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3 billion bases long[...]we were able to recover roughly 70 per cent

It's impressive how resilient DNA is as a data storage medium. That's the equivalent of ~500MB of raw data they've recovered, if my calculations are correct.

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They didn't sequence the whole human genome (~3 billion bases) for multiple reasons. I am not an expert on ancient DNA but I will try to explain the paper as best I can:

1. Contamination with other flora and fauna DNA 2. Relative low proportions of human DNA 3. The DNA is usually highly degraded, which limits the analyses to short read sequencing (in this case they used 76 bp reads). The halflife of human DNA is ~521 years.

To mitigate these problems they used multiple targeted approaches including one to isolate mitochondrial DNA, where they managed to sequence the whole ~16kb human mtDNA, where each base was covered by 62 sequencing reads on average (62x coverage).

They used another to isolate specific regions containing single nucleotide polymorphisms (SNPs), which are DNA mismatches known to be related to ancient human DNA and humans. They targeted 470,724 single nucleotide polymorphisms of which 70% (336,429) were recovered.

They did perform shotgun sequencing on all of the DNA isolated, but due to species assignment issues they again focused on fragments that contain diagnostic SNPs in these cases they only recovered a small number of SNPs per sample, again due to the relatively low proportion of human DNA and its degradation (20,526, 3,734, 124,862, 85,901, 34,756, 41,632, 34,677 and 72,992) as per the legend in figure 3.

That analysis makes me think of matching more than recovery.

"matching" is exactly how we do DNA sequencing right now. The current technology is called next generation sequencing (NGS), we multiply the DNA and perform matching digitally to construct the full DNA.

It's quite fascinating. It's like if order to figure out the shape of a teacup, we generate thousands of identical copies, smash them all to rather small bits, and then try to count the different types of shards as a first step to piecing together one full copy. Impressive that it works.

> It's like if order to figure out the shape of a teacup, we generate thousands of identical copies, smash them all to rather small bits, and then try to count the different types of shards as a first step to piecing together one full copy. Impressive that it works.

Yes, but you've got the order wrong.

The teacup is smashed before all of the identical copies are created.

(I wrote DNA analysis software for 6.5 years)

It's not fascinating; it's an endless source of trouble. We only do it because we don't have sequencers that produce extremely long (chromosome length) high quality reads, especially in sequences that contain a lot of repetition. This has been a source of errors and ambiguity for as long as we've used shotgun.

This is a great analogy. One small change is that there are two ways to reassemble it. One is to try to blindly put the pieces together and fork a teacup (read assembly) vs trying to use a picture of the teacup to figure out where the pieces go (read alignment / mapping)

Would it be possible to clone an ancient human being from DNA?

Probably not, not nearly enough material remained to make an accurate clone. The article mentions 70% recovery rate; according to the internet, humans share 98% of DNA with chimpanzees (and 35% with daffodils), so unless you have 100% or 99.9999% of the DNA, the clone will be imperfect at best and a Thing That Should Not Be at worst.

I think your ethical board would probably stop you first.

Keep in mind that this is survivorship bias. The vast majority of DNA from this period has lots. Sure, there is tons that exists but we haven't found but without a doubt almost all of it has been lost.

This is DNA that happened to be the right conditions to survive. It isn't so much that the medium is resilient but that if stored in the correct conditions it can survive.

It makes me think about how many ancient ruins don't exist simply because the people nearby didn't see reason not to reuse all that convenient unowned pre-quarried rock.

Even today, it's not a very compelling plea: "No, don't tear down the recently-abandoned building, it would look cool several hundred years after you die."

So too on the microscopic label, if there are convenient molecules nobody else is using...

"Spolia" is a fun architectural term for this sort of material reuse, particularly with the more interesting decorative pieces. Many of those stones taken from ancient buildings have become notable newer ancient buildings in their own right.

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

> It makes me think about how many ancient ruins don't exist simply because the people nearby didn't see reason not to reuse all that convenient unowned pre-quarried rock.

In the case of Ostia near Rome, they mined it for building material until it became a malaria swamp. It wasn't drained until the 20th century. Around 20% of the workers draining the swap contracted malaria.

So this is how I should be storing family photos.

In a sense your DNA is your family photo.

I was going to say... except without that mole on your arm. But then I thought, it probably has all kinds of battle scars with disease and other adversity coded in it, making a mole inconsequential.

Thinking on how to save things long term is a fun exercise. If I were super rich and felt that highly of myself, I would totally build a monument to myself built to last the ages; elevated (against flooding), tonnes of erosion resistant rock, a library of all human knowledge in many different formats, sealed off. But with an exact copy near it for tourists.

You'd find yourself in company with many religious organizations. The Mormon Church has a couple of records vault carved into the granite outside SLC, while the church of Scientology has 3 geographically separated primary vaults dug into the mountains (Petrolia and Creston CA, and a place in the desert outside Albuquerque).

You’ve gotta have a series of timed vaults that give access to precious metals every few generations.

It’s even more impressive when you compare it to rna, which “lives” minutes. Take away the pair strand, add a hydroxyl group and a uracil, and it’s a totally different thing.

Im fascinated, any noob friendly reading material?

Honestly, scientific papers. The pain of jargon will be less than the pain of a popsci book. Especially with all the tools to rewrite/summarize/search these days.

Yes, but which ones? There are so many out there... It seems like you're educated on the subject, so you may be able to recommend good ones.

A good start would be the review articles listed here: https://scholar.google.com/scholar?q=rna+half-life&hl=en&as_.... If there's a paywall, use sci-hub or check the lab's page for a pdf. I should caveat that there is no one rna half life, some live much longer

It's ok if you don't have recommendations, but sending a google link is a bit out of pocket :(

Ha! I'm sorry. not trying to be cagey/dismissive. There's no paper that must be read: they're all nodes in a network. All I can do is point you to a cluster, w/ the right filter and jargon search terms. Apologies if I came off out of pocket.

Check out the review articles in the “Nature Reviews” journals, like “Nature Reviews Genetics”. These articles are written by experts but designed for a non-specialist audience (with undergraduate science education).

I think of the error correction codes used by CDs.

But for DNA, the data is needed to literally stay alive as replication occurs constantly through our bodies. And this has been refined over maybe billions of years.

When can I start storing passwords in mine?

You can order DNA sequences from all sorts of companies. IDT is by far one of the most popular, using classical biochemical means:

https://www.idtdna.com/pages/products/genes-and-gene-fragmen...

https://www.idtdna.com/pages/products/custom-dna-rna/dna-oli...

And a newer player that uses tech from integrated circuit manufacturing (I think?) is Twist Biosciences:

https://www.twistbioscience.com/twist-ordering-platform

Retrieval of information has a bit of latency, however.

Sooner than you'd think! https://wyss.harvard.edu/technology/dna-data-storage/

(though passwords aren't a great application)

Oh great when i get into old age not only will I forget my password but my DNA will have mutated to the point that it technically isn't my password any longer

lol

Why do you have all those eyeballs on your arm?

Oh, that... yeah, they said I had a lot of special characters in my LinkedIn password, and this is the best way to encode those.

You could likely store them in the junk DNA without much risk, as long as you avoid encoding sequences that are the start of coding regions. That said, if you managed to inject them into every cell of your body, this would be the biological equivalent of dropping pamphlets containing your passwords everywhere you go.

They require at least one emoji and an uppercase character

- Your password has expired. You must choose a new one.

- Uh, oh. How am I going to see behind me, then?

Might be a poor idea if anyone who can collect and sequence your DNA gets your passwords.

Yeah, you'd be vulnerable to pepper shakers and divulging all your passwords in a sneeze.

All of my passwords are encoded in pi…somewhere

Well, probably! But it hasn't actually been proven yet that pi is a "normal number" [0], though most mathematicians think it must be.

[0] https://en.wikipedia.org/wiki/Normal_number#

That's a stronger claim anyhow. We'd merely need Pi to be a rich number, ... which hasn't been proven either.

https://en.wikipedia.org/wiki/Disjunctive_sequence#Rich_numb...

It's not necessary that pi be normal in order for it to contain every possible sequence. Sufficient, but not necessary.

If the OP is anything like me, then they have no trust in number theory researchers and deliberately choose passwords like "141592" so they can be sure

I enjoy thinking about this. Not only is a sequence of digits encoding the complete works of Shakespeare in there somewhere, it's in there again. And again, an infinite number of times.

In my encoding I represent the works of Shakespeare by the digit 0, anything else by the digit 1 followed by its ASCII representation.

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