[HN Gopher] Scientists create simple synthetic cell ___________________________________________________________________ Scientists create simple synthetic cell Author : sdht0 Score : 230 points Date : 2021-03-30 07:25 UTC (1 days ago) (HTM) web link (www.nist.gov) (TXT) w3m dump (www.nist.gov) | [deleted] | koeng wrote: | JCVI-Syn3A has been around for a while. Here is the genome | sequence from 2018 - | https://www.ncbi.nlm.nih.gov/nuccore/1241355755 | | Back at FreeGenes we synthesized all of the genes from this | organism with codon optimization for Escherichia coli | (https://stanford.freegenes.org/collections/gene- | sets/product...), the workhorse of synthetic biology. If you | combine the right transcriptional and translational elements, you | should be able to build a fully modular genome from this gene | set! We also did a couple other organisms in pursuit of this | modular genome. As a nice bonus, you can also easily do in-vitro | cell-free experiments since the codon tables are nice (and I've | heard from Kate Adamala's group that JCVI-Syn3 has pretty bad | cell free, though that was a couple years ago) | | It's important to note that JCVI-Syn3A has a LOT of problems when | it comes to its practical use. There just isn't enough energy | being put into making an understandable and practical | modular/minimal genome. | mercurywells wrote: | What is "pretty bad cell free"? | fiftyfifty wrote: | So can we say science has finally achieved a biological "Hello | World"? | TimTheTinker wrote: | Not exactly. These lines of cells weren't created from scratch. | From the article: | | > Scientists at JCVI constructed the first cell with a | synthetic genome in 2010. They didn't build that cell | completely from scratch. Instead, they started with cells from | a very simple type of bacteria called a mycoplasma. They | destroyed the DNA in those cells and replaced it with DNA that | was designed on a computer and synthesized in a lab. This was | the first organism in the history of life on Earth to have an | entirely synthetic genome. They called it JCVI-syn1.0. | dnautics wrote: | "Hello World" isn't exactly created from scratch either. | You're using libc in most cases. | tambourine_man wrote: | Someone wrote it though. It's not a blackbox that's evolved | independently for millions of years. We as a species know | how to build one, since we did. | blakesley wrote: | I suppose this makes sense, but at a personal level, the | two scenarios seem similar. Interpreters & compilers are | blackbox to me, at least. I have no idea how they work, | and I wouldn't be able to make one for myself. But sure, | someone could teach me. | maverick74 wrote: | Exactly what i was writing!!! :) | | Now, i guess that - like last time - we're going to have news | everywhere claiming that scientists "created life" (again). | | LOL | booleandilemma wrote: | Those gaps keep getting smaller and smaller though, don't | they? | thereisnospork wrote: | I'm curious if they are going to 'ship of Theseus' it. First | replace the dna, done, then the lipid membrane, then feed it | C13 labelled amino acids to prove that the entirety of the | cell proteom is from their synthetic genes. | | Not quite creating life but definitely hijacking it. | dnautics wrote: | Not specifically with C13, but that _is_ what is going on. | lupire wrote: | What would that mean? | maverick74 wrote: | No, because like in JCVI-syn1.0 | | "They didn't build that cell completely from scratch. Instead, | they started with cells from a very simple type of bacteria | called a mycoplasma. They destroyed the DNA in those cells and | replaced it with DNA that was designed on a computer and | synthesized in a lab. This was the first organism in the | history of life on Earth to have an entirely synthetic genome." | | In another words, like in the previous attempt (in which i was | equally amazed - at first - only to then became disappointed | latter) THEY DID NOT CREATE LIFE!!! | | They picked up an already living organism and "reprogrammed | it". | | Its like having a computer. They are learning to program, and | remove all the unnecessary parts but they still don't have a | clue on to build the hardware. | | The problem, it seems, is in transforming bare lifeless | quimicals into something "alive". | | Creating life, it seems, is still something reserved only to | God Himself! (and i suspect it's going to be like that for a | loooong time, if we ever manage to accomplish it anyway) | camjohnson26 wrote: | Intelligent Design as a theory for life's origins has | received a lot of unfair criticism because people think it's | code for "young earth creationism". It's not though, it's an | observation that random natural processes are too slow at | generating information to be responsible for life on earth. | | It's the same deductive logic you would use if you found an | artifact in the middle of the desert. Yes natural forces | could have carved an image from the rock, but the more | detailed the image the less likely it arose naturally. | | The fact that even now, no one has any idea of how to create | the basic forms of life shows the astonishing amount of | information that exists in even a simple cell. It's time to | reconsider intelligent design, even if the designer is an | alien species or a programmer of a simulation. There's too | much information to spontaneously generate, and we have never | seen life come from non life. | | The theory has been essentially banished from academia for | political, not scientific, reasons, but Michael Behe and | Stephen Meyer's books, specifically Darwin's Doubt and | Signature of the Cell, lay out the case in detail. | yumraj wrote: | So if you say that alien scientists created life on Earth | and is hence intelligent design, sure why not. Earth could | be some alien civilization's lab for all we know.. | | But then at some point those aliens, or the ones that | created them, or the ones that ...... created them ..., | must have been created spontaneously. | camjohnson26 wrote: | Totally, it just moves the problem but potentially moves | it to a larger search space. If you find a piece of | marble isolated on top of a cliff it's not cheating to | deduce that it came from a larger group of similar rocks. | You would calculate the probability that it was formed | there, vs the probability it was formed somewhere else | and moved there. | yumraj wrote: | I think there is a flaw in the logic. | | Life forms spontaneously. Just because this life evolves | into higher beings who can also create above life in lab, | the fundamental fact that life formed spontaneously is | not affected in any way. | mssundaram wrote: | Sorry for your down votes. I'm grateful that you would | share this perspective. As a Hindu, science and religion | are not conflicting. I'm looking forward to reading those | two books you cite - thank you for sharing! | selimthegrim wrote: | It's been banished from non religious parts of academia | because it's not falsifiable or testable, so it belongs in | the theology department. | camjohnson26 wrote: | It is testable, if a scientist creates life in a | laboratory then intelligent design exists. It is | falsifiable, you can compute the amount of information | contained in biological structures, and compute whether | known natural processes can create that amount of | information on the timescale of the universe. If they | can, intelligent design is falsified. | | Regardless, where the theory lives in the org chart is | irrelevant to whether it is true or not, and it's | certainly no worse than all the other origin of life | speculation. | whatshisface wrote: | > _If they can, intelligent design is falsified._ | | That's not true, demonstrating that process A could have | resulted in the observed effect does not show that | process B did not cause it. | camjohnson26 wrote: | If that's true every paper that references life's origins | needs to be retracted. If natural processes can be | responsible for abiogenesis then intelligent design | becomes much less likely, which is as close to | falsifiable as you can get for a statement of history. | api wrote: | The larger metaphysical claims are not testable. Some of | the narrower claims are, such as that self-replicating | evolvable structures cannot arise naturally. | | This basically amounts to the claim that the complexity | floor of life is too high for such a structure to arise | naturally over terrestrial time spans. | | Obviously a demonstration of abiogenesis would invalidate | that claim. This could also be challenged by | computational models that are sufficiently physically | plausible, or the discovery or creation of even simpler | lifeforms that extend the lower complexity bound of life | down to regions that challenge the argument. | | Of course another possibility is that this is our Fermi | paradox answer: life is in fact so profoundly unlikely | that its frequency of occurrence is e.g. less than once | per billion years per galaxy! | camjohnson26 wrote: | Exactly, these are major themes in the books I posted. | Darwin's Doubt deals specifically with the Cambrian | Explosion and the explosion of information over a short | time span that it represented. It digs deep into the | search space of protein folds and epigenetic information | and whether known evolutionary processes can be | responsible for the original emergence of the simplest | forms of life, or if there are even simpler forms of life | possible that lived before the Cambrian Explosion. | hnitbanalns wrote: | I appreciate your posted alternative theory on this | subject. It's refreshing. | api wrote: | We don't know how much information was required for the | Cambrian explosion because we don't have DNA sequence | information from that era. We can only guess based on the | DNA sequence information of today or from recent (in | geological terms) fossils frozen in ice cores, etc. All | the DNA sequence info we have is actually extremely | recent. | | It's possible that the very long "boring" period before | the Cambrian explosion was in reality when a whole lot of | stuff was being evolved that later all came together to | allow large scale cellular cooperation. | | An analogy I like is a barn raising. If you watched a | barn raising from very far away it would appear that | nothing is happening and then boom, you get a barn. In | reality the structure is being assembled slowly on the | ground for a long time before anything "macro" happens. | This analogy also comes up in regard to macroevolution | and perhaps even abiogenesis. | | BTW it's important to remember that modern evolutionary | theory does not include a theory of abiogenesis. Life is | assumed to exist and evolutionary theory deals with how | it changes over time. The origin of life is a separate | (albeit related) scientific question and one for which we | do not currently have an established answer. There are | many credible hypotheses but so far no way to really test | them. | eloff wrote: | The theory is banished because there is no supporting | evidence for it - compared to evolution which has an | enormous amount of supporting evidence. That's science | working at its best, and nothing political. | | I say this as someone who once believed as you do, that | you've been fooled, perhaps like me, by not honestly | examining the evidence for the other side with an open | mind. May you also find enlightenment. | camjohnson26 wrote: | Intelligent design is not incompatible with evolution, it | deals with the origin of life not the process by which it | adapts. | maverick74 wrote: | Ok... Let's put a end to this! | | GOD CREATED LIFE! | | There it is! I said it! | | And I'm going to say even more: there is absolutely no | scientific proof that shows otherwise. | | In fact the complexity points keeps pointing this way. | It's just a question of keeping the mind open. :) | | Ok... You can now ban me for my comment! | eloff wrote: | That's a very different intelligent design to what I've | come across. I guess people had to try to salvage it | somehow. | sdht0 wrote: | I want to clarify the idea here. | | 1) We don't know how life originated on Earth. | | 2) We don't have a full idea of what happened during the | Cambrian explosion. | | 3) We don't know how human consciousness manifests itself | in the brain. | | 4) Evolution by random natural processes is not possible | without deliberate nudges. | | Is the claim here that 1-3 is simply not possible without | an intelligent entity intervening in the natural laws? If | so, I'm personally fine with it. God (who is the most | popular potential Intelligent Designer) has always been a | God of the Gaps. In the future, I am pretty confident we'll | figure out the explanations using just the physical laws of | the universe. | | But if the claim also includes 4, then I think it can be | discarded with a high confidence. We can already observe | how evolution works at the virus and bacteria level. We | have found the transitional fossils [0]. The science of | evolutionary development biology [1] is already giving us | great insights into how organisms translate the genetic | code to build our complex bodies. It also shows how the | same genes have been reused across species (e.g., the genes | for eyes in the house fly and humans are the same). We | don't need the Intelligent Design hypothesis to explain | evolution. | | (EDIT: I see from another comment that you already agree to | the above point.) | | The claim Intelligent Design supporters can make at best is | that God created the first cells, perhaps nudged them a | little during the Cambrian explosion, and perhaps again | intervened before the evolution of Homo Sapiens. But all | the rest happened the boring way, following the natural | laws. | | > we have never seen life come from non life. | | Does not imply we never will. Given the countless other | times this argument has been used to justify an Intelligent | Creator when we didn't know something, I give very low | credence to the idea that /this/ time is truly it. Unless | someone can show mathematically why life cannot possibly | emerge from the natural laws, naturalism remains the best | hypothesis. | | [0] https://en.wikipedia.org/wiki/Transitional_fossil [1] h | ttps://en.wikipedia.org/wiki/Evolutionary_developmental_bio | ... | kens wrote: | You recommend Behe's book; I read his earlier book | "Darwin's Black Box"a while back. I found it interesting, | well-written, and superficially convincing but | fundamentally flawed and ultimately a waste of time. | camjohnson26 wrote: | Thanks for actually engaging the arguments, do you | remember what you found fundamentally flawed? | kens wrote: | I read "Darwin's Black Box" over 20 years ago so I can't | give a lot of details. His fundamental idea was | "irreducible complexity", a system that won't work if you | take away any piece, such as a mousetrap. He claimed that | a lot of biological mechanisms were like this. The | fundamental argument was that something irreducibly | complex can't be formed by evolution because it won't | work if is anything missing, so you can't evolve part | way. E.g. a mousetrap that lacks the spring doesn't work | at all. Therefore, evolution couldn't create the | irreducibly complex mechanisms found in biology. QED. | | The big flaw that I see is that he looks at the problem | of creating irreducibly complex mechanisms by addition, | but they can easily be produced by _subtraction_. As an | analogy, an arch is irreducibly complex because if you | take out any stone, it collapses, so you can 't build it | one stone at a time. But you don't build an arch this | way. Instead, a support is built and the stones are put | on top of the support, one at a time. When you take the | support away, now you have an irreducibly complex | structure. Similarly with biology, something can evolve | step by step with redundancy, and then pieces are removed | by evolution, ending up with an irreducibly complex | mechanism that Behe views as impossible. | | I should reiterate that I read the book decades ago so | I'm probably wrong on the details of Behe's argument. I | figured I should answer your question but I'm not | particularly interested in having a debate on evolution. | camjohnson26 wrote: | Me either just interested in other perspectives, thanks. | yread wrote: | More like proof of concept of a buffer overflow vulnerability. | It's smart but we have no idea what do all these transistors do | kazinator wrote: | Yes ... using a copy and paste of seven existing functions, | knowing what two of them do. Oh, and bootstrapped using a copy | of an existing execution environment. | mrguyorama wrote: | So basically the React tutorial app? | svachalek wrote: | It's a 480 line (gene) Hello World. For this to be the minimum | viable cell, when we don't even know what so many of the genes | do, would be surprising to me. It would mean pre-cellular life | somehow gathered these genes or equivalents without the | benefits a cell provides. Not saying it's impossible, but it | would be pretty interesting. | swiley wrote: | Perhaps "Hello world copy and pasted from StackOverflow." | tgv wrote: | More like a quine, isn't it? Pretty impressive. | tmabraham wrote: | While this top-down approach (removing unnecessary parts of an | organism and keeping the essential parts) is really impressive, I | personally find the bottom-up approach more interesting: building | an "artificial cell" by adding all the transcription and | translation machinery into a lipid vesicle, allowing for this | "artificial cell" to produce proteins to do various tasks. For | example, people have developed "artificial /synthetic cells" that | communicate with each other [1] and even bacteria [2]. There has | also been some recent study on dividing cell-sized lipid vesicles | with membrane proteins [3]. I know there were some comments about | science has achieving a biological "Hello World", and I think | this sort of work is what is going to get us there. | | [1]: | https://www.nature.com/nchem/journal/v9/n5/abs/nchem.2644.ht... | | [2]: https://pubs.acs.org/doi/abs/10.1021/acsami.8b10029 | | [3]: https://www.nature.com/articles/s41467-020-14696-0 | cambalache wrote: | Meh, if you are not doing the atoms yourself from leptons and | quarks then I am not interested. | pmiller2 wrote: | Of course, there's a relevant xkcd: https://xkcd.com/378/ | kens wrote: | The approach of removing unnecessary parts from a genome to | find the minimum brings to mind Muntzing. In the 1940s, Earl | Muntz was a TV seller who reduced manufacturing costs by | cutting out unnecessary components. He walked around the lab | with diagonal cutters and snipped out components until the TV | stopped working. He'd put the last component back and have a | new lower-cost design. The TVs only worked in high-signal | areas, but were much cheaper than the competition and sold a | ton. | | https://www.electronicdesign.com/technologies/boards/article... | callesgg wrote: | What do you mean? Like creating every protin without a | ribosome? Why would you need to go to that lengths of artfical? | Seams to like you have to start from the top up in one way or | another. Starting from the complete bottom just seams over the | top. | faeyanpiraat wrote: | If you can figure out how to go bottom up, it will result in | new innovations in microscopic manufacturing methods. | [deleted] | callesgg wrote: | Or... you can just use the top up built cell to manufacture | things. Why build your own nanorobots when there are pre | made nanorobots that already works. | hutzlibu wrote: | Starting from the bottom means, you really did understand it | all, once completed .. | callesgg wrote: | If that is the ultimate purpose and you have a way to | slowly progress towards full understanding sure. | hutzlibu wrote: | Oh, I would say many researchers have that goal, but | probably not many would consider it a realistic goal to | be achieved in their lifetime .. | | (all assumed, biology is not my area) | tmabraham wrote: | > Starting from the complete bottom just seams over the top. | Is it really? | | "What I cannot create, I do not understand." - Richard | Feynman | | And to clarify, currently the ribosomes are provided as part | of the cell-free transcription/translation system. | Additionally, amino acids, tRNA (plus tRNA synthetase), RNA | polymerase, and a primitive energy source (ATP with some | extra energy in creatine phosphate) are all provided. | | Here are the components of the most common cell-free | transcription/translation systems (PURE): | https://www.nature.com/articles/nprot.2015.082/tables/1 | laurent92 wrote: | Yes. Starting from the bottom, we might in the process | discover that 90%-99% of cell components are | cruft/inefficient, and discover how to make cells 10 or 100 | times smaller. Imagine being able to inject neurons in the | brain that are 100 times smaller. | sizzle wrote: | Couldn't messing around with these artificial cells expose us | to the risk of creating some second order mutations in humans | from accidentally introducing these cells to our microbiome | from the lab akin to the COVID-19 escaping a 'gain of function' | virus lab theory? | pmiller2 wrote: | It would be extremely unlikely that such an artificial cell | could colonize humans in any way, and even more unlikely that | such a cell would be pathogenic. | stadium wrote: | Source? | pmiller2 wrote: | Look at the proportion of natural cells that can colonize | humans versus those that can't. Similarly, look at the | proportion of pathogenic organisms versus non-pathogenic | organisms. Assuming the _goal_ wasn 't to produce a | pathogen, I find it unlikely we'd produce one | accidentally. | jchrisa wrote: | If you can create something living by a combination of non | living parts, I think that would be an interesting first. All | of the life we know of, presumably has living ancestors. Hence | the notion of a "spark" of life that is passed on like the | flame of a torch. If we can create life from raw parts and | supply the spark ourselves, it increases the relevance of | science. Suddenly the idea of sending seeds of ecosystems in | the form of printers and data would become viable. | throwaway889900 wrote: | We didn't create life from nothing, but we can certainly get | close. | https://en.wikipedia.org/wiki/Miller%E2%80%93Urey_experiment | noxer wrote: | Close? Yeah no, I dont think so. The experiment was | basically a complete failure. It just happens to be | interesting to analyses what actually happened and why. Its | also based on assumed condition on earth that are now | consider extremely unlikely. | sliken wrote: | So grey goo version 0.01? | stcredzero wrote: | _We_ are grey goo version 0.0.1!!! That is, life on Earth. Life | has already become a solar powered self replicator that caused | a global catastrophe, burying the whole Earth in a toxic gas. | mrguyorama wrote: | I always get angry about the conservative idea that "It's | hubris to think humanity is so powerful that we could | possibly change the whole environment!" (occasionally | sprinkled with "only god is that powerful") | | Guess what? Such simple creatures as an early bacteria did it | even harder over 2 billion years ago, making the earth nearly | inhabitable by anything that came before it. | stcredzero wrote: | Not all conservatives. There are some who actually advocate | for a carbon tax. | | Also, lots of religious people are socialist as all git- | out, and some organizations advocate those political | positions _officially_. | | It's easy to hate on the stupid, uninformed conservatives. | Just like it's easy to hate on the stupid, uninformed | leftists. | stevenpetryk wrote: | Worth pointing out that the parent comment said | conservative "idea", not conservative people. | relax88 wrote: | Eh, this biological grey goo is likely so crappy at surviving | that it would get snuffed out or out competed by any random | culture from the bottom of your shoe. | | I'd be more concerned about viral gain of function research and | the weaponization of synthetic biology in general. | lgats wrote: | https://en.wikipedia.org/wiki/Gray_goo | Freestyler_3 wrote: | Could they make cells that can regulate, if there is abundance of | X = do something? I mean that would end a lot of problems. | Starting with diabetes. | mschuster91 wrote: | For that to end diabetes, you'd need to keep the cells in the | body... which has two difficulties: first, the cells need to be | protected from the immune system destroying them and second, | the cells need to find a place in the body to live... and then | you have to find a way to keep their numbers regulated. | ChuckMcM wrote: | This is an interesting result. Basically cellular biologists | debugging cells the same way folks who don't understand how a | program works debug it, by chopping parts off until it fails and | then adding back bits one by one until it works again :-). | | At some point, not today and perhaps not in the next 20 years, | humans will understand exactly how cells and DNA "work" from | first principles to final behavior. At that point, humans will | either cease to age and never suffer from disease (Venter would | have liked that), or humanity will be wiped out by a malicious | organism that is designed by a deranged practitioner. | | Yet another technology produced Lady or the Tiger challenge. | darkteflon wrote: | I had to look this up: | | https://en.m.wikipedia.org/wiki/The_Lady,_or_the_Tiger%3F | okl wrote: | There's a fun Smullyan book with that title. | novaRom wrote: | We already understand exactly how cells and DNA "work", the | problem is methabolic networks are very large and hard to | simulate with sufficient certainty. | andrewflnr wrote: | That's rather the point. Those metabolic networks are not | meaningfully separable from "how cells and DNA work". | dooopy wrote: | Lol what are you talking about | WalterBright wrote: | Knowing how something works is not at all the same thing as | knowing enough to make significant improvements. It's just a | first step. | ChuckMcM wrote: | True, but knowing how something works enables you to walk the | path to learn how to make improvements. It allows you to make | reasoned changes vs random changes. | lujim wrote: | Ahh boy that title. Clicking on the link to probably realize that | this is totally harmless and my initial reaction is due to how | much I've been stuck inside for a year. | dang wrote: | I've truncated the title to try to make it less baity. If | anyone wants to suggest a better--i.e. more accurate and | neutral--title, preferably using representative language from | the article, we can change it again. | Traubenfuchs wrote: | Stunning and beautiful: We are on our way to truly intelligently | designed life. | Giorgi wrote: | So at some point we can just print humans (or better organism) | making organic life obsolete. | gulli1010 wrote: | Are we creating new organisms that can kill us? | breck wrote: | Loved the full article, thank you for helping science Elsevier! | | 606,520 Americans died of Cancer last year. With your help | restricting access to information, I bet we can hit 1,000,000 by | 2030! | | /s | | #ElsevierSupportsCancer (100% truth) | f6v wrote: | > Of the seven genes added to this organism for normal cell | division, scientists know what only two of them do. | | This gives you an appreciation of how little we know. I work in | bioinformatics, and every one in the field will tell you that | there's been an explosion in the number of datasets. However, try | finding recent data on your condition of interest! The number of | experiments grows incredibly fast, but we're not there yet to | build a comprehensive model even of a simple organism. | dnautics wrote: | so fyi I worked in that lab, we called many of them MUFs | ("membrane proteins of unknown functions")... We kind of | suspect that all they do is maintain membrane integrity and | isotonicity _just by being present_. One easy way for a cell to | do to increase the yield of a stuff is to have literally more | genes. | | So there are a lot of interesting things to do (which I don't | know if they did), like instead of having those last five genes | in there, copying one of those five genes five times... | azernik wrote: | > One easy way for a cell to do to increase the yield of a | stuff is to have literally more genes. | | Wat | | How does this work? Do they encourage expression of the genes | that actually make stuff? | f6v wrote: | Maybe parent meant that gene duplication (paralogs) results | in increased gene product. | dnautics wrote: | Thank you for clarifying. | [deleted] | koeng wrote: | https://vizbi.org/Posters/Images/2021/vB26.png | | They're working towards it :) | choeger wrote: | I wonder if this is going to be incredibly useful or totally | over the top for research. Imagine a development like the | BioNTech vaccine. With an atomic-resolution cell simulator, | you could verify your mRNA code, including the delivery into | the cell itself and watch it perform. | | But would that be like watching my CPU decode and fetch | instructions, interesting but completely useless for most | practical applications, or like a debugger introspecting a | running process, an incredible useful tool? | akiselev wrote: | _> But would that be like watching my CPU decode and fetch | instructions, interesting but completely useless for most | practical applications, or like a debugger introspecting a | running process, an incredible useful tool?_ | | It would be like watching the cloud of electrons moving | over transistors across an entire chip, without the benefit | of knowing quantum mechanics. Except in this analogy, | everyone is in the same boat and working on a single | codebase that's the surviving vestige of billions of years | of "just good enough" coders fighting it out, so every | little bit helps. ___________________________________________________________________ (page generated 2021-03-31 23:00 UTC)