tag:blogger.com,1999:blog-4948885059517209129.post7085269764143531890..comments2023-10-29T08:04:00.488-07:00Comments on Quintessence of Dust: How the bat got its wingStephen Mathesonhttp://www.blogger.com/profile/05057004085073574659noreply@blogger.comBlogger17125tag:blogger.com,1999:blog-4948885059517209129.post-90734595829270895362008-06-02T20:06:00.000-07:002008-06-02T20:06:00.000-07:00Ichneumon--When techniques for ES cell propagation...Ichneumon--<BR/>When techniques for ES cell propagation and gene targeting are developed in chiropterans, some decades from now, I would bet that the authors will be interested in performing that currently-impossible experiment. Regarding your second idea, it might be interesting to examine the relevant region in other mammals.Stephen Mathesonhttps://www.blogger.com/profile/05057004085073574659noreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-74792729642307077102008-05-30T14:12:00.000-07:002008-05-30T14:12:00.000-07:00A few thoughts:1. They deleted the regulatory seq...A few thoughts:<BR/><BR/>1. They deleted the regulatory sequence from the mouse genome and found no obvious change in phenotype, but did they also delete it from the *bat* genome to see what would happen? I'd think that would be an obvious test.<BR/><BR/>2. It seems to me that mice have pretty stubby forelimbs compared to the average mammal. Perhaps this regulatory sequence in mice is "dialed down" all (or most of) the way, thus removing it results in little change. If this is the case, this sequence (in mice) might be a minimized version of what was, in the mouse's longer-limbed ancestors, a sequence with a more functional use.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-47200824637790415602008-05-23T11:24:00.000-07:002008-05-23T11:24:00.000-07:00There is something that puzzles me and should be s...There is something that puzzles me and should be shared by scientists and creationists. If I read well Darwin, and this article, there exists a genetic cursor that does nothing else but extend the limb. Therefore, from mouse to bat, the spectrum of limb shapes is completely obvious (what is called a one degree of freedom problem in physics), and in order for a bat to exist, all shapes in between should be somewhat good.<BR/>Therefore there exists an arrow of evolution, from mouse to bat, it is just the one way shift of the cursor, and all animals in between are predictable, in terms of shape.<BR/>There is even no need to look for them in quarries, it suffices to morph down or up the bat limb into the mouse limb. <BR/>The problem is that mathematics tell you that a one degree of freedom only evolution will necessary happen, eventually. Therefore, the bat was actually <BR/>"already present" in the mouse, and bound to appear.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-2572265846735564462008-05-22T18:49:00.000-07:002008-05-22T18:49:00.000-07:00Hi Claire--Thanks for the kind words, and for the ...Hi Claire--<BR/><BR/>Thanks for the kind words, and for the criticism. If your aim is to steer me away from "mud-slinging," I welcome the feedback, and I'll pay attention. I should note, though, that I do not refer to anyone as an ignoramus merely for holding to special creation, or even for believing odd or silly things. (See my <A HREF="http://sfmatheson.blogspot.com/2007/09/and-your-horse-now-would-make-him-ass.html" REL="nofollow">strong support</A> of the work of the <A HREF="http://www.creationbiology.org/content.aspx?page_id=22&club_id=201240&module_id=37881" REL="nofollow">BSG</A>, a group of young-earth creationist biologists.) Those who make inexcusably inaccurate claims – i.e., those who are badly wrong and should know better – are the ones who earn the title of "ignoramus." If you follow the link in the blog post, you'll read a remarkably bad series of blog posts in which, among other simplistic and laughable dismissals of evolutionary theory, you will see evolution referred to as "myth" as opposed to science. When people with Ph.D.'s write stuff like that, <A HREF="http://sfmatheson.blogspot.com/2008/03/when-its-not-just-disagreement.html" REL="nofollow">something other than mere disagreement</A> is called for.<BR/><BR/>So I'll keep working at tempering the language. But truth-telling will always trump manners here, and there's a place for exposing the misconduct of Christians who abuse science (and theology) in desperate and disreputable attacks on evolutionary science, all because they falsely believe that common descent is an obstacle to faith in Christ.Stephen Mathesonhttps://www.blogger.com/profile/05057004085073574659noreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-90269377449991433882008-05-22T15:13:00.000-07:002008-05-22T15:13:00.000-07:00Great blog, most informative. Having taken a (ver...Great blog, most informative. Having taken a (very extended!) maternity leave break from teaching/research this gives the old grey matter a good work out!<BR/><BR/>But is it helpful to label those who believe in special creation as creationist ignorami? They're not going to be uplifted by such titles or encouraged to investigate the truth further. I just think as Christians we should leave the mud-slinging to the world.Clairehttps://www.blogger.com/profile/18312634455397243949noreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-66561363544859038422008-05-20T19:33:00.000-07:002008-05-20T19:33:00.000-07:00Anonymous--Your criticism is noted, and thanks for...Anonymous--<BR/>Your criticism is noted, and thanks for backing off on the "fraud" claim. I think it's appropriate for you and others to note the potential for overstating the importance of the study, especially if/when it is interpreted as the discovery of <I>the</I> explanation for mouse-bat limb length divergence. One thing though: you say "no change in the mouse when prx1 is deleted" but that's wrong. There was no change when the <I>1-kb regulatory element</I> was deleted; deletion of the <I>gene</I> leads to significant reductions in forelimb length, as shown by the authors (Fig. 3A) and <A HREF="http://www.genesdev.org/cgi/content/abstract/9/10/1237" REL="nofollow">by others in 1995</A>.Stephen Mathesonhttps://www.blogger.com/profile/05057004085073574659noreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-53310385959726879072008-05-20T18:43:00.000-07:002008-05-20T18:43:00.000-07:00after all, you are right, it is not fraud, because...after all, you are right, it is not fraud, because the data are honnest. Let me withdraw the word. <BR/>The report I mentionned was in<BR/><BR/>http://www.sciencedaily.com/releases/2008/01/080114173923.htm<BR/><BR/>Nevertheless, it seems to me the finding is extremely modest. I would expect a 6% change of mouse limb extension by many other genetic mutations, for example in fgf's. as there is no change in the adult, and no change in the mouse when prx1 is deleted, I find the overal rationale rather weak, and the claims disproportionate.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-84072478268790427962008-05-20T17:52:00.000-07:002008-05-20T17:52:00.000-07:00Hey Karen (nunatak)--Thanks for the kudos. I just...Hey Karen (nunatak)--<BR/>Thanks for the kudos. I just looked at your most recent unheralded papers, and I'd like to herald it sometime soon. :-) I'll be in touch.<BR/><BR/>AIGBusted--<BR/>That recent bat fossil is cool, but most people have interpreted it to show that echolocation arose after flight. I agree it seems somewhat transitional, but it doesn't help much with the limbs-to-wings issue. It was a good month or two for bat evolution, though, eh?<BR/><BR/>NiK0--<BR/>Hmmm. I did read that part of the paper, but I think I see it as much less of a problem than you do. First, I agree with the authors' interpretation: that limb development regulates, and that the effects during mid- and late gestation were overridden by later processes. After all, neither the authors nor any of the commenters (including myself) have claimed that Prx1 is <B>the</B> major player in limb length, and any subsequent process that can regulate could lead to compensation. But more importantly, I think that the significance of the paper derives from the finding that the swapping of an enhancer alone, in the absence of structural differences in coding regions, can generate significant morphological change, and change that is both "positive" and correlated with the known evolutionary trajectory. Of course you're right that changes in mid- and late gestation aren't visible to selection, and it's certainly disappointing that the adults aren't different (this probably answers the "Why <I>Genes & Development</I> and not <I>Nature</I> or <I>Science</I>" question). But I'm not sure that the authors oversold their results. The emphasis has been on the evo-devo connection, specifically on the regulatory element-morphology connection, and not on some overarching claim that we found the gene that makes wings. Good point, though, and thanks for the comment.<BR/><BR/>Anonymous: not sure where you read "mouse given bat like forelimb" but that's at worst a minor exaggeration and is not something the authors themselves claimed. Your hilarious claim of fraud suggests to me that you should continue posting anonymously till you get some basic concepts of ethics straight.Stephen Mathesonhttps://www.blogger.com/profile/05057004085073574659noreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-81294360603771189252008-05-20T08:56:00.000-07:002008-05-20T08:56:00.000-07:00@if you read closely (p146, end of the second left...@if you read closely (p146, end of the second left para), they couldn't find any significant limb length difference in the BatE/BatE adults. <BR/><BR/>also the difference between the control and the experiment in the paper is only a 6% difference. Between the mouse and the bat, how much is the difference 1000% or so, no? <BR/>The review of the article was "Mouse given bat like forelimb". Is not that fraudulent?<BR/><BR/>Reminds me the Speeman's organizer graft experiment, supposedly giving a mirror frog, which never was.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-30816544999421240622008-05-20T08:17:00.000-07:002008-05-20T08:17:00.000-07:00It seems to me that such a fact renders the set of...It seems to me that such a fact renders the set of possible animal morphologies completely predictable. Is not that annoying?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-2501006461097163872008-05-19T13:05:00.000-07:002008-05-19T13:05:00.000-07:00John: That's a tricky case to make, because it rel...John: That's a tricky case to make, because it relies on secondary selection. If a trait (redundant regulatory areas) is only useful when a mutation occurs somewhere else (e.g., by the radiation damage you suggest), then its selective advantage will be apparently only rarely. If it's only useful in rare cases, then it would have to be *very* useful to avoid being lost by drift. This scenario is possible, it just requires extreme parameters.<BR/><BR/>A simpler explanation is that the redundant bits are harmless, rather than useful. They're not selected for, they just aren't selected out, and because these kinds of duplications happen fairly often, some of them become common in the population by chance (drift). The vast quantity of apparently useless-but-harmless noncoding DNA in mammalian genomes supports the idea that this is the process going on. In this scenario, the redundant bits are free to undergo mutations and subfunctionalize without damaging the fitness of the organism, and that's how they can be around to provide new functionality.Sarah S.https://www.blogger.com/profile/12816412712141575337noreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-73825265350359754152008-05-19T06:41:00.000-07:002008-05-19T06:41:00.000-07:00The maintentance of these redundant enhancers can ...The maintentance of these redundant enhancers can be interpreted as the diversity reservoir of a particular individual. All organims change themselves in responce to pressures of all kinds, some are capable of more drastic changes then others. While we can't breathe methane or simply not breath like some little microscopic beasties, one of the ways we <B>can</B> respond is to have these backup sections of useful but not essentail information. The backup is there in case something goes wrong, like a toxin or radiation damage, or as a reserve bit of diversity to throw at the coming selective pressure. I am imagining some kind of analogue to the inate immune responce. But in this case, the immunity is to extinction, heh.<BR/>This same sort of redundancy can be seen in kinases, where elimination of many kinase enzymes from an organism can show no phenotype. The concept the Evo-Devos are selling is the molecular tool box; a powerful evolutionary tool that would certainly have significant benefits for a species who had one. No foresight is needed, just natural selection!Alabastahhttps://www.blogger.com/profile/05286769711619408349noreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-39297941495772373732008-05-19T00:31:00.000-07:002008-05-19T00:31:00.000-07:00Redundancy in this case is a technical term. The r...Redundancy in this case is a technical term. The regulatory element is redundant in the mouse because removing it has no discernible effect. That does not mean it has no function, only that its function is dispensable, perhaps the slack taken up by other mechanisms. <BR/><BR/>Many whole gene knockouts have no discernible effect on their own. The point is that such elements are the most plastic bits that can be played with when the variations are being selected against.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-24631981024921968022008-05-18T22:24:00.000-07:002008-05-18T22:24:00.000-07:00I am alarmed by this quote "Maintenance of redunda...I am alarmed by this quote "Maintenance of redundant enhancers for essential developmental control genes would allow changes in expression pattern to arise ..." As I read it, it implies some sort of planning (genome manager A: "maybe we should chuck this junk"; genome manager B "nah, let's keep it; it might be useful someday") Evolution has no foresight!Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-53256066016478655102008-05-18T19:07:00.000-07:002008-05-18T19:07:00.000-07:00hey there, i thought your post was great, but i ju...hey there, i thought your post was great, but i just don't really like the article you chose.<BR/><BR/>i went over it in journal club and thought it was a lemon. if you read closely (p146, end of the second left para), they couldn't find any significant limb length difference in the BatE/BatE adults. a phenotype that is only expressed prenatally doesn't seem like one that selection might act on... but then again who says the path to wings can't be paved with neutral mutations?<BR/><BR/>i personally think that it's a bit hasty to conclude that the regulatory sequence the authors found is responsible for any significant part of the morphological difference between birds and bats.<BR/><BR/>the authors begin their abstract referring to natural selection's action on variation within a population. but since their sequence maintains creates no significant variation, how can they say that cis-regulatory regions like theirs are responsible for the greater part of heritable variation?<BR/><BR/>i mean, sure, they're probably right. but i don't think that their evidence is strong enough to support their sweeping conclusions.<BR/><BR/>all that aside, i think it's an awesome proof technique and a stunning example of what molecular techniques can do these days.<BR/><BR/>i agree with you entirely that for every sheet of creationist dribble there are at least 30 unheralded scientific studies advancing our understanding of how evolution works. this one just isn't my favorite of the bunch.DJ FUCKING PRETENTIOUShttps://www.blogger.com/profile/01505716875626887040noreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-45318058185625608892008-05-18T18:32:00.000-07:002008-05-18T18:32:00.000-07:00Very Neat! I do have one thing I'd like to add to ...Very Neat! I do have one thing I'd like to add to the article: It states that "The fossils can't yet show us how paws gave rise to wings". This is true, there is not a sequence of fossils that show this transition (Bats are too fragile to fossilize well). However, there was a fossil reported a few months ago which <A HREF="http://aigbusted.blogspot.com/2008/02/cool-new-fossils.html" REL="nofollow">definitely represented a transitional stage between tree climbers and bats</A>.<BR/><BR/>I wrote about this on my blog:<BR/>http://aigbusted.blogspot.com<BR/><BR/>Peace,<BR/>RyanAIGBustedhttps://www.blogger.com/profile/03232781356086767207noreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-22212545904276513382008-05-18T14:02:00.000-07:002008-05-18T14:02:00.000-07:00What an excellent post. You not only gave a good ...What an excellent post. You not only gave a good overview of the paper but explained how it related to the evo-creo debate. As a big fan of evo-devo myself (and author of one of those unheralded papers in the literature you mentioned), I thank you for writing this post.Karen Jameshttps://www.blogger.com/profile/03597701284348386435noreply@blogger.com