- gene expression is far more important than the quantity of genes themselves,
- a number of important genes (the Hox genes) might be traced back to the Cambrian explosion,
- the number of genes across all species is smaller than expected, and
- there is high commonality of genes across species.
One of my acquaintances made an even stronger claim: that evo-devo has determined that our global gene pool has been stable for half a billion years or more. Let's call this the stable genome theory. I think this is an extreme claim, and I'm not certain what evidence one could possibly find that would support it.
The evidence for such extreme stability of our planet's genome is a bit slim, as far as I can tell. For example, we only suspect that Hox genes were present since the Cambrian explosion 540 million years ago because we know they are capable of creating all of the morphologies we have seen since. However, it's also possible that we evolved completely new genes that perform the same functions. If nothing else, the stable genome theory seems a bit single-minded in its dismissal of gene mutations over the last few hundred million years.
Still, it's a very interesting theory.
My colleague was making this extreme claim in the context of an argument for intelligent design (ID). From his perspective, our planet's gene pool had remained roughly intact since the dawn of life, and yet it provided the source of all variation within and across species. He interpreted our gene pool as something akin to a pre-written library of computer code for all life, a situation which he felt contrary to evolution. Until recently, it was believed that ongoing mutations of the genes themselves were the root source of variation between and within species. So if we discover that all of the mutation that powers evolution happened very early in Earth's history, what does that say about evolution? And why hasn't our genome continued to evolve new genes since the Cambrian?
His argument for design is flawed in several different ways.
First, evolution never depended on any specific mechanism to explain the source of variation. Evolution is a fact of the fossil record, and the theory is true independent of the mechanism that generates variation. That's why evolution was an accepted scientific theory before DNA was discovered. We have not "found fossil rabbits in the Precambrian."*
Second, if evo-devo is correct, the genes aren't parts of a master computer program, they are just raw materials. It is the regulating factors that control the expression of those genes which form the programming for any given life form. The early production of our genome is no different than the early production of amino acids or the DNA replication mechanism itself. In this scenario, it is the regulating factors that are mutated and which evolve, not the genes. Genes would be raw materials for life much the way atoms are raw materials for chemistry; the genome would be akin to the periodic table of elements.
Third, if our genome has not mutated since the Cambrian (or before), then there must be some simple explanation. One explanation would be that our genome consists of all compatible, stable genes. Any other gene sequences would be toxic because they would create killer proteins or interfere with the expression of vital genes. Another possible explanation would be that creating genes requires an environment that facilitates certain kinds of mutations, perhaps primitive supernuclei** in the primordial soup were the only efficient way to create a spectrum of genes. That is, today's mutations are too clumsy to create whole new genes, so no new genes were created since the early Earth supported supernuclei. Since the early Precambrian, the Earth has not seen conditions capable of creating new genes.
The fourth flaw is that intelligent design isn't a theory at all. It has no explanatory power. No matter what connections we deduce, no matter what emergent beauty uncover, intelligent design advocates will always point to whatever mysteries still lie ahead as evidence for a creator. Intelligent design can never, ever be falsified. To the ID believer, nothing is as elegant as the words "God did it."
Arguments about ID aside, the stable genome theory is a very interesting one. One can imagine a scenario in which conditions 3.8 billion years ago generated substantially all of our genes (and those of other species). Since then, evolution has mixed and matched genes and tweaked the expression of those genes to create the diversity of life we see today.
If this theory were true, and again, I can think of no easy ways to prove it, then either modern mutations cannot create new genes, or they can only create poisonous ones.
I suspect that reality is not as simple as this. We probably have a blend of genes, many of which were created billions of years ago, many that were created since.
* To quote the British scientist, J.B.S. Haldane.
** Supernuclei are something I just made up. They would be giant versions of the nuclei within normal cells, but they would hold thousands of chromosomes, and run amok with sloppy gene replication. Okay, it's far-fetched. Dammit Jim, I'm a physicist, not a biologist!