tag:blogger.com,1999:blog-37148773.post1868285915638772712..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: More Junk DNA FallaciesLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger20125tag:blogger.com,1999:blog-37148773.post-51404247203326214542009-10-05T15:21:24.804-04:002009-10-05T15:21:24.804-04:00Thank you, Nils Reinton, for calling these bozos o...Thank you, Nils Reinton, for calling these bozos on their sh--.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-23019710277647367792009-09-23T14:09:24.411-04:002009-09-23T14:09:24.411-04:00All these conjectures about what junk DNA is for a...All these conjectures about what junk DNA is for are begging the question. I've not heard any reasonble evidence to suggest that the majority of junk DNA is 'for' anything.<br /><br />Given what's known about copying errors, sequence duplication, mobile genetic elements, etc., the simplest explanation still seems to me that junk DNA is exactly that. Junk that has no particular function, but doesn't cause enough of a fitness burden to be purged faster than it's created.<br /><br />The idea that junk DNA serves as some kind of reservoir to support 'evolvability' is intriguing. But, without some supporting evidence, it sounds to me like an ad hoc conjecture based on the unstated and irrational belief that junk DNA <i>must</i> be doing <i>something</i>.qetzalnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-58675061070035397692009-09-23T12:50:36.058-04:002009-09-23T12:50:36.058-04:00I could be wrong, but one significant difference m...I could be wrong, but one significant difference might be that bacteria have relatively rapid generational turn over vs. us bigger creatures. Thus maybe sleek genomes, aren't as much of a problem.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-15680859127172442522009-09-23T10:49:44.141-04:002009-09-23T10:49:44.141-04:00Thus, the “less junk” kind may have a lower probab...<i>Thus, the “less junk” kind may have a lower probability than the “more junk” kind of having acquired any useful digital information. More junk becomes more common – we observe this and try to figure out why.</i><br /><br />Your argument is interesting, but I am not really convinced.<br />Bacteria get by with very sleek genomes, and they can rapidly adapt. Thus, there seems to be no need for huge reserves of non-functional DNA to sustain adaptability. Also, within taxa there is a huge variation in the DNA content. It is really hard to explain this in your scenario, as directional selection for increased genome size would minimize differences.Corneelhttps://www.blogger.com/profile/02884855837357720225noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-34170154617446171122009-09-22T17:12:07.915-04:002009-09-22T17:12:07.915-04:00What is selected for is that which aids in the sur...What is selected for is that which aids in the survival and reproduction of a given organism in a given environment - but environments change, we know this. The adaptation of new traits requires the shuffling, deleting, adding, copying, and changing of digital information- the genome (we know this too). <br /><br />If having less junk means a decrease in the ability to do the above tasks, then an organism with less junk (by chance) may also have less of a chance at survival and proliferation given some pressure. Thus, the “less junk” kind may have a lower probability than the “more junk” kind of having acquired any useful digital information. More junk becomes more common – we observe this and try to figure out why.N. Ataiehttps://www.blogger.com/profile/12909551501290741641noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-31636960563753729112009-09-22T16:53:10.684-04:002009-09-22T16:53:10.684-04:00Are genes for eye color junk do you suppose, or is...<i> Are genes for eye color junk do you suppose, or is eye pigmentation essential? </i><br /><br />No definition of junk DNA includes a recognizable, functional protein gene.The Other Jimhttps://www.blogger.com/profile/17570666738076378921noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-68282712059628261572009-09-22T15:18:14.544-04:002009-09-22T15:18:14.544-04:00If junk DNA is defined as non-essential, then this...<i>If junk DNA is defined as non-essential, then this is not a false dichotomy.</i><br /><br />Yes, but that's a silly way to define junk DNA. Are genes for eye color junk do you suppose, or is eye pigmentation essential?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-70876768581083742172009-09-22T12:21:50.574-04:002009-09-22T12:21:50.574-04:00The logical fallacy in your "More Junk DNA Fa...<i>The logical fallacy in your "More Junk DNA Fallacies" argument is the false dichotomy that DNA must be either essential or alternatively must be junk with no middle ground possible.</i><br /><br />If junk DNA is defined as non-essential, then this is not a false dichotomy.<br /><br /><i>Or perhaps, the “junk” has a role to play in the evolvability of organisms: a large, stocked, laboratory; a spacious art studio.</i><br /><br />This is what IDers refer to as "front-loading," which is an ad hoc rationale they came up with which does not refute the claim that the DNA in its current form is in fact junk, because this idea implies that the DNA has to change and be different to be non-junk.ALnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-58089430675004156822009-09-22T09:26:52.715-04:002009-09-22T09:26:52.715-04:00@N. Ataie
Or perhaps, the “junk” has a role to pla...@N. Ataie<br /><i>Or perhaps, the “junk” has a role to play in the evolvability of organisms: a large, stocked, laboratory; a spacious art studio.</i><br />Maybe, but nonfunctional DNA is not maintained for that reason, as you seem to suggest. The one thing you cannot select for is future reproductive success. If the benefits of a large genome are not immediately apparent within one or a few generations, than it is not adaptive. Until it acquires a function, it still is junk.Corneelhttps://www.blogger.com/profile/02884855837357720225noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-78433967532484495842009-09-22T02:07:00.884-04:002009-09-22T02:07:00.884-04:00I say the anti-junkists should go play around with...I say the anti-junkists should go play around with some maize or dinoflagellates or something...<br /><br />Although transposons <i>are</i> actually functional and non-junk - for themselves! Somebody think of the parasites please!Psi Wavefunctionhttps://www.blogger.com/profile/10829712736757471647noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-10481981638996970682009-09-21T22:37:40.651-04:002009-09-21T22:37:40.651-04:00Those on the sidelines of science need something t...Those on the sidelines of science need something to write about. They need to get published in some manner. What better way than to exaggerate. <br /><br />Move along - nothing to see here. Next exaggeration around the corner.Linzelhttps://www.blogger.com/profile/01514267602859699974noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-5860504564483452382009-09-21T19:26:07.228-04:002009-09-21T19:26:07.228-04:00Oh scientific journalism! Where Asn stands for ...Oh scientific journalism! Where Asn stands for 'Asinine'.GossipGuyhttps://www.blogger.com/profile/11229370109545377375noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-68264802680897563952009-09-21T19:00:37.855-04:002009-09-21T19:00:37.855-04:00Even if 99% of the genome had no “function”, as de...Even if 99% of the genome had no “function”, as determined by observations that organisms seem to get by without it, that is still only a very small portion of the mass of that organism. <br /><br />The economy of nature predicts that the mass of the organism, the substance, need be accounted for, it should have some function or the survival game favors its removal or degeneration. Experiments show that most macromolecules have functions that rely on the agency of all, most, or many of the atoms that makes up that molecule. <br /><br />The “waste” observed in the genome seems to makeup a relatively large portion of the “wasted mass”. Perhaps the energy and resources conserved by the removal of portions of the genome are negligible, and thus, do not offer an advantage to species that have less of the “junk”. <br /><br />Or perhaps, the “junk” has a role to play in the evolvability of organisms: a large, stocked, laboratory; a spacious art studio. Thus, the trade-off of mass-spared may be a decreased ability to evolve – which we may not see with “function” experiments aimed at affects on one or few generations. Function may stretch beyond our measurements.N. Ataiehttps://www.blogger.com/profile/12909551501290741641noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-4047490679120704352009-09-21T18:27:39.643-04:002009-09-21T18:27:39.643-04:00Nils,
I find it amusing, and a bit bizarre, that ...Nils,<br /><br />I find it amusing, and a bit bizarre, that you are criticizing others for their <i>"bombastic (and misleading?) statements."</i><br /><br />This from someone who titles a blog post <a href="http://biopinionated.com/2008/10/28/hammering-nails-in-the-junk-dna-coffin/" rel="nofollow"><i>Hammering nails in the junk-DNA coffin</i></a>.<br /><br />You don't think that title is bombastic? To me, it implies that the "junk-DNA" hypothesis is dead. It's certainly not my idea of a nuanced message.<br /><br />Honestly, which do you think is more consistent with available data: that the junk-DNA hypothesis is dead, or that most of our genome is in fact junk?qetzalnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-31758864758663877482009-09-21T17:11:15.579-04:002009-09-21T17:11:15.579-04:00I'm just pointing out what the literature actu...I'm just pointing out what the literature actually says, as I have been for quite some time. <br /><br />Here's another one you may find interesting. It's by Comings (1972), in the first explicit discussion of "junk DNA" (Ohno only used the term in the title).<br /><br /><em>These considerations suggest that up to 20% of the genome is actively used and the remaining 80+% is junk. But being junk doesn't mean it is entirely useless. Common sense suggests that anything that is completely useless would be discarded. There are several possible functions for junk DNA.</em><br /><br />So, by my count, we still await evidence for functions in another 15% before we even get to the original expectation from 35+ years ago.<br /><br />I don't think I'll continue in a back and forth, but you can see the <a href="http://genomicron.blogspot.com/2008/02/junk-dna-quotes-of-interest-series.html" rel="nofollow">Quotes of Interest</a> for lots more.T Ryan Gregoryhttps://www.blogger.com/profile/17028390880937952573noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-74428027881092549842009-09-21T16:51:00.726-04:002009-09-21T16:51:00.726-04:00DG. By your logic: Unless we find that half the po...DG. By your logic: Unless we find that half the population is not evil, then the statement "half of the population is evil" is true. Not a valid argument as you can see. Therefore the headlines are not false and if anything only slightly misleading. That's nevertheless besides the point I am making: bombastic (and misleading ?) statements from scientists will necessarily bring about tabloid headlines. <br />Gregory. Nice quote. By using that are you implying that what Orgel and Crick are saying is what you yourself have been saying all along ? If so you have communicated that in a strange manner. If you had communicated this correctly, then maybe the science reporters would have gotten the point by now.SciPhu (Nils Reinton)http://biopinionated.com/noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-86905328461968400992009-09-21T16:32:35.402-04:002009-09-21T16:32:35.402-04:00The logical fallacy in your "More Junk DNA Fa...The logical fallacy in your "More Junk DNA Fallacies" argument is the false dichotomy that DNA must be either essential or alternatively must be junk with no middle ground possible.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-53601878372300596892009-09-21T16:16:24.124-04:002009-09-21T16:16:24.124-04:00When more and more promoters, enhancers, repressor...<em>When more and more promoters, enhancers, repressors and other regulatory elements are discovered, claim that this of course was not included in the definition of “most of the genome”.</em><br /><br />"It would be surprising if the host genome did not occasionally find some use for particular selfish DNA sequences, especially if there were many different sequences widely distributed over the chromosomes. One obvious use ... would be for control purposes at one level or another."<br /> - Orgel and Crick 1980T Ryan Gregoryhttps://www.blogger.com/profile/17028390880937952573noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-32280670524165637002009-09-21T14:50:37.124-04:002009-09-21T14:50:37.124-04:00Unless we discover that 50% of our genome is not J...Unless we discover that 50% of our genome is not Junk than the statement "most of our genome is junk" is factually correct. The poitn of the posts here by Larry, and by T. Ryan Gregory is that any study or headline that essentially says "this isn't true!" while showing that some percentage less than this isn't junk is false and misleading.-DGhttps://www.blogger.com/profile/16018033631187602248noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-75440919410628324822009-09-21T13:59:29.717-04:002009-09-21T13:59:29.717-04:00I have linked to your response in the post so that...I have linked to your response in the post so that both sides are represented, bringing me back on the narrow path. Just to clarify, I'm not upset about the presentation of the paper. What upsets me is the way you and Gregory keep blaming these "not junk after all" headlines on reporters. The message you send is that our genome mostly junk, of course you'll get these headlines then - expecting anything else would be naive. If you wanted nuances, then you should have included them in the first place.SciPhu (Nils Reinton)http://biopinionated.com/noreply@blogger.com