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."

Science is a moving target

[davidwr]

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."

Proof?

[Amorymeltzer]

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.

Ummm....

[Otter]

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.

Three levels of truth (maybe more...)

[gillbates]

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. Which does much to explain why religious institutions are very conservative when it comes to accepting new ideas.
• Mathematics is provably correct. That is, apart from an error in the proof, what is true today will always be true.
• Science is experimentally correct. That is, the hypotheses called true today may be shown false tomorrow with the discovery of additional data.

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.

Re:Not really a tree...

[MightyMartian]

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:Proof?

[MightyMartian]

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:So, what you are saying is.....

[MightyMartian]

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.

Re:Three levels of truth (maybe more...)

[NIckGorton]

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:Proof?

[LWATCDR]

"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 but not so open that your brain falls out.

Anyone that says that the current theory of evolution is fact isn't being scientific.

Re:Three levels of truth (maybe more...)

[zulater]

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 cleanse sin. Abortion is murder in the eyes of the church because in most cases the church believes that life begins as conception or when the zygote attaches to the uterus. Many passages speak of God forming the child in the womb (Job 31:15, Psalm 139:15, Isaiah 44:2, Isaiah 49:5 etc). I agree that many do take the scriptures out of context and try to twist them into what they want to hear not what is actually meant. This is the folly of man trying to interpret scripture outside of other scripture.

Re:Proof?

[Tsiangkun]

The aquisition or modification of gene function over time is fact.
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-centromeres are stability propagated over time is a fact.

Evolution is not limited to changes in DNA, it is also caused via chromosomal rearragements that change the environment where the gene is expressed.

It is a fact that retrovirus change gene expression and function. We use them as mutagens all the time in screens for new mutations.

Evolution of mitochondrial sequences is one of the best known ways for mapping the history of the human race.

Science is a process

[2short]

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. :)

Re:Three levels of truth (maybe more...)

[MorePower]

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."

Re:Three levels of truth (maybe more...)

[Citizen of Earth]

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 millions of religions around the world all actually true, or only the ones of your personal religion?

Re:Proof?

[Fastolfe]

The things that you observe are facts. One can clearly see that life evolves over time. For long-term study, we have the fossil record. For short-term study, we have bacteria, fruit flies and other organisms that have short life-spans. We can directly observe evolution. This aspect is fact.

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 many even throw in abiogenesis, which makes things worse). Evolution is, in fact, both fact and theory. If one succeeds in completely destroying the theory of evolution, it does nothing to disprove the facts that led us to that theory. Life still evolves over time.

http://en.wikipedia.org/wiki/Evolution_as_theory_and_fact [wikipedia.org]