AndrewC: “How do you know that?”
Allmendream: “By its rate of conservation between species, and the fact that it is incapable of making a full length transcript precluding function as a gene or as a stabilizing transcript producing pseudogene.”
AndrewC: “It has a rate of conservation based upon the assumption that it started from the ‘same’ object(as the others which may be used to gauge difference). The other assumption is that it has no function apart from its classification as a potential/actual protein producer.”
I have to agree with Andrew here. As I have pointed out numerous times now, the more pseudogenes are studied the more they prove functional. Moreover, even our ideas of what constitutes function are rapidly changing. For instance, the Darwinists over at Panda’s Thumb assume that if a “pseudogene’s DNA is extensively modified by methylation” it is a “known hallmark of transcriptional inactivity.”
http://www.pandasthumb.org/archives/2006/08/rumors_of_pseud.html
However, the scientists over at Panda’s Thumb are directly contradicted by an international team of scientists who conducted the “first large-scale study of the human genome detailing the sections that are not strictly DNA-sequence based.” In addition to estimating that up to one in six genes might be influenced by external factors, they also concluded that “regions called evolutionary conserved regions (ECRs), lying distant from genes, out in the ‘junk’ DNA, had high concentrations of methylation.” And most importantly, they concluded that said methylation “may indicate that these regions have an undiscovered role to play in gene or chromosome activity.”
http://ec.europa.eu/research/headlines/news/article_06_11_21_en.html
Thus, not only are pseudogenes proving to be increasingly functional, we are also finding that there are numerous functional epigenetic elements that can have a major impact on gene activity/expression. In short, given the rapidly accumulating evidence to the contrary, it is probably best to err on the side of prudence and take pseudogenes out of the “junk” category pending further study of the same.
Not all pseudogenes show conservation of sequence. If you find a function for one that is as divergent as other DNA that hasn’t been shown to have a function and has been shown to change at the neutral mutation rate THEN you break the linkage between function and conservation.
Many elements in DNA are highly divergent and shown to be selectively neutral. Why do you think the group that discovered the first functional pseudogene had a COW when their transgenic mouse showed a phenotype for an insertion within what was thought to be a non-functioning element? They KNEW that this was more interesting than whatever protein/gene they were looking at in the first place. And unlike most pseudogens, this one that had a functional transcript showed conservation, as if it were a gene.
None of the examples you have brought up have broken the linkage between conservation and function. Maybe the Discovery Institute should look into that as a line of research, if they did research.