pretend to have authority on a subject you know nothing about? Feel free to take a genuiune (not AIG) class in paleontology some time.

      -Anaxyrus

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  18. Anonymous
    Actually you make a good point to me. I have been vague in my mind what percentages of fossils are casts of former life and what are original skeleton material. Unless its 100% of the former.
    Still its just a snapshot at a moment in biological time for that creature.
    Drawing conclusions or criticisms, ID folk do this a lot because they reject YEC criticisms of geology, by comparing these moments in biological time with "other" moments is not based on biological investigation.
    Rather its based on geological presumptions and then a line of reasoning.
    The fossils tell very little and its the gaps between the fossils, the processes and results, that is being figured out. USING the fossils at either end.

    Folks too quick thought fossils were a part of biological investigation of origins.
    they can be evidence but not biological evidence for conclusions on processes.
    Evolutionary biology wrongly thought fossils were evidence for biological evolution.
    A logical flaw that has persisted too long.

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  19. "Balancing selection of some sort is a way out of the problem but there aren't many examples of balancing selection (sickle cell alleles in countries with malaria is one)."

    are you seriously equating balancing selection on a single allele with stabilizing selection on morphological phenotypes (the only evidence for 'stasis')? Do you know anything about quantitative genetics approaches to the inheritance of multigenic traits?

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    1. I've struggled with trying to understand quantitative trait analysis and other theoretical models of the inheritance of multigenic traits but, I confess, the mathematics is just gibberish to me.

      Can you explain, in simple terms, the important differences between stabilizing selection and balancing selection? Is it just a question of single genes vs multiple genes?

      Do you think that most of the variation within populations is maintained by some form of balancing selection or stabilizing selection? Or is it just multiple alleles affecting morphological traits that are maintained and the rest are drifting to fixation or extinction?

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    2. Can you explain, in simple terms, the important differences between stabilizing selection and balancing selection? Is it just a question of single genes vs multiple genes?

      I'll give it a try, though I might easily get it wrong.

      Balancing selection describes a mathematical result in theoretical population genetics. Two different alleles have higher fitness when they are together. When the heterozygous fitness is high enough it can overcome even hard selection against the homozygotes. In the distant past each interesting variation on this idea led to a published paper.

      Some examples of balancing selection are known in nature.

      If they are duplicated and become different genes, that should be selected over balancing. But that's rare. More likely in a large population? The longer the duplication happens, the more likely the environment no longer selects for that combination.

      Stabilizing selection is different. An idea that came from observation and experiment. People see that in most species, the individuals look pretty much alike. The wolves mostly look alike. So do the foxes, the wild roses, etc. But artificial breeding easily gets different shapes. Dogs vary tremendously and they probably came from wolves or something that all looked like. People who breed foxes today get lots of variation. Ditto roses.

      There is lots of genetic variability, and some of it can be expressed. But it does not get expressed much. Why? Maybe most of the observed variation in DNA is neutral mutations. But breeders easily create phenotypic variation ....

      If there's no selection against phenotypic variation, why doesn't it happen a lot in nature? On the other hand, if selection in nature prevents it, why don't the extra alleles disappear from populations, or at least be present at much lower frequencies?

      It's hard to study complicated combinations of genes in natural populations. Maybe there is strong selection for "normal behavior and appearance", and the genes which would cause phenotypic change are indeed rare. Present at such low frequencies that they don't get expressed much, and the few individuals that do show observable difference tend to get weeded out before you notice them. Breeders find the rare genes with inbreeding.

      Or maybe there is some sort of genetic mechanism to hide the variability. How would that be selected? Well, imagine a population getting "pulled" by selection in various directions. It can fit different niches with contrasting requirements. New niches open up and close down quickly. A species that responds too fast will suffer -- if it speciates slow it gets some sort of average genome that might do badly at each niche. If it's fast to speciate it may turn into many small populations each filling a niche that does not consistently support enough individuals to survive. Better to pick one stable niche and freeze the design. When that fails then adapt and find a new niche, and freeze the design again.

      How could such a mechanism evolve? How would individuals who expressed it be selected over individuals? I can imagine ways, but it's hypothetical selection for a hypothetical mechanism in a hypothetical ecology. Still maybe species that do this tend to go extinct slower than species that don't, and if they do fill new stable niches often enough then they might take over the world.

      A third choice is that by accident many combinations of genes produce the same result, and no one of them is very important so somehow you get the same phenotype all over while keeping a high genetic diversity without much selection going on. I can't say how this would happen, I have to wave my hands and say it just works somehow, more than with the other two ideas.

      Basicly, balancing selection is a theoretical construct looking for examples, and examples have been found. Stabilizing selection is a puzzling observation looking for a theory, and the theory has not quite been found.

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    3. Do you think that most of the variation within populations is maintained by some form of balancing selection or stabilizing selection?

      Selection reduces variability. Balancing selection is a special case where selection can't reduce variability below some particular floor. In general you can't expect selection to "maintain" variation.

      Still, it can happen. Start with a gene duplication. Two copies are free to evolve in two different directions. But if you depend on two separate mutations to make that happen, there's a 50% chance they'll both happen at the same site instead of different sites. Then you have to wait for a new mutation, or recombination, or another duplication event and you get balancing selection in the meantime.

      Or is it just multiple alleles affecting morphological traits that are maintained and the rest are drifting to fixation or extinction?

      Every site that isn't selected, will tend to drift. But the selected sites can affect that strongly. When one site is selected, everything in its linkage group is selected with it. Some neutral mutations will get wiped out and others will be greatly advanced, and the variability at linked neutral sites will be greatly reduced.

      For neutral mutations to dominate the picture, you need whole linkage groups with no selection for a long time. This does not seem very plausible to me, but of course my intuition has been wrong many times before.

      I prefer a third choice. Perhaps there are genetic mechanisms that have been selected to hide the variability. Dominant/recessive genes could be one primitive approach to that. Some dominance can be explained as the dominant form does something: a functional enzyme, say, while the recessive form does nothing: maybe a nonfunctional enzyme. This fits some known examples. But there could also be a specific genetic mechanism which can get that result. If genes switch between dominant and recessive at a relatively high rate, say 10^-4 per generation, then genes which tend to spread will spread faster when they become dominant while genes which tend to lose out will lose slower when they become recessive.

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  20. Negative Entropy. I know you think “evolution is no longer in dispute.” I certainly do not and will likely never understand evolution as well as you do. I have read Larry’s “Evolution is a fact and a theory.” Part of it says, “evolution is a theory. It is also a fact. And facts and theories are different things.” Many would take that statement to be less than clarifying and more confusing. I have seen explanations at Sandwalk that deny that the modern understanding of evolution as simple random chance events (in the conventional sense of the words), and consequently part of a completely unguided unintelligent process. I have seen some Sandwalk fans imply that evolution has virtual guided intelligent aspects to it, through the process of natural selection, but not in any mysterious supernatural way (which also seems a little contradictory to me). Furthermore, as far as I know, the “fact” of evolution has not one serious testable proposition for life’s origin on earth, as alluded to in Larry’s blog, “Changing Ideas About The Origin Of Life.” It’s OK not to know. It does not seem OK to me to pronounce evolution a fact, when it can’t even make a serious scientific proposition for its beginning.

    Here’s something I’ve noticed. The people who are so sure that evolution is a fact and not a theory, are typically very intelligent, educated and work in direct or related scientific endeavors, and are most often atheists. Those people, whose work is invaluable, are as confident that evolution is a fact as they are that there is no God. The rest of the world, except for those who passively believe in evolution, are skeptical of both evolution as a fact and the non-existence of God. It seems logical to me that the former group of atheists could think that their intelligence, education and work qualifies them to render a more informed and accurate opinion on the factual qualities of evolution. That opinion could render the opinions of others as invalid, and maybe even worse (IDiots).

    I don’t buy the proposition that informed scientific opinion coupled with an a priory view on God’s existence or non-existence makes for the most objective view, no matter whether one is a theist or atheist. Empirical scientific data is subject to interpretation. It’s hard to put aside theistic or atheistic biases during interpretation. The Creationist view has an advantage that is absent for evolutionists. The Creationist view allows historical and modern scientific interpretations to be matched against an independent historical human record compiled by hundreds of culturally and geographically unrelated people who lived over millennia in the same natural world we do where observable natural phenomena occurred. When the best modern scientific data and its various interpretations are matched against the claims and record of the Bible, and are found to be in harmony, that (I think) makes a better case for a valid corroborating view of what empirical science says and what it may mean for living life in this world (For, what good is science, if is does not inform how and why we live?). You may interpret periods of stasis and the periods of rapid change as part of an unguided (purposeless) process. I interpret them as a reflection of God’s supernatural intervention is His creation - not as corrections, and therefore indicative of a logically imperfect or illogical god. I see a God that wants us to detect Him being active and personally interested in us and the creation that sustains us, as a sign of His love for us.

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  21. Wow. I'll take the time to respond to some of that.

    " 'evolution is a theory. It is also a fact. And facts and theories are different things.' Many would take that statement to be less than clarifying and more confusing.":

    Let's look at some more examples with the same structure:
    "Water is a liquid. It is also important for human survival. And liquids and substances that are important for human survival are different things."
    "Gold is a metal. It is also precious. And being a metal and being precious are different things."
    What is confusing about that?

    "I have seen explanations at Sandwalk that deny that the modern understanding of evolution as simple random chance events":

    There is no such understanding among scientists - it is a misunderstanding promoted by creationists. A better summary of the modern understanding of evolution is that it involves a combination of simple random chance events and the non-random effects of those events. E.g. if you went into an orchard and (randomly) picked a lot of fruit but (non-randomly) discarded all the rotten ones, you would end up with a collection of non-rotten fruit.

    "the “fact” of evolution has not one serious testable proposition for life’s origin on earth":

    It's not clear what you mean by "proposition", but evolution has nothing to do with the origin of life. Expecting the fact of evolution (i.e. the observation that allele frequencies change over time) to explain the origin of life is like expecting the fact of gravity (i.e. the observation that things fall downward) to explain the origin of the solar system.

    The practical use of our understanding of evolution has to do not with the origin of life (which happened long ago) but with the fact that it is an ongoing process. This is particularly important in fast-evolving organisms such as viruses and bacteria, where we observe evolution happening on a month-to-month basis (rather than a millenium-to-millenium basis). E.g. I recommend this excellent article: http://www.nytimes.com/2012/06/26/science/the-evolution-of-bird-flu-and-the-race-to-keep-up.html

    "The rest of the world, except for those who passively believe in evolution, are skeptical of both evolution as a fact and the non-existence of God.":

    I don't know what it means to believe something "passively", but you should be aware that most Christian denominations (including the Catholic church: http://en.wikipedia.org/wiki/Catholic_Church_and_evolution) accept the reality of evolution. Creationists do not speak for Christianity in this regard.

    "I don’t buy the proposition that informed scientific opinion coupled with an a priory view on God’s existence or non-existence makes for the most objective view":

    Views on the existence or non-existence of God are not relevant to the question of whether evolution happens, unless your particular view is about the existence of a God who (per definition of that particular notion of God) must necessarily prevent evolution from happening. Most theists do not place such a restriction on their concept of God, nor do they see any reason why God should want to prevent evolution from happening.

    "When the best modern scientific data and its various interpretations are matched against the claims and record of the Bible, and are found to be in harmony":

    Unfortunately they are not generally found to be in harmony. For instance, Joshua 10:13 is not in harmony with the modern understanding of planetary motion, and John 2:9 is not in harmony with the modern understanding of chemistry. The usual interpretation of these passages is to incorporate our understanding of the way stories usually propagate and give up on interpreting them as literally true. There are not many people who would interpret them as casting doubt on our understanding of planetary motion and chemistry.

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  22. Diogenes, I accidentally put these responses under Larry’s “On this Day in 1945.”

    Diogenes – Existentialism, as defined by Webster: “a chiefly 20th century philosophical movement embracing diverse doctrines but centering on analysis of individual existence in an unfathomable universe and the plight of the individual who must assume ultimate responsibility for acts of free will without any certain knowledge of what is right or wrong or good or bad.”

    Diogenes said, “Why is OK to define good and bad according to the preferences of spooks, whose existence can't be proven-- but it's not OK to define good and bad according to the preferences of humans, whose existence can be proven?” - What are the preferences of humans?

    Diogenes said, “The Bible orders …” - When you read a book, do you read it through a straw?

    Additionally. It’s plain to see that you have read at least portions of the Bible out of context or through a theistic denial (atheistic) lens, rendering accurate interpretation unlikely. You probably expect me to understand evolution and something of the naturalistic lens through which it is viewed. I try. Doing so, and adhering to evolution’s jargon, it’s plain to me that evolution is a accidental unguided process that gained some mutational sophistication and complexity during the process called natural selection – leading to life as we know it – a (human) life that has no other purpose or meaning than to temporarily take up space on planet earth, while it waits for all the hydrogen in the universe to be exhausted and (long previous) for life to be extinguished. Now, Diogenes, do you know the Bible well enough to do more than cite passages that you believe contradictory or nonsensical? Do you know its core proposition, based on the assumed existence of a supreme holy deity, a proposition that can be discerned by non-scientific minded people, as well as scientific minded people?

    Diogenes. In Larry’s blog, “The Paradox of Stasis?” Jud sarcastically said, “Evolution cannot explain everything yet, therefore it is untrue. You'll need to tell the quantum physicists and general relativists, Denny - in fact every last scientist, since by general agreement no one knows or can explain every last thing yet.” – First, Jud accuses me of saying that evolution is untrue, because it cannot explain everything. I do not say that. I say that a statement like ‘evolution is a fact’ is untrue. It is in part untrue because scientists certainly don’t know everything, as Jud says. The Bible doesn’t tell us everything either, in passages like Joshua 10:13 and John 2:9. I do not blindly deny evolution. I view it as an intellectually logical model for how things came to be – better than any previous scientific model. But, I do not think it is the best or most logical model. One doesn’t even have to be a theist to see that the universe and earthly life is less likely a big accident, and more likely designed. My thinking is based on all the scientific data that points less to an unguided accident and more to purpose, which is (as I said) in harmony with the Bible.

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  23. The "explanation" of stasis offered in his post is not an explanation for stasis at all. It invokes drift in isolated populations to explain why invaders have different phenotypes. That isn't stasis, that's change. Explaining stasis would involve explaining why species morphology stays the same for extended periods of time. The offered explanation clearly does not qualify.

    Developmental constraints are a silly explanation for stasis, since we know how strong these are, and it is nowhere near enough to explain extended periods of stasis. Stabilizing selection is the obvious explanation for stasis. That's why people invoke it and look for it. It's not because they don't understand the alternatives, it's because the alternatives suck.

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