tag:blogger.com,1999:blog-5255808252082956251.post6326280843936934244..comments2024-02-16T01:48:30.016-08:00Comments on mathbionerd: ENCODE: The good, the bad, and the uglymathbionerdhttp://www.blogger.com/profile/17525536407206138695noreply@blogger.comBlogger2125tag:blogger.com,1999:blog-5255808252082956251.post-61255284792581473452013-05-24T09:47:39.606-07:002013-05-24T09:47:39.606-07:00Hi Dr. Drey,
I think you are spot on. That has be...Hi Dr. Drey,<br /><br />I think you are spot on. That has been the crux of the "ugly" portion. Many scientists agree with you that understanding function as it affects the cell is more important that the broad definition of any biochemical activity decided upon by the main ENCODE consortium. <br /><br />There are many labs in the ENCODE consortium that are working on understanding this more specific question. I cannot imagine how frustrated they must be they their research is being overshadowed by this debate.<br /><br />Unlike "the human genome" (which we now know varies much more across humans than originally expected), we know that "the human transcriptome" is highly variable between tissues of the same individual, let alone across individuals. That doesn't mean that we shouldn't look for consensus across individuals and populations that can help make broad statements, but it is a much more nuanced process... kind of like clinical work. :)mathbionerdhttps://www.blogger.com/profile/17525536407206138695noreply@blogger.comtag:blogger.com,1999:blog-5255808252082956251.post-46171628239305334122013-05-23T05:17:39.480-07:002013-05-23T05:17:39.480-07:00I'm still lurking on your posts and think they...I'm still lurking on your posts and think they are excellent! :-)<br /><br />Here I'd like to half comment half question since the deep details are far outside my expertise but much more up your alley -<br /><br />Namely, as you note, the question of the definition of functionality. "any biochemical activity" to me seems like a pointless definition in light of what we (admittedly relatively recently) know about proteomics, epigenetics, siRNA, etc. it would seem to me that pretty much ALL DNA should actually have SOME biochemical activity. It is, after all, a very biologically active molecule. <br /><br />The better question for me would be "what is the functionality and us it significant" rather than "does it have ANY"<br /><br />I can imagine it likely that there are sequences of DNA that are functional by accident - simply because it happens to be reactive - with or without specific compensation in cellular processes for the activity. I can also see much of it being of little or no significance. After all, water in the cell is also functional and necessary in the biochemical processes. <br /><br />Maybe it is just the clinician in me talking (though of course I would love to ultimately characterize every single atomic movement if a cell for as perfect a model as out friend Heisenberg will allow) but it seems a better task to focus on a more narrow definition with a specific focus as to what the functionality is to better build our understanding of the major interactive systems within a cell to build a model we can use to make predictions at the -omic level. This would, ass I see it, allow us to actually better understand and predict the effects if plieotropic phenotypes which are, after all, the cause of most disease and pathology (and variation). <br /><br />Am I totally off base in my (albeit brief and rough) thinking? Dr. Dreyhttps://www.blogger.com/profile/02723658004615108572noreply@blogger.com