tag:blogger.com,1999:blog-37148773.post3260150866416138655..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: Evolution's Hidden ForceLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger15125tag:blogger.com,1999:blog-37148773.post-32226849639084155782011-02-11T17:08:22.070-05:002011-02-11T17:08:22.070-05:00"Ask them what causes the variation in phenot..."Ask them what causes the variation in phenotypes seen within any species."<br /><br />Right, we've never encountered terms like penetrance or even bothered to enumerate what mechanisms could possibly be behind phenomena like that...<br /><br />And don't say 'random'; use the term 'stochastic'.Argonnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-54090092261291265012011-02-10T16:21:02.123-05:002011-02-10T16:21:02.123-05:00I gave up my long time subscription to New Scienti...I gave up my long time subscription to New Scientist (off and on since the sixties) after the 'Darwin was Wrong' article. I realised that the New Scientist was now featuring opinion and entertainment rather than science.<br /><br />The epigenetics article was another example of this trend.DiscoveredJoyshttps://www.blogger.com/profile/05300239909689336895noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-5902733792860757422011-02-10T08:15:37.847-05:002011-02-10T08:15:37.847-05:00OK, here's a challenge. Conduct a straw poll o...OK, here's a challenge. Conduct a straw poll of some of your biologist colleagues who haven't read the article. Ask them what causes the variation in phenotypes seen within any species.<br /><br />I bet the majority will say it is a combination of genetic variation and environmental variation - and the interaction between the two. A few might mention developmental noise. If they mention epigenetics at all, they probably have in mind adaptative changes that are genetically programmed.<br /><br />What Feinbergy is claiming, by contrast, is that a lot of the variation is due to random epigenetic changes, and that this is not mere "noise" in the system, but that there is actually a special mechanism for producing it.Michael Le Pagenoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-65479810211537517262011-02-09T19:11:44.485-05:002011-02-09T19:11:44.485-05:00Michael Le Page says,
Larry, what the article act...Michael Le Page says,<br /><br /><i>Larry, what the article actually said was:<br /><br />"What's written on the piece of paper could fundamentally alter the way we think about epigenetics, evolution and common diseases."<br /><br />I think cutting out key parts of the quote and then criticising the mutilated version, rather than the ours, is unfair. It's not the sort of thing you'd take to kindly if creationists did it.</i><br /><br />Gimme a break. My posting was supposed to be a quiz and including the word "epigenetic" would have sort of given it away, no?<br /><br />Besides, if you check your cover page you'll see that criticizing you for overblown statements about evolution isn't exactly out of line.<br /><br /><i>I'm sorry if you feel we lied to you. But Henry and I (the editor of the feature) worked hard to try to ensure the piece was balanced and put Feinberg's ideas in context for a general readership, and I still think we did a pretty good job.</i><br /><br />I didn't say you lied but you sure did try and turn a molehill into a mountain. Are you aware of the fact that we've known about methylation of DNA sequences for 35 years? Mutations that affect methylation in bacteria and bacteriophage have been well-studied for decades and natural variants of methylation in bacterial strains are hardly new.<br /><br />There was even a Noble Prize in 1978.<br /><br />It's too bad the bartender didn't have a copy of a microbiology textbook. :-)<br /><br>Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-38532663374756085822011-02-09T11:47:54.231-05:002011-02-09T11:47:54.231-05:00Larry, what the article actually said was:
"...Larry, what the article actually said was:<br /><br />"What's written on the piece of paper could fundamentally alter the way we think about <b>epigenetics</b>, evolution <b>and common diseases</b>."<br /><br />I think cutting out key parts of the quote and then criticising the mutilated version, rather than the ours, is unfair. It's not the sort of thing you'd take to kindly if creationists did it.<br /><br />Further down in the piece, we clearly state:<br /><br /><i>"As surprising as Feinberg's idea is, it does not challenge the mainstream view of evolution."</i><br /><br />The piece also reflects some of the scepticism expressed here:<br /><br /><i>Jerry Coyne, an evolutionary geneticist at the University of Chicago, is blunter. "There is not a shred of evidence that variation in methylation is adaptive, either within or between species," he says. "I know epigenetics is an interesting phenomenon, but it has been extended willy-nilly to evolution. We're nowhere near getting to grips with what epigenetics is all about. This might be a part of it, but if it is it's going to be a small part."</i><br /><br />I'm sorry if you feel we lied to you. But Henry and I (the editor of the feature) worked hard to try to ensure the piece was balanced and put Feinberg's ideas in context for a general readership, and I still think we did a pretty good job.Michael Le Pagehttp://www.newscientist.com/article/dn13620noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-72635509781230647602011-02-09T09:09:04.663-05:002011-02-09T09:09:04.663-05:00Although not disputing an important contribution o...<i>Although not disputing an important contribution of Lamarkcian inheritance, ..</i><br /><br />Not the most lucky expression!<br /><br />In quantitative genetics good theoretical studies on variances exist. Feinberg did not even try to find out whether anybody had done a model more or less like this before.heleenhttps://www.blogger.com/profile/17358426050959144140noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-63065240771010858402011-02-08T20:43:18.186-05:002011-02-08T20:43:18.186-05:00DK says:"I read the paper to see what the dea...DK says:<i>"I read the paper to see what the deal is about. As far as I can see, the relation to evolution is tangential.</i>"<br /><br />Exactly. Even Feinberg himself is quoted in NS article (full text online <a href="http://www.thebigview.com/forum/showthread.php?t=5113" rel="nofollow">here</a>) saying that methylation is not typically transmitted between generations, so doesn't have much to do with long term genetic or morphological change. <br /><br />But - he is arguing that proneness to methlyation (i.e. CpG dinucleotides) is non-randomly distributed in the genome, making for a mechanism of sorts that may enhance fitness in variable environments. <br /><br />Let's say that it probably won't be an idea that shakes the world of evolutionary biology to its very core.PaulMnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-53640420250232855132011-02-08T12:35:41.450-05:002011-02-08T12:35:41.450-05:00"The sad thing is that Andy Feinberg isn'..."The sad thing is that Andy Feinberg isn't a hack--here's the actual science to which this article refers:<br />http://www.ncbi.nlm.nih.gov/pubmed/20080672"<br /><br />I don't agree; one can publish an article in a respectable journal and still do poor science and be labelled a hack. I'm not commenting on Dr. Feinberg here, but merely noting that your assertion is not necessarily correct. The journal that published Dr. Feinberg's article is PNAS, and there have been occasions where bizarre papers have made it in (e.g. search Margulis and PNAS).Alexhttps://www.blogger.com/profile/02590604089043425452noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-84473714980272074932011-02-08T06:47:42.476-05:002011-02-08T06:47:42.476-05:00DK says,
I read the paper to see what the deal is...DK says,<br /><br /><i>I read the paper to see what the deal is about. As far as I can see, the relation to evolution is tangential.</i><br /><br />I haven't read the article but what you're saying can't be true.<br /><br />We were told that, "what's written on the piece of paper could fundamentally alter the way we think about ... evolution ...."<br /><br /><i>New Scientist</i> wouldn't lie to me, would it?<br /><br>Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-49495944070338469812011-02-08T00:03:54.495-05:002011-02-08T00:03:54.495-05:00Anonymous, thanks for the "the actual science...Anonymous, thanks for the "the actual science to which this article refers"! <br /><br />I read the paper to see what the deal is about. As far as I can see, the relation to evolution is tangential. I can't judge technical side of the massive methylation mapping. What I am missing there is an indication of the noise/errors. I.e., how much of their findings can be reasonably attributed to pure chance? But that's the experimental part and the one that's not directly related to evolution and is not IMHO very linked to the paper's main thesis. <br /><br />The rest as I see it: <br />1. A hypothesis that an increased variance of the trait's expression increases fitness. <br />2. Simulations aimed to prove self-evident propositions that a) when selective pressure favors large X, large X with small variance gets selected, b) when selective pressure favors alternately large X or small X, organisms with large variance of X get selected. <br /><br />#2 in no way proves #1. I am very sympathetic to #1 and I am sure there are instances where it is true and where it is false. It will be a lot of fun to think of experiment(s) that can test it most easily. All in all, however, a far cry from "Uncertainty principle: How evolution hedges its bets"!DKnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-36220865426584992162011-02-07T21:14:25.511-05:002011-02-07T21:14:25.511-05:00The sad thing is that Andy Feinberg isn't a ha...The sad thing is that Andy Feinberg isn't a hack--here's the actual science to which this article refers:<br />http://www.ncbi.nlm.nih.gov/pubmed/20080672Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-7620495724088713892011-02-07T20:13:35.951-05:002011-02-07T20:13:35.951-05:00Knowing Larry's trigger points and New Scienti...Knowing Larry's trigger points and New Scientist's predilection to getting thngs wrong, that word is probably "epigenetics". So we have "eigenetics might inject a Heisenberg-like uncertainty into the expression of genes". <br /><br />Whatever. As Larry pointed for a few zillion times, a good start would be to define the damn term. It's not like an idea that randomness plays a role in many biological phenomena is particularly new. Else, I don't know WTF the analogy to the uncertainty principle might mean.DKnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-64565816771821701752011-02-07T20:11:25.144-05:002011-02-07T20:11:25.144-05:00The article was about epigenetics and how epigenet...The article was about epigenetics and how epigenetic control can maintain diversity in a population. In other words, as Bjørn Østman, commented none of your options seem to fit very well.Michael Mnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-35426925283386763072011-02-07T18:53:00.362-05:002011-02-07T18:53:00.362-05:00Amateurism and sensationalism is the major problem...Amateurism and sensationalism is the major problem with the <i>New Scientist</i>. I have noticed that the contributors on Evolution don't read the scientific papers they cite and offer a very superficial analysis. You can be interesting and stick to good standards of scientific journalism.<br /><br />Sure, NS is a science magazine and not a journal, but it should be more critical of what eminent scientists, such as Larry Moran, have to say. Always question, never accept anything when there is even an iota of reasonable doubt: That is my motto.Unknownhttps://www.blogger.com/profile/18226525473904632047noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-76156961077556404932011-02-07T17:42:34.286-05:002011-02-07T17:42:34.286-05:00Stochasticity? None of the answers you provided se...Stochasticity? None of the answers you provided seems to fit.Bjørn Østmanhttps://www.blogger.com/profile/08859177313382114917noreply@blogger.com