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Cheap DNA Sequencing Is Here – Writing DNA Is Next
- astazangasta 11y agoWriting genomes, once we can do it, will be the technology that drives this century (sorry, nodejs). Imagine printing a bamboo tree programmed to grow into a bed frame.
- jacquesm 11y agoI don't see how being able to write DNA will give you the ability to grow bamboo bedframes.
- ilurk 11y agoWill DNA be Turing Complete? :) Not the same, but quite related: https://www.youtube.com/watch?v=2JNSpMhJLvg https://www.youtube.com/watch?v=2JNSpMhJLvg
- udp 11y ago> Will DNA be Turing Complete? :) Actually... quite possibly. Check out the first slide in [1]. You can basically build genetic logic gates using promoters to conditionally (i.e. depending on the presence of light, a protein, etc.) produce a protein to induce or repress another promoter, thereby increasing or decreasing the expression of another gene. It's still pretty early stages and there are a lot of factors that make this more complicated (life isn't binary), but the ultimate goal of synthetic biology is to be able to program DNA in the same way you might program a computer. [1] http://co.mbine.org/events/COMBINE_2015/agenda?q=system/files/combine2015-Utah_101615_v3.pdf http://co.mbine.org/events/COMBINE_2015/agenda?q=system/file...
- dekhn 11y agoYes, DNA (with a combination of some enzymes) is capable of universal computation. So far, this has not turned out to be anything particularly interesting from an engineering standpoint,
- crusso 11y agoWill DNA be Turing Complete? DNA (with supporting cell machinery) create us, so...
- cge 11y agoYes, even without enzymes and cells. I have DNA crystallization based tiling systems that can implement essentially arbitrary 1d cellular automata and could implement Turing machines directly. People have implemented neural networks with branch-migration-based systems, and DNA gates can be used to implement systems of logic gates and a wide class of chemical reaction networks. There's a whole field of DNA and molecular computing.
- astazangasta 11y agoDNA is code, we just don't have a compiler yet.
- eli_gottlieb 11y agoPhenotype = genotype + environment + reproductive phenotype (that is, the seed shell for a plant, egg for a bird, or the uterus for a mammal). Being able to rewrite the genotype doesn't give you total customization of the resulting phenotype.
- mylons 11y agoand this is just our current understanding, which is certainly going to shift as measurement becomes cheaper and more accurate. iterative science!
- ethbro 11y agoWouldn't the reproductive phenotype in this case also be genetically controlled (albeit in the previous generation's)?
- eli_gottlieb 11y agoExcept that it's also subject to its own environmental influences, separately from those which impact the new individual after its birth.
- refurb 11y agoExactly! Identical twins have the same DNA, but they don't have the same fingerprints. Why? Different environment in the womb. Could we tweak things like eye color? Sure. Things like intelligence? Much, much harder.
- mylons 11y agothis is overly simplistic
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- dekhn 11y agobamboo is already a fine construction material, it's much more efficient to just grow long straight pieces and join them after the fact. That way you don't have to do any genome engineering, or have special growth facilities for oddly shaped bamboo (for one, bamboo that doesn't grow straight up is going to take a lot more space on the ground).
- hyperbovine 11y agoi think it would be much easier to just grown the bamboo into the frame, a la the square watermelon. But I digress: we are many, many decades away from being able to do things like that. Possibly centuries. Even programming single-celled organisms to assemble simple hydrocarbons is barely within our reach, at present.
- astazangasta 11y agoConsider how we went from nothing to cell phones in a century; this is not that far away.
- hyperbovine 11y agoNot sure what you imagine the early 20th century to have been like ... I mean, general relativity just turned 100. Anyways, in terms of our understanding the genetic architecture of even basic traits like height (to say nothing of complicated ones like the morphology of a bamboo shoot) we're practically in the Dark Ages. I know it's a bitter pill to swallow for the "Singularity is near" crowd.
- TeMPOraL 11y agoI think right now, your best approach to growing bamboo bed frames would be to a) first make a frame-shaped template, and b) make bamboo cells grow according to the template. Encoding it in just cell DNA is beyond our current state of knowledge and probably insanely tricky - Fourier-transforming a square and encoding it into chemical feedback loops and encoding that into DNA kind of tricky.
- jacquesm 11y agoSad to see you downvoted, that's exactly how certain wooden rakes are made (hence my reference to that upthread).
- adrianN 11y agoWriting genomes and understanding protein folding will be the gateway to full nanotech. Think about it: proteins are already tiny machines that perform specific functions. If we learn how to make them ourselves the sky's the limit.
- mistralx01 11y agoGene doping is upon us!
- cenal 11y agoExciting and scary at the same time. Here's to hoping people don't go overboard.
- crusso 11y agoSome always do go overboard no matter what the technology.
- ilurk 11y agoScience trumping nature. (pun not intended but given the political circumstances the expression does give pause for thought, maybe a better term would be:) Determinism over randomness.
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- skosuri 11y agoSynthesis is still quite expensive at a penny a base, much less a dime a base. To give a comparison to sequencing, costs are about a penny a megabase (~7 orders of magnitude cheaper). We have a long way to go. Even for a small bacterial genome (1Mbp) that's $10,000 at a penny a base. To have any real power, I'd want to build at least thousands of them which is a little out of my price range.
- hyperbovine 11y agoAlso, what are the error rates? This was a major problem for NGS in the early days. (Still is, on certain platforms.)
- TeMPOraL 11y agoI guess today is my day of not groking English, but I have to ask - what do you mean by "a penny a base" and "a dime a base"? EDIT: I know what's a base pair. I didn't understand the "penny" and "dime" in this context.
- skosuri 11y agoSorry, it's short for basepair (bp) of DNA (eg a, c, t, or g). Currently it costs about ten cents a bp to synthesize a particular stretch of sequence from one of the companies in the article (dime a base). An average protein can be encoded by 1 kilo basepair, a small bacterial genome by 1 mega basepair, and a human genome by 6 giga basepair.
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- angrow 11y agoThey are the American one-cent and ten-cent coins, respectively. The words are also used to indicate costs of $0.01 and $0.10.
- fisk 11y agoMaybe the confusion here is that prices are sometimes spoken of as 'a [currency unit] a [item]' which can be understood as 'one [currency unit] per [item]'.
- namespace 11y agoInteresting times! Can we recursively keep on creating our better (or worse) selves for ever? How will copyright work for genetic designs?
- udp 11y ago> How will copyright work for genetic designs? Or, rather, how does copyright work for genetic designs? Syn Bio papers are published all the time, and their designs are copyright like any other invention.
- toomuchtodo 11y agoGreat question! I'm assuming that if AI and genetic engineering hit their stride at the same time, copyright is the least of our concerns. We engineer machine intelligence just enough for it to spark (tipping point, runaway, whatever you want to call it), and then it'll engineer us "better". Is "better" what we consider better? Or what it considers better? Interesting times.
- ggreer 11y agoWhen it comes to people, you don't need much writing of DNA to get really interesting stuff. Nick Bostrom (author of Superintelligence: Paths, Dangers, Strategies) has fleshed-out the idea of iterated embryo selection.[1] IES lets you do the equivalent of a millennia-long human breeding experiment in a couple of months in a lab. The result would be phenotypes that have never existed in history. These people would be smarter and healthier than anyone who lived before. It would utterly change the human condition. The key enabling technology is the ability to (in-vitro) turn embryonic stem cells into gametes. This has been done in mice, but not humans. 1. http://www.nickbostrom.com/papers/embryo.pdf http://www.nickbostrom.com/papers/embryo.pdf
- frozenport 11y agoNot clear how you translate the behavior of single cells into phenotypes, especially when that phenotype may show after many years.
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- imaginenore 11y agoCan't you gene edit adult yourself to become healthier and smarter?
- jakobegger 11y agoI don't think it's quite as easy. With embryo selection you are selecting genotypes, not phenotypes. The paper you link is pretty handwavy regarding that point; Bostrom seems tho think that if we just had more data we will be able to find a model that links genotypes and phenotypes. However, this is far from certain. There are too many degrees of freedom in our genome, and there are too many factors that contribute to something generic like "cognitive ability". Each individual contribution is so tiny that the effect is lost in noise, even if we sampled all humans. And even if someone comes up with a novel statistical method and finds a reasonable model, optimising that model would be pretty dangerous. If you just optimise for one trait, the chances you'll even end up with a viable embryo after a dozen iterations are pretty slim. There's a lot of selective pressure on cognitive abilities; so there must be reasons why we aren't smarter than we are. These reasons will probably kill your experimental embryo.
- agumonkey 11y agoI'm a bit scared, so far I've never read anything leading me to believe we can understand organic complexity. To my eyes writing DNA will only be a spectacular show of nopes.
- crusso 11y agoso far I've never read anything leading me to believe we can understand organic complexity That's a bit hyperbolic, isn't it? We understand the basics many organic systems and our knowledge and tool sets are improving at an accelerating rate. Look at the recent gene therapy used to cure leukemia: http://www.techtimes.com/articles/104545/20151109/babys-leukemia-reversed-by-new-gene-editing-technique-therapy-may-also-work-for-other-diseases.htm http://www.techtimes.com/articles/104545/20151109/babys-leuk... To my eyes writing DNA will only be a spectacular show of nopes But we'll be able to learn so much from the failures. We'll finally have the coding and debugging tools to make a serious stab at reverse engineering life.
- agumonkey 11y agoRight, hyperbole it is. I understand that research is making very large steps these days. But too often when things get too cheap, people use it without deep enough thoughts, with something as large as an organism.... Cheap rant from my side but that's my belief. The sooner we get real insights and are able to find new cure the better. We'll see.
- musha68k 11y agoRelevant xkcd: https://xkcd.com/1605/ https://xkcd.com/1605/
- tim333 11y agoSo maybe this will lead to open source Jurassic Park style dinosaur code on GitHub that you can write to DNA and breed?
- melted 11y agoSequencing will only be truly "here" when companies like 23andme offer both sequencing and interpretation of human genome directly to consumers for $1k or less. Preferably much less.
- peter303 11y agoDNA has been proposed as a long term digital storage medium. Magnetic and optical digital storage generally last less than a decade. You need to copy annually to be sure. As others pointed out, writing DNA efficienty is the bottleneck. Reading is getting cheap.
- gourneau 11y agoIf you think this sounds awesome and want to be a part of a Founders Fund startup working on related things contact me at josh@synthego.com