Category Archives: Evolution

There ain’t no flies in us.

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So I am reading Neil Shubin’s Your Inner Fish, which as noted I was eagerly anticipating. My immediate reaction is that it will be a good little book for non-experts, but the very basic overview of topics and stilted writing style (think of the exact opposite of Stephen Jay Gould’s long, comma-filled, complex sentence constructions) will be less engaging to biologist readers. I suspect that I do not reflect the target audience, though, so no major complaint here.

The title of the book refers to species such as Tiktaalik roseae (which Dr. Shubin and his colleagues discovered, to much deserved acclaim), an extinct species that, in retrospect, held characteristics that we may consider transitional between fishes and terrestrial tetrapods. Whereas Tiktaalik itself is probably not a direct ancestor of ours, I don’t have much of a problem with the “inner fish” idea on the basis of this comparison. After all, we’re talking about extinct ancestors (or things similar to ancestors) that were fishes and from whom we have inherited some persistent characteristics despite the many changes that have occurred in our lineage.

But then on p. 59, in a discussion of developmental regulatory genes which are similar in sequence and effect in different model organisms, we find:

An “inner fly” helped find an “inner chicken”, which ultimately helped Randy [Dahn, one of Shubin’s students] find an “inner skate”. The connections among living creatures run deep.

Here is a phylogeny of the organisms being discussed, all of them modern species:


At no time was there a fly in vertebrate ancestry. There was no skate in the ancestry of terrestrial vertebrates. The ancestral amniote was not a chicken. (And, while we’re on the subject, the ancestor of humans was not a chimp). There is a common ancestor shared by all of these contemporary animals, but it was not a fly any more than it was a human. Humans do not have inner flies — and equally, flies do not have inner humans. If anything, both have an “inner-common-ancestor-of-metazoans”, but admittedly that is more accurate than it is memorable.


Incidental DNA revisited.

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Note – this post has been updated since originally posted.

In the recent exchange regarding my post about genome size and code bloat, one of the authors of the study in question made the following claim:

In its conclusion prof. Gregory suggests that we claim that “Non-coding DNA does
accumulate “so that” it will result in longer-term evolutionary advantage”.
We ABSOLUTELY NEVER stated such a non-sense. It is curious that the same accuse was moved by prof. Gregory in its article “Coincidence, coevolution, or causation? DNA content, cell size, and the C-value enigma”, that we cite in our paper, to an article by Jain that we also cite in our paper. So, either prof. Gregory has a very poor opinion of our intelligence, or he thinks that we do not read the articles that we cite. Let us state, unambiguously, what we and Jain really say: “IF does exist a mechanism for genome size increase, THEN maybe the resulting long-term advantage can overcome the short-term disadvantage” (Jain was referring to the selfish dna as the genome increasing mechanism while we do not give any preference). Prof. Gregory reverts the implication: “IF there is a long-term advantage THEN the mechanism of genome increase is the product of selection”, and then explains us that it can’t be true. Incidentally, in the case of Jain, I think that what he was really intending can be clearly understood just by the title: “Incidental DNA”.

When someone suggests that one has misinterpreted the claims of an author, the appropriate thing to do is to consult the original article to be sure. So, I looked up the Jain (1980) letter, some quotes from which are given here (with emphasis):

Natural selection is concerned not only with the existing variability but even more so with mechanisms which ensure its continued availability. If there is intragenomic selection leading to rapid build-up of some of the DNA sequences (the selfish DNA of Doolittle and Sapienza and Orgel and Crick) we must treat this part of DNA as incidental to the fundamental process of mutability so vital for ensuring continued supply of raw material for the production of new genes. It does not follow that all of the DNA produced in this manner will, in fact, acquire a function. A large part of it (or even all of it) may not do so and may be eliminated only on an evolutionary time scale. Meanwhile, new DNA of the same and similar kind may continue to be produced so that at a given point of time there will always be large amounts of non-specific DNA. This fraction is best described as ‘incidental’ rather than ‘selfish’ DNA. We may call it incidental because it is a byproduct of the inherent property of mutability of the genome, a characteristic to which natural selection attaches great importance even if it leads to the production of repeated sequences and a wasteful deployment of energy. Viewed in this light, non-functional DNA is very much a product of natural selection — a selection operating for mutability per se. Its relative abundance is probably a function of its nonfunctional nature for any other DNA which carries information of one kind or another would create genetic imbalance and would be quickly rejected.

…

Nature places considerable premium on playing safe so that it will not run short of raw material even if this means indiscriminate production leading to sequences which are destined to remain functionless.

Now, Dr. Musso may interpret this very differently, but I take it to mean that Jain argued that non-coding DNA was preserved by natural selection specifically because it may become useful as a source of new genes. Moreover, this would have to be non-coding DNA that was preserved in this way because adding coding regions for future use would create complications in genic function. I have discussed in various posts (e.g. here, here) why this notion is untenable.

UPDATE: My interpretation of Jain (1980) was that he was arguing that non-coding DNA is preserved by selection because it contributes to mutability. Further discussion with Jonathan Badger, and another re-read of Jain (1980) in the context of alternative interpretation, has bolstered the conclusion that he was in fact suggesting something different from what I said. The much more reasonable interpretation, and what I now think he was actually arguing, is that the genome is inherently unstable for reasons unrelated to non-coding DNA and that this is maintained by selection (though, it must be said, not in the usual sense but interlineage level) and the accumulation of non-coding DNA is a byproduct of this. I will accept that the authors of the paper that began the discussions saw it this way — though their phrasing “IF does exist a mechanism for genome size increase, THEN maybe the resulting long-term advantage can overcome the short-term disadvantage” is easily confused with arguing that non-coding DNA generates some long-term advantage that overcomes its immediate disadvantage (rather than representing a side-effect of some other process with a long-term advantage). And then, there is still the issue of what the original article stated:

From this point of view, we can think of TMs in our simulations as organisms trying to increase their gene pools adding new genes assembled from junk DNA. If the organisms possess more junk DNA it is possible to test more “potential genes” until a good one is found.

Though I doubt he will read this post, I do apologize to Dr. Jain if indeed I misinterpreted his argument. That said, I do think his phrasing of selection is imprecise and that this probably contributed to the confusion. In my original citation written 8 years ago, I cited Jain as an example of a “noncoding DNA is there because it might be useful” line of thinking, and while he may have been an inappropriate example, this notion is still around and needs to be fixed. In any case, I have not changed my opinion that the article that started this discussion drew undue links between a model and biological genome evolution, and that their results have little bearing on the genome size question.

________

Update, part two

I hate to keep updating this post (though I have preserved the original form with strikeouts), but I just knew I was not the only person to have interpreted Jain (1980) as suggesting that noncoding DNA was preserved because of its potential long-term benefits. It seems W.F. Doolittle (an originator of the “selfish DNA” idea, and whose paper Jain was commenting on) got the same impression. I will quote at length from Doolittle (1982), in which he discussed the varying reactions to the notion of selfish DNA shortly after it was proposed (italics in original, most in-line references omitted).

(c) The long-term evolutionary advantage of genomic rearrangements. Transposable elements promote genetic rearrangements, and the kinds of rearrangements (transpositions, deletions and inversions) seem similar in both prokaryotes and eukaryotes. This (and the occasional turning on and off of genes adjacent to the site of insertion) appears to be all that many, perhaps most, transposable elements actually do for the organism which bears them and it does not seem to be a good thing. Selection operating on individuals should eliminate such elements. Thus many have claimed that transposable elements are maintained because they play important “evolutionary roles”. This is not a straw man which Carmen Sapienza and I set up in order to have a hypothesis against which to pit the notion of selfish DNA. I can only document this with quotations not, I hope, taken out of context:

“Whether they (insertion sequences) exert functions at these positions or are simply kept in reserve as prefabricated units for the evolution of new control circuits remains unclear.”

“It is possible that the sole function of these elements is to promote genetic variability…”

“A tenable hypothesis regarding the function of transposition is that it allows adaptation of a particular cell to a new environment.”

“All these alterations could lead to changes in structural gene function and in the control of gene expression and could provide organisms with a means of rapid adaptation to environmental change.”

Evolutionary roles have similarly been invoked for heterochromatic highly repetitive DNAs, whose presence does affect recombination in neighbouring and distant regions and whose characteristics may (although the experimental evidence is not strong) affect chromosome pairing.
Neither we [Doolittle and Sapienza] nor Drs Orgel and Crick denied that transposable elements or heterochromatic highly repetitive DNAs have such evolutionary effects, nor that these effects might not be important, perhaps even as the basis for macroevolutionary change. What we were arguing against was the assumption that these elements arose through and are maintained by natural selection because of these effects.
This assumption is often only implicit in the writings of many who suggest that the only roles of mobile dispersed and tandemly reiterated DNAs are evolutionary ones. Thus we have been accused by some of these of misrepresenting their positions and thus indeed of attacking straw men after all. I apologize to those who feel we have put words in their mouths. But I do not see how statements that the only “functions” of transposable elements or highly repetitive DNAs are to generate or modulate genetic variability can mean anything other than that natural selection maintains, and probably even gave rise to, such elements through selection for such “functions”. Shapiro (1980) has been brave enough to articulate this view outright:

“Why, then, are insertion elements not removed from the genome? I think the answer must be that there is a selective advantage in the ability to generate new chromosome primary structure.”

Those who speculate on the function of excess DNA have formulated this position in a more extreme way. For instance, Jain (1980) states

“at a given point of time there will always be large amounts of non-specific DNA. This fraction is best described as ‘incidental’ rather than ‘selfish’ DNA. We may call it incidental because it is a byproduct of the inherent property of mutability of the genome, a characteristic to which natural selection attaches great importance even if it leads to the production of repeated sequences and a wasteful deployment of energy. Viewed in this light, non-functional DNA is very much a product of natural selection — a selection operating for mutability per se.“

The question of whether natural selection operates in this way, that is of whether the evolutionary process itself evolves under the direct influence of natural selection, lies at the root of the real controversy over whether self-maintaining, structured, genomic components without phenotypic function can properly be called “selfish”. This may seem like a small and metascientific quibble. In fact it is not; it is one of the most troublesome questions in evolutionary biology today. It manifests itself in debates over the origin and maintenance of mechanisms involved in the optimization of mutation rates, recombination, sexual reproduction, altruistic behaviours of all sorts and even speciation. Such mechanisms are not clearly advantageous to, and can be detrimental to, the fitness of the individual. Yet they may increase the long-term survival properties of the group to which the individual belongs, thus seeming to be the product of what has been called “group selection”.

________

Doolittle, W.F. (1982). Selfish DNA after fourteen months. In: Genome Evolution (G.A. Dover and R.B. Flavell, eds.), Academic Press, New York, pp.3-28.

Jain, H.K. (1980). Incidental DNA. Nature 288: 647-648.



Modern Synthesis dead?

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There seems to be new interest in the blogosphere regarding what Stephen Jay Gould had to say about evolution, invigorated, at least in part, by Jerry Coyne’s post on The Loom. This appears to have grown into the creation of a “ScienceBlogs Book Club” which will discuss Gould’s massive book, The Structure of Evolutionary Theory. I read it when it came out. I am certain that Larry Moran has read it. But we’re not on ScienceBlogs (he declined, and I was never approached). I also am fairly sure that PZ Myers has read it, so maybe he can provide some perspective.

My last post dealt briefly with one aspect of this discussion, namely a misinterpretation of punctuated equilibria as representing a saltatationist mechanism. In no small part, this has been based on cherry picking quotes from Gould’s diverse writings, which did indeed cover mutations of substantial effect in addition to patterns of speciation in geological timescales.

This time I want to revisit one of Gould’s most famous quotes, and certainly his most infamous. The version that is most familiar, I believe, is the one cited in Charlesworth et al. (1982), who quote Gould thus:

I have been watching it [neo-Darwinism] slowly unravel as a universal description of evolution … I have been reluctant to admit it … but … that theory, as a general proposition, is effectively dead, despite its persistence as a text-book orthodoxy.

Strong claims, to be sure. But evolutionary biologists, I should hope, are always wary of ellipses, and that passage has several.

Here is Gould’s (1980) quote in full (emphasis added):

I well remember how the synthetic theory beguiled me with its unifying power when I was a graduate student in the mid-1960’s. Since then I have been watching it slowly unravel as a universal description of evolution. The molecular assault came first, followed quickly by renewed attention to unorthodox theories of speciation and by challenges at the level of macroevolution itself. I have been reluctant to admit it — since beguiling is often forever — but if Mayr’s characterization of the synthetic theory is accurate, then that theory, as a general proposition, is effectively dead, despite its persistence as textbook orthodoxy.

The question is, what was Mayr’s characterization that Gould considered effectively dead as a general proposition?

Ernst Mayr (1963) (emphasis added):

The proponents of the synthetic theory maintain that all evolution is due to the accumulation of small genetic changes, guided by natural selection, and that transspecific evolution is nothing but an extrapolation and magnification of the events that take place within populations and species.

Polyploidy. Genetic drift. Mass extinction. Gould said many controversial things, but his claim, without ellipses, that the modern synthesis so defined had perished was pretty neutral.

_____________

References

Charlesworth, B., R. Lande, and M. Slatkin. 1982. A neo-Darwinian commentary on macroevolution. Evolution 36: 474-498.

Gould, S.J. 1980. Is a new and general theory of evolution emerging? Paleobiology 6: 119-130.

Mayr, E. 1963. Animal Species and Evolution. Harvard University Press, Cambridge, MA.


Punctuated equilibria is not saltationism.

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If I get more time, I may weigh in on the debate that has erupted of late on several blogs, namely regarding saltationism in evolution. This was sparked by Olivia Judson’s post, and fanned by Jerry Coyne’s guest critique on Carl Zimmer’s blog, The Loom.

For the moment, I will sidestep the issue of small mutations of large effect (and the additional issue of large mutations, like genome duplications) and will focus briefly on the claim that Coyne makes in the post and in various articles that Eldredge and Gould’s idea of punctuated equilibria is, or at least was, saltationist in mechanism.

It isn’t. It never was. Gould did maintain an interest in macromutations in his discussion of development in the 1970s and 80s, but this was separate from punk eek. Linking them just because the same author discussed them would be like calling natural selection a Lamarckian theory because Darwin considered the inheritance of acquired characteristics in the Origin.

I am pleased to note that Niles Eldredge will provide an article entitled “The early evolution of punctuated equilibria” as his Editor’s Corner of the forthcoming issue of Evolution: Education and Outreach, so look for that in the spring and for additional discussions in future issues of the journal.

You can also consult Gould’s The Structure of Evolutionary Theory, or the chapter on the topic that was published alone as Punctuated Equilibrium.

Meanwhile, I will simply direct you to the summary of punctuated equilbria by Bruce Lieberman and Niles Eldredge at Scholarpedia:

Punctuated equilibria actually comprises several different and related observations. These include:

  1. the fossil record contains a rich source of data useful for developing important evolutionary hypotheses;
  2. speciation typically happens allopatrically, in narrow and geographically restricted populations containing relatively few individuals;
  3. species are not slowly and gradually adapting and evolving over long stretches of geological time;
  4. species lineages that show stasis – or an absence of morphological change – dominate the fossil record and provide useful information about the tempo and mode of evolution;
  5. the first appearance of a new species in the fossil record usually does not represent its point of evolutionary origin but rather the migration of a new geographically isolated species back into its ancestral range, with concomitant expansion in abundance; and
  6. speciation typically takes on the order of 5,000 to 50,000 years to occur – far shorter than the average duration of species in the fossil record.

This is, in essence, an extrapolation into deep evolutionary time, of Ernst Mayr’s ideas regarding allopatric speciation. Mayr himself thought so:

I believe I was the first author to develop a detailed model of the connection between speciation, evolutionary rates, and macroevolution (Mayr, 1954). Although long ignored, my new theory of the importance of peripatric speciation in macroevolution is now widely recognized. “Mayr’s hypothesis of peripheral isolates and genetic revolution must of necessity be a centerpiece of the punctuated equilibria theory; it is the theory, for all practical purposes” (Levinton, 1983:113). I once more presented my theory in great detail (Mayr, 1963:527-555). Under these circumstances it is most curious that the theory was completely ignored by paleontologists until brought to light by Eldredge and Gould (1972).

Mayr, E. 1992. Speciational evolution or punctuated equilibria. In: The Dynamics of Evolution (eds. A. Somit and S.A. Peterson), pp. 21-53. Cornell University Press, Ithaca, NY.

Indeed, here is what he said in the 1954 paper:

…rapidly evolving peripherally isolated populations may be the place of origin of many evolutionary novelties. Their isolation and comparatively small size may explain phenomena of rapid evolution and lack of documentation in the fossil record, hitherto puzzling to the palaeontologist.

Mayr, E. 1954. Change of genetic environment and evolution. In: Evolution as a Process (eds. J.S. Huxley A.C. Hardy, and E.B. Ford), pp. 157-180. George Allen & Unwin, London.

Several bloggers have discussed Coyne’s critique, and you can find summaries here and here. The one to which I most enthusiastically direct you is by Larry Moran. Larry puts it clearly, and points out that even one of Gould’s major detractors agreed that Gould never proposed punctuated equilibria as a saltationist process. Incidentally, I am not the only person to endorse that post. As Niles Eldredge told me when I mentioned the blog discussions, “PS: Larry Moran says it all!”.

Your inner fish.

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Neil Shubin was on the Colbert Report recently, just one of a growing list of scientists who have appeared on the show (including, for example, Craig Venter and Ken Miller). You may also remember seeing Shubin interviewed for the NOVA program Judgment Day: Intelligent Design on Trial. Shubin was the man behind the discovery of the transitional fossil Tiktaalik roseae, which represents a superb example of the predictive power and massive wealth of supportive evidence within evolutionary biology.

Shubin’s book Your Inner Fish was released today, and I have been waiting eagerly for it. The excerpt I read was very well written and interesting, and the idea of having examples of human characteristics that are holdovers from our evolutionary history is very exciting for teaching. Plus, anyone who discovers such an awesome transitional species — in Canada, no less — will find his way onto my reading list.

HT: Pharyngula


The Moral Instinct by Steven Pinker in the New York Times.

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In my experience in dealing with anti-evolutionists, the fundamental motivation for dismissing evolution is not its adverse implications for religion itself (real or imagined, depending on your view), but the sense (definitely imagined) that accepting evolution subverts any basis for morality. One can go around and around with an anti-evolutionist only to discover in the end that he or she is really arguing from a moral perspective: “A naturalistic approach cannot show why it is absolutely wrong to kill someone, only divine moral laws can, thus evolution is unacceptable and hence incorrect.”

In this regard, it was with much interest that I read the piece by Steven Pinker in the New York Times on The Moral Instinct.

Now, I am not a major advocate of evolutionary psychology. Many of the “just-so stories” that come out of that circle make me either roll my eyes or cringe, depending on the usually overblown ratio of strength-of-claim to quantity-of-data. On the other hand, I would not argue that the human brain and the behaviours it exhibits are somehow exempt from the evolutionary processes that apply to every other organ in every other living species. However, that is not to say that all behaviours are adaptive — far from it. I suspect that some behaviours are (or were) adaptive, and some are not and never were.

Speaking specifically of innate human behaviours that are (or were) adaptive, I prefer to think of them as a series of “rules” or “guidelines” that are supplemented by details from culture. Nature via nurture. Language is a good example, and one that I use with students. The ability to learn a language is innate. Which language one learns is cultural. These are inseparable.

I have long thought that morality is rather similar. There is an innate moral compass that all normal humans possess (e.g., “the golden rule”, known to biologists as the basis of reciprocal altruism), but many of the specifics of what constitutes “good” versus “bad” are filled in by culture. Pinker takes a similar view, although he (I think correctly) distinguishes between societal conventions and moral principles, the former of which are especially culturally malleable. He also notes five basic themes that comprise the moral sense: harm, fairness, community (or group loyalty), authority, and purity (see also Haidt 2007). The proportions and expressions of these may vary among cultures, but they are universally identifiable in human beings. I quite like this formulation as a useful way to think about the differences and unities in moral judgments among people.

Finally, and perhaps most importantly, Pinker points out that studying and even explaining morality does not destroy it: if anything, it may help us to behave morally in a more effective way by adding some rationality to the equation.

The article is excellent, and I recommend it very highly.


Huckabee is right for all the wrong reasons.

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Over at Pharyngula, PZ points to an interview with former Arkansas Governor and presidential hopeful Mike Huckabee. As a Canadian, I have long been amused by Huckabee for reasons you can see here. The prospect of this guy becoming president is unnerving, but then so is the fact that our neighbours saw fit to elect (or at least, not not-elect) Bush. Twice.

Here is what Huckabee has to say about evolution. I have omitted the bit about teaching non-scientific alternatives in science class that preceded it, because it’s too silly to repeat (he says “all views”, but presumably he means “one other view” only).

Because, frankly, Darwinism is not an established scientific fact. It is a theory of evolution, that’s why it’s called the theory of evolution.

He’s right. “Darwinism” — a term used mostly by creationists, but also historically (e.g., Wallace) and to an extent today (e.g., Dawkins), especially in Britain — refers to natural selection as a mechanism of evolution. And it is a theory. In science, a theory is an explanation for an observed or inferred condition of the natural world that is well established through multiple lines of empirical evidence (i.e., a fact). Darwin’s theory of natural selection is one explanation for the fact that species are related through descent, which in turn has been well established in science for well over a century on the basis of fossils, biogeography, embryology, morphology, and genetics. Darwinian natural selection is not the only available explanation, and therefore represents a subset of modern evolutionary theory. That natural selection happens is an established fact (witness antibiotic resistance), but what its role is in causing large-scale evolution remains a subject of discussion among biologists.

So “Darwinism,” in the sense of meaning that the majority of evolution occurs via natural selection, is indeed not an established fact, it is a theory. Huckabee’s words are correct, even if his intent is terribly muddled. Scientific theories explain facts. If there is no established fact, then there is no theory needed.

I invite Gov. Huckabee to read more about this in a recent paper that is freely available here.


News stories of interest.

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In keeping with my recent minimalist approach to the blog, here are some links to stories by others that I think you may find interesting.

US ‘doomed’ if creationist president elected: scientists (PhysOrg)

I think this is a great line:

“The logic that convinces us that evolution is a fact is the same logic we use to say smoking is hazardous to your health or we have serious energy policy issues because of global warming,” University of Michigan professor Gilbert Omenn told reporters at the launch of a book on evolution by the National Academy of Sciences (NAS).

Evolutionary idea
Scientists rally to explain and defend the cornerstone of biological study
(Houston Chronicle)

An interesting piece (especially given the venue), and I am happy to say that it makes a note of the new journal Evolution: Education and Outreach, which I hope you’re all planning to read.