30 August 2007

Which came first, the bird or the smaller genome?

ResearchBlogging.orgIt’s easy to think of a genome as a collection of genes, perhaps because so many of the metaphors used to explain genes and genomes (blueprint, book of life, Rosetta Stone) can give one the impression that everything in a genome is useful or functional. But genomes are, in fact, packed with debris. Many genomes contain huge collections of fossil genes: genes that have been inactivated by mutation but were never discarded, sort of like the old cheap nonfunctional VCRs in my basement. And many genomes contain even more massive collections of another kind of fossil-like DNA: mobile elements, or their remnants. The human genome, for example, contains over 1 million copies of a single type of mobile genetic element, the Alu transposon. Together, the various types of mobile genetic elements comprise nearly half of the human genome.

Think about that. Almost half of the human genome is made up of known mobile elements, pieces of DNA that can move around, either within a genome or between genomes with the help of a virus. This extraordinary fact -- and many of the specifics surrounding it -- constitutes one of the most compelling sources of evidence in favor of common descent, the kind of data for which only common ancestry provides a complete (or even reasonable) explanation. I’ll come back to this topic regularly.

Now it turns out, not surprisingly, that differences in genome size among types of organisms are determined primarily by the numbers of these mobile elements, and not by the number of genes. In fact, there is wild variation in genome size among types of organisms, and the variation has little to do with the numbers of genes expressed by those organisms. Consider birds, the subject of this week’s Journal Club (“Origin of avian genome size and structure in non-avian dinosaurs,” Organ et al., Nature 446:180-184, 8 March 2007).

Birds have remarkably small genomes, averaging 1/2 to 1/3 of the size of typical mammalian genomes. (The chicken genome, for example, is less than half the size of the mouse genome.) Why might this be? In other words, how might we explain this difference? The authors point to two important ideas. First, the chicken genome has been fully sequenced and analyzed, and it contains far less of the debris mentioned above. It seems that the processes that create (or multiply) mobile genetic elements are significantly less active in birds than in mammals and other vertebrates. Second, small genome size is intriguingly correlated with flight. Bats, compared to other mammals, have small genomes, and flightless birds, compared to other birds, have larger genomes. This has led to the proposal that small genome size might offer a selective advantage to flying animals, by reducing the energy cost associated with hauling all that debris around. So, it seems that a smaller genome is advantageous for flying vertebrates, and that genome size can be reduced by restraining the production of mobile genetic elements. And this raises several interesting questions, including this one: did the reduction in genome size accompany the origin of bird flight, or did it happen in advance? In other words, we can propose at least two alternative scenarios:
  • 1) flight drove the genome change, by favoring small genomes, or
  • 2) the genome change happened first, and helped to get flight off the ground. ;-)
How can we even hope to distinguish between these possible explanations? We would need, somehow, to look at the genomes of the ancestors of birds. And all evidence indicates that the relevant ancestors of birds are dinosaurs; in fact, today's birds are considered to be flying dinosaurs. The recent description of protein sequences from T. rex bone provided strong confirmation of the birds-from-dinosaurs hypothesis, but no DNA was recovered from the samples, and no information about genome structure can be inferred from those otherwise fascinating studies. If only, a la Jurassic Park, we could get some dino DNA...

Enter Organ et al. with a wonderfully creative idea. It turns out that, in organisms alive today, cell size is strongly correlated with genome size. In other words, organisms with large genomes tend to have larger cells. This relationship was first described in red blood cells, but Organ et al. show that it holds quite well in bone cells as well. Using bones from living species, they created a statistical model that enabled them to infer genome size by looking at the size of bone cells. Then they combined their model with measurements of bone cell size from fossilized bones of long-extinct animals, and were able to estimate the genome size of dozens of extinct species, including 31 dinosaur species and several extinct bird species. Their results are remarkable: small genomes are found in the entire lineage (with one interesting exception, Oviraptor) that gave rise to birds, all the way back to the theropod dinosaurs that are the typical reference point in the dinosaur-to-bird story. Here's how the authors put it: "Except for Oviraptor, all of the inferred genome sizes for extinct theropods fall within the narrow range of genome sizes for living birds." Even if you don't have access to Nature, you can have a look at the cool family tree in Figure 2, which shows small genomes in red and larger ones in blue. It's a compelling image.

The results suggest that small genomes arose long before dinosaurs took to the air, and raise some interesting questions about the interplay of physiological function (e.g., energy consumption associated with flight) and genome structure. Certainly scenario #1 above is not favored by these findings: flight apparently arose in organisms that already had much smaller genomes than many of their earthbound cousins. The relationship between flight and small genome size, then, remains unclear and even mildly controversial. Organ et al. acknowledge that the two characteristics did not arise together, but after reference to the larger genomes in flightless birds, they conclude their paper by noting that "the two may be functionally related, perhaps at a physiological level." And they postulate that small genome sizes may have been favored by warm-bloodedness and its associated energetic demands. But a minireview of the paper raises several criticisms of these hypotheses, and it is clear that the evolutionary forces acting on genome size are complex and yet poorly understood.

Notwithstanding the unanswered questions regarding genome evolution, this paper is the kind of scientific article that should be carefully considered by those who deny common descent. Following are some aspects of the story that create interesting questions for creationists and/or design advocates.

Consider the results presented in Figure 2. Outside of common ancestry, how are we to account for these data? The strong correlation between flight and small genome size in living organisms might look like some kind of "design" to someone who favors that sort of thinking, but Organ et al. have conclusively uncoupled genome size and flight. Of course those of us who see the universe as a creation will be happy to marvel at the advantages presented by small genomes to flying organisms, and perhaps we'll all think of these wonders as evidence of brilliant "design." But it seems to me that "design" does not serve a significant explanatory role here. On the contrary, I maintain that the work of Organ et al. demonstrates the following: in dinosaur lineages, the best way to predict genome size in an extinct species is to know the ancestry of the species. Common design aspects don't help. Common descent explains the pattern.

And yet, I think it gets much worse than that for anti-evolution thinkers. I regularly see certain old-earth creationists (e.g. the folks at Reasons To Believe) and design proponents (e.g. William Dembski) arguing that "junk DNA" (which includes, but is not limited to, the 45% of the human genome composed of mobile elements and their debris) is not "junk" but can have important functions. (The arguments of these critics are flawed in several ways, which I'll detail some other time.) While it's true that mobile elements have contributed to the formation of new genes from time to time, and are thought to be significant sculptors of genomic evolution, it's also true that mobile elements are indiscriminate in their jumping, and their continued hopping about is a documented cause of harmful mutation. Here, though, is a significant quandary for a design advocate considering a bird genome: if these mobile elements have important functions in the organism, then how is it that birds can get by with 1/4 as many of them as, say, squirrels? Why, if these elements have important functions in the organism, do bats seem to need far fewer of them than, say, rats? (The genome of the big brown bat is 40% the size of the genome of the aardvark. Hello!) It seems to me that these facts are best understood when one considers the possibility that most of this DNA is essentially parasitic, and that some types of organisms have benefited by restraining its spread. A "design" perspective with regard to genome size is just not helpful, and if that perspective insists on excluding common ancestry, then it's worse than worthless.

Article(s) discussed in this post:

  • Organ, C.L., Shedlock, A.M., Meade, A., Pagel, M. and Edwards, S.V. (2007) Origin of avian genome size and structure in non-avian dinosaurs. Nature 446:180-184.

19 August 2007

Introducing me: on common descent and explanation

What is the evidence for common descent?

To even ask the question, it seems to me, is to suppose that common descent is a proposal, or a hypothesis, and that a certain body of evidence supports the proposal. And that, of course, is quite true: common descent is a scientific theory, and a certain body of evidence supports that theory. But it is my view, and one of the themes of this blog, that the theory of common descent does not derive its main strength, its immense scientific success, from the collection of evidence that supports the proposal that organisms alive today are related through ancient common ancestors. In other words, I think that to claim that “there is a lot of evidence for common descent” is to significantly understate the strength of the theory.

The strength of the theory arises not from the evidence that supports it, although one can certainly build an overwhelmingly compelling case on that basis alone. The strength of the theory arises from its vast explanatory power. The data that make common descent so scientifically compelling are not just the data that “support” the theory. To really understand why common descent is such a powerful theory, one must focus on data that are explained by the theory, findings that just don’t make sense without an explanatory framework of common ancestry.

So I find common descent to be a scientific explanation with extensive and pervasive explanatory power, an explanation that allows data from widely varying areas of biology to just make sense. There is no competing scientific explanation for these data. Many of my weekly journal article reviews will deal with recent scientific findings that are beautifully explained by common ancestry.

But wait: this idea of explanation can be tricky. One can offer various explanations for a particular event or phenomenon, and no single explanation need be identified as the only explanation, or even as the best one. John Haught has famously noted this fact, using an illustration originally created by John Polkinghorne. Suppose someone walks into my kitchen and discovers a tea kettle boiling, then asks, “why is the water boiling?” I could offer several explanations: 1) the water is transitioning from a liquid to a gas, under certain kinetic or thermal influences; 2) an intense blue flame is burning beneath the kettle; or 3) I wanted to make a pot of coffee. (Haught prefers tea. I had to change something.) All of these explanations are correct, and none is better than any of the others. If the question was “why is the water boiling?” then a perfectly true answer can take many forms.

So, when I claim that common descent has no competition as a scientific explanation, I am focusing on the scientific nature of the explanation. If we want to know, for example, why there are highly conserved retroelements at homologous locations on certain mammalian chromosomes, the best scientific explanation is common ancestry. Might there be other true explanations? I can think of several alternative explanations, among them this one: “Because God made the chromosomes that way.” And that’s certainly true. So that alternative explanation is correct, but it’s not an explanation that competes with common ancestry. After all, it doesn’t say how God made the chromosomes that way. And what about this one: “The chromosomes are that way because God made them that way, de novo and without common ancestry, and the evidence for common descent is contrived or illusory.” That’s an interesting explanation, with lots of problems, one of which is this: it’s not a scientific theory in my view. In a future article, I’ll unpack some of the issues here for Christians. Suffice it to say for now that I see that last proposal as an alternative explanation, but not as a competing scientific explanation.

And do I really mean that the theory has no scientific competition at all? Well, no, for in fact there are perhaps innumerable scientific explanations that could account for the observations in question. Maybe, for example, there are unknown and utterly mysterious scientific laws that govern the formation of living things, such that every species acquires its unique characteristics independently of other species. The problem with this proposal is not so much that it isn’t scientific, but that it’s scientifically vacuous. It explains the observations, but has no basis within them. It’s an explanation, but it’s a worthless one.

And yes, that does mean that science employs an interesting and largely unseen set of values, a collection of assumptions and criteria by which explanations are judged. We all know that some explanations are better than others, in that they provide an account that we all judge to be superior to those of other explanations. How does this work? Maybe that question will come up occasionally in my articles or in the discussion.

So that’s what I think about common descent and scientific explanation. And what about natural selection? I’m a big fan of Darwin’s big idea, for sure, but I think the explanatory issues are different in that arena. More to come.

Now you know where I stand on evolution. I’m an NCSE Steve, and I think evolutionary theory is fascinating, powerful (as an explanation) and awe-inspiring (as a view of life’s history). Are there problems for Christians? Sure. But they’re not insurmountable, and there’s nothing to fear in exploring God’s world.

05 August 2007

Why "Quintessence of Dust?"

What a piece of work is a man, how noble in reason, how infinite in faculties, in form and moving how express and admirable, in action how like an angel, in apprehension how like a god: the beauty of the world, the paragon of animals and yet, to me, what is this quintessence of dust?

Hamlet, Act II, Scene II (Arden Shakespeare)

When I consider your heavens, the work of your fingers, the moon and the stars, which you have set in place,

what are mere mortals that you are mindful of them, human beings that you care for them?

You have made them a little lower than the heavenly beings and crowned them with glory and honor.

Psalm 8:3-5 (Today's New International Version)

Then the Lord God formed a man from the dust of the ground and breathed into his nostrils the breath of life, and the man became a living being.

Genesis 2:7 (Today's New International Version)

03 August 2007

Kicking off my blog

Well, it's August 3, 2007, and I'm setting up my blog. It's called Quintessence of Dust, and it will deal with issues of science and Christian faith, focusing on genetics, development, evolution, neuroscience and topics related. I'll regularly address intelligent design and creationism, among other scientific issues that attract the attention of evangelical Christians. My main theme will be scientific explanation.

Most typically, I will base my comments on a very recent article in the scientific literature. I'm shooting for one of these article-based commentaries ("Journal clubs") per week. Minor entries will be interspersed as I feel inspired.

I anticipate errors and correction, and I'll post corrections prominently.

Theology, philosophy and Shakespeare will also figure semi-prominently. I don't really care about politics, so it won't often contaminate the blog unless and until a politician speaks on a topic of interest. (And, of course, they often do.) Boston Red Sox baseball will always trump politics.

So, here's Hamlet getting the first big quote (ripped unceremoniously out of context):

"...there is something in this more than natural, if philosophy could find it out."
--Hamlet, Act II, Scene II