tag:blogger.com,1999:blog-37148773.post8428828360531148210..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: Perspectives on the Tree of Life: Day OneLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger10125tag:blogger.com,1999:blog-37148773.post-14708612389649950692009-08-09T22:25:45.621-04:002009-08-09T22:25:45.621-04:00Konrad: good point, the talk was indeed about a hy...Konrad: good point, the talk was indeed about a hypothetical computational approach (seeded maximum likelihood inference of phylogenetic networks) which may have been implemented already (Luay Nakhleh? Barbara Holland? Daniel Huson?) but I haven't had time to check.<br /><br />But it's true that almost everyone and their poodle has tried out neighbor-net, MJ, split decomposition nets, etc. etc., by now.Rob Beikonoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-68196509536450630732009-08-05T17:36:25.012-04:002009-08-05T17:36:25.012-04:00Rob - I agree; my point was that these ideas are n...Rob - I agree; my point was that these ideas are not new, but already in the iterative improvement stage. This is in contrast to the impression created by the post: referring to a "hypothetical computational approach" and saying it "may be possible to construct networks—as opposed to trees—using computer programs" sounds strange when we have been doing it (albeit imperfectly) for years.Konradnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-26790179084438182192009-08-04T14:31:28.062-04:002009-08-04T14:31:28.062-04:00NickM says,
Hi Larry -- you concede at various po...NickM says,<br /><br /><i>Hi Larry -- you concede at various points that disagreements are often not huge, and that much of the pattern even in high-LGT situations is still treelike. Yet you persist in making unqualified declarations about the death of the tree of life -- much like the sensationalist cover of New Scientist -- despite the fact that you yourself regularly bash New Scientist for sensationalism and hype on almost every other topic!<br /></i><br><br>Sorry if I haven't been clear.<br /><br />One of the things I'm trying to do is to show everyone that there is a legitimate scientific controversy about the tree metaphor. The people at the meeting are not a bunch of kooks. There really is a problem that's due largely to the confounding effects of lateral gene transfer.<br /><br />My own position is that the root of the tree of life is unknown and it will probably always be unknowable. The best representation of the total tree of life has a web or net at the base. <br /><br />Thus, the so-called "tree of life" that's found in most textbooks—the one with three domains and eukaryotes on the same branch as archaebacteria—is almost certainly false.<br /><br />In that sense the "tree of life" is deader than a doornail. However, this does not mean the end of all treelike thinking in biology. The upper parts of the representation are very treelike. <br /><br />Some scientists would dispute this point of view and they cannot be as easily dismissed as you seem to think.Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-34189151709484190342009-08-04T02:59:21.992-04:002009-08-04T02:59:21.992-04:00Hi Larry -- you concede at various points that dis...Hi Larry -- you concede at various points that disagreements are often not huge, and that much of the pattern even in high-LGT situations is still treelike. Yet you persist in making unqualified declarations about the death of the tree of life -- much like the sensationalist cover of New Scientist -- despite the fact that you yourself regularly bash New Scientist for sensationalism and hype on almost every other topic!<br /><br />Why can't we be a little sophisticated about this, admit that "right" and "wrong" come in degrees in science, and that this applies to the Tree of Life metaphor like everything else.<br /><br />In other words, why not apply some balance along the lines of Asimov's famous line?<br /><br />"[W]hen people thought the earth was flat, they were wrong. When people thought the earth was spherical, they were wrong. But if you think that thinking the earth is spherical is just as wrong as thinking the earth is flat, then your view is wronger than both of them put together."<br /><br />Isaac Asimov (1989). "The Relativity of Wrong." The Skeptical Inquirer, 14(1), 35-44. Fall 1989. <br />http://chem.tufts.edu/AnswersInScience/RelativityofWrong.htmNickMhttps://www.blogger.com/profile/04765417807335152285noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-18879668264133322372009-08-03T08:00:25.789-04:002009-08-03T08:00:25.789-04:00While it is certainly true that many very good net...While it is certainly true that many very good network methods have been developed to examine recombination, these methods are still improving as well, and in many cases are heuristic or need arbitrary thresholds to be chosen (e.g., median networks).<br /><br />Networks that represent non-homologous LGT are not exactly analogous to recombination networks too, given the possibility of drastic changes in gene content in the former.Rob Beikonoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-3945099955491822172009-07-31T18:22:59.048-04:002009-07-31T18:22:59.048-04:00We weren't aware of the fact that a species wa...<i>We weren't aware of the fact that a species was considered a unit of evolution.</i><br /><br />What do you mean by that? You know better than that, Larry—of course in the study of macroevolution and paleontology species are considered the "natural" units of evolution.Ford Prefectnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-54441352570437441902009-07-31T17:47:46.539-04:002009-07-31T17:47:46.539-04:00People have been inferring phylogenetic networks f...People have been inferring phylogenetic networks for years - nothing new there. The problem is that the principled ways are computationally feasible only for a handful of taxa. There are also fast, heuristic ways, but they leave questions in terms of interpretation and reliability.<br /><br />Have a look at the recombination and viral evolution literature. There's really not much difference between recombination in viruses and LGT in bacteria - I'm wondering if some of the bacterial folk are in danger of reinventing the wheel here.Konradnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-10121736019094929042009-07-31T13:49:46.358-04:002009-07-31T13:49:46.358-04:00Ford may be right that we can't infer a basal ...Ford may be right that we can't infer a basal tree for all organisms from the sequences of extant organisms. But this doesn't mean that basal evolution was not tree-like, any more than the abundance of transfered sequences in extant microbial genomes means that most microbial inheritance is now by LGT. <br /><br />We know that vertical inheritance is vastly more frequent in extant bacteria than LGT, so we shouldn't rashly assume otherwise for ancient microbes (no matter how cool the idea is). <br /><br />What's needed is some serious simulation work, to determine whether rare ancient LGT can mask tree-like inheritance. What would a billion years of evolution look like if one gene was transfered by LGT per 1000 organismal replications, or per 1,000,000 organismal replications? <br /><br />There's no point in fussing about philosophy or politics until we know how much LGT would be needed to give the evolutionary relationships we see.Rosie Redfieldhttps://www.blogger.com/profile/06807912674127645263noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-46873480940549755672009-07-31T09:48:51.118-04:002009-07-31T09:48:51.118-04:00Wow, sounds like a fascinating day!Wow, sounds like a fascinating day!Joelhttp://blog.motheyes.comnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-17441390095521973702009-07-31T09:34:48.151-04:002009-07-31T09:34:48.151-04:00In this post you say of Yan Boucher's talk, &q...In this post you say of Yan Boucher's talk, "The main idea was that we should not consider species as the unit of evolution, instead, the appropriate unit is a piece of DNA. This was by far the most controversial talk. Several participants, including me, were quite confused by the presentation. We weren't aware of the fact that a species was considered a unit of evolution."<br /><br />But a couple of posts down, you quote Ford Doolittle as saying, "[W]hat molecular phylogeny ultimately seeks is The Tree of Cells (TOC), a tracing back from the present of all speciation events...."<br /><br />Could it have been in this sense that Yan Boucher spoke of species as a unit of evolution, i.e., that we detect and follow the occurrence of evolution through speciation events?Judnoreply@blogger.com