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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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  • Not really a tree... (Score:5, Interesting)

    by myowntrueself (607117) on Tuesday January 22, 2008 @04:57PM (#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)
  • by verbalcontract (909922) on Tuesday January 22, 2008 @05:01PM (#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.

  • by KublaiKhan (522918) on Tuesday January 22, 2008 @05:02PM (#22144878) Homepage Journal
    In the pursuit of knowledge, every day something is added.
    In the pursuit of understanding, every day something is removed.
  • by Anonymous Coward on Tuesday January 22, 2008 @05:31PM (#22145414)
    Taxonomy is an extremely confused science. Our marine biology teacher used to amuse himself by showing us different new 'trees'. I got the distinct feeling that taxonomists has their own Religious Wars.

    Oh, they used to sort by similarity but genetics changed that. Now they are sorting by heritage, which is saner, but the "official" tree is pretty fucked up. It being an unholy mix.

    I missed that class.
  • by Angostura (703910) on Tuesday January 22, 2008 @05:43PM (#22145622)
    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.
  • What now? (Score:2, Interesting)

    by glwtta (532858) on Tuesday January 22, 2008 @06:26PM (#22146272) Homepage
    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 by "the five groups...", but I'm pretty sure their little unreadable graphic (which, by the way, wtf?) doesn't cover all of Eukarya - is this groundbreaking research transforming one mostly unknown pet classification into another?

    Then there's this: "Previously, these species were thought to be completely unrelated."

    Unless I slept through something fairly major, all currently living organisms on Earth are still considered to have arisen from a common origin (or created by the gods in a flash of omnipotence, etc, etc.), so all species are related.

    And of course it explains that to arrive at these conclusion they have "studied" the genes - I'm sure anything more specific would make our poor little heads hurt.

    Can someone summarize what they actually did?
  • by JeanPaulBob (585149) on Tuesday January 22, 2008 @06:33PM (#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?
  • by JeanPaulBob (585149) on Tuesday January 22, 2008 @11:19PM (#22149234)

    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 equivalent & interchangeable), or it could make a world of difference (for instance, if the latter is used primarily or exclusively in contexts of ceremonial "uncleanness").

    The problem is, everyone jumping on the Bash the Fundie wagon--yourself included, apparently--doesn't care about discerning what the Hebrew Scriptures--the Torah, the Mosaic Law--actually mean. You have your easy excuses for dismissing, demonizing, or denigrating Christians. You don't have to know whether your criticisms have actual merit before leveling them; you don't have to know if your simplistic, at-first-glance readings will bear up to the facts. Since you're a "skeptic", the facts are obviously going to be on your side--you don't have to actually check them.
  • Re:Pretty good guess (Score:5, Interesting)

    by RockDoctor (15477) on Wednesday January 23, 2008 @03:28AM (#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.)

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