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From: Ernest Major <{$to$}@meden.demon.co.uk>
Newsgroups: talk.origins
Subject: Re: Life: Turn it upside down!
Date: Wed, 10 Apr 2024 14:10:37 +0100
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On 10/04/2024 11:37, Arkalen wrote:
> On 10/04/2024 12:00, Arkalen wrote:
>> On 10/04/2024 11:25, Ernest Major wrote:
>>> On 10/04/2024 07:58, Arkalen wrote:
>>>> On 09/04/2024 23:41, Ernest Major wrote:
>>>>> On 09/04/2024 19:17, Arkalen wrote:
>>>>>>
>>>>>> Sorry, I thought you'd excluded viruses with the "step down from 
>>>>>> there" bit. The gulf is still huge between viruses and cellular 
>>>>>> life but I guess it's true the gulf between cellular life and 
>>>>>> nonlife is smaller if you include them. The issue in terms of 
>>>>>> abiogenesis is that it's unclear whether they're true 
>>>>>> intermediates or if they arose after or parallel to cellular life.
>>>>>
>>>>> It's conceivable that all three models for the origins of viruses 
>>>>> (relicts of pre-cellular life, highly reduced descendants of 
>>>>> parasitic cells, rogue genes) are true, for different groups of 
>>>>> viruses.
>>>>>
>>>>> Mimivirus has a bigger genome and more genes than some cellular 
>>>>> organisms, including some genes involved in metabolism and in 
>>>>> protein synthesis. This, and nucleocytoplasmic large DNA viruses in 
>>>>> general, seem to go some of the way in filling the gap between 
>>>>> viruses in general and cellular organisms.
>>>>>
>>>>
>>>> I agree with all of that. Just to clarify: when I talk about the 
>>>> huge gulf in complexity between viruses and cellular life I'm not 
>>>> talking about genome size, I'm talking very specifically about 
>>>> everything cellular life is that viruses aren't, with cellular 
>>>> structure & components, metabolism, translation mechanisms, all the 
>>>> resulting behavior... I don't think even mimivirus begins to compete 
>>>> in that field but I'm happy to learn more.
>>>>
>>>
>>> I don't know what mimivirus does with all its genome. The following 
>>> may give an idea of how much is actually known. (It's more than I 
>>> expected.)
>>>
>>> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9133948/
>>>
>>> Autotrophs have "complete" metabolisms. Heterotrophs need not. For 
>>> example, human lack the ability to synthesis essential amino acids 
>>> and various essential metabolic cofactors (aka vitamins).
>>
>> I don't agree with that definition of "complete" metabolism. It's not 
>> like any living thing can exist completely within itself, even 
>> autotrophs live off of external energy & nutrient sources. I think a 
>> better distinction between "full metabolism" and "not full metabolism" 
>> might be that cells pair exergonic and endergonic reactions in order 
>> to do work. In this they gain a measure of independence: they depend 
>> on the environment for the energy that powers the exergonic reactions 
>> and the basic building blocks they're made of but there are many 
>> degrees of freedom in how they can obtain them. This also both affords 
>> and requires a level of complexity that things that don't pair 
>> reactions that way don't have.
>>
> 
> Idly continuing to think on that and wondering why this pairing would 
> matter. I said "degrees of freedom" which I'm sure is part of the 
> answer. I wonder if something dumber is just storage capacity? 
> Thermodynamic reactions don't think and don't wait, there is no notion 
> of "the energy is here, you can do the reaction" let alone "the energy 
> will be here and it will balance out, you can do the reaction now" 
> (quantum phenomena excepted lol but that's a very small discrepancy they 
> allow). There needs to be a very specific *way* one reaction causes 
> another reaction to occur and notions of "energy" are just an 
> abstraction we use to think about some constraints on which reaction can 
> make which other happen.
> 
> 
> So basically if you're a system that relies on a lot of endergonic 
> reactions to happen you're kind of stuck. You need to not only exist in 
> an environment with lots of free energy, you need the *form* of that 
> free energy to very precisely match up to the specific endergonic 
> reactions you're doing. That's never going to happen is it, and if it 
> does you're completely stuck in that environment. You can't change 
> (different endergonic reactions might not work) and you can't leave (the 
> second you leave the environment your endergonic reactions stop).
> 
> 
> Compare that with a cell. It depends on its environment, that's for 
> sure! Cut it off from necessary energy and nutrient sources and it will 
> die as surely as our purely endergonic system would. But it won't die 
> *immediately*. The very critical bit - the pairing of endergonic & 
> exergonic reactions - is all done inside instead of relying on the free 
> energy of the environment, and even that's made much more flexible by 
> using ATP as a universal intermediate. That makes many more reactions 
> possible, they don't need to be paired *exactly* you just need the 
> supply of ATP to stay stable overall. There's some storage capacity 
> there albeit not much. But what really changes the game is being able to 
> run your exergonic reactions off of otherwise-inactive molecules that 
> you *can* store indefinitely. Now you can go seconds, minutes, even 
> hours without critical environmental input! There's some breathing room 
> (ha) to move or adapt.
> 
> 
> Maybe that storage ability alone is what changes the game really, it's 
> what makes the "degrees of freedom" thing possible & evolveable and 
> justifies the way we think of life as uniquely self-sustaining when we 
> know it's not. We go "life is self-sustaining. Is it? No, we die without 
> oxygen right? We're only self-sustaining for a few minutes, that's 
> nothing" without realizing that the counterfactual is a microsecond so a 
> minute is HUGE.

Humans can't survive very long without external inputs (oxygen being the 
most critical on the shortest time scales). That may not be the case for 
all species. Tardigrade tuns, bacterial cysts and plant seeds may be 
counterexamples. (They're not absolutely isolated from the environment, 
but do they depend on inputs? or do they run a minimal maintenance 
metabolism on stored reserves?)

A quick search informs me that norovirus can survive on surfaces for 
weeks. Elsewhere, concern has been expressed at ancient pathogens, 
including viruses, being released by melting permafrost, so some people 
would seem to think that survival for thousands of years is possible.
> 
> <snip>
> 

-- 
alias Ernest Major