[HN Gopher] DNA has a 521-year half-life (2012)
___________________________________________________________________
DNA has a 521-year half-life (2012)
Author : marcodiego
Score : 113 points
Date : 2022-02-05 11:56 UTC (11 hours ago)
(HTM) web link (www.nature.com)
(TXT) w3m dump (www.nature.com)
| fbn79 wrote:
| Is not in contrast with the sequencing of 1.6M old mammoth DNA?
| https://www.nature.com/articles/d41586-021-00436-x
| dav_Oz wrote:
| For 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-d...
| [deleted]
| samarama wrote:
| For 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
|
| 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.
| mchusma wrote:
| I like your thinking! A couple of points:
|
| (1) we don't really know the threshold yet to be beyond repair
| I think. It may be 1% but may be 20%.
|
| (2) as others noted, it's 15 years for 0.1% damage using your
| math.
|
| (3) your timeline directly contradicts the article doesn't it,
| which suggests keeping people in ideal conditions would have a
| DNA half life of millions of years.
|
| (4) it's not a given that you need to wake people up to repair
| DNA. Maybe you just need to bring them to 1 degree Celsius or
| something. Or maybe nanobots can work on you while completely
| frozen. I think we are quite far from knowing right now.
|
| So yes, for long term travel DNA repair will be important but
| how it actually works I think we know little about.
| samarama wrote:
| Good points, but why is it 15 years for 0.1%?
| ReaLNero wrote:
| A 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 wrote:
| >>> log(0.99, (1/2)**(1/10000)) 144.99569695122509
| jdmoreira wrote:
| I don't understand this. Does half-life even say anything
| else about the probability distribution? aren't you assuming
| specific distribution here?
| dekhn wrote:
| half 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 wrote:
| It'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 (?).
| cochne wrote:
| Your 15 years number is for 0.1%
| stocknoob wrote:
| This shows the importance of mental gut checks.
|
| If indeed 1% break after 15 years, then 10% (ignoring
| compounding) break after 150 years, and 50% after 750 years.
| That doesn't square with a half life of 10,000.
| ReaLNero wrote:
| I always forget Bernoulli's inequality. Your gut isn't as
| clever as mine :)
| xorencrypted wrote:
| At the speed of travel you would want to traverse space,
| wouldn't the time dilation make the half life of passengers
| less of a problem?
| sandworm101 wrote:
| >> crew would probably be awake at all times for repairs etc
|
| If the ship requires human crews to conduct regular repairs,
| then the ship probably won't last long enough to get where it
| is going. A ship that is going to last for 10,000 years will
| need to be built like an Egyptian pyramid, solid enough to last
| forever and be functional despite millennia of erosion. Putting
| someone on that pyramid to conduct repairs might sound good,
| but after 10,000 years those repairs would become just another
| source of erosion. The activities of that one person would wear
| down any system with which they interact.
| sixQuarks wrote:
| Erosion in space is much different than on earth. Even the
| rovers left on the moon 50 years ago should in theory still
| work.
| flatiron wrote:
| And it's silly to think about. Who cares. 300 years from
| now people will be taking trash out in mars and people will
| be picking it up. We will spread our disease at least
| within out universe.
| sandworm101 wrote:
| Except the batteries on that rover are long dead. Many, if
| not all, of the plastic and paper insulators exposed to
| vacuum are now brittle and broken. All labels or painted
| surfaces are likely bleached white. Differential expansion
| during lunar daylight cycles has likely snapped a few
| things here and there too. Fifty years of exposure to
| static electric charges on the moon has put lunar dust in
| all sorts of places it doesn't belong. Powering up the
| electrical systems would be interesting/scary. Any metal
| parts that have been touching each other, again in vacuum,
| are now contact/cold-welded together. The wheels might
| still turn, but the bearings are likely shot. And that is
| all before any talk of micrometeors.
| mlindner wrote:
| The above poster is talking about physical erosion by human
| interaction. There are ruts worn into solid rock in many
| parts of the world with old roads that are only 1000 or
| 2000 years old. Over 10,000 years anything that is touched
| by humans will be worn away to no material at all.
| samarama wrote:
| In a ship with 20 million parts, 19.9 million can probably be
| automated, but there's simply 100k parts that can't always be
| fixed 100% in advance.
| lettergram wrote:
| Even in a -80C freezer with dehydrated and frozen cells they
| don't recommend over 5 years.
|
| https://www.researchgate.net/post/How-long-can-fresh-frozen-...
| rthomas6 wrote:
| If you go fast enough, accelerating and decelerating at 1 g,
| you can travel a million light years in a perceived time of
| about 27 years.
| IncRnd wrote:
| That's a more difficult problem compared to DNA repair, crew
| rotation, or material erosion.
| mlindner wrote:
| Yes, but you also need nearly infinite fuel.
| rthomas6 wrote:
| Nah, just 3e18 kg ;)
| opportune wrote:
| An efficient engine could use antimatter as its
| battery/fuel source and move itself forward by using
| antimatter to eject propellant close to the speed of light
| in the opposite direction right? That probably wouldn't
| require a large mass of antimatter/propellant. Especially
| since you can collect propellant from the interstellar
| medium wherever you're going
| ben_w wrote:
| Even antimatter has limits, and those limits deny
| reaching a relativistic gamma of 1e6/27:
|
| http://www.projectrho.com/public_html/rocket/enginelist3.
| php
|
| But even if you ignore that limit, at that kind of speed
| you also need to account for your outer hull undergoing
| significant damage as each stray intergalactic hydrogen
| you hit has a kinetic energy of 34.75 TeV in your frame
| of reference, and while this will create a large supply
| of antimatter, it will do so in a way significantly less
| helpful to your goal than the fact we can transmute lead
| into gold by using the former as a radiation shield in a
| nuclear reactor is useful to someone who wants to get
| rich quick.
|
| Bonus fact: this energy level is higher than the LHC, so
| you may have some extra weird mass-modification effects
| besides relativity as the front of your spaceship is now
| a Higgs Boson torch.
| Zenst wrote:
| I'm sure there are ways in which we are still learning and
| right out of the plot of a film that needs no mention:
| https://newatlas.com/science/extract-insect-dna-amber/
| takinola wrote:
| Don't we have highly durable generational spaceships already?
| They're called asteroids. If we find an asteroid that's large
| enough to have internal geothermal activity, you could put a
| bunch of people in an underground system and nudge it into a
| trajectory towards another star system.
|
| As long as it can support crops, oxygen generation, etc the
| passengers just proceed to live a "normal" life for the next
| couple generations until they arrive in orbit around a brand
| new star.
|
| The hardest part would be maintaining culture to still identify
| with the purpose of the mission after there's no one of the
| original passengers left over
| tremon wrote:
| I don't think most asteroids are large or dense enough to
| have adequate geothermal heat to sustain a human population?
|
| Anyone got a back-of-the-envelope calculation for what size
| asteroid we'd need for this?
| Qem wrote:
| https://arc.aiaa.org/doi/10.2514/6.2014-4373
| justinator wrote:
| _Don't we have highly durable generational spaceships
| already? They're called asteroids._
|
| A planet. You're describing a planet. And we're doing a
| pretty terrible job keeping this planet we're traveling on
| sustainable for human habitation.
| takinola wrote:
| Well the one we're on has made it 4 billion years. Getting
| one to last 10,000 years should be a lot easier
| beaconstudios wrote:
| It has only been about 5000 years since humans became
| sedentary and formed civilisations and we're already
| seriously disrupting the ecosystem. That's the timeline
| you'd have to look at.
| smrtinsert wrote:
| Less than a flash in the physical history of this world.
| Crazy!
| awb wrote:
| What about water?
| takinola wrote:
| I do concede a certain amount of hand waving in this
| proposed solution
| brnt wrote:
| How structurally solid are asteroids, comets? I thought they
| were mostly balls of 'snow'.
| blagie wrote:
| .... 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?)...
| handol wrote:
| There 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
| adrian_b wrote:
| That 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 wrote:
| Look 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/7/4/815/57629
| 99?login=f...
| Qem wrote:
| The 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 wrote:
| that would be the worst needle in a haystack problem
| ever.
| adrian_b wrote:
| For 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.
| peter303 wrote:
| Still 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.
| RivieraKid wrote:
| So the chances that Jurassic Park will be feasible in the future
| is zero?
| johnhenry wrote:
| The feasibility of Jurassic Park went out the window millions
| of years ago.
| kingcharles wrote:
| Obligatory "Life finds a way"
|
| https://www.youtube.com/watch?v=oijEsqT2QKQ
| jll29 wrote:
| I 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 wrote:
| Yes 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
|
| 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 wrote:
| Your 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 wrote:
| https://en.wikipedia.org/wiki/Homologous_recombination
| friedturkey wrote:
| How 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-...
| dekhn wrote:
| Bdelloid 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.
| axg11 wrote:
| I 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.
| LinuxBender wrote:
| If 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?
| dekhn wrote:
| you 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.
| bgroat wrote:
| Do we know the half-life of a digital record?
| LinuxBender wrote:
| I 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 wrote:
| As 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 wrote:
| Sorry 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)
| aristophenes wrote:
| I 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.
| credit_guy wrote:
| Oh, 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.
| ChrisLomont wrote:
| Read the page. Half life is precisely defined.
|
| Your claim half-life doesn't apply is incorrect. All atoms
| undergo radioactive decay, so half life applies as precisely to
| all matter as is does to uranium.
| credit_guy wrote:
| > All atoms undergo radioactive decay
|
| Are you sure about that?
| ChrisLomont wrote:
| So far the isotopes called "stable isotopes" are ones with
| unobserved decay, and slowly over time ones that used to be
| called stable are being found to decay (e.g., Bismuth 209).
| Quantum uncertainty (and still theoretical proton decay,
| expected to happen, just not measured well yet) are
| expected to get the rest.
|
| Ultimately quantum tunneling will get them all. There is no
| known mechanism to prevent it.
| kloch wrote:
| I think the term "effectively stable" is what is meant in
| this context.
| baremetal wrote:
| i guess he has never heard of a stable isotope.
| d_tr wrote:
| Stable isotopes decay but at much slower rates. Even
| protons decay.
| addaon wrote:
| While neutrons do decay in the standard model (half life
| on the order of 10 minutes, observed), protons do not
| decay in the standard model, nor has proton decay ever
| been observed -- and folks have looked.
| morelisp wrote:
| Even if it were true that all atoms had a half-life, "DNA" is
| not an atom.
| ChrisLomont wrote:
| Doesn't matter. Half life is used for anything that is
| modeled with exponential decay: energy systems, medicine
| effectiveness, caffeine in a body, oscillations.
|
| So if the essence of a thing breaks down, and the model for
| it is exponential decay, then it has a half life.
|
| Thus DNA has a half life, just as the paper in Nature, one
| of the premier scientific publications in the world,
| demonstrates.
| morelisp wrote:
| Nonetheless, "atomic radioactive decay exists and DNA is
| made of atoms" is _not_ the reason DNA has its half-life,
| as your post claimed.
| noname120 wrote:
| 1. From the article:
|
| > By comparing the specimens' ages and degrees of DNA
| degradation, the researchers calculated that DNA has a half-
| life of 521 years. That means that after 521 years, half of the
| bonds between nucleotides in the backbone of a sample would
| have broken; after another 521 years half of the remaining
| bonds would have gone; and so on.
| yladiz wrote:
| Oh, man, what negativity.
|
| Even if the term "half life" isn't really appropriate here,
| it's clear enough (and explained well enough) in the article.
| This isn't a published scientific paper, this is an article
| likely meant for a more general audience, so, jeez, cut it some
| slack.
| credit_guy wrote:
| Fair enough, I was too negative. I'll leave my comment
| unedited, so people won't get confused about the exchange.
|
| The article itself is ok, and the researchers had good
| intentions. The problem is the idea took a life of its own.
| It almost became a meme. I heard this article many times
| quoted on HN. And the idea itself is definitely wrong, and
| needs to be debunked.
|
| If the 521-year half-life were remotely true, we couldn't
| hope to ever sequence something older than 100 or 1000 half
| lives (i.e. half a million years). Well, we did that just the
| year after (this article was published in 2012, we sequenced
| a 500k year old fossil in 2013) We also sequenced a one
| million year fossil in 2021 [1])
|
| [1] https://www.nature.com/articles/d41586-021-00436-x
| JackFr wrote:
| You should read the article and not comment based on the title
| and your preconceptions. All of your questions are addressed in
| the text of the article.
| jaybrendansmith wrote:
| Agree. 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 wrote:
| Is 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 wrote:
| No. 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.
___________________________________________________________________
(page generated 2022-02-05 23:01 UTC)