6 ms·

Life will find a way

by powmedia 9y ago

HankB99 9y ago
I wonder if we can get some DNA from it.
- notlob 9y ago
  > I wonder if we can get some DNA from it. From the article: “McKellar said that soft tissue and decayed blood from the tail were found in the amber but no genetic material was preserved.”
- delecti 9y ago
  The half life of DNA is roughly 521 years [1]. The sample was 99 million years old, so you could expect roughly 3.33347 × 10^-57200 [2] percent of the DNA to be left. And considering humans have about 7 billion base pairs [3], you could reasonably expect no real recoverable information to remain. [1] http://rspb.royalsocietypublishing.org/content/early/2012/10/05/rspb.2012.1745 http://rspb.royalsocietypublishing.org/content/early/2012/10... [2] https://www.wolframalpha.com/input/?i=0.5%5E(99+million+%2F+521) https://www.wolframalpha.com/input/?i=0.5%5E(99+million+%2F+... [3] https://en.wikipedia.org/wiki/Human_genome https://en.wikipedia.org/wiki/Human_genome
  - throwaway613834 9y ago
    In what sense does DNA have a half-life? It can't be radioactivity so is it seems to be just about molecular disintegration? Which is weird because why should a stable structure have a half-life?
    - anamexis 9y ago
      The introduction of the first citation explains it a little bit: > DNA has limited chemical stability and decays without the enzymatic repair mechanisms of living cells [18]. Following cell death, nucleases start to cleave the DNA into fragments [19] and during decomposition, the DNA is digested by micro-organisms [18,20]. In determining long-term DNA decay, it is believed that hydrolysis of amino groups accelerates the loss of purine residues (depurination), resulting in strand cleavage [21,22]. This random DNA fragmentation generates a characteristic negative exponential correlation between DNA fragment length and number of molecules (figure 1a) [23,24,26,27].
      - throwaway613834 9y ago
        Thanks! I even clicked on the link and read every sentence that had "half" in it but didn't see anything... didn't expect it to be somewhere else in the introduction haha.
        delecti 9y ago
        As a general rule, it's safe to assume every word in the abstract of a paper is significant.
        throwaway613834 9y ago
        > As a general rule, it's safe to assume every word in the abstract of a paper is significant. ...what? The sentence quote above was from the introduction, not the abstract. Nothing in the abstract answered my question of why a stable structure like that of DNA should undergo disintegration. (Did you read the abstract yourself?)
      - garmaine 9y ago
        To be fair, many of those processes are things that I would presume halt at some point in an isolated chemical environment. Also, what kind of breakdown? If segments up to a certain sizer were stable, that would be enough to reconstruct a full genome of the sequencers were sensitive enough and the final segments long enough.
    - skadamou 9y ago
      This link might help answer your questions. Also, half-life in this context is just referring to how long it takes the number phosphodiesterase linkages (bonds holding the DNA backbone together) to decrease by 1/2. Half-life can refer to other types of decay as well :-) https://www.nature.com/news/dna-has-a-521-year-half-life-1.11555 https://www.nature.com/news/dna-has-a-521-year-half-life-1.1...
    - jacquesm 9y ago
      DNA has a half life, but the real question here is how being trapped in amber would affect that half life. So there may be more - or less - than one would expect if the DNA would be in some other environment. At a guess the time span involved is long enough that no matter how this would be influenced there still would not be any usable DNA fragments.
      - yread 9y ago
        Another question is what sort of artifacts would sequencing material in amber produce. Considering the quality of data from formaldehyde fixed paraffin embedded (FFPE) samples I think it would be quite a struggle
    - crooked-v 9y ago
      Everything has a half-life. Even plain old protons have a theoretical half-life of of 10^31 to 10^36 years. https://en.wikipedia.org/wiki/Proton_decay https://en.wikipedia.org/wiki/Proton_decay
      - whatshisface 9y ago
        Proton decay is not a feature of the standard model, it comes from other theories with far less experimental evidence behind them; by no means at this point can we say that protons "have" a half-life.
    - barrkel 9y ago
      All exponential decay processes have half-lifes - or rather, half-life is a metric that describes the scale of an exponential decay rate. https://en.wikipedia.org/wiki/Exponential_decay https://en.wikipedia.org/wiki/Exponential_decay
  - BurningFrog 9y ago
    Even so... the broken fragments would lie next to each other, and with some future technology it's not unthinkable that they could be reconstructed. Or is there something fundamental I'm not aware of?
    - yjftsjthsd-h 9y ago
      It really depends; entropy is a harsh mistress. The output of a paper shredder can theoretically be reformed into the source paper, but below a certain size fragment there's not enough information left to recover.
- anilakar 9y ago
  If that's the case, you better start learning to use those UNIX systems soon.

Life will find a way

HankB99 9y ago

I wonder if we can get some DNA from it.

notlob 9y ago
> I wonder if we can get some DNA from it. From the article: “McKellar said that soft tissue and decayed blood from the tail were found in the amber but no genetic material was preserved.”
delecti 9y ago
The half life of DNA is roughly 521 years [1]. The sample was 99 million years old, so you could expect roughly 3.33347 × 10^-57200 [2] percent of the DNA to be left. And considering humans have about 7 billion base pairs [3], you could reasonably expect no real recoverable information to remain. [1] http://rspb.royalsocietypublishing.org/content/early/2012/10/05/rspb.2012.1745 http://rspb.royalsocietypublishing.org/content/early/2012/10... [2] https://www.wolframalpha.com/input/?i=0.5%5E(99+million+%2F+521) https://www.wolframalpha.com/input/?i=0.5%5E(99+million+%2F+... [3] https://en.wikipedia.org/wiki/Human_genome https://en.wikipedia.org/wiki/Human_genome
- throwaway613834 9y ago
  In what sense does DNA have a half-life? It can't be radioactivity so is it seems to be just about molecular disintegration? Which is weird because why should a stable structure have a half-life?
  - anamexis 9y ago
    The introduction of the first citation explains it a little bit: > DNA has limited chemical stability and decays without the enzymatic repair mechanisms of living cells [18]. Following cell death, nucleases start to cleave the DNA into fragments [19] and during decomposition, the DNA is digested by micro-organisms [18,20]. In determining long-term DNA decay, it is believed that hydrolysis of amino groups accelerates the loss of purine residues (depurination), resulting in strand cleavage [21,22]. This random DNA fragmentation generates a characteristic negative exponential correlation between DNA fragment length and number of molecules (figure 1a) [23,24,26,27].
    - throwaway613834 9y ago
      Thanks! I even clicked on the link and read every sentence that had "half" in it but didn't see anything... didn't expect it to be somewhere else in the introduction haha.
      - delecti 9y ago
        As a general rule, it's safe to assume every word in the abstract of a paper is significant.
        throwaway613834 9y ago
        > As a general rule, it's safe to assume every word in the abstract of a paper is significant. ...what? The sentence quote above was from the introduction, not the abstract. Nothing in the abstract answered my question of why a stable structure like that of DNA should undergo disintegration. (Did you read the abstract yourself?)
    - garmaine 9y ago
      To be fair, many of those processes are things that I would presume halt at some point in an isolated chemical environment. Also, what kind of breakdown? If segments up to a certain sizer were stable, that would be enough to reconstruct a full genome of the sequencers were sensitive enough and the final segments long enough.
  - skadamou 9y ago
    This link might help answer your questions. Also, half-life in this context is just referring to how long it takes the number phosphodiesterase linkages (bonds holding the DNA backbone together) to decrease by 1/2. Half-life can refer to other types of decay as well :-) https://www.nature.com/news/dna-has-a-521-year-half-life-1.11555 https://www.nature.com/news/dna-has-a-521-year-half-life-1.1...
  - jacquesm 9y ago
    DNA has a half life, but the real question here is how being trapped in amber would affect that half life. So there may be more - or less - than one would expect if the DNA would be in some other environment. At a guess the time span involved is long enough that no matter how this would be influenced there still would not be any usable DNA fragments.
    - yread 9y ago
      Another question is what sort of artifacts would sequencing material in amber produce. Considering the quality of data from formaldehyde fixed paraffin embedded (FFPE) samples I think it would be quite a struggle
  - crooked-v 9y ago
    Everything has a half-life. Even plain old protons have a theoretical half-life of of 10^31 to 10^36 years. https://en.wikipedia.org/wiki/Proton_decay https://en.wikipedia.org/wiki/Proton_decay
    - whatshisface 9y ago
      Proton decay is not a feature of the standard model, it comes from other theories with far less experimental evidence behind them; by no means at this point can we say that protons "have" a half-life.
  - barrkel 9y ago
    All exponential decay processes have half-lifes - or rather, half-life is a metric that describes the scale of an exponential decay rate. https://en.wikipedia.org/wiki/Exponential_decay https://en.wikipedia.org/wiki/Exponential_decay
- BurningFrog 9y ago
  Even so... the broken fragments would lie next to each other, and with some future technology it's not unthinkable that they could be reconstructed. Or is there something fundamental I'm not aware of?
  - yjftsjthsd-h 9y ago
    It really depends; entropy is a harsh mistress. The output of a paper shredder can theoretically be reformed into the source paper, but below a certain size fragment there's not enough information left to recover.
anilakar 9y ago
If that's the case, you better start learning to use those UNIX systems soon.