3 ms·

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 radioi

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)...
  - nemo 6y ago
    When I first said the half-life of DNA is ~521 years at 13.1°C I was careful to include that temperature which made it clear that the decay of any organic material over time has more variables than merely time. Here's the article where that number comes from. https://royalsocietypublishing.org/doi/full/10.1098/rspb.2012.1745 https://royalsocietypublishing.org/doi/full/10.1098/rspb.201... Mammoth DNA preserved in permafrost can last longer. Temperature is a variable. But dinosaurs lived in a very warm time, much warmer than the Ice Age the mammoths lived in so there's no possibility of nature somehow preserving Jurassic fossils in ice/permafrost.
  - perl4ever 6y ago
    Well, what half-life do you think that article implies? I took a shot at the calculation, and I got 1375 years.* That suggests to me that, yes, the popular figure may be off, but what difference does it make when you're talking about dinosaurs? I mean it seems like you are implicitly saying that it's a huge exaggeration to claim 120,000 half-lives since the dinosaurs went extinct whereas it might be as little as 47,000. I don't think you're wrong. But raising 2 to either power overflows my calculator, so I don't see how it matters. *my calculation is very imprecise and ignorant of biology, but I think orders of magnitude are good enough when talking about exponentials. - the sample was 180 mg - the number of cells in that size sample might be 8e10.[1] - they had 17x coverage - log2(17/8e10) is about -32 - 44,000 years / 32 = 1375 [1] I got a number for cells/kg by assuming a human weighs 180 lbs and has the number of cells mentioned in this reference: https://pubmed.ncbi.nlm.nih.gov/23829164/ https://pubmed.ncbi.nlm.nih.gov/23829164/
    - credit_guy 6y ago
      I don't think it works quite like that. A DNA molecule (some people prefer to call it a "strand") has billions of nucleotides (or "DNA letters"). There is one DNA molecule per chromosome, and a few dozens chromosomes in every single cell. For all practical purposes, the same chromosome in various cells has the exact same copy of the DNA molecule. After the organism's death, each DNA molecule will probably break down in a matter of days, at most. From this point of view a half-life of 521 years is an astronomic number, and totally false. After a few years there will be exactly zero intact DNA strands. But that won't make a difference anyway, as we are not able to read a full strand in one read anyway. Instead we read fragments and stitch them together. Like you see a "GATACA" and then a "TACACCG" and hypothesize that they were both parts of the longer string "GATACACCG". The longer the intersection string, the most likely the stitching is correct. In the mammoth case, they had fragments longer than 60 letters. Stitching together all these fragments, they were able to produce the full string (of billions of letters) 17 independent times. That gives them a high level of confidence that what they did is correct. In the case of dinosaurs. Will we ever be able to read fragments of tens of letters and stitch them together? Maybe, maybe not. If the DNA breaks down so much that you won't be able to see even pairs of letters, then we are totally out of luck. If we see pairs of letters, we probably see triplets, quadruplets, etc. Can we stitch together a long string out of quadruplets? Most likely not, but if we have 10-letter strings, probably yes. Are we going to have a contamination problem? If most of the DNA fragments come from bacteria rather than the original dinosaur, will we be doomed? Most likely we'll be able to come up algorithms that will eliminate bacterial DNA genes out of the reconstituted genome. We are quite smart. Is Jurassic Park in the near future. Not before we are able to revive mammoths. And a mammoth is difficult to create for the simple reason that it takes a very long time to gestate a baby elephant. If each iteration in your experiment takes one year, you are in danger of shipwrecking your career. Can we overcome these challenges? You bet. Anytime soon? My guess is that not during my lifetime, at least. But then Bill Gates states that we overestimate what we can do in one week but underestimate what we can do in a decade. So, you never know.
nemo 6y ago
When you're looking at things this old the reality is any DNA found has a very good chance of being from bacteria & other organisms/contamination from the more recent than 100 million years ago past. Even if you come up with a really clever tool to find ancient DNA you have no guarantees of finding dino DNA nor any way to filter out the DNA from all the organisms of the past, virtually all unsequenced, that could be contaminants.
nemo 6y ago
While this thing is being referred to as "mummified" the fossil itself is a result of gradual processes that replaced the original form of the corpse with minerals. It's not dried meat in there. The find was a few years ago, so much has been written on the topic, and you should read what the discussions of experts on the topic had to say. I'm not sure if you read this link before but I encourage you to - it includes a nice summary of the issues. https://www.scientificamerican.com/article/possible-dinosaur-dna-has-been-found/ https://www.scientificamerican.com/article/possible-dinosaur...

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)...
- nemo 6y ago
  When I first said the half-life of DNA is ~521 years at 13.1°C I was careful to include that temperature which made it clear that the decay of any organic material over time has more variables than merely time. Here's the article where that number comes from. https://royalsocietypublishing.org/doi/full/10.1098/rspb.2012.1745 https://royalsocietypublishing.org/doi/full/10.1098/rspb.201... Mammoth DNA preserved in permafrost can last longer. Temperature is a variable. But dinosaurs lived in a very warm time, much warmer than the Ice Age the mammoths lived in so there's no possibility of nature somehow preserving Jurassic fossils in ice/permafrost.
- perl4ever 6y ago
  Well, what half-life do you think that article implies? I took a shot at the calculation, and I got 1375 years.* That suggests to me that, yes, the popular figure may be off, but what difference does it make when you're talking about dinosaurs? I mean it seems like you are implicitly saying that it's a huge exaggeration to claim 120,000 half-lives since the dinosaurs went extinct whereas it might be as little as 47,000. I don't think you're wrong. But raising 2 to either power overflows my calculator, so I don't see how it matters. *my calculation is very imprecise and ignorant of biology, but I think orders of magnitude are good enough when talking about exponentials. - the sample was 180 mg - the number of cells in that size sample might be 8e10.[1] - they had 17x coverage - log2(17/8e10) is about -32 - 44,000 years / 32 = 1375 [1] I got a number for cells/kg by assuming a human weighs 180 lbs and has the number of cells mentioned in this reference: https://pubmed.ncbi.nlm.nih.gov/23829164/ https://pubmed.ncbi.nlm.nih.gov/23829164/
  - credit_guy 6y ago
    I don't think it works quite like that. A DNA molecule (some people prefer to call it a "strand") has billions of nucleotides (or "DNA letters"). There is one DNA molecule per chromosome, and a few dozens chromosomes in every single cell. For all practical purposes, the same chromosome in various cells has the exact same copy of the DNA molecule. After the organism's death, each DNA molecule will probably break down in a matter of days, at most. From this point of view a half-life of 521 years is an astronomic number, and totally false. After a few years there will be exactly zero intact DNA strands. But that won't make a difference anyway, as we are not able to read a full strand in one read anyway. Instead we read fragments and stitch them together. Like you see a "GATACA" and then a "TACACCG" and hypothesize that they were both parts of the longer string "GATACACCG". The longer the intersection string, the most likely the stitching is correct. In the mammoth case, they had fragments longer than 60 letters. Stitching together all these fragments, they were able to produce the full string (of billions of letters) 17 independent times. That gives them a high level of confidence that what they did is correct. In the case of dinosaurs. Will we ever be able to read fragments of tens of letters and stitch them together? Maybe, maybe not. If the DNA breaks down so much that you won't be able to see even pairs of letters, then we are totally out of luck. If we see pairs of letters, we probably see triplets, quadruplets, etc. Can we stitch together a long string out of quadruplets? Most likely not, but if we have 10-letter strings, probably yes. Are we going to have a contamination problem? If most of the DNA fragments come from bacteria rather than the original dinosaur, will we be doomed? Most likely we'll be able to come up algorithms that will eliminate bacterial DNA genes out of the reconstituted genome. We are quite smart. Is Jurassic Park in the near future. Not before we are able to revive mammoths. And a mammoth is difficult to create for the simple reason that it takes a very long time to gestate a baby elephant. If each iteration in your experiment takes one year, you are in danger of shipwrecking your career. Can we overcome these challenges? You bet. Anytime soon? My guess is that not during my lifetime, at least. But then Bill Gates states that we overestimate what we can do in one week but underestimate what we can do in a decade. So, you never know.

nemo 6y ago

When you're looking at things this old the reality is any DNA found has a very good chance of being from bacteria & other organisms/contamination from the more recent than 100 million years ago past. Even if you come up with a really clever tool to find ancient DNA you have no guarantees of finding dino DNA nor any way to filter out the DNA from all the organisms of the past, virtually all unsequenced, that could be contaminants.

nemo 6y ago

While this thing is being referred to as "mummified" the fossil itself is a result of gradual processes that replaced the original form of the corpse with minerals. It's not dried meat in there. The find was a few years ago, so much has been written on the topic, and you should read what the discussions of experts on the topic had to say. I'm not sure if you read this link before but I encourage you to - it includes a nice summary of the issues. https://www.scientificamerican.com/article/possible-dinosaur-dna-has-been-found/ https://www.scientificamerican.com/article/possible-dinosaur...