tag:blogger.com,1999:blog-37148773.post3447274732647692217..comments2024-03-19T09:50:39.449-04:00Comments on <center>Sandwalk</center>: What Should We Teach About the "Tree of Life"?Larry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger57125tag:blogger.com,1999:blog-37148773.post-69615167378854277842013-12-11T17:50:33.909-05:002013-12-11T17:50:33.909-05:00Paper in Nature today arguing for two domains, arc...Paper in Nature today arguing for two domains, archaea and bacteria:<br /><br />http://www.nature.com/nature/journal/v504/n7479/full/nature12779.htmlSteveFhttps://www.blogger.com/profile/06089429778294973157noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-62310512288071485172013-07-23T21:51:07.011-04:002013-07-23T21:51:07.011-04:00Jonathan,
I wonder if you could elaborate on the d...Jonathan,<br />I wonder if you could elaborate on the discussion of "archaea" as an entity? or just point me and other readers to a good recent reference on this? I certainly use the Woesian (sp?) tree in my micro class as a jumping off point, and discuss the shrublike aspects, and discuss whether species makes sense as a category for microorganisms, in the context of LGT. I would like to be able to go further with this, especially in my more advanced courses. When I'm teaching about this, I find that most students really like reading about the debates and arguments among scientists on these topics. Things like LUCA and deep phylogeny really get them interested.Paul Orwinhttps://www.blogger.com/profile/10772086513700172720noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-59842825512599179202013-07-23T19:57:56.909-04:002013-07-23T19:57:56.909-04:00Isn't there a point in time after which the Tr...Isn't there a point in time after which the Tree of Life becomes a true representation of particular clades? Is it that big a deal to admit that before that time, with a lot of horizontal gene transfer and so forth, that things are a lot messier? I think undergraduates ought to be able to handle that.<br /><br />"There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one;" or, for that matter, into many.<br /><br />Does it really matter if the lines of descent are somewhat blurred up to a point?John Krehbielhttps://www.blogger.com/profile/10078079001156415151noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-12706070405563006502013-07-21T14:22:08.339-04:002013-07-21T14:22:08.339-04:00In their article entitled “What Is a Prokaryote? T...In their article entitled “What Is a Prokaryote? The Prokaryotes: Prokaryotic Biology and Symbiotic Associations” Doolittle and Zhaxybayeva write:<br /><br />“At issue is whether living organisms on this planet are two kinds (prokaryotes and eukaryotes) or instead, three (Bacteria, Archaea, and Eukarya).”<br /><br />We have known now for many, many years that viruses are the most abundant life forms on this planet, and that the repertoire of viral genes is greater than that of cellular genes. Interestingly, there is an article just published in Science (http://www.sciencemag.org/content/341/6143/281.abstract) describing some very large viruses (Pandoraviruses) which have a genome larger than those of some protozoa.<br /><br />Therefore, not including viruses in the discussions on the Tree of Life (ToL) is poor science any way you look at it. Maybe it is time for people who write, with apparent authority, about the kinds of organisms on our planet and about the ToL to take a refreshing introductory course in Biology.<br /><br />Claudiu Bandeahttps://www.blogger.com/profile/04987489537796352657noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-14191137767220185882013-07-21T13:29:04.651-04:002013-07-21T13:29:04.651-04:00I think that a Tree of Life (or more accurately a ...I think that a Tree of Life (or more accurately a Shrub of Life) works well for Eukaryotes, despite a relatively small amount of lateral gene transfer. I've taught it and would again. I think arguing about the value of this Shrub is like pointing out the problems of using a 2-D photograph to teach about a 3-D house; the limitations are real, but the photo can still provide a good first approximation of the truth.<br /><br />With regards to prokaryotes (a useful descriptive term, though not a clade), I've taught a kind of Shrub of Life with the eukaryote nucleus evolving within Archaea. I've commented that lateral gene transfer makes the picture messy. If I were teaching this again, I'd emphasize the messiness even more, the eukaryote nucleus as a chimera. (Reading Sandwalk is useful.) I like these topics where I can say, "This is the best I know now but this is an area of active research." (I often have to say, "This is the best I know but I don't know much," so it feels good to have a reason to not know.) Some of the students aren't happy with the uncertainty but it's good for them. Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-37895816607526511002013-07-21T10:32:44.304-04:002013-07-21T10:32:44.304-04:00Why are so many of these "honest, God-fearing...<i>Why are so many of these "honest, God-fearing" zealots like this?</i>?<br /><br />Just a few, I think, but those individuals are very industrious. AllanMillerhttps://www.blogger.com/profile/05955231828424156641noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-51917517263985329342013-07-21T10:13:26.641-04:002013-07-21T10:13:26.641-04:00"I'm neither, as I only follow the eviden..."I'm neither, as I only follow the evidence, wherever it may lead me."<br /><br />Right... And let me guess - it amazingly leads you to Yahweh?<br /><br />Pathetic.nmanninghttps://www.blogger.com/profile/14767343547942014627noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-70358051085213295852013-07-21T10:12:31.194-04:002013-07-21T10:12:31.194-04:00"Are you mentally retarded? Aren't you su..."Are you mentally retarded? Aren't you supposed supposed to be a scientist and no fairy-tale-teller?"<br /><br />The deceptive creationist projects.<br /><br />Why are so many of these "honest, God-fearing" zealots like this?nmanninghttps://www.blogger.com/profile/14767343547942014627noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-80676521194051186412013-07-21T10:10:30.685-04:002013-07-21T10:10:30.685-04:00Of course, your "beliefs" align with den...Of course, your "beliefs" align with denying evolution, so of course you take what your psych professor declared about evolution as Gospel, since it aligned with your faith. Pretty transparent.nmanninghttps://www.blogger.com/profile/14767343547942014627noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-64636835921765643102013-07-21T07:21:12.848-04:002013-07-21T07:21:12.848-04:00The biological species concept is reproduction-bas...The biological species concept is reproduction-based in the sense that sexual intercompatibility draws its boundaries. It only applies to sexual eukaryotes. Asexuals should more nearly approach the 'tree ideal' - eukaryotic sex is a kind of wholesale LGT, though sexual <i>speciation</i> remains tree-like.<br /><br />When you replicate any DNA base pair, you get two. Those can be further replicated, and you end up with a 'tree' for each bit. Any two descendants at the twig-tips can trace back to a node at which their ancestral bases were paired in the same DNA molecule. <br /><br />Neighbouring bases should follow the same pattern, so you would expect to be able to superimpose the trees from two close neighbours. And if replication were perfect, and gene transfer nonexistent, it would be trees all the way down. But obviously, there are confounding forces at work when you try to <i>infer</i> the actual phylogeny from modern material - mutations, deletions, duplications, LGT fragment incorporation.<br /><br />Because it derives from a fundamental property of the genetic material, the 'ideal' phylogeny would be treelike for any base, and if the whole genome is replicated, the same tree will apply across the genome. But with LGT, threads connect different branches. At the level of the individual base, passage from one lineage to another does not invalidate the tree concept at base level, but blurs it at genome level. A lot of this (and gene loss etc) over time makes the 'vertical', idealised tree harder to recover from any dataset.<br /><br />Some authors hold that this net-effect is not simply an artefact of vertical descent + a dripfeed of LGT + time, however. AllanMillerhttps://www.blogger.com/profile/05955231828424156641noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-20182192158746034312013-07-20T23:52:44.842-04:002013-07-20T23:52:44.842-04:00Jerseyboy
What exit?
If you are really from Jer...Jerseyboy <br /><br />What exit?<br /><br />If you are really from Jersey, you know what I'm asking.<br /><br />If you are another sock puppet for the banned Vashti/Witten, you don't.Diogeneshttps://www.blogger.com/profile/15551943619872944637noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-11998600438584343942013-07-20T19:40:48.679-04:002013-07-20T19:40:48.679-04:00As I said, I have no opinion on this specific ques...As I said, I have no opinion on this specific question and I am not teaching or researching anything beyond the flowering plants anyway. I am merely afraid that some readers might be prompted to throw out the baby with the bathwater if they get the impression that LGT means the absence of tree structure. Some people make the same argument even for within the plants or animals, where LGT is definitely much less frequent than in bacteria.Alex SLhttps://www.blogger.com/profile/00801894164903608204noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-59640504515661565612013-07-20T18:07:33.863-04:002013-07-20T18:07:33.863-04:00Second, just because there is LGT or introgression...<i>Second, just because there is LGT or introgression even between Eukaryote lineages does not mean that there is no tree</i><br /><br />Let's assume that there IS a tree buried somewhere in all that data. Are you absolutely certain that it will show eukaryotes as a sister group of Eocytes? If you are not certain, would you teach it anyway?<br /><br /><i>In other words, the history of a species is not equal to the history of its genes ...</i><br /><br />Exactly. That's why it's wrong to teach that eukaryotes are most closely related to Eocytes just because a small subset of genes shows that phylogeny. Don't you agree?Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-26439651855087102402013-07-20T12:52:41.625-04:002013-07-20T12:52:41.625-04:00It's the basic theist double standard. If you&...It's the basic theist double standard. If you're not a scientist, then any science you understand to be true is 'scientism' and you merely have a faith position, but if you *are* a scientist, you're a member of a priesthood and speaking in a hidden tongue known only to fellow-believers.<br /><br />What I find amusing about that is that the scope of the ambition of that claim is 'you're as deluded as we are'. It's not claiming superiority, merely parity. It's accusing us of being confused because we have faith and priesthoods. <br /><br /><br /><br />Jemhttps://www.blogger.com/profile/10359685574788608040noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-33341376022820023802013-07-20T11:47:10.502-04:002013-07-20T11:47:10.502-04:00If you ever want to have a really deep discussion ...If you ever want to have a really deep discussion about "species:" John S Wilkins.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-34673959872923921202013-07-20T11:42:14.024-04:002013-07-20T11:42:14.024-04:00What I really find amusing about jerseyboy is that...What I really find amusing about jerseyboy is that he thinks that discussions between scientists about the meaning of the details of their work is somehow indicative of a failure of the scientific method, or that they are "not doing science" if they do not have absolute certainty about how new discoveries in their field should be understood.<br /><br />He probably assumes that all knowledge should be handed down from on high, and received without comment. As if that happens even in religious scholarship. Last I checked, there were innumerable religious sects which could not agree even on basics.<br /><br />Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-63527098008454289912013-07-20T11:35:34.119-04:002013-07-20T11:35:34.119-04:00I think that 10^2860 is a high enough probability ...I think that 10^2860 is a high enough probability for scientists to use the term "certainty" with regard to LUCA. Of course, if the arguments ever suggest otherwise I am willing to revise my conclusion. Pray, tell, what is it you do under those circumstances?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-90739819460386002382013-07-20T11:27:39.136-04:002013-07-20T11:27:39.136-04:00Part of my comment was lost. I was referring to u...Part of my comment was lost. I was referring to using the nested hierarchy in K-12, and necessarily in undergraduate when that fails. The concept of the nested hierarchy had never completely occurred to me until John Harshman pointed it out to me many years ago on Usenet. Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-75048453627223056532013-07-20T06:40:25.135-04:002013-07-20T06:40:25.135-04:00I am not really qualified to judge prokaryote phyo...I am not really qualified to judge prokaryote phyogenetics so I don't really take a position on the three domains controversy. And for all I know it might be correct that there is so much LGT going on. But that being said:<br /><br />First, I know that there are people who are more qualified than I am and who argue that at least a good deal of the mush that is interpreted as being indicative of rampant LGT might stem from the difficulty of establishing sequence homology between lineages that diverged from each other a really really damn long time ago. The host of this blog <a href="http://sandwalk.blogspot.ca/2008/10/bacteria-phylogeny-facing-up-to.html" rel="nofollow">has written about the problem himself</a>, of course.<br /><br />Second, just because there is LGT or introgression even between Eukaryote lineages does not mean that there is no tree. We systematists and phylogeneticists are, after all, not interested in producing a classification of gene copies, we merely use them as data. What we want to produce is a classification of species, and species can still form a mostly tree-shaped species phylogeny even if there is some gene flow between them.<br /><br />In other words, the history of a species is not equal to the history of its genes, and to think otherwise is to succumb to the <a href="http://en.wikipedia.org/wiki/Fallacy_of_composition" rel="nofollow">fallacy of composition</a>.<br /><br />Finally, ...<br /><br /><i>The most likely explanation is that euakryotes are chimeras resulting from fusion of an archaebacterium and a eubacterium</i><br /><br />It is clear that we have very different visions of what "most likely" means. To me it sounds too much like <a href="http://whyevolutionistrue.wordpress.com/2009/09/04/worst-paper-of-the-year/" rel="nofollow">this</a>. But again, I work on flowering plants, not on the really deep phylogenetics.Alex SLhttps://www.blogger.com/profile/00801894164903608204noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-74337485425947272622013-07-20T06:01:24.147-04:002013-07-20T06:01:24.147-04:00This creationist feigning-to-be-confused moron is ...This creationist feigning-to-be-confused moron is getting tiresome. <br /><br />Is anyone even in doubt about this particular and specious individual? His "strange" confusion about problems that just so <i>mysteriously happens</i> to relate with anything that touches on evolution, atheism and/or morality and humanism - is more obvious and transparent than intergalactic vacuum is to neutrino radiation. <br /><br />It really is curious how many different individuals of this specific type that end up on this blog. Or mabye they're mostly the same idiot posting under a new acronym. Hmmm... ?Mikkel Rumraket Rasmussenhttps://www.blogger.com/profile/07670550711237457368noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-34101917528544113882013-07-20T03:41:43.340-04:002013-07-20T03:41:43.340-04:00Are you mentally retarded? Aren't you supposed...<b>Are you mentally retarded? Aren't you supposed supposed to be a scientist and no fairy-tale-teller? What kind of scientific statement is this? Basically, one can believe in anything he wants, as long as my "scientific view" is not effected.</b><br />It seems you're the retarded one. None of these veiews were expressed in that post. Mikkel Rumraket Rasmussenhttps://www.blogger.com/profile/07670550711237457368noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-10700964169350738322013-07-20T02:27:40.271-04:002013-07-20T02:27:40.271-04:00I largely agree, and it turns out that the "p...I largely agree, and it turns out that the "problem" here isn't all it's made out to be. The web of life in single-celled organisms still tends statistically towards a tree. <br /><br />In any case, I don't see any issue with just teaching the facts here. Trees are fine for humans, dogs and other large multicellular eukaryotes for the most part, but most of evolution has happened in single-celled life where it's much more messy and life a web(though still tending statistically towards a tree). As long as it is explained how and why these concepts apply and where they apply. Mikkel Rumraket Rasmussenhttps://www.blogger.com/profile/07670550711237457368noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-63626576005327032292013-07-20T02:20:38.021-04:002013-07-20T02:20:38.021-04:00Just to make sure I'm not misunderstood, I'...Just to make sure I'm not misunderstood, I'm not saying we shouldn't teach them that the tree of life is a web, we should. But the concept of a tree can be taught, and where and why it applies and where and why it doesn't. That would be teaching the facts. Mikkel Rumraket Rasmussenhttps://www.blogger.com/profile/07670550711237457368noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-20172109029346578672013-07-20T02:16:23.847-04:002013-07-20T02:16:23.847-04:00Then you shouldn't be having any problems. Thi...Then you shouldn't be having any problems. This discussion is about how to best present that evidence, not about whether evidence exists. Your confusion is of your own making. Mikkel Rumraket Rasmussenhttps://www.blogger.com/profile/07670550711237457368noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-56989162840144961692013-07-20T02:08:49.385-04:002013-07-20T02:08:49.385-04:00Because no matter what, the majority of genes are ...Because no matter what, the majority of genes are transferred vertially, not horizontally. For most of that kind of evolution "normal" people think about, that is, plants and animals. Humans and their dogs and cats, cows, flowers etc. For those organisms, the tree of life is actually pretty solid and indeed pretty much a tree. <br /><br />Of course, as people who really know biology knows, most of the evolution that has taken place on this planet has happened in single-celled organisms. There the "tree of life" is a web, it only "trends" towards a tree. <br /><br />So, by analogy, teaching people newtonian mechanics(a useful approximation) is like teaching them about the "tre of life". See: <br /><b>Seeing the Tree of Life behind the phylogenetic forest</b><br /><i>Pere Puigbò, Yuri I Wolf and Eugene V Koonin</i>*<br /><a href="http://www.biomedcentral.com/1741-7007/11/46" rel="nofollow">http://www.biomedcentral.com/1741-7007/11/46</a>Mikkel Rumraket Rasmussenhttps://www.blogger.com/profile/07670550711237457368noreply@blogger.com