700,000-Year-Old Horse Found in Yukon Permafrost Yields Oldest DNA Ever Decoded | Hacker News Reader

700,000-Year-Old Horse Found in Yukon Permafrost Yields Oldest DNA Ever Decoded

westerndigs.org

100 pointssalemh10 comments

I love seeing modern 2-legged dinosaur depictions with feathers. I wondered why, growing up, everyone didn't see that they were just giant birds with teeth and weird little arms.

When I was growing up, I thought crocodiles were the closest thing to dinosaurs. I’m fairly sure that’s what I was taught in school. Then came all the drawings of dinosaurs with feathers and my mind was blown when I read that birds are actually more closely related to dinosaurs than crocodiles are.

> the half-life of a DNA molecule is estimated to be about 521 years. By this reckoning, even under the best conditions, DNA could remain intact for no more than 6.8 million years.

I just love how they skip inferences...

If its an exponential decay process, as it supposedly is, then its more of a statistical game where the median helix would have cracked into 1 base pair at 6.8Myr.

That would really suck if you only had one single helix to work with. However I'd think theoretically given an infinite amount of genetic data (unlikely) you could analyze every molecule in the sample separately and then put it back together.

There's a radiation analogy... if you've got a speck of Co-60 of a certain almost infinitely small size, its not too hard to do the math to prove that after 1M years theres less than one atom left of Co-60. Say you want a 1 Kg pile of Co-60 thats 1M years old. Yes, indeed, it is very true that if you start with exactly and only one speck of Co-60 the odds exceed 50% chance that there will be less than one atom left. The solution is simple, start with a bigger piece than an infinitely small speck and use a lot more than one speck.

This isn't a silver bullet, being exponential, if I were not so lazy I could work out that if you wanted the DNA from the first known life on the planet, you'd need a multiple of the entire mass of the universe as a starting sample size or something crazy like that.

Just saying if you want 6.80001 Myr DNA its not impossible its just going to be a huge expensive PITA compared to existing techniques for stuff merely 100 years old.

The guy who divided 6.8e6/521 I think is trying to tell you how many base pairs long an average DNA helix probably would be, I think, sorta? So the average 1/2 life of a base pair is 521 years, and half of an entire helix is 6.8M years.

"Just saying if you want 6.80001 Myr DNA its not impossible its just going to be a huge expensive PITA compared to existing techniques for stuff merely 100 years old."

That's kind of an interesting problem. I wonder how much material you'd need to get decent coverage of a averaged sized organism (few gigabases) given the decay rates they calculated.

So, this statement assumes that anything bigger than ~ 13k half-lives (how did they get this number?)

And in the case of the decoded sample this is ~ 1300 half-lives

Where can I read more about "Single Molecular Sequencing", looks very interesting..

Based on the sequencing read archives for that publication[1], it looks like they used Helicos[2]. PacBio[3] is another form of it.

[1] http://www.ncbi.nlm.nih.gov/sra?LinkName=pubmed_sra&from_uid...

[2] http://en.wikipedia.org/wiki/Helicos_single_molecule_fluores...

[3] http://en.wikipedia.org/wiki/Single_molecule_real_time_seque...

The Helicos stuff would have to be pretty old, they've been effectively out of business for some time (having filed for bankruptcy in 2012).

The paper suggests they mostly used Illumina, with one guy using Helicos:

"J.S. did ancient and modern DNA extractions and constructed Illumina DNA libraries for shotgun sequencing"..."X.W. did Illumina libraries on donkey extracts"..."A.S.-O. performed Illumina sequencing for the Middle Pleistocene".."Ji.M. and X.W. performed Illumina sequencing for the Middle Pleistocene and the donkey genomes at BGI".."J.F.T. headed true Single DNA Molecule Sequencing of the Middle Pleistocene genome"

It's worth noting that while Illumina sequencing isn't true single molecule, you are getting a read signal from a single fragment of DNA.

“But also we pioneered the usage of what is called true Single Molecular Sequencing that basically reads through molecules as they stand, without further manipulation,” Orlando added. By tracking a full, single DNA molecule, the team was able to avoid having to “amplify” fragments, which can often introduce errors.

This is utterly silly because the technique they used (illumina) amplifies fragments anyways, and the error introduced by PCR (1 in 40,000 if you use good polymerases) would pale in comparison to the molecular degradation; it should be simple to run control experiments and "back out" the amount of error caused by the manipulation.

It's also worth noting that this is not a full genome, they just sequenced PARTS of the genome.

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