Try this. Seriously, *This!* Try this:

What is the most complex non-life?

Probably a virus. Yes a virus. Viruses do not
technically meet the definition of life.

Technically.

So step down from there: What is the most
complex non-living material/compound, other
than viruses?

Prions? Crystals?

What?

The point is, if and when you identify the
most complex example of non living things,
you just identified the gap that must be
bridged in order to produce life.

Right?

People tend to think of life as a starting
point when in all seriousness it's part of
a spectrum.

For real.

Life if part of a spectrum.

There's lots & lots of amazingly complex
structures out there that aren't alive. And
if you look at the most complex of them all,
and compare them to the least complex life
forms, THEN you start seeing where the
missing pieces have to fit.

What am I saying?

I'm saying that if you want to understand the
origins of life, stop looking at life. Start
looking at non living forms.

--
https://jtem.tumblr.com/tagged/The%20Book%20of%20JTEM/page/5

On 09/04/2024 14:17, JTEM wrote:
>
> Try this. Seriously, *This!* Try this:
>
> What is the most complex non-life?
>
> Probably a virus. Yes a virus. Viruses do not
> technically meet the definition of life.
>
> Technically.
>
> So step down from there:  What is the most
> complex non-living material/compound, other
> than viruses?
>
> Prions? Crystals?
>
> What?
>
> The point is, if and when you identify the
> most complex example of non living things,
> you just identified the gap that must be
> bridged in order to produce life.
>
> Right?
>
> People tend to think of life as a starting
> point when in all seriousness it's part of
> a spectrum.
>
> For real.
>
> Life if part of a spectrum.
>
> There's lots & lots of amazingly complex
> structures out there that aren't alive. And
> if you look at the most complex of them all,
> and compare them to the least complex life
> forms, THEN you start seeing where the
> missing pieces have to fit.
>
> What am I saying?
>
> I'm saying that if you want to understand the
> origins of life, stop looking at life. Start
> looking at non living forms.
>

It's been done, the gap was identified, and it's an unbelievably huge
gulf that's the reason the field struggled for decades to make any
headway. Turns out evolution is pretty powerful for generating complexity!

I think the alkaline hydrothermal vent theory is making good headway now
but "what's the most complex non-living system" wasn't really the
foundational insight there. More like "is there a non-living system that
could generate energy like modern cells do".

Arkalen wrote:

> It's been done

Not by everyone, not here.

> the gap was identified, and it's an unbelievably huge
> gulf

Not really. Pretty small, actually. Especially when you're
looking at the dividing line there. There's a genuine
argument over viruses, for example.

> I think the alkaline hydrothermal vent theory is making good headway now

You're doing it again. Looking at life instead of non
life, even as you argue that you're not or at least
not so much (maybe just a little?).

I talked about the study of non life.

> but "what's the most complex non-living system" wasn't really the
> foundational insight there. More like "is there a non-living system that
> could generate energy like modern cells do".

As you recall, part of the dogma is that the conditions no
longer exist. That, the conditions were perfect for spawning
life, abiogenesis occurred then immediately got up and left,
presumably searching for tea...

If conditions persisted, abiogenesis should be observed!

So take the emphasis off of life.

--
https://jtem.tumblr.com/tagged/The%20Book%20of%20JTEM/page/5

On 2024-04-09 19:03, JTEM wrote:
>  Arkalen wrote:
>
>> It's been done
>
> Not by everyone, not here.

I meant in the field.

>
>> the gap was identified, and it's an unbelievably huge gulf
>
> Not really. Pretty small, actually. Especially when you're
> looking at the dividing line there. There's a genuine
> argument over viruses, for example.

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.

>
>> I think the alkaline hydrothermal vent theory is making good headway now
>
> You're doing it again. Looking at life instead of non
> life, even as you argue that you're not or at least
> not so much (maybe just a little?).

Maybe you're not familiar with the hypothesis? It's not looking at
modern hydrothermal vent life, it starts with a fully abiotic scenario.

>
> I talked about the study of non life
>
>> but "what's the most complex non-living system" wasn't really the
>> foundational insight there. More like "is there a non-living system
>> that could generate energy like modern cells do".
>
> As you recall, part of the dogma is that the conditions no
> longer exist. That, the conditions were perfect for spawning
> life, abiogenesis occurred then immediately got up and left,
> presumably searching for tea...
>
> If conditions persisted, abiogenesis should be observed!
>
> So take the emphasis off of life.
>

The alkaline hydrothermal vent hypothesis doesn't involve modern
alkaline hydrothermal vents, in fact it relies on the assumption the
chemistry would have worked out differently in an acidic, non-oxygenated
ocean.

--
Cet e-mail a été vérifié par le logiciel antivirus d'Avast.
www.avast.com

Arkalen wrote:

> The alkaline hydrothermal vent hypothesis doesn't involve modern
> alkaline hydrothermal vents, in fact it relies on the assumption the
> chemistry would have worked out differently in an acidic, non-oxygenated
> ocean.

It's Faith-Based.

If you study non life you study things that actually exist.

And I don't mean you begin with viruses or prions, either.

"Spectrum."

Create a "Complexity Spectrum" the way you might construct
a color spectrum.

Wait. That's not it.

"Electromagnetic Spectrum."

Because it doesn't begin with visible light, and it doesn't
even end there!

Who knows? Maybe if we framed life within a proper spectrum
is wouldn't end with our concept of life!

God?

Forms of intelligence we have yet to imagine?

That's pure speculation... speculating the spectrum... I
love it! I'm too clever by at least half! Or at least that's
what I say...

Okay, but properly framed within a spectrum, we certainly
don't start with life. We know that.

Where is such a spectrum published?

--
https://jtem.tumblr.com/tagged/The%20Book%20of%20JTEM/page/5

On 2024-04-09 20:34, JTEM wrote:
>  Arkalen wrote:
>
>
>> The alkaline hydrothermal vent hypothesis doesn't involve modern
>> alkaline hydrothermal vents, in fact it relies on the assumption the
>> chemistry would have worked out differently in an acidic,
>> non-oxygenated ocean.
>
> It's Faith-Based.

No, it's based on general knowledge of chemistry and the data we have on
early Earth conditions.

>
> If you study non life you study things that actually exist.

That can be true or false whether you study life or nonlife. In this
case while we no longer have an oxygen-less ocean we can simulate such
conditions when doing experiments; those experiments involve things that
actually exist.

>
> And I don't mean you begin with viruses or prions, either.
>
> "Spectrum."
>
> Create a "Complexity Spectrum" the way you might construct
> a color spectrum >
> Wait. That's not it.
>
> "Electromagnetic Spectrum."
>
> Because it doesn't begin with visible light, and it doesn't
> even end there!
>
> Who knows? Maybe if we framed life within a proper spectrum
> is wouldn't end with our concept of life!
>
> God?
>
> Forms of intelligence we have yet to imagine?
>
> That's pure speculation... speculating the spectrum... I
> love it! I'm too clever by at least half! Or at least that's
> what I say...
>
> Okay, but properly framed within a spectrum, we certainly
> don't start with life. We know that.
>
> Where is such a spectrum published?
>

I don't know if any such spectrum is explicitly published, to my
knowledge its contents are basically what you listed in your OP. So not
exactly warranting a paper but maybe there are review papers or
subject-matter papers with good introductions that address your idea.
I'll keep you posted if I look it up.

--
Cet e-mail a été vérifié par le logiciel antivirus d'Avast.
www.avast.com

Arkalen wrote:

> JTEM wrote:

>> It's Faith-Based.

> No, it's based on general knowledge of chemistry and the data we have on
> early Earth conditions.

That is literally Faith-Based! Because you have no idea what
is required to spontaneously form life, or even if it were
ever possible. Abiogenesis is not the only game in town, not
even the only scientific game.

So it's based on beliefs. Plural.

>> If you study non life you study things that actually exist.

> That can be true or false whether you study life or nonlife.

Working out abiogenesis is studying things that do not exist,
including the theorized environment... not to mention HOW
this environment could manage it.

Study non life is actually studying things that exist.

> In this
> case while we no longer have an oxygen-less ocean we can simulate such
> conditions when doing experiments; those experiments involve things that
> actually exist.

If those experiments ever succeeded, which they haven't, that
would prove that Creationism is real. After all, it would be
an example of an intelligence bringing into existence life by
intent, by design. But it wouldn't and couldn't "Prove" that
it ever happened in nature.

> I don't know if any such spectrum is explicitly published

Well there's your problem!

> to my
> knowledge its contents are basically what you listed in your OP.

Oh, dude; I was woafully under performing there! We're talking
a HUGE spectrum, from the most basic forms of matter to the
most complex examples of non-living structures... onto the very
simplest forms of life...

Think of it like the "Electromagnetic Spectrum." We're talking
BIG here, very BIG -- the opposite of small.

> So not
> exactly warranting a paper

Lol! It's exactly what papers need to be written about!

THAT IS THE POINT!

It's an approach that needs to take over, be completed in order
to make any legitimate discoveries.

> but maybe there are review papers or
> subject-matter papers with good introductions that address your idea.
> I'll keep you posted if I look it up.

Science is gone anyways. It's all driven by money: Grants.

If it doesn't have a direct military or financial benefit, it's
politics now.

So don't hold your breath.

--
https://jtem.tumblr.com/tagged/The%20Book%20of%20JTEM/page/5

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.

--
alias Ernest Major

On 09/04/2024 21:37, JTEM wrote:
>  Arkalen wrote:
>
>>  JTEM wrote:
>
>>> It's Faith-Based.
>
>> No, it's based on general knowledge of chemistry and the data we have
>> on early Earth conditions.
>
> That is literally Faith-Based!  Because you have no idea what
> is required to spontaneously form life, or even if it were
> ever possible. Abiogenesis is not the only game in town, not
> even the only scientific game.
>
> So it's based on beliefs. Plural.

Sorry; your reply of "it's Faith-based" was to the following:

"The alkaline hydrothermal vent hypothesis doesn't involve modern
alkaline hydrothermal vents, in fact it relies on the assumption the
chemistry would have worked out differently in an acidic, non-oxygenated
ocean."

I thought the "faith" you were referring to was "our partial knowledge
of the conditions of early Earth" but I take it you just meant the
hypothesis overall?

The alkaline hydrothermal vent hypothesis starts out focusing on the
proton motive force that all cells use for energy and noticing that the
conditions for the proton gradient it involves would have existed in
alkaline hydrothermal vents in early Earth oceans: alkaline fluid caused
by the serpentinization reaction between water and rock seeps into the
ocean through rocky pores, inducing a pH gradient across the walls of
those pores that's very like the pH gradient across prokaryotic cell
membranes today. They further noticed that the minerals in such pores
match up with the cores of enzymes like acetyl CoA involved in carbon
fixation, up to their crystalline structure, and have some catalytic
activity of their own.

https://nick-lane.net/wp-content/uploads/2016/12/Sojo-et-al-Astrobiology-review.pdf

They ran experiments exploring how carbon fixation could work under such
chemical conditions and there's been a lot of recent progress:

The paper where they actually pulled off reducing CO2 to formose IIRC:
https://www.pnas.org/doi/full/10.1073/pnas.2002659117

Exploration of the synthesis of various other relevant biomolecules:
https://www.nature.com/articles/s41467-021-26158-2
https://www.liebertpub.com/doi/10.1089/ast.2021.0125
https://www.mdpi.com/2075-1729/13/5/1177

Something about trying out simpler ATP precursors & coming up with
insights why ATP might be use now:
https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001437
https://link.springer.com/article/10.1007/s11084-018-9555-8

Recent years have shown a merging of this pure metabolism-first
hypothesis with other strains of abiogenesis research, including the
idea the earliest cells could have self-assembled from lipids, which
this fits well with (and gives a source for the lipids!). Again with
experiments into how that could work in the Hadean AHV conditions:

https://www.nature.com/articles/s41559-019-1015-y
https://royalsocietypublishing.org/doi/10.1098/rsfs.2019.0067

And they're even closing the circle on the biggest bootstrap problems in
abiogenesis - after all you're metabolism first OK but then whence
genes? And how does it resolve RNA first vs protein first? These are
mostly computational models so far, but of course very much rooted in
the known chemistry and ongoing experiments into that chemistry:

https://royalsocietypublishing.org/doi/10.1098/rsfs.2019.0067
https://www.mdpi.com/2075-1729/13/5/1129

The circle closes as follows: the pH gradient in those early vents would
have reduced CO2 and basically been an ongoing reaction continuously
generating simple organic molecules in the vent. Lipids & such would
spontaneously form protocells, and peptides would bind to vent minerals
& the membranes and some would catalyze the reduction of CO2, causing
more organic molecules to be formed. This would induce a very limited
kind of reproduction & heredity and therefore natural selection in those
protocells: membranes with peptides that catalyzed CO2 reduction well
would grow and split faster, causing a feedback loop that increased the
catalysis of CO2 reduction and the resulting concentration of organic
molecules. Nucleotides could emerge in such an environment and this in
turn solves one of the issues with RNA World - if RNA is selected for
speed or accuracy of replication then that pushes it towards *shorter*
chains, not complex ones. But if RNA is selected *from the start* for
increased CO2 reduction because it's part of a protocell that's already
multiplying & under selective pressure for that parameter, then that's
no longer an issue.

The most exciting aspect of the hypothesis IMO is how well it fits with
looking at the question from the other direction: inferring the
properties of LUCA from a phylogenetic analysis of modern life. This
reveals that archae and bacteria have common mechanisms for most things
- RNA replication, translation, ATP synthesis, etc, but have different
mechanisms for all things membrane-related. They both rely on the proton
gradient across their cells for ATP, and do it in the same way, but they
*generate* that gradient in different ways! This is perfectly explained
by LUCA being an organism that relied on a natural proton gradient, and
bacteria & archaea being two branches of that tree that independently
evolved ways of pumping protons across their membranes using the Ech
protein, which allowed them to live outside the vents. (the first
article I linked might get into that aspect)

You know what I just saw this review article that seems to sum
everything up and that I should probably read because it's from 2023, so
truly the latest dirt:
https://www.annualreviews.org/content/journals/10.1146/annurev-ecolsys-110421-101509

(Also sorry to all the non-Nick Lane folk working on this, his website
is still my best link list in a pinch)

Anyway this is all just to say the alkaline hydrothermal vent hypothesis
is a normal scientific hypothesis, relying on inferences from current
knowledge, hypotheses & models on possible causes and experiments to
test those hypotheses & models and gather further knowledge.

>
>>> If you study non life you study things that actually exist.
>
>> That can be true or false whether you study life or nonlife.
>
> Working out abiogenesis is studying things that do not exist,
> including the theorized environment... not to mention HOW
> this environment could manage it.
>
> Study non life is actually studying things that exist.

Well you might be reassured then to find that all the experimental work
linked above is very much into non-life that exists.

>
>> In this case while we no longer have an oxygen-less ocean we can
>> simulate such conditions when doing experiments; those experiments
>> involve things that actually exist.
>
> If those experiments ever succeeded, which they haven't, that
> would prove that Creationism is real. After all, it would be
> an example of an intelligence bringing into existence life by
> intent, by design. But it wouldn't and couldn't "Prove" that
> it ever happened in nature.

That seems to assume the only possible abiogenesis experiment is "making
a cell from scratch" but that's never how science or experiments work.
Experiments are always about testing some testable aspect of a
hypothesis. That would be like saying we never tested the theory of
relativity until we put GPS satellites into orbit or something.

>
>> I don't know if any such spectrum is explicitly published
>
> Well there's your problem!
>
>> to my knowledge its contents are basically what you listed in your OP.
>
> Oh, dude; I was woafully under performing there!  We're talking
> a HUGE spectrum, from the most basic forms of matter to the
> most complex examples of non-living structures... onto the very
> simplest forms of life...

And I'm telling you most of that spectrum is empty, shows a huge gulf.
I'll give you that I could add some things to your list, most notably
dissipative systems like tornadoes. But if you think the spectrum is
full then you should have no trouble at all populating it better than
you did there.

I mean, obviously every element of that spectrum has to have been
realized at some point, or abiogenesis couldn't have happened. But you
seem focused on only looking at things that exist now, so.

>
> Think of it like the "Electromagnetic Spectrum." We're talking
> BIG here, very BIG -- the opposite of small.
>
>> So not exactly warranting a paper
>
> Lol!  It's exactly what papers need to be written about!
>
> THAT IS THE POINT!
>
> It's an approach that needs to take over, be completed in order
> to make any legitimate discoveries.
>
>> but maybe there are review papers or subject-matter papers with good
>> introductions that address your idea. I'll keep you posted if I look
>> it up.
>
> Science is gone anyways. It's all driven by money:  Grants.
>
> If it doesn't have a direct military or financial benefit, it's
> politics now.
>
> So don't hold your breath.
>

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.

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). Parasites,
especially intracellular parasites (including parasitic plants, which
invade their hosts at the intracellular level) lack even more of the
metabolism, scavenging chemicals from their hosts. With 1,000 or so
genes, mimivirus also has a truncated metabolism (I don't know how it
compares to say Wolbachia, but with comparable numbers of genes a
comparison seems an obvious thing to investigate.) A difference between
mimiviruses and intracellular parasites is that the latter have their
own cytoplasm, while the former utilises the host cytoplasm as a
substrate for its metabolism. That's still a big difference - but is it
the only difference in kind between mimiviruses and the simplest
intracellular parasitic organisms? (According to the above paper
mimivirus has an immune system, which is something one could imagine a
cellular organism lacking.)

One can imagine an intermediate condition - where the parasite has its
own cytoplasm, but also exports enzymes into the host cytoplasm to
extend its metabolism into the host cytoplasm. (At a grosser scale
venoms are somewhat analogous, but being associated with predation
rather than parasitism are purely destructive. However fungal parasites
modify the behaviour of their hosts may be getting closer to this
intermediate, though I suspect this also is more interference with the
host metabolism rather than parasitising it.)

A contrary hypothesis is that large parts of the mimivirus genome are
junk DNA - remnants not yet eliminated of a ancestral cellular state, or
alternatively host genes accidentally incorporated in the mimivirus
genome, the retention of which is permitted by the large size of the
mimivirus capsid. I would expect that mimiviruses, like bacteria, would
be under effective selection for the removal of superfluous DNA, but one
could postulate a structural role - the excess DNA serving as packing to
maintain the integrity of the capsid. There is a wide variety of genome
sizes among mimivirus and its relatives, which would seem to allow this
hypothesis to be tested by looking for a correlation between capsid
volume and genome size.

--
alias Ernest Major

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.

In that sense heterotrophs and autotrophs both have full metabolisms,
it's their energy sources that differ.

(and this is me now remembering that this is actually the whole point of
the word "metabolism" - the union of catabolism with anabolism)

> Parasites,
> especially intracellular parasites (including parasitic plants, which
> invade their hosts at the intracellular level) lack even more of the
> metabolism, scavenging chemicals from their hosts. With 1,000 or so
> genes, mimivirus also has a truncated metabolism (I don't know how it
> compares to say Wolbachia, but with comparable numbers of genes a
> comparison seems an obvious thing to investigate.) A difference between
> mimiviruses and intracellular parasites is that the latter have their
> own cytoplasm, while the former utilises the host cytoplasm as a
> substrate for its metabolism. That's still a big difference - but is it
> the only difference in kind between mimiviruses and the simplest
> intracellular parasitic organisms? (According to the above paper
> mimivirus has an immune system, which is something one could imagine a
> cellular organism lacking.)

I agree those are much more similar than I'd been thinking; I was
thinking of viruses as they are outside of the cell but you're right
that when you consider their activity inside of the cell then there's
much less reason to say that activity isn't "metabolism". Except for
that whole "meta" part of "metabolism" : does mimivirus do catabolism?
Do intracellular parasites?

I'll look it up after posting but I notice you point out the difference
that intracellular parasites have their own cytoplasm. I will hazard the
guess that this means they have their own *membranes*, and further
hazard the guess that they use respiration to generate a proton motive
force across that membrane to regenerate ATP. I could see it if they
didn't, after all they can get ATP from the host cell can't they. But if
they do, that would be metabolism with the "meta".

>
> One can imagine an intermediate condition - where the parasite has its
> own cytoplasm, but also exports enzymes into the host cytoplasm to
> extend its metabolism into the host cytoplasm. (At a grosser scale
> venoms are somewhat analogous, but being associated with predation
> rather than parasitism are purely destructive. However fungal parasites
> modify the behaviour of their hosts may be getting closer to this
> intermediate, though I suspect this also is more interference with the
> host metabolism rather than parasitising it.)
>
> A contrary hypothesis is that large parts of the mimivirus genome are
> junk DNA - remnants not yet eliminated of a ancestral cellular state, or
> alternatively host genes accidentally incorporated in the mimivirus
> genome, the retention of which is permitted by the large size of the
> mimivirus capsid. I would expect that mimiviruses, like bacteria, would
> be under effective selection for the removal of superfluous DNA, but one
> could postulate a structural role - the excess DNA serving as packing to
> maintain the integrity of the capsid. There is a wide variety of genome
> sizes among mimivirus and its relatives, which would seem to allow this
> hypothesis to be tested by looking for a correlation between capsid
> volume and genome size.
>

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.

<snip>

On 10/04/2024 11:00, 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.

Don't sweat the choice of scare-quoted word (and I don't think that full
versus non-full is semantically different from complete versus
incomplete) - the point was to establish a spectrum of the degree of
dependence on other organisms as a source of biochemical molecules, with
a hypothetical endpoint (which I suspect is achieved in some autotrophs)
of no dependence of all, so I could place mimiviruses on that spectrum
as close to intracellular parasites.

At the far (lower) end of the spectrum are viroids. Viroids like the
Potato Spindle Tuber Viroid have no metabolism - they're passively
replicated by the host machinery. Viroids like the Avocado Sum Blotch
Viroid are a miniscule step along the spectrum - they're self modifying
ribozymes.

https://www.mdpi.com/1422-0067/22/7/3476

"Classic" viruses can be considerably less complex. A minimal virus
would be an RNA which code for structural proteins, which on synthesis
by the host cell spontaneously assemble, in conjunction with host
replicated genomes, to form virus particles. Some viruses have also have
enzymes, either packaged in the viral particle, or synthesised in the
host cytoplasm, providing a minimal metabolism. For example DNA viruses
that replicate in the cytoplasm rather than the nucleocytoplasm, require
reverse transcriptases to convert their genomes to RNA which can then
hijack the host machinery. As I said, I don't know what mimivirus is
doing with its genome, but with a 1000+ genes, I suspect that it's at
least approaching intracellular parasites in metabolic complexity.
>
> In that sense heterotrophs and autotrophs both have full metabolisms,
> it's their energy sources that differ.
>
> (and this is me now remembering that this is actually the whole point of
> the word "metabolism" - the union of catabolism with anabolism)
>
>> Parasites, especially intracellular parasites (including parasitic
>> plants, which invade their hosts at the intracellular level) lack even
>> more of the metabolism, scavenging chemicals from their hosts. With
>> 1,000 or so genes, mimivirus also has a truncated metabolism (I don't
>> know how it compares to say Wolbachia, but with comparable numbers of
>> genes a comparison seems an obvious thing to investigate.) A
>> difference between mimiviruses and intracellular parasites is that the
>> latter have their own cytoplasm, while the former utilises the host
>> cytoplasm as a substrate for its metabolism. That's still a big
>> difference - but is it the only difference in kind between mimiviruses
>> and the simplest intracellular parasitic organisms? (According to the
>> above paper mimivirus has an immune system, which is something one
>> could imagine a cellular organism lacking.)
>
> I agree those are much more similar than I'd been thinking; I was
> thinking of viruses as they are outside of the cell but you're right
> that when you consider their activity inside of the cell then there's
> much less reason to say that activity isn't "metabolism". Except for
> that whole "meta" part of "metabolism" : does mimivirus do catabolism?
> Do intracellular parasites?
>
> I'll look it up after posting but I notice you point out the difference
> that intracellular parasites have their own cytoplasm. I will hazard the
> guess that this means they have their own *membranes*, and further
> hazard the guess that they use respiration to generate a proton motive
> force across that membrane to regenerate ATP. I could see it if they
> didn't, after all they can get ATP from the host cell can't they. But if
> they do, that would be metabolism with the "meta".

Microsporidia have lost the ability to generate their own ATP. The same
is said of Giardia.
>
>>
>> One can imagine an intermediate condition - where the parasite has its
>> own cytoplasm, but also exports enzymes into the host cytoplasm to
>> extend its metabolism into the host cytoplasm. (At a grosser scale
>> venoms are somewhat analogous, but being associated with predation
>> rather than parasitism are purely destructive. However fungal
>> parasites modify the behaviour of their hosts may be getting closer to
>> this intermediate, though I suspect this also is more interference
>> with the host metabolism rather than parasitising it.)
>>
>> A contrary hypothesis is that large parts of the mimivirus genome are
>> junk DNA - remnants not yet eliminated of a ancestral cellular state,
>> or alternatively host genes accidentally incorporated in the mimivirus
>> genome, the retention of which is permitted by the large size of the
>> mimivirus capsid. I would expect that mimiviruses, like bacteria,
>> would be under effective selection for the removal of superfluous DNA,
>> but one could postulate a structural role - the excess DNA serving as
>> packing to maintain the integrity of the capsid. There is a wide
>> variety of genome sizes among mimivirus and its relatives, which would
>> seem to allow this hypothesis to be tested by looking for a
>> correlation between capsid volume and genome size.
>>
>

--
alias Ernest Major

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

Ernest Major wrote:

> 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.

There are claims for life surviving dormant for up to a quarter of
a billion years. Though this is not entirely accepted, there's not
an over abundance of counter claims, and bacteria north of 100k
years in age is considered established.

--
https://jtem.tumblr.com/tagged/The%20Book%20of%20JTEM/page/5

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>
>>
>

Arkalen wrote:

> Sorry; your reply of "it's Faith-based" was to the following:
>
> "The alkaline hydrothermal vent hypothesis doesn't involve modern
> alkaline hydrothermal vents

So, nothing that exists.

> in fact it relies on the assumption

Faith based.

> I thought the "faith" you were referring to was "our partial knowledge
> of the conditions of early Earth" but I take it you just meant the
> hypothesis overall?

The faith begins with the belief that abiogenesis even happened.

Panspermia is equally as valid.

There's also creationism, yes.

It's also possible that abiogenesis did occur, on Mars or even
in another solar system, only for life to be deposited on Earth
via some cross contamination...

It's a variation on Panspermia, I know, but classical Panspermia
has life forming as a consequence of the Big Bang.

> That seems to assume the only possible abiogenesis experiment is "making
> a cell from scratch" but that's never how science or experiments work.
> Experiments are always about testing some testable aspect of a
> hypothesis. That would be like saying we never tested the theory of
> relativity until we put GPS satellites into orbit or something.

A hypothesis explains the evidence/observations AND serves as the
basis of predictions. These predictions, in turn, lend themselves
to scientific testing -- experimentation, observation. This testing,
if failed, falsifies the hypothesis. There was less than
compelling confirmation of an Einstein prediction almost right
away, but it did take a few years before the first solid
scientific test confirmed a prediction.

However...

'Tis the nature of "Evidence" to support more than one conclusion.
A positive test result of a prediction IS CONSISTENT WITH a
hypothesis, but in almost all cases is also consistent with other
explanations. So scientifically confirming a prediction of an
abiogenesis hypothesis isn't as convincing as some might believe.

Ideas are really only good or bad in comparison to other ideas,
not themselves.

>> Oh, dude; I was woafully under performing there!  We're talking
>> a HUGE spectrum, from the most basic forms of matter to the
>> most complex examples of non-living structures... onto the very
>> simplest forms of life...

> And I'm telling you most of that spectrum is empty, shows a huge gulf.

That would be more convincing if either one of us could point to
such a spectrum -- mapped out, scientifically. But we can't. So
you are arguing... what?

My point from the beginning is that we need this spectrum laid out.
The work has to be done. BECAUSE it hasn't been.

The spectrum isn't empty, it's ignored.

> I'll give you that I could add some things to your list, most notably
> dissipative systems like tornadoes. But if you think the spectrum is
> full then you should have no trouble at all populating it better than
> you did there.

My point is that people are approaching this all wrong. That, nobody
has done this basic work.

Did you know homosexuality was originally classified as a mental
illness, a disorder? Do you know why they stopped? Because someone
got the idea to look for gay men who were NOT being treated for
mental health issues. Turns out that if the only gay men you ever
look at are the ones in therapy, you get the idea that all gay men
suffer from mental health issues!

What you are NOT looking at is important. Sometimes it's more
important than what you are looking at.

> I mean, obviously every element of that spectrum has to have been
> realized at some point, or abiogenesis couldn't have happened.

We're back to being faith-based. Abiogenesis is not the only
game in town. And even if it did happen somewhere on the
surface of a planet, this may not have been that planet! It
may literally be impossible to identify any environment that
had ever existed on this Earth which might've resulted in
abiogenesis... if it ever happened anywhere.

So switch the focus. Study things that are real, that actually
exist.

> But you
> seem focused on only looking at things that exist now, so.

That's me, focused on what I can see instead of what doesn't
exist!

--
https://jtem.tumblr.com/tagged/The%20Book%20of%20JTEM/page/5

On 10/04/2024 16:16, JTEM wrote:
>  Arkalen wrote:
>
>> Sorry; your reply of "it's Faith-based" was to the following:
>>
>> "The alkaline hydrothermal vent hypothesis doesn't involve modern
>> alkaline hydrothermal vents
>
> So, nothing that exists.
>
>> in fact it relies on the assumption
>
> Faith based.
>

You're repeating your original reaction to that sentence in a way that
makes it clearer that you really are just reacting to the word
"assumption" that refers to pretty well-accepted facts about the
primordial Earth. I would take it as a confirmation that you think
things like "there wasn't free oxygen in the atmosphere in that Hadean"
are faith, but then you say this:

>> I thought the "faith" you were referring to was "our partial knowledge
>> of the conditions of early Earth" but I take it you just meant the
>> hypothesis overall?
>
> The faith begins with the belief that abiogenesis even happened.

So it doesn't seem you're applying that word in a very consistent way.

>
> Panspermia is equally as valid.
>

No, the alkaline hydrothermal vent hypothesis is far and away superior
to all others in scope, specificity, evidential support and predictive
power. It's especially superior to panspermia which isn't even so much a
hypothesis as a vague notion that doesn't actually explain the origin of
life.

> There's also creationism, yes.

Sure. I figured that since you were talking about a spectrum of
complexity in things that actually exist from life to nonlife that the
context of this thread was naturalistic explanations.

>
> It's also possible that abiogenesis did occur, on Mars or even
> in another solar system, only for life to be deposited on Earth
> via some cross contamination...

Way more likely that it was in alkaline hydrothermal vents.

>
> It's a variation on Panspermia, I know, but classical Panspermia
> has life forming as a consequence of the Big Bang.
>
>> That seems to assume the only possible abiogenesis experiment is
>> "making a cell from scratch" but that's never how science or
>> experiments work. Experiments are always about testing some testable
>> aspect of a hypothesis. That would be like saying we never tested the
>> theory of relativity until we put GPS satellites into orbit or something.
>
> A hypothesis explains the evidence/observations AND serves as the
> basis of predictions. These predictions, in turn, lend themselves
> to scientific testing -- experimentation, observation. This testing,
> if failed, falsifies the hypothesis. There was less than
> compelling confirmation of an Einstein prediction almost right
> away, but it did take a few years before the first solid
> scientific test confirmed a prediction.
>
> However...
>
> 'Tis the nature of "Evidence" to support more than one conclusion.
> A positive test result of a prediction IS CONSISTENT WITH a
> hypothesis, but in almost all cases is also consistent with other
> explanations. So scientifically confirming a prediction of an
> abiogenesis hypothesis isn't as convincing as some might believe.
>
> Ideas are really only good or bad in comparison to other ideas,
> not themselves.

Sure, and the alkaline hydrothermal vent hypothesis is really good in
comparison to pretty much all of the other ideas on abiogenesis I'm
aware of, although I'd love to see that challenged.

In this case though the competing ideas are so different that the
experimental results linked in the papers I linked are mostly relevant
to this hypothesis. Certainly they can suggest different variants of
this hypothesis, in which case scientists can figure out different
predictions those variants make and come up with experiments that would
distinguish them. But it's hard for, say, an experimental result showing
you can fix CO2 into formate in alkaline-hydrothermal-vent conditions to
support or not support panspermia, or a hypothesis that abiogenesis
happened on land or whatever. What that experimental result does to is
increase the specificity and plausibility of the AHV hypothesis, which
turns it into a better hypothesis, which if the others *don't* also
become better hypotheses via their own experimental results means it
becomes better than those others.

>
>>> Oh, dude; I was woafully under performing there!  We're talking
>>> a HUGE spectrum, from the most basic forms of matter to the
>>> most complex examples of non-living structures... onto the very
>>> simplest forms of life...
>
>> And I'm telling you most of that spectrum is empty, shows a huge gulf.
>
> That would be more convincing if either one of us could point to
> such a spectrum -- mapped out, scientifically. But we can't. So
> you are arguing... what?

Here's me pointing->:
....water&lower -> Tornadoes, crystals, abiotic autocatalytic reactions,
alcohol -> polycyclic aromatic hydrocarbons, long alkanes -> [huge gap]
-> most viruses -> giant viruses, intracellular parasites? ->
prokaryotic cells -> eukaryotic cells & higher...

Shouldn't be too hard for you to fill that gap if what you're saying is
true.

>
> My point from the beginning is that we need this spectrum laid out.
> The work has to be done. BECAUSE it hasn't been.
>
> The spectrum isn't empty, it's ignored.
>

How could we tell the difference ?

>> I'll give you that I could add some things to your list, most notably
>> dissipative systems like tornadoes. But if you think the spectrum is
>> full then you should have no trouble at all populating it better than
>> you did there.
>
> My point is that people are approaching this all wrong. That, nobody
> has done this basic work.
>
> Did you know homosexuality was originally classified as a mental
> illness, a disorder? Do you know why they stopped? Because someone
> got the idea to look for gay men who were NOT being treated for
> mental health issues. Turns out that if the only gay men you ever
> look at are the ones in therapy, you get the idea that all gay men
> suffer from mental health issues!
>
> What you are NOT looking at is important. Sometimes it's more
> important than what you are looking at.
>
>> I mean, obviously every element of that spectrum has to have been
>> realized at some point, or abiogenesis couldn't have happened.
>
> We're back to being faith-based. Abiogenesis is not the only
> game in town. And even if it did happen somewhere on the
> surface of a planet, this may not have been that planet! It
> may literally be impossible to identify any environment that
> had ever existed on this Earth which might've resulted in
> abiogenesis... if it ever happened anywhere.

Nah it's not impossible, several perfectly cromulent candidates were
identified including the one it actually happened in which is alkaline
hydrothermal vents. (I'm being cheeky of course; what's more to the
point for your point is that it's definitely and unambiguously an
environment which MIGHT'VE resulted in abiogenesis)

>
> So switch the focus. Study things that are real, that actually
> exist.

I'm extremely confused. Are you saying there are tons of entities that
exist today that are intermediate steps between life and non-life such
that no complexity gap between the two exist, but also life didn't start
from non-life? Or all the entities are somewhere other than Earth?

>
>> But you seem focused on only looking at things that exist now, so.
>
> That's me, focused on what I can see instead of what doesn't
> exist!
>
>
>
>

Arkalen wrote:

> You're repeating your original reaction to that sentence in a way that
> makes it clearer that you really are just reacting to the word
> "assumption"

I am responding to what is said, correct.

I think I can speak for everyone, and if I can't I certainly should
be able to, when I say that amongst the more annoying things on
usenet is when people ignore what you say and, instead, react to
something that was never stated.

But I'm just brilliant, that's all. What do I know?

> that refers to pretty well-accepted facts about the
> primordial Earth.

Yet we both know that we don't have all the answers, because if
we did we'd never even have discussions such as this.

There are working assumptions. Abiogenesis is a working assumption
and it's wrong it assume that it's a fact, much less a well
accepted fact.

There are other ideas out there, including other scientific ideas.

There's a lot of interesting things, published online, on the
topic of a-priori assumptions. I know you're plenty familiar
with the concept and the pitfalls but maybe a reminder?

> I would take it as a confirmation that you think
> things like "there wasn't free oxygen in the atmosphere in that Hadean"
> are faith, but then you say this:

If abiotic oxygen is a myth, life has already been discovered
on Mars. Ganymede. Europa.

>> The faith begins with the belief that abiogenesis even happened.

> So it doesn't seem you're applying that word in a very consistent way.

That does not follow.

There's more than one potential answer. A BELIEF, a FAITH in
one in particular is FAITH BASED.

>> Panspermia is equally as valid.
>>

> No

Of course it is.

> the alkaline hydrothermal vent hypothesis is far and away superior
> to all others in scope, specificity, evidential support and predictive
> power.

Lol! Nothing is useful unless and until life is spontaneously
formed under laboratory conditions. AND THEN that's when the
debate begins! Because it won't "Prove" that it ever happened
in nature, only that it is not excluded.

> It's especially superior to panspermia which isn't even so much a
> hypothesis as a vague notion that doesn't actually explain the origin of
> life.

Science is about stepping outside of yourself. That is literally
why it exists. Humans are so biased that we need a specific
set of rules, a process we must follow to keep up from latching
onto whatever our knee-jerk tells us.

Science was created to remove the human element.

You're insisting that the human element is what validates the
work.

>> There's also creationism, yes.
>
> Sure. I figured that since you were talking about a spectrum of
> complexity in things that actually exist from life to nonlife that the
> context of this thread was naturalistic explanations.

The problem with Creationism is that abiogenesis, in a lab, would
be an example of same. So you're not escaping Creationism with
such goals, you're trying to validate it with an actual example!

Ironic, I know.

>> It's also possible that abiogenesis did occur, on Mars or even
>> in another solar system, only for life to be deposited on Earth
>> via some cross contamination...

> Way more likely that it was in alkaline hydrothermal vents.

It's not a vote. And there is no outcome to such a pursuit that
would "Prove" abiogenesis over, say, Creationism.

> Sure, and the alkaline hydrothermal vent hypothesis is really good in
> comparison to pretty much all of the other ideas on abiogenesis

Rather circular, that. And anyone proposing a different answer
would be definition be disagreeing with you.

What do you have in common with all of them? That's a start.

>>> And I'm telling you most of that spectrum is empty, shows a huge gulf.
>>
>> That would be more convincing if either one of us could point to
>> such a spectrum -- mapped out, scientifically. But we can't. So
>> you are arguing... what?

> Here's me pointing->:
> ...water&lower -> Tornadoes, crystals, abiotic autocatalytic reactions,
> alcohol -> polycyclic aromatic hydrocarbons, long alkanes -> [huge gap]
> -> most viruses -> giant viruses, intracellular parasites? ->
> prokaryotic cells -> eukaryotic cells & higher...

This is usenet. The internet. I just read a claim that the exact same
scientists who worked out the date, time & location of the eclipse
are the people who have determined that Gwobull Warbling is REEL!

Matter exists along a spectrum. All matter. Map it out. Speaking
rhetorically. Not saying you should do it but I am saying that it
needs to be done.

> Shouldn't be too hard for you to fill that gap if what you're saying is
> true.

And yet we both know that it's never been done.

>> The spectrum isn't empty, it's ignored.

> How could we tell the difference ?

Someone could attempt to map out all life and non life: Matter.

The claim is that the very same nature which produced diamonds
and forms lithium can also produce life. This life is not a
separate and distinct form of matter, it lies along a spectrum.

This much is a fact.

To claim anything else is to argue divine intervention!

So if we understand that spectrum we understand life, and an
understanding of that spectrum begins with actually mapping
it out.

>>> I mean, obviously every element of that spectrum has to have been
>>> realized at some point, or abiogenesis couldn't have happened.
>>
>> We're back to being faith-based. Abiogenesis is not the only
>> game in town. And even if it did happen somewhere on the
>> surface of a planet, this may not have been that planet! It
>> may literally be impossible to identify any environment that
>> had ever existed on this Earth which might've resulted in
>> abiogenesis... if it ever happened anywhere.

> Nah it's not impossible, several perfectly cromulent candidates were
> identified including the one it actually happened in which is alkaline
> hydrothermal vents.

Nah, you're trolling.

>> So switch the focus. Study things that are real, that actually
>> exist.

> I'm extremely confused. Are you saying there are tons of entities that
> exist today that are intermediate steps between life and non-life such
> that no complexity gap between the two exist, but also life didn't start
> from non-life? Or all the entities are somewhere other than Earth?

Is that how you see the Electromagnetic Spectrum? As a series of
intermediate steps?

--
https://jtem.tumblr.com/tagged/The%20Book%20of%20JTEM/page/5

On 10/04/2024 22:50, JTEM wrote:
>  Arkalen wrote:
>

<snip>

>
> There are working assumptions. Abiogenesis is a working assumption
> and it's wrong it assume that it's a fact, much less a well
> accepted fact.

I'm not talking about abiogenesis in that (snipped) sentence, I'm
talking about the conditions on early Earth, which is what you continue
to seem to claim you were referring to when you talked about "faith".
Can you clarify for me which if any of these claims you'd be willing to
grant as plausible enough to draw inferences from in this conversation?

1) Earth existed as a planet 4 billion years ago
2) Earth did not exist as a planet 6 billion years ago
3) Earth formed by accretion around the same time the rest of the Solar
System did
4) Photosynthetic life did not exist in the earliest stages of Earth's
existence
5) in the lade Hadean/Archean period Earth had a solid crust and oceans
6) alkaline hydrothermal vents exist today
7) alkaline hydrothermal vents are created by the reaction of
serpentinization between mantle minerals like olivine and water
8) the conditions for the existence of hydrothermal vents were as or
more common in the lade Hadean/Archean vs today
9) the atmosphere in the late Hadean/Archean was reducing, with
low-to-negligible levels of oxygen and higher-than-today levels of
carbon dioxide and methane

>
> There are other ideas out there, including other scientific ideas.
>
> There's a lot of interesting things, published online, on the
> topic of a-priori assumptions. I know you're plenty familiar
> with the concept and the pitfalls but maybe a reminder?
>
>> I would take it as a confirmation that you think things like "there
>> wasn't free oxygen in the atmosphere in that Hadean" are faith, but
>> then you say this:
>
> If abiotic oxygen is a myth, life has already been discovered
> on Mars. Ganymede. Europa.

Sure, very low free oxygen then. In terms of the reason I originally
brought it up (the chemistry of alkaline hydrothermal vents) it works
out the same.

<snip>

>> the alkaline hydrothermal vent hypothesis is far and away superior to
>> all others in scope, specificity, evidential support and predictive
>> power.
>
> Lol!  Nothing is useful unless and until life is spontaneously
> formed under laboratory conditions. AND THEN that's when the
> debate begins!  Because it won't "Prove" that it ever happened
> in nature, only that it is not excluded.

I didn't say "useful", I said "superior to all others in scope,
specificity, evidential support and predictive power". I'm happy to
justify each of those claims, is there one you have particular
objections to or that you want me to start with?

>
>> It's especially superior to panspermia which isn't even so much a
>> hypothesis as a vague notion that doesn't actually explain the origin
>> of life.
>
> Science is about stepping outside of yourself. That is literally
> why it exists. Humans are so biased that we need a specific
> set of rules, a process we must follow to keep up from latching
> onto whatever our knee-jerk tells us.
>
> Science was created to remove the human element.
>
> You're insisting that the human element is what validates the
> work.

I wasn't aware I was doing that, could you clarify? The criteria I
listed are actual rules science uses to evaluate hypotheses, they're
very much a part of the "stepping outside of yourself" and "removing the
human element" that you describe.

>
>>> There's also creationism, yes.
>>
>> Sure. I figured that since you were talking about a spectrum of
>> complexity in things that actually exist from life to nonlife that the
>> context of this thread was naturalistic explanations.
>
> The problem with Creationism is that abiogenesis, in a lab, would
> be an example of same. So you're not escaping Creationism with
> such goals, you're trying to validate it with an actual example!
>
> Ironic, I know.

Not really; the lab is a controlled environment that allows one to
narrow down the causes of any given phenomenon. This includes natural or
nonsentient causes.

Take for example the Todd Willingham case and the debunking of the
forensic science used to convict him. Forensic scientists had some ideas
on how human-caused fires differ from accidental ones and based on those
they argued that various patterns were evidence that Todd Willingham had
committed arson. Then a guy called Gerald Hurst discredited all this
evidence based in part on experiments where he re-created those patterns
in ways that showed that they can occur in non-human-caused fires.

Now I can see there is a fun little conceptual paradox there that I'd be
happy to work through, but just for a start: do you think what Gerald
Hurst did was inherently impossible or invalid?

<snip>

>> Sure, and the alkaline hydrothermal vent hypothesis is really good in
>> comparison to pretty much all of the other ideas on abiogenesis
>
> Rather circular, that. And anyone proposing a different answer
> would be definition be disagreeing with you.

It's not circular, it's a positive claim that I gave a number of
justifications for earlier and am happy to give more (but I already
proposed that higher up so we can keep it there). And of course anybody
making a contradictory claim is disagreeing with me, that's the nature
of positive claims. The next step is for me to defend my claim, those
that disagree to make counter-arguments, etc.

>
> What do you have in common with all of them? That's a start.
>
>
>>>> And I'm telling you most of that spectrum is empty, shows a huge gulf.
>>>
>>> That would be more convincing if either one of us could point to
>>> such a spectrum -- mapped out, scientifically. But we can't. So
>>> you are arguing... what?
>
>> Here's me pointing->:
>> ...water&lower -> Tornadoes, crystals, abiotic autocatalytic
>> reactions, alcohol -> polycyclic aromatic hydrocarbons, long alkanes
>> -> [huge gap] -> most viruses -> giant viruses, intracellular
>> parasites? -> prokaryotic cells -> eukaryotic cells & higher...
>
> This is usenet. The internet. I just read a claim that the exact same
> scientists who worked out the date, time & location of the eclipse
> are the people who have determined that Gwobull Warbling is REEL!
>
> Matter exists along a spectrum. All matter. Map it out. Speaking
> rhetorically. Not saying you should do it but I am saying that it
> needs to be done. >
>> Shouldn't be too hard for you to fill that gap if what you're saying
>> is true.
>
> And yet we both know that it's never been done.
>
>>> The spectrum isn't empty, it's ignored.
>
>> How could we tell the difference ?
>
> Someone could attempt to map out all life and non life:  Matter.
>
> The claim is that the very same nature which produced diamonds
> and forms lithium can also produce life. This life is not a
> separate and distinct form of matter, it lies along a spectrum.
>
> This much is a fact.
>
> To claim anything else is to argue divine intervention!
>
> So if we understand that spectrum we understand life, and an
> understanding of that spectrum begins with actually mapping
> it out.
>

I assume you're proposing something that you think is possible to do,
even somewhat practical given you think it's a better approach than all
other ones, so for example it wouldn't involve mapping every individual
particle of matter including those contained in the paper or computers
this map would be published in. Some categorization would be involved.
What level of category do you have in mind? Like, what might a typical
entry in the database look like? What size database do you think would
be possible or reasonable?

I'm also a bit curious what mechanism in your mind would cause such a
map to help use understand the origins of life. By which I mean there's
some intuitive reasons it seems obvious it would help, but ISTM those
same reasons say that instantiating elements of that spectrum in the lab
would help us understand just as much, and you seem to think it wouldn't
help at all.

>>>> I mean, obviously every element of that spectrum has to have been
>>>> realized at some point, or abiogenesis couldn't have happened.
>>>
>>> We're back to being faith-based. Abiogenesis is not the only
>>> game in town. And even if it did happen somewhere on the
>>> surface of a planet, this may not have been that planet! It
>>> may literally be impossible to identify any environment that
>>> had ever existed on this Earth which might've resulted in
>>> abiogenesis... if it ever happened anywhere.
>
>> Nah it's not impossible, several perfectly cromulent candidates were
>> identified including the one it actually happened in which is alkaline
>> hydrothermal vents.
>
> Nah, you're trolling.

On 10/04/2024 14:52, Ernest Major wrote:
> On 10/04/2024 11:00, Arkalen wrote:
>> On 10/04/2024 11:25, Ernest Major wrote:
>>> On 10/04/2024 07:58, Arkalen wrote:

snip

>>> Parasites, especially intracellular parasites (including parasitic
>>> plants, which invade their hosts at the intracellular level) lack
>>> even more of the metabolism, scavenging chemicals from their hosts.
>>> With 1,000 or so genes, mimivirus also has a truncated metabolism (I
>>> don't know how it compares to say Wolbachia, but with comparable
>>> numbers of genes a comparison seems an obvious thing to investigate.)
>>> A difference between mimiviruses and intracellular parasites is that
>>> the latter have their own cytoplasm, while the former utilises the
>>> host cytoplasm as a substrate for its metabolism. That's still a big
>>> difference - but is it the only difference in kind between
>>> mimiviruses and the simplest intracellular parasitic organisms?
>>> (According to the above paper mimivirus has an immune system, which
>>> is something one could imagine a cellular organism lacking.)
>>
>> I agree those are much more similar than I'd been thinking; I was
>> thinking of viruses as they are outside of the cell but you're right
>> that when you consider their activity inside of the cell then there's
>> much less reason to say that activity isn't "metabolism". Except for
>> that whole "meta" part of "metabolism" : does mimivirus do catabolism?
>> Do intracellular parasites?
>>
>> I'll look it up after posting but I notice you point out the
>> difference that intracellular parasites have their own cytoplasm. I
>> will hazard the guess that this means they have their own *membranes*,
>> and further hazard the guess that they use respiration to generate a
>> proton motive force across that membrane to regenerate ATP. I could
>> see it if they didn't, after all they can get ATP from the host cell
>> can't they. But if they do, that would be metabolism with the "meta".
>
> Microsporidia have lost the ability to generate their own ATP. The same
> is said of Giardia.

Do you have a cite on that? This paper suggests that Giardia does have
metabolism, using fermentation (but then maybe it varies by Giardia
species, this paper seems to be looking at one specific one):

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC88984/

It explicitly describes it as generating its own ATP unless I'm
seriously missing something:

"However, certain eukaryotes, including Trichomonas spp., Entamoeba
spp., and Giardia spp., are characterized by their lack of mitochondria
and cytochrome-mediated oxidative phosphorylation. They rely on
fermentative metabolism (even when oxygen is present) for energy
conservation. Glycolysis and its brief extensions generate ATP, with
generation dependent only on substrate level phosphorylation."

I'm not sure you're even completely right on Microsporidia, cf this paper:
https://link.springer.com/article/10.1007/s00436-020-06657-9

It does describe microsporidia as using the host's ATP, but also of
using glycolysis to generate ATP:

"These parasites have lost canonical mitochondria and the oxidative
phosphorylation pathway, so that glycolysis is the only way to
generate ATP (Heinz et al. 2012; Corradi 2015). During the
intracellular development stage, microsporidia apparently do
not use their energy metabolism (Dolgikh et al. 2011) and
instead satisfy their energy demands by “stealing” ATP from
the host cell using unique nucleotide carriers acquired via
horizontal transfer from bacteria (Tsaousis et al. 2008;
Alexander et al. 2016)."

As an aside I think it's really interesting that those are both
eukaryotes; it actually tracks with what I said earlier about how
"having their own cytoplasm" implied "having their own membranes" which
implied "respiring across those membranes" because I realized later that
this applied to bacteria but not necessarily eukaryotes! Eukaryotes
respire using mitochondria, not their outer membrane. I still think it's
interesting that the examples we'd find of endocellular parasites that
(maybe, partially) gave up on metabolism would be eukaryotes. Does it
means bacteria don't do this? And if so why is it eukaryotes can give up
on metabolism more easily than bacteria can? It seems to intuitively
make sense that getting rid of organelles would be easier than getting
rid of a function that's fundamental to your cellular structure, but
seeing eukaryotic modularity potentially confirmed this way is still
pretty interesting.

It also means I still have doubts about the notion that intracellular
parasites can be as simple as even giant viruses. It seems entirely
possible in principle don't get me wrong; my argument is that metabolism
is what separates cellular life's complexity from that of viruses so it
would perfectly track that cellular life that got rid of metabolism
could simplify to virus level. But the idea of *eukaryotes* - not just
cellular life but *eukaryotic* cellular life containing organelles and
all that jazz even if mitochondria are no longer in their number - could
be as simple as viruses, giant as they might be, still begs disbelief
for me. Possible in principle but pretty remarkable to witness in
reality, and I'm not sure Microsporidia or Giardia reach that level.

Thank you for drawing my attention to the possibility, it's definitely
something I'll look into more.

On Tue, 9 Apr 2024 13:03:18 -0400, JTEM <jtem01@gmail.com> wrote:

> Arkalen wrote:
>
>> It's been done
>
>Not by everyone, not here.
>
>> the gap was identified, and it's an unbelievably huge
>> gulf
>
>Not really. Pretty small, actually. Especially when you're
>looking at the dividing line there. There's a genuine
>argument over viruses, for example.
>
>> I think the alkaline hydrothermal vent theory is making good headway now
>
>You're doing it again. Looking at life instead of non
>life, even as you argue that you're not or at least
>not so much (maybe just a little?).

Alkaline hydrothermal vents are far removed from living systems.

>I talked about the study of non life.
>
>> but "what's the most complex non-living system" wasn't really the
>> foundational insight there. More like "is there a non-living system that
>> could generate energy like modern cells do".
>
>As you recall, part of the dogma is that the conditions no
>longer exist. That, the conditions were perfect for spawning
>life, abiogenesis occurred then immediately got up and left,
>presumably searching for tea...
>
>If conditions persisted, abiogenesis should be observed!
>
>So take the emphasis off of life.

If the conditions of abiogenesis persisted, what do you suppose you
would observe? Do you imagine something resembling complex life would
crawl out fully formed? If so, your imagination is analogous to those
who assumed spontaneous generation of mice from bundles of rags.

Instead, consider the greater likelihood of an environment which
created an acidic gradient between layers of porous rocks. There
would be, could be, nothing remotely resembling modern life, yet the
system as a whole would metabolize chemicals seeping from the ground
to build abiotic molecules enclosed within sheets of bilayer
phospholipids. If you were to analyze these molecules, you would
notice nothing distinguishable from the products of extant life. So
how could you prove these molecules were in fact created abiotically?

--
To know less than we don't know is the nature of most knowledge

jillery wrote:

> Alkaline hydrothermal vents are far removed from living systems.

Context, my delectable nutted cheese ball. This was raised
as an environment in which abiogenesis might occur.

> If the conditions of abiogenesis persisted

Assuming that there were such conditions on our planet.

Assuming that abiogenesis ever occurred.

So that's not one but two a-priori assumptions, my
delightful bouquet of candied fruit.

> Instead, consider the greater likelihood of an environment which
> created an acidic gradient between layers of porous rocks. There
> would be, could be, nothing remotely resembling modern life, yet the
> system as a whole would metabolize chemicals seeping from the ground
> to build abiotic molecules enclosed within sheets of bilayer
> phospholipids.

So you're countering my proposal that we study non-life with this
talk of non-life.

Oo! There's a reason why you are my spicy enchilada of love, and
this is it!

*Hugs!*

--
https://jtem.tumblr.com/tagged/The%20Book%20of%20JTEM/page/5

On 11/04/2024 14:41, Arkalen wrote:
>>> I agree those are much more similar than I'd been thinking; I was
>>> thinking of viruses as they are outside of the cell but you're right
>>> that when you consider their activity inside of the cell then there's
>>> much less reason to say that activity isn't "metabolism". Except for
>>> that whole "meta" part of "metabolism" : does mimivirus do
>>> catabolism? Do intracellular parasites?
>>>
>>> I'll look it up after posting but I notice you point out the
>>> difference that intracellular parasites have their own cytoplasm. I
>>> will hazard the guess that this means they have their own
>>> *membranes*, and further hazard the guess that they use respiration
>>> to generate a proton motive force across that membrane to regenerate
>>> ATP. I could see it if they didn't, after all they can get ATP from
>>> the host cell can't they. But if they do, that would be metabolism
>>> with the "meta".
>>
>> Microsporidia have lost the ability to generate their own ATP. The
>> same is said of Giardia.
>
> Do you have a cite on that? This paper suggests that Giardia does have
> metabolism, using fermentation (but then maybe it varies by Giardia
> species, this paper seems to be looking at one specific one):
>
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC88984/
>
> It explicitly describes it as generating its own ATP unless I'm
> seriously missing something:
>
> "However, certain eukaryotes, including Trichomonas spp., Entamoeba
> spp., and Giardia spp., are characterized by their lack of mitochondria
> and cytochrome-mediated oxidative phosphorylation. They rely on
> fermentative metabolism (even when oxygen is present) for energy
> conservation. Glycolysis and its brief extensions generate ATP, with
> generation dependent only on substrate level phosphorylation."
>

I'd misinterpreted this, by not paying sufficient attention to the
context of a statement "but there is no ATP production".

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8404698/

In my defence, your mention of respiration above distracted me from
considering non-mitochondrial (non-respiratory) ATP production. Not all
intracellular parasites act as you proposed, but I overstepped the mark
in baldly stating that they don't produce ATP.
--
alias Ernest Major