tag:blogger.com,1999:blog-37148773.post2188939277386200709..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: What Does the Bladderwort Genome Tell Us about Junk DNA?Larry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger7125tag:blogger.com,1999:blog-37148773.post-82092433441407166662013-05-31T06:36:35.396-04:002013-05-31T06:36:35.396-04:00You are not the first person to offer such a specu...You are not the first person to offer such a speculative explanation for junk DNA. Since you can be certain that ideas like yours have been around for at least four decades, ask yourself why they haven't been accepted by the experts. There must be a reason. Do your homework.<br /><br />Does it pass the Onion Test?Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-72449407143950994052013-05-31T04:49:07.882-04:002013-05-31T04:49:07.882-04:00"An easy and very plausible answer is that ge..."An easy and very plausible answer is that genomes record and store information for reference purposes when the need arise. It explains why nothing happens when its so-called junk DNA is deleted.<br /><br />Any effects would not be seen in terms of the survivability of the genome after deletion...but certainly would have an effect if/when that information was needed to adapt to new environmental conditions."<br /><br />Yes, that has been proposed before and does make sense as an hypothesis. But that doesn't make it any less "junk" by the definition. Junkyards are full of junk, but the reason why they are profitable is because sometimes people find them useful later on. That's why we keep "junk" around at home but not "trash".<br /><br />Functional DNA means that the DNA is either regulatory or gets transcribed/translated into useful RNA/proteins. Gene duplication generates many pseudogenes that are free to change, eventually maybe turning into something useful under certain conditions. But while they are not useful they are "junk" with no function that can be deleted. This is perfectly accepted in molecular evolution. If you delete them nothing happens, but they may turn into something useful on the long haul. But all these pseudogenes and other forms of nonfunctional DNA are still "junk" as per the definition of the term. What ENCODE proposes is something far different (for which they really have no evidence at all). Pedro A B Pereirahttps://www.blogger.com/profile/15195139833344839287noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-70296944083985764402013-05-31T03:04:41.411-04:002013-05-31T03:04:41.411-04:00An easy and very plausible answer is that genomes ...An easy and very plausible answer is that genomes record and store information for reference purposes when the need arise. It explains why nothing happens when its so-called junk DNA is deleted.<br /><br />Any effects would not be seen in terms of the survivability of the genome after deletion...but certainly would have an effect if/when that information was needed to adapt to new environmental conditions. <br /><br />IN principle, this explanation could be tested by exposing a plant to a wide variety of conditions and record the results....then knock out a sizable portion of the genome (several times; each time knocking out a different area) and run it through the same conditions as before the knock-out and compare the difference in performance. <br /><br />This would be a big undertaking like the Lenski experiments but could conceivably provide evidence that in fact the so-called junk DNA is useful if not essential to a genome.<br /><br />That would answer the reason why genome sizes are not proportional to their complexity.<br /><br /><br />Stevehttps://www.blogger.com/profile/15246115342112568778noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-30454099024112686342013-05-30T21:26:29.964-04:002013-05-30T21:26:29.964-04:00Larry has also addressed your comments about the c...Larry has also addressed your comments about the cost of junk DNA to the organism (negligible from what I recall) and the protection it might provide against radiation induced mutations (none as John Harshman indicates) in previous posts.steve oberskihttps://www.blogger.com/profile/14067724166134333068noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-7662264472281784422013-05-30T21:22:56.055-04:002013-05-30T21:22:56.055-04:00Randy, I believe some work has been done with mice...Randy, I believe some work has been done with mice were some of the junk DNA was removed with no observed deleterious effects.steve oberskihttps://www.blogger.com/profile/14067724166134333068noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-22608813469960856952013-05-30T20:41:16.063-04:002013-05-30T20:41:16.063-04:00Probably not. A bigger target just means more hits...Probably not. A bigger target just means more hits and doesn't change the probability that any particular spot gets hit. If there were some quota for number of mutations per genome, you would have a point.<br /><br /> But be careful. You might attract the attention of Claudiu Bandea.John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-54266272630579093192013-05-30T19:12:28.118-04:002013-05-30T19:12:28.118-04:00Can we now, or perhaps soon, simply eliminate junk...Can we now, or perhaps soon, simply eliminate junk DNA and see what happens? I think of defragmenting the free space on a hard drive. The files are all preserved, but it's a lot neater.<br /><br />I don't know anything about the subject, but maybe by filling up the space with more junk, perhaps it protects the important DNA by providing a larger target for harmful radiation or whatnot to hit. If it harms the junk DNA, perhaps that's not bad. Is this a reasonable guess?Randyhttps://www.blogger.com/profile/06294841118508802764noreply@blogger.com