Half-Life of DNA is 521 Years, Jurassic Park Impossible After All

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."

Comments

Someone forgot to tell these guys

[pkbarbiedoll]

Russian and Korean Researchers Will Inject Mammoth DNA Into Elephant Eggs, Resurrecting 10,000-Year-Old Beast

Re:Someone forgot to tell these guys

[dpilot]

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

[sed quid in infernos]

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.

Re:Someone forgot to tell these guys

[busyqth]

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

[mdfst13]

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

[Groo Wanderer]

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

[Lonewolf666]

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 ;-)

Re:Someone forgot to tell these guys

[gewalker]

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 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)

Re:Someone forgot to tell these guys

[irtza]

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 relatively low correlation coefficient suggesting a good deal of variability in this decay rate. One pointed to factor looked at was temperature of ground soil, which for a mammoth preserved in frost may be a significantly longer period.

Re:Someone forgot to tell these guys

[Gninnaf]

Also in Jurasic Park the DNA was sealed in amber. Wouldn't that extend the half life. Does this mean Walt Disney and Ted Williams only have 521 years to be revived :)

Re:Someone forgot to tell these guys

[funwithBSD]

No problem, we will just swizzle the results until we hatch a qualitaitve T-Rex instead of a gecko.

Re:Someone forgot to tell these guys

[Groo Wanderer]

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

Re:Someone forgot to tell these guys

[mishu2065]

521 years should be enough for anybody.

Re:Someone forgot to tell these guys

[buchner.johannes]

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

[Wraithlyn]

10,000 years is roughly 20 half-life periods

Hey now there's no need to exaggerate, Gabe said HL3 will be done when it's done.

Re:Someone forgot to tell these guys

[Anonymous Coward]

You mixed up the , and . there.

Only in some countries. http://en.wikipedia.org/wiki/Decimal_mark#Countries_using_Arabic_numerals_with_decimal_comma

Re:Someone forgot to tell these guys

[shaitand]

The last thing Disney corp would want is walt disney revived.

Re:Someone forgot to tell these guys

[Hal_Porter]

He's a creationist! BURN HIM!

Re:Someone forgot to tell these guys

[Lonewolf666]

True. I got the digit grouping symbol and the decimal separator mixed up. For a US discussion forum, in Germany it would have been correct. Oops, but with mitigating circumstances...

Re:Someone forgot to tell these guys

[ancienthart]

Can't give you links, but examples of his ass-ery were:
- strongly supporting the Nazi Party prior to WWII
- abused and severely underpaid his animators, and fired them if they tried to unionize.

Mammoths?

[Culture20]

Quick, what does this mean regarding mammoth burgers?

Cryogenics

[SJHillman]

Does this have any bearing on cryogenics or would that preserve the DNA?

Re:Cryogenics

[biodata]

Cryogenics would pretty much stop most of the reactions that break the bonds, so half-life would be hugely increased, especially if material is properly dried first. Seeds can last for many decades and still grow if dried to 5% moisture content and frozen at -80. Not sure about animal embryos, but sperm and eggs also.

Re:Cryogenics

[Spottywot]

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.

The hell with dinosarurs...

[cayenne8]

...for God's sake, lets get samples and clone Keith Richards before its too late!?!?!?

Re:The hell with dinosarurs...

[NEDHead]

Isn't he already older than 521 years? I suspect his DNA is suspect as it is.

Re:The hell with dinosarurs...

[BluBrick]

...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.

Re:Ummmm

[biodata]

It is an English phrase meaning 'putting an end to' but using fewer words.

No water, no air, no bonds broken?

[Doofus]

So in amber, or some other similar impermeable substance, the chemical reactions requiring water or air might well be prevented or dramatically slowed, thus the degradation of DNA might be substantially slower than the 521 years described in the summary.

Not necessarily the end of the Jurassic Park idea.

Re:No water, no air, no bonds broken?

[Sparticus789]

Also worth mentioning, what about the tar pits? If an animal is surrounded by tar and sealed in, what happens to the DNA degradation?

Re:No water, no air, no bonds broken?

[Maximum Prophet]

"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

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.

Question...

[Savage-Rabbit]

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?

Re:Question...

[MaXintosh]

Scientist here (you can tell by my hat, and the fact that something like 90% of my comments on /. start with "I'm a biologist"). First, the DNA we get is from better preserved remains, which kicks the half life back further (It's in TFA, but not mentioned in the summary). There's still a 'deadline' around 7 MYA, where (allegedly) all the bonds would have pretty much been broken at that point - Frozen remains supposedly have a halflife around 158 kya. It's that dang phosphate backbone that's too willing to run off and go have reactions with any trallop of a molecule that wanders on by.

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).

Re:Question...

[MaXintosh]

We can, and do, try this. It's called 'ancestral state reconstruction' and its what I make my students do each year. There's a ton of assumptions that go into it, though, and few few are likely to be correct over long timescales. We can do that with closely related taxa (I can make some educated statements about the last common ancestor of, say, black-tailed and white-tailed deer DNA-wise), but the further back in time you go, the more homoplasy (convergent/parallel evolution), atavism, and just plain weird crap (macro-mutations) happens. Heck, for some species, we have two+ chromosome counts running around at the same time. Dinosaurs are probably beyond our reconstructive ken.

OTOH, people are clever. I'm open to someone coming up with an interesting statistical approach that proves me wrong for these deep coalescenceses.

Re:So wait...

[Electricity Likes Me]

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.

Building a dinosaur from a chicken

[John Bokma]

An option (?) still open:

Jack Horner: Building a dinosaur from a chicken | Video on TED.com - Renowned paleontologist Jack Horner has spent his career trying to reconstruct a dinosaur. He's found fossils with extraordinarily well-preserved blood vessels and soft tissues, but never intact DNA. So, in a new approach, he's taking living descendants of the dinosaur (chickens) and genetically engineering them to reactivate ancestral traits — including teeth, tails, and even hands — to make a "Chickenosaurus".

What about the 30,000 year old seed that sprouted?

[erotic_pie]

What about the 30,000 year old seed that sprouted? http://www.popsci.com/science/article/2012-02/russian-scientists-resurrect-pleistocene-era-plants-buried-siberian-permafrost-30000-years

But Jurassic Park wasn't bsaed off fossil DNA

[91degrees]

It was based off DNA from blood from an insect trapped in amber.

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.

Uh, what?

[Daetrin]

Wikipedia seems to have a page all about doing what this article says is impossible: http://en.wikipedia.org/wiki/Ancient_DNA

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?

Re:Uh, what?

[Anonymous Coward]

"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 wikipedia page.

Practical limit,~1.5 million years

[slew]

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.

Re:But what about...

[MRe_nl]

Well, that would be "One hell of a mosquito and an only slightly less impressive glob of amber", or "A very small dinosaur" obviously.

Not impossible

[michaelmalak]

It's not impossible. You just show the computer a photo of a dinosaur, let it start from the DNA of a Komodo Dragon, and let it try different "what if" changes to the DNA, simulating the growth of the each resulting organism. Could even happen within the lifetime of Randall Munroe.

Re:Not impossible

[ColdWetDog]

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?

Re:Ummmm

[Anonymous Coward]

If you don't pay for your putting, you can't have any meat. How can you have any meat if you don't pay for your putting?

Re:Oh don't worry

[ColdWetDog]

All you need is C-span.

Although 'alive' is pushing it a bit.

So what did MarySchweitzer find?

[Zinho]

Is this why we haven't heard much from Mary Schwietzer 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.

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.

Re:Ummmm

[Raenex]

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.

News for nerds

[Hadlock]

But we're going to explain to you how half-lives work anyways.

Hmm

[kiriath]

I wonder if 521 years is how long we'll be waiting for Half Life 3?

Ladies and gentlemen..

[jd2112]

Welcome to Dodo Park.

Sorry, it just doesn't have the same ring to it.

Re:But what about...

[Anonymous Coward]

If the dinosaur is encased in amber, why do we need to wait for a mosquito? Why would we want to wait for a mosquito that can bite through amber... drill the thing then get the hell out of there.

There is still hope.

[TsuruchiBrian]

This doesn't fundamentally change anything. Even if half your DNA is destroyed every 521 years, large multicellular organisms have trillions of cells containing copies of their DNA. You don't need to find a single complete correct set. That is already hard enough to do in living organisms. You can assemble a mostly complete set from many incomplete sets. Recovering data from a harddrive with corrupted data is very hard. Recovering the data from a trillion copies of the same data that was corrupted in different random ways is much much easier. As long as every section of data survived in some of the copies, it can be reassembled. Even if there is not enough DNA in a single organism to do this, the differences between the DNA of individuals of the same species is very small. This is what makes sexual reproduction possible. Maybe we can't clone a T-Rex, but if we find enough genetically similar DNA from multiple T-Rexs, we can theoretically make a T-Rex "offspring" of all of them. We don't really care about cloning an specific individual T-Rex anyway. A genetic T-Rex that never existed, but does now, is perfectly acceptable. Maybe there isn't enough T-Rex DNA in the whole world to make a coherent set of DNA. That's possible. All I am saying is that we still have some more good tricks up our sleeve, and we shouldn't give up yet. We will certainly clone some kind of Pleistocene organism like a mammoth as an earlier step anyway. No reason to decide what are limits are so early in the game.

Jurassic Park still possible

[captaindomon]

Even given the half life, we may be able to resurrect dinosaurs. Remember that we are talking about information that is encoded, with billions of copies hanging around. Given we can find enough samples, even if they are all missing different portions, we may be able to piece together the complete sequence by combining the portions of each sample that survived. Throw in extremely cold temperatures like the article talks about, and some Jurassic-park style replacement of certain portions from modern animals, and it is still very possible. Maybe not today, but in 100 years I can see it being very possible.

250M-year-old bacteria were revived in 1999...

[jeffb (2.718)]

...or so researchers claimed. I know there was some skepticism around their claim, but was it ever refuted?

Re:But what about...

[fahrbot-bot]

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. :-)

"Impossible After All"

[jlv]

One of the best ways to make it happen is to declare it's "impossible". It gives people something to strive for.

Re:But what about...

[somersault]

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.

Re:But what about...

[fragtag]

He meant frogs not "frog's". Dino DNA is of course really large (Were talking a T-Rex afterall), so all they have to do is inject a whole frog directly in sequence. AAAATSAATTTTS(frog)AAA

Re:What about possible cells from t. Rex fossil?

[ledow]

Actually, it was 1993.

https://en.wikipedia.org/wiki/Mary_Schweitzer

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.

Re:Oh don't worry

[dkleinsc]

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.

I don't see the problem

[masman]

Since dinosaurs went extinct just 6000 years ago, it shouldn't be all that hard to find some DNA that's not too terribly degraded.

Re:Oh don't worry

[kiriath]

Hitler is a fixed point in time and thus cannot be killed.

Re:Ummmm

[rpresser]

The half-life of unusual British phrases in the US is less than 18 years.

Re:But what about...

[EGSonikku]

Yes, he's sure. No Jesus riding Velociraptors on Slashdot, please.

Re:DNA mapping Egyptian Qharaohs and families

[MozeeToby]

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 the overlapping sections (between the *), you can construct one longer sequence:
123412321*242213422332*1323451234.

Which can then be combined with other sequences in turn. A few hundred thousand iterations later you can do you genealogical research on your 2000 (or 10000) year old mummy.

the mammoth DNA is frozen

[circletimessquare]

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:So wait...

[funwithBSD]

It's 98% chicken DNA,

With 2% Samuel Jackson mixed in to make it a Bad Ass Mother Fucker.

Re:I prefer to transfer my DNA

[dietdew7]

Via kleenex?

Re:What about possible cells from t. Rex fossil?

[Zinho]

Actually, it was 1993.

https://en.wikipedia.org/wiki/Mary_Schweitzer

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.

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 number of qualified researchers.

I'm not saying that we should start conspiracy theories that "the Man" is keeping her down, nor that we should look at her results with unskeptical credulity. On the other hand, your response to her research sounds like an ad hominem attack instead of an actual argument about the research's merit. Cut the girl some slack; if she's wrong she'll have plenty of rope to hang herself with. If she's right, though, we shouldn't reject her results just because they disagree with our preconceived notions.