Homeobox, Sweet Homeobox

There Goes the Neighborhood, or what the protochordate said to the other invertebates when it learned that vertebrates had let four copies of the Hox genes move into one genome instead of the traditional single Hox cluster dwelling. Truer words have rarely been more unspoken.

Viewed at the species level, evolution can seem random, chaotic, and rapid - at least if you consider 100,000 years rapid. From the genome's eye view, not so much. Genomes tend to be staid, conservative neighborhoods. The pace of change at the genome level is two or three orders of magnitude slower, but it tends to be cumulative. There are no "new" genes, just variations on the old ones. If one of these variations has the right accent, and can fit in with the guys at the club, it might be allowed to hang around.

The discovery of the homeobox genes about a quarter of a century ago was perhaps the most important in the history of embryology. They are a sort of Rosetta stone for the whole of developmental biology. A subset of the homeobox genes, the Hox genes, provide the solution for a long standing developmental problem: since each cell contains the same genes, how does it know what genes to express? How does a cell know to become the appropriate part of finger, heel, heart or brain? Their discovery had an amazing bonus: though they were first found in fruit flies, a nearly identical set of genes turns out to play the same role in almost the whole animal kingdom. It's as if the Intelligent Designer could think of only one way to control development. The genes are so similar that if you insert the mouse's version of the "make an eye here" gene into an embryonic fruit fly leg, it makes a fruit fly eye on that leg.

Hox and the homeobox are the subject of "The fruit fly's tale" in Dawkins' The Ancestor's Tale but despite it's 2004 publication date, some details are already a bit out of date. He is aware that vertebrate genomes are more complex than their invertebrate counterparts, but does not seem to know that the quadrupling of Hox domain took place between Amphioxus and the vertebrates. He knows that developmental patterns in plants are controlled by a non-homologous MADS box set of genes, but doesn't seem to know that both homeobox genes and MADS box genes are found in all the branches of the eukaryotes - though last I heard, it was not clear what they are up to in single-celled creatures. Consequently, both sets of genes seem to date back before the dawn of the metazoa (multi-cellular life) a billion or more years ago.

Change is slow and gradual in the genome neighborhood.