tag:blogger.com,1999:blog-37148773.post2898954095937178176..comments2024-03-19T00:24:23.577-04:00Comments on <center>Sandwalk</center>: Genetic Load, Neutral Theory, and Junk DNALarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger13125tag:blogger.com,1999:blog-37148773.post-27537541427572353842015-08-14T08:46:48.182-04:002015-08-14T08:46:48.182-04:00No, it isn't. Mutations strike stochastically....No, it isn't. Mutations strike stochastically. There won't be 'one or two' lethal mutations every spermatocyte generation. Some spermatocytes will have 4 lethal mutations and some will have 0 lethal mutations. The ones with 0 lethal mutations are the ones that go on to form the next generation of spermatocytes. Mutations in junk regions will not be similarly selected against - so more of those 130 mutations will be in the junk region than chance would suggest.Tim Tylerhttps://www.blogger.com/profile/06623536372084468307noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-35373336669315241142015-08-14T08:35:44.933-04:002015-08-14T08:35:44.933-04:00You are referring to dominant lethal mutations tha...You are referring to dominant lethal mutations that affect developing sperm cells. Let's assume, as you do, that such mutations are a significant proportion of mutations in functional DNA. The genetic load argument stills applies. It says that if all of the genome were functional, such mutations would lead rapidly to extinction because there's bound to be one or two every generation. <br /><br />Is that your point?Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-2543103267256539172015-08-14T06:50:56.600-04:002015-08-14T06:50:56.600-04:00Alas, within-organism selection acting on germ-lin...Alas, within-organism selection acting on germ-line cells will concentrate those 130 mutations in non-coding regions. If a mutation will kill or sterilize an adult, there's at least a fair chance that it will kill or sterilize the cells ancestral to gametes. 399 generations of spermatocytes in each male results in a significant opportunity for selection to act in this way. This blunts the strength of the argument for most of the genome being junk from genetic load.<br />Tim Tylerhttps://www.blogger.com/profile/06623536372084468307noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-81125351225870106152009-11-28T17:07:24.582-05:002009-11-28T17:07:24.582-05:00So instead of 'junk', maybe we should call...So instead of 'junk', maybe we should call it 'padding', or 'protective'.<br /><br />Chicken or egg? Do we have a high genetic load because we have a largely neutral genome or do we have a largely neutral genome because we have a high genetic load?<br /><br />If 80% of the human genome can be successfully deleted (as Dawkins claims) does the human mutation rate somehow go down? Wouldn't this lead to unacceptable numbers of deleterious mutations?<br /><br />Data point: The enslaved genome of a rhizarian alga, the chlorarachniophyte Bigelowiella natans nucleomorph, has only 331 genes and is the world's smallest eukaryote nucleous. 3 chromosomes. It is still 27% 'junk' DNA, mostly in telemere and subtelemere regions. Doesn't have centromeres, which is interesting. The genes still have original introns although they are 9-21 bp. The exons remain even where the transcription promoters are on adjacent genes. Also, it has a pseudogene! Five copies of one gene.<br /><br />Complete nucleotide sequence of the <br />chlorarachniophyte nucleomorph: Nature’s smallest nucleus<br /><br />PR Gilson et al, PNAS 2006Unknownhttps://www.blogger.com/profile/06704810560064858160noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-5528133044113374272009-11-23T08:30:00.619-05:002009-11-23T08:30:00.619-05:00I understand that, but Larry was talking about pro...I understand that, but Larry was talking about protein-coding regions.Alexanderhttps://www.blogger.com/profile/01908428123363294967noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-1720194962066960042009-11-23T08:13:55.063-05:002009-11-23T08:13:55.063-05:00Sorry, I meant to write DNA elements, such as prom...Sorry, I meant to write DNA elements, such as promoters, enhancers and other regulators of chromosomal structure.Alex Palazzohttp://scienceblogs.com/transcriptnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-40533461996913612672009-11-23T08:12:26.782-05:002009-11-23T08:12:26.782-05:00Alexander,
About 2% of the genome codes for prote...Alexander,<br /><br />About 2% of the genome codes for proteins and ncRNAs with some function, and roughly another 2-3% contains DNA coding elements. This 5% of the genome is conserved - so by chance alone 95% of all mutations will land in "junk" DNA. That cuts the level of non-junk DNA mutation by a factor of 20 fold.Alex Palazzohttp://scienceblogs.com/transcriptnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-34147722907266915422009-11-17T19:33:45.623-05:002009-11-17T19:33:45.623-05:00LM said: "This is one of the arguments in fav...LM said: "This is one of the arguments in favor of Neutral Theory. Most mutations are neither deleterious nor beneficial. They are simply neutral with respect to natural selection."<br /><br />As we are talking here about mutation, and not fixation, this alone does not support neutral theory. Neither neutral theory nor selection theory differ substantially with respect to the distribution of selection coefficients entering a population through mutation. Perhaps neutralists are more likely to downplay the possiblity of beneficial mutations. Selectionists have always maintained that many new mutations may be neutral, they have simply argued that such mutations are unimportant at the population genetics level.<br /><br />So, the differences lie in the population level processes that determine the fate of mutations. Neutral theory predicts that the mutations that fix are primarily neutral and fixed by drift, selection theory predicts a primary role for positive natural selection.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-91361781424213176162009-11-17T17:00:21.634-05:002009-11-17T17:00:21.634-05:00About the finding that only 20% of point mutations...About the finding that only 20% of point mutations in genes are non-neutral: how was this determined? By looking at the effects of individual substitutions in isolation?<br /><br />Given the existence of highly conserved gene regions, it seems a bit odd if 80% of nucleotides in a gene are free to mutate randomly. I'm guessing there must be lots of epistasis (in which case you oversimplified a bit when you went from 120 to 26).Alexanderhttps://www.blogger.com/profile/01908428123363294967noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-13408326832994515332009-11-17T16:52:22.168-05:002009-11-17T16:52:22.168-05:00"Darwinian evolution doesn't recognize ne..."Darwinian evolution doesn't recognize neutral mutations and random genetic drift"<br /><br />Sure? Let's read Darwin:<br /><br />"I am inclined to suspect that we see, at least in some [cases], variations which are of no service to the species, and which consequently have not been seized on and rendered definite by natural selection.… Variations neither useful nor injurious would not be affected by natural selection, and would be left either a fluctuating element, as perhaps we see in certain polymorphic species, or would ultimately become fixed.… We may easily err in attributing importance to characters, and in believing that they have been developed through natural selection;… many structures are now of no direct use to their possessors, and may never have been of any use to their progenitors.… [On the other hand,] we are much too ignorant in regard to the whole economy of any organic being to say what slight modifications would be of importance or not."<br /><br />It's a well known quotation from The Origin. Perhaps Darwin was not being "darwinian" all the time, or maybe he was not writing about "darwinian" evolution but about the evolution of someone else ;o)El PaleoFreakhttps://www.blogger.com/profile/11323149141956089390noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-87793840724632634082009-11-17T15:11:25.684-05:002009-11-17T15:11:25.684-05:00Kate asks,
Why do the mutations almost always com...Kate asks,<br /><br /><i>Why do the mutations almost always come from the chromosomes from the father?</i><br><br>I explain this in <a href="http://sandwalk.blogspot.com/2007/07/mutation-rates.html" rel="nofollow">Mutation Rates</a>. <br /><br />Between zygote and egg there are about 30 cell divisions while between zygote and sperm there are about 400 cell divisions. <br><br>Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-63546137895891737102009-11-17T15:04:30.132-05:002009-11-17T15:04:30.132-05:00Anon, there are a lot more rounds of replication i...Anon, there are a lot more rounds of replication in the male zygote (about 10-15x more IIRC).Chris Harrisonhttps://www.blogger.com/profile/11383092030160768244noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-71399675275308428652009-11-17T13:46:22.545-05:002009-11-17T13:46:22.545-05:00thanks. I found this very interesting. Why do the...thanks. I found this very interesting. Why do the mutations almost always come from the chromosomes from the father? Did I read that right?<br />-KateAnonymousnoreply@blogger.com