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I don't think the genome sequence coverage number can be used to infer anything about how fast DNA decays, or even how much DNA was available to the researchers

I don't think the genome sequence coverage number can be used to infer anything about how fast DNA decays, or even how much DNA was available to the researchers. For example, from wikipedia [1], I found out that the African elephant's genome was sequenced in 2009; the details can be found in [2], where the sequencing coverage is listed at 7x. Why 7x and not 1000x, or more? Most likely there are some limiting factors, such as compute costs, and people are not chasing higher coverage numbers for their own sake. >If you think the half life could be millions of years I don't think the half life could be millions of years. I simply think half life is not a meaningful concept for DNA. Books decay. What's the half-life of books? How many books from a hundred years ago are still around nowadays? Let's be generous and say 0.1%, that's a half-life of about 10 years. That means there should be no books older than 300 years, yet I have seen with my own eyes a Gutenberg bible, printed well before 1500. [1] https://en.wikipedia.org/wiki/List_of_sequenced_animal_genomes#Mammals https://en.wikipedia.org/wiki/List_of_sequenced_animal_genom... [2] http://genome.ucsc.edu/cgi-bin/hgGateway?org=Elephant&db=loxAfr3&hgsid=154866831 http://genome.ucsc.edu/cgi-bin/hgGateway?org=Elephant&db=lox...

perl4ever 6y ago
I don't understand why you insist that a number that has a large uncertainty cannot be meaningfully specified, when you yourself demonstrate putting constraints on it. That is giving it a meaning. There are about 49 Gutenberg bibles known to remain of 158-180 copies, I read. log2(49/169) = -1.8; 570/1.8 = 316 years for half of them to disappear. It's very meaningful to say that a number is between 10 and 1000. It's not 10,000; it's not 100,000, or 1,000,000. There are maybe 10^82 atoms in the universe. That's about 2^272 so saying I am confident the half life of even the best preserved, most cherished books is less than 1000 years means that a 300,000 year old book could not exist. Because even if there were 10^82 of them, not one would be left. If you really insist you cannot quantify it, you're saying there's a chance! Aren't you? With DNA, it's not that I know the half life is 1375 years precisely, or have hardly any biological knowledge, but the little knowledge I have combined with exponential rates of loss constrains it so I can't imagine the upper bound is above 10,000 years. The thing I am trying to express is that even huge uncertainty and almost total ignorance give you far more to work with than "nothing".
- credit_guy 6y ago
  What if the decay does not follow an exponential law? For example a power law? Here's an interesting quote from the wikipedia article on ancient DNA [1] "Researchers in 2016 measured chloroplast DNA in marine sediment cores, and found diatom DNA dating back to 1.4 million years. This DNA had a half-life significantly longer than previous research, of up to 15,000 years. Kirkpatrick's team also found that DNA only decayed along a half-life rate until about 100 thousand years, at which point it followed a slower, power-law decay rate" [1] https://en.wikipedia.org/wiki/Ancient_DNA https://en.wikipedia.org/wiki/Ancient_DNA
  - perl4ever 6y ago
    I mean, you're looking at figure 3 and the description thereof, but that seems to be a relative amount of DNA. I'd consider figure 1 instead. It appears that the half life is about 200,000 years for site U1343. At that rate, you still wouldn't have any dino DNA left even if the whole universe was made of it.

perl4ever 6y ago

I don't understand why you insist that a number that has a large uncertainty cannot be meaningfully specified, when you yourself demonstrate putting constraints on it. That is giving it a meaning. There are about 49 Gutenberg bibles known to remain of 158-180 copies, I read. log2(49/169) = -1.8; 570/1.8 = 316 years for half of them to disappear. It's very meaningful to say that a number is between 10 and 1000. It's not 10,000; it's not 100,000, or 1,000,000. There are maybe 10^82 atoms in the universe. That's about 2^272 so saying I am confident the half life of even the best preserved, most cherished books is less than 1000 years means that a 300,000 year old book could not exist. Because even if there were 10^82 of them, not one would be left. If you really insist you cannot quantify it, you're saying there's a chance! Aren't you? With DNA, it's not that I know the half life is 1375 years precisely, or have hardly any biological knowledge, but the little knowledge I have combined with exponential rates of loss constrains it so I can't imagine the upper bound is above 10,000 years. The thing I am trying to express is that even huge uncertainty and almost total ignorance give you far more to work with than "nothing".

credit_guy 6y ago
What if the decay does not follow an exponential law? For example a power law? Here's an interesting quote from the wikipedia article on ancient DNA [1] "Researchers in 2016 measured chloroplast DNA in marine sediment cores, and found diatom DNA dating back to 1.4 million years. This DNA had a half-life significantly longer than previous research, of up to 15,000 years. Kirkpatrick's team also found that DNA only decayed along a half-life rate until about 100 thousand years, at which point it followed a slower, power-law decay rate" [1] https://en.wikipedia.org/wiki/Ancient_DNA https://en.wikipedia.org/wiki/Ancient_DNA
- perl4ever 6y ago
  I mean, you're looking at figure 3 and the description thereof, but that seems to be a relative amount of DNA. I'd consider figure 1 instead. It appears that the half life is about 200,000 years for site U1343. At that rate, you still wouldn't have any dino DNA left even if the whole universe was made of it.