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The Tree of Life Consolidates
Posted by
kdawson
on Tue Jan 22, 2008 04:46 PM
from the pruning-it dept.
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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Science is a moving target (Score:5, Insightful)
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."
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Oh wait...
Science is a process (Score:3, Insightful)
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
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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.
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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
Re:Just hoopla over definitions (Score:5, Informative)
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.
Parent
Re: (Score:3, Informative)
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.
Re:Pretty good guess (Score:5, Interesting)
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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Oops, my bad (Score:5, Funny)
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First we lose pluto and now we lose this. (Score:5, Funny)
At the risk of being called a Tao-rrorist... (Score:5, Interesting)
In the pursuit of understanding, every day something is removed.
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Not really a tree... (Score:5, Interesting)
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)
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Someone helpfully linked the paper [plosone.org] (and was modded down for his trouble); they address that concern extensively.
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So, what you are saying is..... (Score:2)
That sounds a little....incestuous....no?
Re:So, what you are saying is..... (Score:5, Insightful)
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.
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Archaea (Score:5, Informative)
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Re:Archaea (Score:4, Informative)
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.
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Proof? (Score:5, Insightful)
Three levels of truth (maybe more...) (Score:3, Insightful)
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:
Re:Three levels of truth (maybe more...) (Score:5, Insightful)
Well, unless you are someone who strictly interprets the OT: http://www.godhatesshrimp.com/ [godhatesshrimp.com]
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Re:Three levels of truth (maybe more...) (Score:4, Informative)
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.)
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Re:Three levels of truth (maybe more...) (Score:5, Interesting)
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?
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Re:Three levels of truth (maybe more...) (Score:5, Insightful)
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."
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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
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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.
I can agree with the axiom part, but are all the mutually-conflicting divine revelations of the mil
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Re:Proof? (Score:5, Insightful)
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.
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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
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The accumulation of DNA modifications over time is a fact.
The aquisition of gene function due to alteration of DNA sequence is a fact.
The modification of gene function due to alteration of DNA sequence is a fact.
The modification of gene function due to transposable element insertions, and remobilizations, is a fact.
The alteration of gene function due to chromosomal rearrangements is a fact.
The generation of neo-centromeres is a fact.
That neo-
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The theory is how evolution occurs. What causes life to evolve over time? The theories that we have are simple, direct, and have no counter-evidence.
Both sides of this "debate" commonly confuse the two issues (and
two? (Score:2)
Two? For several decades, I thought most biologists considered life as being divided into three main branches ("domains"): eukaryotes, prokaryotes, and archaea.
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Taxonomy especially is inexact. (Score:4, Interesting)
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.
Rather, you haven't been keeping up. (Score:5, Informative)
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.
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Ummm.... (Score:4, Insightful)
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.
Correction: "Tree of Life" is an old expression (Score:2)
But the circle of life... (Score:5, Funny)
- Born, Live, Read
/., Die
Non-geeks, substitute "ReadNo! (Score:4, Funny)
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So Charles Darwin, born in the 1809, predates the Kabbalah? [wikipedia.org]
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