10 ms·
DNA has a 521-year half-life (2012)
- deleted 5y ago[deleted]
- handol 5y agoThere has been some evidence that DNA can be preserved far longer than the half-life would suggest. https://academic.oup.com/nsr/article/7/4/815/5762999 https://academic.oup.com/nsr/article/7/4/815/5762999
- adrian_b 5y agoThat half-life is obviously applicable only at a given temperature and at a given humidity, because water or similar substances are required to hydrolize, i.e. break, the bonds between nucleotides. If the DNA molecule is immobilized in a solid, either by freezing or by extreme drying, the half-life will be much longer. That half-life was for bird bones preserved at 13.1 Celsius degrees. Even in this paper it was mentioned that at minus 5 Celsius degrees some information from the DNA should remain even after 1 million years. Unfortunately, there are very few, if any, places on Earth where ancient DNA would have the chance to be preserved for a long time either by freezing or by extreme drying.
- Robotbeat 5y agoLook at the link! Claim of possible DNA from a dinosaur. It’s a bold claim (although carefully caveated) but doesn’t seem crackpot to me, especially considering there are other surviving macromolecules like proteins in soft tissue from dinosaurs. https://academic.oup.com/nsr/article/7/4/815/5762999?login=false https://academic.oup.com/nsr/article/7/4/815/5762999?login=f...
- adrian_b 5y agoFor now the claim is for possible DNA fragments from the cartilage of a dinosaur, with a length of at least 6 nucleotides, but there is no evidence yet that the fragments are long enough to have preserved any useful information. It is likely that fragments with a length of at least a few hundred nucleotides would be needed. The paper that started this thread was not about the decomposition of the individual nucleotides, which might be preserved even from dinosaurs, but about the speed of the fragmentation of the DNA molecule, which causes a continuous loss of information until the fragments are so short that no useful information remains. I certainly hope that we will find cases of extremely lucky preservation of long DNA fragments that are more ancient than what was found until today. Until now, the oldest DNA that was preserved well enough to allow sequencing of significant parts of it had an age of up to a few tens of thousands of years, e.g. from mammoths, woolly rhinoceroses, cave bears, cave lions, Neanderthal humans etc.
- Qem 5y agoThe impact that killed the dinosaurs surely ejected some rocks into space. I wonder, what are the odds there's still some space rock floating around the solar system today, holding some ancient DNA, preserved by the cold of space. Perhaps even in nearby Moon or Mars surface?
- dekhn 5y agothat would be the worst needle in a haystack problem ever.
- credit_guy 5y agoOh, man, what non-sense. 1. A DNA molecule is billions of pairs long. What does half-life measure? When does a DNA molecule count as destroyed? When one pair breaks, when 10% of the pairs break, when 99.9% of them break? 2. Even if pairs break, so what? When we sequence DNA from various organisms, we start by breaking the strands in small pieces anyway. 3. Even if this half-life had any meaning, it would not be a constant number. Half-life is a constant number for radioactive decay. For other things, it's just a somewhat helpful concept. How long do onions keep until they spoil? Maybe they have a half-life of one week. But, the storage conditions make a huge difference. If you put a lot of onions in a plastic bag, and leave them in a hot, humid and unventilated place, they'll spoil much faster than if you keep them well separated, in a dry and cool place. The same with DNA. In fact DNA's half life is probably days, not hundreds of years. In exceptional conditions, some animal or human remains get exposed to some conditions that make them "fossilize". So, if the 521 year half-life has any meaning, it's a conditional expectation given some exceptional situations. But then some situations are more exceptional than others. The 521 years (ha, just think of it, not 500, but 521! ) is already millions of times longer than the normal decay time of animal tissues. What is to say there are no more exceptional conditions under which the DNA half-life won't be 5 million years? 4. And even if 521 was an exact number, for every type of animal tissue, for all places in the world, that still does not mean we can't reconstitute the DNA's of the dinosaurs. Dinosaurs had both ancestors and successors. The successors are the birds, the ancestors lead to crocodiles, and maybe other animals as well. They have common ancestors with lots of other animals, or more precisely, with all animals. DNA is information. Information propagates. Science comes up all the times with better and better methods to retrieve information. Just look at how your iPhone is able to take a picture at night now, versus 10 years ago. Sure, part of that quality leap is the sensor, but a huge part is the Machine Learning algorithms used for denoising. In other words, for information retrieval.
- jaybrendansmith 5y agoAgree. It's unclear from the article that information cannot still be reliably obtained from the sample. Sure the bonds break, but since the construction of nucleotide bases are well understood, does that mean these cannot be distinguished in the sample?
- xbar 5y agoIs it reasonable to conclude that no animal that has gone extinct in the last millennium should be unsequencible, given a modest amount of genetic material?
- dekhn 5y agoNo. Mammoth DNA has been sequenced (15K years old). Perfect conditions for preserving tissue, small fragments can be extracted. Since all cells have the same DNA, fragments that are long enough and have low enough base error rates can be aligned to reconstruct longer fragments (really the same thing as regular shotgun genome assembly). I would expect if you could find ancient (1Mya) tardigrades preserved as tuns, they could probably be extracted and sequenced.
- friedturkey 5y agoHow does DNA half-life factor into cells and seeds that last thousands of years and are still viable? [1] I assume seed cells probably aren’t dividing, but I guess maybe they could be using energy and slowly reproducing? And apparently bacterial spores can basically freeze themselves in time for thousands of years and wake themselves up once conditions are favorable. [1] https://www.newscientist.com/article/dn14125-jesus-era-seed-is-the-oldest-to-germinate/amp/ https://www.newscientist.com/article/dn14125-jesus-era-seed-...
- axg11 5y agoI believe here they’re referring to the half-life of free DNA. In cells (plant or human) the DNA will be bound by a range of different proteins, wrapped up and packaged (e.g histones, but there are many other types too). Presumably the half-life of these proteins is shorter than free DNA but their presence will still change the overall half-life. Environmental conditions are another factor. The inside of a seed could have a more controlled pH, temperature, humidity when compared to the surrounding environment. That would also change the effective half-life.
- dekhn 5y agoBdelloid rotifers over 20K years old have been revived and propagated, and these are actual animals, so we know that in the case of creatures capable of cryptobiosis, there's enough high quality DNA after 20K to sustain life. To reach cryptobiosis involves packing the interior of cells with materials and reducing metabolism tremendously (I suspect there is still some tiny residual activity, barely measureable), and probably also some repair enzymes for the inevitable strand breaks.
- dav_Oz 5y agoFor clarification: Half-life of atoms as in "radioactive decay" (weak, strong and EM force) cannot really be modified by perservations methods. Here [0] a precise answer. The decay-time of bio-molecular strucutres/bonds (containing information like DNA) can be modified in many ways very easily: low temperatures, exclusion of oxygen (amber) ... I guess "half-life" of DNA is just some fast and crude laboratory proxy for chemical "stability" in a specific setting. [0] https://www.wtamu.edu/~cbaird/sq/mobile/2015/04/27/can-the-decay-half-life-of-a-radioactive-material-be-changed/ https://www.wtamu.edu/~cbaird/sq/mobile/2015/04/27/can-the-d...
- samarama 5y agoFor those wondering about interstellar travel in sleeping pods, at room temperature humans could only be “frozen” for 10 years (1% bonds broken) before too much DNA damage would have occurred. However, in temperature below zero at -5 degrees Celsius for example, half life of DNA is actually 10,000 years or more. https://en.m.wikipedia.org/wiki/Ancient_DNA https://en.m.wikipedia.org/wiki/Ancient_DNA Still, this would also only allow 200 years of freezing before more than 1% of bonds would have been broken. The third and probably most viable option is to wake up the crew every 200 years to repair accumulated DNA damage. Also, a small percentage of the crew would probably be awake at all times for repairs etc., so the crew could rotate every 200 years.
- ReaLNero 5y agoA half-life of 10,000 years means the fraction (0 to 1) of healthy bonds at year t can be modeled by (1/2)^(t/10000). To have 1% bonds broken, it would take an expected 145 years. EDIT: Fixed the numbers, my bad!
- vient 5y ago>>> log(0.99, (1/2)**(1/10000)) 144.99569695122509
- jdmoreira 5y agoI don't understand this. Does half-life even say anything else about the probability distribution? aren't you assuming specific distribution here?
- dekhn 5y agohalf lives (specifically, the "decay" of any individual thing is stochastic but the aggregate of many molecules models exponential decay (in radioactivity. I have no idea what happens in a complex mash of DNA)
- sannee 5y agoIt's not a terrible assumption to make. We just need to assume[1] that the decay events are independent, that is, every bond flips a coin every 500 years and if it comes up heads, it breaks, independent of what the other bonds do. That is, the process is inherently "local", individual bonds having no way of knowing what the other bonds are doing. [1] It may be a bit worse in the long run, since if many bonds break, the higher order DNA structure gets damaged and that may change the rate of decay experienced by individual bonds (?).
- RivieraKid 5y agoSo the chances that Jurassic Park will be feasible in the future is zero?
- johnhenry 5y agoThe feasibility of Jurassic Park went out the window millions of years ago.
- kingcharles 5y agoObligatory "Life finds a way" https://www.youtube.com/watch?v=oijEsqT2QKQ https://www.youtube.com/watch?v=oijEsqT2QKQ
- jll29 5y agoI wonder if you could re-assemble the broken (due to decayed bonds) strands to the most likely sequence, given DNA sequence statistics similar to n-gram language models for human language (= languages with an alphabet of more than 4 letters).
- bognition 5y agoYes you can, this is how most genomes are sequenced these days. You break the DNA up into a lot of smaller segments that are sequenced in parallel, you then combine them into the larger unified sequence. https://www.genome.gov/genetics-glossary/Shotgun-Sequencing https://www.genome.gov/genetics-glossary/Shotgun-Sequencing You cannot unfortunately do this for dinosaur DNA. The longest human chromosome has 250M basepairs. With a half life of ~500 years it only takes about 14K years for the chromosome to break down into individual nucleotides. 2^(14000/500) is roughly 170M
- tgb 5y agoYour body does this itself. You have two copies of every chromosome and they’re practical identical. A break in one will be repaired by using the other chromosome. Similarly, even a base change in one strand of one chromosome will be repaired based off the other strand (with a chance that the wrong strand is chosen tho). DNA repair mechanisms like these are exploited by CRISPR and other gene modification strategies: break the part you want to change and then trick the repair mechanism into making the modification you want by providing it with an appropriate template to work off. (Not all CRISPR based techniques use this.)
- dekhn 5y agohttps://en.wikipedia.org/wiki/Homologous_recombination https://en.wikipedia.org/wiki/Homologous_recombination
- LinuxBender 5y agoIf ones goal was to preserve DNA, might it be more feasible to build a digital representation of the DNA and create multiple copies with parity data stored in multiple mediums and distributed to reduce risk of physical damage? Could the DNA be regenerated from the digital data? If not now, in the future perhaps?
- bgroat 5y agoDo we know the half-life of a digital record?
- LinuxBender 5y agoI suspect that depends on the chosen stored medium. I am assuming perhaps incorrectly that we could find a medium more durable than genetic material with known degeneration rates. The first thing that comes to mind is the fictional society from the planet Krypton. They stored data in crystals, likely artificially created diamond material. I suspect we could do this today without consideration for cost.
- nexuist 5y agoAs far as I'm aware stone doesn't erode in space, so we could always just laser in bumps on a stone and read it like a CD. The primary concern then becomes avoiding getting hit by micro debris.
- bgroat 5y agoSorry if my parent comment came of antagonistic. I was really just asking. Either way there must be advantages in multiple backups: - DNA - Digital sequence - Crystals - Stone etching Even with different decay rates they won't all decay in the same way. We can diff multiple records and reproduce a probable original. (I think - I'm not expert in digital storage or the mechanics of DNA)
- dekhn 5y agoyou could absolutely make enormous numbers of stone tablets with tiny lithography marks to encode information. Combined with replication and a redundancy code, you could store enormous amounts of information for enormous amounts of time. But it seems better to just make a dark dry cold repository and store DNA in a matrix that lasts for a long time.
- aristophenes 5y agoI love how the article says that ground water and microbes are responsible for most of the degradation, then blithely quote the computational evolutionary biologist “This confirms the widely held suspicion that claims of DNA from dinosaurs and ancient insects trapped in amber are incorrect" though things trapped in amber are protected from exterior microbes, groundwater, and even oxygen. If they did the study on things trapped in amber they could have come to that conclusion, but they didn’t. Scientists are people and have the same flaws as the rest of us.
- blagie 5y ago.... I don't buy the conclusion. Science progresses. What's possible in the future can't be predicted today. Let's start with what we can do in 2022 which we couldn't imagine in 1922. * Of course, we can sequence DNA now (and we know it exists). * We can also trace back sequences of DNA by when they were created (from splits in evolutionary trees) and extrapolate portions of old DNA of organisms long gone. * We can probably use machine learning to predict portions of DNA. Now, let's imagine 2122. * Will we be able to make inferences from partially-degraded DNA? Perhaps. * Will we be able to make inferences from the structure about the organism about the corresponding DNA? Perhaps. * Will our ability to combine inferences grow? Perhaps. Overall, one thing I've learned is to not predict what's /im/possible. Eventually, engineering finds a way to do some truly counter-intuitive things (and conversely, can't solve problems we'd think would be solved by now; where's my rocket car?)...
- fbn79 5y agoIs not in contrast with the sequencing of 1.6M old mammoth DNA? https://www.nature.com/articles/d41586-021-00436-x https://www.nature.com/articles/d41586-021-00436-x
- peter303 5y agoStill DNA may be superior to retaining written human records on just about every other media, save stone and metal. Especially longer than recent magnetic media.
- simonblack 5y agoI wonder how long any DNA sealed in plant gum/amber would last.
- WalterBright 5y agoThe only way we can travel to the stars is as information. Unfortunately, that requires a receiver at the other end.