Monthly Archives: January 2008

Modern Synthesis dead?

Posted on by

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.

Posted on by

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!”.

Welcome Pharyngulanchers.

Posted on by

I see PZ has linked here in a discussion of yet more IDist nonsense regarding junk DNA. To help you find what you’re after, here is a list of relevant posts on the subject:


1,000 genomes on the way (sort of).

Posted on by

ScienceNOW and ScienceDaily are reporting the announcement of the 1000 Genomes Project, which will be supported by agencies in the UK, China, the US, and elsewhere. It will include analyses of the genomes of 1000 individual humans, and will build upon the International HapMap Project.

ScienceDaily describes the early phases of the project:

In the first phase of the 1000 Genomes Project, lasting about a year, researchers will conduct three pilots. The results of the pilots will be used to decide how to most efficiently and cost effectively produce the project’s detailed map of human genetic variation.

The first pilot will involve sequencing the genomes of two nuclear families (both parents and an adult child) at deep coverage that averages 20 passes of each genome. This will provide a comprehensive dataset from six people that will help the project figure out how to identify variants using the new sequencing platforms, and serve as a basis for comparison for other parts of the effort.

The second pilot will involve sequencing the genomes of 180 people at low coverage that averages two passes of each genome. This will test the ability to use low-coverage data from new sequencing platforms to identify sequence variants and to put them in their genomic context.

The third pilot will involve sequencing the coding regions, called exons, of about 1,000 genes in about 1,000 people. This is aimed at exploring how best to obtain an even more detailed catalog in the approximately 2 percent of the genome that is comprised of protein-coding genes.

So, it’s really six “complete” sequences like those available for Jim Watson and Craig Venter, plus low-redundancy coverage for 180 additional people. Then the rest are subsets of genes (1,000 of around 20,000) from 1,000 people, or about 0.075% of the genome.

Though it isn’t 1000 genomes sensu stricto, it is definitely a very exciting project.


A quick shot of the thrill of science.

Posted on by

PZ has posted this video, and I liked it so much that I thought I would share it as well. It is meant to contrast “biblical science” with science, but really this is a minor point. The more relevant aspect is the, quite frankly, thrilling tour of a tiny portion of what science has achieved.


What’s wrong with this figure? (Round three).

Posted on by

In the process of finishing up a paper, I came across this figure (Gilbert 2007).

Figure 1. Drosophila species assemblies, showing assembly sizes and coverage of these by D. melanogaster genome DNA (top and middle lines, in megabases, left ordinate), and counts of chromosome segments inverted relative to Dmel (bottom line, right ordinate). Species on abscissa are taxonomically ordered with Dgri most distant from Dmel.

Two questions. One, why are these points joined by lines? Two, what does “taxonomically ordered” mean? I suspect it is equivalent to “phylogenetic sequence”, which was discussed in a previous edition of “What’s wrong with this figure?“.

Here is the phylogeny that is most often seen in discussions of the 12 Drosophila genome sequences (in this instance, based on Crosby et al. 2007).


Pop quiz: Are D. grimshawi and D. melanogaster the most distantly related species in this subsample of the genus?


The blogosphere overreacts!

Posted on by

I am not interested in getting into a battle with any of my fellow bloggers on this issue, especially since I actually read all of the blogs involved and appreciate what each one of them has to say. But I do have to point out that sometimes the blogosphere overreacts, and things get blown out of proportion. Also, the sun rises in the morning and snow is cold.

On his new powerblog (seriously, Seed must have told him he has to post something every 15 minutes), Greg Laden made the following statement:

The “Junk DNA” story is largely a myth, as you probably already know. DNA does not have to code for one of the few tens of thousands of proteins or enzymes known for any given animal, for example, to have a function. We know that. But we actually don’t know a lot more than that, or more exactly, there is not a widely accepted dogma for the role of “non-coding DNA.” It does really seem that scientists assumed for too long that there was no function in the DNA.

What I actually said was, I think, pretty innocuous and mostly accurate:

Over on his blog, Greg Laden points to some new work by John Mattick’s group on non-coding RNA expression in mouse brains. It’s interesting stuff, and worth a look. Please bear in mind as you do, however, that non-protein-coding but functional RNA is nothing new. Ribosomes are made of non-coding RNA, for one thing. Sadly, Greg seems to have bought into the distortions (several promoted by Mattick) about what people have said about non-coding DNA.

That was the extent of my discussion of Greg in particular. I then provided a list of examples of functions that have been suggested, and concluded by giving my opinion about how the results of this quite interesting paper should be interpreted realistically.

Larry says I have “already tried to teach Greg some real science about junk DNA”. RPM says I “put Greg in his place”. Genome Technology Online says I “blasted” Greg. And SF Matheson says Greg is “being spanked a little too hard” (he could be referring to commenters, but this follows a line about what Larry and I wrote).

In his reaction and in the comments to others, Greg decides to:

1) School me on why genome size is relevant, with special reference to birds and flying. Since this is based partly on my own work, I find this curious.

2) Insinuate that objection to claims of function for all eukaryotic DNA are cultish, and that those who agree with Larry Moran and me are “disciples”.

3) Say (to RPM) “…this post of yours, Moran’s writing on this, and to a much lesser extent T.R. Gregory’s work, is sufficiently impolite and tending sometimes to the obnoxious that it makes it hard for people to engage in learning, as opposed to debate.” (I get a qualifier, but am listed).

Again, here is what Greg claimed:

The “Junk DNA” story is largely a myth, as you probably already know. DNA does not have to code for one of the few tens of thousands of proteins or enzymes known for any given animal, for example, to have a function. We know that. But we actually don’t know a lot more than that, or more exactly, there is not a widely accepted dogma for the role of “non-coding DNA.” It does really seem that scientists assumed for too long that there was no function in the DNA.

And yet again, here is what I actually said about Greg’s statement — no more, no less:

Sadly, Greg seems to have bought into the distortions (several promoted by Mattick) about what people have said about non-coding DNA.

I think they are distortions. And I think Greg’s statement shows he agrees with them. Judge for yourself if the blogosphere got this one right with regard to what I, myself, actually wrote.

___________

Update:

I feel I should provide some clarification, so let me address the statements that Greg made and explain why they are inaccurate.

(1) The “Junk DNA” story is largely a myth.
This is false. There is good reason to expect that much or most of the genome is non-functional, and it takes evidence to show otherwise.

(2) DNA does not have to code for one of the few tens of thousands of proteins or enzymes known for any given animal, for example, to have a function. We know that. But we actually don’t know a lot more than that…
Yes, we do. We know that about half of the genome in humans is made of inactive transposable elements. We know that many mechanisms can add or subtract DNA without being related to function. We know the patterns of diversity in genome size for 10,000 species of eukaryotes.

(3)… or more exactly, there is not a widely accepted dogma for the role of “non-coding DNA.”
This implies that there is a role and we just don’t have the details about it, but the premise is not something you can assume as a given.

(4) It does really seem that scientists assumed for too long that there was no function in the DNA.
This is not true, but it is the claim made by Mattick and others (usually non-scientists). People assumed function from the very beginning, either for all DNA or simply a lot of it. This is true right back to the very first use of the term “junk DNA”, and it was true when people had to explicitly challenge the assumption of function, and it has continued up to the present. Some people, mostly sequencers, may have ignored the rest of the genome and focused on genes, but that does not reflect the range of views that have always been expressed.


How much DNA could be deleted from the human genome?

Posted on by

Larry Moran asks an interesting set of questions about human DNA:

How much of it could be removed without affecting our species in any significant way in terms of viability and reproduction? Or even in terms of significant ability to evolve in the future? In other words, how much is junk?

The options are:

  • None
  • less than 10%
  • between 11% and 49%
  • between 50% and 74%
  • between 75% and 89%
  • 90% or more

I hope people take his poll, because I think it will be intriguing to see what most people think. However, I have to admit that I won’t really be able to vote, for the reason I outlined in the comments to his article:

I think this is where a distinction between nonfunctional and inconsequential is important [see Effect versus function for more details]. In terms of whether most DNA is functional, I would agree on the basis of what we currently know that much of it could be deleted in principle. However, this would also affect cell size, and therefore organs, and therefore organisms. And yet, I would not necessarily consider the influence of DNA amount on the cell as a function. It could very well be that there is upward pressure from transposable elements and other mechanisms that cause DNA to accumulate, and downward pressure against this accumulation through selection on organisms. The balance that has been reached is not necessarily adaptive for either side. However, deleting a lot of it could have impacts on development and morphology nonetheless. Maybe it would even be a beneficial change, maybe deleterious, but I can’t assume that there would be no effect.

In some ways, it’s a little like asking, how much of the bacteria in your gut could you kill without having an effect on your health? In principle, a lot of it is clearly not functional, and none of it is there just to function on your behalf. But if you cleared the gut of all bacteria, or even just the commensal and parasitic species, would there be no effect? And if there were adverse consequences, would you take this as evidence that all those bacteria had a function after all?



Genome Technology Online is still confused.

Posted on by

I mentioned once before that Genome Technology Online is confused about non-coding DNA. Today they confirmed this: The Semantics of “Junk” DNA — We’re Confused, Too.

Greg Laden points out a recently published paper in PNAS that gives credence to the theory that non-coding RNA has specific function. The work identified 849 ncRNAs (of 1,328 examined) that are expressed in the adult mouse brain, the majority of which they also found were associated with and expressed in specific regions, cell types, or cellular compartments. He’s blasted here and here for his supposed naivety, but he maintains that the “paper is interesting and the evidence for ncRNA having some function is reasonable.”

Funny, that’s pretty much what I concluded about the paper too:

I am not about to claim that the study hasn’t shown evidence of function for these non-coding regions. I think it’s quite interesting, and it wouldn’t surprise me if lots of non-coding RNA turned out to have a regulatory function.

Greg wasn’t “blasted” by me, but I did point out his misinterpretation of the evidence for function in non-coding DNA, of which these non-coding RNAs are a tiny fraction. The extrapolation from this to “junk DNA” in general is what I was noting. I think aggregating services like Genome Technology Online are useful, but not when they do little more than give inaccurate comment.


Your inner fish.

Posted on by

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