Friday, May 1, 2009

Dinosaurs, immunity, and yeast

The latest issue of Science has some good stuff. Mary Schweitzer is back with evidence of hadrosaur collagen. I know lots of creationists that get charged up by this sort of thing, since this is supposed to be evidence that the fossils must be younger than conventional claims by millions of years. I've never been very excited about this, mainly because the Flood throws a real monkey wrench into these arguments. A major source of degradation of biomolecules is water. So anything that died in the Flood and floated in water for a year shouldn't really have many biomolecules left, right? Seems like if you believe fossils are millions of years old or are the remains of carcasses from the Flood, the outcome is the same: very little preservation of biomolecules. In this case, Schweitzer is finding collagen, which is pretty tough, so I guess it makes sense that it might be preserved in some extraordinary cases. In any case, finding the rare, hardy biomolecule from dinosaurs is nothing to get excited about, since the conventional model and the Flood model both predict the same thing: this should be very, very unusual.

There's also an interesting essay on the origin of the immune system from John Travis. He doesn't make Behe look very good, but then... well, the less said about that, the better. He does highlight an intriguing idea emerging in the immunology community, which the editorial summary describes with this question:
Did the immune system evolve to keep out harmful organisms, or is it like a bouncer at a nightclub, trained to allow the right microbes in and kick the less desirable ones out?

Now that's a cool idea: The immune system is supposed to let the right bugs in. Maybe keeping things out is secondary? Maybe that's why it sometimes doesn't work so well? (Sometimes I wish ID advocates would pay attention to things that are actually interesting.)

Most interesting is the paper from Tirosh et al. on the evolution of gene expression in yeast. Yeah, that's right. Yeast is more interesting than dinosaur protein. At least this yeast is. I love how the genome age has finally provided us with tools to begin probing really interesting questions. In this case, they "designed designed a microarray that enables the measuring of allele-specific expression in a hybrid of Saccharomyces cerevisiae and S. paradoxus." What does that mean? Well, it means they can monitor in detail how genomes react to the stress of hybridization, which is kind of like rewinding the clock on speciation. From a neodarwinian perspective, speciation commences by the accumulation and selection of genetic variation, and many, many creationist criticisms of evolution focus on this model, for right or wrong.

For a long time, hybridization has made me suspicious of the simplicity of this model. Maybe it's just my own overly simplistic conception of neodarwinism, but I would guess it is an oversimplification shared by many creationists. Hybridization does weird things, from reorganizing a genome in a kangaroo hybrid to plain old hybrid vigor. These phenomena suggest that phenotypic or even genomic divergence can be accomplished in ways we haven't even begun to imagine. The real key seems to be gene expression, which is why I'm excited about this yeast paper.

To be clear: This paper from Tirosh et al. does not invalidate the neodarwinian model. It actually confirms an important part of that model, namely that variations in the DNA "account for most of the expression divergence." In other words, the main reason that S. cerevisiae and S. paradoxus are phenotypically different is because they have different DNA sequences (duh). They also found that novel gene expression patterns in the S. cerevisiae x paradoxus hybrid are often the result of complex interactions between regulatory proteins and the environment. So as often happens in genetics, the combined expression of two genes is not additive, it's synergistic. Unexpected things happen.

What does that have to do with speciation (or creation for that matter)? I think we creationists need to stop thinking as if the gene is everything, as if a change in a gene sequence or regulatory sequence is "the" problem. Changing the entire system is "the" problem, and that can happen in very unexpected ways, sometimes without very large changes to the DNA. This doesn't alleviate the problem of how the DNA sequences change, but it forces us to rethink both critiques of neodarwinism and our own models of intrabaraminic diversification.

My point is probably still unclear, but I've rambled on long enough in this post. Maybe I should write up something on the fascinating subject of "synergistic epistasis" and why we need to pay attention to it.

Schweitzer et al. 2009. Biomolecular characterization and protein sequences of the Campanian hadrosaur B. canadensis. Science 324:626-631.

Travis. 2009. On the origin of the immune system. Science 324:580-582.

Tirosh et al. 2009. A yeast hybrid provides insight into the evolution of gene expression regulation. Science 324:659-662.