The debate not only between Darwinists vs ID continues:
Are viruses dead or alive?
If viruses are dead, what makes them “animated”?
If viruses are alive, are they another life form?
142 thoughts on “Are viruses dead or alive?”
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Therefore, using ID “logic” they cannot have arisen naturally, is that right?
Of course, according to ID “logic” arches are impossible to build as well.
Yes, killing people. According to their design, right?
The debate not only between Darwinists vs ID continues:
That is in the OP, attempting to frame the question.
And yet it seems everything J-Mac is saying has nothing to do with intelligent design at all.
Are you afraid to address the very issue you raised in the OP J-Mac? What does Intelligent Design have to do with viruses?
Were viruses designed? Did they evolve?
What’s your position J-Mac?
If you are afraid to say, that’s also OK. You join the many many other fence sitters in the ID camp afraid to say what they believe, just waiting for the third crow.
Viruses incorporate themselves into the host cell and thus the host cell becomes the body of the virus. Once the viral genome becomes incorporated within the the cell they are not separate entities. The cell is taken over by the virus, it becomes the virus and the virus becomes it, they become one. If people don’t like labelling it a virus I’m happy to call it a viral unit. And of course that also includes its metabolic processes and homeostasis.
Copying lengths of DNA involves taking a string and adding matching units along the length. In other words the new string is grown on the original. There can be no replication without growth.
Reproduction is the higher level process of creating new viruses.
That’s tricky territory. How about multicellular organisms for example? Do you become a rhinovirus-human chimera everytime you catch a cold?
They resemble plant seeds in that they can lay dormant for a time and given a suitable environment become active.
They take over individual cells, not all body cells. Of course it all belongs to the unity that is life.
If one takes autopoeisis or biological autonomy as a necessary condition of life, then viruses are not alive. But they do evolve — and they could not exist without biologically autonomous systems to co-opt — so they are on the periphery of life.
But the individual cells are not separate entities either; they belong with the organism.
Mind you, I am not saying you are wrong. Just pointing out that you are taking arbitrary decisions in order to fit viruses into the definition of life I offered. That’s fine. You can also change the definition of life so it includes viruses, like Allan did. That’s fine as well. But it’s arbitrary.
The boundary between chemistry and life is a fuzzy one. That is why the answer to J-Mac’s question is an arbitrary decision.
Why would the issue of whether viruses are “dead or alive” be a debate between “Darwinists” and “IDists”?
I, for one, welcome my new snotty overlords.
Corneel,
But fundamental. Without replication, the rest could not happen. The peripheral definitional additions are all in service of replication. So I see it not as mere semantic preference, but somewhat deeper.
The obsession with producing a definition of life is the same as the definition of a ‘planet’.
Is Pluto any different, now that it is not defined as a planet ?
Did a (changed) book entry change our view of the universe ?
You defined life by its dependence on nucleic acid replication. I’d agree that replication (with modification!) is crucial, but argue that the use of nucleic acids as the carrier of heritable information is incidental. However, just “replication” is insufficient to define living beings. Or better: it fails to exclude things that we do not view as living things (e.g. computer viruses). “Template based replication” may be better for that reason.
I am also going to go all Charlie on you and argue that, without metabolism, replication of nucleic acid polymers would not happen. I could easily defend the position that the transmission of heritable information is in the service of maintaining metabolic homeostasis. There are even theories that posit that metabolism predates the origin of replicators. Hence, your preference may be more than semantic, but I predict it will not garner consensus.
Definitions can be useful, even if there remain border cases. For example, in research into the origin of life it helps to know what features characterize life.
Without self-sustaining self-replicators, evolution can’t happen. Viruses cannot replicate without a host. But that just eliminates viruses as anything to do with life’s origins.
Or does it?
J-Mac?
Viruses must be ancient, but I do not recall them having anything to do with origin of life. Significant for origin of life research would be that all living things have a cellular organization and share key features of metabolism and processing of heritable information.
No, with or without modification. The point being that replication (I agree, template-based replication would be better) permits the message to survive deterioration in instances of the medium. Without this tendency to persistence, nothing else can happen.
It is true that modern replicators have evolved many strategies to improve their replication capacity.
I dare say. You could also defend the position that sex is ‘for’ diploids. But as in that case, you’re taking the modern, derived cycle and deciding that all stances are arbitrary. Starting at the beginning, that may not be justified. In an admittedly imaginary world where naked replicators were able, poorly, to achieve template-copying without elaborate metabolism, but gradually evolved improvements in that capacity to the point of extinction of all examples of the ancestor, it would not be an equal stance to say that the nucleic acids serve the needs of the metabolism. It’s a hypothetical of course, the chemical difficulties are immense, but the existence of the possibility counters the insistence that both stances are equivalent – particularly when we peer behind the veil of the proposed alternative:
Ha! I laugh in the face of consensus! Depending how defined, of course, Metabolism-First theories suffer from a lack of rationale to long-term persistence, and a total handwave as to the means by which such systems transition to one in which a complementary template system takes over. You start with ‘metabolism’, and then somehow a base-complementary polymer with the same capacity arises, replicating the ‘metabolism’ two for one … a stretch, I submit.
If the message just persists unaltered, nothing is happening either. In my view, the absence of the ability to adapt just makes for a mildly interesting chemical process, not a living being.
It is true that modern metabolisms have evolved many strategies to improve their persistence
Perhaps, but the real question is why the naked replicator qualifies as life, and the naked metabolism does not, when both are required in all modern living organisms. I’d say that is an arbitrary decision.
That’s quite an assumption. That cells didn’t evolve simplifies evolution’s task but that puts quite a burden on origin-of-life hypotheses. Couldn’t metabolic pathways operate in some inorganic environment? Pores in some substrate? Why could this not happen prior to cellular structure?
Sure, lack of fidelity is where things get really interesting. But ‘sufficient’ fidelity, coupled with exponential increase, is vital. You can get persistence of lineage with no change; without that persistence, nothing. ‘Change’ is not a defining characteristic of life, but reproduction is, and the reason (somewhat cryptically, perhaps, in a definition derived from observation rather than principle) is its effect on persistence.
How? Is lactate dehydrogenase engaged in modifying sequence?
I’m not so sure that is ‘the real question’, even though it is the semantic matter under discussion!
If one were to follow a template-copying sequence back to its inception, we might puzzle as to exactly where we would apply our ‘life/non-life’ razor, but I’m pretty sure we would not continue to be mystified by that question as we progressed from that point into a hypothetical ‘pre-metabolism’. Life starts when reproduction does.
J-Mac? Have you broken out of lockdown?
It could, but it would not be life if “organized in cellular structure” would be part of the definition. 😎
For clarity: I am not claiming that a definition of life should only include features that are relevant for abiogenesis research, but merely that it will provide guidance to what features are interesting to start looking. Compartmentalization could have been important for early life.
Yes it is. If it doesn’t evolve, it is not life in my book. Several definitions of life I have seen include evolution as an explicit requirement, including the one I linked to. You are free to use your own definition of course, but I will not be sharing it.
To continue turning your arguments around 180 degrees, I might as well be asking how nucleic acids are engaged in energy metabolism. Indirectly they are, because metabolism and expression of heritable information are interdependent in modern organisms. That is why I think both should be part of the definition.
Again, I beg to differ. A primitive metabolism would definitely be in the demilitarized zone between inanimate chemistry and full-fledged life for me. I would probably choose your side, and declare it “not-life”, but I do not feel confident enough to tell off people choosing otherwise.
For those like myself who don’t know much about viruses, here are a few things I’ve found.
In this video by Vincent Racaniello he gives his current definition of a virus as ‘an infectious, obligate, intra-cellular parasite comprising genetic material, can be DNA or RNA, often surrounded by a protein coat and sometimes a membrane’.
He mentions that there are a couple of million viruses in every teaspoon of sea water. He also mentions that all the ocean’s viruses if laid head to tail would reach over 100 million light years.
On the question of life, Racaniello’s solution is to say that a virus has two phases, one that’s not living which is the particle and one that is which is the infected cell.
Well that is a step towards what I am saying. It should be looked at from the point of view of the whole life cycle and not just an arbitrary snapshot of one instant in time. Any living creature is a being in time and this cannot be disregarded as if it has no part to play when trying to define it.
Here they marvel at the virus:
And here capsid formation is described:
According to this report the capsid is assembled without the assistance of the host cell. The more details that are uncovered, the more remarkable viruses turn out to be.
Below is a chart from the video linked to above. It’s taken from Racaniello’s blog.
I agree.
Fair enough, but I am having trouble imagining a replicating entity that achieves 100.000% fidelity: the nature of chemistry is against you. Even my imagined ‘metabolism-first’ entities suffer variation in the counter-ions floating around…
Many proposed criteria in the metabolism and ‘independence’ departments seem to be the results of desperate lawyering to exclude viruses whilst retaining auxotrophs.
I did not take J-Mac to be making any such claim. Any claim at all, in fact.
Ever.
Rather, I see J-Mac as a practitioner of the “Airplane food, what’s up with that?” school of comedy, and the mangled grammar of the OP may simply mean “Here’s another debate”.
A colleague of mine retired a few years ago, and because he had an interest in philosophy he also affiliated himself with our Philosophy Department and was allowed to give an undergraduate course on philosophy of biology. The course had a Reddit discussion group, and I was asked to join it as an outside biology expert. The first question that came up was, what was the definition of life. Someone said that we needed to get that straightened out before we could do anything else. I disagreed. I said that I had been working in biology for over 40 years (then) and had never had a definition of life. It didn’t seem to prevent me from being able to do the research I wanted to. I predicted that they would get tangled up in that discussion and never resolve it — the discussion would be a black hole that swallowed them up.
They disagreed, and off they went to settle the matter once and for all. I never heard back.
Do you take this to mean that you were right and they were wrong?
There are some scientists who tend to think their science covers all existence. Most terribly this is affecting economists and lawyers, but also physicists, mathematicians, and biologists. It happens when they fail to define the domain of their science.
Then there are other scientists who tread with proper caution because they know the limits of their science. For example, you do not get to be an archeologist without having a clear idea of what archeology is and what it is not.
Then there are the philosophers, whose domain is in fact defined to cover existence itself and everything in it, and indirectly also what is outside of it. It would be only right for them to speak out more bravely.
Of course, nothing may prevent you from working in biology, but when you fail to define what it is you are working with, there will be astonishingly little to learn from you – about biology, specifically.
Well, I already figured out some time ago that you are a statistician and a programmer rather than a biologist. Good at numbers, not so good at what is behind the numbers. You work “in biology” in a similar way one works “in politics” or “in Hollywood” – famous and thus successful in the trivial sense, but possibly better qualified to do something entirely different.
And they’re still probably trying to arrive at a suitable definition.
If you imagine that there is no variation in the monomers that make up a polymer replicator, it is inevitable. But I admit that given the sloppy nature of chemical reactions, something interesting was bound to happen.
Good point. I was thinking of problems with obligate symbionts (e.g. lichens) myself.
Because numbers have nothing to do with biology, I suppose.
LMFAO
How dare you question the biological credentials of someone who
(1) has a small noctuid moth species, which eats cottonwood leaves in the mountains of Arizona, named after him, and
(2) caught the first Southern Bog Lemming ever found on Mount Desert Island, Maine?
And, oh, I seem to have missed the part of your comment in which you established your own biological credentials.
He has none.
Joe Felsenstein,
I got a hearty belly laugh out of this. Thank you for that.
J-Mac,
I think you misunderstand. I was stating that you were ignorant of the joke being made, and that you then called someone else ignorant. Hence you lacking ground to stand on. It was intended to play on the irony of the situation. It also had a double meaning, which is that your arguments imply a fundamental ignorance of the fact of evolution, the theory of evolution by natural selection, and also how basic logic and evidence work.
Well, it all boils down to personal preference. In that spirit, I find the necessity for change to be a peculiar one. A 100%-faithful replicating system would not be alive? 🤔 Fidelity is improved by evolution. So hypothetically, a system could evolve to become non-living! Of course practically, 100% is not achievable, because the closer it got, the less it could change. On this requirement, they are kept ‘alive’ by constraint!
By producing transcripts that are translated into the molecules of energy metabolism. I don’t think these stances are anywhere near symmetrical; information flow is in 1 direction, and the benefit accumulates to the template, not the materials templated. They keep popping up; they don’t persist.
Those nucleic acid stretches that produce variants beneficial to their bearers tend towards increase in frequency. The alternative stance, that it’s the polymers of metabolism that are the central actors, happening to store their essence in ‘inert’ nucleic acid form, seems as absurd as insisting that it’s the shell of sand grains, not the larval genome thereby protected, that is what caddis flies are really all about. Genetic sequence is the beneficiary of its actions, over multiple generations. Its products are ephemeral, assisting one or two iterations: useful secretions.
CharlieM,
Something to do while at a loose end, I suppose.
Erik,
By that logic, someone who only works at night will never get anything done because he can’t precisely define when ‘night’ starts or ends.
As you may have noted, I tend to be very pragmatic in how I approach definitions of life. Yes, in theory a population could evolve to the point where it escapes my definition of life. For the reasons you’ve mentioned, I think this is not something I should worry about. If we were to encounter some life form that has accomplished this feat, I would treat that as I would treat viruses: they fall outside of my definition, but I will study them anyway 😜
I do not occupy that alternative stance (though I could easily go on defending it; caddis flies are not naked strands of DNA as far as I am aware). My position is very Charlie-like in that I want reproduction AND metabolism on board, as well as development, growth, and cellular organisation. As a geneticist I am sympathetic to the view that the transmission of heritable information occupies a special position, but I don’t want to blind myself to the fact that there is a whole lot more that characterizes living organisms.
Lockdown has that effect on me.
Another very important question is if virologists are biologists or chemists. If we don’t know this, how can we ever hope to find a cure?
Corneel,
You think I’m blind to these things? 🤣 I don’t talk to my wife as if she is a shell wrapped around her DNA, nor is my relationship with my dog affected by this stance! That’s a curious position adopted by many ‘anti-reductionists’ I encounter, that emphasising the evolutionary relationship between genotype and phenotype somehow demands the abandonment of all system-level considerations. I’ll see your ‘as a geneticist’ and raise you an ‘as a biochemist’ that I’m well aware of the broader interplay of the system in organismal physiologies. But it remains a fundamental fact that genotype is the basic currency of evolution, preserved by its effects in the environment in which it finds itself. Which, for any gene, includes the other genes with which it is covalently linked or commonly encapsulated, some of which translate it, replicate it, supply its product with energy, etc, during one or more iterations.
Who are you calling an “anti-reductionist”? If you really were a reductionist you would be writing shorter OPs.
Anyway, given your purported appreciation of the wide interdependence of all players in organismal physiology, I do not understand why you insist on restricting the definition of life to the replication of nucleic acid polymers (which is what got this discussion started). Why not include all features that characterize living things, even if you perceive some to be more significant than others?
It will be good enough when they are virologists. The problem is the virus, not chemistry or biology.
Whereas when a non-biologist thinks he is a biologist, we do not have much hope.
Right. I knew you never really believed in materialism.
ROFL
From where I’m standing, it appears that Corneel is addressing the Charliesque question “What is life?”, or even the J-Mackian “Life, what’s up with that?”, whilst Allan is addressing the narrower “How do we unambiguously define life?”