8 ms·

Obligatory question: DNA?

by Ericson2314 6y ago

ericlewis 6y ago
DNA half-life basically wouldn’t be able to survive this long, no matter how well preserved I believe.
- Ericson2314 6y ago
  That is my understanding too. Also they mention mineral deposits so it seems like this is still at least somewhat a fossil?
- epicureanideal 6y ago
  Even if DNA itself can't, it seems possible that with advanced enough technology there might be hope of recovery of something other than DNA that could be used to figure out what the DNA was. Imagine for example a machine that takes off 1 layer of atoms at a time, painstakingly charting them, and then another layer of software that figures out probabilistically whether the arrangement of atoms means that a decayed strand of DNA was here... and then probabilistically adds together the the billions of decayed shreds of DNA. Maybe the relative positions of the base pairs are still probabilistically informative despite decaying and many of them breaking apart. I don't know. But it seems like there's a plausible way to try to extract data from fossilized DNA.
  - shrimp_emoji 6y ago
    With advanced enough technology, we might train an ML model to generate a genome that morphologically approximates the dinosaur, simulating the trillions of protein foldings and chemical interactions involved in each trial, until we have a genome that produces the dinosaur, physically. Because we have no certain model of the dinosaur, behaviorally, we can guess at that and ML our way to that, too. And boom: you have your ersatz sim dino, and it only took like three Matrioshka brains.
  - nemo 6y ago
    The half-life of DNA is ~521 years at 13.1°C. This dino is more than 100 million years old. Scientists have been working very diligently to try to recover DNA from millions of years ago, but the reality is any DNA found has a very good chance of being from bacteria & other organisms from the more recent past. Still there are (disputed) claims to have found DNA that's millions of years old: https://www.scientificamerican.com/article/possible-dinosaur-dna-has-been-found/ https://www.scientificamerican.com/article/possible-dinosaur...
    - credit_guy 6y ago
      Not clear to me how this meme that the half-life of DNA of about 500 years appeared. There is no concept of half-life for chemicals, there's one only for radioisotopes. For this particular mummified dinosaur, if they found lots of somewhat preserved soft tissue, maybe hundreds of pounds, chances are that there could be trillions of DNA segments. Very likely no single gene will be unbroken, but with many fragments broken in different places the theoretical possibility to reconstitute the genetic code is there. You also don't start from zero knowledge. Humans and birds share about 65% of the genetic code [1], and dinosaurs are closer to birds than humans are. [1] https://education.seattlepi.com/animals-share-human-dna-sequences-6693.html https://education.seattlepi.com/animals-share-human-dna-sequ...
      - rolph 6y ago
        >There is no concept of half-life for chemicals< https://www.sciencedirect.com/topics/medicine-and-dentistry/plasma-half-life https://www.sciencedirect.com/topics/medicine-and-dentistry/... https://en.wikipedia.org/wiki/Biological_half-life https://en.wikipedia.org/wiki/Biological_half-life half life is a general term that is frequently used in biochemistry, enzyme kinetics, chemistry and nuclear physics as a general term it is converse of doubling time and is simply a measure of stability or observed activity https://en.wikipedia.org/wiki/Half-life https://en.wikipedia.org/wiki/Half-life
        credit_guy 6y ago
        Ok, there's a concept of biological half-life, including the famous 5 hours for caffeine. Living bodies are extraordinarily similar though, for example we all have about the same temperature of 36 deg Celsius. Chemicals out in the open, that's a completely different story. To be more specific: [1] is a published article in Current Biology where they state they were able to fully sequence the genome of two mammoths, one of which was 44.8k years old. That would be 86 half-lives according to the meme of 521y half-life for DNA. 2^(-86) is roughly 10^(-26). By the logic of DNA half-life, reconstituting a 44.8k y.o. mammoth genome would be beyond utterly ridiculous. Still, here we are. [1] https://www.cell.com/current-biology/fulltext/S0960-9822(15)00420-0 https://www.cell.com/current-biology/fulltext/S0960-9822(15)...
teraflop 6y ago
Not likely. According to the research I've seen, the half-life of DNA nucleotide bonds in fossilized samples is on the order of a few hundred thousand years. But that's the half-life of each bond, which means sequences of non-trivial length will become fragmented much more quickly. After 110 million years, it seems very unlikely that anything sequenceable still exists, even in trace amounts. https://royalsocietypublishing.org/doi/10.1098/rspb.2012.1745 https://royalsocietypublishing.org/doi/10.1098/rspb.2012.174...
- epicureanideal 6y ago
  But if they're fossilized, those broken bonds would still be roughly in the same locations, right? So not useful for sequencing, but maybe the information can still be recovered by some future not-yet-possible means.
- staticautomatic 6y ago
  Could someone knowledgeable in pchem explain how this works? I'm guessing that half of the substance doesn't deterministically decay after a specific amount of time. I imagine that the decay follows some probability distribution, which should mean some portion of the substance decays much faster or slower, right? Does some of it never decay at all?
  - throwaway_pdp09 6y ago
    See link to previous discussion, posted above https://news.ycombinator.com/item?id=14326913 https://news.ycombinator.com/item?id=14326913 Might help.
- starpilot 6y ago
  DNA doesn't have a "half-life," there's no consistent inverse exponential decay that continues in perpetuity. It's like saying what's the half-life of a steak? Degradation depends on conditions.
jbay808 6y ago
An interesting question might be, assuming this animal has some descendants alive today, has its original gene sequence been better preserved in that heritage than within its own body?

Obligatory question: DNA?

ericlewis 6y ago

DNA half-life basically wouldn’t be able to survive this long, no matter how well preserved I believe.

Ericson2314 6y ago
That is my understanding too. Also they mention mineral deposits so it seems like this is still at least somewhat a fossil?
epicureanideal 6y ago
Even if DNA itself can't, it seems possible that with advanced enough technology there might be hope of recovery of something other than DNA that could be used to figure out what the DNA was. Imagine for example a machine that takes off 1 layer of atoms at a time, painstakingly charting them, and then another layer of software that figures out probabilistically whether the arrangement of atoms means that a decayed strand of DNA was here... and then probabilistically adds together the the billions of decayed shreds of DNA. Maybe the relative positions of the base pairs are still probabilistically informative despite decaying and many of them breaking apart. I don't know. But it seems like there's a plausible way to try to extract data from fossilized DNA.
- shrimp_emoji 6y ago
  With advanced enough technology, we might train an ML model to generate a genome that morphologically approximates the dinosaur, simulating the trillions of protein foldings and chemical interactions involved in each trial, until we have a genome that produces the dinosaur, physically. Because we have no certain model of the dinosaur, behaviorally, we can guess at that and ML our way to that, too. And boom: you have your ersatz sim dino, and it only took like three Matrioshka brains.
- nemo 6y ago
  The half-life of DNA is ~521 years at 13.1°C. This dino is more than 100 million years old. Scientists have been working very diligently to try to recover DNA from millions of years ago, but the reality is any DNA found has a very good chance of being from bacteria & other organisms from the more recent past. Still there are (disputed) claims to have found DNA that's millions of years old: https://www.scientificamerican.com/article/possible-dinosaur-dna-has-been-found/ https://www.scientificamerican.com/article/possible-dinosaur...
  - credit_guy 6y ago
    Not clear to me how this meme that the half-life of DNA of about 500 years appeared. There is no concept of half-life for chemicals, there's one only for radioisotopes. For this particular mummified dinosaur, if they found lots of somewhat preserved soft tissue, maybe hundreds of pounds, chances are that there could be trillions of DNA segments. Very likely no single gene will be unbroken, but with many fragments broken in different places the theoretical possibility to reconstitute the genetic code is there. You also don't start from zero knowledge. Humans and birds share about 65% of the genetic code [1], and dinosaurs are closer to birds than humans are. [1] https://education.seattlepi.com/animals-share-human-dna-sequences-6693.html https://education.seattlepi.com/animals-share-human-dna-sequ...
    - rolph 6y ago
      >There is no concept of half-life for chemicals< https://www.sciencedirect.com/topics/medicine-and-dentistry/plasma-half-life https://www.sciencedirect.com/topics/medicine-and-dentistry/... https://en.wikipedia.org/wiki/Biological_half-life https://en.wikipedia.org/wiki/Biological_half-life half life is a general term that is frequently used in biochemistry, enzyme kinetics, chemistry and nuclear physics as a general term it is converse of doubling time and is simply a measure of stability or observed activity https://en.wikipedia.org/wiki/Half-life https://en.wikipedia.org/wiki/Half-life
      - credit_guy 6y ago
        Ok, there's a concept of biological half-life, including the famous 5 hours for caffeine. Living bodies are extraordinarily similar though, for example we all have about the same temperature of 36 deg Celsius. Chemicals out in the open, that's a completely different story. To be more specific: [1] is a published article in Current Biology where they state they were able to fully sequence the genome of two mammoths, one of which was 44.8k years old. That would be 86 half-lives according to the meme of 521y half-life for DNA. 2^(-86) is roughly 10^(-26). By the logic of DNA half-life, reconstituting a 44.8k y.o. mammoth genome would be beyond utterly ridiculous. Still, here we are. [1] https://www.cell.com/current-biology/fulltext/S0960-9822(15)00420-0 https://www.cell.com/current-biology/fulltext/S0960-9822(15)...

teraflop 6y ago

Not likely. According to the research I've seen, the half-life of DNA nucleotide bonds in fossilized samples is on the order of a few hundred thousand years. But that's the half-life of each bond, which means sequences of non-trivial length will become fragmented much more quickly. After 110 million years, it seems very unlikely that anything sequenceable still exists, even in trace amounts. https://royalsocietypublishing.org/doi/10.1098/rspb.2012.1745 https://royalsocietypublishing.org/doi/10.1098/rspb.2012.174...

epicureanideal 6y ago
But if they're fossilized, those broken bonds would still be roughly in the same locations, right? So not useful for sequencing, but maybe the information can still be recovered by some future not-yet-possible means.
staticautomatic 6y ago
Could someone knowledgeable in pchem explain how this works? I'm guessing that half of the substance doesn't deterministically decay after a specific amount of time. I imagine that the decay follows some probability distribution, which should mean some portion of the substance decays much faster or slower, right? Does some of it never decay at all?
- throwaway_pdp09 6y ago
  See link to previous discussion, posted above https://news.ycombinator.com/item?id=14326913 https://news.ycombinator.com/item?id=14326913 Might help.
starpilot 6y ago
DNA doesn't have a "half-life," there's no consistent inverse exponential decay that continues in perpetuity. It's like saying what's the half-life of a steak? Degradation depends on conditions.

jbay808 6y ago

An interesting question might be, assuming this animal has some descendants alive today, has its original gene sequence been better preserved in that heritage than within its own body?