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What appear to be biochemical processes may be a natural feature of geology

quantamagazine.org

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Re: What appear to be biochemical processes may be a natural feature of geology

#101
post #41

It's been speculated for at least a decade now that geochemistry spawned biochemistry and life as we know it. This appears to be the latest instance of this pattern. One of the most notable examples is geothermal processes simply creating calm energy gradients that are stable for billions of years (e.g., underwater alkaline vents), which can then essentially "manufacture" organic compounds, which naturally assemble i…

I almost agreed with your comment, but then I remembered there are countless planets with conditions unsuitable for life (as we know life). We have found a couple planets that are optimisticly closer to Earth conditions, but very few, and there is usually some characteristic that makes it a stretch still.

With that said, if Earth was compared to a super computer, the initial conditions and perturbations (weights and biases, or probabilistic inference) are very important, as most planets that are also performing ~10^38 ops/sec will never succesfully manufacture biochemistry/life.

Re: What appear to be biochemical processes may be a natural feature of geology

#102

Earlier quoted context omitted.

Yet, there is only one form of life on earth exhibiting cellular metabolism and DNA/RNA replication. That original life form formed as soon as the earth became suitable for life. In the 3+ billion years since, there has been no new life form created that we know of despite the ongoing unfathomable computations.

Is that still the case with the discovery extremophiles that exist on chemical vents deep under the ocean and far away from the sun? Or rather, how sure are we that they're the same form?

Yes. All known life shares an (assumed) last common universal ancestor (LUCA, presumed extinct), and there is significant evidence pointing that way.

We can infer properties and function by looking at genes shared between archea and bacteria that most likely came from such an ancestor; this paints a picture of a DNA-based anaerobic thermophile (think hydrothermal vents) with a membrane and simple anti-virus defenses (CAS).

Re: What appear to be biochemical processes may be a natural feature of geology

#103
post #101
post #41

It's been speculated for at least a decade now that geochemistry spawned biochemistry and life as we know it. This appears to be the latest instance of this pattern. One of the most notable examples is geothermal processes simply creating calm energy gradients that are stable for billions of years (e.g., underwater alkaline vents), which can then essentially "manufacture" organic compounds, which naturally assemble i…

I almost agreed with your comment, but then I remembered there are countless planets with conditions unsuitable for life (as we know life). We have found a couple planets that are optimisticly closer to Earth conditions, but very few, and there is usually some characteristic that makes it a stretch still. With that said, if Earth was compared to a super computer, the initial conditions and perturbations (weights and…

I've actually thought about this. My personal interpretation (which I admit is absolutely a bit playful, but I also find it very fulfilling) is that gravity acts like a resource allocator. It clumps matter together into stars, planets, etc., forcing it to interact, while keeping those objects far enough apart that they generally can run independently of each other for very long periods of time.

If you allow me to exercise some creative liberty with language, it's almost as if gravity is just launching countless trillions of parallel instances of the same computation, with nearly all possible initial starting conditions. Some of those initial conditions allow the local compute capacity to "descend" into finding more and more optimal ways to increase entropy and heat dissipation by exploiting local energy gradients (i.e., life).

In terms of the frequency of life, I'd expect basic microscopic life to be somewhat common, as it's "just" a way of exploiting geochemical energy gradients for local entropy maintenance. That doesn't necessarily even mean fully functioning cells, genetic codes, etc. It really just means molecular compounds or assemblies that exploit or create energy gradients. However, generally once that's kicked off, it's reasonable to consider that this generally would lead to the kinds of selection pressures that favor the development of what we'd know as basic cellular machinery and replication.

However, complex life I would expect to be almost vanishingly rare. The Earth only managed to figure it out a single time so far as we know (generating eukaryotes from bacteria/archaea) in billions of years. How many other planets feature roughly the same chemical computation which just never explored the right niche of chemical possibility to give rise to that complexity? This suggests to me the universe must expend unbelievably vast amounts of computation to overcome the threshold to complex life. I don't think it'd be unreasonable to assume that it requires thousands of separate "planetary computers", each with basic life, for only a single one to generate something like complex life (eukaryotes or equivalent), and that's to say nothing of the millions or billions of planets that don't generate any life at all.

Re: What appear to be biochemical processes may be a natural feature of geology

#104
post #40

This is like saying "wood burns, even when the tree is dead" but much, much slower. The disequilibrium (sugars and free O₂) were produced by living organisms, and this is just the gradual drift back to a lower energy state. CO₂ is common in the universe, and not at all a sign of life. O₂ and sugars are rare.

This seems like the better explanation of my laybrain reading this and thinking; why would you start with soil? If it were a true geological phenomenon then shouldn’t they use a sterile jar of granite dust or something that only existed on earth prior to life? It seems like pointing at a jar of bio matter and saying we can’t stop it is not really a good methodology to base much upon. I barely ever even took a chemistry class in my life but something just feels wrong with this approach to me. I assume that’s what the other scientists who doubt the sterilization were thinking too.

Re: What appear to be biochemical processes may be a natural feature of geology

#105
The actual publication is available here: https://www.science.org/doi/10.1126/sciadv.adw9065

  The present study challenges the traditional view that the *respiration of 
  organic carbon to CO2* is an exclusively intracellular process, revealing that 
  *organic compound respiration can occur spontaneously in an extracellular 
  context in soils*.
On the surface, it looks like they rediscovered that oxidation of organic / carbonaceous compounds occurs at low temperatures independently of presence of living organisms. The real contribution of the paper would be in elucidation of the specific mechanisms of oxidation of these organic compounds (e.g. via abiotic catalysis).

Compare to this paper from 2003:

https://sci-hub.kvnp.top/10.1016/s0360-1285(03)00042-x

  Coal oxidation at low temperatures is the major heat source responsible for 
  the self-heating and spontaneous combustion of coal and is an important source 
  of greenhouse gas emissions. This review focuses on the chemical reactions 
  occurring during low-temperature oxidation of coal. Current understanding 
  indicates that this process involves consumption of O2, formation of solid 
  oxygenated complexes, thermal decomposition of solid oxygenated complexes and 
  generation of gaseous oxidation products. Parameters, such as mass change, 
  heat release, oxygen consumption, and formation of oxidation products in the 
  gas or solid phase, have been used to qualitatively and quantitatively 
  describe the oxidation process. Reaction mechanisms have been proposed to 
  explain the characteristics of consumption of O2, and formation of oxidation 
  products in the gas and solid phases. Various kinetic models have also been 
  developed to describe the rate of oxygen consumption and the rates of 
  formation of gaseous oxidation products in terms of the rate parameters of the 
  relevant reactions, oxidation time, temperature, and initial concentration of 
  oxygen in the oxidising medium.

Re: What appear to be biochemical processes may be a natural feature of geology

#106
post #84

Earlier quoted context omitted.

Sugars are just chains of hydrocarbons with alcohol groups, they are probably going to be ubiquitous. ATP is useful because the phosphate groups make a stable bond that nevertheless can be hydrolyzed, releasing a lot of energy. But the adenosine "backbone" of the ATP is more-or-less arbitrary. Other forms of life can use something different. Or they might use the phosphorus bonds themselves where terrestrial life use…

I also do not believe that our RNA and complex amino acids are likely to be universal. On the other hand, the simple amino acids are known to be universal, both from chemical analyses of celestial bodies and from abiotic syntheses in laboratories. In theory, sugars can be produced abiotically by the polymerization of formaldehyde. However, sugars are not very stable chemically and suitable catalysts for formaldehyde…

Great post! Thank you.

Is it conceivable that instead of water, some other solvent can be used? Those ethane/methane lakes on Titan ...

Re: What appear to be biochemical processes may be a natural feature of geology

#107
post #34

Earlier quoted context omitted.

That's a bit odd - why wouldn't wind blown non-sterile organic matter from the surrounding forest re-colonize the area?

There's nothing unusual there. Typically natural forests grow out in stages, with different generations of trees replacing each other. Because they actually killed off everything, the "older" trees are not propagating there because they are not adapted for that. That's also why natural forests have clearings that can last for a while.

What's unusual (or "unnatural") is that it's not just the macro level that was annihilated, but even the subterranean fungal network. Fire won't do that (unless the soil is very thin). Drought won't.

What is happening is apparently the entire cycle of repopulation of a food source for the most fundamental of ecosystem anchors.

What surprising is that this should be the equivalent of planting a garden with fuly sterilized soil. As someone else noted, why aren't wind-borne spores and nematode corpses revitalizing the subterranean ecosystem?

Re: What appear to be biochemical processes may be a natural feature of geology

#108

Reminds me of the abiogenic petroleum: https://en.wikipedia.org/wiki/Abiogenic_petroleum_origin

That's a wild, out-there hypothesis. This is a factual observation that currently has no strong explanation hypotheses.

Re: What appear to be biochemical processes may be a natural feature of geology

#109

Earlier quoted context omitted.

I also do not believe that our RNA and complex amino acids are likely to be universal. On the other hand, the simple amino acids are known to be universal, both from chemical analyses of celestial bodies and from abiotic syntheses in laboratories. In theory, sugars can be produced abiotically by the polymerization of formaldehyde. However, sugars are not very stable chemically and suitable catalysts for formaldehyde…

Great post! Thank you. Is it conceivable that instead of water, some other solvent can be used? Those ethane/methane lakes on Titan ...

Theoretically yes, but honestly I doubt it. Simple hydrocarbons are too stable, water molecules disassociate naturally (that's what pH means!). Water is also polar and can dissolve significant quantities of polar compounds. Ethane is non-polar.

But crucially, the speed of chemical reactions goes down by 2-3 times for every 10C. Ethane liquefies at -160C so most chemical reactions would be around 100000 times slower than at 0C. And many chemical reactions would not work at all because of the high activation energy.

It's possible that low-temperature life might utilize some highly unstable (at room temperature) compounds. But there are few low-energy pathways that can be used to _synthesize_ these compounds in the first place in nature.

Re: What appear to be biochemical processes may be a natural feature of geology

#110
post #40

This is like saying "wood burns, even when the tree is dead" but much, much slower. The disequilibrium (sugars and free O₂) were produced by living organisms, and this is just the gradual drift back to a lower energy state. CO₂ is common in the universe, and not at all a sign of life. O₂ and sugars are rare.

Indeed.

They suggest that the soil can somehow catalyze metabolic reactions and break down complex carbohydrates without life but where would the complex carbohydrates come from?

I'm also curious how they could demonstrate that there isn't some sort of very constrained extremophile producing all their results that doesn't exactly colonize very well but will still function.

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