28 March 2010

Introns and design

Mike Gene has posted an interesting series on introns that's worthy of a few comments. His thesis is that "introns facilitated the evolution of multicellular life."

A. The idea is interesting and rational but not novel. Research on introns and evolution is active and lively, and one prominent scientist in the field, Eugene Koonin, has proposed that introns drove many aspects of the evolution of eukaryotes (i.e., non-bacteria).

B. The more general proposal that mobile genetic elements have facilitated evolution of multicellular life is somewhat new (the first major review of the idea appeared in 2004) but also uncontroversial. Thus the notion that non-coding DNA elements are important evolutionary forces is not novel and is clearly not an explanatory problem for evolutionary biology. (And Mike did not claim that it is.)

C. Mike's overall design argument is based on front-loading, i.e., he postulates that "unicellular life was designed to frontload the appearance of metazoan life." The idea is that early unicellular life contained elements which were included mainly to facilitate the development of multicellular life. I'm not a fan of this kind of reasoning, but there's nothing profoundly irrational about it, and Mike can certainly claim to be in distinguished company on this one – Simon Conway Morris once referred to sponges as "animals in waiting," making a similar front-loading allusion without the emphasis on teleology.

Both Mike and Conway Morris are referring to the fact that various genetic elements that seem to be animal-specific or vertebrate-specific are nevertheless found in species thought to represent much more ancient lineages. Conway Morris talks of seemingly brain-specific components found in sponges (which lack a nervous system) and Mike notes that introns are found in single-cell eukaryotes, specifically the kind of organism (a choanoflagellate) that is not an animal but is thought to be related to the single-celled creatures that gave rise to plants and animals. Whether this should be called "front loading," I don't know. But it's pretty clear that the earliest eukaryotic cells, including those which probably gave rise to multicellular life, already had a lot of introns in them.

D. But Mike makes some mistakes that I want to focus on, because one of them illustrates a particularly serious intellectual danger of design-think.

1. Mike asserts that bacteria don't have introns. This is not quite true. The group II introns are present in many bacteria – in some genes – and are thought to be forebears of the group I introns that are so widespread in animal genomes. The implication is that the intron table was already set long before the eukaryotic (much less multicellular) party had started. The "front-loading" would appear to have occurred in bacteria themselves. (Mike alludes to this in the first post of the series.) And that matters because...

2. ...Mike says something really strange early in his series. His first "clue" that introns facilitated multicellular life is the observation that bacteria don't have introns and that bacteria don't make multicellular organisms. He concludes that bacteria are disabled by their lack of introns, and thus are unable to accomplish the feat of generating the wonders of the animal and plant worlds. He asks the bizarre question, "Where are the prokaryotic mice?" He points to the difference in complexity between prokaryotic cells (bacteria, basically) and eukaryotic cells (cells with nuclei, the cells that make up all plants and animals) and summarizes the diversity of cell types that can be generated by eukaryotic cells (brain cells, muscle cells, etc.) in contrast to the simplicity of prokaryotic cell types.  All true. But look carefully at his conclusion:

Note that while the vertebrate expression of the eukaryotic cell has been able to spawn 120 different cell types, both eubacteria and archaebacteria have not moved beyond a meager 2, even though these prokaryotes are both more numerous and older than eukaryotes.
It sounds reasonable, until you think about the tree of life and the reality of common descent, explanations which Mike Gene readily acknowledges. In the context of an unfolding tree of life, his statement reduces to "animals are eukaryotes" and nothing more. Let me explain.

Mike asserts that prokaryotes haven't spawned multicellular life. But that's not true. In fact, all indications are that prokaryotes spawned all multicellular life. The first eukaryotic cells are thought to have been forged by combinations of prokaryotic cells (this is the well-known endosymbiotic hypothesis) and the presence of group II introns in bacteria is just one of numerous observations that point to common ancestry between eukaryotes and prokaryotes. In other words, unless Mike is disavowing common ancestry (the trunk of the tree of life), then his conclusion doesn't make any sense. Prokaryotes really did give rise to multicellular life, by giving rise to ever more complex cell types.

Now, maybe you don't think there's a big mistake here. Mike is just saying that simple cells can't make complex multicellular assemblages, right? Well, no, he's saying something more than that. He's saying that through vast numbers and vast ages, they should have done so. He thinks it's notable that prokaryotes, even after almost 4 billion years and countless individual lives, haven't formed a mouse. I think this is crazy talk.
  • Bacteria actually do form very interesting multicellular assemblages. Organisms? Not really. But let's not ignore the fact that prokaryotes do know how to live in complex and cooperative environments. 
  • Most importantly, Mike's thinking here shows a weakness that I believe arises most commonly in design-oriented analyses of evolution. He seems to think that the presence of prokaryotes today, in all their lame simplicity, is notable because they coexist with those majestic miracles of design and performance, the awe-inspiring flora and fauna of metazoan life.  But that's nonsense. Prokaryotes are successful – wildly successful – in countless niches which have never been colonized by multicellular organisms. Why not ask why they are so successful? Why not write a series in which the presence of introns and mobile elements and organelles is put forth as an explanation for the disastrous failure of multicellular life to dislodge the humble archaea and bacteria from these positions of ecological dominance?
Do you see the mistake? It's in the assumption that a simple species is a failure, and a complex one is a success. Mike didn't ask why the most extreme environments on earth are populated by archaea, those ancient and simple prokaryotes, and not by highly-complex animals. That imbalance, I believe, arises from the emphasis on design, and it's an error we all wrestle with.

Mike's right about introns and their likely role in the origins of multicellular organisms. But he's wrong to associate complexity with success, and I think he's wrong to assert that introns in particular were necessary for the evolution of multicellularity and its associated complexity. I suspect that there are lots of ways to encourage genetic diversity and modularity, but that introns and splicing, dating to the RNA world, made the contribution because they were there when others weren't.

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