tag:blogger.com,1999:blog-37148773.post8640497425649714773..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: The Three Domain Hypothesis (part 3)Larry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger8125tag:blogger.com,1999:blog-37148773.post-62453051332917123262006-11-28T00:05:00.000-05:002006-11-28T00:05:00.000-05:00Pace "Because it has long been used by all texts o...<em>Pace "Because it has long been used by all texts of biology, it is hard to stop using the word, prokaryote. But the next time you are inclined to do so, think what you teach your students: a wrong idea."<br /><br />Larry: "Do you agree? Do you think the Three Domain Hypothesis is so solidly established that all other hypotheses are just plain wrong?"</em><br /><br />I don't think that's what Pace is saying -- as I interpret it, all he is saying is that it doesn't seem plausible to maintain Haeckel's 19th century idea of Kingdom Monera where all organisms lacking nuclei were assumed to be more or less the same; we know too much about the biochemical and genetic differences between bacteria and archaea to believe it any more. And I agree.<br /><br />But that doesn't mean that the Three Domain Hypothesis in the traditional sense is the One True Answer to explain these differences. It could well be that in the future people will believe that only the eukaryotic nucleus is related to archaea and that the cytoplasm arose from a bacterium or even some other form of life that we haven't discovered yet. Science gets more and more complicated as we learn more. <br /><br />But just as flaws in Einstein's theories of gravity don't send physicists rushing back to Newton, possible flaws in Woese's Three Domains won't send biologists back to Haeckel.Jonathan Badgerhttps://www.blogger.com/profile/04921990886076027719noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-14107142856531193102006-11-27T21:49:00.000-05:002006-11-27T21:49:00.000-05:00Martin may be guilty of hyperbole—aren't we ...Martin may be guilty of hyperbole—aren't we all from time to time?—but he makes a valid point. The proponents of the Three Domain Hypothesis have been very forceful in pushing the idea. They're currently acting as if it's a done deal and all the textbooks should be changed.<br /><br />For example, Pace argues in "Time for a Change" (Nature 441:289 (2006)) that the word "prokaryote" should be abandoned now that we "know" for sure that the earliest split was not between eukaryotes and prokaryotes. He says ...<br /><br /><i>The use of the term 'prokaryote' fails to recognize that an idea about life's origins has been proved wrong.</i><br /><br />I don't know about you but that sure sounds to me like he already knows the answer. Pace closes with some strong language ...<br /><br /><i>I believe it is critical to shake loose from the prokaryote/eukaryote concept. It is outdated, a guesswork solution to an articulation of biological diversity and an incorrect model for the course of evolution. Because it has long been used by all texts of biology, it is hard to stop using the word, prokaryote. But the next time you are inclined to do so, think what you teach your students: a wrong idea.</i><br /><br />Do you agree? Do you think the Three Domain Hypothesis is so solidly established that all other hypotheses are just plain wrong? <br /><br />In my opinion, that's not a good example of how scientists should behave when they know that respected colleagues disagree with their favorite hypothesis.Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-43926821594894829822006-11-27T16:22:00.000-05:002006-11-27T16:22:00.000-05:00Bill Martin, as quoted by Larry "Thus, it seems to...<em>Bill Martin, as quoted by Larry "Thus, it seems to me that there is a schisma abrew in cell evolution, with the rRNA tree and proponents of its infallibility on the one side and other forms of evidence, proponents of LGT, or proponents of a symbiotic origin of eukaryotes on the other. The former camp is well organized behind a unified view (be it right or wrong, still a view) and is arguing that we already have the answers to microbial evolution." </em><br /><br />I think Bill Martin is creating a straw man here; *nobody* on the "rRNA side" (really, the three domain side) thinks that "we already have the answers to microbial evolution". <br /><br />Everybody knows that there are a lot of unanswered questions in evolution and studies of whole genome phylogeny, LGT and the possible symbiotic origin of eukaryotes are of interest to everybody in the field of microbial evolution. Much of the research in these subjects is conducted by people who support the three domains (not surprisingly, since that is the current majority view).Jonathan Badgerhttps://www.blogger.com/profile/04921990886076027719noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-32317512571426852592006-11-27T09:11:00.000-05:002006-11-27T09:11:00.000-05:00All the articles are from the book. I haven't got ...All the articles are from the book. I haven't got time to do a complete review of the literature so I decided to concentrate on the articles in the book in order to higlight the controversy.<br /><br />Most people don't realize that there's a fight going on.Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-37278990964659275532006-11-27T07:25:00.000-05:002006-11-27T07:25:00.000-05:00Would it be possible to cite journal and year in a...Would it be possible to cite journal and year in addition to author’s name and article title? Or are all the mentioned articles chapters in the book edited by Sapp?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-24410818684567189712006-11-26T17:59:00.000-05:002006-11-26T17:59:00.000-05:00There are many assumptions in using the "predicted...There are many assumptions in using the "predicted" secondary structure as a guide. First, you have to assume that your predictions are correct. Second, you have to assume that there has been no migration of secondary structure as double-stranded regions expand and contract over time. Third, you have to assume that secondary structure is conserved. <br /><br />Even if all these assumptions hold you still have the problem of only four possible bases at each position and you still have the problem of deciding where the gaps should be placed.<br /><br />If you've ever tried aligning ribosomal RNA sequences you'll find that it's much more difficult than aligning highly conserved amino acid sequences, even when you have predictions of double-stranded regions. <br /> <br />There's a large aligned sequence database of ribosomal RNAs so it's not that hard to fit in another related sequence. What we don't know is how accurate the original alignments were in the first place. (Some work has been done on this. If you have references, I'd appreciate hearing about them.)Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-78406696486624298142006-11-26T17:27:00.000-05:002006-11-26T17:27:00.000-05:00About you proposed criteria number 5: The predicte...About you proposed criteria number 5: The predicted secondary structure of rDNA could be used as a guide in the alignment process, and this will make it as acurate as a protein alignment.Anonymoushttps://www.blogger.com/profile/09534342181196680440noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-46064756927711131572006-11-26T17:21:00.000-05:002006-11-26T17:21:00.000-05:00The old idea that we need to choose "the right gen...The old idea that we need to choose "the right gene" is part of the problem. We shouldn't infer evolutionary relationships from a single gene any more than we should infer them from a single bone.<br /><br />The "right gene' idea dates from the time when getting the sequence of even one gene was expensive. The question now is how much (and what kind of) sequence or non-sequence characters do we need to get a satisfactory approximation of evolutionary histories? <br /><br />Maybe the best approach would be to take those organisms with whole-genome sequences and see how much information can be left out without seriously weakening the tree.<br /><br />(I think Bill Martin's camp also has its share of politics and charismatic leaders.)Rosie Redfieldhttps://www.blogger.com/profile/06807912674127645263noreply@blogger.com