Gaia Hypothesis

[studiot]

58 minutes ago, Agent Smith said:

Those intermediary reactions were building up to what we see now, a stable system that (autocorrects) 😄

 

In exactly what way is

n(CO₂ + H₂S + O₂ + H₂O)  =  (CH₂O)_n + n(H₂SO₄)

intermediate between

n(H₂O + CO₂)  = n(CH₂O) + n( O₂)

 

and

 

Catabolism

[joigus]

9 hours ago, sethoflagos said:

For me, the evolution of photosynthesis is quite a serious challenge to GH.

This is more or less what I meant when I said,

On 7/18/2024 at 9:58 PM, joigus said:

When something catastrophic happens --whether cosmic, in the form of an asteroid, or internal, in the form of, e.g., an unpredictable mutation-- from the POV of the mathematician modelling it-- you would have to assume time-dependent coefficients that implement this catastrophic behaviour.

Photosynthesis by cyanobacteria leading to the GOE no doubt came from mutations in prokaryotes, which is a genetic event, but catastrophic nonetheless.

As @StringJunky said, all bets are off then. It's like the Earth setting the course to a whole new "Gaia deal" so to speak.

What I fail to see is the presence of an immutable condition defining the stasis. In the case of thermodynamics, it's the equation(s) of state. In the case of living organisms, it's parameters such as pH, osmotic pressure, temperature...

What on Earth (pun intended) is the go-back-to condition that defines Gaia?

 

On 7/22/2024 at 3:27 PM, studiot said:

But it just does not happen to be in effect on Earth.

Agreed.

[sethoflagos]

7 hours ago, joigus said:

What on Earth (pun intended) is the go-back-to condition that defines Gaia?

I think the default condition comprises a moderately stable environment populated by a biota optimally adapted to thrive in those specific environmental conditions. If a genetic or behavioural change occurs in one species such that it starts to significantly alter the conditions in which it thrives, then that seems to be a recipe for evolutionary suicide does it not?

As presented, this is a relatively straightforward, self-sustaining mechanism that provides the basics of Gaia without appealing to evolutionary foresight (or new age spiritualism).

But...

The empirical background came predominantly from the studies of modern (at least, pre-industrial) ecosystems. These in turn have been shaped by a global climate that from the close of the last glaciation 10 kya has until very recently been unusually stable by geological standards. It may well be atypical.

7 hours ago, joigus said:

Photosynthesis by cyanobacteria leading to the GOE no doubt came from mutations in prokaryotes, which is a genetic event, but catastrophic nonetheless.

We should also point out that it was initialised ~3.5 bya with the development of photosynthesis and advanced gradually raising free oxygen levels from ~1 ppm to ~2% by ~1.9 bya, with the GOE proper occurring over the final half billion years or so of that period. Obviously, we have a fairly coarse-grained perspective on such distant times, and there may well have been a series of lethal pulses in O₂ concentration as each stage in the sequence of oxygen reducing buffers reached saturation point in turn. However, the picture we see is one of sustained hostility to life for one third of the planet's existence. This was not an overnight catastrophe like the Chixulub impact. For an immense period of time, this was situation normal (afu).

7 hours ago, joigus said:

As @StringJunky said, all bets are off then. It's like the Earth setting the course to a whole new "Gaia deal" so to speak.

GOE is not an isolated example: plants had another good go at wiping us out when they conquered the land in the Devonian and sent atmospheric O₂ levels shooting up to ~30%; the advent of sea floor burrowing destroyed the highly productive seabed bacterial mats of earlier times. I'd make the case that such stability we observe is never more than transitory - the seeds of revolution are always ready in the wings. Indeed, imho they need to be in order to periodically begin anew. 

It's very tempting to write these off as 'special cases' when they threaten such such a seductive idea as Gaia. But nature is, as someone once said, red in tooth and claw. We idealise and anthropomorphise it at our peril.       

Edited July 23 by sethoflagos
sp

[StringJunky]

5 hours ago, sethoflagos said:

I think the default condition comprises a moderately stab environment populated by a biota optimally adapted to thrive in those specific environmental conditions. If a genetic or behavioural change occurs in one species such that it starts to significantly alter the conditions in which it thrives, then that seems to be a recipe for evolutionary suicide does it not?

This is why it's important to have as many players in a biosphere as possible to minimize the effect of a significant population alteration of a single species. If populations are moderated by competition, so is a biosphere. Catastrophic population change is ok as long some form of life can persist in the adverse environment until organism diversity can resume and evolution begin again. I think no species is favoured, only that DNA/RNA, as the information/pattern/signal carriers, can persist. As long as the minimum information survives, so can life as it is. It doesn't have to start all over again from basic molecules compounded from astronomical events.

Edited July 24 by StringJunky

[Agent Smith]

@studiot, Je ne sais pas. The sulphur-based reaction, my guess is, was not sustainable and collapsed. Not exactly an intermediary stage towards the photosynthesis-respiration system we have, but more like a dead end. What say you?

[studiot]

5 hours ago, Agent Smith said:

@studiot, Je ne sais pas. The sulphur-based reaction, my guess is, was not sustainable and collapsed. Not exactly an intermediary stage towards the photosynthesis-respiration system we have, but more like a dead end. What say you?

Certainly not a dead end.

The sulphur process (sulphur is in the same periodic table group as oxygen)  is still active today. Both NASA and NOAA and many other authorities now have reports on it.

You intrduced the word  intermediate, which implies to me that it was a necessary calling point to get where we are.

The fact remains that there are many organisms that do not rely on photosynthesis alive and well today, some do not even need oxygen.
they are competitive species, not stepping stones.
Remember also that if the Chixelub metorite had not happened we would not be here, the dinosaurs would still rule the Earth.

 

On 7/23/2024 at 9:26 AM, studiot said:

Time to trot out the parable of the puddle ?

I first heard the parable of the puddle on ScienceForums and I think it offers an amazing insight. I posted the invitation to give some other member a chance to post it.
Since no one has, here is my version.

 

Somewhere in a hot country lies a dusty road full of potholes.
Every night it rains and puddles form in the potholes.
Every day the puddles evaporate in the heat.

One morning a pudle woke up (became self aware) and thought "what a wonderful world and how lucky am I ?"
This pothole is exactly right for me. It is me shaped.
During the day, the puddle evaporated and the traffic passed, extending the pothole.

The next morning the puddle woke up and thought.......

 

I have been watching a TV detective series and in the last episode he says an interesting thing.

"We should not look for facts to fit our theory of what happened; we should look for theories to fit the facts."
 

Edited July 24 by studiot

[dimreepr]

21 hours ago, Agent Smith said:

That's ok, I fully respect your skepticism. 

Thanks, however that's not evidence of my wrongism, or more pertinately any sort of support for your claim.

 

[joigus]

12 hours ago, sethoflagos said:

I think the default condition comprises a moderately stable environment populated by a biota optimally adapted to thrive in those specific environmental conditions.

Yes, but see how dangerously close to a tautology we get? The default condition is whatever can sustain biota that will keep that condition. It's like the puddle suggested by @studiot. That was a brilliant analogy btw.

12 hours ago, sethoflagos said:

Obviously, we have a fairly coarse-grained perspective on such distant times, and there may well have been a series of lethal pulses in O₂ concentration as each stage in the sequence of oxygen reducing buffers reached saturation point in turn. However, the picture we see is one of sustained hostility to life for one third of the planet's existence. This was not an overnight catastrophe like the Chixulub impact. For an immense period of time, this was situation normal (afu).

Yes, I think this has to do with biodiversity being very low back during those eons --see last point by @StringJunky. Higher biodiversity will conceivable smooth out these patterns of variations. That's probably why we see those sharp banded-iron formations corresponding to the GOE. It's been speculated (but very plausibly so) that they must correspond to pulses of massive death of aerobic/anaerobic organisms and their re-births. It's like the oscillating pattern of daisy world, but with generations of aerobic/anaerobic prokaryotes playing the role of the black/white daisies, and oxygen abundance in the interstices of their bacterial mats (rather than the atmosphere) playing the role of the albedo. Well, perhaps the oversimplified way I've come to look at it.

13 hours ago, sethoflagos said:

GOE is not an isolated example: plants had another good go at wiping us out when they conquered the land in the Devonian and sent atmospheric O₂ levels shooting up to ~30%; the advent of sea floor burrowing destroyed the highly productive seabed bacterial mats of earlier times. I'd make the case that such stability we observe is never more than transitory - the seeds of revolution are always ready in the wings. Indeed, imho they need to be in order to periodically begin anew. 

I agree with this. In fact, I've thought for some time that we usually focus too much on particular episodes just because of the particularly dramatic footprint they left behind, but the reason why we divide at all Earth time into these periods is because towards the end of each one of them, something had to give (biologically speaking) under one kind of stress or another, be it biological, cosmic, or geologically driven, or all of them together. 

[dimreepr]

7 hours ago, Agent Smith said:

@studiot, Je ne sais pas. The sulphur-based reaction, my guess is, was not sustainable and collapsed. Not exactly an intermediary stage towards the photosynthesis-respiration system we have, but more like a dead end. What say you?

There's a reason why fermentation stops when the alcohol level reaches a pitiful 15%, it's not a dead end but it sure does seem like Gaia is looking out for us alcoholics.

But if you want some fun, sing 

 

[sethoflagos]

2 hours ago, joigus said:

Yes, but see how dangerously close to a tautology we get? The default condition is whatever can sustain biota that will keep that condition. It's like the puddle suggested by @studiot. That was a brilliant analogy btw.

Exactly! Hence my earlier comment:

On 7/17/2024 at 10:13 PM, sethoflagos said:

At best, GH seems to say no more than stable is stable, unstable is unstable. What is there to disagree?

 

2 hours ago, joigus said:

Yes, I think this has to do with biodiversity being very low back during those eons --see last point by @StringJunky. Higher biodiversity will conceivable smooth out these patterns of variations.

A good point indeed, and yet I have a lingering reservation. High species diversity tends to be associated with highly specialised niche partitioning and complex, often Byzantine levels of species interdependence and coevolution. In times of stress, these tend to be the systems most vulnerable to collapse and they do so quite quickly. I'm not sure they provide that much of a defence. Born survivors tend to have much less fussy lifestyles.  

[Agent Smith]

3 hours ago, dimreepr said:

There's a reason why fermentation stops when the alcohol level reaches a pitiful 15%, it's not a dead end but it sure does seem like Gaia is looking out for us alcoholics.

But if you want some fun, sing 

Si, that seems to be the case and I don't know how exactly fermentation works (I was told it's partial respiration/oxidation. Do you know?), but it's an apropos example for reactions that come to an end because it's unsustainable ... as far as I can tell. Do you have other examples? 

 

Sorry the link to the song is broken, must be a good song.

3 hours ago, dimreepr said:

Thanks, however that's not evidence of my wrongism, or more pertinately any sort of support for your claim.

 

That's correct. No need to respond.

5 hours ago, studiot said:

Certainly not a dead end.

The sulphur process (sulphur is in the same periodic table group as oxygen)  is still active today. Both NASA and NOAA and many other authorities now have reports on it.

You intrduced the word  intermediate, which implies to me that it was a necessary calling point to get where we are.

The fact remains that there are many organisms that do not rely on photosynthesis alive and well today, some do not even need oxygen.
they are competitive species, not stepping stones.
Remember also that if the Chixelub metorite had not happened we would not be here, the dinosaurs would still rule the Earth.

That's correct, underwater vents, the human gut, volcanoes and even hot springs have their own microbiota; photosynthesis ain't the only game in town. However, do you have more ... put some meat on the outline you've provided of how TGH is untenable or at least per the chemical reactions you've cited and other non-oxygen dependent chemical interactions you mention ... wrong?

Edited July 24 by Agent Smith

[joigus]

2 hours ago, sethoflagos said:

Exactly! Hence my earlier comment:

 

A good point indeed, and yet I have a lingering reservation. High species diversity tends to be associated with highly specialised niche partitioning and complex, often Byzantine levels of species interdependence and coevolution. In times of stress, these tend to be the systems most vulnerable to collapse and they do so quite quickly. I'm not sure they provide that much of a defence. Born survivors tend to have much less fussy lifestyles.  

I see your point. My take is that specialist vs generalist occurs in a direction with respect to the evolutionary tree, while a taxon vs another taxon occurs along a different direction. What I mean is any specialist in a given taxon has a cousin that is a generalist. It stands to reason that the more species there are, the more likely it is that a genetically-close generalist is there to fill the gap.

There is no doubt that diversity is bound to take a blow any time a catastrophic event happens. Swarms of specialists will fall, and along with them relatively closely interdependent sub-niches. Conceivably, it's the generalist cousins that remain there to plant the seeds of the future biodiversity.

Edited July 24 by joigus
minor correction

[CharonY]

6 hours ago, Agent Smith said:

(I was told it's partial respiration/oxidation. Do you know?)

I think that is not entirely wrong but also (in my mind) not very helpful. A more specific way to think about it is to view fermentation as a means to regenerate NAD+. During glycolysis (as well as during oxidative decarboxylation of pyruvate and the TCA cycle under oxic conditions) NADH is generated which can power an electron transport chain, which we refer to as respiration (with the ultimate purpose to generate energy). In aerobic respiration the electrons are ultimately transferred to oxygen, but those able to respire under anaerobic conditions can also use e.g. sulfate or metals and so on.

But if respiration is not an option, and the cell e.g. only uses glycolysis for energy generation, it will accumulate NADH that it has to convert back to NAD+, otherwise glycolysis will stop. This is where fermentation kicks in during e.g. ethanol formation NADH is converted to NAD+.

Perhaps that is also not very intuitive, but if you look at the mechanisms, it is quite a bit more precise.

[Agent Smith]

7 hours ago, CharonY said:

I think that is not entirely wrong but also (in my mind) not very helpful. A more specific way to think about it is to view fermentation as a means to regenerate NAD+. During glycolysis (as well as during oxidative decarboxylation of pyruvate and the TCA cycle under oxic conditions) NADH is generated which can power an electron transport chain, which we refer to as respiration (with the ultimate purpose to generate energy). In aerobic respiration the electrons are ultimately transferred to oxygen, but those able to respire under anaerobic conditions can also use e.g. sulfate or metals and so on.

But if respiration is not an option, and the cell e.g. only uses glycolysis for energy generation, it will accumulate NADH that it has to convert back to NAD+, otherwise glycolysis will stop. This is where fermentation kicks in during e.g. ethanol formation NADH is converted to NAD+.

Perhaps that is also not very intuitive, but if you look at the mechanisms, it is quite a bit more precise.

I don't recall seeing C2H5OH in human biochemistry except as alochol-induced hepatitis, but I do know about how alcoholics are susceptible to malnutrition because of the calories they get from alcohol, which spoils their appetite, making them skip meals, the usual way nutrients enter the body.

 

I also don't get why fermentation and its product alcohol was brought into the discussion.

@CharonY

So, looking for confirmation here ... 

1. NADH comes from NAD+

2. NADH drives the electron chain (that generates ATP/some other energy molecule)

3. In respiration, during the final stage the electron gets transferred to oxygen and we replenish our NAD+

4. In anaerobic conditions, NADH is converted to NAD+ via fermentation, C2H5OH being a byproduct. Is that why we have to seal the container when we make alcohol? 

Edited July 25 by Agent Smith

[Agent Smith]

@studiot

[studiot]

19 hours ago, Agent Smith said:

That's correct, underwater vents, the human gut, volcanoes and even hot springs have their own microbiota; photosynthesis ain't the only game in town. However, do you have more ... put some meat on the outline you've provided of how TGH is untenable or at least per the chemical reactions you've cited and other non-oxygen dependent chemical interactions you mention ... wrong?

Voila

We seem to be making some progress.

Did you catch what the detective said in my last post ?

Because you should be setting out the facts and looking for a theory to fit them.

Not setting out Gaia and looking for facts to fit the theory.

 So what is a summary of the facts ?

Well the Earth began almost 5 billion years ago.

And throughout that time conditions have been changing, sometimes steadily and slowly, sometimes quickly and dramatically.
Some of these changes have resulted in great change in lifeforms at any one time.
Some of these changes have been rapid enough to cause great change to the human population.

How is this compatible with the conditions laid down in the Gaia Hypothesis of persistency of the conditions in comfortable late 19th century Europe ?
Planet Earth does not fit Gaia, but somewhere else might.

 

Note I see you have posted something about my 'Food Diagram' but I don't see any comment or question  ?

[Agent Smith]

18 minutes ago, studiot said:

 

Voila

We seem to be making some progress.

Did you catch what the detective said in my last post ?

Because you should be setting out the facts and looking for a theory to fit them.

Not setting out Gaia and looking for facts to fit the theory.

 So what is a summary of the facts ?

Well the Earth began almost 5 billion years ago.

And throughout that time conditions have been changing, sometimes steadily and slowly, sometimes quickly and dramatically.
Some of these changes have resulted in great change in lifeforms at any one time.
Some of these changes have been rapid enough to cause great change to the human population.

How is this compatible with the conditions laid down in the Gaia Hypothesis of persistency of the conditions in comfortable late 19th century Europe ?
Planet Earth does not fit Gaia, but somewhere else might.

 

Note I see you have posted something about my 'Food Diagram' but I don't see any comment or question  ?

I'm glad you see progress in our discussion. You're on the mark as to how science has to be conducted. Do you mean to say James Lovelock did science backwards? He was a chemist and these come in various flavors and I know next to nothing about which tier of chemists he belonged to. Coming up with a globally impactful hypothesis like Gaia suggests he was not just any chemist. Do you have anything on him that suggests his work was shoddy? 

Please review your diagram of energy production in a cell. I have a question in red. It's Acetyl CoA (from Google), right? Also, which book is that? Is it a downloadable PDF?

Edited July 25 by Agent Smith

[studiot]

40 minutes ago, Agent Smith said:

Please review your diagram of energy production in a cell. I have a question in red. It's Acetyl CoA (from Google), right? Also, which book is that? Is it a downloadable PDF?

Here is some more information.

Yes it's acetyl-thiolCoA

Everything to the left of my marker arrow is expanded as previous diagram.
Everything to the right is rolled into the CoA.

 

It's from

McMurray  Organic Chemistry

 

mine is the 4th ed.

 

Sorry about the flatbed scanning but there 1350 pages so it doesn't sit well

[Agent Smith]

@studiot, well-above my paygrade. Interesting book though. I did a quick google search, the CoA unfolds into a complex ring structure (like the one in your illustration). Gracias. Good day.

[studiot]

42 minutes ago, Agent Smith said:

@studiot, well-above my paygrade. Interesting book though. I did a quick google search, the CoA unfolds into a complex ring structure (like the one in your illustration). Gracias. Good day.

You might find this one simpler and more digestible.

 

[sethoflagos]

On 7/24/2024 at 5:36 PM, joigus said:

What I mean is any specialist in a given taxon has a cousin that is a generalist. It stands to reason that the more species there are, the more likely it is that a genetically-close generalist is there to fill the gap.

You've got me thinking now! 

If instead of the black and white flowers of daisyworld, we had two species of flower that were simply different and a nectar feeding 'generalist' bird that could feed from either though not particularly efficiently.

Would there be an evolutionary advantage in splitting into two closely related species that each were optimised for just one flower species? Would the potential gains in feeding efficiency offset the doubling(?) of the average distance between their preferred flowers? Providing one of the flowers survived a catastrophe, then both the generalist and one of the specialists might too. Both the energy budget and survivabilty factors are not as clearcut as I imagined.

This case actually blurs the lines between generalist and specialist for me. A group of closely related specialists could simply be viewed as a generalist hedging his bets. Another case of the dangers of making sweeping generalisations in regard to complex systems?     

 

[CharonY]

12 hours ago, Agent Smith said:

I don't recall seeing C2H5OH in human biochemistry except as alochol-induced hepatitis, but I do know about how alcoholics are susceptible to malnutrition because of the calories they get from alcohol, which spoils their appetite, making them skip meals, the usual way nutrients enter the body.

 

I also don't get why fermentation and its product alcohol was brought into the discussion.

@CharonY

So, looking for confirmation here ... 

1. NADH comes from NAD+

2. NADH drives the electron chain (that generates ATP/some other energy molecule)

3. In respiration, during the final stage the electron gets transferred to oxygen and we replenish our NAD+

4. In anaerobic conditions, NADH is converted to NAD+ via fermentation, C2H5OH being a byproduct. Is that why we have to seal the container when we make alcohol? 

1) yes, or more precisely we have the interconversion of

NADH <-> NAD+ + H+ + 2e-

2) Not quite, it is the initial donor. The chain is basically a redox gradient, starting with NADH and ending with the terminal electron acceptors.

3) Also not quite, NAD+ is regenerated during the first step of the electron transport chain, following the reaction shown in 1). The electrons then continue to move through the chain, which powers the proton pumps. That is not part of regeneration of NAD+ per se, but just the process necessary to ultimately gain energy from the whole ordeal (the gradient in turn powers an ATP synthetase).

4) Simply put, yes. When there is oxygen, cells can use respiration to get more energy rather than having to rely on fermentation. That being said, under the right conditions (e.g. very high glucose surplus) some cells also conduct fermentation even in presence of oxygen. 

Here, cells prioritize rapid energy generation via glycolysis over the more efficient, but slower process of respiration. But this is only possible if glucose is not a limiting factor (as it is often the case in nature).

 

[joigus]

25 minutes ago, sethoflagos said:

Would there be an evolutionary advantage in splitting into two closely related species that each were optimised for just one flower species? Would the potential gains in feeding efficiency offset the doubling(?) of the average distance between their preferred flowers? Providing one of the flowers survived a catastrophe, then both the generalist and one of the specialists might too. Both the energy budget and survivabilty factors are not as clearcut as I imagined.

I don't think the distinction between generalist and specialist can be unambiguously drawn in a scenario of just 2 or 3 species. The lines get blurred, I think, precisely because the distinction is only precisely defined if/when there are plenty of resources. After all, the specialist's motto is something like "from all these so and so many resources I can only exploit this particular one". With only resources A and B, the specialist and the generalist cannot be told apart. That's what my common sense dictates anyway. I hope it makes sense.

So you're right to say, I think,

34 minutes ago, sethoflagos said:

This case actually blurs the lines between generalist and specialist for me.

It's kind of like trying to define the pressure of a collectivity of two molecules!

[sethoflagos]

6 hours ago, joigus said:

I don't think the distinction between generalist and specialist can be unambiguously drawn in a scenario of just 2 or 3 species. The lines get blurred, I think, precisely because the distinction is only precisely defined if/when there are plenty of resources. After all, the specialist's motto is something like "from all these so and so many resources I can only exploit this particular one". With only resources A and B, the specialist and the generalist cannot be told apart. That's what my common sense dictates anyway. I hope it makes sense.

Yes, there has to be more distance between the two for the distinction to make sense, doesn't there.

Sanity seems to restored when I consider them as extremes of a spectrum with eg. the raccoon at one end and the xanthopan at the other.

[Agent Smith]

10 hours ago, CharonY said:

1) yes, or more precisely we have the interconversion of

NADH <-> NAD+ + H+ + 2e-

Ok. What we have to focus on is the 2 electrons? 2e-?

10 hours ago, CharonY said:

2) Not quite, it is the initial donor. The chain is basically a redox gradient, starting with NADH and ending with the terminal electron acceptors.

Yes, a (redox) gradient, but what exactly does that mean? A gradient of increasingly more "electron-philic" compounds? Are you saying the chain of redox reactions are thermodynamically favored? 

11 hours ago, CharonY said:

3) Also not quite, NAD+ is regenerated during the first step of the electron transport chain, following the reaction shown in 1). The electrons then continue to move through the chain, which powers the proton pumps. That is not part of regeneration of NAD+ per se, but just the process necessary to ultimately gain energy from the whole ordeal (the gradient in turn powers an ATP synthetase).

Can you explain this a bit more? NADH is the electron donor, oui? Hence it depletes as the TCA cycle is activated? We would need more NADH to sustain the reaction and so there's got to be a way to replenish the stock of NADH. This is achieved (ultimately) via oxygen???  

11 hours ago, CharonY said:

4) Simply put, yes. When there is oxygen, cells can use respiration to get more energy rather than having to rely on fermentation. That being said, under the right conditions (e.g. very high glucose surplus) some cells also conduct fermentation even in presence of oxygen. 

I suppose it's not a question of either this/that, but more of which reaction dominates a particular set of circumstances.

 

Gracias.