• genes for rRNA and histones, for which there is constant demand, fall into this category

• One copy may by mutation develop a new and useful function
  • Color vision in Homo sapiens and Old World primates is an example

  • The gene for the visual protein opsin was duplicated, and the second copy mutated to provide a different absorption maximum

  • Only 15 amino acids are different between the two opsins and three of them appear to account for the wavelength difference

    Position in Sequence	180	277	285
    Green Pigment	Alanine	Phenylalanine	Alanine
    Red Pigment	Serine	Tyrosine	Threonine

  • The duplication must have occurred after the split between Old World and New World primates, which happened between 30 and 40 million ybp

• Both copies may be subfunctionalized: mutated so their total activity is the same as the one original

• Mutation may silence one copy while the other is maintained functional by selection

Silenced copies are molecular fossils, or pseudo genes. For example, the gene (MYH16) controls the development of the temporalis muscle, which is involved in moving the jaw during chewing:

Which came first: the mutation or the diminishing of the muscle by other pathways? We can't tell, but a good guess would be that the changed diet of Homo sapiens relative to the great apes made a huge temporalis muscle less important, and hence mutations in the gene were less likely to be repaired.

The accumulation of mutations in a fossil gene may be used to study the overall dynamics and evolution of the genome.

For example, one of the largest gene families in mammals is the family of more than 1,000 olfactory genes

• In humans, fewer than 500 of these are still functional

• More than 300 of our disfunctional ones are still functional in rats and mice

• The great apes lie in between humans and rats

• The greatest loss of olfactory genes among the apes occurs among those that have developed color vision - a sensory trade-off?

That we carry around fossil evidence of an ancestral olfactory system clearly is inconsistent with the idea that we were somehow "designed" or "intended" to be as we are.

Is it possible to raise the dead? May some genes that are fossilized in the sense of no longer having their original function still be transcribed and functional in a new way? Maybe.

• Cows have an RNase gene with a duplicate pseudogene that also is expressed; in all other ruminants, the gene is a fossil
  • The simplest explanation is that the pseudogene was revived in the cow after the evolutionary split from other ruminants

• In the snail L. stagnalis, a pseudogene for nitric oxide (NO) synthesis is expressed and inhibits the expression of the actual NO synthase gene

Overall, several hundred expressed pseudogenes have been identified, but no function has been attributed to most of them. [Gerstein et al., Nucleic Acids Research, 2005, 33, 2374].