tag:blogger.com,1999:blog-1812431336777691886.post3273819410232201337..comments2024-02-29T03:57:00.088-05:00Comments on The Mermaid's Tale: More advertising, yet a lesson to learnAnne Buchananhttp://www.blogger.com/profile/09212151396672651221noreply@blogger.comBlogger17125tag:blogger.com,1999:blog-1812431336777691886.post-78114192410756868522012-09-10T08:17:02.014-04:002012-09-10T08:17:02.014-04:00They would not consider themselves to be a 'jo...They would not consider themselves to be a 'journal'? A surprise to me, though the truth is that they are a mix of journal and magazine. And while they're for a membership organization and should not in that sense be out pandering credit cards and so on and all their hyping, they might argue that this is the way to do the "Advancement of Science"<br /><br />I have never used LaTeX, so I may have to give it a look, or more likely, explore LyX.....except that journals want Word.<br /><br />It must be that old-style typesetting isn't done any more, and the new machine-editor interfaces are Word based, for better or worse.Ken Weisshttps://www.blogger.com/profile/02049713123559138421noreply@blogger.comtag:blogger.com,1999:blog-1812431336777691886.post-56388429730096817042012-09-09T14:26:09.309-04:002012-09-09T14:26:09.309-04:00Ken,
I meant that Science explicitly cites itself ...Ken,<br />I meant that Science explicitly cites itself as "Science magazine", not a journal.<br /><br />There are Word to LaTeX translators (as well as the reverse), but few of them work all that well. But my point was just how bizarre it is that the leading science publication uses a proprietary (and clumsy) word-processing program to typeset its articles, when the scientists submitting the articles are already using a brilliant, open-source typesetting language/system (i.e., TeX/LaTeX). For those who are convinced that a Word-like system is the only way to write, there is LyX---an open source, TeX/LaTeX system with a WYSIWYG interface.John R. Vokeyhttps://www.blogger.com/profile/03822243132435056442noreply@blogger.comtag:blogger.com,1999:blog-1812431336777691886.post-71870817851831248192012-09-08T07:05:09.252-04:002012-09-08T07:05:09.252-04:00And John, of course your point about LaTeX reflect...And John, of course your point about LaTeX reflects the larger issues about publication that are yet to be settled, as reflected in the Elsevier boycott and increasing use of arXiv and the push for open access and so on. As long as scientists feel the benefits of publishing in Science are greater than the benefits of having control over the process, they'll keep submitting to Science in Word. And of course Science counts on just that. Anne Buchananhttps://www.blogger.com/profile/09212151396672651221noreply@blogger.comtag:blogger.com,1999:blog-1812431336777691886.post-61475655703463994442012-09-08T06:56:25.835-04:002012-09-08T06:56:25.835-04:00where did they admit that? I would like to see it!...where did they admit that? I would like to see it!<br /><br />I have never used LaTeX, and wonder if there isn't a Word-LaTeX translator program avaiable. In any case, I assume this has to do with the practical aspects of physical publication, that is, how compositors--whatever they're called these days--actually set up the printing machines. Not just to treat scientists like secretaries (who use Word because you don't have to know much to type things*).<br /><br /><br />*Well, actually, I've insulted secretaries: they know a hell of a lot more about how to use Word and all its excessive features than I do!Ken Weisshttps://www.blogger.com/profile/02049713123559138421noreply@blogger.comtag:blogger.com,1999:blog-1812431336777691886.post-22852367783459005502012-09-08T02:43:29.565-04:002012-09-08T02:43:29.565-04:00A propos of the larger (largest?) point, at least ...A propos of the larger (largest?) point, at least Science admits it is but a magazine, not a true (any more) scientific journal. As it now relegates the methods to ephemeral web sources, it can no more be considered a scientific journal of record. Nature has yet to admit the same, but we all know it is but a matter of time.<br /><br />But, I want to raise a smaller (smallest?) point: Science (the magazine) assumes/almost demands that submissions be in MS Word format. Despite the fact that many (most?) real scientists prepare their manuscripts in LaTeX, Science provides at most pitiful/useless TeX/LaTeX/BibTeX submission support. Why do we, as the academic science community, tolerate this? We should shun Science magazine for that reason alone, never mind the fact that it publishes inadequate reports, and has lately become the mag for professional science shills.John R. Vokeyhttps://www.blogger.com/profile/03822243132435056442noreply@blogger.comtag:blogger.com,1999:blog-1812431336777691886.post-61386270486908334372012-09-06T23:11:28.081-04:002012-09-06T23:11:28.081-04:00First, the amino acid predictions are based on che...First, the amino acid predictions are based on chemical properties etc. and suffer from the problem of predicting in isolation rather than, as you say, context.<br /><br />For non-coding variation, there is little current way to predict harmfulness. Even regulatory binding sites tolerate variation.<br /><br />What it boils down to is that empirically we have to _estimate_ effects from data--that is, retrospectively and in the contexts of our particular sample, because we have no good theory for most of the non-coding sites.<br /><br />Certainly deleteriousness depends on contexts--including ecology, climate, other members of same or other species, other cells in the body, and so on.<br /><br />And with so many sites contributing to sites, and many if not most contributing simultaneously to many traits ('pleiotropism'), the problems we face with current methods are clear.<br /><br />Proper science in the classical sense predicts from theory, but we are constrained, in the absence of adequate theory to make inferences of a general statistical kind from limited past data and hope it will predict future data.<br /><br />This is far to vast a topic for this reply, but we've dealt with some of it in past blog-posts.<br /><br />You are sensing, I think, the nature and vastness of the challenge!Ken Weisshttps://www.blogger.com/profile/02049713123559138421noreply@blogger.comtag:blogger.com,1999:blog-1812431336777691886.post-24802406316119660182012-09-06T21:11:15.126-04:002012-09-06T21:11:15.126-04:00Regarding genetic load, there are so many computat...Regarding genetic load, there are so many computational methods of predicting deleteriousness (for lack of a better term) of amino acid changing polymorphisms I've lost track. But extending this to non-coding sites seems to be very open question. Especially if deleteriousness depends on genetic background. Amithttps://www.blogger.com/profile/17374419504359860299noreply@blogger.comtag:blogger.com,1999:blog-1812431336777691886.post-48819761480195264822012-09-06T13:30:44.067-04:002012-09-06T13:30:44.067-04:00Today, no, and it's worse. It has to be sold ...Today, no, and it's worse. It has to be sold as having to do with disease. No more could we spend what we do on space, these days, without the promise of finding life out there.<br /><br />Too bad. It didn't used to be nearly so bad in this respect. Science journals, even the big ones, were black and white, with boring covers and no hype to speak of. It was better that way, for science at least. <br /><br />But this also has to do with public support for science. Whether that is more or less than decades ago, or whether scientists just always want more, I can't say.Ken Weisshttps://www.blogger.com/profile/02049713123559138421noreply@blogger.comtag:blogger.com,1999:blog-1812431336777691886.post-14352805466003622602012-09-06T13:21:28.129-04:002012-09-06T13:21:28.129-04:00A question I have about these ‘new’ findings is: W...A question I have about these ‘new’ findings is: Would this hype even work if we weren’t talking about humans? <br />I think that most of these findings won’t be at all surprising for people who work at the molecular level. I don’t think I’ve heard someone mention ‘junk DNA,’ at least in a serious manner, in quite a while. However, I sometimes think people act a little silly when we start thinking and talking about humans. In the medical literature people get hyped up about those cures that are just around the corner and have a tendency to exaggerate findings too (e.g. reduced drug sensitivity becomes drug resistance in certain journals, etc.) But would this ‘discovery’ have a mass of articles (~30) and front page news if we were talking about a parasite? Or what if it was an organism that has very little or nothing to do with humans? <br />Anonymoushttps://www.blogger.com/profile/05068601494828074316noreply@blogger.comtag:blogger.com,1999:blog-1812431336777691886.post-46468355043637425782012-09-06T10:39:40.615-04:002012-09-06T10:39:40.615-04:00A scary prospect! You're right.A scary prospect! You're right.Ken Weisshttps://www.blogger.com/profile/02049713123559138421noreply@blogger.comtag:blogger.com,1999:blog-1812431336777691886.post-88856807584057690182012-09-06T10:38:14.302-04:002012-09-06T10:38:14.302-04:00I don't think it's niceness as much as wei...I don't think it's niceness as much as weighing the worse of two evils... unseemly antics by egomaniacal ladder climbers don't actually matter compared to the real crisis in public science education. Creationists LOVE to talk about junk DNA. Every day another human who has been raised by lies gets closer to voting age. Holly Dunsworthhttps://www.blogger.com/profile/05260104967932801186noreply@blogger.comtag:blogger.com,1999:blog-1812431336777691886.post-91763171024803313002012-09-06T10:33:23.946-04:002012-09-06T10:33:23.946-04:00I think reporters, even Gina Kolata who is usually...I think reporters, even Gina Kolata who is usually very good, should not be so gullible, and if they're science reporters they ought to learn more before writing about it. But also, this is clearly part of the hype-machinery. The scientists themselves, when talking to the reporters, are probably saying they're dramatically over-turning the idea of 'junk' DNA, because that's a way to promote their work...and they see that reporters eat it up because it makes for a good story line.<br /><br />So, you are probably right in many ways, but I am far less charitable to the System, which I think more or less knowingly is a mutual reinforcement, exaggeration phenomenon.<br /><br />As I recently heard in another context, only bad news really gets reported. In the past even science reporters for major media clearly said that only 'controversy' sells. That is what is really going on here: overturning, revolutionary, transformative,.... are the kind of concepts they can write about.<br /><br />And the journals know this and play the same game. At least, that's my view. You're just too nice a person compared to me!Ken Weisshttps://www.blogger.com/profile/02049713123559138421noreply@blogger.comtag:blogger.com,1999:blog-1812431336777691886.post-20392426714620642102012-09-06T10:24:38.688-04:002012-09-06T10:24:38.688-04:00That so many ENCODE reporters thought that junk DN...That so many ENCODE reporters thought that junk DNA needed to be overturned is indicating that maybe there still is a great need to overturn the notion of junk DNA in the pop mind. Repetition is important with science news and education. And not all news stories reach all people. Non-scientists don't get the exposure that scientists do. It takes time to overturn them in the popular mind. I think we should be more patient about that. Holly Dunsworthhttps://www.blogger.com/profile/05260104967932801186noreply@blogger.comtag:blogger.com,1999:blog-1812431336777691886.post-39658022799824228902012-09-06T09:56:29.897-04:002012-09-06T09:56:29.897-04:00It is a sad commentary on our advertising-based ti...It is a sad commentary on our advertising-based times. Young people need to raise grass-roots objections, or they (you!) are trapped in decades of playing this Red Queen rat-race just to stay employed.<br /><br />It is worse than the fact that many scientists know that we stopped talking about junk DNA years and years ago, because many scientists--especially those in the health and medical sciences--don't know that and have a very cartoonishly naive idea about evolution and genetic architecture.<br /><br />The real work of science should be done more quietly, slowly, deliberately and with fewer mega-projects so that more people working under the constraints of limited budgets and hence forced to think harder, can raise the chance of somebody actually coming up with new ideas.Ken Weisshttps://www.blogger.com/profile/02049713123559138421noreply@blogger.comtag:blogger.com,1999:blog-1812431336777691886.post-26102430335480054642012-09-06T09:50:22.724-04:002012-09-06T09:50:22.724-04:00Did you see this piece by Mike Eisen? Reading that...Did you see this piece by Mike Eisen? Reading that press release he links to, you would think that NHGRI spent $200M to conclude that junk DNA doesn't exist! http://www.michaeleisen.org/blog/?p=1167Amithttps://www.blogger.com/profile/17374419504359860299noreply@blogger.comtag:blogger.com,1999:blog-1812431336777691886.post-694066072246407452012-09-06T09:13:44.118-04:002012-09-06T09:13:44.118-04:00Yes, and to the degree, which is clearly rather mo...Yes, and to the degree, which is clearly rather more the case than the exception, that traits are controlled by many genes, the selection intensity is distributed even more widely.<br /><br />Humans clearly are viable (til we blow ourselves all up or pave over all arable land), yet very slow reproducers, a long-term legacy from primates. And most mammals are slow reproducers, relative to all of this, as well.<br /><br />So all of this DNA function may have been put in place gradually, our own genomes reflecting that very, very ancient legacy. But there is so much variation, and genome rearrangement among species, that clearly these many functions are minimally important (tolerate variation).<br /><br />It is not seriously conceivable that the hundreds of thousands of distributed or repeat elements across the genome, comprising half or more of it, would have 'function' in the sense of all this hyperbole in the media.Ken Weisshttps://www.blogger.com/profile/02049713123559138421noreply@blogger.comtag:blogger.com,1999:blog-1812431336777691886.post-47213681911989303752012-09-06T08:48:05.864-04:002012-09-06T08:48:05.864-04:00The genetic load argument is interesting. I also ...The genetic load argument is interesting. I also recall that genetic load is greatly diminished if soft selection prevails, which was likely the case in the evolution of humans (since population regulation was likely local and we roamed in smallish groups). Hence, the cost of selection would be weakened even further, even if 80% of the genome was under the scrutiny of selection. rich lawlerhttps://www.blogger.com/profile/13353965284524429553noreply@blogger.com