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From: Arkalen <arkalen@proton.me>
Newsgroups: talk.origins
Subject: Re: Life: Turn it upside down!
Date: Wed, 10 Apr 2024 16:06:02 +0200
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On 10/04/2024 15:10, Ernest Major wrote:
> 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:

<snip>

>>>>
>>>> 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).

Like I said, minutes is still orders of magnitude longer than any 
nonliving dissipative system can sustain its activity without its energy 
source. An additional point that occurred to me after posting is that 
even though the system always still depends on the environment, 
metabolism also reduces the *number* of environmental factors it depends 
on, which is a flexibility evolution can work with. In modern life "how 
long you can go without X resource" is almost never a pure chemical 
constraint but is also the outcome of adaptive tradeoffs. Humans can't 
survive more than minutes without oxygen, but we live where oxygen is 
abundant. Sperm whales can survive over an hour without it.

> 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?)


I was deliberately excluding dormancy here, partly because it's an 
evolved adaptation to begin with that's not that relevant to the 
complexity gap between life and nonlife but mostly because dormancy 
involves trading off thermodynamic work for thermodynamic stability, 
often (as with viruses but not only, I seem to recall an example 
mentioned in "The Vital Question" but I don't remember the organism) not 
doing thermodynamic work at all. In that sense I'd think of it as 
"self-preserving" more than "self-sustaining", as the reduced dependence 
on environmental inputs is directly related to the (temporary) sacrifice 
of the organism's normal living activities. In the most extreme examples 
where dormancy involves no thermodynamic work it also changes the very 
definition of "survival", from "avoiding thermodynamic equilibrium" to 
"avoiding accidental disruptions to one's current state of thermodynamic 
equilibrium that would prevent revival".

Having said that it's still an important part of how life in general 
sustains itself through unfavorable environmental conditions, so fair 
enough.

> 
> 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>
>>
>