tag:blogger.com,1999:blog-37148773.post824782431628746651..comments2024-03-18T09:58:09.828-04:00Comments on <center>Sandwalk</center>: What's in Your Genome?Larry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger49125tag:blogger.com,1999:blog-37148773.post-32697535508818159122011-12-06T06:39:01.602-05:002011-12-06T06:39:01.602-05:00Furthermore...the idea of ancient virus integratio...Furthermore...the idea of ancient virus integrations in ancestral genomes is non-sensical. <br /><br />Viruses have there origin in genomes. That is standard textbook knowledge:<br /><br />http://www.nature.com/scitable/topicpage/the-origins-of-viruses-14398218<br /><br />The only remaining & possible explanation is found here:<br /><br />http://blog.drwile.com/?p=1106<br /><br />Cheers,<br />PBpeter borgernoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-18660358417651202812011-12-06T06:33:17.097-05:002011-12-06T06:33:17.097-05:00Question:
Why would anybody call genetic elements...Question:<br /><br />Why would anybody call genetic elements that actually and actively participate in inducing variation in offspring JUNK DNA?<br /><br />I really don't get that, Mr Moran? Isn't variation a very relevant parameter in evolutionary processes? <br /><br />A better name for these highly repetitive genetic elements, which affect gene expression through position effect and as enhancers/silencers, would be variation-inducing genetic elements.<br /><br />Variation-inducing genetic elements...remember that name.<br /><br />Cheers,<br />Peter Borger, PhDpeter borgernoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-75409396414612160172011-06-08T18:42:51.800-04:002011-06-08T18:42:51.800-04:00Anonymous, I appreciate that you have taken the ti...Anonymous, I appreciate that you have taken the time to list some references. <br />Please copy and paste from them the sentences that you think are relevant to the discussion. <br />I used to read references people gave, only to find that my time had been wasted. I do not do that any more. <br />You could start by just taking one of them.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-1178650010583018912011-06-08T09:01:24.224-04:002011-06-08T09:01:24.224-04:00When a difficult question arises about evolution t...When a difficult question arises about evolution theory, Moran just goes quiet. As does everyone else. <br /><br />As if by ignoring issues they will go away.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-1537649316641310212011-06-08T00:13:50.003-04:002011-06-08T00:13:50.003-04:00@Anonymous Tuesday, June 07, 2011 6:03:00 PM
Your...@Anonymous Tuesday, June 07, 2011 6:03:00 PM<br /><br />Your reading assignment.<br /><br />http://www.genetics.org/content/101/3-4/519.long<br /><br />http://www.nature.com/nature/journal/v315/n6017/pdf/315283b0.pdf<br /><br />http://www.imb.uq.edu.au/download/large/Introns_1994.pdf<br /><br />http://www.sciencedirect.com/science/article/pii/S0960982204002957<br /><br />http://www.nature.com/nrg/journal/v7/n3/full/nrg1807.html<br /><br />http://www.sciencemag.org/content/330/6006/920.full<br /><br />http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09992.html<br /><br />http://www.biology-direct.com/content/1/1/22Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-1383229485619666712011-06-07T18:03:36.390-04:002011-06-07T18:03:36.390-04:00How can people in this field, not have an answer t...How can people in this field, not have an answer to the basic question about the existence of "junk" introns in protein-coding genes? <br />That is about as basic as it gets.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-77756442560308816822011-06-07T12:50:08.863-04:002011-06-07T12:50:08.863-04:00Evolution theory is left with the odd idea that th...Evolution theory is left with the odd idea that the exons in the gene are perfectly organized to provide the RNA and then the proteins for the functioning of the creature. <br />But right beside all these exons are introns that are just "junk". <br /><br />Please explain using evolution principles such as drift, mutation, selection etc how in the world that could happen.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-40232646560775966382011-06-06T14:12:13.220-04:002011-06-06T14:12:13.220-04:00The question might be better put as:
Why are "...The question might be better put as:<br />Why are "introns" considered to be a percentage of the <i>genome? </i><br /><br />Are introns part of the genome?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-24029439376360436562011-06-06T12:24:23.906-04:002011-06-06T12:24:23.906-04:00I am talking about the introns in protein-coding g...I am talking about the introns in <b>protein-coding </b>genes. <br />It appears that Moran considers those particular introns (in protein-coding genes) to be "junk". <br />It appears that he considers those particular introns (in protein-coding genes) to be 9.6% of the entire genome. <br /><br />I am hoping he can explain why he thinks that they are "junk". None of his other posts address this question.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-61038476941849220642011-06-06T10:57:02.197-04:002011-06-06T10:57:02.197-04:00anonymous says,
It would be great if he could exp...anonymous says,<br /><br /><i>It would be great if he could explain his thinking about that. </i><br /><br />I do not believe that all introns sequences are junk. <br /><br /><a href="http://sandwalk.blogspot.com/2010/06/idiots-do-arithmetic-second-time-same.html" rel="nofollow">IDiots Do Arithmetic a Second Time - Same Result</a><br /><br /><a href="http://sandwalk.blogspot.com/2008/02/junk-in-your-genome-intron-size-and.html" rel="nofollow">Junk in Your Genome: Intron Size and Distribution</a><br /><br /><a href="http://sandwalk.blogspot.com/2008/02/junk-in-your-genome-protein-encoding.html" rel="nofollow">Junk in Your Genome: Protein-Encoding Genes</a><br /><br />All these links can be found in <a href="http://sandwalk.blogspot.com/2008/02/theme-genomes-junk-dna.html" rel="nofollow">Genomes & Junk DNA</a>. Anonymous would know that if he had bothered to do any homework before commenting. <br /><br />But who am I kidding? IDiots don't do homework! That's why they're IDiots.<br /><br>Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-68108830820395994592011-06-06T09:53:42.866-04:002011-06-06T09:53:42.866-04:00CORRECTION:
Well it looks like Moran is not intere...CORRECTION:<br />Well it looks like Moran is not interested in discussing this further. But it is worth looking at. <br />Moran covers the topic of introns in this thread:<br />http://sandwalk.blogspot.com/2011/05/junk-jonathan-part-7chapter-4.html<br />From there we get the distinct impression that Moran considers introns in protein-encoding genes to be "junk". <br />And he appears to think that this "junk" constitutes 9.6% of the genome. <br /><br />Why consider introns to be junk? <br />Do they perform no useful function?<br />It seems that they perform the function in the gene of separating the exons. That seems useful. The exons can be distinguished from each other by these separators.<br />It seems Moran considers them junk because they are spliced out in the process of transcription to <b>RNA.</b> <br />I wonder if that is why Moran considers them "junk". <br />It would be great if he could explain his thinking about that.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-5178708597084450842011-06-05T15:59:47.351-04:002011-06-05T15:59:47.351-04:00I have asked:
"Are you saying that the intron...I have asked:<br />"Are you saying that the introns within coding DNA is "junk"?"<br /><br />Is this too difficult a question to answer?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-74071414121178205232011-06-04T15:24:17.419-04:002011-06-04T15:24:17.419-04:00I have a question about this part:
Protein-encodi...I have a question about this part:<br /><br />Protein-encoding genes: (9.6% junk)<br /> transcribed region: <br /> essential 1.8% <br /> intron junk (not included above) 9.6% d<br /><br />dIntrons sequences account for about 30% of the genome. Most of these sequences qualify as junk but they are littered with defective transposable elements that are already included in the calculation of junk DNA."<br /><br />Are you saying that the introns within coding DNA is "junk"?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-74379212331661664942011-06-04T13:02:40.844-04:002011-06-04T13:02:40.844-04:00Dr. Moran, I was looking at your list in your post...Dr. Moran, I was looking at your list in your post. <br />Where do chaperone proteins fit into the picture? Are they produced by coding DNA or non-coding DNA. <br />Which of your categories does the DNA which produces chaperone proteins fit?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-68378164507804018932011-05-18T15:24:43.036-04:002011-05-18T15:24:43.036-04:00I would appreciate dr Moran's comment on:
Tit...I would appreciate dr Moran's comment on:<br /><br />Title: Transposable element insertions have strongly affected human evolution <br />Author(s): Britten RJ <br />Source: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Volume: 107 Issue: 46 Pages: 19945-19948 Published: NOV 16 2010heleenhttps://www.blogger.com/profile/17358426050959144140noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-27185128174491208242011-05-17T03:21:26.222-04:002011-05-17T03:21:26.222-04:00Proud to read that centromeric DNA is considered f...Proud to read that centromeric DNA is considered functional, even though it is not.<br /><br />Various articles have shown that the kinetochore can form on unique (non-repetitive) DNA. One chromosome in orangutan lacks alpha-satellite DNA, as does one chromosome in horses, whereas most chromosomes in chicken lack repetitive DNA at the centromeric locus all together. In addition, neocentromeres (centromeric relocalizaton on a chromosome) formation in humans happens relatively frequent (in term of evolutionary time), although it is commonly associated with clinical manifestations.<br /><br />At the same time, tandem repeat arrays have been observed on holocentric chromosomes (lacking a primary constriction or regional/localized centromere), which (currently) have not been shown to associate with kinetochore/centromere function.<br /><br />For these reasons, I would argue that your estimations of functional DNA in our genome is overestimated by 2%.Daniël P. Meltershttps://www.blogger.com/profile/12794987401481805447noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-75295073782113339542011-05-13T19:54:29.118-04:002011-05-13T19:54:29.118-04:00@Atheistoclast
"You've been told *over a...@Atheistoclast<br /><br />"You've been told *over and over* again, Larry, that just because you don't know the exact function of something doesn't make it junk."<br /><br />Conversely, just because you can imagine a function for something doesn't mean it evolved for an adaptive reason.<br /><br />A function can be imagined for anything, it's just an exercise in speculation, and very little to do with actual science.Psi Wavefunctionhttps://www.blogger.com/profile/10829712736757471647noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-88223861756987874132011-05-12T15:37:18.551-04:002011-05-12T15:37:18.551-04:00Jud wrote:
What unmitigated junk, pun fully inten...Jud wrote:<br /><br /><i>What unmitigated junk, pun fully intended. I must have something with no benefit (or deleterious) because someone else does, and that leads to an "arms race"? So if my neighbor is in hock up to his eyeballs, I better accumulate massive debt as well or be left behind?</i><br /><br />OK...perhaps an analogy would be useful. Say I invest in a backup to my hard drive and you do not. We are both given some deadlined assignment to do on our computers that we both save every night to our respective HD.<br /><br />Now, one night 2 weeks down the line we both experience some physical failure and we lose the data on our hard drives. However, my backup has been storing all of my data all along.<br /><br />As a result, I am at an advantage over you since you have to start all over again whereas I don't. <br /><br />This is one reason why duplicate genes become accumulated in the genome. They may not offer anything beneficial <i>per se</i> other than it always is good to have a backup - those who don't are at a disadvantage compared to those who do.Atheistoclastnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-46641040154141839132011-05-12T15:27:58.054-04:002011-05-12T15:27:58.054-04:00Steve wrote:
If element A is useless now how can...Steve wrote:<br /><br /><i><br />If element A is useless now how can there be any selection for it, other than a negative selection (probably very small if any) making carriers less prevalent due to the cost of carrying a useless function.</i><br /><br />You don't understand. Element A may have no use at present but it could do in the future - that is the nature of variation. Therefore, its preservation is beneficial in the evolutionary long-run.<br /><br /><i>If element A is "useless" (your word) then by definition it can not have any beneficial effects.</i><br /><br />At the moment. But in the future it might. Therefore, my argument is that in the future those individuals with in-tact element As will be reproductively better off compared to those with degenerate elementAs.<br /><br />For example, if some LTR retotransposon is doing nothing at the moment in some obscure part of the genome but relocates to a become a new cis-regulatory element in some gene 100 years from now, then selection will favor those individuals who possess the functional element compared to those who have lost it or have let it become defective.<br /><br />Larry, unfortunately, can't even begin to understand this. The reason is that he is not a population geneticist - he is a biochemist. That's all he is, that's all he'll ever be.Atheistoclastnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-42276443672513336972011-05-12T14:38:26.583-04:002011-05-12T14:38:26.583-04:00Atheistoclast said on Junk & Jonathan: Part 3—...Atheistoclast said on <a href="http://sandwalk.blogspot.com/2011/05/junk-jonathan-part-3-preface.html" rel="nofollow">Junk & Jonathan: Part 3—The Preface</a>,<br /><br /><i>I completely agree with Wells.<br /><br />Moran is wrong.<br /><br />His argument is essentially an argument from personal incredulity and poor analysis. </i><br /><br />Thanks for clearing that up.<br /><br />Now I can ignore you with a clear conscience.<br /><br />Goodbye.<br /><br>Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-90878809968151317792011-05-12T11:58:10.995-04:002011-05-12T11:58:10.995-04:00If Larry were a cosmologist ,heaven forbid, he wou...If Larry were a cosmologist ,heaven forbid, he would be arguing that dark matter and energy (that make up 96% of the universe) were simply "junk".<br /><br /><a href="http://www.ift.uam.es/workshops/DarkMatters/img/DarkMatterPie.jpg" rel="nofollow">Dark matter mirrors dark genomes</a><br /><br />I think that pretty much sums up his approach.Atheistoclastnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-25123621774493724592011-05-12T10:11:53.937-04:002011-05-12T10:11:53.937-04:00@Atheistoclast If element A is useless now but tur...@Atheistoclast <i>If element A is useless now but turns out to be useful later on, then those individuals with the most preserved (functioning) element As in their genomes will feel its beneficial effects compared to those with defective and degenerate ones. As such, they will become more prevalent because of differential reproduction. OK?</i><br /><br />Not OK.<br /><br />If element A is useless now how can there be any selection for it, other than a negative selection (probably very small if any) making carriers less prevalent due to the cost of carrying a useless function.<br /><br />I'm not even arguing from a genetic basis (good thing as I have no background) but from a logical basis and your statement seems to be logically incoherent.<br /><br />If element A is "useless" (your word) then by definition it can not have any beneficial effects.steve oberskinoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-31351552770630401942011-05-12T08:33:52.292-04:002011-05-12T08:33:52.292-04:00Atheistoclast writes:
In fact, I can see how both...Atheistoclast writes:<br /><br /><i>In fact, I can see how both the accumulation of duplicate genes (80% of eukaryotic genes are paralogs of others) and ncDNA might set off evolutionary arms races. It is a case of must having something only because someone else does - the actual net benefit needs not exist.</i><br /><br />What unmitigated junk, pun fully intended. I must have something with no benefit (or deleterious) because someone else does, and that leads to an "arms race"? So if my neighbor is in hock up to his eyeballs, I better accumulate massive debt as well or be left behind?Judnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-7186478541130865432011-05-12T08:22:40.553-04:002011-05-12T08:22:40.553-04:00Atheistoclast writes:
It is a brave new world you...Atheistoclast writes:<br /><br /><i>It is a brave new world you want to destroy, Larry.</i><br /><br />How unintentionally appropriate. Consider this excerpt from The Tempest, from which the phrase "brave new world" comes:<br /><br /><br />MIRANDA: ...O brave new world, <br /> That has such people in't! <br /><br />PROSPERO <br /><br /> 'Tis new to thee.<br /><br />...and compare that to Larry's comment on a previous posting of yours:<br /><br />Atheistoclast: <i>If I were a researcher I would investigate possible reasons for a relationship rather than just dissing it.</i><br /><br />Larry: <i>Investigations have been underway for at least forty years.... Why do I get the feeling that all this is new to you?</i>Judnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-77802264299517173612011-05-12T07:53:04.312-04:002011-05-12T07:53:04.312-04:00Larry,
Both introns and UTRs play an important pa...Larry,<br /><br />Both introns and UTRs play an important part in molecular stability. That is increasingly obvious. Their utility is subtle.<br /><br /><i>Let me assure you that there cannot be SELECTION for potential future uses. Evolution doesn't work that way.</i><br /><br />No, you don't seem to understand how selection can have a long reach into the future - I am very disappointed. Here is an example:<br /><br />If element A is useless now but turns out to be useful later on, then those individuals with the most preserved (functioning) element As in their genomes will feel its beneficial effects compared to those with defective and degenerate ones. As such, they will become more prevalent because of differential reproduction. OK?<br /><br /><i>In species with small genomes the average insertion will be lethal and quickly weeded out of the population.</i><br /><br />That is precisely the point. Both ncDNA, and also duplicate protein-coding genes, serve as buffers against harmful effects in the *individual* organism. In fact, I can see how both the accumulation of duplicate genes (80% of eukaryotic genes are paralogs of others) and ncDNA might set off evolutionary arms races. It is a case of must having something only because someone else does - the actual net benefit needs not exist.<br /><br />Now, the reason why I mentioned "<b>illegitimate recombination</b>" is because uni-chromosomal prokaryotes don't recombine their DNA as eukaryotes do. Since illegal recombinatory events can cause frameshifts in coding DNA, ncDNA (especially intergenic sequences) serves as a protective shield against them.<br /><br /><i>Don't you think it's time we started to entertain the idea that there may not be a reason why closely related species have vastly different amounts of DNA?</i><br /><br />I would be more interested in why amphibians have so much ncDNA compared to others. I know you think of this as coincidence and accidence but I think that is a lazy answer. Also, 40 years ago we didn't have the genomic analysis tools we have now. It is a brave new world you want to destroy, Larry.Atheistoclastnoreply@blogger.com