tag:blogger.com,1999:blog-37148773.post5378567978292189379..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: Evolution and Variation in Folded ProteinsLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger7125tag:blogger.com,1999:blog-37148773.post-59523178322946054202014-02-17T16:16:03.345-05:002014-02-17T16:16:03.345-05:00I think you mean 20^200 (20 possible residues in e...I think you mean 20^200 (20 possible residues in each of 200 different positions) not 200^20 (200 possible residues in 20 positions). 20^200 is 2^20 x 20^160 times bigger!. Not that that helps the creationists much.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-16304372871974211882008-03-17T09:53:00.000-04:002008-03-17T09:53:00.000-04:00Martinc asks,Larry, have you any opinions on the h...Martinc asks,<BR/><BR/><I>Larry, have you any opinions on the hypothesis of Drummond that expression levels are important in the rate of evolution of coding sequences ? - principally through the negative effects of high levels of misfolded proteins.</I><BR/><BR/>Of course I have an opinion! :-)<BR/><BR/><A HREF="http://sandwalk.blogspot.com/2007/03/silent-mutations-and-neutral-theory.html" REL="nofollow">Silent Mutations and Neutral Theory</A><BR/><BR/>Biology is messy. For every generality there will be many exceptions. The trick is not to let the existence rare exceptions distort one's view of the big picture.<BR/><BR/>Most silent mutations are neutral and so are most amino acid substitutions. The fact that some of these will affect protein folding and, therefore, the rate of gene expression does not mean that most of them will. Similarly, the fact that some codons will be translated faster than others is a well-known fact but it doesn't seem to be very important in the vast majority of cases.Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-13479789554209390342008-03-17T07:11:00.000-04:002008-03-17T07:11:00.000-04:00A paper that describes a genetic basis for the mal...A paper that describes a genetic basis for the malate/lactate change you describe in the post: http://mbe.oxfordjournals.org/cgi/content/full/21/3/489Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-64724681472220177522008-03-17T04:32:00.000-04:002008-03-17T04:32:00.000-04:00Larry, have you any opinions on the hypothesis of ...Larry, have you any opinions on the hypothesis of Drummond that expression levels are important in the rate of evolution of coding sequences ? - principally through the negative effects of high levels of misfolded proteins. <BR/>http://www.pubmedcentral.nih.gov/picrender.fcgi?tool=pmcentrez&artid=1242296&blobtype=pdfSigmundhttps://www.blogger.com/profile/00262375488263086844noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-33595483363443711572008-03-15T12:57:00.000-04:002008-03-15T12:57:00.000-04:00Richard Dawkins makes the same point in The Ancest...Richard Dawkins makes the same point in <I>The Ancestor's Tale</I>, p.589 (paperback)<BR/><BR/><I>Indeed,there are lots of different amino acid sequences that will yield the same shape, which is one reason to doubt naive calculations of the astronomical 'improbability' of a particular protein chain, obtained by raising 20 to the power of its length.</I><BR/><BR/>If I remember correctly that is exactly how Durston derives his estimates of improbability, which is why I was interested in knowing if the spring smackdown was still in the works.<BR/><BR/>It's as if I lost a hand holding 3 deuces to someone who had a four of clubs, a four of hearts, a four of diamonds, a King of spades and an eight of hearts; and concluded that I needed exactly that hand to beat three deuces, when in fact there is a whole family of hands containing three of something that could do the job.paul01https://www.blogger.com/profile/06306440944379183875noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-9710394219946083252008-03-15T08:36:00.000-04:002008-03-15T08:36:00.000-04:00I've been waiting for this post. This point needs ...I've been waiting for this post. This point needs following up:<BR/><BR/><I>The point is that there are literally billions of different proteins that have the same shape as globins and still function as carriers of oxygen. This is an important point. Opponents of evolution often take a single globin from a single species and calculate the probability that such a structure will form. They assume that only one out of twenty amino acids can be found at each position and the resulting probability (e.g., 200^20) is enormous. Thus, they conclude, such a protein could never form by chance. They don't seem to appreciate the fact that we already know of billions of different proteins that can function as globins. </I><BR/><BR/>I'll keep tabs on it!Timothy V Reeveshttps://www.blogger.com/profile/03913020911593893925noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-81482244044214833792008-03-14T16:42:00.000-04:002008-03-14T16:42:00.000-04:00In contrast, one can consider the recent transitiv...In contrast, one can consider the recent transitive homology studies of Cro proteins carried out by the Cordes lab (see <A HREF="http://dx.doi.org/10.1073/pnas.0711589105" REL="nofollow">PNAS</A> for their paper). They found two proteins with 40% sequence identity and identical functions, but very different folds. That this is <I>surprising</I> essentially proves the rule that we expect enormous sequence flexibility for a given structure.<BR/><BR/>Temperature and ionic strength have also been found to occasionally dicate structure, and not just in terms of denaturation or aggregation. Brian Volkman's work on lymphotactin indicates that these conditions can cause transitions between different stably folded structures.Sparkyhttps://www.blogger.com/profile/10444352252473400411noreply@blogger.com