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Baffling 400,000-Year-Old Clue to Human Origins

Scientists have found the oldest DNA evidence yet of humans’ biological history. But instead of neatly clarifying human evolution, the finding is adding new mysteries.

In a paper in the journal Nature, scientists reported Wednesday that they had retrieved ancient human DNA from a fossil dating back about 400,000 years, shattering the previous record of 100,000 years.

The fossil, a thigh bone found in Spain, had previously seemed to many experts to belong to a forerunner of Neanderthals. But its DNA tells a very different story. It most closely resembles DNA from an enigmatic lineage of humans known as Denisovans. Until now, Denisovans were known only from DNA retrieved from 80,000-year-old remains in Siberia, 4,000 miles east of where the new DNA was found.

The mismatch between the anatomical and genetic evidence surprised the scientists, who are now rethinking human evolution over the past few hundred thousand years. It is possible, for example, that there are many extinct human populations that scientists have yet to discover. They might have interbred, swapping DNA. Scientists hope that further studies of extremely ancient human DNA will clarify the mystery.

“Right now, we’ve basically generated a big question mark,” said Matthias Meyer, a geneticist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, and a co-author of the new study.

http://www.nytimes.com/2013/12/05/science/at-400000-years-ol...



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http://www.notjustatheory.com/

http://www.notjustatheory.com/

That's like saying everything Newton discovered was wrong because Einstein improved our understanding of gravity.

But regardless, you have to concede that knowledge based on objective scientific research is implicitly more logically sound than "feelings" or "beliefs" about religious ideas written thousands of years ago?

Check out http://ronpaulforums.com for activism and news.

We can spend all day going back and forth

But what I will say about religion is that at least with the bible, my personal view is that it is more of a telling of historical events, from a religious view point. In other words, there is archilogical evidence to support occurrences in the Bible, but not how they occurred. For example, written in the bible it says the God split the Red Sea; there is evidence that over history the Red Sea has split, but it appears to be a natural occurrence, not one caused by God. Now it could have been caused by God at the time, but we will never know, but what we do know is that when it has happened, there is scientific facts to show that it happened naturally.

It is a theory - that is all

Evolution is a theory. The question is why do they hold it so tightly and doggedly. It is a theory and if science does not support it you pose a new theory at least, yet they do not. More and more it looks like a belief system or a simple desire to undermine some other belief system.

Like gravitation and photosynthesis

Just theories. Testable, reproducible, verifiable. Not guesses, not fantasies, not hypotheses, THEORIES.

If you are going to denigrate a concept, try to use the proper terminology, otherwise your bias will remain unconcealed.

dynamite anthrax supreme court white house tea party jihad
======================================
West of 89
a novel of another america
https://www.smashwords.com/books/view/161155#longdescr

"otherwise your bias will

"otherwise your bias will remain unconcealed."

Well gee, is that not a good thing? Otherwise that would be intellectual dishonesty to conceal your bias would it not?

I think you need to understand the definition of theory. Allow me to provide it for you according to Merriam-Webster:

1: the analysis of a set of facts in their relation to one another

2: abstract thought : speculation

3: the general or abstract principles of a body of fact, a science, or an art

4 a : a belief, policy, or procedure proposed or followed as the basis of action

b : an ideal or hypothetical set of facts, principles, or circumstances —often used in the phrase in theory

5: a plausible or scientifically acceptable general principle or body of principles offered to explain phenomena

6 a : a hypothesis assumed for the sake of argument or investigation

b : an unproved assumption : conjecture

c : a body of theorems presenting a concise systematic view of a subject

Elsewhere it is given as, "a well-established principle that has been developed to explain some aspect of the natural world. A theory arises from repeated observation and testing and incorporates facts, laws, predictions, and tested hypotheses that are widely accepted."

I give you that evolution is well-established and was developed to explain some aspect of the natural world. It is widely accepted though it's support is falling away. Why? Due to the lack of the rest of the definition. Evolution says there would be transitional species, that is the hypotheses it is based on. So, repeated observation? None. Testing the hypotheses? The predictions? For 150 years and the tests have failed. Facts? Where? Laws? And I don't mean the kind out of Government saying you can only teach evolution. No, scientific laws like thermodynamics which actually fit creationist theory better than evolution.

When does theory become law?

People refer to the law of gravity, but the theory of relativity, and theory of evolution. In physics, one learns many laws: laws of thermodynamics, conservation of mass-energy, motion, momentum, etc..

GoodSamaritan's picture

Citations, please

Gravity? Check. Easy to repeat experiments that demonstrate its effect.

Photosynthesis? Check. See it happening over and over again every day.

One kind of organism changing into another kind? When and where was this observed? Was it repeated? Why wasn't it widely reported?

Ron Paul - Honorary Founding Father

Isn't the guy on the far

Isn't the guy on the far right of that image, in fact, one of the Duck Dynasty Taliban?

Looks like my Journeyman.

When I was a Electrical apprentice. Maybe he's up in Toronto getting lights back on after the ice storm. He be about 85 now. 340 in a dogs life. The moral of the story The older you get the less you count birthday years.

Money talks and dogs bark

LOL

No, but I bet he would not be singing the blues, if he were living in Louisiana in the 50's.

“Although it was the middle of winter, I finally realized that, within me, summer was inextinguishable.” — Albert Camus

Delete

Delete

Old thread

But had to suggest that's not the case. In recent times, DNA trace evidence has been successfully extracted from a fossilized dinosaur bone.

"Hell is empty, and all the devils are here" (Shakespeare)
RP 2012~ Intellectual Revolution.

GoodSamaritan's picture

Proving the fossil was nowhere near 68 million yo

if you're referring to the DNA extracted from a T-Rex. The half-life of DNA is now known to be 521 years at a maximum under perfect conditions for preservation.

Assuming roughly six trillion base pairs per strand for the dino DNA, and assuming it was immediately dried, vacuum-packed, and frozen at about –80 degrees Celsius, the likelihood of finding two conjoined pairs would be virtually zero after only 22,000 years.

Ron Paul - Honorary Founding Father

GoodSamaritan's picture

There is no 400,000-year-old DNA

The story is propaganda and/or bad science. Studies of the rate of breakdown of DNA in laboratory conditions indicate that "no DNA would remain intact much beyond 10,000 years." Sykes, B., The past comes alive, Nature 352(6334):381–382, 1991.

Dr. Sykes is currently Professor of Human Genetics at Oxford and a recognized world authority on DNA.

Ron Paul - Honorary Founding Father

This says the current record

This says the current record is 500,000 years-

http://www.popsci.com/science/article/2013-02/whats-half-lif...
http://www.nature.com/news/dna-has-a-521-year-half-life-1.11555

I highly doubt that Dr. Sykes disputes this. More likely, his statement is being taken out of context.

Check out http://ronpaulforums.com for activism and news.

GoodSamaritan's picture

The authors are duplicitous

They agree that the half-life is 521 years so either they failed to do the extrapolation - a trivial task - or else they're too agenda-driven to bother with facts.

Your assumption about the quote being taken out of context is simply wrong and the onus is on you to prove otherwise. Writing about magnolia leaf fossils (and others in the same layer found to also have DNA, including oak, cypress and tulip tree fossils) he says:

This means these compression fossils defy the prediction, from in vitro estimates of the rate of spontaneous hydrolysis, that no DNA would remain intact much beyond 10,000 years. What a good job not everybody knew that, grant reviewers included.

He's being sarcastic. Sykes is not denying that the fossils are multimillions of years old. He is saying that if the inferences from the laboratory data had been completely trusted, no one would have bothered to look for DNA in such old sediments. The fact that it exists is to him evidence that the inferences were wrong, not the age. Another brilliant evolutionist who places agenda over facts.

Ron Paul - Honorary Founding Father

a paper from 1991 is your evidence?

You realize you are quoting a paper from 1991? Do you think that the understanding and science of DNA has changed much in the last 22 years?

And Bryan Sykes is not a young Earth creationist.

You are just quoting some creationist website. Anyone who uses something that inherently conflicts with objective reason as a basis for a scientific theory is not a scientist.

Sykes does not dispute the age of the Earth nor evolution.

Check out http://ronpaulforums.com for activism and news.

GoodSamaritan's picture

I'm sorry about your reading comprehension problem

I'll try to make it a little easier for you to digest.

Dr. Sykes believes the earth is billions of years old and life evolved from molecules to man. With me so far? That's what you should have deduced from my statement that, "He's being sarcastic. Sykes is not denying that the fossils are multimillions of years old."

He made it clear in a 1991 Nature article that "...no DNA would remain intact much beyond 10,000 years" and then completely disregarded his own evidence because it didn't fit his world view. Still with me?

In two separate but related responses in the immediate vicinity of your pointless reply, I presented facts from an October 2012 article in Nature that corroborated Dr. Sykes' estimate of 10,000 years as an upper limit on DNA survivability. As the palaeogeneticists in that article reported, the half-life of DNA under perfect preservation conditions is now known to be 521 years.

I'm not doing the exponentiation for you so I suggest you ask your math teacher for assistance. The bottom line is that the probability of finding DNA that's even 22,000 years old is vanishingly small and there is absolutely no 400,000-year-old DNA in existence anywhere under any circumstances.

Ron Paul - Honorary Founding Father

Correct me if I'm wrong

You seem to understand, or think you understand, this stuff way more than I understand it. I must have missed your reference to a 2012 Nature article in this thread but I did find an article in the Procedings of the Royal Society B (Biological Sciences):
http://rspb.royalsocietypublishing.org/content/279/1748/4724...

It says the *average* half-life of DNA is 521 years, but that's not an upper limit as you're suggesting, it's an average. If you look at the bottom of page 4729 in that article (seventh page of the pdf), there's a table showing the half-life of DNA as it varies with temperature. At 25C it's ~500 years, but that increases with lower temperatures. They conclude: Still, the results indicate that under the right conditions of preservation, short fragments of DNA should be retrievable from very old bone (e.g. greater than 1 Myr). However, even under the best preservation conditions at 258C, our model predicts that no intact bonds (average length 1 bp) will remain in the DNA ‘strand’ after 6.8 Myr

You say in another reply: They agree that the half-life is 521 years so either they failed to do the extrapolation - a trivial task - or else they're too agenda-driven to bother with facts.

But based on skimming this article, perhaps another possibility here is that you've latched onto the idea that the half-life is 521 years, as if the half-life of DNA were comparable to the half-life of a radioactive element, and missed the fact that the half-life of DNA is not a constant but is highly variable, and 521 years is not an upper bound based on ideal conditions but rather an average that would apply in far from ideal conditions.

GoodSamaritan's picture

Good try

From the Nature article:

By comparing the specimens' ages and degrees of DNA degradation, the researchers calculated that DNA has a half-life of 521 years. That means that after 521 years, half of the bonds between nucleotides in the backbone of a sample would have broken; after another 521 years half of the remaining bonds would have gone; and so on.

http://www.nature.com/news/dna-has-a-521-year-half-life-1.11555

From the RS article:

By analysing mitochondrial DNA (mtDNA) from 158 radiocarbon-dated bones of the extinct New Zealand moa, we confirm empirically a long-hypothesized exponential decay relationship. The average DNA half-life within this geographically constrained fossil assemblage was estimated to be 521 years for a 242 bp mtDNA sequence,...

[Note that they are the ones who claim an exponential decay rate.]

The decay rates do not account for the potential initial post-mortem phase of rapid DNA decay governed by nucleases.

[In other words, they assume no decay between death and fossilization - an highly unlikely scenario.]

We have demonstrated that in situ DNA decay is described by first-order kinetics, confirming that long-term post-mortem DNA fragmentation can be treated as a rate process. This closes the gap to theoretical in vitro observations made four decades earlier. We argue that equation (3.3) represents the best available approximation of the rate of mtDNA decay in fossil bone.

On p. 4729 that you reference, the chart shows that the exponential decay associated with the average half-life of 521 years is the longest estimate given of the seven data sets measured. The other data sets show significantly shorter half-lives. So, yes, the 521 figure is an average, but it is their most generous average.

You're quoting their claims of model predictions but that is merely speculation on their part. I'm referring to the actual measurements of actual fossils - not guesses about what they think or hope they might find in the future as predicted by their model.

Ron Paul - Honorary Founding Father

Well now I could be wrong

But you did write "As the palaeogeneticists in that article reported, the half-life of DNA under perfect preservation conditions is now known to be 521 years."

From what I can tell that's not even close to a fair summary of what they said. The average they calculated wasn't "under perfect preservation conditions." Not even in that Nature article that turns out to be just a summary of the paper in the Proceedings of the Royal Society B that I provided a link for.

Could you perhaps either show where they claim that result to be the "half-life of DNA under perfect preservation conditions," or retract that characterization of the research?

I'm not clear on what your objection is to the table on 4729. Is that they're extrapolating based on the fact that decay would be slower under colder conditions? Are you trying to say that it's unreasonable to assume that under colder conditions than their samples (which were, if I understand it, stored at similar temperatures) the decay would slow? Or do you agree that this is a reasonable assumption but your point is that their model is speculative? If it's the latter, then that again doesn't fit with your earlier claim that the research was about "perfect preservation conditions."

GoodSamaritan's picture

Their terms were "right conditions of preservation"

and "best preservation conditions". I took those terms to mean "ideal" or "textbook" or "perfect", as in best possible.

Their assumptions:

No postmortem decay from nucleases.
Steady-state temperature from burial.
Constant pH.

There were other, less relevant assumptions. But all of their assumptions are built into the model from which they then made predictions.

So, yes, my summary was fair.

As for the table, I don't have an objection. The numbers are generated from their model. My position is that their numbers appear reasonable, though very generous given the assumptions above. They injure their credibility, however, when they then proceed to speculate about possible DNA finds in the future that are orders of magnitude older than the ages of the bones they measured. Just because they can extend the line on a graph doesn't make conjecture reality.

Ron Paul - Honorary Founding Father

I must be misunderstanding you

because now you're quoting the phrases "right conditions of preservation" and "best preservation conditions" as if they were talking about the conditions under which the half life would be 521 years, when that's clearly not the case. In context what they said was:

Still, the results indicate that under the right conditions of preservation, short fragments of DNA should be retrievable from very old bone (e.g. greater than 1 Myr). However, even under the best preservation conditions at -5 C, our model predicts that no intact bonds (average length 1 bp) will remain in the DNA ‘strand’ after 6.8 Myr

This is in the caption for Table 1 on page 4729.

Note that the phrase isn't just "best preservation conditions" but "best preservation conditions at -5 C", and if you look just below that at the chart the half-life they give for -5 degrees C is 158,000 years, not 521 years. This is why their conclusion about recoverable DNA very old bones, greater than a million years under best preservation conditions, is different from the conclusion you've been claiming based on your inaccurate summary.

Again, your claim was that their research found a half-life for DNA of 521 years under best conditions. That's not what the paper says at all, and now that you've explained the phrases you had in mind, we can look at the context and see that where they talk about "best preservation conditions" they are very clearly *not* saying the half life would be 521 years under those conditions, but much longer than that.

So can you retract your inaccurate summary of their research (and the various other things you've said that would only be valid inferences starting from that faulty assertion), or find a different place in the paper where they do say what you claim they said?

GoodSamaritan's picture

I understand what you're saying

as well as what they said. Perhaps what I'm not making clear is the connection between those assumptions I listed and all of the half-lives, including the 521 years.

I'll say it this way. They built a model based on analysis of 158 bones. That model has significant assumptions behind it that are not actually found in the real world. Those assumptions simplified the analysis but also extended the half-life values. Nucleases break down DNA, temperatures fluctuate, pH changes, oxygen corrodes, free radicals break bonds, and water dilutes.

Removing such real-world factors from the model leaves an ideal circumstance for DNA preservation. The conditions are more ideal at colder temperatures. Either way, their model is assuming "best preservation conditions" found nowhere on earth.

They are *speculating* that DNA can survive 158,000 years at -5C. There is no justification for that speculation based on analysis of bones that are only 600 to 8,000 years old. There is no place on earth that has been -5C for 158,000 years. Both the Arctic and Antarctic were tropical at one time. Hopes and dreams are not science.

Ron Paul - Honorary Founding Father

That's starting to sound more accurate

You started out saying: The half-life of DNA is now known to be 521 years at a maximum under perfect conditions for preservation.

It's simply false to say that the half-life of DNA is "known to be 521 years at a maximum." The paper cited doesn't say that. You mashed up a claim about longer half-lives for DNA under best conditions, with a claim about the average (not maximum) being 521 years under less-than-ideal conditions, to come up with a bogus assertion.

Now you seem to be admitting that the half-life of DNA would be greater than 521 years, for samples preserved under better conditions than the ones they used in their tests, but you argue that their projected "best case" of a half-life of 158,000 years is based on unrealistic assumptions. Well, of course it is, they're calculating an upper bound there, under idealized conditions, in part to refute the claims made in ref [1].

BTW, they cite the current record as being 450-800 kyr DNA recovered from Greenlandic ice cores (their ref 47).

GoodSamaritan's picture

That's not my admission

There are no "samples preserved under better conditions" because those better conditions - given their assumptions - do not exist and have never existed.

I could have been more exacting in my initial remark, but the fact remains that their estimates are exaggerated - all of them. I'm being kind in even accepting their 521-year half-life. And, as I already indicated, for them to extrapolate unearthly preservation conditions and suggest that DNA could/maybe/perhaps/hopefully someday be found that is hundreds of thousands of years old is just science-fiction fantasy.

If their model is the best available to date, and it might be, then the citation of 450-800 kyr DNA is propaganda. Or else let them provide proof that such supposedly ancient DNA was preserved under their ideal assumptions for its entire existence up to discovery.

Ron Paul - Honorary Founding Father

That's not your admission, but it should be

It's not a matter of being "more exacting." You misrepresented what the authors of the paper were saying, and misrepresented it over and over until just recently. When you tried to explain where you got that idea out of the paper you referred to a couple of phrases that occurred in a context that was very clearly *not* saying what you claimed.

So your summary of their research was wrong, and if you got that idea from the paper at the place you claimed, at best you were misreading them, mashing up their discussion of calculating an upper bound on DNA half-life (for which they come up with a half-life of 158,000 years) with an earlier figure of 521 years which was not a maximum at all, but the average for a specific set of samples.

And you kept repeating the error. You said: The half-life of DNA is now known to be 521 years at a maximum under perfect conditions for preservation. Saying that the half-life of DNA is "known" to be 521 years makes it sound like scientists have accepted that as the upper bound on DNA half-life under perfect conditions. But obviously the authors of the paper you've been citing wouldn't agree that they "know" this, since they in fact argue for an upper bound of 158,000 years, not 521 years.

Then you said: As the palaeogeneticists in that article reported, the half-life of DNA under perfect preservation conditions is now known to be 521 years. But that's not what they reported.

Later you said: If you want to believe that DNA can be found intact after 500,000 years then you will necessarily have to disbelieve that the half-life of DNA is 521 years. I choose to believe the palaeogeneticists. But again, what you say you are choosing to believe from those authors is not at all what the authors are saying.

Now you say: There are no "samples preserved under better conditions" because those better conditions - given their assumptions - do not exist and have never existed.

But the ice cores (at 450-800 kyrs) are very clearly an example of DNA preserved under better conditions than the ones they studied in their sample. They estimated the fossil burial temperature of the bones they studied to be 13.1 C. Ice cores, of course, would be at around zero C. Lower temperature = better conditions. Better conditions = longer half-life.

GoodSamaritan's picture

I can't make it any clearer for you

If you want to believe that their assumptions justify pretending that DNA can survive hundreds of thousands of years, then you go right ahead. That's a ridiculous position, in my opinion, given that they state very clearly impossible - perfect - conditions that artificially maximize the predicted longevity to impossible numbers. The half-life isn't anywhere near 521 years (or any of the longer numbers at colder temperatures).

You keep harping on "The half-life of DNA is now known to be 521 years at a maximum under perfect conditions" as if that is an incorrect summary. I didn't state which temperature - and it doesn't matter - because there are not now, and never have been, the conditions which they presume for their predictions. If they had been more thorough, or honest, they would have made it clear that the half-lives listed for each temperature band are wildly optimistic.

"Saying that the half-life of DNA is 'known' to be 521 years makes it sound like scientists have accepted..." That's your interpretation. I didn't claim that's what they said and I'm permitted to simplify points wherever I want for the sake of brevity.

The ice cores prove nothing since they are not as old as claimed. I know how they get those dates and - again - gross, simplifying assumptions are made as to the rate of layering. Hundreds of layers can and do form in a single year.

Ron Paul - Honorary Founding Father

Disagreeing vs. misrepresenting

You said, repeatedly, that the authors of the paper were claiming that DNA had a half-life of 521 years maximum. But that's very clearly not what they were claiming. You were claiming to agree with them at that point, but misrepresenting what they were saying. You were attributing a claim to them that they were not making. You were wrong.

I asked you where you got that idea. You referred to a particular section of the paper where certain phrases were used. They were indeed arguing for an upper bound on DNA half-life in that section, but not an upper bound of 521 years as you repeatedly claimed up to that point. You were wrong, and the source for your claim turned out to be saying something very different from what you were claiming.

Now you're focused on disagreeing with their model, which is fine, but disagreeing with their argument is not the same thing as misrepresenting their argument.

GoodSamaritan's picture

Thanks for the clarification

Perhaps the best way for me to represent their work, rather than giving them any credence as I did, is to simply point out their baseless assumptions and fantastical predictions, and show the reader why their work provides strong evidence for an upper limit of DNA survival in the range of 10-20,000 years.

Ron Paul - Honorary Founding Father