I’m aware of several stabs at The Biogenesis Question and I’m wondering how to reconcile the Nick Lane’s book’s claims with some of them.
The best take I know, in terms of a beautifully reasoned presentation about the idea that maybe biogenesis wasn’t an accident but rather might have been necessary. Here’s a roughly 60 minute talk (that works at 2X speed) from Eric Smith, of the Santa Fe Institute.
Maybe the biggest point of disagreement is here?
Life that isn’t harvesting negentropy isn’t alive. For life to exist it needs a barrier between its ordered self and its chaotic environment. Life on Earth uses a cell wall composed of a lipid membrane. Since the inside of the cell is ordered and the outside is chaotic, there is an entropy gradient across the cell wall. Here’s where the primordial soup theory becomes implausible. A primordial soup is at chemical equilibrium. A cell is at chemical disequilibrium.
In contrast with this, Eric Smith’s model also has life “requiring” a gradient, however, from his perspective initially there was a geochemical disequilibrium (with no “selfs”, plausibly no “cells”, and thus no “evolution as such”) but instead something similar to: (1) the electrical disequilibrium based on electrons that makes lightning necessary, or (2) the tornado that releases the stress of high dry cold air ABOVE low wet warm air.
The geophysical stress he points to is the production of excess CO2 (from white smokers) and the combination of this with some source of hydrogen, and the construction of lower energy O2 and CH4… which is a giant jump that has no particularly obvious catalysts.
In this theory metabolism came first. Maybe a “metabolic biome” came first? Then the leakage from the “stress releasing vortex in chemistry” was mixed and remixed to build up larger biomolecules (maybe more than one) and some “best catalyst of itself” fell out of the process.
Then the fact that the modern catalytic facilitators all have a subunit which is the “A” of ACTG… turns out not to be that surprising. So maybe the “A” (adenine) was already around, and then its re-use in RNA and DNA (and the A of “ATP” and so on) is like… yeah, that just makes sense?
But anything that facilitated that metabolic hurricane would probably have been OK… It probably didn’t have to be specifically adenine. Any enzymes (or before that ribozymes) or even just any specific nucleotides and so on… are just the director and the stagehands, not the irreplaceable “story” and its core players.
So I guess a first question I have is whether The Vital Question talked about metabolism and autocatalysis or Eric Smith or the reverse Kreb cycle or adenine or any of this stuff?
It seems like it is very focused on the formation of membranes into cells which I had previously always just sort of assumed (maybe naively) would happen automatically through the self-assembly of micelles. Maybe micelles make the autocatalytic processes go faster, in which case they could show up just from thermodynamics?
It could be that my imagination is too free here, but I could imagine that there might be micelles that form as little “processing bubbles” and the faster they go inside the bubble the faster they can pop open and seed the water with their kind of chemistry… that is pre-dispossed to form more micelles?
By contrast:
Nick Lane proposes that LUCA was a membrane capped pore in an olavine rock.
It seems like Nick Lane thinks the hard part is… membranes? Really?
Thus my second question is what Lane’s evidence was for why membrane formation is so hard, and are such a big part of the story (in comparison to other factors).
I feel like the most likely answer will have has something to do with Sodium pumps?
An antiporter is like a turnstile to a building which lets exactly one person into a building for every person which leaves except instead of people it operates on ions. A Na⁺/H⁺ antiporter lets in one sodium ion for every hydrogen ion it lets out and one hydrogen ion in for every sodium ion it lets in. If there is more hydrogen on one side of the membrane, a Na⁺/H⁺ antiporter acts as a hydrogen-powered sodium pump
But, like… maybe the early waters were just more potassium rich than modern sodium rich seawater? This isn’t my area of expertise, (I’m just curious about everything and have big gaps in my knowledge about… basically everything), but I’m curious for more details in this possible version of the story.
I’ve read Nick Lane’s book, but I’m not familiar with Eric Smith’s stuff (yet).
Lane agrees that life started from a geochemical disequilibrium, in Lane’s model it’s serpentinization.
Lane’s book spends a lot of time talking about the Acetyl-CoA cycle, which is a key part of the Citric Acid cycle, as well as many other metabolic cycles. But he doesn’t mention the reverse Krebs cycle or adenine specifically, AFAICT. He cites Eric Smith favorably as going into more details on the specific biochemistry involved.
Regarding membranes, his model is that the first membranes were very leaky with respect to ions. Which is a good thing in the disequilibrium environment, since otherwise the cell would get too full of ions, and die! But there are two big problem for cells with such membranes: 1. their gradient will quickly equilibriate if they leave the sea vent, thus killing them. 2. Evolving a less leaky membrane will reduce their ability to use the sea-vent gradient, and thus by itself will not be selected for. A proton pump will not give an advantage in this case (the argument is a bit complex). The key is that a Sodium antiporter pump needed to come after the leaky membrane. This by itself gives an advantage, by also creating an Na+ gradient across the membrane, and this advantage is strengthened by making the membrane incrementally less leaky. (Lane explicitly claims that the oceans were high in Sodium ions, and low in Potassium ions 4 billion years ago, FWIW.)
But just the Sodium pump wasn’t enough to allow the cells to survive autonomously, since it trades positive ions for positive ions one to one. However, it now makes it advantageous to evolve a proton pump. And that was what finally facilitated the ability for cells to become fully autonomous. He goes on to claim that the direction the proton pump was “installed” across the membrane creates different problems, and that Bacteria and Archea are the result of this happenstance.
If I had a hunch it would route through the idea of metal atoms that fit into larger enzymes like rock knives wielded by squishy caveman hands.
As wikipedia says of inorganic biochemical co-factors:
In nutrition, the list of essential trace elements reflects their role as cofactors. In humans this list commonly includes iron, magnesium, manganese, cobalt, copper, zinc, and molybdenum.
So the thing I would naively do, to find candidate minerals, would be to try to sift conserved co-factors, especially with a focus on ribozymes that do the same trick, and then these “metalloribozymes” (some of which do exist in evolved systems still) might suggest typical mineral environments where things first started and never stopped being essential…
...but I don’t seem much mention of Olivine playing well with copper or zinc, and [manganese olivine] goes to its own name: Tephroite. But there was no mention of Tephroite in the review.
So this is where my own naive priors would send me looking: for minerals full of elemental cofactors common to ancient metalloribozymes. Lots of data sifting seems likely to be useful, over ribozyme and enzyme databases, and mineral databases, which I have not done.
Did Nick Lane do this kind of data sifting to find the name “Olivine”, or did he use some other method?
One idea is that he got the name from the literature, and perhaps cites whoever proposed Olivine? When I search [olivine biogenesis] I get Serpentinization results which echo the link you offered (and youtube on [serpentization] gives a fun experimental video that is interesting but sheds no particular light for me).
Synthesizing this… maybe the practical upshot is just “most normal mantle material reacting with seawater” could be loosely called “something-like-olivine turning to something-like-serpentine” and since there is so much mantle, and so much seawater, priors say that “this general reaction” is the key reaction at a high and fuzzy level of description. Maybe?
It looks like he got it from Mike Russell, though he disagrees with Russell on the details.
Regarding cofactors, the important thing (in Lane’s version of this model) about serpentinization is that it is alkaline. This would cause iron to precipitate out (as iron hydroxides and iron sulphates), and dissolve minerals such as nickel and molybdenum.
He points out nickel-doped greigite (Fe5NiS8) as a mineral with a crystal structure similar to several ancient metalloribozymes, and which he thinks was likely to have deposited on the walls of pores in the rock (serpentine?).
I’m aware of several stabs at The Biogenesis Question and I’m wondering how to reconcile the Nick Lane’s book’s claims with some of them.
The best take I know, in terms of a beautifully reasoned presentation about the idea that maybe biogenesis wasn’t an accident but rather might have been necessary. Here’s a roughly 60 minute talk (that works at 2X speed) from Eric Smith, of the Santa Fe Institute.
Maybe the biggest point of disagreement is here?
In contrast with this, Eric Smith’s model also has life “requiring” a gradient, however, from his perspective initially there was a geochemical disequilibrium (with no “selfs”, plausibly no “cells”, and thus no “evolution as such”) but instead something similar to: (1) the electrical disequilibrium based on electrons that makes lightning necessary, or (2) the tornado that releases the stress of high dry cold air ABOVE low wet warm air.
The geophysical stress he points to is the production of excess CO2 (from white smokers) and the combination of this with some source of hydrogen, and the construction of lower energy O2 and CH4… which is a giant jump that has no particularly obvious catalysts.
On this reading, “some aqueous chemistry” that self-catalyzes, to turn energy dense molecules into waste products HAD to autocatalyze SOMEHOW in order to release the stress.
In this theory metabolism came first. Maybe a “metabolic biome” came first? Then the leakage from the “stress releasing vortex in chemistry” was mixed and remixed to build up larger biomolecules (maybe more than one) and some “best catalyst of itself” fell out of the process.
Then the fact that the modern catalytic facilitators all have a subunit which is the “A” of ACTG… turns out not to be that surprising. So maybe the “A” (adenine) was already around, and then its re-use in RNA and DNA (and the A of “ATP” and so on) is like… yeah, that just makes sense?
But anything that facilitated that metabolic hurricane would probably have been OK… It probably didn’t have to be specifically adenine. Any enzymes (or before that ribozymes) or even just any specific nucleotides and so on… are just the director and the stagehands, not the irreplaceable “story” and its core players.
So I guess a first question I have is whether The Vital Question talked about metabolism and autocatalysis or Eric Smith or the reverse Kreb cycle or adenine or any of this stuff?
It seems like it is very focused on the formation of membranes into cells which I had previously always just sort of assumed (maybe naively) would happen automatically through the self-assembly of micelles. Maybe micelles make the autocatalytic processes go faster, in which case they could show up just from thermodynamics?
It could be that my imagination is too free here, but I could imagine that there might be micelles that form as little “processing bubbles” and the faster they go inside the bubble the faster they can pop open and seed the water with their kind of chemistry… that is pre-dispossed to form more micelles?
By contrast:
It seems like Nick Lane thinks the hard part is… membranes? Really?
Thus my second question is what Lane’s evidence was for why membrane formation is so hard, and are such a big part of the story (in comparison to other factors).
I feel like the most likely answer will have has something to do with Sodium pumps?
But, like… maybe the early waters were just more potassium rich than modern sodium rich seawater? This isn’t my area of expertise, (I’m just curious about everything and have big gaps in my knowledge about… basically everything), but I’m curious for more details in this possible version of the story.
I’ve read Nick Lane’s book, but I’m not familiar with Eric Smith’s stuff (yet).
Lane agrees that life started from a geochemical disequilibrium, in Lane’s model it’s serpentinization.
Lane’s book spends a lot of time talking about the Acetyl-CoA cycle, which is a key part of the Citric Acid cycle, as well as many other metabolic cycles. But he doesn’t mention the reverse Krebs cycle or adenine specifically, AFAICT. He cites Eric Smith favorably as going into more details on the specific biochemistry involved.
Regarding membranes, his model is that the first membranes were very leaky with respect to ions. Which is a good thing in the disequilibrium environment, since otherwise the cell would get too full of ions, and die! But there are two big problem for cells with such membranes: 1. their gradient will quickly equilibriate if they leave the sea vent, thus killing them. 2. Evolving a less leaky membrane will reduce their ability to use the sea-vent gradient, and thus by itself will not be selected for. A proton pump will not give an advantage in this case (the argument is a bit complex). The key is that a Sodium antiporter pump needed to come after the leaky membrane. This by itself gives an advantage, by also creating an Na+ gradient across the membrane, and this advantage is strengthened by making the membrane incrementally less leaky. (Lane explicitly claims that the oceans were high in Sodium ions, and low in Potassium ions 4 billion years ago, FWIW.)
But just the Sodium pump wasn’t enough to allow the cells to survive autonomously, since it trades positive ions for positive ions one to one. However, it now makes it advantageous to evolve a proton pump. And that was what finally facilitated the ability for cells to become fully autonomous. He goes on to claim that the direction the proton pump was “installed” across the membrane creates different problems, and that Bacteria and Archea are the result of this happenstance.
Thanks! Does he explain “why Olivine”?
If I had a hunch it would route through the idea of metal atoms that fit into larger enzymes like rock knives wielded by squishy caveman hands.
As wikipedia says of inorganic biochemical co-factors:
So the thing I would naively do, to find candidate minerals, would be to try to sift conserved co-factors, especially with a focus on ribozymes that do the same trick, and then these “metalloribozymes” (some of which do exist in evolved systems still) might suggest typical mineral environments where things first started and never stopped being essential…
...but I don’t seem much mention of Olivine playing well with copper or zinc, and [manganese olivine] goes to its own name: Tephroite. But there was no mention of Tephroite in the review.
So this is where my own naive priors would send me looking: for minerals full of elemental cofactors common to ancient metalloribozymes. Lots of data sifting seems likely to be useful, over ribozyme and enzyme databases, and mineral databases, which I have not done.
Did Nick Lane do this kind of data sifting to find the name “Olivine”, or did he use some other method?
One idea is that he got the name from the literature, and perhaps cites whoever proposed Olivine? When I search [olivine biogenesis] I get Serpentinization results which echo the link you offered (and youtube on [serpentization] gives a fun experimental video that is interesting but sheds no particular light for me).
Synthesizing this… maybe the practical upshot is just “most normal mantle material reacting with seawater” could be loosely called “something-like-olivine turning to something-like-serpentine” and since there is so much mantle, and so much seawater, priors say that “this general reaction” is the key reaction at a high and fuzzy level of description. Maybe?
It looks like he got it from Mike Russell, though he disagrees with Russell on the details.
Regarding cofactors, the important thing (in Lane’s version of this model) about serpentinization is that it is alkaline. This would cause iron to precipitate out (as iron hydroxides and iron sulphates), and dissolve minerals such as nickel and molybdenum.
He points out nickel-doped greigite (Fe5NiS8) as a mineral with a crystal structure similar to several ancient metalloribozymes, and which he thinks was likely to have deposited on the walls of pores in the rock (serpentine?).