The Tree of Life Consolidates 266
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."
Archaea (Score:5, Informative)
Re:First used by Darwin? (Score:3, Informative)
So Charles Darwin, born in the 1809, predates the Kabbalah? [wikipedia.org]
Re:Not really a tree... (Score:3, Informative)
Someone helpfully linked the paper [plosone.org] (and was modded down for his trouble); they address that concern extensively.
Re:Proof? (Score:3, Informative)
Just hoopla over definitions (Score:2, Informative)
Hey the journal finally loaded, here is a link to the actual paper: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000790 [plosone.org], although its taking a long time to load for me, and it's not even slashdotted yet.
Re:two? (Score:3, Informative)
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.
Re:Archaea (Score:1, Informative)
Although you can slice and dice as Eukaryotes/Prokaryotes, it's commonly accepted that Archaea are as different genetically from Eubacteria as Eubacteria are to Eukaryotes. In fact, it is usually said that Archaea are more closely related to Eukaryotes than they are to Eubacteria, so grouping Eubacteria and Archaea together as "Prokaryotes" because they lack a nucleus makes as much sense as grouping bats and birds together because they can fly.
Re:Not really a tree... (Score:2, Informative)
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 species, thus allowing organisms to have more than two parents. A cycle would mean that some individual received genetic material from one of its descendents. If you define an individual as a set of genes that is available to pass on to descendents, then a cycle, by definition, cannot exist.
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.
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.)
Re:Just hoopla over definitions (Score:3, Informative)
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 reviewed of course) to show that they believe in the Open Access concept and let everyone with a digital connection have access to it.
Re:Just hoopla over definitions (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]
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:So, what you are saying is..... (Score:2, Informative)
I saw an interesting article on speculation that placental mammals may have "learned" how to share fluids between fetus and mother by borrowing immune-suppression genes from a virus that used such tricks to escape the immune system.
Unlike what the poster is saying, these don't make producing the tree more difficult
Only in newer and complex species does a fairly clear tree path appear. However, for simpler organisms and perhaps further back in time, cross-gene transfer seems to be more common such that tree-ness may get really murky. Bacteria, for example, create plasmids whose sole purpose appears to be to share genes with other strains.
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.