Hi All,
I'm happy I have stimulated some discussion about this subject matter. For some reason I can't imagine it looks this whole thing is going to be somehow personal and I have not posted this last e-mail to the list as a consequence. Joe, unfotunately I never attended a lecture of yours, and didn't raise trivial distinctions and objections to a grant proposal you submitted. My intention was not to be critical about BM or ICs, or whatever. I just wanted to point it out that things are sometimes a bit too complex and some unreliable predictions from our models may slip out unnoticed evey now and then, as I believe it is apparent reading the literature (including my own, of course). Having said that, my guess was that we *may* use the BM and computations at nodes to see where (in which lineages) do phenotypes appear very different from predictions. For instance, I think it could be somehow possible to use estimated ancestral charactes to see how much the inclusion of some fossil (or new) species changes the estimated value (e.g. by creating a polytomy by the inclusion of the new species), or even back-calculate branch lenghts (under BM assumption) for these unusual phenotypes to see how much evolution accelerates in these lineages (by comparison with real branch lengths). I hope I spoke my mind more clearly at this time. Pas >----Messaggio originale---- >Da: dwba...@uchicago.edu >Data: 05/08/2011 20.23 >A: "Joe Felsenstein"<j...@gs.washington.edu> >Cc: "r-sig-phylo@r-project.org"<r-sig-phylo@r-project.org> >Ogg: Re: [R-sig-phylo] R: Re: R: ancestral state reconstruction for tips > >As the diversity of explicit models of trait evolution grow, it will >be interesting to see if any consensus develops about which models >hold most often in general and whether any insight is gained into >which conditions predict appearance of different models. > >I think Joe is right that realizing a model is an inaccurate or >imprecise description of reality should impel us to develop better >models of the world around us, because this partly how science moves >forward. However, I don't think pointing out that a model is deficient >requires that that person must themselves develop an alternative. >After all, an alternative model that capture a more realistic level of >complexity may not be possible in some situations (it is certainly >possible in trait evolution models, however.) Requiring such a thing >would put too much pressure on scientific whistle-blowers, who play a >very important role in reminding the rest of us that the world is more >than the models we use to understand it and make our predictions. > >-Dave > > > > >On Fri, Aug 5, 2011 at 10:51 AM, Joe Felsenstein <j...@gs.washington.edu> wrote: >> >> Pasquale Raia said: >> >>> Of course Ted is right, but my problem with this computation, or >>> with the >>> simple exercise I was proposing is well another: as a >>> paleontologist I often >>> come across pretty exceptional phenotypes (dwarf hippos and >>> elephants, huge >>> flightless birds, to make a few examples). When you use methods >>> like this (I >>> mean Garland and Ives') and compare the output with those >>> phenotypes, as I did, >>> you immediately realize what the the bottom line is: no matter if >>> they are >>> nodes or tips, by using the expected (under BM) covariance the >>> estimated >>> phenotypes are dull, perfectly reasonable but very different from >>> anything >>> exceptional you may find yourself to work with. This is why I feel >>> it is >>> difficult to rely on those (unobserved) values to begin with. >> >> I think that what is being said is that Brownian Motion is too sedate >> a process >> and does not predict some of the large changes actually seen in the >> fossil >> record. >> >> That's a legitimate point but does put the onus on the maker of the >> point to >> propose some other stochastic process that is tractable and has these >> large >> changes (and that fits with known Mendelian and Darwinian mechanisms). >> Just complaining that the Brownian stochastic process is no good is >> insufficient. >> >> If we want to add the fossils to the calculation, then they will of >> course >> pressure the Brownian Motion process to change more in their vicinity, >> which may help some. >> >> Joe >> ---- >> Joe Felsenstein j...@gs.washington.edu >> Dept of Genome Sciences and Dept of Biology, Univ. of Washington, >> Box 5065, Seattle Wa 98195-5065 >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> R-sig-phylo mailing list >> R-sig-phylo@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >> > > > >-- >David Bapst >Dept of Geophysical Sciences >University of Chicago >5734 S. 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