Curing cancer with beer and speculative genetics

Carl Zimmer has an excellent piece in today's Science Times focusing on the notion of deep homology in genes. Deep what, you ask? Zimmer begins by writing about research to find genes that play a role in the growth of blood vessels. The hope is that if these genes can be identified, they can be turned off and slow the growth of tumors. The genes are part of the yeast genome which doesn't even have blood, let alone blood vessels, and Zimmer's article reveals why cancer researchers would bother to look at genes that repair cell walls in yeast.

Deep homology is the concept that body structures do not arise anew, but evolve from existing structures. Drs. Shubin, Tabin, and Carroll explain it well in the abstract to their 2009 article in Nature:

Advances in developmental genetics, palaeontology and evolutionary developmental biology have recently shed light on the origins of some of the structures that most intrigued Charles Darwin, including animal eyes, tetrapod limbs and giant beetle horns. In each case, structures arose by the modification of pre-existing genetic regulatory circuits established in early metazoans. The deep homology of generative processes and cell-type specification mechanisms in animal development has provided the foundation for the independent evolution of a great variety of structures.

In other words, new structures share common genetic ancestry with older structures. The human eye and the contemporary jellyfish eye, for example, evolved not from anything that looks remotely like an eye, but from cells in aquatic species that also had light-sensitivity. What these structures have in common is a genetic sequence that provides the template for the assembly of c-opsin - a light-sensitive protein. And that is the most important point that Zimmer's article and the articles by Shubin and Carroll make to me. Genes rarely directly make disease, they don't directly encode complex behavior, and they aren't even "designed" for the purpose of building a given anatomic structure per se. Genes sequence proteins and in the context of different organic substrates those proteins can be adapted for specific functions. It is fun to get lost in the speculative connections that books like Richard Powers's latest make about "happiness genes," and the like. But it is worth being cautious about allowing such dreams to drive scientific terminology. This is well illustrated by the following excerpt from Zimmer's article:

Scientists are also discovering that our nervous system shares an even deeper homology with single-celled organisms. Neurons communicate with each other by forming connections called synapses. The neurons use a network of genes to build a complete scaffolding to support the synapse. In February, Alexandre Alié and Michael Manuel of the National Center for Scientific Research in France reported finding 13 of these scaffold-building genes in single-celled relatives of animals known as choanoflagellates.

No one is sure what choanoflagellates use these neuron-building genes for. The one thing that is certain is that they don’t build neurons with them.

Then maybe we shouldn't call them neuron-building genes? It's easy, if one is driven by a passion for a narrow sliver of knowledge, to see everything as related to that expertise. It makes sense to drive hypothesis-making with our knowledge of genes, since their action precedes any biological function or structure we can observe, but this article reads like a cautionary tale regarding attaching structural significance to a gene if knowldge of its function is not secure. Genes sequence proteins. Genes sequence proteins. Read Zimmer's article - it combines clear writing about contemporary basic science with a good story about current newsy science. A really good piece.