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FrostReaver t1_jbnfnyw wrote

There is a concept call the minimum viable cell, where researchers attempt to splice almost all genes from a Mycoplasma mycoides except what is needed for survival. The genes that are necessary include metabolic proteins that handle essential functions like reproduction, fermentation, and amino acid synthesis.

"It has a smaller genome (531,490 bp) than that of any known organism that can be grown in axenic culture. There are only 438 protein-coding genes and 35 RNA-coding genes (Hutchison et al. 2016)."

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5710109/#:~:text=A%20minimal%20cell%20is%20one,genes%20and%20components%20are%20understood.

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Jale89 t1_jbnh2q1 wrote

As far as I am aware, this is currently our best answer. I saw a talk by the Primary Investigator in 2015 - I recall that they were basically knocking out every gene. We had a brief conversation about an area they hadn't explored where they could potentially go even further, if there are genes sets where knocking out only single components was lethal, but knocking out the whole set was survivable, so there's potential to go even further.

OP, the virus mentioned doesn't really represent an organism because it requires the mechanisms of a cell to replicate. The organism that FrostRever mentions here exists in "axenic culture", which means there are no other species present at all.

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Nymaz t1_jbovj2r wrote

> doesn't really represent an organism because it requires the mechanisms of a cell to replicate.

Is there a specific definition of "organism" that includes this requirement? Not trying to be snarky I'm genuinely curious. I always thought that "organism" just meant a unit of "life" which just requires the ability to reproduce, and doesn't include the mechanism.

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Nietzschemouse t1_jbowwcd wrote

Eh. Not really any more than there is a concrete definition of "species".

Lots of biologists don't refer to viruses as organisms, but there's a fair argument that they're no less alive than any other parasite.

I'd say, noting this is tangential to my field of study, that the (EDIT: agreed upon) minimum requirement is a cell membrane. Viruses may have capsules, but it's not quite the same. I believe this to be unnecessarily arbitrary, but it's consistent with keeping viruses out of the alive category

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InfamousAmerican t1_jbp0ugv wrote

Would replication of RNA/DNA not be sufficient to be considered an organism?

I see why the parasite/virus case is similar. Does the difference stem from the necessity of a host for viral replication?

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ayelold t1_jbp4m0g wrote

Viruses don't have a metabolism. Generally speaking, using energy is part of being alive. Also, a virus doesn't replicate its own DNA. It co-opts the replication mechanisms of a host cell and forces the cell to do the replication.

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rickdeckard8 t1_jbp714o wrote

There are no easy dividers like these to separate life from non-life. The short answer is that it depends on how you define life. Others define it in another way and include viruses among live organisms. Just like there is no clear definition on what a game is.

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Nietzschemouse t1_jbp3fdp wrote

In my opinion, that's enough, but the taxonomists of the world disagree.

There are so many organisms that are obligated to have a host to survive. Granted, they mostly need one condition or another that the host provides, rather than invading its cells, but I much find the distinction between virus and obligate pathogen to be just one that is being held onto rather than one that is meaningful. I'm open to someone giving me a real definition, though I've never encountered one I feel satisfying.

Worth noting, my opinion on the lack of consensus for species is that there genuinely can't be one. Humans try to classify biology, but biology doesn't care. You can look at the clostridium or clostridioides clades or the bacillus cereus groups and see examples of biology laughing at us trying to name a species when there is so much intermingling and genetic transfer or so little genetic difference between "species". Dengue virus subtypes might be even clearer, though that's an example of what should arguably be four species being lumped into a single one. Also, why would a non living entity be granted living entity taxonomy like "species" or "genius"? I think that's a matter of convenience, but it does raise an eyebrow because viruses have evolutionary histories as rich as bacteria or animals.

Then there's the "there's no such thing as a tree" argument, that I personally subscribe to.

Long story short, between understood "convention", attempts at classification (taxonomy) that can only approach but never reach the truth, the complicated phylogenetic nature of the world - the fuzzy line between the same and different, and the general resistance to change, I don't think there's really a clear answer for what constitutes an organism and why. Again, I'm open for debate or education.

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CreaturesLieHere t1_jbq7yb9 wrote

I think the answer lies in quantum physics, we may find some mechanism there that exists in typical life but doesn't exist in atypical thing like viruses and self-replicating RNA. Either that, or it lies in chemistry and we just haven't found the right experiment to make the discovery with. Because the line between "a mix of compounds/elements that can do complex things" and "life" has to be drawn somewhere right?

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TheNorthComesWithMe t1_jbqhi7s wrote

There doesn't have to be any fundamental measurable difference between something that is or is not life. Reality doesn't really care about our need to define things.

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Elladan71 t1_jbrmf6j wrote

This is undeniable. But when we're talking about definitions, aren't we talking about human constructs, attempts to approximate truth? Isn't it the same impulse that birthed the scientific method? Drawing lines between things is *useful!

Plus, anything that provides conversation like this thread is worth talking about, if you ask me.

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CreaturesLieHere t1_jbqo3rx wrote

There are several measurable differences between cells and viruses.

Defining what viruses are, and thus whether or not they're considered "life", is quite scientifically important. We need to define things based on what their uses and limitations are. Viruses are already known to have unique characteristics; if we further define those characteristics and are able to distinguish them from organisms, we can potentially discover new things about life, or new things about almost-life as a whole that fits certain parameters. We dont know what we don't know. Everyone freaking out over labels is missing the point, as usual.

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Nietzschemouse t1_jbq98ao wrote

I mean, sure. Maybe such a thing exists, but if we don't know of that, we're just making things up.

Not that it matters, but I don't personally draw a line between a bunch of molecules and an animal. Granted, that's not a common opinion

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blacksheep998 t1_jbp6ca6 wrote

There exist self-replicating strands of RNA. All they are is RNA in solution that can gather and assemble loose nucleotides into copies of itself.

But if a virus is alive, then they could probably be considered alive too.

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omgu8mynewt t1_jbphzq3 wrote

I work with viruses, some virologist like 'genetic material replicating and closed in a membrane' which makes me laugh

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dave-the-scientist t1_jboxhrl wrote

It really depends who you ask. Some consider viruses to be alive, others do not.

True, a virus can't function unless it's inside a cell with access to those nutrients/cofactors, and existing proteins and other components. But a bacteria also can't function unless it's in an environment with appropriate nutrients/cofactors and existing proteins and other components. The only difference is that those proteins etc already exist when the bacteria is born (divides into daughter cells), while a virus has to go and find them. Does that difference define life?

But then, if you consider a virus to be alive, what about self-replicating plasmids? They're really not much different from a virus. What about transposable elements in a genome? Are they alive too? They're not much different than a virus in latent phase.

The definition of life is something that sounds like it should be easy, and high school textbooks do give a precise definition. But the reality is a lot more complicated and murky than it seems.

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Dachannien t1_jbozrot wrote

For that matter, what about a prion? Does nothing when not in the presence of similar amino acid chains that are in a vulnerable conformation, but makes more of itself when those resources are available.

Then again, prions don't breathe and eat and grow, and that is how we know they're not alive.

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dave-the-scientist t1_jbpdrcx wrote

Right? The concept of "life" is surprisingly tricky. But I personally would not consider prions to be alive.

I will say though, prions definitely "eat", when they destroy the normal form of the protein. They "grow" by increasing their population, much like bacteria / viruses. Breathing is not a requirement for life.

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mdielmann t1_jbq3wst wrote

By these definitions for eat and grow, a fire is alive. I'd consider prions no more alive than fire, while still being as dangerous as fire.

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dave-the-scientist t1_jbq760p wrote

Behold, a man!

But yes, examples like fire (nice idea on that one btw) are why "life" is weirdly tricky to define.

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mdielmann t1_jbq8clj wrote

I get the edges are very blurry when defining what something is or isn't in biology, but I wouldn't equate destroy or alter with consume, or grow with reproduce, either.

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dave-the-scientist t1_jbqteik wrote

When you hear "consume" or "metabolize", it doesn't just mean destroying or altering a molecule. The important bit is that energy is removed from the molecule and used by the "organism" in question. Fire definitely does count for that particular one, as the reaction to burn something is almost exactly what we do in our bodies. We burn our food, just much more slowly. A prion though, does not meet that criteria. It does alter a molecule (the non-dangerous form of the prion protein), and energy is removed (the dangerous form of the prion is at a slightly lower energy level, I believe), but the original prion doesn't do anything with that energy. It is unchanged.

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Elladan71 t1_jbrnlfg wrote

I think you're on the right track, here. A virus needs a cell to function. A bacterium needs a nutrient-rich environment to function. An animal needs gravity oxygen, water, and food. Plants and animals are *environments for other kinds of life, so it's no wonder that the question is difficult to answer. When asked in the other direction, you're confronted with whether the Earth itself is alive.

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theSPOOKYnegus t1_jboxtqq wrote

Viruses aren't dead but they don't fit the definition of alive either, it's just a coded set of genetic information that uses the cells processes to reproduce. They float without direction until they hit a cell they can hijack

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Krail t1_jbrbzeh wrote

I've heard one interpretation that a virus particle could be thought of as analogous to a seed, and that an infected cell effectively becomes a virus organism.

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rickdeckard8 t1_jbp807r wrote

Everything alive is dependent on something else in their environment to stay alive. If you define life by function instead of properties you can arrive at a different conclusion.

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czyivn t1_jbp0x3h wrote

The problem is that parasites can range such a gamut that range from selfish genetic elements like transposons all the way up to like, head lice and remora. It's not clear where the line is between organisms and not, because it's really a gradient that depends on your opinion to draw a line. "Capable of living on it's own" is a good line to draw, though, when you're asking how many genes you need to live. It would be like asking how much money you need to live in NYC and including people in a survey who live with their parents. Not totally relevant to the question being asked.

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Awwkaw t1_jbowzou wrote

No, but a virus doesn't have the ability to reproduce. It has the ability to be reproduced. But so does many things, such as chairs, phones, books, and possibly other stuff. Much like a virus however, neither chairs, phones or books can reproduce.

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sfurbo t1_jboxrx0 wrote

Viruses require very specific environments to reproduce (the inside of the right kind of cell), but so does humans. Put humans in 2000 degrees, and they won't reproduce. Put them in the vacuum of space, and they won't reproduce. Without food, humans won't reproduce. Without water, humans won't reproduce. How is that fundamentally different from viruses?

A much more convincing argument for viruses not being alive is that they don't have a metabolism.

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Awwkaw t1_jbp08d0 wrote

In those conditions humans are dead, so they do not fulfill the definition of life.

A virus has no ability to reproduce, and as such it is not life.

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sfurbo t1_jbq50cl wrote

The virus can reproduce, it just requires a very specific environment to do so, including specific molecules that are only produced by other life, such as ribosomes.

Humans require very specific environments to survive, including a long list of chemicals that are only produced by other life, such as vitamins.

The requirements for the virus are a lot more specific, but there is nothing fundamentally different in them.

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Awwkaw t1_jbq6bqd wrote

No, the virus cannot reproduce.

It simply does not have the parts to reproduce. Only instructions on how to produce it. A virus is even worse at reproducing than Ikea chairs:, the chairs bring both the parts and the manual, the virus only comes with the manual. The extremely specific conditions you mention do not allow the virus to reproduce, it allows the host cell to produce the virus.

You might not like the definition of the word, but it is what it is.

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Solesaver t1_jbp0b4x wrote

A chair requires a very specific environment to reproduce. Inside a carpentry shop with a human carpenter capable of measuring, cutting, and machining new parts to assemble, or otherwise a factory designed to create more chairs. /s

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SirNanigans t1_jbr0i9b wrote

Viruses can be fairly complex, but imagine the very basic form of what they are: A string of DNA floating around and getting into cells, and causing them to produce more copies of itself. Obviously viruses are more than just rogue DNA, but that's their function - they corrupt other cells. They don't eat, photosynthesis, reproduce, etc. They're much closer to a chemical reaction, like how fire causes wood to create more fire, except orders of magnitude more complicated.

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LTEDan t1_jbqhwx4 wrote

This probably gets into more philosophy than science maybe, but there's not really a clear-cut line between "life" and "non-life" which is why it's hard to classify where viruses fall. If you instead think of life as less of a binary state and more like a process of self-preservation/self-propagation, then viruses certainly fit that bill. I would imagine the usage of the term "organism" predates thinking of life as a process and more of a state.

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stellarfury t1_jbqop8n wrote

I honestly think that most microbial stuff (prions, viruses, even bacteria to some extent) is closer to machinery than anything a layman would consider "life."

Sure, it's autonomous self-replicating machinery that actively seeks and processes its own fuel, but... well, you could design a macroscale machine that does this.

You wouldn't want to, because you'd be Ted Faro, but it's possible.

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Elladan71 t1_jbrpzwp wrote

Heck, who's to say that having achieved sapience, those self-replicating machines aren't alive? Racists, that's who!

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ANGLVD3TH t1_jbp2nf9 wrote

I've heard some think it's best to define an infected cell as the living virus, treating virions as reproductive material. I don't know how widespread this idea is, but I thought it was an elegant way to define them as living.

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nayhem_jr t1_jbqi6fj wrote

> they could potentially go even further, if there are genes sets where knocking out only single components was lethal, but knocking out the whole set was survivable, so there's potential to go even further.

That’s got to be maddening, having to account for various combinations within your original problem.

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screen317 t1_jbsngi7 wrote

> OP, the virus mentioned doesn't really represent an organism because it requires the mechanisms of a cell to replicate

There are a slew of obligate parasitic eukarotes that this definition disqualifies as an organism.

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RaptureAusculation t1_jbnh8ry wrote

Would this be a likely candidate for what the first life on Earth looked like since the structure is so simple?

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Jale89 t1_jbnneoi wrote

No: this is more like comparing a Raspberry Pi to a full modern PC - all the same modern bits but simpler. Comparing to the first life on earth would be like the first computers, with radically different components and operating principals to achieve the same functions.

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Ragondux t1_jbni1gv wrote

For this to work you need to have a cell will enzymes and ribosomes to be able to use the DNA to make proteins It's likely that the first living organisms were simpler and then built all this machinery.

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FrostReaver t1_jbnianq wrote

The first cells could've been a couple strands of RNA in a micelle with a protein.

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Ragondux t1_jbnieqh wrote

There's even a theory that proteins appeared later, since RNA can do a lot of stuff by itself and have enzymatic functions.

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Beliriel t1_jbnsf2e wrote

Yeah the base pairs of RNA can spontaneously form in nature and RNA can act like an enzyme or protein itself. Last I heard, evidence strongly hints that the world was an RNA (single strand) world before double stranding and then the more stable DNA double helix developed. But it's not conclusive.

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HermanCainsGhost t1_jbon0d6 wrote

The “RNA world hypothesis” was what I was taught in my upper level genetics class back in 2004, so unless I am out of the loop and it has been discarded in the 20 years since, it sounds accurate to me

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UnfinishedProjects t1_jbo8q53 wrote

I've seen this before, and I understand it, and I understand life can be created spontaneously by lightning striking in the perfect place. But what does that early early, minimal life do?? Is it about to hunt for "food"? How does it survive and replicate if it's just a few proteins that got shocked?

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Dr_Vesuvius t1_jboah5t wrote

You’re thinking of “life” as if it were a soul, some chemicals gain a “spark of life” and then they are alive.

It’s more helpful to think of life as being those things which reproduce. This isn’t a perfect definition either, of course.

You have a primordial soup full of basic organic chemicals. Some bits of RNA, some proteins, some sugars. These chemicals are already undergoing natural selection, as more stable ones survive longer, but they aren’t undergoing evolution because there is no “descent with modification”. Maybe some chemicals, through chance, form a very simple precursor to a cell which dramatically increases their survival. They can absorb small molecules while protecting themselves from the environment. Great. Does not mean they are alive. Can that structure divide into two parts which can then both grow and divide again? That’s what makes something alive.

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UnfinishedProjects t1_jbou27j wrote

You made me understand primordial soup for the first time. I mean I understood what they meant but I never thought about it being an actual soup of all the required ingredients.

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Shadver t1_jbog0eo wrote

To sort of echo the other response in a different way, I find it easier to think of early life in a chemistry sense rather than a biology sense. Chemical reactions can "reproduce"(autocatalysis), and they can compete with other reactions over the starting ingredients for the reaction. We can get these sort of lifelike qualities from very simple structures that could be outcompeted by more complex and better replicating structures over time. If you're interested in more about origin of life research, I found that the YouTube channel "Professor Dave Explains" does a really good job of giving easy enough to understand explanations for stuff like this.

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UnfinishedProjects t1_jbotuuf wrote

Okay now that actually makes perfect sense. Life is just an ongoing chemical reaction after all.

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Teslapunk1891 t1_jboeonb wrote

I find the concept of prions to be useful in understanding this. Ofc, prions are complex proteins and massively more complex and durable than any early life-precursor would have been, but they can fold other proteins into copies of themselves. Early protoliving assemblages could have been amino acid assemblages that generally tend to replicate through a few stages, and more effective/ more complicated versions of them were able to keep replicating and working together until eventually they could form something that would be considered living.

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triklyn t1_jbop8ul wrote

what does a prion do?

makes non-prions into prions. self-replication is the most important step. from there, imperfection will enable natural selection.

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danby t1_jbol01z wrote

Probably not. The last universal common ancestor (LUCA) of all life, circa 3.6 billion years ago, was bacteria-like and most likely to be free living (or somewhat colony forming). It's unlikely that a free living organism could have a genome as small as 438 genes. We also know that most major protein structural families data back to that period so a fairly complete repertoire of possible biochemical functions would have been within evolutionary reach to the LUCA. So it seems likely the LUCA was quite sophisticated from a biochemical function POV. We see that contemporary bacterial genomes tend to favour minimum levels of redundancy but that isn't the same as having smaller numbers of genes. Different types of bacterial genomes have very diverse counts of the number of genes present. Between these observations there's little reason to suspect that the LUCA's genome was minimal.

Anything older than the LUCA, such as pro-genotes (things before "modern" genomes appeared) or even earlier forms would have been substantially different to an organism with an organised genome of 438 genes. The further back in time you go towards the abiotic origin of life the more "weird" and less cellular early life probably was. There remains a reasonable chance that the earliest self replicating systems were just soups of nucleotide chains, which would arguably be the earliest life-like things on earth (circa 4.6 bya), and that's quite unlike a genome-containing cellular organism.

It remains a very open question what the earliest self-replicators that gave rise to cells might have been but all the options are pretty weird. Here's a somewhat decent summary of some models

https://www.bionity.com/en/encyclopedia/Origin_of_life.html

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ThorsTacHamr t1_jbommjb wrote

They are using this approach or a very similar one to try to find LUCA ( the lasts universal common ancestor). Not necessarily the first living thing but the oldest living thing that all current organisms can trace their lineages back to.

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danby t1_jbopbwg wrote

Minimal genome experiments generate organisms that aren't free living so they aren't really aimed at generating something like the LUCA. Mostly these experiments are trying to discover the minimal set of house keeping genes that can maintain a living cell, there's no reason to believe the LUCA was like that, nor any reason to believe that the LUCA had a minimally sized genome.

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severoon t1_jbouxw9 wrote

Also consider that "life" is likely to be an arbitrary feature in this discussion.

If you have a molecule that happens to be an enzyme which builds itself, you have yourself a self-replicating thing. Is it "alive"? Definitely not.

Well that's one feature of "life" but it's one that most people tend to think of only in the context of life. But all the features we typically think of in the context of life exist in much simpler, not-alive things.

By looking for the simplest thing we consider "alive," no matter how we define that, it's likely to end up being much simpler than what we would feel comfortable calling "life."

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helm t1_jbo91uq wrote

An MVC with 500k base-pairs … that’s quite far removed from self-replicating RNA strands!

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RatMannen t1_jbvej80 wrote

I had no idea geneticists also did tiny code challenges, as well as programmers.

Though thinking about it, genetics is just soggy programming

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