The article (which is from 2023 by the way) doesn't discuss the findings of the DNA analysis, so I went and looked up the original - https://doi.org/10.1038/s41586-023-06035-2
> with estimates of present-day human and faunal contamination both below 1%. Comparisons with present-day human populations²⁶ using ƒ3-statistics and D-statistics²⁷,²⁸ show high affinities to Native Americans (Extended Data Fig. 5). When projected into a principal component analysis with other ancient human individuals (Fig. 3c), DCP1 falls within a group of Ancient North Eurasian individuals from further east in Siberia, which includes the approximately 24 ka Mal’ta 1 and the approximately 17 ka Afontova Gora 3 individuals²⁹,³⁰. Both of these individuals are genetically closer to DCP1 than non-Ancient North Eurasian individuals when tested with D-statistics (Extended Data Fig. 6b), and all three show similar affinities to ancient Siberians and Native Americans with ƒ3-statistics and D-statistics
4 days ago [-]
4 days ago [-]
userbinator 5 days ago [-]
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.
gww 5 days ago [-]
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.
dexwiz 5 days ago [-]
That analysis makes me think of matching more than recovery.
thangngoc89 5 days ago [-]
"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.
vintermann 4 days ago [-]
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.
inetknght 4 days ago [-]
> 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)
dekhn 4 days ago [-]
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.
gww 4 days ago [-]
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)
sweeter 5 days ago [-]
Would it be possible to clone an ancient human being from DNA?
Cthulhu_ 5 days ago [-]
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.
saagarjha 5 days ago [-]
I think your ethical board would probably stop you first.
kevincox 5 days ago [-]
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.
Terr_ 5 days ago [-]
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...
wlesieutre 5 days ago [-]
"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.
> 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.
5 days ago [-]
Waterluvian 5 days ago [-]
So this is how I should be storing family photos.
saagarjha 5 days ago [-]
In a sense your DNA is your family photo.
m463 3 days ago [-]
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.
Cthulhu_ 5 days ago [-]
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.
AlotOfReading 4 days ago [-]
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).
Waterluvian 4 days ago [-]
You’ve gotta have a series of timed vaults that give access to precious metals every few generations.
biophysboy 5 days ago [-]
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.
bloqs 5 days ago [-]
Im fascinated, any noob friendly reading material?
biophysboy 4 days ago [-]
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.
skyyler 4 days ago [-]
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.
biophysboy 4 days ago [-]
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
skyyler 4 days ago [-]
It's ok if you don't have recommendations, but sending a google link is a bit out of pocket :(
biophysboy 3 days ago [-]
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.
kirsebaer 4 days ago [-]
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).
m463 3 days ago [-]
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.
bloomingkales 5 days ago [-]
When can I start storing passwords in mine?
epistasis 5 days ago [-]
You can order DNA sequences from all sorts of companies. IDT is by far one of the most popular, using classical biochemical means:
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
brianmaurer 3 days ago [-]
lol
almosthere 5 days ago [-]
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.
ryao 5 days ago [-]
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.
SlightlyLeftPad 5 days ago [-]
They require at least one emoji and an uppercase character
selcuka 5 days ago [-]
- Your password has expired. You must choose a new one.
- Uh, oh. How am I going to see behind me, then?
Y_Y 5 days ago [-]
Might be a poor idea if anyone who can collect and sequence your DNA gets your passwords.
rolandog 5 days ago [-]
Yeah, you'd be vulnerable to pepper shakers and divulging all your passwords in a sneeze.
egillie 5 days ago [-]
All of my passwords are encoded in pi…somewhere
magneticnorth 5 days ago [-]
Well, probably! But it hasn't actually been proven yet that pi is a "normal number" [0], though most mathematicians think it must be.
It's not necessary that pi be normal in order for it to contain every possible sequence. Sufficient, but not necessary.
Y_Y 5 days ago [-]
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
billforsternz 4 days ago [-]
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.
Y_Y 4 days ago [-]
In my encoding I represent the works of Shakespeare by the digit 0, anything else by the digit 1 followed by its ASCII representation.
throw0101c 4 days ago [-]
> The cool and dry conditions in the cave have made it possible for scientists to recover preserved DNA left behind by ancient Denisovans, Neanderthals and humans, all of whom occupied the cave at different times over 40,000 years.
That's a long time to have people live in a particular area generally, and a particular "home" in particular.
AIUI, some of the oldest writing we have dates to Ur III at 2000 BC, so that's 'only' 4000 years ago, or perhaps the Uruk period, which at 3500 BC, is 5500 years old:
So the oldest document(s) we have are only about 1/10th how long this cave was occupied.
Some of these time scales are mind-boggling.
sitkack 5 days ago [-]
Send that to a consumer DNA analysis company and find her closest living relatives!
bbarnett 5 days ago [-]
It's basically everyone!
theWreckluse 5 days ago [-]
Or, it could be no one at all!
hackeraccount 4 days ago [-]
If you go back far enough (and I don't know if this is) isn't the answer always everyone or no one but never "some".
sitkack 5 days ago [-]
I know that person!
5 days ago [-]
metalman 5 days ago [-]
this is just the begining of DNA as a tool in archiology.
Earlier work with densovian dna, showed not only a genetic profile,of indivuals, it showed a familial relationship, father/daughter.
The implication is that we will start to get a clearer look into human migration patterns ,including tribal, and familial groups, which while interesting, will also be prone to every kind of abuse in the forwarding of various agendas,...racial,ethnic,religios, nationalistic.
Makes me want to stir the pot sometimes, and feed
back in a lurid interpretation of ancient DNA, proving, i dont know, how about our ancestors throwing off our alien overlords, but now the death star has activated and is beaming alien DNA
data right into us from the 5G, but, but, (marketing angle), ....eating , "product xx" or product xy, strengthens your imune system and prevents the alien download from finishing.
The real issue in my blathering, is that fiction
is fighting an uphill battle, to be stranger than reality.
TeMPOraL 5 days ago [-]
I thought that it was already established that we're descendant of the ancient astronauts from the 12 Colonies of Kobol, and that the "mitochondrial Eve" was a child of a human and a Cylon.
(Part of me wishes to see this resurface as a bona fide religion, oblivious to the source material.)
throwaway173738 4 days ago [-]
All of this has happened before, and all of it will happen again.
mparnisari 5 days ago [-]
How did they know to explore this cave in particular? Blows my mind. Or was it by accident?
AlotOfReading 5 days ago [-]
Denisova cave has been known for about 150 years or so. Back in the 1970s, the Soviet Union sent some archaeologists out to see what was in the cave. They found some upper paleolithic stuff (e.g. like what the article is about), as well as some mousterian stuff (very weird this far north and east). They did excavations over the next couple of decades and eventually, some of the dating/sequencing technology improved to the point where it could actually be used on the cave artifacts. That's when they discovered denisovans and immediately made the cave one of the most important archaeological sites on the planet. There's been no lack of funding since.
5 days ago [-]
jvandonsel 4 days ago [-]
...and also showed that she had antlers.
(Sorry, I couldn’t resist)
4 days ago [-]
peeingpoop 5 days ago [-]
[flagged]
fastball 5 days ago [-]
It says a lot about the state of discourse and gender science that I can't tell if you genuinely don't understand or if you are being facetious.
But assuming you are being genuine: your sex (faka gender) is encoded in your DNA on the 23rd chromosomal pair. If you have two X chromosomes (XX), you are a female human (woman). If you have one X and one Y (XY), you are male human (man). These chromosomes dictate your sexual development (organs/hormones/etc). There are some people (estimated at 1-2% of the human population) who are "intersex", in that they don't have an XX or XY pair, but some variation thereof (XXY, XYY, etc). However even these variations generally fall under one or the other umbrella of male or female. e.g. Klinefelter syndrome (XXY) is generally going to present as male (albeit frequently with poorly developed testicles and other complications). Genes are complicated so this is a bit of an oversimplification.
To make this more about sex itself (since humans are a sexually reproducing species and that is why we are having this conversation at all), there are effectively three options for all humans: you produce small gametes (sperm / male) or you produce large gametes (eggs / female), or you produce neither due to some complication and therefore cannot participate in procreation. This is dictated almost wholly by your DNA.
So, back to the article: they know the DNA in the deer tooth was from a woman because (presumably) the 23rd chromosome was an XX pair.
noneeeed 5 days ago [-]
Just to add one more wrinkle to the link between DNA and the presentation of sex, there is also androgen insensitivity syndrome, in which the person has a Y chromosome, but the developing body does not react to the testosterone produced by the testes.
The result is someone who may appear to be female, have female genitals, but has testes where ovaries would be expected. It's often not discovered until puberty doesn't happen as expected, and they discover they can't have children.
Like all these conditions, this is on something of a spectrum depending on how total it is.
As you say, genes are complicated. So much more so than is often implied in reporting of discoveries of "a gene for X".
epistasis 5 days ago [-]
DNA has a very strong signal for man, woman, and everyone in between.
epistasis 5 days ago [-]
I was a little blithe with my reply here, and feel bad about the scientific inaccuracy I'm perpetuating. The "everyone in between" spectrum often has strong signals, but sometimes it's not very strong straight from DNA alone! And it's also incredibly complex, far far more complex than doing mutation calls, to the point that automating it is quite difficult. Sure, finding XX, XY, XXY, and the many other combinations of sex chromosomes as they appear in nature is easy. Finding subtle inactivations of the genes on the Y chromosome is much harder. In fact analysis of genomes of intersex people is a common use of consumer whole genome and whole exome sequencing, so any consumer sequencing company that simply reports XX as female and XY as male is laughably amateurish, and your customer support lines will be swamped with extremely knowledgeable self-educated intersex people that will being providing tons of information for the company to up their game.
fastball 5 days ago [-]
> so any consumer sequencing company that simply reports XX as female and XY as male is laughably amateurish
To my knowledge there is no XX person who can produce sperm and there is no XY person who can produce eggs. So while "XX is female" is over-simplified, "XX is not male" seems fairly clear.
TeMPOraL 5 days ago [-]
> your customer support lines will be swamped with extremely knowledgeable self-educated
In no other field this combination (self-educated, actually knowledgeable, and calling customer support) seems to exist, so that alone might be worth further study.
epistasis 4 days ago [-]
They are highly motivated people trying to understand the genetic basis of themselves better, and have usually been seeing doctors throughout their lives towards that end, and usually they'll know more than their doctors because of the rarity of their phenotypes. I have tons of respect for that.
dgfitz 5 days ago [-]
> "It was clear that a human handled it…”
Ah, science.
fortran77 4 days ago [-]
My first thought, after reading the headine, was that the deer bit her.
dgfitz 4 days ago [-]
We have vastly different experiences with deer I suppose.
Cthulhu_ 5 days ago [-]
It's like IT, gotta make sure you have the basics right like whether it's plugged in before you start with more advanced stuff.
jdiff 5 days ago [-]
There actually was human DNA in it so I don't know why we're scoffing as successful methods as if they're unreasonable.
ursuscamp 5 days ago [-]
The article says that it belonged to a species of deer called “wapiti”. Since I never heard of it, I looked it up and it’s just an elk. Why didn’t the article just say “elk” which is the much more common term?
chmod775 5 days ago [-]
Two reasons:
- Elk is ambiguous. There's an Elk/Wapiti in North America, Central Asia, and East Asia, and another species of deer referred to as an "Elk" by people in Eurasia, but which is known as a "Moose" in North America.
- Because journalists these days don't have time to look these kinds of things up. The original paper only refers to it as wapiti/cervus canadensis/deer. If the whoever wrote that article knew it refers to an elk, they'd have pointed that out for the reader.
dan-robertson 5 days ago [-]
Elk is pretty ambiguous — it refers to different species depending on the context (in Europe, ‘elk’ refers to what in north America is called a moose. Wapiti is a name for what ‘elk’ refers to in North America). You get a similar problem with the words ‘hawk’ and ‘buzzard’
jhbadger 4 days ago [-]
And badger -- In Europe they are small adorable members of the Meles genus. In the Americas, Africa, and Asia the word refers to larger and more aggressive animals in the Taxidea and Mellivora genera that just look superficially like Meles.
bregma 4 days ago [-]
The wapiti is the animal on the reverse of the Canadian 25 cent definitive coin. Perhaps the folks who write the article are just educated and worldly.
Rendered at 22:33:41 GMT+0000 (Coordinated Universal Time) with Vercel.
> with estimates of present-day human and faunal contamination both below 1%. Comparisons with present-day human populations²⁶ using ƒ3-statistics and D-statistics²⁷,²⁸ show high affinities to Native Americans (Extended Data Fig. 5). When projected into a principal component analysis with other ancient human individuals (Fig. 3c), DCP1 falls within a group of Ancient North Eurasian individuals from further east in Siberia, which includes the approximately 24 ka Mal’ta 1 and the approximately 17 ka Afontova Gora 3 individuals²⁹,³⁰. Both of these individuals are genetically closer to DCP1 than non-Ancient North Eurasian individuals when tested with D-statistics (Extended Data Fig. 6b), and all three show similar affinities to ancient Siberians and Native Americans with ƒ3-statistics and D-statistics
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.
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.
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)
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.
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...
https://en.wikipedia.org/wiki/Spolia
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.
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.
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.
(though passwords aren't a great application)
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.
- Uh, oh. How am I going to see behind me, then?
[0] https://en.wikipedia.org/wiki/Normal_number#
https://en.wikipedia.org/wiki/Disjunctive_sequence#Rich_numb...
That's a long time to have people live in a particular area generally, and a particular "home" in particular.
AIUI, some of the oldest writing we have dates to Ur III at 2000 BC, so that's 'only' 4000 years ago, or perhaps the Uruk period, which at 3500 BC, is 5500 years old:
* https://en.wikipedia.org/wiki/List_of_oldest_documents
* https://www.sfu.ca/~poitras/jesho_UR_14.pdf
So the oldest document(s) we have are only about 1/10th how long this cave was occupied.
Some of these time scales are mind-boggling.
(Part of me wishes to see this resurface as a bona fide religion, oblivious to the source material.)
(Sorry, I couldn’t resist)
But assuming you are being genuine: your sex (faka gender) is encoded in your DNA on the 23rd chromosomal pair. If you have two X chromosomes (XX), you are a female human (woman). If you have one X and one Y (XY), you are male human (man). These chromosomes dictate your sexual development (organs/hormones/etc). There are some people (estimated at 1-2% of the human population) who are "intersex", in that they don't have an XX or XY pair, but some variation thereof (XXY, XYY, etc). However even these variations generally fall under one or the other umbrella of male or female. e.g. Klinefelter syndrome (XXY) is generally going to present as male (albeit frequently with poorly developed testicles and other complications). Genes are complicated so this is a bit of an oversimplification.
To make this more about sex itself (since humans are a sexually reproducing species and that is why we are having this conversation at all), there are effectively three options for all humans: you produce small gametes (sperm / male) or you produce large gametes (eggs / female), or you produce neither due to some complication and therefore cannot participate in procreation. This is dictated almost wholly by your DNA.
So, back to the article: they know the DNA in the deer tooth was from a woman because (presumably) the 23rd chromosome was an XX pair.
The result is someone who may appear to be female, have female genitals, but has testes where ovaries would be expected. It's often not discovered until puberty doesn't happen as expected, and they discover they can't have children.
Like all these conditions, this is on something of a spectrum depending on how total it is.
As you say, genes are complicated. So much more so than is often implied in reporting of discoveries of "a gene for X".
To my knowledge there is no XX person who can produce sperm and there is no XY person who can produce eggs. So while "XX is female" is over-simplified, "XX is not male" seems fairly clear.
In no other field this combination (self-educated, actually knowledgeable, and calling customer support) seems to exist, so that alone might be worth further study.
Ah, science.
- Elk is ambiguous. There's an Elk/Wapiti in North America, Central Asia, and East Asia, and another species of deer referred to as an "Elk" by people in Eurasia, but which is known as a "Moose" in North America.
- Because journalists these days don't have time to look these kinds of things up. The original paper only refers to it as wapiti/cervus canadensis/deer. If the whoever wrote that article knew it refers to an elk, they'd have pointed that out for the reader.