Half-Life of DNA is 521 Years, Jurassic Park Impossible After All 315
another random user writes with this quote from Nature News:
"Few researchers have given credence to claims that samples of dinosaur DNA have survived to the present day, but no one knew just how long it would take for genetic material to fall apart. Now, a study of fossils found in New Zealand is laying the matter to rest — and putting paid to hopes of cloning a Tyrannosaurus rex (abstract). After cell death, enzymes start to break down the bonds between the nucleotides that form the backbone of DNA, and micro-organisms speed the decay. In the long run, however, reactions with water are thought to be responsible for most bond degradation. Groundwater is almost ubiquitous, so DNA in buried bone samples should, in theory, degrade at a set rate. Determining that rate has been difficult because it is rare to find large sets of DNA-containing fossils with which to make meaningful comparisons. To make matters worse, variable environmental conditions such as temperature, degree of microbial attack and oxygenation alter the speed of the decay process. 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."
Someone forgot to tell these guys (Score:4, Funny)
Russian and Korean Researchers Will Inject Mammoth DNA Into Elephant Eggs, Resurrecting 10,000-Year-Old Beast [popsci.com]
Re:Someone forgot to tell these guys (Score:5, Insightful)
That just says that they're going to inject the DNA - it doesn't say that they're going to get viable embryos out of it.
Re:Someone forgot to tell these guys (Score:4, Informative)
Re:Someone forgot to tell these guys (Score:5, Insightful)
Why do they need to know? 10,000 years is roughly 20 half-life periods, so they should expect roughly 1-millionth of the DNA to remain.
Since the wooly mammoth genome is approximately 4.7 billion in 58 chromosomes, for an average of 81 million base pairs per chromosome, the DNA fragments would be, on average 81 base pairs long, which should be enough to figure out the original sequence after duplicating and matching. So a full reconstructed mammoth genome should be possible.
Re:Someone forgot to tell these guys (Score:5, Interesting)
Heck, 81 base pairs would save you a lot of time chopping strands for PCR, you would already have the pieces. :)
Seriously though, given those numbers are for a single cell, how many do you have with a mammoth carcass? More than 1, in fact more than 1 million. If you can find a lab blender big enough to stuff a mammoth carcass in to, the rest should be trivial. I would also venture that after a while, the fact that a dinosaur bone didn't degrade to dust means that it is better preserved than your average thing stuffed in to the ground so the half life would, after a point, extend.
Given a few dinosaur samples, you could probably get enough to reassemble most of the genome. With some not all that complex math, you can compare it to a few key reptile sequences and likely get some strong hints or even direct sequences that are missing. Some things change a lot over time, others do not or can not.
And yes, I did do this in college. No, not on dinosaurs though, that would have been a bit more fun to talk about at the bars.
-Charlie
Re:Someone forgot to tell these guys (Score:4, Informative)
With the numbers of busyqth (mammoths died out 4500 years ago by the way):
If you have 1 DNA in pieces of 1000 base pairs length from one mammoth, it must not be older than 8500 years.
If you have 1 DNA in pieces of 81 base pairs length from one mammoth, it must not be older than 10000 years.
If you have a million DNA pieces of 81 base pairs length from a million mammoths, they must not be older than 30000 years.
The returns are diminishing quickly. 10000 years can not be exceeded significantly.
Re:Someone forgot to tell these guys (Score:5, Funny)
Yes, but back then we called them 'Safety goggles'. They had a precursor to a holographic UI called 'scratches'. It worked much the same in practice.
-Charlie
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The last thing Disney corp would want is walt disney revived.
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- strongly supporting the Nazi Party prior to WWII
- abused and severely underpaid his animators, and fired them if they tried to unionize.
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I think your way of looking at the decay is not the way I would expect decay to occur. At each half-life, there is a 50% chance that base pair bonds are broken, so at one half life, I would expect a poisson distribution of base pair lengths that remain rather than at one half life for the chromosome to be broken in two. This would imply that at one half life most sequences will be single digits in length and that at 20 half lifes, there will be very few sequences longer than 2.
Also, they do show a relativ
Re:Someone forgot to tell these guys (Score:5, Funny)
the mammoth DNA is frozen (Score:5, Interesting)
the assumptions in the 521 year half life number is that we are above freezing temperatures. so mammoth DNA has a different experience
there are arguments to make that frozen water would lengthen the half life (frozen water is not as chemically active) or shorten it (ice crystals shredding the dna physically rather than chemically)
i'm not knowledgeable enough to guess if the frozen effect would save the DNA better or shred it even worse, but i think it is a valid to say that the half life would be a lot different if you are dealing with a corpse that was frozen at death and stayed that way in permafrost the entire thousands of years time before getting to a modern biotech lab
Re:Someone forgot to tell these guys (Score:5, Funny)
Hey now there's no need to exaggerate, Gabe said HL3 will be done when it's done.
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There is a big difference between finding 10,000 year old mammoth DNA under near perfect conditions (the bodies froze quickly because it was already freezing and stayed frozen until they were found) and hoping to find 65 million year old Tyrannosaurus rex DNA under bad conditions (the processes that preserve fossilized bones are bad for DNA--too much heat and pressure). As cold weather animals, mammoths are ideal candidates for something like this. The dinosaurs required much warmer climates.
Re:Someone forgot to tell these guys (Score:5, Informative)
Something must be wrong with the 521 years. 65 million years / 521 years = 124.760 half lifes.
That means only 1 / (2^124.760) = 1 / (3,1787695069134767997232294562089e+37556) of the original DNA should be available for analysis today. Those guys would be lucky to find a single base pair that has not decayed. Hardly a sufficient basis to make a quantitative analysis ;-)
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No problem, we will just swizzle the results until we hatch a qualitaitve T-Rex instead of a gecko.
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The abstract seems to suggest that even if a t-rex were found in "mammoth trapped in ice" conditions, which as far as we know is an absurd scenario, it'd still be unusable, right?
The team predicts that even in a bone at an ideal preservation temperature of -5 C, effectively every bond would be destroyed after a maximum of 6.8 million years. The DNA would cease to be readable much earlier â" perhaps after roughly 1.5 million years, when the remaining strands would be too short to give meaningful information.
Tyrannosaurus roamed the earth, what, 65-67 million years ago? That's 9x's older than the maximum listed here. But maybe I've misunderstood...?
Re:Someone forgot to tell these guys (Score:5, Insightful)
Even more importantly, this ignores a previous published article on "DNA Sequence from Cretaceous Period Bone Fragments" -- Science 266 (5188) 1229-1232, here is a PDF [myweb.dal.ca] of the article in Science. Either 80 mya (Cretaceous) is horribly wrong, the 521 year half-live of DNA is horribly wrong, Woodruff, et al were horrible deceived (or frauds) or some combination of these.
You would hope evidence would be the deciding factor, but scientists are human too, and the interpretation of evidence is often more important than the actual evidence -- it is very hard to upset to prevailing opinion (as it should be when the opinion is well founded)
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He's a creationist! BURN HIM!
Mammoths? (Score:4, Funny)
As I'm not personally familiar with it; (Score:2)
How does roadkill taste?
(And no, I don't know how mammoth tastes either).
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How does roadkill taste?
It's a little bit earthy, with a slight aftertaste of rubber.
Oh don't worry (Score:2)
Nobody has scientifically disproved time travel yet... we may yet get to see dinosaurs alive!
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All you need is C-span.
Although 'alive' is pushing it a bit.
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If time travel was possible, dinosaurs would have come to us in their time travel machines long before now.
-Charlie
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But it's easy to disprove time travel:
1. Anyone capable of time travel at any point in the future would immediately take the opportunity to kill Hitler while he was a no-name artist.
2. Nobody killed Hitler before WWII started.
3. Ergo, there exists no future where time travel exists. Q.E.D.
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Hitler is a fixed point in time and thus cannot be killed.
Cryogenics (Score:4, Interesting)
Does this have any bearing on cryogenics or would that preserve the DNA?
Re:Cryogenics (Score:5, Informative)
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FTA:
The calculations in the latest study were quite straightforward, but many questions remain. “I am very interested to see if these findings can be reproduced in very different environments such as permafrost and caves,” says Michael Knapp, a palaeogeneticist at the University of Otago in Dunedin, New Zealand. Moreover, the researchers found that age differences accounted for only 38.6% of the variation in DNA degradation between moa-bone samples. “Other factors that impact on DNA preservation are clearly at work,” says Bunce. “Storage following excavation, soil chemistry and even the time of year when the animal died are all likely contributing factors that will need looking into.”
Clearly the researchers are aware of the effects of different conditions and levels of preservation and are looking into it. Would be a bit worrying if they didn't.
No water, no air, no bonds broken? (Score:5, Insightful)
Not necessarily the end of the Jurassic Park idea.
Re:No water, no air, no bonds broken? (Score:5, Interesting)
Also worth mentioning, what about the tar pits? If an animal is surrounded by tar and sealed in, what happens to the DNA degradation?
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"there were several reports, including the one in 1992, that claimed that DNA fragments had been recovered from insects that had died between 25 and 125 million years ago. These reports caused considerable excitement, but despite intensive efforts no other researchers, including the team at The Natural History Museum, have been able to repeat and verify these results. As a result of these findings, most scientists now agree that DNA doesn't survive in fossilized insects in amber."
http://www.nhm.ac.uk/resources-rx/files/12feat_dna_in_amber-3009.pdf [nhm.ac.uk]
Short answer: It was plausible, but now is considered debunked. Unless a dino got frozen for 150 mega-years, there's no Jurassic to be.
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That particular method has been (mostly) debunked. But the article here does make substantial assumptions about the environment the DNA is subjected to, any situation that leaves DNA in a different environment from that envisioned by the authors is also likely to have a different result.
So I'd say that neither this article, nor the lack of ability to reproduce the DNA in insects in amber reports, proves the impossibility of getting a hold of Jurassic DNA in some form.
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Not necessarily the end of the Jurassic Park idea.
From the beginning, it was obvious that Jurassic Park is to genetic engineering as Star Trek is to astronautics: good entertainment, a captivating story, an even better sound track, but nothing even remotely related to reality.
Question... (Score:5, Insightful)
If the half-life of DNA is 521 years how are scientists able to sequence 30.000 year old Neanderthal DNA? Presumably this applies to regular DNA, did Svante Pääbo and his team sequence mtDNA?
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It has taken folks decades to get the technology to sequence such DNA. It's very degraded. IIRC, they rely on multiple overlaps of small fragments and the technology has been pushing that fragment size down over the years. I'm sure you could look it up. To tired at the moment.
Re:Question... (Score:5, Informative)
This means even in the relatively recent past, the amount of DNA we're looking at is pretty dang tiny. Part of the reason ancient DNA is so dang tricky is because the much of what you sequence is not actually what you're interested in - doubly so when you're sequencing something closely related to humans. For example, did some spot sequencing of ancient/historic polar bear remains, and had to toss out a chunk of the data we got back, as it was soil bacteria(/fungi/pollen) contamination. How do we know which is which? We had good scaffolds to align our bear sequences back up again, though not everyone is as fortunate as us.
In addition to being rare, what is left is fairly short. You can imagine if you start putting breaks in at random, your average length is going to start declining rapidly, and then level out at some small value that takes quite a while to get smaller. It'll get there, and given geologic time scales, a lot of what we want is that far back, but it'll take a while.
Finally, what isn't mentioned in this summary is that there was massive variance in the estimates of half-life. Supposedly only 40% of the variance in halflife was explained by age. Preservation, inter-lab differences, and good old fashioned luck probably contribute considerably to variance in half-life.
There are other factors too, but they're boring, and I should probably get work done instead of dragging out this reply.
(And to answer your latter question, Neanderthals have been sequenced whole genome, not just mtDNA).
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A major piece of data for creationists... (Score:2)
Maybe Neanderthals are not that old.... The better question, is how do we have dinosaurs with red blood cells? If DNA can barely survive for 500+ years, and cannot survive more than 1.5 million, how do red blood cells last 65 million years since the presumed extinction impact event?
Creationists will be VERY interested in this article.
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From TFA:
So 30,000 years doesn't seem to be beyond recoverable, as long as you get enough material from a body kept under roughly ideal conditions.
So you are saying that the DNA is fragmented but it can still be 'stitched' together even If the DNA degrades. How do you re-assemble the DNA of an archaic hominid accurately when it had DNA that was different from ours? I suppose you could use the DNA of modern humans as a clue but if that is the case (and I'm not saying it is), what about animals that are extinct and have no close genetic relative today like, say, a terror-bird. What I mean is that with Neanderthal DNA being sequencable we could theoretic
Building a dinosaur from a chicken (Score:3)
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Exactly. Much of the "lost" DNA is still very much available, in the form of the dinosaurs' descendants.
Not only that, but any sample of nontrivial size will contain plenty of redundant DNA strands. This "half-life" business can be dealt with through instrumentation and data analysis, if not through chemistry or biology alone.
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I thought Mosanto already invented the chickensaurus. And that's why chicken breasts today are the size of yesteryear's turkey breasts?
What about the 30,000 year old seed that sprouted? (Score:2, Interesting)
But Jurassic Park wasn't bsaed off fossil DNA (Score:2)
Now, the enzyme degradation will no doubt be an issue, as well as the rareness of mosquitoes preserved in amber, but that's another matter.
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An article on this at The Register pointed out that even in amber, the DNA had very little chance of surviving 1.5M years, let alone the 62M years that would have been required for Jurrassic Park to have happened.
If its left exposed... sure. (Score:2)
What if it is sealed in a way that microbes, oxygen, etc can not interfere with it? Say amber, a tar swamp, a deep freeze?
No I did not read the article nor do I have any knowledge on the subject beyond that leaving a steak on a counter in 100 degree heat has a very different outcome than putting it in a sealed bag in a freezer.
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The article actually addresses this and DNA is capable of lasting 1.5 to 6 million years.
Typical crap Slashdot summary pandering to the Anti-Cloning lobby.
Uh, what? (Score:4, Insightful)
It claims there are multiple cases of Neanderthal DNA being sequenced, and a couple quick google searches seem to indicate there are many other similar situations where DNA was recovered.
So i'm wondering, did this study perhaps prove that if nothing is done to preserve the DNA after death then... surprise! The DNA isn't preserved?
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"Wikipedia seems to have a page all about doing what this article says is impossible"
No, it doesn't. Dinosaurs (non-avian ones) are 65 million years old or older. The oldest ancient DNA that isn't regarded as bogus or probably so is less than a million years old. People had hopes that DNA extracted from dinosaur bones was real, but upon more careful testing, it was discovered to all be contamination. Neanderthals are a lot younger than dinosaurs. That time range works.
This is all explained on the wikip
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You're correct that dinosaurs and Neanderthal existed on completely different time scales, but you're completely ignoring that the claims made by this paper would make getting DNA samples impossible for _both_ of them.
Practical limit,~1.5 million years (Score:5, Informative)
The 521 year half-life is if the DNA is exposed to water in typical situations, ITFA (in the article) they give an estimate for the best case situation...
The team predicts that even in a bone at an ideal preservation temperature of 5 C, effectively every bond would be destroyed after a maximum of 6.8 million years. The DNA would cease to be readable much earlier — perhaps after roughly 1.5 million years, when the remaining strands would be too short to give meaningful information.
“This confirms the widely held suspicion that claims of DNA from dinosaurs and ancient insects trapped in amber are incorrect,” says Simon Ho, a computational evolutionary biologist at the University of Sydney in Australia. However, although 6.8 million years is nowhere near the age of a dinosaur bone — which would be at least 65 million years old — “We might be able to break the record for the oldest authentic DNA sequence, which currently stands at about half a million years,” says Ho.
As other posters point out, the famous mammoth recreated from DNA was from about 10,000 years ago, much less than the 1.5 million year practical limit estimated by this research team.
Fill in the gaps? (Score:2)
If ape and human DNA are 5-10% different, then perhaps dinosaur and some current reptile DNA are very similar as well, since now you have 90% of the DNA already, you have to find much less, and if you have billions of samples of DNA, perhaps they could be reconstructed. I would think that by the time we are able to do such a thing we won't be far from being able to create our own dinosaur from scratch.
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...of a sample... (Score:2)
Okay, but there were how many billion copies of the sample when the creature died? If there were two, after 521 years I still have (on average) at least one copy of 3/4 of the data, extending the half-life to (check my math here) 737 years. With 15 billion copies or so, the half-life gets up to, hey!, about 65 million years, and there are trillions of cells (and so trillions of copies of DNA) in a human-
Not impossible (Score:3)
Re:Not impossible (Score:5, Funny)
OK. I just showed my computer a picture of a Komodo Dragon. It just is sitting there, doing nothing.
Now what am I supposed to do?
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Pick up the damned mouse and talk to it. It didn't work for Scotty, but things have gotten more advanced since then. Do it in public for better results.
-Charlie
Frog DNA (Score:2)
So what did MarySchweitzer find? (Score:5, Interesting)
Is this why we haven't heard much from Mary Schwietzer [discovermagazine.com] lately? Six years ago she isolated soft tissue remnants from inside a T-rex femur.
More recently, Charlotte Oskam (Biologist at Murdoch University in Australia) identified DNA in fossilized egg shells [metro.co.uk].
We've always known that DNA was unlikely to survive the passage of aeons, this just puts a number to it. Specific conditions could still allow better than typical preservation, and so I dislike making an absolute statement that we'll never find it. Hopefully those who are still looking for the elusive ancient DNA will take this study as a way to focus their search rather than have their funding cut.
News for nerds (Score:4, Funny)
But we're going to explain to you how half-lives work anyways.
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If there's one thing you should have learned from Slashdot it's that simply being a nerd doesn't make one less stupid, less ignorant, or less technically inclined.
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At the same time, it also shouldn't make you less capable of googling a term you don't understand.
Hmm (Score:5, Funny)
I wonder if 521 years is how long we'll be waiting for Half Life 3?
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Nope, that's the release date for Duke Nukem 4D!
Ladies and gentlemen.. (Score:5, Funny)
Sorry, it just doesn't have the same ring to it.
There is still hope. (Score:2)
Jurassic Park still possible (Score:4, Interesting)
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Reproduce a T-Rex exactly like it was: -> Not so Likely.
250M-year-old bacteria were revived in 1999... (Score:3)
"Impossible After All" (Score:4, Insightful)
One of the best ways to make it happen is to declare it's "impossible". It gives people something to strive for.
What about possible cells from t. Rex fossil? (Score:2)
Story 1 [msn.com]
Storey 2 [smithsonianmag.com]
Story 3 [pbs.org]
IF, and that's a big if, what this paleontologist has found is un-fossilized bits of t. Rex, would it be possible to see if any bits of DNA remain? As she states in the third article, she is not equipped to look for DNA and so can't do it.
Not doubting what the res
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Actually, it was 1993.
https://en.wikipedia.org/wiki/Mary_Schweitzer [wikipedia.org]
And it's been pretty discredited since then.
If all else fails, Google these things and look for the magic words: Consensus between independent researchers with respectable backgrounds.
Without that, nothing means anything. Just this woman career path and the subjects of her official qualifications are enough to worry me.
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Actually, it was 1993.
https://en.wikipedia.org/wiki/Mary_Schweitzer [wikipedia.org]
And it's been pretty discredited since then.
If all else fails, Google these things and look for the magic words: Consensus between independent researchers with respectable backgrounds.
Without that, nothing means anything. Just this woman career path and the subjects of her official qualifications are enough to worry me.
From the wikipedia article you quoted:
A more recent study (October 2010) published in PLoS ONE contradicts the conclusion of Kaye and supports Schweitzer's original conclusion.[14]
14^ Peterson, JE; Lenczewski, ME; Reed, PS (October 2010). Stepanova, Anna. ed. "Influence of Microbial Biofilms on the Preservation of Primary Soft Tissue in Fossil and Extant Archosaurs". PLoS ONE 5 (10): 13A. doi:10.1371/journal.pone.0013334. [doi.org]
It sounds like her research isn't as discredited as you make it sound.
What part of her official qualifications are in question? Would you rather that her Ph.D. in Biology come from an institution more prestigious than Montana State University? The field she's working in is quite new; there are very few specimens of intact tissue from that long ago, and not many people are working on it. Broad consensus is hard to reach in young fields, if only because of the small nu
I don't see the problem (Score:2)
water ubiquitous except where its not (Score:2)
My house is built on layers of rock containing some amazingly well preserved ~400M year old fossils, and there appears to be very little water because the iron in the clay is not rusted, making it bright blue instead of brown. It is brown however where the rocks have been cracked and water can get through.
The hell with dinosarurs... (Score:5, Funny)
Re:The hell with dinosarurs... (Score:5, Funny)
Isn't he already older than 521 years? I suspect his DNA is suspect as it is.
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Why? He is already so well preserved that we have plenty of time. Just keep him away from coconut trees and we are golden.
-Charlie
(Note: There is also a strong possibility that if we sequence Keith, we might get a few extraneous dinosaur chromosomes for free....)
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...for God's sake, lets get samples and clone Keith Richards before its too late!?!?!?
It's already too late. He died in 1983, but no-one had the heart to tell him.
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Well, that would be "One hell of a mosquito and an only slightly less impressive glob of amber", or "A very small dinosaur" obviously.
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Re:But what about... (Score:4, Funny)
A mosquito that bit a dinosaur encased in amber....
Forget that. I'd like to see the tree that generated the sap to encase a dinosaur in amber. :-)
Re:But what about... (Score:5, Funny)
Why is the parent modded 'Funny' - that is the story behind how the scientists in Jurassic Park found dinosaur DNA...
You just explained why it's funny.
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It could just be tens or hundreds of thousands...or depending on if you're a Creationist or not, it could be [ n] thousand years.
http://www.nytimes.com/1990/05/31/us/errors-are-feared-in-carbon-dating.html?pagewanted=all&src=pm [nytimes.com]
http://physicsworld.com/cws/article/news/2001/may/10/carbon-clock-could-show-the-wrong-time [physicsworld.com]
Re: (Score:3, Funny)
Yes, he's sure. No Jesus riding Velociraptors on Slashdot, please.
Re:But what about... (Score:5, Funny)
Re:Ummmm (Score:5, Informative)
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It is an English phrase
To be precise, it's "chiefly UK". Another alternative in idiomatic American English would be "putting to rest", which wins the Google fight against "putting paid to" by a large margin.
Re:Ummmm (Score:5, Funny)
The half-life of unusual British phrases in the US is less than 18 years.
Re:Ummmm (Score:5, Funny)
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That the actual research is about the rate of degradation of DNA in fossils, and not the viability of cloning from DNA recovered?
It should be obvious that the half-life doesn't imply ubiquitous degradation, and with 25-bases ensuring a very reliably unique match, it's conceivable you could recover enough to start a cloning project provided the initial reservoir was very large.
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You're telling me no manner of preservation could get us T-Rex dna?
Ah, but it's just for *original* T-Rex DNA. Once you get good enough with DNA manipulation, you can make a T-Rex from scratch!
Re:So wait... (Score:4, Funny)
It's 98% chicken DNA,
With 2% Samuel Jackson mixed in to make it a Bad Ass Mother Fucker.
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About 6% of the links would still be present, not 5% of the DNA. That means the vast majority of the available sequences are very very short, but statistically there's going to be longer sequences mixed in. And you'll have a massive number of copies of the total DNA strand. So long as they are long enough to be unique, you can start merging them together to expand what you have.
For instance, if you have one sequence that goes 123412321*242213422332* and another that goes
*242213422332*1323451234, based on
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