tag:blogger.com,1999:blog-37148773.post3611995901771325563..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: Must a Gene Have a Function?Larry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger6125tag:blogger.com,1999:blog-37148773.post-26851130588804092422012-02-10T21:01:31.795-05:002012-02-10T21:01:31.795-05:00Larry,
"Genes that Encode Functional RNAs&qu...Larry,<br /><br />"Genes that Encode Functional RNAs"<br /><br />Encode?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-52084560234519332402012-02-08T20:28:39.994-05:002012-02-08T20:28:39.994-05:00Since the best (or at least the easiest) test for ...Since the best (or at least the easiest) test for functionality is evolutionary conservation, it would probably be a good idea if you're looking for <i>de novo</i> genes not to look at a terminal node but at some internal node, old enough that we could distinguish neutral evolution from purifying selection. I would suggest looking for sequences present and conserved in hominids (<i>sensu lato</i>) but not present in other primates.John Harshmannoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-62588677274219900142012-02-08T15:52:04.677-05:002012-02-08T15:52:04.677-05:00But it's always the exceptions to the rule--hu...But it's always the exceptions to the rule--human-specific duplications with implications for disease and evolution--that make for good research projects and likely create a bias among researchers about function.gilltnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-66558790698335568742012-02-08T15:51:56.785-05:002012-02-08T15:51:56.785-05:00Given this very stringent definition of "func...Given this very stringent definition of "function" (with which I largely agree), is your earlier challenge here really a fair one?<br />http://sandwalk.blogspot.com/2011/01/challenge-to-fans-of-alternative.html<br /><br />I suspect that even if you restrict yourself to the primary splice isoforms of genes conserved across several species, there just isn't enough evidence out there yet to demonstrate function for more than a fraction of them, unless you allow yourself to infer function from sequence conservation.<br /><br />Conversely, even where there's a demonstrable biological effect, it can be arguable as to whether that constitutes a <i>function</i>. Consider the case of a newly-evolved miRNA, that alters the expression levels of a few dozen protein-coding genes and has some phenotypic consequence when deleted. Can we say that this miRNA truly has a function? Or is rather that the miRNA is a bit of rubbish left over from RNA processing, and which interferes with the expression levels of a number of genuinely functional genes. The fact that the functional genes subsequently evolved workarounds to maintain their function in the presence of the interfering detritus doesn't mean that the detritus itself plays a meaningful role.Peterhttps://www.blogger.com/profile/12559721137290332762noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-41891969173427409882012-02-08T14:46:39.599-05:002012-02-08T14:46:39.599-05:00Everything is subject to natural selection but tha...Everything is subject to natural selection but that's probably not what you meant.<br /><br />You meant to ask whether it has to be adaptive. The answer is no. There are many identical copies of some genes and it's likely that the extra copies are redundant. That's why they usually "die" by mutation.Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-87174004227567468992012-02-08T13:48:06.227-05:002012-02-08T13:48:06.227-05:00To qualify as a a "function" within this...To qualify as a a "function" within this definition, must a character be subject to natural selection? For example, there are evidently so many bits of transcribed RNA floating around that no doubt there are some that, just by chance, will have a measurable biochemical effect on something else somewhere in the cell. However, if the effect of the RNA was not selected for in the first place, and if it is not subject to selection because the effect in question has no impact on reproductive success -- then does this piece of RNA have a "function" within the contemplation of the definition?FitzRoynoreply@blogger.com