Fossil protein breakthrough will probe evolution

NewScientist.com news service ^ | 19:00 13 November 02 | Fred Pearce

[dead]

The first complete sequencing of protein from a fossil bone suggests that proteins can survive for millions of years - long enough to probe the evolution of many extinct species, including the ancestors of modern humans.

For many years, biologists have deduced evolutionary relationships from the visible features of living animals and fossils. Molecular biology has given them a new tool for living animals - comparing DNA sequences. However, DNA survives for only a short time after death, so paleontologists have been limited to comparing the shapes and sizes of the bones of extinct species.

But analyzing ancient proteins now gives them a new option, says Christina Nielsen-Marsh of the University of Newcastle, because their amino acid sequences reflect genetic codes.

The big advantage of proteins is their stability in suitable environments. Pieces of DNA large enough to sequence using sensitive amplification techniques can survive for 100,000 years in permafrost. But osteocalcin, a structural protein that bonds directly to the minerals of bone, lasts much longer.

Matthew Collins, also at Newcastle University, estimates that osteocalcin can survive for more than 100 million years at 0 °C, and for some 10 million years at 10 °C. That would be long enough to look back some six or seven million years to the last common ancestor of humans and chimpanzees.

Exact match

To show the potential of their technique, Nielsen-Marsh and colleagues sequenced the amino acids in osteocalcin extracted from bones of the extinct steppe bison (Bison priscus) found in permafrost in Siberia and Alaska. Both bones are a minimum of 55,000 years old, the limit of carbon dating.

The complete sequences of amino acids exactly matched that of the modern bison (Bison bison). They differ by a single amino acid from modern cattle, which are thought to have diverged from bison at least a million years ago. Previous work has detected - but not isolated or sequenced - proteins in 120 million year old dinosaur bone.

Although osteocalcin sequences diverge slowly, they can probe evolution over millions of years. "Human evolution, is the most exciting of the possibilities," says Peter Hauschka of the Harvard Medical School, US, who worked with Nielsen-Marsh. Osteocalcins differ by a few amino acids in humans, chimps and orangutans, he says, so they could help identify the nearest living relatives of suitable fossils.

Hominid fossils are few and far between, and it could be hard to persuade anthropologists to give them up for the destructive analysis. Yet teeth also contain osteocalcin, and they are much more common fossils.

Osteocalcin itself may not be able to determine the puzzling lineages of australopithecines and humans over the past two million years, but the method could be applied to other proteins that might give a clearer picture.

Journal reference: Geology (vol 30, p 1099)

[asformeandformyhouse]

Using your criterion, there would be no science textbooks left.

No, using my criterion science textbooks would include science and not religion.

[AndrewC]

I'm sorry. I must have misinterpreted some of your more cryptic posts...

Okay, but if you recall, it was your theory on the viewpoint of ID. I responded with ---"You don't know what you are talking about, do you?" or some such thing. In any case, I find the article's main hypothesis a big stretch considering a tenfold decrease in stability for a 10 degree change in temperature. But further analysis will determine whether this is another turkey sandwich dino or something useful.

[general_re]

We all post here at the pleasure of the owners and operators of this (private) site. Ted knew the rules and chose to violate them, despite being personally warned by the moderators not to.

[Nebullis]

No, using my criterion science textbooks would include science and not religion.

That's great!

[CalConservative]

It's all over both sides of the evidence. If it works, it's re-used. If it's different, it's because the designer knows something we don't know.

Well, I hardly think evolutionary theory is the model of consistency we should all aspire to.

In the engineering side of my company, we can re-use design components where appropriate and that is certainly most efficient where it is applicable. There are other situations where we have to start nearly from scratch, because the solution demands a different design from the ones that we already have stored in our AutoCAD templates file.

It's design to fit the specified operating parameters. We do it all the time.

[CalConservative]

So why is the cow protein different then?

Uh, because a cow is different from a bison? My understanding from the article posted that it wasn't different by very much.

[asformeandformyhouse]

That would include the religion of Evolution.

[<1/1,000,000th%]

It's design to fit the specified operating parameters. We do it all the time.

At random, with no rhyme or reason. Just as predicted by ID.

[edsheppa]

Uh, because a cow is different from a bison?

In what functional way are cow bones different from bison bones?

[f.Christian]

The molecule reproduced too accurately — there is no possibility of neo-Darwinian evolution by mutation and natural selection.11

[jennyp]

(And, of course, as libertarians get the republican party to do more and more of their bidding -- that is, privatize more and more of our society -- then what happens at "private sites" becomes even more interesting.)

If there is competition, as in the science examples, there's no problem with privatization. If there is inherently little or no chance of privatization, as in gov't services, then the private contractor(s) have to operate under clear gov't guidelines.

I doubt that the GOP is going to be influenced at all by the anarchist wing of the libertarian movement.

[jennyp]

Osteocalcin itself may not be able to determine the puzzling lineages of australopithecines and humans over the past two million years, but the method could be applied to other proteins that might give a clearer picture.

I find it amazing that evos blast christians or IDers for their 'faith' but they readily accept this article as proof of whatever they want it to be without reading the last sentence. IOW, "We are concerned that this discovery will fail to provide any conclusive evidence just as many others have failed, but we'll trumpet the discovery long enough to get in included in textbooks long after it's been discredited."

As I think Nebullis mentioned, this is just one protein of many. Here's what happens when they examine a range of sequences:

MULTI-GENE COMPARISONS

Cytochrome c phylogenies are sometimes imperfect, since they are based on a single gene, and mutations can occasionally reverse previous mutations. In Figure 1, the lamprey [cytochrome c] appears closer to humans than does that of tuna fish, contrary to evolutionary expectations*. Biologists have addressed this problem by looking at more and more genes. Some genes evolve faster than others, some slower. Of course, the fact that some genes change faster or slower than others doesn't disprove evolution.

A recent study (Kumar and Hedges 1998) involved hundreds of genes, for dozens of species. In Figure 3, the 50 genes used to compare old world monkeys to humans have a strong "peak" indicating 23 million years (MYa) since the last common ancestor of these species. The bell-shaped curve centered at 23 MYa is nothing less than a strong biotic "signal." When 107 genes of primates and rabbits are compared, these differences correspond to 90 MYa since the primate/rabbit common ancestor. The "message" is clear: humans are genetically much closer to old world monkeys than they are to rabbits. This accords perfectly with evolutionary expectations: the last common ancestor of primates and rabbits is much farther back in time than the last common ancestor of humans and old world monkeys. Had the genes turned out otherwise, Darwin's "fantasy" would have evaporated.

Figure 3. Comparisons of hundreds of genes. (Data from Kumar & Hedges1998)

- Dave Thomas, NMSR/TCCSA Debate, round 1a

[general_re]

Modern science has become, to a large extent, an "owner and operator" endeavor, where individual researchers work and publish "at the pleasure" of the handful of CEOs who have the resources to make go/no-go decisions on funding.

Yes, yes, I know - the concept of private property is sooooo tiresome to those who wish to enter into houses and rummage through fridges without fear of interference from those who mistakenly think they "own" a thing.

Ted Holden has the right to speak freely, as do you. But having the right to speak is most assuredly not the same as having a right to a particular forum. Ted Holden continues to speak freely despite being denied a platform here - if you wish, I will be more than happy to direct you to some of his other haunts where you may verify for yourself that no vast libertarian conspiracy has bound and gagged him to prevent him from expressing his opinion.

Aside from that, seeing that the only alternative to private ownership is public ownership of fora, scientific and otherwise, I am sure that I speak for many when I say that I await with great interest your proposals for solving this "problem" you have so breathlessly elucidated for us all...

[gore3000]

But further analysis will determine whether this is another turkey sandwich dino or something useful.

Yes, the turkey sandwich story is quite humorous and shows quite well the total absurdity of paleontologists:

THE DINOSAUR AND THE TURKEY SANDWICH

On the second day of the symposium, William Garstka reported that he and a team of molecular biologists from Alabama had extracted DNA from the fossil bones of a 65-million-year-old dinosaur. Although DNA from other studies suggests that DNA older than about a million years cannot yield any useful sequence information, Garstka and his colleagues amplified and sequenced the DNA. compared, it with known DNA from other animals, and found that it was most similar to bird DNA . They concluded that they had found "the first direct genetic evidence to indicate that birds represent the closest living relatives of the dinosaurs". Their conclusion was reported the following week by Constance Holden in Science.

The details of the discovery, however, are revealing. First the dinosaur from which Garstka and his colleagues allegedly recovered the DNA was Triceratops. According to paleontologists there are two main branches in the dinosaur family tree. One branch included the three-horned rhinoceros-like Triceratops which millions of people have seen in museum exhibits and movies. But birds are thought to have evolved from the other branch. So according to evolutionary biologists, Triceratops and modern birds are not closely related, their ancestors having gone thier separate ways almost 250 million years ago.

Even more revealing, however, was that the DNA Garstka and his colleagues found was 100 percent identical to the DNA of living turkeys.. Not 99 percent, not 99.9 percent, but 100 percent. Not even DNA obtained from other birds is 100 percent identical to turkey DNA (the next closest match in their study was 94.5 percent with another species of bird). In other words, the DNA that had supposedly been extracted from the Triceratops bone was not just similar to turkey DNA - it was turkey DNA. Gartska said he and his colleagues considered the possibility that someone had been eating a turkey sandwich nearby, but they were unable to confirm that.
FROM: Jonathan Wells, Icons of Evolution, page 130, 131.

Just comes to show the professionalism and dedication of paleontologists! And remember, your tax dollars paid for this wonderful discovery!

[asformeandformyhouse]

Nice chart. Of course this all assumes that the common ancestor exists. When you start with the result, it's not as hard to find an equation that works. As the article stated:

Biologists have addressed this problem by looking at more and more genes.

Had the single gene shown what the biologists already assumed, they would never have looked at the 50. If it had taken 100, 200 or 3000 genes, then they would have continued until they recieved the desired result.

My point is that there is a science to evolution and there is a religion. The creationists will jump on every failure of evolution as proof of creation and the evos will continue massaging the equation until the results yield the already pre-assumed outcome, which seems to be that there is no 'intelligence' of any kind in the process, and that chance, time and law are enough to yield information-enhancing mutations. Which I personally doubt.

The faith of the evo is just as great as the faith of the creationist. So great in fact, that known hoaxes and errors will continue to be presented loud and far as fact, rather than face the prospect of admitting wrong. The evo acts exactly the same way when confronted with something such as ID as the creationist does when confronted with evolution. These threads are proof of that.

[AndrewC]

Nice Chart

Man

Monkey

Rabbit

Rock