"junk DNA" a useful term or not?

mispost, sorry having trouble with the boardThis message has been edited by mick, 05-19-2005 11:54 AM

mispostThis message has been edited by mick, 05-19-2005 11:53 AM

Hi,I'm picking up a discussion that was taking place on the simple evidence for ID thread. AdminBen requested that the discussion be moved here. The discussion concerned repetitive elements and pseudogenes. Junk DNA replicates itself during cell division in the same way as any other DNA. But I guess you are asking how repetitive elements duplicate themselves and spread around the genome.There are some pictures of the process at the following locations:http://www.anselm.edu/...age/jpitocch/genbio/transposons.JPG
(I think the "transposon enzyme" must refer to reverse transcriptase)http://www.gmuender.org/bt/genetik/img046.gif
(This looks like a viral insertion)Here is a nice overview of the different types of repetitive element: Sticking with repetitive elements for a moment - there is a good way to tell that repetitive elements are of viral origin rather than degradation of old human genes. Each retrovirus contains a set of characteristic genes - these are called gag, pol and env. Gag is the gene that codes for the viral capsid (the outer shell of the virus), pol is the gene that codes for reverse transcriptase, and env is the gene that codes for proteins that stick out of the coat of the virus. When you look at the larger repetitive elements (like LINEs) you find that you can identify viral env genes within the nucleotide sequence. So the viral origin of these repetitive elements is clear.Moving to pseudogenes, you are right that these are old degraded genes. But they tend to be degraded duplicates of extant genes, not degraded ancestral genes. Usually, for every pseudogene you have, you also have a functional copy of the same gene. Pseudogenes tend to have a relatively recent origin in random gene duplication. When a gene (or part of a gene) is accidentally duplicated, the genetic control systems of that gene are usually not duplicated along with it. So the new duplicate never gets to be expressed.If you want to find some ancient remnants of ancestral genes, the best place to look is our housekeeping genes! We share many such genes with yeast, for example, and they are still functional and expressed. I suspect that ID would like to find a function for things like repetitive elements. But it's pretty clear that they have no function other than their own duplication, and hence are good evidence for Darwinian processes operating within the genome. They don't appear to have any biological function in the cell. If anything they impose a cost in terms of the rapidity with which a cell can divide. Pretty much the same goes for pseudogenes. Pseudogenes are coding genes that are never expressed - therefore they are genes that have LOST their function. The propogation of repetitive elements is probably consistent with your view, yes. Although the phylogenetic patterns implied by the distribution of repetitive elements in different species are not consistent with YEC.MickThis message has been edited by mick, 05-19-2005 12:13 PM

The only thing I would add is that there is evidence that (some) introns do actually have a function, and play a role in gene expression.First, some introns are self-splicing (they fold themselves up and remove themselves from the mrna autocatalytically, which is a function of a sort).Second, some of the intron-coded mrna can act as a transcription regulator for the gene of which it is a part, and for transcription in general (google snoRNA).Third, it is also possible that introns act as spacers that put the exons into positions accessible to transcription factors.Last, there is at least one example of a gene in which all the functional sequences are contained within the introns rather than exons (I think the introns all code for snoRNA, and the exons are destroyed without doing anything).While we can be pretty sure that repetitive elements (30-40% of the human genome) and pseudogenes are genuinely junk, the position on introns is less clear.MickThis message has been edited by mick, 05-19-2005 01:23 PM