On 11/04/2024 14:41, Arkalen wrote:
> 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)."
>

Microsporidia are a large group (1500 named species, but estimates of
the actual number runs to a million or more), so statements may be true
of some rather than all microsporidia. Repeating my original web search
I find

"Indeed, one group of microsporidia, the Enterocytozoonidae, has lost
multiple proteins in the glycolytic pathway, effectively inhibiting ATP
generation"

--
alias Ernest Major

On 11/04/2024 14:41, Arkalen wrote:
>
> 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.

Your original mention of ATP production associated with membranes
pointed me in the direction of amitochrondriate eukaryotes for
counterexamples (and I had a recollection of microsporidia as "energy
parasites"). I don't see a reason to conclude that loss of ATP can't
also occur among parasitic prokaryotes.

My first candidate - Mycoplasma - came out negative; they do generate
ATP, but by an atypical path. Further searching however found putative
energy parasites among the acutalibacteraceous clostridia.

https://www.nature.com/articles/s41396-023-01502-0

On the other, a paywalled paper reports that Chlamydia trachomatis was
erroneously considered an obligate energy parasite for nearly 40 years.
Google Scholar then finds what it perhaps the debunking paper.

https://onlinelibrary.wiley.com/doi/full/10.1046/j.1365-2958.1999.01464.x

Quite a number of prokaryotes are energy parasites. But we're looking
for obligate energy parasites (and even that may not be enough - one
could imagine a parasite which has some ATP-production capability, but
not enough to meet its needs).
>
>
> 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.

There's even a amitochondriate animal - Henneguya zschokkei. (Looking at
the Wikispedia article for this I discover that there is a hypothesis
that myxozoa evolved from transmissible cancers.)

However microsporidia and Giardia were brought up in response to your
specific claim about ATP; not as a claim of comparable complexity to
mimiviruses. Personally I doubt (pace the problem of generating an
operational definition of complexity giving an ordering), even with the
overlap in genome sizes and gene counts, that any cellular organisms are
simpler than mimivirus, but it strikes me that this is some that needs
to be demonstrated rather than assumed. I would look among parasitic
prokaryotes for candidates, with Wolbachia pipientis and Buchnera
aphidicola as first ports of call. (I suspect that treating these two
clades as single species in incorrect, and each of these is comprised of
many species.)

Based on the overlap in genome sizes and gene counts my provisional
position is that the gap between viruses and cellular organisms is
narrower than generally expected.

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

--
alias Ernest Major

On 2024-04-13 11:25, Ernest Major wrote:
> On 11/04/2024 14:41, Arkalen wrote:
>> 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)."
>>
>
> Microsporidia are a large group (1500 named species, but estimates of
> the actual number runs to a million or more), so statements may be true
> of some rather than all microsporidia. Repeating my original web search
> I find
>
> "Indeed, one group of microsporidia, the Enterocytozoonidae, has lost
> multiple proteins in the glycolytic pathway, effectively inhibiting ATP
> generation"
>

Yes I saw that too when I read the whole paper later, very cool! IIRC
they don't know how it manages the spore stage as a consequence, I think
I have another tab open I haven't read yet that talks about those in
more detail.

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

On 13/04/2024 11:21, Ernest Major wrote:
> 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.

To further strengthen your defense, when I made that comment about
membranes I had also forgotten there were other ways of making ATP :)

On 13/04/2024 12:12, Ernest Major wrote:
> On 11/04/2024 14:41, Arkalen wrote:
>>
>> 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.
>
> Your original mention of ATP production associated with membranes
> pointed me in the direction of amitochrondriate eukaryotes for
> counterexamples (and I had a recollection of microsporidia as "energy
> parasites"). I don't see a reason to conclude that loss of ATP can't
> also occur among parasitic prokaryotes.

Definitely not. This was less of a conclusion and more of an idea,
sparked by the examples you'd mentioned but clearly not fully or even
partly justified by them. And also thinking of how the most famous and
ancient bacteria endosymbionts gave up everything *except* ATP
production, which seemed like a cute contrast. But of course
endosymbioses would have different dynamics than parasitism to begin with.

>
> My first candidate - Mycoplasma - came out negative; they do generate
> ATP, but by an atypical path. Further searching however found putative
> energy parasites among the acutalibacteraceous clostridia.
>
> https://www.nature.com/articles/s41396-023-01502-0
>
> On the other, a paywalled paper reports that Chlamydia trachomatis was
> erroneously considered an obligate energy parasite for nearly 40 years.
> Google Scholar then finds what it perhaps the debunking paper.
>
> https://onlinelibrary.wiley.com/doi/full/10.1046/j.1365-2958.1999.01464.x
>
> Quite a number of prokaryotes are energy parasites. But we're looking
> for obligate energy parasites (and even that may not be enough - one
> could imagine a parasite which has some ATP-production capability, but
> not enough to meet its needs).

Right, Microsporidia would be a good example of those - aside from the
one variety that seems to not generate ATP at all all the others seem to
generate ATP only during the spore phase and depend entirely on stealing
host ATP otherwise.

Given the context which was comparing cellular life to viruses and my
argument that the big thing that separated viruses from cellular life
with implications on complexity was that cellular life did both
catabolism & anabolism and viruses only the latter I think it's fair
enough to set the bar here at "actually no ATP production/catabolism at
all".

Maybe there is something else you could clarify for my mind - I got from
Nick Lane the idea that 100% of life that generates ATP does so via the
proton motive force across a membrane (for prokaryotes, their own
membrane). Bringing up glycolysis and fermentation made me doubt this a
bit (and made me realize I'd been confusing the PMF with oxygenic
respiration even though the latter obviously isn't universal) but
looking up different bacterial metabolisms they still seem to end up
using the PMF? But I haven't found a clear or solid enough source to be
sure. It would also raise the question of how eukaryotes without
mitochondria but doing glycolysis or fermentation do it, but a figure in
a paper on Microsporidia does kind of suggest the mitosome membrane is
involved.

Do you know whether using the PMF is universal in ATP-generating life?

(just writing this also makes me realize I'd confused my catabolism &
anabolism a bit: I was conflating ATP generation with catabolism but
actually that's a kind of anabolism, with catabolism being whatever
reaction maintains the PMF. Which suggests the possibility of an
organism that generates ATP while using outside energy to maintain the
PMF but that's the alkaline hydrothermal vent hypothesis' LUCA; all
actual parasites that gave up on catabolism seem happy to just import
ATP while they're at it)

>>
>>
>> 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.
>
> There's even a amitochondriate animal - Henneguya zschokkei. (Looking at
> the Wikispedia article for this I discover that there is a hypothesis
> that myxozoa evolved from transmissible cancers.)
>
> However microsporidia and Giardia were brought up in response to your
> specific claim about ATP; not as a claim of comparable complexity to
> mimiviruses. Personally I doubt (pace the problem of generating an
> operational definition of complexity giving an ordering), even with the
> overlap in genome sizes and gene counts, that any cellular organisms are
> simpler than mimivirus, but it strikes me that this is some that needs
> to be demonstrated rather than assumed. I would look among parasitic
> prokaryotes for candidates, with Wolbachia pipientis and Buchnera
> aphidicola as first ports of call. (I suspect that treating these two
> clades as single species in incorrect, and each of these is comprised of
> many species.)
>
> Based on the overlap in genome sizes and gene counts my provisional
> position is that the gap between viruses and cellular organisms is
> narrower than generally expected.

I haven't finished reading the paper on Mimivirus but you seem to know
quite a bit about it - I saw something about part of its genome being
pretty stable and the other highly variable and apparently borrowed from
the host. Is that accurate to your understanding or did I misunderstand?
And if it's accurate, could it suggest that Mimivirus' genome is being
used in a different way from the "standard" way we think of (if such a
thing exists), and this might imply a different relationship between
genome size and complexity from that of cells or other viruses?

Like the prokaryotes thing it's not a claim, just an idea. I'd been
wanting to dig into it a bit but haven't yet so I thought I'd ask you
for thoughts anyway.

On 13/04/2024 15:11, Arkalen wrote:
>> Based on the overlap in genome sizes and gene counts my provisional
>> position is that the gap between viruses and cellular organisms is
>> narrower than generally expected.
>
>
> I haven't finished reading the paper on Mimivirus but you seem to know
> quite a bit about it - I saw something about part of its genome being
> pretty stable and the other highly variable and apparently borrowed from
> the host. Is that accurate to your understanding or did I misunderstand?
> And if it's accurate, could it suggest that Mimivirus' genome is being
> used in a different way from the "standard" way we think of (if such a
> thing exists), and this might imply a different relationship between
> genome size and complexity from that of cells or other viruses?

This is not just a feature of mimivirus and allies. I expect that gene
content is fairly uniform with vertebrate families. But in plants there
is turnover in membership of gene families - cycles of duplication
followed by neofunctionalisation, subfunctionalisation or loss - so you
end up with a core genome and genes found within some but not all
species of a group. Places to look at this are Gossypium, where we have
genomes for at least 25 species, including 6 species of subgenus Karpas
which have a common allotetraploid ancestry and which may show
differential loss during the ongoing process of diploidisation, and
other agriculturally important groups such as Brassica and Triticum.

Generally as you go towards "simpler" organisms the magnitude of the
contrast between the core genome and pangenome increases.

In E. coli strains have between 4,000 and 5,500 genes (4,288 in the
first sequenced strain), with a soft core (found in the great majority,
but not all strains) of around 3,000 genes, a core genome of 1,000
genes, an a pangenome of 16,000 or more genes.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9205054/
https://en.wikipedia.org/wiki/Escherichia_coli

Wolbachia pipientis gene contents are strikingly variable between
strains symbiotic with different hosts.

Mycoplasmas have a gene content of the order of 1,000 genes, a core
genome of around 500 and a pangenome of well in excess of 30,000.

https://www.nature.com/articles/s42003-021-02105-1

Giant viruses (and pox viruses), with core genomes and substantial
lineage specific genomes, don't seem out of line.

The question that needs to be asked is to what extent this a genuine
phenomenon, and to what extent it is an artefact of greater taxonomic
splitting in charismatic megabiota. Is it correct to treat Buchnera
aphidicola, Wolbachia pipientis and Escherichia coli as single species,
or are they equivalent to a vertebrate genus, family, order or class?
>
> Like the prokaryotes thing it's not a claim, just an idea. I'd been
> wanting to dig into it a bit but haven't yet so I thought I'd ask you
> for thoughts anyway.

--
alias Ernest Major

On Fri, 12 Apr 2024 22:00:21 -0400, JTEM <jtem01@gmail.com> posted yet
another self-parody:

> 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.

Yes, and so is a non-living system by definition.

>> If the conditions of abiogenesis persisted
>
>Assuming that there were such conditions on our planet.
>
>Assuming that abiogenesis ever occurred.

As stated. What part of "if" do you not understand?

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

Are you a-priori assuming otherwise?

>> 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.

How do you propose to study non-life without speaking of non-life?

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

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

Arkalen wrote:

> 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".

No. You're talking about abiogenesis. You're saying that it likely
occurred under the conditions you referenced. You introduced an
abiogenesis "hypothesis" that was centered on a proposed environment,
these conditions. Abiogenesis.

> Can you clarify for me which if any of these claims you'd be willing to
> grant as

I grant that a better technique would be to study that which exist,
instead of that which does not exist.

You might as well study God, because you can't see him either!

And, non coincidentally, such pursuits are incapable of establishing
that abiogenesis ever occurred in nature. If you managed to
replicate a particular environment and spawn life form non-life, all
that would "Prove" is that creationism is real. It would be an act
of CREATION, where an intelligence created life by intent, by design.

So i don't find it as useful as you imply.

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

> Sure, very low free oxygen then.

Sure, very low levels of life then.

Doesn't matter how low or high it is, either life on these other
worlds HAS BEEN DISCOVERED or there is such a thing as aboitic
oxygen.

> I didn't say "useful", I said "superior to all others in scope

That's circular.

"Assuming I am right, this is the right answer! And the right
answer is superior to all the others!"

That's religion not science.

> specificity, evidential support and predictive power".

This is a little bit bigger than that.

Evidence is rarely if ever exclusive. It supports more than
one conclusion. It's also interpreted. So it's never enough
to just concentrate on one answer.

In the end, it's always a comparison. Someone is only ever
tall so long as others are shorter than they are. And a
scientific "Answer" is only the best answer if others have
been satisfactorily explored.

>>> 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.

This is a very odd thing to say. Because we have no explanation
for the origins of life, least of all one that has been
confirmed scientifically.

This is about what strikes you as good or not.

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

> I wasn't aware I was doing that

Well hopefully I clarified.

>> 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;

Yes, really. LITERALLY. It would literally be an example of
creationism.

> the lab is a controlled environment that allows one to
> narrow down the causes of any given phenomenon.

No. That's the opposite of science.

You merely decided that you know something happened.

All scientific experimentation can ever accomplish is to
establish that something MAY happen given specific,
measurable conditions. It doesn't mean that it ever
happened nor that those conditions ever existed.

> 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.

It was an excellent example of how people defer to "Authority"
and why an "Appeal to Authority" is not a valid argument.

As I recall from the case, the investigators found that the fire
burned in a star like pattern and this "Proved" in their minds
that it was an intentional Satanic act, while in reality the fire
seemed to burn towards oxygen sources.

What is lost on most people is that in both cases, the evidence
is exactly the same. Both were looking at patterns, the exact
same patterns. Both saw this "Star."

> 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?

It's not really a paradox. The evidence was the evidence was the
evidence. Everyone saw it.

>>> 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

Of course it's circular. You're concluding with your starting premise.

>> 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

Why wouldn't it be?

It's just studying what exists.

> 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.

Every type of matter, yes.

> 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?

Doesn't really matter. In my day you could locate an item inside of
a 20 million entree database in seconds, if that long.

...milliseconds.

Of course things are significantly faster now...

> I'm also a bit curious what mechanism in your mind would cause such a
> map to help use understand the origins of life.

I'm at a lot here. I can't explain how you can't see it.

Life isn't unique. It isn't separate and distinct. It is merely a
form of matter along a spectrum. Period. So let's map out and try
to understand that spectrum.

Because "Abiogenesis" isn't even science. It's "True" no matter
what, can't be falsified, just like God. And even if you somehow
produced it under laboratory conditions, you'd just be "Proving"
creationism. Because that's exactly what it would be: An
intelligence creating life.

So move on to the study of things that really do exist.

> I'm sad you snipped the parenthetical right after that where I confessed
> to cheekiness but added the actual serious answer, which was that
> alkaline hydrothermal vents are definitely, indubitably an environment
> that ever existed on this Earth which MIGHT've resulted in abiogenesis.

Such pursuits are theoretically -- and only theoretically -- useful
in that they could identify environments to search for on other
worlds.

Exobiology.

Or...

Astrobiology.

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

On 15/04/2024 19:36, JTEM wrote:
>  Arkalen wrote:
>
>> 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".
>
> No. You're talking about abiogenesis. You're saying that it likely
> occurred under the conditions you referenced. You introduced an
> abiogenesis "hypothesis" that was centered on a proposed environment,
> these conditions. Abiogenesis.

I talk about many things, it's unfortunate you seem to struggle to keep
track of them. All this extreme snipping can't be helping.

>
>> Can you clarify for me which if any of these claims you'd be willing
>> to grant as
>
> I grant that a better technique would be to study that which exist,
> instead of that which does not exist.

So that's a "no" then. Oh well.

snip
>
>> I didn't say "useful", I said "superior to all others in scope
>
> That's circular.
>
> "Assuming I am right, this is the right answer! And the right
> answer is superior to all the others!"

Not "superior"; superior *in scope* (and specificity, evidential support
and predictive power). And I'm not assuming it's superior in those ways,
I'm observing it:

*Scope:* All the abiogenesis hypotheses I've seen focus on a small
aspect of the problem - looking for sources of organic molecules,
looking for nonliving processes by which RNA could form, looking for
nonliving processes by which cell-like structures could form, looking at
whether some functions of life like RNA replication can happen
spontaneously. The alkaline hydrothermal vent hypothesis OTOH covers
almost all of the problem space and extends even beyond, from nonliving
precursors of metabolism capable of generating the building blocks of
life to the divergence of archaea and bacteria, blowing right past LUCA.
It incorporates the formation of cell-like structures, fixes some
conceptual problems with RNA world and recent papers are tackling the
origins of protein translation.

*Specificity:* Even within their narrow scope the other abiogenesis
hypotheses I've seen aren't able to narrow possibilities down much -
they basically open the door for questions but don't find much in the
way of answers, not enough to narrow down to a single one at least. The
AHVH OTOH is increasingly specific in its claims, from the
protometabolic pathways that are increasingly fleshed out and
constrained by experimental results, specific ways protocells would form
and what factors would constrain their growth, specific antecedents to
ATP and why ATP might be the universal energy currency, a specific order
in which the genetic code might have formed and protein formation might
have started given patterns in the genetic code, the path by which
archaea and bacteria would have acquired their respective proton-pumping
schemes, etc etc.

*Evidential support:* That kind of goes with the scope and specificity
really - every part of the hypothesis makes has different independent
lines of evidence supporting it and it has many parts. From the physics
of serpentinization to the phylogenetic signal in archaea and bacteria
and going through the increasing volume of experimental results into
various aspects of the hypothesis. No other abiogenesis hypothesis has
that convergence of independent lines of evidence; many have as their
only line of evidence the observations that made someone come up with
the hypothesis to begin with.

*Predictive power:* That kind of goes with scope and specificity too.
Other abiogenesis hypotheses I know of aren't specific enough to make
good predictions and don't have a scope that would allow them to make
predictions about much. A lot of the evidential support mentioned above
also doubles as predictions made and satisfied by earlier versions of
the hypothesis. In its current forms it suggests predictions about
plenty of things, like the ability of specific reactions to be done
under hydrothermal vent conditions that haven't been done yet, the order
in which purine nucleotides vs pyrimidine nucleotides would have been
created, that a hairpin RNA loop could catalyze peptide bonds, details
in how archaea and bacteria differ...

snip
>>>> 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.
>
> This is a very odd thing to say. Because we have no explanation
> for the origins of life, least of all one that has been
> confirmed scientifically.
>
> This is about what strikes you as good or not.

There is a big difference between an explanation we aren't sure is true,
something that's a partial explanation and something that's not an
explanation at all. The alkaline hydrothermal vent hypothesis is a
partial explanation well on its way to being a full one that we aren't
sure is true. Panspermia isn't an explanation at all - not for the
origin of life at least.

snip
>> the lab is a controlled environment that allows one to narrow down the
>> causes of any given phenomenon.
>
> No. That's the opposite of science.
>
> You merely decided that you know something happened.
>
> All scientific experimentation can ever accomplish is to
> establish that something MAY happen given specific,
> measurable conditions. It doesn't mean that it ever
> happened nor that those conditions ever existed.

Are you confused about the subject of conversation again? That sentence
was a general description of the nature of experiment, all this
"something happened" makes it look like you're treating it like
abiogenesis, meaning your "that's the opposite of science" is misapplied.

>
>> 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.
>
> It was an excellent example of how people defer to "Authority"
> and why an "Appeal to Authority" is not a valid argument.
>
> As I recall from the case, the investigators found that the fire
> burned in a star like pattern and this "Proved" in their minds
> that it was an intentional Satanic act, while in reality the fire
> seemed to burn towards oxygen sources.
>
> What is lost on most people is that in both cases, the evidence
> is exactly the same. Both were looking at patterns, the exact
> same patterns. Both saw this "Star."
>
>> 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?
>
> It's not really a paradox. The evidence was the evidence was the
> evidence. Everyone saw it.

I'm talking about the experiments Gerald Hurst ran to undermine the
claims the prosecutors made about that evidence. Were they adequate to
that purpose? Is that even a possible thing to do?

>
>>>> 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
>
> Of course it's circular. You're concluding with your starting premise.

You're confusing a circular argument with a simple statement.

>
>>> 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
>
> Why wouldn't it be?
>
> It's just studying what exists.
>
>> 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.
>
> Every type of matter, yes.
>
>> 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?
>
> Doesn't really matter. In my day you could locate an item inside of
> a 20 million entree database in seconds, if that long.
>
>      ...milliseconds.
>
> Of course things are significantly faster now...

On 14/04/2024 18:50, Ernest Major wrote:
> On 13/04/2024 15:11, Arkalen wrote:
>>> Based on the overlap in genome sizes and gene counts my provisional
>>> position is that the gap between viruses and cellular organisms is
>>> narrower than generally expected.
>>
>>
>> I haven't finished reading the paper on Mimivirus but you seem to know
>> quite a bit about it - I saw something about part of its genome being
>> pretty stable and the other highly variable and apparently borrowed
>> from the host. Is that accurate to your understanding or did I
>> misunderstand? And if it's accurate, could it suggest that Mimivirus'
>> genome is being used in a different way from the "standard" way we
>> think of (if such a thing exists), and this might imply a different
>> relationship between genome size and complexity from that of cells or
>> other viruses?
>
> This is not just a feature of mimivirus and allies. I expect that gene
> content is fairly uniform with vertebrate families. But in plants there
> is turnover in membership of gene families - cycles of duplication
> followed by neofunctionalisation, subfunctionalisation or loss - so you
> end up with a core genome and genes found within some but not all
> species of a group. Places to look at this are Gossypium, where we have
> genomes for at least 25 species, including 6 species of subgenus Karpas
> which have a common allotetraploid ancestry and which may show
> differential loss during the ongoing process of diploidisation, and
> other agriculturally important groups such as Brassica and Triticum.
>
> Generally as you go towards "simpler" organisms the magnitude of the
> contrast between the core genome and pangenome increases.
>
> In E. coli strains have between 4,000 and 5,500 genes (4,288 in the
> first sequenced strain), with a soft core (found in the great majority,
> but not all strains) of around 3,000 genes, a core genome of 1,000
> genes, an a pangenome of 16,000 or more genes.
>
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9205054/
> https://en.wikipedia.org/wiki/Escherichia_coli
>
> Wolbachia pipientis gene contents are strikingly variable between
> strains symbiotic with different hosts.
>
> Mycoplasmas have a gene content of the order of 1,000 genes, a core
> genome of around 500 and a pangenome of well in excess of 30,000.
>
> https://www.nature.com/articles/s42003-021-02105-1
>
> Giant viruses (and pox viruses), with core genomes and substantial
> lineage specific genomes, don't seem out of line.
>
> The question that needs to be asked is to what extent this a genuine
> phenomenon, and to what extent it is an artefact of greater taxonomic
> splitting in charismatic megabiota. Is it correct to treat Buchnera
> aphidicola, Wolbachia pipientis and Escherichia coli as single species,
> or are they equivalent to a vertebrate genus, family, order or class?
>>
>> Like the prokaryotes thing it's not a claim, just an idea. I'd been
>> wanting to dig into it a bit but haven't yet so I thought I'd ask you
>> for thoughts anyway.
>

Ron Dean has just, indirectly, reminded me of Helacyton. Given the
genomic instability of cancer lineages I suspect that also has a core
genome, and a larger pangenome.

--
alias Ernest Major

Arkalen wrote:

>> No. You're talking about abiogenesis. You're saying that it likely
>> occurred under the conditions you referenced. You introduced an
>> abiogenesis "hypothesis" that was centered on a proposed environment,
>> these conditions. Abiogenesis.

> I talk about many things,

Sadly, then, that right now you chose to talk about nothing.

If you are now walking back your abiogenesis position, good.
Glad to see you do that.

>> I grant that a better technique would be to study that which exist,
>> instead of that which does not exist.

> So that's a "no" then. Oh well.

"No"... what? "No I won't run off on your tangent.

Seriously, I do NOT want this to degraded into yet another
narcissism-fueled meltdown, not after you were doing so
good!

My position is consistent. Go back to my initial post: Unchanged
view.

Sorry that consistency is so offensive.

>> "Assuming I am right, this is the right answer! And the right
>> answer is superior to all the others!"

> Not "superior"; superior *in scope* (and

Typical narcissist.

>> This is a very odd thing to say. Because we have no explanation
>> for the origins of life, least of all one that has been
>> confirmed scientifically.
>>
>> This is about what strikes you as good or not.

> There is a big difference between an explanation we aren't sure is true,
> something that's a partial explanation and something that's not an
> explanation at all.

Not that it'll help but, my point was about HOW we go about
exploring the origins of life. You advocate studying that
which does not exist and I advocate studying that which does
exist.

> The alkaline hydrothermal vent hypothesis

Oh who cares? Really. Even if one of these stabs in the dark
ever got it right -- scientists are able to spawn life from
non life under laboratory conditions -- it would simply be an
example of CREATIONISM.

> is a
> partial explanation

It's not an explanation at all.

To pretend that it's half an explanation or 33% of an explanation
or even 5% of an explanation is a declaration of your beliefs,
not a statement of fact.

>> All scientific experimentation can ever accomplish is to
>> establish that something MAY happen given specific,
>> measurable conditions. It doesn't mean that it ever
>> happened nor that those conditions ever existed.
>
> Are you confused about the subject of conversation again?

No, I actually began the discussion! And I've remained
consistent while you have repeatedly denied your very own
words!

We should change our focus, study those things that actually
exist, that we can study.

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

On 17/04/2024 04:35, JTEM wrote:
>  Arkalen wrote:
>
>>> No. You're talking about abiogenesis. You're saying that it likely
>>> occurred under the conditions you referenced. You introduced an
>>> abiogenesis "hypothesis" that was centered on a proposed environment,
>>> these conditions. Abiogenesis.
>
>> I talk about many things,
>
> Sadly, then, that right now you chose to talk about nothing.
>
> If you are now walking back your abiogenesis position, good.
> Glad to see you do that.
>
>>> I grant that a better technique would be to study that which exist,
>>> instead of that which does not exist.
>
>> So that's a "no" then. Oh well.
>
> "No"... what? "No I won't run off on your tangent.
>
> Seriously, I do NOT want this to degraded into yet another
> narcissism-fueled meltdown, not after you were doing so
> good!
>
> My position is consistent. Go back to my initial post:  Unchanged
> view.
>
> Sorry that consistency is so offensive.

The issue isn't your position, it's your inability to parse sentences
for meaning and give answers that relate to that meaning. If your
position is solid it should be able to survive an actual conversation
where you temporarily allow the words of others to live in your head to
see where they go. I won't say "if it can't survive that then you
shouldn't hold it" because I agree that what we think of as "rational
discussion" is less reliable than we think and people can absolutely be
swayed from a correct position to a wrong one based on arguments that
look convincing but shouldn't have been. But there are other ways of
avoiding that fate; for example allowing ourselves to hold positions
based on strong feeling and not just rational analysis. The issue is
that once we're talking with someone then rules of logic and
conversation come into play.

Well, all this conversation on abiogenesis has made me hungry, I'll go
have a tuna sandwich. I think tuna sandwiches are delicious.

JTEM wrote:
"WRONG! Circular! Abiogenesis isn't delicious because abiogenesis didn't
happen!"

>
>
>>> "Assuming I am right, this is the right answer! And the right
>>> answer is superior to all the others!"
>
>> Not "superior"; superior *in scope* (and
>
> Typical narcissist.
>

I appreciate that out of the looooong explanation/defense of my position
I made that you snipped you still kept juuuuuuust enough to show my
disagreement was valid. You could have snipped right after the second
"superior" but didn't, bravo. (I assume you agree with all the rest as
you have no objection to it)

>
>>> This is a very odd thing to say. Because we have no explanation
>>> for the origins of life, least of all one that has been
>>> confirmed scientifically.
>>>
>>> This is about what strikes you as good or not.
>
>> There is a big difference between an explanation we aren't sure is
>> true, something that's a partial explanation and something that's not
>> an explanation at all.
>
> Not that it'll help but, my point was about HOW we go about
> exploring the origins of life. You advocate studying that
> which does not exist and I advocate studying that which does
> exist.

See, that specific sub-exchange for example was about whether panspermia
is an explanation for the origin of life or not.

>
>> The alkaline hydrothermal vent hypothesis
>
> Oh who cares? Really. Even if one of these stabs in the dark
> ever got it right -- scientists are able to spawn life from
> non life under laboratory conditions -- it would simply be an
> example of CREATIONISM.

Ah I see my questions about Gerald Hurst and the Todd Willingham case
also went the way of the snip; I take it this "reproducing abiogenesis
in the lab would prove creationism" claim isn't a claim you feel
comfortable defending? If so you could just avoid making it.

>
>> is a partial explanation
>
> It's not an explanation at all.
>
> To pretend that it's half an explanation or 33% of an explanation
> or even 5% of an explanation is a declaration of your beliefs,
> not a statement of fact.

I think it's a pretty straightforward consequence of the features of the
hypothesis and the meaning of the word "explanation" but I take it you
disagree. How do you decide whether something is an explanation for
another thing and to what extent?

>
>>> All scientific experimentation can ever accomplish is to
>>> establish that something MAY happen given specific,
>>> measurable conditions. It doesn't mean that it ever
>>> happened nor that those conditions ever existed.
>>
>> Are you confused about the subject of conversation again?
>
> No, I actually began the discussion!  And I've remained
> consistent while you have repeatedly denied your very own
> words!
>
> We should change our focus, study those things that actually
> exist, that we can study.
>

I could have a computer print out that very sentence a thousand times
and it would be "consistent" too and it wouldn't be holding a
conversation either, let alone convincing anyone the sentence is true or
a good idea. It would be reaching to even describe that sentence *as* an
idea in such a scenario, a random string of letters would yield the same
behavior.