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The Tree of Life Consolidates
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."
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."
Knowledge is how to play a game, intelligence is how to win, wisdom is knowing what game to play.
I should be more careful with that chainsaw. Poor tree, only 5 branches , I hope it survives...
mcgrew's razor: Never attribute to stupidity that which can be explained by greedy self-interest
What else will science rob from us before we decide enough is enough?
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)
In the free world the media isn't government run; the government is media run.
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
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.
I live in constant fear of the Coming of the Red Spiders.
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.
In the pursuit of knowledge, every day something is added.
In the pursuit of understanding, every day something is removed.
In Xanadu did Kubla Khan
A stately pleasure dome decree
So Charles Darwin, born in the 1809, predates the Kabbalah? That's cosmology, not biology.
You can't take the sky from me...
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.
What I'm listening to now on Pandora...
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:
The key, I think, is not to confuse the various levels of truth. 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. There is a large difference between the three, and understanding the subtle limitations of each is just as important as understanding the ideas they espouse.
The society for a thought-free internet welcomes you.
- Born, Live, Read
/., Die
Non-geeks, substitute "ReadIt must have been something you assimilated. . . .
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 an organism has x+2 mutations in a histone protein/gene it gets slotted into one kingdom or another?
:P
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, although its taking a long time to load for me, and it's not even slashdotted yet.
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.
The world's burning. Moped Jesus spotted on I50. Details at 11.
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
Sigs are too short to say anything truly profound so read the above post instead.
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.
I stole this sig from someone cleverer than me.
4 supergroups? Wait, did Journey break up? Who stopped believing!
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 refined our approximation, and it appears two of those groups are more closely related that the rest.
So, certain single-celled organisms are understood to be more closely related to certain other single celled organisms than previously thought. Compared to any of the organisms involved, you're still more closely related to certain other single celled organisms, as well as all animals and fungi. If that shakes your world view, you need to get out more.
For the most part, these viral sequences are in neutral or junk genome stretches, so they don't have any influence on the organism.
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.
Table-ized A.I.
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.)
Birds are not dinosaur descendants;birds are dinosaurs, for all useful meanings of "birds", "are" and "dinosaurs"