Tiny microbe challenges the definition of cellular life
nautil.us146 points by jnord a day ago
146 points by jnord a day ago
Fascinating!
The article should have at least tipped its hat to mitochondria:
>But unlike a virus, Sukunaarchaeum has its own ribosomes, cellular structures that synthesize proteins, and it can replicate itself without the help of a host.
Yes and this is true of mitochondria as well: Their own DNA, a own complex set of membranes, a private customized set of ribosomal proteins and tRNAs, and the ability to replicate within the “host”. Mitochondria are also perfectly happy to be swapped from cell to cell.
I wonder if or how these nanobiobots contribute to the fitness of their hosts.
So, from my amateur perspective, Sukunaarchaeum + mitochondria = bacterium?
ok so we knew about bacteria, tiny cells that don't have a nucleus, responsible for lots of disease. Bacteria do not look like the bigger cells that have a nucleus, they noticeable differences in how they work. Those big cells do have mitochondria in them which very much do look like bacteria that started living in those other cells.
Later on archaea were discovered they are the size of bacteria but the look like the bigger cells in how some of the key things in side of them work. Archaea don't cause any known diseases so that's one of the reasons it took so long to find them, but we can now find them all over the place by their DNA and it's now pretty clear that the ancestor of all big celled (and multi cellular life) was an archaea and they've even found the group of archaea that multi cellular life evolved out of.
Well, no, because (from the article) "Archaea are similar to bacteria, but distinct in their structure, genetics, and metabolism."
I've always felt like the biological definition of life isn't useful or meaningful when it comes to borderline replicators like viruses.
In my opinion, a virus in the environment is quasi-dead, but once it enters a cell and it hijacks its components, it becomes alive.
This does not differ that much from bacterial or fungal spores, or even from plant seeds, which can also be almost "dead", i.e. without detectable metabolism or internal changes, even over many thousands of years, until they reach a favorable environment that triggers their revival.
The difference between a virus and a bacterial spore is that the viral particle contains only a subset of the parts of a living organism, so it could never be brought back to life in an environment where nothing is already alive. However, once the virus takes control over many parts of a cell, which provide the functions that it is missing, like the machinery for protein synthesis, the ensemble formed by the parts brought by the viral particle and the parts formerly belonging to the invaded cell, can be considered as alive and distinct from what the invaded cell was previously.
In any case, the evolution of the viruses and the evolution of the cellular forms of life are entangled, with a lot of genetic material exchanged between them, so considering the viruses as non-living is definitely counter-productive, because neither the viruses nor the cellular forms of life can be understood separately.
The word you're looking for is cryptobiosis/anabiosis no need to invent a new one. Something thats later alive almost by definition is not dead. The entire living system has been alive since abiogenesis.
We have to agree on the basic definition of ultra-basic terms.
You just proposed a definition. Good. It's not complete, but necessary, conditionally.
Basically, we shouldn't use "alive" and "dead" as dualities. There's at least three states: "dead/inert/never gonna get there", "meets a definition of life (see next category) when supplemented by a host cell or something else complex and exterior", "can self-replicate and grow on its own, in a friendly environment with sufficient food/fuel/inputs available = life".
Maybe more. But let's stop pretending biology is dead versus alive, because viruses definitely ruin that.
That's a pretty cool framework for the alive or dead debate. I've always been firmly on the alive side but now I can do a better job of presenting the argument concretely instead of just ' nuh-uh '
The virus behaves a bit like the seed of certain plants (like many orchids) that need obligatory symbionts. The seed by itself is not viable.
> so it could never be brought back to life in an environment where nothing is already alive
I always thought of a virus as purely a "modifier", not having the characteristics of "life" independently. If this was a game, the virus might be a runestone or skin for your character.
Anything that doesn't need external "life" to come alive, I would consider as "life" in various states. Maybe it's in hibernation, or stasis, or dormant but the life is there. Maybe to keep the silly game analogy, this might be the extra character on your roster.
> Anything that doesn't need external "life" to come alive, I would consider as "life" in various states
Doesn't almost any biological entity need external life to come alive via, e.g. reproduction or mitosis or what have you?
Yes but you are talking about the threshold of existence, and the cell is alive as soon as it starts existing. For a virus you also have the threshold of "application", when the viral code is applied to something alive. Before that the virus exists but is not alive itself. After the application it's modifying other life which maybe technically can be considered alive.
This is why I said "to come alive" instead of "to be created". The virus is something that just exists but only becomes alive when mixed with something that's already alive.
Most concepts in biology break down on the borderline cases, because the phenomena are so complicated with all the little variations, the concepts have an inherent fuzziness.
Instead of the concepts being like a box where something is definitely in the box or not in the box like in mathematics or maybe physics, the concepts are more like a clustering of characteristics in a high-dimensional space or landscape of variation, where things are classified according to their similarity to a central paradigm case. (This seems to be how our minds model at least some concepts as well, as evidenced by our being faster at categorising cases that are closer to some paradigm case)
One notorious example is the concepts of male and female: yes, there are borderland examples of individuals who can't be classified as either, but almost everyone clusters sufficiently closely to the distinct paradigmatic cases that the concept has an obvious utility.
But the same thing happens everywhere in biological classification: whether something is a mammal or not becomes fuzzy as we go back in evolutionary time, and whether something is alive or not is similar.
> the concepts are more like a clustering of characteristics [...]
> This seems to be how our minds model at least some concepts as well [...]
Since we have existed for 100's of thousands of years, and formal thinking only a couple hundred as a widespread practice, only habitually by a modern minority, and then for a tiny minority of daily concepts -- that is very nearly the only way we encode concepts.
In fact, we no doubt actually encode formal concepts using clustered characteristic thinking. We have just intentionally narrowed characteristics down to the point that the result is formal thinking.
Yeah, I think that's an interesting feature of linguistic thought: it builds on and exists within our deep evolutionary heritage of percetion and fuzzy classifications, but by the nature of words as being discrete items it also predisposes us to think naively that the phenomena referred to by words are also discretely organized into this box-like either/or structure, but the reality is more complex
Sure, but considering how central and defining the concept of "life" is to biology (the study of life and living organisms) you'd think we wouldn't have a fuzzy definition for that specific concept. I can see why it's tricky, though.
Life is very useful as a term because it allows you to define a 'not living' term as well: dead. And it has meaning at the highest level. But if you start looking at things in a more detailed way even death doesn't arrive 'all at once' for multi cellular organisms, for instance a dead person's hair still grows to the point that corpses need to be shaved. And a virus may be dead by one persons view on what 'life' is all about but alive by someone else's definition. And depending on the context both of them may be right.
The definition is fuzzy because the concept is fuzzy! Even something that we in every day life see as settled such as a species is not always clear-cut. Cat or dog? That's usually easy. Member of a species yes or no? Not so easy, and in some cases subject to considerable debate and even then unresolved.
For instance:
https://en.wikipedia.org/wiki/Species_complex
And:
https://en.wikipedia.org/wiki/Ring_species
Boundaries are hard, just like naming things.
Agree on the fuzzy term.
It is misconception that hair and nails continue to grow. What happens is the that kind and soft tissues dehydrate and shrink and the hairs and whiskers stick out more. Growth stops soon after oxygen and nutrients stop being delivered.
We really only have one example of life (or at least all our examples are interconnected), so I don't expect great definitions.
Just like geology doesn't have a great definition for their subject of study (the earth). They have a definition that works really well, but because they only have one example, the definition ain't stress tested.
Slightly less silly: it took the discovery of lots more bodies inside and outside the solar system (dwarf planets here, exoplanets elsewhere) for astronomers to really nail down the definition of planet.
I find Maturana’s definition satisfactory. Best overview in his book with Francesco Valera:
Autopoiesis and Cognition: The Realization of the Living (1980)
https://en.wikipedia.org/wiki/Autopoiesis_and_Cognition:_The...
Unfortunately out of print.
how does it exclude fire, something well known for making more of itself (which seems to be the main criteria in Autopoiesis)
The problem is that it's really hard to come up with a definition that includes all of the things we agree are obviously life (e.g. mold), does not include fire, and does not just appeal to the particular structure that most or all life on earth seems to have (the cell).
The result is a landscape of fuzzy definitions mostly centered around that last one.
I think that depends on your prior expectations about how biological concepts should be structured. I was trying to make the case that we should expect that they're fuzzy when we're dealing with very complex phenomena that exhibit a lot of variation. The fact that these kinds of phenomena happen to exhibit clustering is what makes (fuzzy) classification possible, but we also find that many phenomena or organisms are in borderland areas between clusters, so the classification doesn't work as well with them.
We only have a single tree-of-life (or possibly, several syncretic trees-of-life from a single planet) as an example. Makes it a little difficult to discern the true principles.
> Most concepts in biology break down on the borderline cases
Most concepts break down on borderline cases, within and without biology. Those motivated will abuse this to argue that those concepts don't meaningfully exist at all.
Because in most cases the categories are invented by us, to make sense of the world. But the penomena themselves are often continuous. Or actually not just us but most life with some kind of sensory system - even paramecium differentiates between food and non-food.
Take our color perception as an obvious example: We clearly see different types of color, despite us being unsure at the thresholds in between, and the actual electromagnetic radiation of visible light being a continuous wavelength range.
That is just a fundamental limit of our reasoning. We mentally make models of the world to make sense of it. These models have to be of less complexity than reality, ergo they have to cluster perceptions, ergo we have to categorize.
> the penomena themselves are often continuous
And even when the attributes are discrete, phenomena tend to be highly combinatorial.
Leaving lots of room for new combinations to be discovered that will upset our taxonomies.
I'd argue that this is FAR more true of the soft sciences - of which biology is perhaps the "hardest".
The definition of steel is pretty hard-edged. A polymer of C, H, and O isn't steel.
The definition of a quasar is similar. There are "maybe quasars", but that's from lack of data, not lack of definition clarity.
A circle is pretty exactingly defined. Mathematicians aren't fuzzy on that.
Similarly, the standard definitions of intelligence break down when we look at borderline cases like simple algorithms, collective insect behavior, or AI systems.
Viruses particularly exemplify “intelligence” is better understood as a spectrum of information-processing and adaptive behaviors rather than a strict threshold.
The issue seems to me that neither concept is wrong, but that we humans keep trying to impose absolute definitions on phenomena that exist along continua, blurring into one another in ways that resist our neat little categorizations.
I would argue viruses exemplify some of the highest evolved intelligence in our world.
If you dropped me off in vacuo (eg in deep space), I wouldn't meet the definition of "alive" either. But the fact that my life require a specific environment doesn't phase us or challenge our definition of life at all.
Not only do I need certain physical conditions (temperature, pressure, molecular gas composition, etc), but I also need to eat, so actually me being "alive" is dependent on specific biological conditions too. My Minimum Viable Environment actually includes other organisms, yet this doesn't challenge the fact that I'm defined as alive.
Certain parasites can only live or reproduce within another organism. This is even more extreme, but it still doesn't challenge our definition of them as being "alive."
This new organism requires a specific "environment," and that "environment" happens to be inside another organism. So what? We're totally un-phased by this requirement when it occurs in other examples.
Perhaps it's better to think of this not as a spectrum between alive and non-living, but as a hierarchy of how constrained (vs unconstrained) is the "environment" required to support life processes.
TL;DR if aliens exist they probably define us as "partly alive" because we can't reproduce outside a planet. :D
I prefer the Erwin Schrödinger's definition more.
PS: There's more recent work done on this:
https://www.quantamagazine.org/a-new-thermodynamics-theory-o...
Useful, but not exact. To go more general in biology. It's kind of like classical pre-cladistics taxonomy. It's helpful to have a definition of reptiles that excludes birds, sometimes, even if birds are evolutionarily reptiles, sometimes you might only want to talk about the cold-blooded species today.
This is just another way to say that the map is not the territory. Anything that tries to describe reality in simpler terms than actual reality is likely just going to end up being a leaky abstraction rather than a hard law. And nature is very fuzzy along the boundaries of whatever concepts you are going to come up with.
I mean, humans are just a definition away from being a single globe-spanning morphing organism.
My biology is a bit rusty but I really have to wonder — are plants and animal cells even “alive”?
Take away the mitochondria and bacteria… can cells live on their own?
If no, then are we that all that different than this microbe?
Might even be sheer arrogance to think that we are the “host” (much like cats/dogs domesticating humans). Maybe we only exist to serve the mitochondria (:->
There are a few weird cases of prokaryotes that don't have mitocondrias. Apparently they had mitocondrias, but they steeled the interesting parts and get rid of them (over gazillions of years). From https://en.wikipedia.org/wiki/Metamonad
> These flagellates are unusual in lacking aerobic mitochondria. Originally they were considered among the most primitive eukaryotes, diverging from the others before mitochondria appeared. However, they are now known to have lost aerobic mitochondria secondarily, and retain both organelles and nuclear genes derived ultimately from the mitochondrial endosymbiont genome. Mitochondrial relics include hydrogenosomes, which produce hydrogen (and make ATP), and small structures called mitosomes.
I think I first came across this on HN: A Symbiotic View of Life: We Have Never Been Individuals [0]
> Take away the mitochondria and bacteria… can cells live on their own?
We can live without bateria if we add with some food supplements.
mitochondria isn't considered alive, as a separate organism, AFAIK. It doesn't even have a species name. It's just a component of the host cell.
As I understand it, these new microorganisms are parasites. They're not essential for the functioning of the host cell like mitochondria are.
Mitochondria were(are?) bacteria, so technically we can't live without bacteria really.
AFAIK no examples of independent mitochondria exist in nature nor the lab currently, so they (almost certainly) WERE bacteria (by some definition), but ARE NOT currently.
Ship of Theseus, obviously.
>We can live without bateria if we add with some food supplements.
Citation needed. I would strongly doubt that this is true, because microbes also play a very important role in eg. immune defense. Remove all the mutualitic microbes from a human (eg skin, digestive tract) and the parasitic and pathogenic bacteria will take their place immediately.
We're talking removing all bacteria. And we know it's possible - even if it can't happen in nature.
There are sterile mice made for scientific uses - 100% mouse, completely microorganism free or your money back. They have health issues, but they can survive and reproduce in the right conditions.
Of course, those "right conditions" include sterile housings and sterilized food, because they'll get contaminated otherwise.
> Take away the mitochondria [...] can cells live on their own?
Neither can live without the other. Too much genetic exchange has taken place in some distant ancestor where critical genes were deleted from mitochondria and moved to the host. Meanwhile host cells became utterly dependent on mitochondria for energy production. Or you might say: the mitochondria were producing so much excess ATP the host cells started evolving to depend on that much energy being available.
The exceptions are later cases (like a few organisms that have copied energy production from the mitochondria genome then later lost the mitochondria entirely).
For all purposes mitochondria are zombie archaea (not bacteria). Hollowed out empty shells retaining just enough function to perform aerobic respiration and reproduce. There is little pressure to evolve away from this local maxima. What benefit would the host cells derive from getting rid of the mitochondria? Not much. And having those critical functions isolated in what amounts to a pseudo-organelle with its own DNA protects it from a lot of sources of damage/error.
So... are we obligate symbiotes? Or have mitochondria hyper-evolved to such a point they are just organelles in our cells - just ones that carry their own DNA instead of relying on the cell's main DNA? Like much of biology... a bit of both in a fuzzy mix without a clear line.
You were a single animal cell at some point. Seems to me that it must have been alive.
Essentially nothing can live on its own, certainly not animals.
Mitochondria can't live without their surrounding cells. Plants are also interdependent with fungi.
I really hate how shitty science reporting has become, you can tell all science journos aren't actually current or well read in the science they report on. This isnt some new miracle find this is a well described and growing phylum https://en.wikipedia.org/wiki/Nanobdellota Having genome reduced symbionts of dinoflagellates is an even more common and general phenomena, its almost the definition of a dino to have a weird zoo of peculiar friends and things becoming endo symbionts. This finding is definitely cool, but I dont understand why the article has to make out its a "breakthrough" or "astounding" rather than actually the more astounding thing is how normal this very weird thing is!
I fell into a rabbit hole when I was looking for coverage of a recent relatively technical biological result and the most prominent Google results were from 'evolutionnews.org' aka 'scienceandculture.com', run by the 'Center for Science and Culture.' Imagine my surprise to find this is all run by a 'Discovery Institute' with tens of millions in funding dedicated to pushing 'intelligent design' and behind the campaign to have anti-evolution views taught in public high school science courses.
Not of course to say these outfits are behind the decline in science reporting, but it's a real tragedy how difficult it is to find actual and competent scientific journalism today, a tragedy that makes the job of such charlatans all the easier. I'm glad that Quanta Magazine seems to be doing well enough, which certainly isn't perfect but I've read some good articles from them.
Out of curiosity, what was the result in question? The director of the DI is a molecular biologist and I've seen his name attached to a paper that reported a pretty humdrum technical result about... (actually checking my notes) the statistical improbability of enzymes arising by purely random assemblage of unrelated protein folds.
that's not humdrum, it's carefully cloaked pseudoscience.
The conclusions as stated in the paper seemed valid, and the methodology seemed to check out, it was just inconsequential; abiogenesis doesn't posit that chemical processes are purely random. The real problem is that creationists were parading the astronomically low probability cited by the paper as evidence that enzymes must have been intentionally constructed.
I agree. It's just a tiny parasite archea. It's common for parasites to get smaller and lose features over time. So it's clearly alive, and the title is linkbait (or totaly wrong).
I made a similar comment in an old thread about this but I can't find it. My biology is not good enough to give details about the phylum (or whatever, I never remember the classification), but I have the same annoyment in many posts about math or physics.
Indeed. This is a cool discovery, but there is absolutely nothing shocking about it. Endosymbionts with reduced genomes are well known, and this is just an extreme case. This new thing is in no way "a new category of life, suspended somewhere between archaea and virus". It's just an archaean.
> Having genome reduced symbionts of dinoflagellates is an even more common and general phenomena, its almost the definition of a *dino* to have a weird zoo of peculiar friends and things becoming endo symbionts.
I spent too long trying to figure out why dinosaurs were a part of this discussion.
IMHO viruses are a horizontal DNA(/RNA) exchange mechanism that took off past the original utility.
Too bad, I was hoping for an electron microscope photo or something.
Oh wow, that looks a lot more complex than I expected for something that's supposed to be extremely "stripped down" from a genomic POV.
I mean, I know the article mentions it "has its own ribosomes, cellular structures that synthesize proteins, and it can replicate itself without the help of a host" but that doesn't always translate to complex structures plainly visible underneath a microscope.
That is a photo of the dinoflagellate that this new thing lives inside. I don't think you can see the new thing in this photo, it's too small.
My bio is rusty but I remember that archaeon are into extreme situations. Is it so weird to find an example of one essentially “offloading” some functionality to its host? Especially in a diluted environment like the oceans
More evidence for the life-exists-on-a-spectrum idea.