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Science

The Tree of Life Consolidates 266

Posted by kdawson
from the pruning-it dept.
Roland Piquepaille writes "The Tree of Life is an expression first used by Charles Darwin to describe the diversity of organisms on Earth and their evolutionary history. There are only two life forms, — eukaryotes, which gather their genetic material in a nucleus, and prokaryotes, such as bacteria, which have their genetic material floating freely in the cell. Until recently, eukaryotes, which include humans, were divided into five groups. But now, based on work by European researchers, the Tree of Life has lost a branch. After doing the largest ever genetic comparison of life forms they concluded that there are only four groups of eukaryotes."
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The Tree of Life Consolidates

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  • by davidwr (791652) on Tuesday January 22, 2008 @05:48PM (#22144588) Homepage Journal
    The more we know, the more we know that what we knew was wrong.

    Or, as a coworker of mine used to say when we realized we didn't know what we were doing: "Everything you know is wrong."
    • Re: (Score:3, Funny)

      This is precisely why we believe in the guy up in the clouds who pulls the strings behind the curtains!

      Oh wait...
    • I never heard of "PLoS ONE", it claims to be a peer reviewed journal at least. If this was ground breaking I'd expect it to be published in Nature though. The "PLoS ONE" website isn't loading for me at the moment, but hopefully I'll be able to read the actual article. This seems to be hoopla over definitions though, we can sort organisms into kingdoms and phyla any way we like, this seems identical to the tug-of-war over whether Pluto is a planet or a planetoid. Is it the size of the planet? Is it if a
      • Re: (Score:3, Interesting)

        by Angostura (703910)
        It's a bit more than that. The question of whether Pluto belongs to the class 'Planet' is basically decide by one metric only: size. A phylogenomic study is rather more interesting than that since it casts light on the actual intrinsic interrelationships between different organisms and their likely evolution paths.

        I've had a quick look at the paper you linked to, and frankly its over my head. My degree was genetics/molecular biology but that was 20 years ago and taxonomy used to bore me rigid.
      • Re: (Score:3, Informative)

        by Seiruu (808321)
        [quote]I never heard of "PLoS ONE"[/quote]

        Then you have also never heard of Open Access, because then you would certainly know what PLoS ONE is. A shame you've never heard of it, because it is a very significant and rapidly growing movement within the scientific community. It puts the emphasis on opening up the access of scientific literature to everyone by switching from reader-pays to author-pays models. And with that said, it is very likely that scholars select PLoS ONE or other OA journals (peer reviewe
      • PLoS ONE is indeed a peer-reviewed journal, and although it's not in the same tier as Nature, it's certainly a respectable publication. Not all major research is published in the Big Two, Nature and Science, you know; there simply isn't room.
        • Re: (Score:3, Informative)

          by FleaPlus (6935)
          PLoS ONE is indeed a peer-reviewed journal

          Mm... not exactly. Perhaps you're thinking of PLoS Biology? Articles submitted to PLoS ONE [wikipedia.org] undergo some very cursory peer review, but in a sense it's undergoing it's primary peer review -now-, with the article out in the open and readers commenting on it. From a news item in Nature:

          http://www.nature.com/nature/journal/v445/n7123/full/445009a.html [nature.com]

          Every paper submitted to the journal is reviewed by at least one member of PLoS One's editorial board of over 200 researchers, but only to check for serious flaws in the way the experiment was conducted and analysed. In contrast to almost all other journals, referees ignore the significance of the result. Notable papers will instead be highlighted by the attention they attract after publication.

          Visitors to the PLoS One website can, for example, attach comments to specific parts of a paper and rate the paper as a whole. Data from those systems, as well as download and citation statistics, will then allow PLoS One's editors to identify and promote the papers that researchers are talking about. "We're trying to make a journal where papers are not the end point, they are the start of a discussion," says PLoS One managing editor Chris Surridge, based in Cambridge, UK.

      • by Anonymous Coward on Wednesday January 23, 2008 @12:30AM (#22149302)
        I never heard of "PLoS ONE", it claims to be a peer reviewed journal at least. If this was ground breaking I'd expect it to be published in Nature though.

        I'm actually surprised you haven't heard of PLoS journals.

        PLoS is an open-access publisher of science journals. Basically, the journals are free to access, and content is published under a creative-commons-type license.

        PLoS journals are excellent, and rival the best journals in their content. There is no "general" science journal like Science or Nature, but there are topical journals like PLoS Biology, PLoS Medicine, etc. I'd argue that the content in these topic journals are comparable to Nature and Science publications.

        PLoS One is a relatively experimental journal published by PLoS that attempts to push the open access model to its limits, by making the peer-review process completely open, where anyone is allowed to comment.

        If anything, the fact that this article was published in a PLoS journal raised rather than lowered my expectations regarding its quality.
    • Or, as a coworker of mine used to say when we realized we didn't know what we were doing: "Everything you know is wrong."


      "Black is white, up is down and short is long."

      Just forget the words and sing along!
    • 5 instead of 4? Well that's a pretty good guess given that the previous generation of scientists did not have a lot of the tools that the new kids on the block have.

      Science is a moving target which is one of the reasonse we should never use terms like "scientifically proven" and should never get ioverconfident.

      • Science is a moving target which is one of the reasonse we should never use terms like "scientifically proven" and should never get ioverconfident.

        I'm not sure "we" ever do. Every time I see that term or those like it (s/scientifically/clinically/) it's always the spew of some scumbag marketroid.
      • Re:Pretty good guess (Score:5, Interesting)

        by RockDoctor (15477) on Wednesday January 23, 2008 @04:28AM (#22150660) Journal

        5 instead of 4? Well that's a pretty good guess given that the previous generation of scientists did not have a lot of the tools that the new kids on the block have.

        The previous "5 kingdoms" model is hardly the result of guesswork. I've been working through a (now-outdated) reference tome on the model on-and-off for about 4 years now, and I'm barely half way through the book (It's Margulis & Schwartz, BTW, "Five Kingdoms: Illustrated Guide to the Phyla of Life on Earth (Paperback) " ISBN 0716730278).
        Given that it's 10 years old now, I was actually expecting this to happen. In the time since I got the book (about 5 years) and started working my way through it, making notes, one of the 137 phyla which they describe has been found to be a grossly degenerated member of another phylum (it's an obscure parasite found normally only on the gills of cephalopod molluscs), another two have been merged (I can't even remember which ones they were. Protoctists of some sort.), and now someone has proposed a different way of slicing up the pie at the super-phylum level. I see that the unikont grouping still stands in this new analysis, which even I could figure out as a natural grouping.

        Trust me (or do the legwork for yourself!), the 5 kingdoms model was not guesswork. It might not be the correct model, but it's based on a lot of evidence.
        (BTW, sitting in my rucksack at this very moment I've got a reprint of one of Margulis' 1995 papers setting out some of the grounds for the 5 kingdoms model. It's my "light reading" on the bus to work, as a change from doing a correspondence course in Java. Next to it is a reference to the geological structure of the South Atlantic, which may be my work place in a couple of years. Lifelong training is a requirement, not an option.)
    • by 2short (466733)

      Our understanding of the world is, and will always be, approximate.

      Science is a process by which we improve that approximation. Nothing we used to know is now wrong. Some things we used to roughly understand we now understand better.

      It appears that the Eukaryotes emerged sometime over a billion years ago. As far back as we could figure out, it looked like there were five groups of them, but we didn't understand which of those groups were more closely related to each other. Further research has now refin
    • "Everything you know is wrong" -- also the title of a very funny Firesign Theatre album.
  • by sm62704 (957197) on Tuesday January 22, 2008 @05:52PM (#22144676) Journal
    I should be more careful with that chainsaw. Poor tree, only 5 branches , I hope it survives...
  • by Anonymous Coward on Tuesday January 22, 2008 @05:54PM (#22144722)
    What else will science rob from us before we decide enough is enough?
  • Not really a tree... (Score:5, Interesting)

    by myowntrueself (607117) on Tuesday January 22, 2008 @05:57PM (#22144770)
    While a tree-structure is algorithmically convenient and very enticing... the "tree of life" is not a tree.

    Ie it is not a "directed, acyclic graph".

    Unfortunately it has 'cycles'.

    Blame retroviruses; they can take genetic material from one species and insert it into the genome of another thereby creating cross-branches.

    As I recall, from my genetics days, baboon retroviruses are a great example of this. Again, IIRC, domestic cats and humans both contain fragments of baboon retroviruses.

    Its possible that the "Cambrian explosion" is a sign of the appearance of retroviruses on the scene.

    The thing is that it is significantly harder to reason about graphs; trees are so much easier to deal with.

    So its very tempting to see things like this as trees and to 'simplify out' the nasty cross-branches.

    (I've studied genetics, computer science, logic and discrete math)
    • Re: (Score:3, Insightful)

      by MightyMartian (840721)
      You're substantially exaggerating the effect that horizontal gene transfer has on the tree. ERVs are taken into account, and are in fact, quite useful in narrowing down where specific species and higher cladistic groupings sit in the tree.
    • Re: (Score:3, Informative)

      by Otter (3800)
      Unfortunately it has 'cycles'.

      Someone helpfully linked the paper [plosone.org] (and was modded down for his trouble); they address that concern extensively.

    • by bar-agent (698856)
      Wouldn't it be a directed, cyclic graph? All connections only go in one direction: forward through time.
    • Your "tree of life" has inter-connecting branches?

      That sounds a little....incestuous....no?

      • by MightyMartian (840721) on Tuesday January 22, 2008 @06:25PM (#22145316) Journal
        There's a small part of most organisms' genomes that are made up of ERVs. These are insertions of retroviral DNA into our genomes. For the most part, these viral sequences are in neutral or junk genome stretches, so they don't have any influence on the organism. Unlike what the poster is saying, these don't make producing the tree more difficult, but in fact are extremely useful in fine-tuning the tree.

        The odd-man out here are some prokaryotes, such as bacteria, where a sort of pseudo-sexual reproduction can take place by direct genome transfers. Still, this does not stop the classification of bacteria, but it does probably mean that the root of the tree of life, those earliest primitive self-replicators, probably swapped genes a helluva lot, so there may be no common ancestor per se, but rather a nest of common ancestors who swapped chunks of their DNA, RNA or whatever the earliest genetic molecules were.
    • by Kjella (173770)

      Ie it is not a "directed, acyclic graph".

      Unfortunately it has 'cycles'.

      I'm sure that's a correct mathematical defintion, but it doesn't apply to common usage. If you take a large family tree you'll almost certainly find some common ancenstors like sharing a great grandfather from the time people found their spouses in small rural communities. That doesn't prevent us from calling it a family tree, as long as it has a direction in time that branches out to multiple individuals/species I don't think a anyone but a mathematician would object.

    • by rucs_hack (784150)
      While the tree of life does have cycles, those are similar adaptations to similar problems, and can occur in diverse species which have been seperate for many millions of years.

      Take the saber tooth adaption. That's been recurring since the pre-dinosaur reptilian era. Always to solve the same basic problem.
      • Not just this.

        Genetic material can be exchanged between without any reproductive connection.

        Retroviruses can lift genetic material from one organism and insert it into the *germ* *line* DNA of another organism.

        This genetic material is then replicated by the second organism in its descendants.

        Two species can share genetic material which they did not inherit from a common ancestor.
    • by phliar (87116)
      Indeed. In fact some (e.g. Lynn Margulis) believe that this is the primary way species evolve, not through mutation. See her book Aquiring Genomes [amazon.com] .
    • Re: (Score:2, Informative)

      by Anonymous Coward
      Tree != Directed, acyclic graph.

      In a tree, each node has exactly one parent. Even if links are bidirectional, non-trivial cycles cannot exist. In a DAG, nodes can have multiple parents; making links bidirectional could create cycles. Every (unidirectional) tree is a DAG, but not every DAG is a tree.

      The "tree of life" IS a directed acyclic graph - even when considering retroviruses, since "higher" organisims have more than one parent. Retroviruses allow gene transfer between individuals of different spec
    • by Antibozo (410516)

      Ie it is not a "directed, acyclic graph".

      Unfortunately it has 'cycles'.

      Blame retroviruses; they can take genetic material from one species and insert it into the genome of another thereby creating cross-branches.

      A tree is not the same thing as a directed acyclic graph (DAG). What you describe, with cross branches, is a directed acyclic graph—cross branches do not necessarily create cycles in a DAG. A tree is a directed acyclic graph with a unique root node from which there is a unique path to every other node. There are many kinds of directed acyclic graphs that do not have this property.

    • Your comments are reasonable, but I think a bit misleading in this context.

      At the scale of this research, life really is a tree. I doubt there are retroviruses which are able to transfer genetic material between (e.g.) plants and animals. Even if there is a low level of horizontal gene transfer, this is just a small perturbation on the tree model: just because there is a canal between two rivers, we don't claim that they are really one river, or that the canal is where the two rivers join.

      At least for eukar
  • Archaea (Score:5, Informative)

    by virology-not for com (841426) on Tuesday January 22, 2008 @05:57PM (#22144774)
    Let's not forget that many scientists think there are three domains (Prokaryotes, Eukaryotes and Archaea). Archaea are very similar to Prokaryotes in that they don't have a nucleus, but they also share many features with Eukaryotes, including several key enzymes. Due to their similarity to the two other lineages, it is thought that Archaea may in fact be the grand daddy of all life. http://en.wikipedia.org/wiki/Archaea [wikipedia.org]
    • That was my big complaint about the summary; glad to see there are other folks here keeping the faith. ;)
    • Re:Archaea (Score:4, Informative)

      by reverseengineer (580922) on Tuesday January 22, 2008 @07:09PM (#22146016)
      The level of organization being discussed in the paper treats a subdivision of the eukaryotes into "superkingdoms." (There's actually not a completely agreed upon term for this level.) This would put these groups a level below the three domains (Eucarya, Eubacteria, Archaebacteria) proposed by Carl Woese. There's a high-level differentiation between the superkingdoms involved based on organization of flagella, with a high-level split between unikonts (one flagellum) and bikonts (two, naturally). This is of course based on evolutionary ancestry- humans are unikonts, but don't have many cells with flagella.

      The unikonts contain the amoebae lineages in one grouping, and the animal and fungi together in another. The bikonts contain the plants and algaes in one grouping, and also a handful of other groupings which take care of the rest of the eukaryotes, most of which are unicellular organisms of various sort. It is the "various sort" that's being ironed out with this paper- the authors argue that on the basis of a common genetic heritage, a couple of the leftover groupings can be consolidated.

      Ironically, this move would actually reunite groupings that were fairly recently separated by the argument that no firm evidence of relation existed. Back when the "five Kingdoms" (Animalia, Plantae, Fungi, Monera, Protista) were considered the top level of organization, Protista existed as a sort of "junk drawer" for simple organisms which did not clearly fit in the other categories. Now it looks as though some of these organisms really are related.

      • Why do biological names look like an explosion in an alphabet soup factory? At first, I thought this was because the classicist biologists had all learned Latin, but I think this vandalism, this hacking a branch off the tree of life reveals the true answer. The vandals ARE setting off explosions in an alphabet soup factory and writing down the words that form.
  • Proof? (Score:5, Insightful)

    by Amorymeltzer (1213818) on Tuesday January 22, 2008 @05:57PM (#22144782)
    Anyone who says "Evolution is taken as faith" or doesn't understand that the theory is based on the evidence, and that new evidence means changing the theory can look at this and shut up. A rather fundamental point was proposed to be rather fundamentally different based on new research and that's just fine. Whether it pans out or not, this is a beautiful example of the glory of science.
    • Yes, being able to correct mistakes is the glory of science. But being right the first time is the glory of religion.

      When religion doesn't get it right, people abandon it completely. When science doesn't get it right, they say, "well, that's just part of the process..."

      Each particular method has its strengths and weaknesses:

      • Religion reveals the truth of divine revelation. Which means that it is true by axiom, not proof. If the "revealed truth" isn't actually true, then it isn't of divine origin
      • by NIckGorton (974753) on Tuesday January 22, 2008 @06:26PM (#22145344)

        When religion doesn't get it right, people abandon it completely.
        No they don't. They just reinterpret the primary tenets of the religion to suit their current desired conclusions. Religious works and religious beliefs are interpreted in the light of the present society and its prejudices. Rather than being taken at face value, they are used to justify what people want to believe. For example, there is no real prohibition against abortion in the Christian Bible. For another example, the selective interpretation of Leviticus as condemnation of homosexuality while ignoring the condemnation of poly-cotton blends and Red Lobster.

        Well, unless you are someone who strictly interprets the OT: http://www.godhatesshrimp.com/ [godhatesshrimp.com]
        • Re: (Score:3, Insightful)

          by zulater (635326)
          But many denominations do try to interpret in context and in light of the culture they were written in. Not to mention that the old law (old covenant/testament) was fulfilled after Christ's death and resurrection. That started the new covenant/testament which has no real limitations on what you eat. This isn't to say that there aren't valid teaching in the old testament but that the rules and regulations for ceremonial cleanliness don't apply anymore since there is no longer a need for sacrificing to cle
        • by yali (209015) on Tuesday January 22, 2008 @07:20PM (#22146184)

          When religion doesn't get it right, people abandon it completely.
          No they don't. They just reinterpret the primary tenets of the religion to suit their current desired conclusions.

          A good demonstration of this is in the classic study When Prophecy Fails [wikipedia.org]. A group of social psychologists studied a doomsday cult whose leader had predicted the end of the world. When the predicted date passed and the world didn't end, people did not leave the cult. Instead, they found reasons to explain it away (God was so impressed with their devotion that he put off the apocalypse on their behalf). The end result was that their beliefs were strengthened, not weakened, by disconfirmatory evidence.

          (As a sidenote, the study was an important early test of Leon Festinger's theory of cognitive dissonance [skepdic.com]; Festinger had predicted the cult's response based on his theory.)

        • by gillbates (106458)

          As one who has had to endure the suffering of a polyester-cotton blend, I, for one, think Moses got that one right the first time. We'd all be much better off without polyester (well, except maybe baseball players, with apologies to George Costanza...)

          But in all seriousness, there are some very good theological reasons why the civil parts of Mosaic law were discarded while the moral parts remained in force. It has to do with the coming of what had been promised by Moses, the fulfillment of prophecy, a

        • by JeanPaulBob (585149) on Tuesday January 22, 2008 @07:33PM (#22146380)

          For example, there is no real prohibition against abortion in the Christian Bible.
          There is also no real prohibition against shooting people in the Christian Bible.

          For another example, the selective interpretation of Leviticus as condemnation of homosexuality while ignoring the condemnation of poly-cotton blends and Red Lobster.
          Far be it from me to interrupt your game of "Bash the Fundies", but...

          The "condemnations" of homosexuality [bible.org] on the one hand and shrimp [bible.org] on the other are not the same, using entirely different words. (Just because the 400 year-old language in the KJV uses the word "abomination" in both passages, doesn't mean the Hebrew is the same.)

          That raises the question, why do you make the peculiar assumption that every command in the OT law is of the same type, for the same kind of reason? Do you allow no distinction between ceremonial rules, and rules involving inherent moral/ethical concerns? Do you think that ancient Hebrews viewed dietary laws (prohibition of shrimp) and the command about mixed fabric as moral issues, in the same sense as murder, adultery, theft, and injustice? If so, why? If not, why base your arguments on absurd equivocation?
          • The "condemnations" of homosexuality on the one hand and shrimp on the other are not the same, using entirely different words. (Just because the 400 year-old language in the KJV uses the word "abomination" in both passages, doesn't mean the Hebrew is the same.)

            What a great example of what the GP was talking about. You have to read those VERY creatively for there to be any difference.

            • Re: (Score:3, Interesting)

              by JeanPaulBob (585149)

              What a great example of what the GP was talking about. You have to read those VERY creatively for there to be any difference.

              What are you talking about? Homosexuality is said to be "tow`ebah". Elsewhere, in a list of dietary laws, certain foods (like shrimp) are said to be "sheqets".

              So, on what basis are you deciding that we have to read them "creatively" for them to be different? What do the two words mean? What's their usage?

              The distinction could be effectively meaningless (if the words are equi

          • Do you allow no distinction between ceremonial rules, and rules involving inherent moral/ethical concerns?

            Oh, you mean like slavery? Lev. 25:44 says its quite hunky-dory as long as they are from neighboring states. Like say for those of us in the USA... Canada.

            Do you think that ancient Hebrews viewed dietary laws (prohibition of shrimp) and the command about mixed fabric as moral issues, in the same sense as murder, adultery, theft, and injustice?

            Quite likely they viewed them differently. But then I also think the issue of the morality of slavery is in the category of injustice rather than fashion and food sense.

            If so, why? If not, why base your arguments on absurd equivocation?

            Its only absurd equivocation if you are unfamiliar with the OT. I'm not, but apparently you are. Why not go have a read and they we can talk a bit more, k?

            Of course you could make th

          • by MorePower (581188) on Tuesday January 22, 2008 @09:33PM (#22147774)
            That raises the question, why do you make the peculiar assumption that every command in the OT law is of the same type, for the same kind of reason?

            Because the basic evangelical argument is that "morality" is based solely on "whatever God said, and humans dare not even try to ask why". If you allow for humans to have some capacity for independent moral awareness, then you would have what us heathen non-believers have been calling for all along, using our own sensibilities to decide what is and isn't acceptable.

            I mean, how else do you condemn homosexuality or pre-marital sex? It's two consenting adults enjoying each other's bodies in mutually pleasing ways without harming others. But the evangelical crowd says "God said 'No', end of discussion."

        • by Kjella (173770)
          Those that can, anyway. Christians have shown a remarkable flexibility in interpreting the Bible, mostly because it's second hand stories and a collection of various books that there's not even an universal agreement on. Plus that most of the Bible is stories and allegories that have some sort of moral in them, but still leaves quite a bit to interpretation. So as long as we just capture the main values, most people are willing to call it Christianity.

          The Quran on the other hand exists in one definitive ver
      • by mike2R (721965)

        Religion reveals the truth of divine revelation. Which means that it is true by axiom, not proof. If the "revealed truth" isn't actually true, then it isn't of divine origin. Which does much to explain why religious institutions are very conservative when it comes to accepting new ideas.

        I'm absolutely fine with that. As far as I'm concerned the big fat red line comes when religious "evidence" is fed back into the scientific process.

        As long as this line isn't crossed religion is just religion, and can be

      • by Angostura (703910)

        When religion doesn't get it right, people abandon it completely.


        So to be clear, are you saying that if any aspect of the Bible were shown to be erroneous, there would be no more Christians a week later?
      • by Belial6 (794905)
        I would describe it differently. It is more an issue of claimed completeness of knowledge vs. margin of error in the information we do have.

        Religion: Claimed Completeness = 70%, Margin of error = 100%

        Mathematics: Claimed Completeness = 70%, margin of error = 20%

        Science: Claimed Completeness = 5%, margin of error 50%

      • by ppanon (16583)
        When religion doesn't get it right, people abandon it completely.
        Sometimes. And sometimes those who try to abandon the religion are called heretics, leading to persecutions and wars that last decades or centuries and cost thousands or millions of lives.

        With science, when somebody's wrong, they might lose their grant and need to investigate something else.

        There's lots to learn from religions about how to be happy and live with others as a productive part of society, to everyone's mutual benefit. But the wor
      • by nagora (177841)
        When religion doesn't get it right, people abandon it completely

        Eh? On what planet? By that argument there would be no religion left.

        Religion reveals the truth of divine revelation.

        No it doesn't. It reveals the ideas of a small group of philosophers and their students.

        Those who take religion as if it were a scientifically-verifiable fact are just as confused as those who think scientific theorems are as reliable and trustworthy as the Gospel or mathematical proofs.

        While I agree with this, I would sa

      • by jgoemat (565882)

        Religion reveals the truth of divine revelation. Which means that it is true by axiom, not proof. If the "revealed truth" isn't actually true, then it isn't of divine origin. Which does much to explain why religious institutions are very conservative when it comes to accepting new ideas.

        You cannot be talking about organized religion then. The only religious people then would be ones that have had divine revelations and the only religion would be based on those personal revelations. I haven't seen any b

      • When religion doesn't get it right, people abandon it completely
        If only that were true!
      • One way to classify Science, mathmatics and religion is by how "truth" can be changed. Mathmatical truth is proved ad once proved (corectly) can never change. In science "truth" is alway subject to change as new data is collected and interpeted. With religion, I can simply decide to become Buddhist tomorrow then get bored and join some New Age group. So with religion "Truth" whatever you currently choose to believe.

        But I do agree 100% that each of Science, mathematics and religion address a different no
      • Re: (Score:3, Insightful)

        But being right the first time is the glory of religion.

        No, pretending to be right the first time and then backpedaling for thousands of years as the divine revelations are increasingly demonstrated to be absurd is the glory of religion.

        Religion reveals the truth of divine revelation. Which means that it is true by axiom, not proof. If the "revealed truth" isn't actually true, then it isn't of divine origin.

        I can agree with the axiom part, but are all the mutually-conflicting divine revelations of the mil

    • Re: (Score:3, Informative)

      by LWATCDR (28044)
      No but Evolution is still mostly theory but it is the best current theory. At least some evolution has been seen in the "wild". Drug resistant bacteria is a good example of evolution in action.

      • Re:Proof? (Score:5, Insightful)

        by MightyMartian (840721) on Tuesday January 22, 2008 @06:21PM (#22145248) Journal
        Define "seen"? Because by your argument, electrons may or may not exist, Proto-Indo-European may or may not have existed and you may or may not have had great-great-grand-parents.

        Evolution is confirmed not just by observing what goes on now, but by observing the fossil record, and just as importantly nowadays, by gathering molecular data. These two lines of evidence fit very well together into the so-called twin-nest hierarchy.

        If you wish to wander down the road of epistemological nihilism, that's your affair, but be aware that everything, and I mean everything you think you know you can't actually know at all. Either you admit that inference is a legitimate means of gathering factual knowledge, or you render the whole show, including what you see, hear, touch, feel and taste irrelevant.
        • Re: (Score:3, Insightful)

          by LWATCDR (28044)
          "electrons may or may not exist", not exactly. A particle wave duality that carries a negative does exist. Some of the theory about what a electron really is still in the realm of theory.

          Evolution is still a theory and as I said it is the theory that fits with all the current data the best. But the theory of Evolution is still just a theory. A lot of questions are still unanswered about how Evolution works. Being scientific means having an open mind about scientific theories. You should keep your mind open
          • You seem on one hand to be pretty deeply confused about the nature of evidence in science, and seem to playing pretty fast and loose with the definition of the word "theory" on the other. Basically you're committing an etymological fallacy, and at the same time trying to create an artificial barrier by which a quantum mechanical explanation of the electron can pass muster, but the twin-nested hierarchy of common descent is somehow a lesser quality of observational science.

            You cannot see an electron directl
          • by ianare (1132971)
            Actually a scientist will say that a scientific theory and fact are not mutualy exclusive. A theory is, simply put, a testable model that makes predictions. That model can be a fact or not, depending on the evidence. It does not have the ordinary usage meaning of 'something which I'm not sure of'.

            Now this does not mean a better theory won't ever be 'found', like when Einstein and his general theory of relativity showed Newton was (partly) wrong with his theory of universal gravitation.

            But for now, the t
  • There are only two life forms, -- eukaryotes, which gather their genetic material in a nucleus, and prokaryotes, such as bacteria

    Two? For several decades, I thought most biologists considered life as being divided into three main branches ("domains"): eukaryotes, prokaryotes, and archaea.

    • Re: (Score:3, Informative)

      by wizardforce (1005805)
      it depends on what you're going after in regard to categorization. three domainss: eucaryotes are cells with nuclei where as procaryotes are cells without nuclei with the third group being archea because of the large genetic and structural differences in comparison with bacteria [eubacteria]. although you could also classify them into archea+eubacteria [from the now defunct monera (5 kingdom classification)], protista, animalia, plantae, fungi under the 6 kingdom classification
    • by Jesus_666 (702802)
      Actually, that can't be true for a simple reason: The three-domain system was introduced in 1990...
  • by verbalcontract (909922) on Tuesday January 22, 2008 @06:01PM (#22144850)

    When I was in 9th grade (I guess about 10 years ago!), there were five "kingdoms": bacteria, protista, fungi, plantae, and animalia. Three years later, there were six: archaea, monera, protista, fungi, plantae, and animalia.

    Now there are branches? And four of them? On a tree? That's news to me. But it's all a matter of naming and grouping, so I guess you say potato, I say tomato.

    • Re: (Score:2, Funny)

      by Tailsfan (1200615)
      THis will really screw up my AP Bio.
    • by IdahoEv (195056) on Tuesday January 22, 2008 @06:42PM (#22145608) Homepage

      When I was in 9th grade (I guess about 10 years ago!), there were five "kingdoms": bacteria, protista, fungi, plantae, and animalia.


      What's happened is that better information has rapidly come to the fore as genetic analysis have been done during the last 15 years. The tree has been revised several times.

      The five kingdom model was already known to be wrong 10 years ago, but that information hadn't propagated to gradeschool and highschool textbooks yet. If you'd studied biology in college, your information would be more up to date.

      These days there are three superkingdoms: Bacteria, Archaea, and Eukarya. (Bacteria and Archaea were formerly grouped together as "monera" or "bacteria" before it was realized that genetically they are as distinct from each other as they are from Eukarya.) Eukarya is broken into a number of kingdoms, and that number has just changed from 5 to 4. Even the 5 they were last year weren't exactly same ones that you learned in school.
  • Ummm.... (Score:4, Insightful)

    by Otter (3800) on Tuesday January 22, 2008 @06:05PM (#22144944) Journal
    The Tree of Life must be re-drawn, textbooks need to be changed, and the discovery may also have significant impact on the development of medicines.

    This is a bit over the top. It's not like there's a single canonical "Tree of Life" that's going to have to be changed across the board; there's endless (mostly self-promoting) squabbling over what should be considered fundamental branches, to which this is yet another entry.

    Frankly, if this were as important as they make out, it would be in Nature, not the if-it's-not-objectively-wrong-it's-in PLoS ONE.

    "...the largest ever genetic comparison of higher life forms on the planet"? Maybe, I guess it depends what dimension you measure "largest" on.

    • by ArsonSmith (13997)
      The Tree of Life must be re-drawn, textbooks need to be changed, and the discovery may also have significant impact on the development of medicines.

      This message brought to you by Learning Resources Publications(r) and the United Drug Association(tm).
    • I would also have thought that the question of whether you draw the phylogenetic tree according to genetic relationships or functional relationships is still open.

      I mean, if organism X shares 92% of its DNA with Y and only 88% with Z, but lives and functions in its ecological niche more like Z than Y, how do you classify them all? Is X closer to Y or Z? I didn't think this question had been settled (assuming it ever can be) among the evolutionary biologists.
      • by Otter (3800)
        I would also have thought that the question of whether you draw the phylogenetic tree according to genetic relationships or functional relationships is still open.

        I think that's been almost entirely settled in favor of the former; DNA sequencing pretty much shut the door on any remaining advocates of polyphyletics.

  • Saying that the "Tree of Life" was first used by Darwin to describe evolutionary relationships should be taken with a grain of salt. The use of a "tree" to describe decendants and family relationships dates back to (at the very least) pre-Roman times. Paintings depicting lineage were long adorned with leaves and fruit. There is a reason that the Bible used a "tree" to signify life -- because the symbolism of a trunk, limbs, shoots and offshoots was well established by mankind long before the Bible was ev
  • by fahrbot-bot (874524) on Tuesday January 22, 2008 @06:13PM (#22145110)
    ...stays the same:
    • Born, Live, Read /., Die
    Non-geeks, substitute "Read /." with "Move Out" and "Have Sex".
  • <sarcasm>This is further proof that the Bible is the Word of God and vindicates Intelligent Design!</sarcasm>
  • No! (Score:4, Funny)

    by waveformwafflehouse (1221950) on Tuesday January 22, 2008 @06:48PM (#22145702) Homepage
    4 supergroups? [apollon.uio.no] Wait, did Journey break up? Who stopped believing!
  • What a worthless article that is.

    2,000 words, and they never listed the "Before" list. And in the text following the "After" list, they implied that there's still a group of organisms not in the list, meaning all these guys really did was move some entries between two branches.

    Worthless. Come back when (a) it's done and (b) it's written-up clearly enough that the facts can be listed in two sentences.
  • What now? (Score:2, Interesting)

    by glwtta (532858)
    Both the summary and the article made no sense whatsoever (and I am not bored enough to read the paper), can someone clarify this for me?

    The "branches" on the "tree" of life are pretty much arbitrary, you could draw a single node called "Life" or you could draw every single individual organism that ever existed - both would be valid.

    Are they saying that they combined two groups on some taxonomic level because they are more closely related than previously thought?

    I don't know what exactly they mean
  • The Tree of Life tells the story of life on Earth, and our research can say something about how quickly life developed. Our discovery suggests that there were fewer big "events" than we have previously assumed in the development of higher life forms.

    I really hate it when your average scientist tries to think. What we can determine (from what we know so far) of the history of life on earth is that there is a fairly large term representing a "winner take all" effect that determines how this tree is ultimately pruned. The insight this scientist was trying to express is that there are relatively few "split pots" on earth's evolutionary tree.

    I've long suspected that a few twinges of our human predilection for genocide stems from a deeply rooted evolution

  • Ultimately, this is all moot. In 2029, the Tree of Life will get what's coming to it, as administered by a giant hexapedal cloaking tank with miniguns for arms.

Arithmetic is being able to count up to twenty without taking off your shoes. -- Mickey Mouse

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