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Comment by jonplackett | Hacker News Reader

This was really exciting until I read the bit where it says it just steals ATP from the host. Thought it could be a whole new way of life but looks more like a clever parasite hack.

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I kind of agree. It also makes this statement a little confusing:

> However, he believes "it's inevitable" that scientists will find more animals like Henneguya among those that have adapted to living in places with almost no oxygen, such as some parts of the ocean floor.

The parasite can live because it's stealing ATP that's being made by an oxygen-burning organism it's attached to. How would you do that with no oxygen-burning organisms around?

The ocean floor has "almost no oxygen," not "no oxygen." There remain oxygen-burning creatures adapted to living beneath in hypoxic conditions.

I dunno if hypoxic is the right term here as it’s usually taken to mean oxygen deprivation / insufficiency, which isn’t what’s happening here, as evidenced by organisms being adapted to the conditions.

The oxygen concentration is actually quite a bit higher in most hadal zones (> 150 µmol/kg [1]) than oxygen minimum zones that exist in the middle layers (< 45 µmol/kg [2]). It's definitely not a hypoxic environment relative to the rest of the ocean.

[1] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5829614/

[2] https://web.stanford.edu/group/MicheliLab/pdf/oceanographica...

Where does the oxygen at the bottom of the ocean come from I wonder?

I guess it could be like, in oxygen-poor places, animals are more likely to evolve to need less oxygen. Some (all that we know of so far) will do this by adapting to extract oxygen more efficiently and to use less energy, and others might do it like this parasite, by finding ways to extract energy directly from a host.

It seems that it would still be surprising that such a parasitical organism could exist in such an environment.

Presumably, if an organism is breathing in a near-zero oxygen environment, they are probably just getting the oxygen they need. If there's enough oxygen to support a parasite stealing from the first, there was enough oxygen to support the parasite getting its own oxygen.

It seems to me much more likely that we'll find these parasites where there is plenty of oxygen:

These organisms didn't evolve as a way of dealing with having no oxygen. They evolved because they adapted so that they did need to bother with mitochondria, because there was a plentiful supply of ATP they could steal. Since they didn't need to burn oxygen, they could do without. And the environment they are in has so much oxygen that the host organism doesn't suffer.

It says only that this may be what they are doing, not that it is for sure... a little late they speculate other alternative as well: _Roger says animals can actually use an oxygen-free process to produce energy from sugar, but it's far less efficient. He suspects this may be what Henneguya is doing_

Yes, it does say that.

It's called glycolysis, and isn't at all exotic. All animals rely on glycolysis when energy requirements outpace oxygen availability.

This little sucker obviously adapted to an environment with little available oxygen and lots of ATP. So the resource gain from losing superfluous stuff outweighed the need for aerobic metabolism.

There are whole different ways of life. For example, before the abundance of oxygen on Earth, the first bacteria lived on sulphur-based biochemistry. It was slow and inefficient, but better than being poisoned by that oxygen plague! Remember that it's an extremely destructive oxidizing agent (even in us it causes aging etc). It actually took millions of years for living organisms to start breathing oxygen (which was the real new and exciting breakthrough of the time).

And this is why I argue when some refer to places like Saturn or Jupiter as "hostile toward life" or "Impossible living conditions". They are certainly hostile to they types of organisms with which we're familiar. But as we often find, nature has a way of surprising us.

I saw the punch line coming when I read that it was a parasite. That being said, it's an extreme form of parasitism.

I guess it depends on how you look at it. Many scientists say that viruses aren't alive because they can't reproduce. But they actually do reproduce by parasitizing a host.

A virus isn't considered life because they do not follow all of the characteristics of life. This lists consists of:

order - meaning systems of cells

response to the environment - can sense, integrate senses, and response

reproduction - can create offspring

growth and development - do the cells grow and mature

regulation - there are mechanisms in place for heat control, thirst, etc

homeostasis - are able to maintain environmental equilibrium/steady state

energy processing - have the ability to convert sun to energy or process something chemically todo so.

If you go through this list, it's quite clear why a virus doesn't make the criteria for life. There is no order, they do not respond to the environment, there is no cell growth or development, they do not have mechanisms for heat, thirst, etc, and they do not maintain an environmental steady state.

If there is no order, response to environment, or growth/development, how can they reproduce?

Assuming reproduction is a characteristic they possess, why is that different from the others they do not possess? Reproduction relies on host cells so it could be said they possess the other characteristics because they rely on the host cells for those as well.

Fire can also reproduce given a reasonable environment - would you call fire alive?

Personally I do

So then that just means everything is alive

Which I also agree with

Energy is life. Life is energy.

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Viruses absolutely do respond to their environment and stuff in spectacular ways, understanding of viruses has come a long way since we thought they were dumb little protein shells

Sorry can you back this statement up? Cursory searching says this is not the case.

The only reference to 'responding to environment' is when that environment is inside of a host/cell. The rest of the time it's inert. When placed in a literal empty box, it is a dumb protein shell.

Took a full virology class, not sure what exactly to source. I went back to the lecture notes and pulled a few examples. They ride cell cytoskeletons, respond to PH changes to escape vescicles during infection (and it's awefully hard to draw the line at "this is just a chemical reponse" when it comes to biology, especially because if proteins doing their thing doesn't count as responding in a lifelike way, then nothing's alive). And also, yes exactly, viruses respond inside of the environment of a host or cell. That is their environment. Obviously you wouldn't expect to see any response to environment if you put them in a box with no environment - we would also be very dead in that case.

Role of receptors - interactions between viral receptor proteins and their hosts are incredibly complex, and include the virus signalling to the host to be more conducive to infection

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3246895/

Virus latency also involved activating replication when the environment is right

https://en.m.wikipedia.org/wiki/Virus_latency

And of course one of the most fascinating parts of virology (in my opinion) is viral surfing and active dissemination (active meaning they do things to infect cells instead of just floating around and bumping things). Viruses bind to a host and then actively move until they reach an ideal entry area

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2171413/

And there are many more but hopefully those are some helpful keywords. But I think you can get a sense of why many virologists treat viruses as living - they are dynamic and interact with their environment, and they evolve under the laws of natural selection. And the more we understand them, the more we realize preconceived notions about them (we originally thought they were just a poison, then some biological chemical, and then dumb protein shells, and now see that they can actually do a lot of crazy stuff - which makes sense because how would a dumb protein she'll be able to stay evolutionarily fit for millions of years against our immune system?

I think those are great rough criteria through which one could perhaps arrive at a distinction between virusses and other life forms.

But let's consider the original concept of the feature based tree of life, which with the advent of genetic sequencing was eventually shown to contain many errors, and to really be a graph of life with a strongly discernible spanning tree.

So if genomes turn out to be a better navigation instrument than behaviors or features, and given how modern understanding of the evolution of life through natural selection, it would appear a better definition for life forms would be to say: patterns in physical nature that can thrive in specific niches (often relying on the presence of other such patterns) having one or more nontrivial / unbounded chemical information stores (say polymers) the contents of which undergo natural selection or the evolutionary algorithm in the environment according to physics.

So prion would not be life forms since their number of chemical states are trivial or bounded, while viruses would still be lifeforms under my definition since their RNA or DNA sequences are non-trivial and in some sense unbounded (their genome could grow or shrink in size over generations).

Also consider that just like living organisms can die because of say UV-C radiation, so can viruses be inactivated by UV-C radiation...

> A virus isn't considered life because they do not follow all of the characteristics of life. This lists consists of:

The list is regrettably a "science-education-ism". My phrase - I don't know of a real one... anyone? A divergence between science-education community practice and science community practice. A rather dramatic one. In actual science practice, "is it alive?" isn't an interesting question, and has none of the importance science-education content often places on it. And people who actually work with viruses, consider them alive. It's perhaps regrettable that so much education content presents the list as science, rather than as an education device. And even as a device it has difficulties, as it doesn't deal well with the richness of biology, including around parasitism, and a binary sort just isn't useful.

> "science-education-ism". My phrase - I don't know of a real one... anyone?

Ever since I first read it in "The Science of Discworld" I've called that "Lies-to-children" (https://en.wikipedia.org/wiki/Lie-to-children):

A lie-to-children (plural lies-to-children) is a simplified explanation of technical or complex subjects as a teaching method for children and laypeople.

Thanks. I also had in mind the idea of a topic that's taught as if it was important to the field, but isn't, independently of its accuracy. So "question doesn't arise", rather than "different answer".

> And people that who actually work with viruses consider them alive.

I know of two people that work with them (create vaccines) that don't consider them alive. I've honestly never heard anyone else that I know working with them talk about considering them alive or not. Not sure why you'd make such a blanket statement unless you are a virologist.

Curious. In this context, I hang out mostly with marine microbiologists. I do go to talks more broadly, but more research biology than medical. Aside from common use of "dead", the question has only come up twice-ish in many years, and both times it the group discussion was unanimous. Actually, it also came up in a talk earlier this year, again environmental microbiology, around a taxonomy of selective pressures? I fuzzily recall they chose a predicate of "capable of adaptive co-evolution". As you say, it rarely comes up, but I'm sensitized to the topic, and I've not previously seen suggestion of an alternate population of thought. Thanks! I wonder if it varies by field? And yes, even if I was a virologist, a blanket statement, especially in a sample-poor context, is just inviting failure by not being true for some unfamiliar subfield or culture.

I think that entire list can (and should) be replaced by one simple criterion: "Is it subject to evolution by natural selection across successive generations? If so, then it's alive."

Fire, no. Prions, no. Viruses, yes.

Prions aren't? I'm not a biologist, I just read wikipedia. I don't understand why a prion couldn't be subject to natural selection.

I can't say, either. I thought they were just inanimate clumps of protein.

Maybe it'd be better to give prions the "maybe" status that we accord to viruses now.

> parasite

Well now I don’t want to look.

>...looks more like a clever parasite hack

We call this "the federal reserve model" IRL

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