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Plan To Build a Genetic Noah's Ark Includes a Staggering 66,000 Species (gizmodo.com)
An anonymous reader quotes a report from Gizmodo: An international consortium involving over 50 institutions has announced an ambitious project to assemble high-quality genome sequences of all 66,000 vertebrate species on Earth, including all mammals, birds, reptiles, amphibians, and fish. With an estimated total cost of $600 million dollars, it's a project of biblical proportions. It's called the Vertebrate Genomes Project (VGP), and it's being organized by a consortium called Genome 10K, or G10K. As its name implies, this group had initially planned to sequence the genomes of at least 10,000 vertebrate species, but now, owing to tremendous advances and cost reductions in gene sequencing technologies, G10K has decided to up the ante, aiming to sequence both a male and female individual from each of the approximately 66,000 vertebrate species on Earth. Cofounders of the project announced the new goal yesterday at a press briefing held during the opening session of the 2018 Genome 10K conference, currently being held at Rockefeller University in New York City. The project will involve over 150 experts from 50 institutions in 12 countries.
I think this is an excellent idea and my first reaction was, "Only 66000 species?" But because of the limited scope of the project that makes sense. However, in order for a project like this to really be useful in a worst-case scenario, all these vertebrates will need some company. Hopefully the other arc-style projects can supply that.
but there's no female in his species. He's like a Moclan, only without the charm.
Maybe they were thinking of the early Hollywood biblical film epics. They cost a lot of money, at the time.
Anyway, to get back to the cynicism, what's the bet this company decides they own those genetic sequences once they've sorted them out?
That way you could create a better model.
I guess once you've sequenced them all, you could beam the info to space, you know, just in case...
if I didn't have google.
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That's actually peanuts, not considering the complexity but seems a right step in a good direction.
Supernatural climate change and divine wisdom leads to antediluvian inbreeding depression. God damn it!
Corruption is convincing someone that the selfless ideal is the same as their selfish ideal.
I hope that when they sequence all these critters they take the time for quality documentation! Would be very annoying for future generations/aliens if they manage to create the first example, only to find out they don't have any food!
Are they trying to get the backing of religious groups? Why the hell would they name it that? Why not DNA Vault or something like the 'Global Seed Vault'
I note that whilst the article has plenty about the challenge of sequencing that many DNA sequences at high quality and low cost, there is no mention of the sheer logistical complexity of getting samples from 66,000 different species some of which are presumably very rare.
No doubt quite a lot can be achieved by contacting a great number of zoos around the world, but it seems to me that there must be a great many species not held in collections. One rarely sees bats in zoos for example and I understand that there are about 1000 species of those. There must be many bird species known only through observation and I dread to think about all the fish species, particularly from the deep sea, which only occasionally get caught.
It might be interesting to know if they can collect DNA from stuffed specimens or those preserved in spirit.
This is by some margin the grossest poem ever written.
We used to have a Bill of Rights. Now, with the rights gone, all we have left is the bill.
Well, technically it is a genetic noah's arc. It has about as many animals as that ship in the old story could hold, it has one male and one female on board without any reasonable explanation how this could possibly not mean death by genetic defect within a handful of generations and it is about as useful for us out here in the real world.
I think the naming is pretty apt.
We used to have a Bill of Rights. Now, with the rights gone, all we have left is the bill.
Considering the number of species, that 66,000 is a drop in the bucket of animal DNA.
I don't consider that as any kind of definition for "staggering" if you are actually trying to do any kind of ark.
The Svalbard Global Seed Vault currently has about 968,000 samples, and can hold up to about 4,500,000, and theirs aren't genetic profiles, it's actual packets of seeds.
As to the VPA, will those "high definition genetic profiles" have enough data to replicate the DNA? Why don't they have tissue samples?
Yes, sure, this is going to be helpful for biologists and others, if the data is accessible, but will it do anything to help SAVE the animals, which is something pretty much considered the prime directive of any kind of ARK
The consortium is spearheaded by InGen.
They're sequencing vertebrate species - add that word and the first Google results say there's only 40,000 instead of the 8.7 million total estimate.
--- Most topics have many sides worth arguing, allow me to take one opposite you.
There is no "death by genetic defect" if the original pair is healthy. Inbreeding doesn't cause genetic problems, it just amplifies existing ones. If the original pair is free of recessive problems as well, then ALL of their descendants will be genetically healthy until such time as new problematic mutations are developed. If they do have problematic recessives then some of their descendants will have problems - fortunately in the wild those are usually the first to be eaten, so the gene-pool has a fair chance of staying reasonably healthy. And with luck (or careful breeding) even the recessives can be largely removed from the population.
You'll still have an astounding lack of genetic diversity (such as seen in cheetahs) , which will make the species extremely fragile in the face of infectious diseases or environmental changes, but you won't necessarily have any genetic problems.
Inbreeding is primarily a problem when you have an artificially protected population, a.k.a. people or pets, where the problematic individuals aren't killed early on. Even then there's plenty of heavily inbred human populations with no serious problems, it all comes down to the genetic health of the founders.
--- Most topics have many sides worth arguing, allow me to take one opposite you.
I believe we may have a Vogon in our midst.
They do it with viruses (easy, since their parasitic nature means you just have to inject their DNA into a susceptible cell for it to suborn to produce the whole virus). They've also done it with some bacteria as well. And yeast. A bit of a step from there to mammals, but a lot of the fundamental techniques are already being developed. Heck, you can mail-order real DNA synthesized to match whatever digital sequence you provide.
Meanwhile, we've been doing nucleus transfers and cloning for decades. Not with astounding success rates, but well enough to know it's feasible and be confident we'll be able to do better in the future. I'm not so sure about replacing just the DNA in the nucleus though - that's likely its own special challenge - though perhaps we could sidestep it a bit by suborning a compatible cell about to undergo mitosis (though that might not be any easier)
Point is, we've already proven it can be done, and some groups are already working on the project to restore already-extinct species - or at least a close approximation of them. A Mammoth cloned using an elephant ovum and host-mother won't be completely a mammoth, it'll have elephant mitochondria at the least, but it'll probably be close enough for ecological purposes.
That won't help us if we manage to completely wipe out most vertebrate life, but so long as we've got one female elephant left that would let us bring back the full complement of elephant species.
--- Most topics have many sides worth arguing, allow me to take one opposite you.
As long as they're healthy the defects are recessive, "good" DNA is present, and some of the offspring will be healthy - several generations of aggressive culling will get you a healthy species, especially if you use genetic screening to advise the culling selection. And of course, if we're bringing a species back from digital DNA records then correcting such defects will be trivial (at least on the second try, once we know what the problems are).
The species will still lack genetic diversity, and be correspondingly vulnerable to disease and environmental change, but it will be genetically healthy, and if it survives long enough will gradually develop new diversity over millions of years via mutation and possibly crossbreeding (either or both of which could be artificially accelerated dramatically)
--- Most topics have many sides worth arguing, allow me to take one opposite you.
Nah, not that bad. It was kinda cool in a dark humor way.
Look back up at my post, now look back down, you're on the Internet. Now look back up. I'm a signature.
Good grief Bobbi Buzkill, next you're going to try to tell us "Library of Congress" is a unit of distance, not time.
the preceding comment is my own and in no way reflects the opinion of the Joint Chiefs of Staff
Pretty precise - there's only about 0.1% DNA difference within the entire human species, Chimpanzees are about 1.2% different than us. Google says our cells own transcription mechanism has an error rate of about one in 10^10 base pairs (a.k.a. the mutation rate), so that gives an upper limit on how accurate any synthesis has to be. But that's a system evolved for long-term replication of the species across millions of generations, you could probably get away with a much higher error rate for a "single-use" creation system, especially if you could effectively screened the results for viability before investing too much time and energy on them.
I don't know if we're there yet, but it's one of those things that's only going to improve. It might be easier up front to store the DNA in deep freeze, but then you have to keep the system powered and frozen in perpetuity against the day it might be needed - one thaw and everything is destroyed. Digital data though can be stored in stable media - there are formats designed for archiving data on geologic timescales, e.g. as molecular-scale patterns etched onto iridium plates with an electron beam. Do that today, while we have the technology and the knowledge, and they could withstand even the collapse of civilization and be available for the survivors to try to restore species diversity once they regain the technology.
--- Most topics have many sides worth arguing, allow me to take one opposite you.
Quite so. The cheetah's in fact have gone through two severe bottlenecks in the last 12,000 years and are virtually clones - you can graft skin between cheetahs willy-nilly without rejection. Also white mice used in laboratories are effectively clones, no diversity at all, and they are healthy (until the researchers get to them).
If you have the genetic technology to actually create an animal from a DNA sequence then you definitely have the technology to edit out defects. And of course a cone/copy of a healthy animal will still be a healthy animal. If it has a deleterious recessive gene, then that will be quickly discovered when a second generation is created, and the deleterious gene can be edited out. By the time we can do this, we will probably be able to spot candidate genetic defects in the sequence itself (we already have some ability to do this using known models of defects).
OTOH it would be a good idea to get a second genome from a different population if possible to retain a high level of genetic diversity. But it does not take many well chosen individuals to capture a high percentage of the total diversity of a species.
Starships were meant to fly, Hands up and touch the sky - Nicky Minaj
Even if they could use the DNA to bring a species back to life...
One of each sex isn't a large enough population to bring them back from the dead. There isn't enough genetic variation in two members. They need to have samples of a lot more of each species.
And this is something that I've never heard brought up in science programs that talk about bringing back extinct animals. (I'm not saying nobody has thought about it, I just haven't heard that they have.) All animals have an extensive micro biome in their digestive system. Cloning an animal doesn't do anything to recreate that.
Does the animal brought back going to have a place to live and food to eat? The animal went extinct for a reason. Most likely it's habitat lose (or illegal hunting). Unless we've recreated a safe place for the animals to live there's no point in bringing them back because they will just become extinct again.
An extreme example is the koala. It's diet consists only of eucalyptus leaves which it can only digest due to the bacteria in it's digestive tract. If it were to go extinct having just the DNA of the koala is completely useless because it will starve if brought back.
Death is one possibility, but competing less effectively is more likely, which could leave the genes in circulation for a long time. Or cancer - lots of cell duplication in a single organism. Biological error rates are probably optimized to maximize the evolutionary advantage of mutation against the disadvantages of crippling developmental defects.
You seem to be saying that problems in *recording* the DNA accurately would be devastating - and I agree. I'm not sure how accurate we are at at this point. Enough? Certainly for microbes, but vertebrates have a much larger genome. My point was that, assuming an accurate recording, problems in the synthesis of new DNA would be tractable. We don't have to understand the system - we just have to be able to duplicate it accurately.
Even with copious recording errors though, the records might still be viable in a future with accurate sequencing and synthesis , simply because there is so much similarity between organisms. You've got two flawed records of most segments, plus accurate records of similar existing organisms. Maybe there's a genuine difference, but probably not. And it's generally unlikely that a replacement of a genuine difference with the "baseline similar organism" will be fatal - it'll probably just remove some minor distinguishing features. You won't get the original organism, but you'll probably get something very similar, and reintroduce most of its genetic distinctiveness to ecosystem.
And of course, we'll also have assembled a wide library of (roughly accurate) genetic information about vertebrates, which would be immensely useful in beginning to understand what makes us different, and the same. Sure there'll be errors - but anything the same between both samples is probably genuine species-level genes - the similarities and differences between species is an immense amount of information to tease apart and advance our understanding of the bio-genetic "language", even if details about specific organisms are often missing. And that understanding, is likely to make it possible to adequately "fix" most lost bits.
Oh, and yes, the oldest ice appears is quite old. But the current Ice Age has lasted 34 million years , and there's a very real chance we may be exiting it more rapidly than ever in the history of the planet. At which point even ice that lasted through the last 8% of it will melt. The Earth's climate is bistable after all, and basically nothing about the climate in the last 34 million years can be expected to project forward across the transition to the radically different realities of a hothouse Earth. The (inter)glacial cycles of the last 30+ million years are nothing in comparison.
--- Most topics have many sides worth arguing, allow me to take one opposite you.
I've heard that humans show genetic evidence of being reduced to But it does not take many well chosen individuals to capture a high percentage of the total diversity of a species.
Chosen *before* sequencing their DNA? (Afterwards, why not just record a broader sample - difference-encoding makes for incredibly efficient compression)
I have my doubts. Obvious differences are easy to spot - disease resistance strategies though, those are far more important to diversity, and not obvious at a glance.
But absolutely - every additional individual helps dramatically when you're starting from 2. *Especially* if your initial sequencing is imperfect. Even just a 3rd sample lets you eliminate most random sequencing errors (A and B are the same, while C is different - C is probably a recording error rather than a genuine mutation. At worst it gets you a more "average" individual than really existed)
--- Most topics have many sides worth arguing, allow me to take one opposite you.
It seems unlikely that the modern DNA replication mechanism "just happened" in the current state from nothing. Far more likely it evolved, which means it *was* designed, by the "unintelligent designer" of natural selection. Some early organisms may even have developed 100% accurate replication - but no mutations means no evolution, especially with asexual reproduction. And such organisms would be rapidly out-competed by their evolving compatriots.
"And it's generally unlikely that a replacement of a genuine difference with the baseline similar organism will be fatal" - because organisms B, C, and D and E all evolved from A. They all used to be A, until mutations accumulated. Revert some of those mutations to the state they were in in A, and you're probably fine - you've just removed some of the differences that had evolved between them. The only way you'd be likely to have a major problem is if some other mutations would cause problems if unchecked, but was held in check by the "deleted" mutation. Replace some sections of human DNA with that from a chimpanzee, and you're probably going to get a more chimpanzee-like "crossbreed" rather than something completely nonviable. The base organisms are almost identical - we're not coding radically different proteins, there's just some minor differences in gene expression. Try to do something similar with a pig and mouse, probably not so successful - there's a lot more generations of divergent evolution there.
>We can't get DNA sequence and predict what kind of organism it would produce. DNA is a very complex program that produces specific result in specific circumstances.
Exactly - we don't understand the "language", so we can't predict what it does. Assmble a "library" of DNA blueprints of practically every vertebrate on Earth, cross-reference it with our biological understanding of the organisms and their similarities and differences, and you've got a dataset to start decoding the language. That'll be a huge project in it's own right - but assembling the "library" is a good starting point.
> This language wasn't made for anyone to read.
Of course it was - unreadable data is just noise. And DNA was designed to be read and implemented by a host of incredibly simple (compared to a human brain) biochemical machines. It as never designed to be easily *summarized*, but being read and obeyed is the entire point. Figuring out what it's saying, and what the implications are, is a big part of genetic research. And it's usually figured out by comparing two similar organisms, one with a particular gene and one without, and seeing what the differences are - very often even independently evolved similar traits will be associated with similar genetic markers, and we're getting increasingly good at identifying them.
>if there is no natural permanent ice on the planet then DNA records are obsolete. No point to revive species if they can't exist in new ecology. Also, at this point humanity will have bigger problems, it will be getting extinct itself.
Nonsense - the survivors of mass-extinctions seem to be fairly random. Surviving such events appears to have less to do with any sort of suitability to the ecology before or after, but rather what's most able to survive the traumatic transition period via flexibility and mobility. Once things have stabilized somewhat then you either resurrect species that didn't survive the transition, or you wait several million years for new species to evolve. And it's extremely unlikely we'll be going extinct. Civilization may well collapse, but we've survived repeated global glaciation (and every previous mass-extinction in the planet's history), despite likely being reduced to only a few thousand individuals at some point. Reason and technology has given us the ability to adapt far faster than evolution allows - an advantage that should preserve the species quite well through a catastrophic global climate transition. Almost everyone might die, but give the survivors a few centuries or millenia, a
--- Most topics have many sides worth arguing, allow me to take one opposite you.
I think you're sim-interpretting what I'm trying to say. I'm not ascribing intention to anything, I'm describing effects. Just as gravity optimizes towards minimum-differential energies, and makes all sufficiently large objects round, evolution optimizes for long term reproductive success of gene-lines. The balance between accuracy and mutation in DNA replication systems is a big contributing factor to that. Mutate too fast, and you don't have the genetic stability to remain a viable gene-line and die out due to endemic genetic diseases. Mutate too slowly, and you're out-competed by faster-evolving gene-lines. Over the long term mutations which bring the mutation rate closer to the theoretical optimum for the organism and environment will tend to spread throughout the population.
Evolution is a design process of the kind that has most successfully dominated human history - trial and error. No knowledge is needed, not even any intent is needed - just an unrelenting culling process weeding out less viable options. Why do dolphins and sharks look so similar despite having such wildly different evolutionary histories? Because they are subjected to many similar evolutionary pressures, which pushed their body shape towards the same optimal solution.
You do make a good point about current sequencing tending to have errors in similar places - if that is the case, then yes, those places will be a problem. Especially if there's something that makes it so that all/almost all sequenced DNA has the same error in the same place - how would you distinguish that fro "legitimate" DNA without being able to actually "read" it's function competently. The counterpoint, is they're only a critical problem if that place actually housed an important difference that can't be copied from similar organisms that survived or avoided the error. And considering just how much of our DNA that we share with yeast, finding something "similar enough" probably won't be a problem for most things.
>Also, "one thaw and everything is destroyed" is nonsense.
I suppose I was being a bit hyperbolic there - sure, thawing for a few days is no problem - but we're trying to preserve information across centuries of climate and likely political chaos. How high a priority do you think preserving a cryogenic facility will get if civilization collapses for a few decades? The caretakers would probably do everything they could to preserve it - but if electrical and fuel supply lines stop running, how longdo you think they can keep it up? Not to
Exactly how long do you think DNA can last relatively unprotected once it thaws?
From what I can tell, recent research suggests that absent any sort of thermal, microbial, etc. activity that would break it down faster, just exposure to ambient moisture breaks down DNA with a half-life of 521 years. That means that after T years, you'll have N=(1/2)^(T/521) of the original sample ( meaning T= -521 log2(N)). To lose 1% of the original DNA requires only 9.6 years of neglect. Of course the losses will be far more random, and it's easy to store a few thousand copies, so you probably have a lot of buffer there.
Both approaches have their value - digital is probably cheaper, and far cheaper in the long term, as well as being far more valuable to current research. And it complements well with even far less comprehensive cryo-vaults, for however long those may last.
--- Most topics have many sides worth arguing, allow me to take one opposite you.
And hey, if you can figure out how to do that to elephants, absolutely! :-D
I mention size and domestication because those are changes we already have a pretty good grasp on, seeing very similar genetic changes in many different species, and they would be useful for quickly making elephants into even more valuable and versatile "industrial equipment" than they are now - and if civilization and it's techno-industrial base collapses, such self-propagating organic technology will persist long after the knowledge to create it disappears - unlike a bulldozer which stops being useful soon after access to parts and fuel is lost.
There's other things that could help mitigate risks - such as crop modifications like grafting in resurrection plant genes to bestow extreme drought tolerance (already showing dramatic successes with some closer relatives).
Basically, if you look at history you see that the collapse of civilization is one of those "when, not if" scenarios, and as civilization becomes global the risk of global collapse increases alongside it. And with massive global ecological and climate problems introducing severe "outside" pressure the risk goes up even further.
--- Most topics have many sides worth arguing, allow me to take one opposite you.
ALL errors are random - and I'm not assuming evolution can fix the errors we introduce at all - I'm proposing we analyze the genome, and revert probable error sections to the state they were probably in a not-too-distant ancestor species.
Here's my assumptions for the future researchers attempting to restore a lost species a few hundred or thousand years from now.
1) They will be able to sequence surviving organisms and organic DNA vaults with ~100% accuracy.
2) They'll be able to identify ~100% of sequencing errors in the digital store, through correlation with accurately sequenced species living and "vaulted", and other stored species sequenced using the same technology (hopefully there'd be well-documented information on the technology used to sequence each sample included in the archive)
3) They will have at least a middling decent understanding of the "language" of DNA (not really necessary, but helpful for repairing some of the non-viable hybrids they'll sometimes create)
Assuming those - if you've got accurate data from a related species with a 1% genetic difference, and lost 1% of the original species DNA to sequencing errors, then by replacing all lost DNA with the sequences from the relative species, you'll end up changing about 1%*1% = 0.01% or 1 part per 10,000 of the original DNA to match a related organism. Effectively creating a new hybrid species that's 99% original and 1% the relative. There's no *guarantee* that it'll be viable, but the odds are pretty good with such a small mixing of "foreign blood".
I certainly won't argue that genuine organic DNA vaults aren't far superior for archival purposes. They are. Not least of which because you have a much better record of DNA methylation and any other still-undiscovered epigenetic factors which are probably at least as important to creating a healthy, complex organism as the DNA sequence itself.
However, organic vaults have two major flaws that interfere with them being created: They're expensive, they're and absolutely useless in the short term. They have absolutely no value until such time as you want to restore a lost species, and we don't currently have the proven ability to restore a species even from long-term cryogenically preserved blastocysts, much less from more readily accessible DNA samples. And they're *far* more expensive to create and maintain than a seed vault, where plants naturally provide incredibly well stabilized and self-sufficient embryos, already primed for long-term preservation and easy restoration (e.g. a few months or years after a plague wipes out the species - which is a constant short-term threat with modern agricultural monocultures). (Heck, we've already managed to resurrect thousand-year-old species preserved by nothing more than a clay pot that ended up in the right environment)
Meanwhile a digital store is utterly useless for restoring species without far more advanced technology than we currently possess - and might ultimately prove to be completely useless for the task on its own. But it is relatively cheap to create, and basically free to maintain. And most importantly it is a valuable and immediately useful resource in expanding our understanding of vertebrate genetics, valuable to both the biological and medical sciences.
And hey, it might also prove useful for last-minute, half-assed organic DNA vault, which seems like it might be as much as we can really hope for on that front. Forget all the painstaking collection and cataloging - just scoop up samples of whatever you can get your hands on, desiccate it, and freeze it all in one big heap (maybe at least in sandwich bags with region labels for the convenience of future geneticists). If Species X was ecologically important, then there's probably at least a little dung in there somewhere to provide a DNA sample. Let future geneticists sort it out if it proves necessary - the digital archive will provide at least a handy mostly-accurate reference sheet to identify the samples after they've been accurately sequenced.
--- Most topics have many sides worth arguing, allow me to take one opposite you.