[AndrewC]

Divergence would be at the neutral mutation rate for those sequences not under selection, so that would be the rate of conservation. It has no function because its transcript is terminated, it cannot make a protein.

Again, assumptions. What sequences are not under selection?(how do you tell things are being selected?) Function and proteins... why do you suppose there was suprise at the "small" of protein coding genes?

"Although the completion of the Human Genome Project was celebrated in April 2003 and sequencing of the human chromosomes is essentially "finished," the exact number of genes encoded by the genome is still unknown. October 2004 findings from The International Human Genome Sequencing Consortium, led in the United States by the National Human Genome Research Institute (NHGRI) and the Department of Energy (DOE), reduce the estimated number of human protein-coding genes from 35,000 to only 20,000-25,000, a surprisingly low number for our species (7). Consortium researchers have confirmed the existence of 19,599 protein-coding genes in the human genome and identified another 2,188 DNA segments that are predicted to be protein-coding genes. "

from --- http://www.ornl.gov/sci/techresources/Human_Genome/faq/genenumber.shtml

[allmendream]

Measurements of divergence at the neutral mutation rate for sequences not under selection confirm the assumptions. You can tell if sequences are not being selected because they do not show conservation and do not have a open reading frame. When comparing genes and pseudogenes between related species the pseudogenes are similar but the genes are even more similar.

The reduction in the estimate of 35,000 genes to 20,000 to 25,000 is very interesting. The predicted protein coded genes are probably predicted based upon genetic conservation and recognizable open reading frames that could code for a protein.