tag:blogger.com,1999:blog-37148773.post3806914196333400356..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: The next step in genomicsLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger108125tag:blogger.com,1999:blog-37148773.post-73298799399100827962015-08-04T21:46:52.438-04:002015-08-04T21:46:52.438-04:00lies,
"A more intelligent question would be:...lies,<br /><br />"A more intelligent question would be: why epigenetics evolved since it is mostly a deterrent of evolution by decreasing the fitness of an organism with cancer and diseases? "<br /><br />Even if this were true, ID/creationists have a lot more explaining to do here. What kind of intelligent design is that?Chris Bhttps://www.blogger.com/profile/04778164246719803780noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-18429280134351371032015-08-04T18:18:32.751-04:002015-08-04T18:18:32.751-04:00What exactly do you think epigenetics is? Your wor...What exactly do you think epigenetics is? Your word salad just above leads me to wonder if you have any notion what you're talking about. If epigenetics had not evolved, there would be no multicellular organisms.John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-60969821337572987822015-08-04T18:11:24.169-04:002015-08-04T18:11:24.169-04:00Mikkel,
A more intelligent question would be: wh...Mikkel, <br /><br />A more intelligent question would be: why epigenetics evolved since it is mostly a deterrent of evolution by decreasing the fitness of an organism with cancer and diseases? <br /><br />Evolutionary suicide? Natural selection, super-selectively and randomly impotent?<br /><br />I'm sure you have a hypothesis just as good as the one that didn't explain the enormous junk DNA differences in similar species. Jasshttps://www.blogger.com/profile/00012083978513644307noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-78264335904611024732015-08-04T16:36:39.783-04:002015-08-04T16:36:39.783-04:00The great thing about actual mutations is that the...The great thing about actual mutations is that they persist forever, so there can be a population response to selection and that response can result in fixation. The shorter the persistence of the epigenetic change, on the other hand, the less time there is for a population response. And even if it gets fixed, in another few generations it won't be again. How can that possibly affect evolution?John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-10406416211472441202015-08-04T15:15:40.727-04:002015-08-04T15:15:40.727-04:00Sceptical Mind,
No one said epigenetics has been ...Sceptical Mind,<br /><br />No one said epigenetics has been discarded as an evolutionary mechanism. There is just no evidence that epigenetic changes can last more than a few generations. I has not been observed yet. That doesn't mean it's impossible, only that there is currently no evidence to support that hypothesis. This is still an active area area of study. It was thought that epigenetic changes (methylation of DNA for example) were reset when DNA replicated, effectively 'wiping the slate' of these changes. In fact, most of these changes do. Some have been observed to persist for several generations, but not longer than that.<br /><br />To be effective over evolutionary time, an epigenetic change would have to persist like a point mutation, for example. Most point mutations are more or less permanent, spreading through the population or droppping out of the population by genetic drift, modified by a positive or negative selection coefficient, if applicable. They become part of the genetic variation on the population. Point mutations don't just revert back to their former state after a few generations.<br /><br />If some epigenetic genetic changes do turn out to be stably inherited over time like point mutation, this would pose no problem for evolutionary theory. It would be another recognized source of heritable genetic variation.Chris Bhttps://www.blogger.com/profile/04778164246719803780noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-41727580476066838212015-08-04T13:01:00.707-04:002015-08-04T13:01:00.707-04:00I was waiting for your links with definite evidenc...<i>I was waiting for your links with definite evidence that epigenetics has been discarded as an evolutionary mechanism, so I guess there is some interesting evidence out there that can change the way people view evolution.</i><br /><br />So could you perhaps share some examples of this "interesting evidence" with the rest of us? Thanks in advance. Faizal Alihttps://www.blogger.com/profile/00937075798809265805noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-12036871411641663762015-08-04T12:49:25.169-04:002015-08-04T12:49:25.169-04:00Several generations 8-10 is enough to make some pe...Several generations 8-10 is enough to make some people investigate further and others mad (look above). Studies are being done so who knows. I was waiting for your links with definite evidence that epigenetics has been discarded as an evolutionary mechanism, so I guess there is some interesting evidence out there that can change the way people view evolution. What's evolutionary time in YOUR VIEW?It seems that your standard model is <b>evolution did</b> it but the disagreement remains on as to HOW EVOLUTION DID IT. How's your view better than mine?<br />Jmachttps://www.blogger.com/profile/04392421995310271733noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-89618441991843628502015-08-04T12:20:01.171-04:002015-08-04T12:20:01.171-04:00Sorry, but "several generations" isn'...Sorry, but "several generations" isn't good enough. It needs to be stable over hundreds of generations, not just three. Nor do I rely on Coyne's opinion. I see you haven't linked to any studies. Show me a case in which epigenetic inheritance is effective over evolutionary time. This is merely your latest attempt to grasp at anything that seems to disagree with the standard model, therefore Jesus.John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-30814287601468657632015-08-04T11:52:17.951-04:002015-08-04T11:52:17.951-04:00If epigenetic can alter the phenotype in heritable...<i>If epigenetic can alter the phenotype in heritable ways and remain stable for several generations, who says that epigenetics can't have any relevance to evolution at all?</i><br /><br />People who have the faintest fucking clue about evolution. That's who.Faizal Alihttps://www.blogger.com/profile/00937075798809265805noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-40824510777999491492015-08-04T11:46:18.186-04:002015-08-04T11:46:18.186-04:00If epigenetic can alter the phenotype in heritabl...If epigenetic can alter the phenotype in heritable ways and remain stable for several generations, who says that epigenetics can't have any relevance to evolution at all?Jmachttps://www.blogger.com/profile/04392421995310271733noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-21558501377362438692015-08-04T11:08:00.892-04:002015-08-04T11:08:00.892-04:00John & Piotr
It looks like both of you rely o...John & Piotr<br /><br />It looks like both of you rely on Coyne's opinion rather than any scientific evidence for epigenetics not having any relevance to evolution. Neither of you have linked any studies that prove your claims. What if there was scientific data suggesting otherwise?Jmachttps://www.blogger.com/profile/04392421995310271733noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-53029215012146941422015-08-04T09:02:57.729-04:002015-08-04T09:02:57.729-04:00"So John, by what evolutionary mechanism (s) ...<i>"So John, by what evolutionary mechanism (s) did the epigenetics evolve?"</i><br /><br />This question is supernaturally dumb. Do you even fucking know what epigenetics is? Mikkel Rumraket Rasmussenhttps://www.blogger.com/profile/07670550711237457368noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-88124895253946991602015-08-04T01:13:13.058-04:002015-08-04T01:13:13.058-04:00"So, it appears that you are saying that the ...<i>"So, it appears that you are saying that the 36% difference between yeast and higher organisms is the maximum for cyt C."</i><br /><br />Nope. I'm saying that it could be lower, but that several factors make it hard to go lower by evolutionary processes. That as divergence goes on, it becomes harder and harder to go lower, but that such thing does not mean that proteins with lower identities would not work. Read much more carefully.<br /><br />Bacteria are not 66% different to eukaryotic organisms. Lots of genes are not even present in one or the other (and/or are so divergent that the homology is no longer detectable). Here you're way off man.<br /><br />This is fun gnomon, but I'm not sure I'll have more time. You're in serious trouble. Your concepts are all over the map. Only semi-right, which makes it hard for you to notice why your conclusions are far off the map. I can see how you go astray. Hopefully you'll notice that one good day. Just try and be much more humble.<br /><br />Huítóu jiànAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-55357597987684595712015-08-02T22:56:41.452-04:002015-08-02T22:56:41.452-04:00How many eukaryotes that aren't opisthokonts h...How many eukaryotes that aren't opisthokonts have cyt c more than 36% different from yeast or humans?John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-52115001659866098542015-08-02T19:11:43.805-04:002015-08-02T19:11:43.805-04:00Yes, I agree mostly. functional constraint!! So, i...Yes, I agree mostly. functional constraint!! So, it appears that you are saying that the 36% difference between yeast and higher organisms is the maximum for cyt C. Any more difference than that may destroy the functional residues. <br /><br />Now, here is another fact: bacteria is ~66% different from all eukaryotic organisms. So, why? Is this 66% the maximum difference? gnomonhttps://www.blogger.com/profile/03362808932731126552noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-86631727625371064422015-08-02T18:26:39.531-04:002015-08-02T18:26:39.531-04:00Who cares. The problem we have with cytC is that i...Who cares. The problem we have with cytC is that it should keep its function. That means that it might be hard to get below the mark you're putting because some unimportant positions might be carried on conserved by proximity with functionally-important ones. Check a multiple alignment. I think you'll find, as I have in many many cases, that even if you have around 36% between yeast's cytC and any-multicellular-organism, you'll find that it's not the very same 36%. The conserved proportion in all of them will be less. That means that at least in theory it can go below 36%, only homoplasy/saturation/carrying on/etc, has kept yeast-whatever pairwise numbers around your preferred "threshold." This is too obvious. By evolutionary processes it might become harder and harder to go lower as the mutation/drift/selection divergence game goes on.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-86921353349301203852015-08-02T17:20:04.026-04:002015-08-02T17:20:04.026-04:00Possibly?Possibly?Anonymoushttps://www.blogger.com/profile/04521153536420798640noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-79321650739319198472015-08-02T13:48:05.330-04:002015-08-02T13:48:05.330-04:00the more specific, the better the theory. just ans...the more specific, the better the theory. just answer the question. is it going to stop at 36% or can it go to 15%. my theory says yes at 36%. what is yours?gnomonhttps://www.blogger.com/profile/03362808932731126552noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-17127366579356719312015-08-02T13:19:20.270-04:002015-08-02T13:19:20.270-04:00Um, thanks?Um, thanks?John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-68953632880637018032015-08-02T11:55:00.853-04:002015-08-02T11:55:00.853-04:00https://xkcd.com/747/
On behalf on my simulationis...https://xkcd.com/747/<br />On behalf on my simulationist friends I would like to express thanks for your work. On behalf of narrativst/gamist hybrid me, who has had to play countless hours of Triplanetary (before it was replaced by Eklunds High Frontier for its more realistic treatment of gravity) to satisfy them (and for which I was rewarded through sessions of InSpectre, Fiasco and various WP-games) I would like to express a somewhat more ambivalent point of view. But since every minute they spent on designing satellites was a miunute not spent on coming up with house rules to make ASL more realistic (because seriously what ASL needed was more rules), I guess you have done good *g*<br />Anonymoushttps://www.blogger.com/profile/04521153536420798640noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-31391074184571786412015-08-02T08:54:44.177-04:002015-08-02T08:54:44.177-04:00gnomon,
I thought that you were mistaking concept...gnomon,<br /><br />I thought that you were mistaking concepts, but it's worse than I suspected. I thought you were talking about saturation and how it makes it difficult to calculate distances, but you;re talking about something that should be obvious. Since yeast's cytochrome C diverged from those of "multicelullar animals" when the two lineages separated (something of a "single" point, provided no HGT and/or gene conversion happens), then its proteins should have somewhat the same distance to their orthologs in multicellular animals. However, phylogenetic analyses rarely give equivalent distances (identity is not a measure of distance), because of confounding factors (like saturation, gene conversion, randomness in fixation of neutral and semineutral changes, etc).<br /><br />Anyway, the sequences keep mutating. But selection keeps some proportion of the protein because of the conservation of function. Not every position in a protein sequence can change without affecting function, and homoplasy can also happen. But the organisms and the sequences continue diverging. Only we can't measure it because of the effects of selection (plus homoplasy and saturation). This is much more evident when we use protein and DNA sequences. So, for example, two cyt C sequences might be 36% identical at the protein level, but very hard to align at the DNA level (unless we used the protein sequence to produce the alignment).<br /><br />Your conceptual framework is in very bad shape.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-29720760387609679532015-08-02T04:37:51.963-04:002015-08-02T04:37:51.963-04:00liesforthedevil, did you bring up epigenetics beca...liesforthedevil, did you bring up epigenetics because you believe that epigenetic effects/results are evidence that an 'outside force' (i.e. your chosen, so-called 'God') influences (or designs, creates, assembles, guides) some or all "traits"? The whole truthhttps://www.blogger.com/profile/07219999357041824471noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-70003922768586636462015-08-02T02:07:35.836-04:002015-08-02T02:07:35.836-04:00"There's no such thing as "equidista..."There's no such thing as "equidistance." Organisms don't stop diverging. Sequences don't stop diverging."<br /><br />Just take cytochrome C. The protein from yest is approximately equidistant to all multicelluar animals, regardless worms or humans (~36% identity). This is just a fact whether one like it or not. Now do you think it could diverge more given more time? could the difference between yeast and human in cyto c be ~15% identity some time in the future, which would be equivalent to the identity between two non-related randomly picked proteins?gnomonhttps://www.blogger.com/profile/03362808932731126552noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-43681147376718316902015-08-02T00:52:16.418-04:002015-08-02T00:52:16.418-04:00gnomon,
You're mischaracterizing the fields o...gnomon,<br /><br />You're mischaracterizing the fields of population genetics and phylogenetics. Here's what you said:<br /><br /><i>"which says there are infinite number of neutral or junk sites for any genome regardless whether it is human or onion"</i><br /><br />Which is false. The model is used when mutations are low enough to assume that few if any mutations fall in the same place. But it is not used for just any analyses. This is why I did not understand what you were talking about. No studies I have checked or reviewed dealt with lowly divergent sequences, and thus none used a linear model, let alone one assuming infinite sites. As I told you, most software will give up estimating distances if there's too many mutations. Researchers will use different models, and often renounce comparing DNA sequences, because of saturation. Researchers will be asked for the models used to infer saturation. Reviewers often demand that appropriate models be used to account for potential mistakes with highly divergent sequences.<br /><br />There's no such thing as "equidistance." Organisms don't stop diverging. Sequences don't stop diverging. It's just that saturation makes it from hard to impossible to actually measure such divergence. You're mistaking the fact that a linear model would stop working with a maximum distance.<br /><br />The "interpretation of the field" is that once there's saturation, we start losing the power to measure distances, and that the molecular clock's ticking can't be measured either. This is what I was taught. I wasn't taught that a molecular clock could be used infinitely. I wasn't taught that mutations never occur in the same site.<br /><br />Maybe you had bad professors. Maybe you had careless teachers who assumed infinite sites no matter what. Maybe you think you're the one who discovered saturation. But you're way off base. Sorry to break the news, but researchers in evolution know about saturation and problematic molecular clocks for eons.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-42165389111794295772015-08-01T20:44:35.862-04:002015-08-01T20:44:35.862-04:00Do you believe that some "traits" can be...<i>Do you believe that some "traits" can be inherited by an organism without altering the sequence of DNA?</i><br /><br />Yes, over the short term (a few generations), but not over a long enough term to be relevant to evolution.<br /><br /><i>Hirschman</i><br /><br />Add an "n" to the end of that and you have the original German spelling. But my autocorrect has no problem. Harshman Harshman Harshman. Easy. Perhaps you shouldn't be using a Microsoft product.John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.com