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Comment by michaelgreshko | Hacker News Reader

Hey, I'm the journalist who wrote the story. A few things: - The organic-rich film preserving the outlines of scales (so, yes, fossilized skin) is only a few millimeters thick. So Mitchell had to prepare the fossil extremely slowly in order to follow the film through the matrix. - The half-life of DNA is ~521 years at 13.1°C, as found in this 2012 paper: http://rspb.royalsocietypublishing.org/content/279/1748/4724 The team's model predicts higher half-lifes at truly freezing temperatures, but even at the extreme end, there's no way DNA would survive 110 million years. - The dating on the site is well constrained to ~110 million years old. The fossil was found in the Wabiskaw Member of the Clearwater Formation, a well-dated rock formation in Alberta. The underlying oil sands have been radiometrically dated to 112±5.3 million years old. (http://science.sciencemag.org/content/308/5726/1293)

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Really awesome writeup of the find. Is Suncor going to be doing any additional, and somewhat more reserved, excavating to understand whether or not there are other important fossils nearby?

Thanks. Interestingly, this is the first large fossil like this that Suncor had run across, in all the digging they had done up in the oil sands. And as you can imagine, finding a land animal like this nodosaur in the middle of what would've been a shallow sea is extraordinarily unlikely. Other mining companies have found other fossils in similar formations, though usually of non-dinosaur marine reptiles (e.g. http://www.sciencemag.org/news/2016/10/ancient-sea-monster-b...).

How much does the DNA degrade (i.e., what does half life mean)? Would it be possible to align any preserved short sequences back together?

If the DNA strands keep getting chopped in half then eventually the strands will be too short to extract anything useful.

What zbyte64 said. Once the animal dies, the enzymes that constantly fix and error-check DNA are no longer around. DNA then degrades over time, cleaving in half every ~521 years on average. So past a million years or two, the fragments are so small, meaningfully putting them back together would be an impossible task, like reconstructing a porcelain bowl you had ground into dust.

Yes, but it is a statistical process. There are many copies of the DNA, so some fragments might still be useful (?)

So, if we assume that the dinosaur has 1 billion base pairs in its genome (huge assumption, see my other comment), it has degraded over 110 million years with a half life of 512 years, there is functionally 0 base pairs left[1] in each dna helix. Even statics can't help much there! I'm wide open to the possibility that I am incredibly wrong in any one of these assumptions however

[1] - http://www.calculator.net/half-life-calculator.html?type=1&n...

I didn't actually look into this or any of the references but I suspect the half-life model is not appropriate in the extreme case. That is, it's an approximation that works on a certain non pathological scale like newtonian physics. Probably need the quantum mechanics version for this.

Not if this really is well-described by independent probabilities, i.e., a chance of being preserved that falls exponentially in time. Even if after 1 million years only half of the strands of DNA have had all their info destroyed, and even if (very unrealistically), the ones that haven't been destroyed are completely intact, then after 100 million years you would need to start with 2^100 = 10^30 DNA strands to have a single one last. And there are < 10^18 cells in a land animal.

No, the only way for something to survive is if the half life model breaks down and the chance of decay during different time periods isn't independent. This would be the case if one of the strands was somehow preserved accidentally.

Yes, but you need fragments of only about 50 basepairs to assemble a genome (or a big part of it) back. A typical DNA strand has on the order of hundreds of millions of basepairs.

The point is that an entire genome (not just 50bp segments) is destroyed in 1 million years.

Why would this be an exponential process? The error is per base pair per unit time. If a DNA fragment is split cleanly in half, each half should have double the expected time to failure as the whole, because there is half the number of base pairs each with the same likelihood of error as before.

It's just like nuclear atomic decay. For each base pair, there is a small chance of decay each small time step. The chance of any given base pair remaining undecayed through some time T is the product of all those probabilities, which fall exponentially in T. The expected number of total surviving base pair is also exponentially falling.

People are talking about two different things in this thread, and that's why people are talking past each other. Some people think halving means "half the number of base pairs remain" which would be an exponential process, yes. The other group thinks that "halving" means literally cut in half -- a failed base pair cuts the DNA strand into two pieces. That would be a linear decay process. As someone with no understanding of the underlying decay processes it's not obvious to me which one is right.

Yes, but 100 million years is quite a few 521-year half lifes.

That half-life is the time it takes for the link between half of the bonds between nucleotides to break (http://www.nature.com/news/dna-has-a-521-year-half-life-1.11...)

So, after 1042 years, only a quarter of the bonds will be intact. After 100 million years, only 1 in every 2^190000 bonds will be expected to still be intact. Taking 2^10 = 1000, that's 1 in every 10^57000. I think that's quite a bit higher than our estimate for the number of particles in the universe (https://www.quora.com/How-many-particles-are-there-in-the-un...)

TL/DR: I wouldn't bet on it.

Mmmm that's not what half-life means. Half-life means that in 521 years, half of the DNA is "gone", not cut in half.

I'm not sure if you're being sarcastic or not...

Edit: Wow a lot of bs going on in the comments. First of all, there's an immense number of ways a DNA strand can degrade, and only one of them splits the strand in two. The relative importance of all these pathways depend on the environment of the DNA, which obviously changes for each and every fossil you have. The global kinetics of "DNA degradation" are supposedly first-order, which implies constant half-life.

http://rspb.royalsocietypublishing.org/content/279/1748/4724

> The relative importance of all these pathways depend on the environment of the DNA, which obviously changes for each and every fossil you have.

And I guess it might for every cell of a single fossil.

How would you know where to align the sequences? I am not an evolutionary biologist so maybe one of those people have a "yes, actually!", but consider modern descendants of dinosaurs have 1 billion base pairs and 20,000-23,000 genes[1], and the fact that we have many many living versions of those fowl to experiment with. Trying to realign chopped up bits of dna with who know how much completely missing, and minimal opportunities to experiment or direct information as to how any particular sequence functions, I can't see any way to extract useful data from highly degraded dna.

More information of degraded dna handling techniques, albeit in the forensics field and aimed toward people, but interesting to me nonetheless [2]

[1] - http://www.nature.com/nature/journal/v432/n7018/full/nature0...

[2] - http://epublications.bond.edu.au/cgi/viewcontent.cgi?article...

Hello? Frog DNA. Duh! :)

Just keep a tight grip on lysine and everything will work out :)

That's exactly how the DNA sequencing works for fresh samples. https://en.m.wikipedia.org/wiki/Sequence_assembly We don't have the technology to do more than a few thousand bases in one go at the moment, so all modern sequencing means chopping up the sample, analysis, and then statistics based reassembly.

I don't know how it relates to million years old samples though. Maybe someone else knows why that's not easily applicable. I'd guess degradation being pretty random leaves chunks which are too small for analysis. (pure speculation, please educate me)

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