Metabolism First and Hydrothermal Vents

The main alternative to RNA-first says chemistry came before genes. Iron drives nine of the eleven Krebs intermediates without enzymes, and minerals fix carbon dioxide at millimolar yields. But no self-sustaining cycle has been demonstrated, Orgel's specificity objection is unanswered, and the field's three camps each hold an objection the other two cannot meet.

Draft:  September 2026

"Lack of specificity rather than inadequate efficiency may be the predominant barrier to the existence of complex autocatalytic cycles of almost any kind." — Leslie Orgel, in an essay finished weeks before his death and published posthumously.1

"Solutions offered by supporters of geneticist or metabolist scenarios that are dependent on 'if pigs could fly' hypothetical chemistry are unlikely to help." — Orgel, in the same essay, aiming at his own side as well.1

Summary

If RNA is too complicated to come first, perhaps chemistry came first and genes came later.  That is the metabolism-first family of theories, and its leading version puts the origin of life in alkaline hydrothermal vents on the Hadean sea floor.

  • The chemistry is real and better than most critics allow. Iron alone, in water at 70 °C, turns pyruvate and glyoxylate into "nine of the eleven Krebs (tricarboxylic acid, TCA) cycle intermediates, including all five universal metabolic precursors," and with hydroxylamine added it makes four amino acids.2 No enzymes and no ATP. This article concedes it.
  • Minerals fix carbon dioxide at real concentrations. Greigite, magnetite and awaruite with hydrogen and carbon dioxide at 100 °C give "formate (up to 200 mM), acetate (up to 100 µM), pyruvate (up to 10 µM)."3 That is the largest yield in this entire literature.
  • And it is achieved with no pH gradient, no membrane and no compartment, which is awkward for the vent theory specifically. The reactor experiments built around a proton gradient produce far less: formaldehyde around 100 nanomolar, "variable and inconsistent between runs,"4 and formate at 1.5 micromolar.5 No such reactor has been reported making a carbon-carbon bond.
  • The strongest objection was written by a founder of the field, and it is about specificity, not probability. Any mineral assembly able to catalyse the eleven steps of a cycle would also catalyse the side reactions that drain it.1 Nobody has answered it. The field worked around it, by abandoning closed cycles for open networks.
  • Orgel is the most misused citation in this area. In the same essay he writes that recognising hydrothermal synthesis "does not necessitate a belief in their ability to self-organize," and that a theory where "metal sulfide–catalyzed reactions provided some or all of the organic molecules… would have many attractive features."1 He is attacking self-organising cycles, not vent chemistry.
  • The vent theory has a physics problem and a partial answer. Baz Jackson calculated that a molecular machine inside a micrometre-thick mineral barrier sees a pH difference "of only about 0.004 units," worth "an insignificant 24 J mol-1."6 Nick Lane's reply is that the machines were never in the rock; they are in lipid membranes lining it, and the rock only has to conduct electrons.7 That answers the geometry and moves the claim.
  • The three mainstream camps refute each other, and each objection is made by a specialist. Deamer says vents cannot make membranes. Jackson says the gradient cannot do the work. Mulkidjanian says no marine setting supplies the potassium and phosphate that all cells require.8 Russell answers the hot-spring camp by denying there was any dry land.

The verdict.  Individual reactions from core metabolism run without enzymes, and that should be conceded loudly.  What has never been demonstrated is a self-sustaining, side-reaction-resistant cycle, which is the thing the theory is named after.

Two theories, not one

The label covers two families that get lumped together, and the objections to them differ.  Keeping them apart is the first thing an honest treatment has to do, and Orgel does it himself.

Self-organising metabolic cycles.  A closed loop of small-molecule reactions, canonically the reverse citric acid cycle, runs on mineral catalysts, fixes carbon dioxide, and is autocatalytic:  one turn makes two copies of an intermediate.  This is the family Orgel destroyed.

Geochemical continuity.  Hydrothermal geochemistry supplies reduced carbon and a proton gradient;  genetically encoded catalysts arrive later and amplify processes already running.  This family requires no self-organising cycle, and Orgel explicitly said it might work.

His own sentence:  "It is important to realize that recognition of the possible importance of prebiotic syntheses that could occur hydrothermally does not necessitate a belief in their ability to self-organize."1

Wächtershäuser's iron-sulfur world

The theory has an author and he should be named.  Günter Wächtershäuser, a patent lawyer with a chemistry doctorate, set it out in 1988.  His proposal:  "at an early stage of evolution, there are precursor organisms drastically different from anything we know.  These organisms are acellular and lack a mechanism for division, yet they can grow…  Although they can barely be called living, they have a capacity for evolution."  Life begins as "an autocatalytic metabolism confined to an essentially two-dimensional monomolecular organic layer," with the organisms "anionically bonded to positively charged surfaces (e.g., pyrite)."9

The energy comes from making pyrite, and his numbers are honest thermodynamics rather than hand-waving.  Iron sulfide plus hydrogen sulfide gives pyrite and hydrogen, releasing 41.9 kJ/mol.  Reducing carbon dioxide to formic acid costs 30.2.  Couple them and the whole runs downhill at −11.7 kJ/mol.9

The idea is also cleverer than critics usually notice.  The products of carbon dioxide fixation are carboxylates, which carry a negative charge and stick to the positively charged pyrite surface as they form.  That is an answer to the dilution problem, which is the standard objection to any chemistry happening in an ocean.

What has actually been demonstrated, and it deserves crediting.  In 1997 Claudia Huber and Wächtershäuser showed that "an aqueous slurry of coprecipitated NiS and FeS converted CO and CH3SH into the activated thioester CH3-CO-SCH3, which hydrolyzed to acetic acid," calling it "the primordial initiation reaction for a chemoautotrophic origin of life."10  In 1998 the same pair converted amino acids into peptides "by use of coprecipitated (Ni,Fe)S and CO," at 100 °C and neutral to alkaline pH.11  Note the inputs in the first case:  carbon monoxide and methanethiol, not carbon dioxide and hydrogen.  That distinction matters and popular accounts drop it.

What has not been demonstrated, sixty years after the idea and nearly forty after the paper, is a closed self-sustaining autocatalytic cycle.  The demonstrated chemistry is a set of linear reactions and open networks.

Orgel's objection, which nobody has answered

Leslie Orgel died on 27 October 2007.  He finished this essay in September and Gerald Joyce submitted it posthumously.  It is the last thing one of the founders of prebiotic chemistry wrote about the field's second-largest research programme, and it is worth reading rather than quoting.

The argument is not about probability.  Orgel grants that each individual step could be made to run.  His objection is that the same mineral surface that catalyses the eleven reactions of a cycle would also catalyse the reactions that drain it.  A cycle is not a set of reactions.  It is a set of reactions running to the exclusion of everything else those catalysts can do.

His sentence:  "Lack of specificity rather than inadequate efficiency may be the predominant barrier to the existence of complex autocatalytic cycles of almost any kind."1

And the qualification that must travel with it.  In the same essay he writes that a theory in which "metal sulfide–catalyzed reactions provided some or all of the organic molecules needed for the formation of a primitive genetic system would have many attractive features."1  Anyone citing Orgel 2008 as a refutation of hydrothermal chemistry is misusing him, and this is the most misused citation in the apologetics literature on this subject.

His closing line is aimed at both camps, including his own.  "Solutions offered by supporters of geneticist or metabolist scenarios that are dependent on 'if pigs could fly' hypothetical chemistry are unlikely to help."1  Orgel spent his career on the genetic side.  He is calling out RNA-first in the same breath.

The vent programme, with its numbers

The alkaline vent theory is the geochemical-continuity family's leading version.  Michael Russell and William Martin proposed that life began "in structured iron monosulphide precipitates in a seepage site hydrothermal mound at a redox, pH and temperature gradient between sulphide-rich hydrothermal fluid and iron(II)-containing waters of the Hadean ocean floor."  Their most-quoted line is a real argument and deserves quoting:  "the question remains of how a solution at equilibrium can start doing chemistry.  Put another way, once autoclaved, a bowl of chicken soup left at any temperature will never bring forth life."12

The theory is attractive because it supplies, for free, three things a cell needs:  a continuous flow of reduced carbon, a natural proton gradient across a thin barrier, and micro-compartments.  Modern cells run on proton gradients, universally, which is a striking coincidence if the gradient was there first.

The experiments are where the argument gets specific, and the numbers should be given rather than adjectives.

Experiment What it produced
Herschy 2014, vent reactor with pH gradient formate at low micromolar; formaldehyde ~100 nM, "variable and inconsistent between runs"
Hudson 2020, microfluidic reactor formate 1.5 µM, at 2.5 × 10-13 mol/s
Preiner 2020, minerals in free solution, no gradient formate up to 200 mM, acetate up to 100 µM, pyruvate up to 10 µM
Muchowska 2019, Fe2+ in water at 70 °C nine of eleven Krebs intermediates; four amino acids

Two readings of that table are both correct and they pull against each other.

The chemistry works.  Carbon dioxide and hydrogen become formate, acetate and pyruvate over ordinary minerals.  Anyone claiming you cannot get organic molecules from inorganic feedstock abiotically is answered by the third row.

The gradient is carrying almost no weight.  The largest yields in the field come from the experiment with no pH gradient, no membrane and no compartment.  The apparatus the theory is named for produces a hundred thousand times less.  That is not a creationist observation;  it is what the papers report.

Hudson's controls are good and the article credits them.  Removing hydrogen, removing the precipitate, acidifying the vent side or alkalinising the ocean side each killed the product completely, and formate rose monotonically with vent-side pH.  That is a dose-response curve, and it answers the charge that the earlier reactor was merely relaxing to equilibrium.5

What no reactor of this kind has been reported doing is forming a carbon-carbon bond.  That is the step that would matter most.

Jackson's objection and Lane's reply

The sharpest technical attack on the vent theory comes from a bioenergeticist with no stake in either camp, and it is worth following because both sides argue well.

Jackson's case.  There is "no evidence for thin inorganic membranes holding sharp pH gradients in modern hydrothermal alkali vents at Lost City."6  The barriers that exist are more than a micrometre thick, two hundred times a lipid bilayer.  A molecular machine sitting in a channel that wide sees a pH difference "of only about 0.004 units," worth "an insignificant 24 J mol-1" against the tens of kilojoules the bulk gradient implies.6  His follow-up adds a consequence about selection rather than chemistry:  organisms using a natural gradient "would have been imprisoned in the vents, unable to escape and become free-living."13

Lane's reply, and it lands.  The machines were never in the rock.  "Jackson conflates thin inorganic barriers with organic membranes (lipid bilayers) throughout his article," and Lane quotes his own 2010 paper to prove the record:  the ancestral ATPase was always envisaged "in organic lipids lining the walls."7  For the prebiotic stage no machine is needed at all:  "there is no requirement for ΔpH-utilizing molecular machines, just an inorganic barrier containing spontaneously precipitated FeS minerals.  Electrons, not protons, are transferred across this barrier from H2 to CO2," so "the barriers need to be semi-conducting for electrons, not protons."7

He also corrects an arithmetic point that is not obvious.  Jackson's figure showed machines on opposite sides of a compartment being driven in opposite directions and cancelling.  But pH is a log scale:  protons at pH 7 are 0.1 µM while hydroxide at pH 10 is 100 µM, a thousandfold difference, so "the pH gradient across the ocean side is much steeper (nearly 3 pH units) than the pH gradient across the vent side (about 0.2 units)."7  That is correct and the article credits it.

Where Lane concedes.  His modelling works "only if the lipid membranes were highly permeable to protons," and "the model assumes steep pH gradients across vent pores, which is plainly a best-case scenario."7  His summary claim after thirty years of work is that natural gradients "could in principle have helped power the origins of life."

And a sentence this article is obliged to print.  Lane complains that Jackson's paper "is already being cited as evidence that life could not have started in alkaline hydrothermal vents.  That is not sustained in his paper."7  That is exactly what a careless citation of Jackson would be doing here, and saying so first is what makes the rest of this section worth reading.

Scoring the exchange honestly.  The geometry objection is answered, twice over.  The "no such membranes have been observed at Lost City" objection is not answered;  Lane relocates the claim to microfluidic laminar-flow experiments rather than evidencing it in a real vent.  And no reply to the escaping-the-vent objection could be found.  An ion pump is useless until the cell is sealed, and the cell cannot seal until it has a pump.

Iron does more than Orgel expected

The result that most damages the strong form of Orgel's objection came in 2019, and this article concedes it without hedging.

Kamila Muchowska, Sreejith Varma and Joseph Moran ran pyruvate and glyoxylate in water with iron(II) at 70 °C.  Within three hours the mixture contained acetate, malate, fumarate, succinate, α-ketoglutarate, isocitrate and aconitate.  In total the network builds "nine of the eleven Krebs (tricarboxylic acid, TCA) cycle intermediates, including all five universal metabolic precursors," and "the intermediates simultaneously break down to CO2 in a life-like regime resembling biological anabolism and catabolism."  Add hydroxylamine and iron metal and it "produces four biological amino acids in a manner paralleling biosynthesis."2

Why this cuts at Orgel.  His claim was that no single mineral or ion could catalyse a suite of unrelated reaction types selectively.  Here iron(II) alone drives aldol chemistry, hydration and dehydration, oxidative decarboxylation and redox steps, in one pot, with reductive and oxidative branches running at the same time.  The specificity problem is smaller than he thought.

Why it does not close the case, on the authors' own terms.  The inputs are pyruvate and glyoxylate rather than carbon dioxide;  the paper describes them as products of abiotic carbon dioxide reduction and cites other work for that step.  It is an open network at sub-millimole scale, not a demonstrated autocatalytic cycle, and a steady state would need continuous feeding.  And of the two missing intermediates, one is citrate, whose lyase reaction is precisely the step Orgel singled out as presenting severe difficulties.2

Three-part verdict:  the chemistry is real, the specificity problem is smaller than Orgel thought, and the closed cycle is still missing.

Autocatalytic sets are mathematics

The theoretical wing of metabolism-first is Stuart Kauffman's autocatalytic set theory:  in a large enough set of peptides, some subset will catalyse its own production, and that closure is what life is.

Orgel's reply is that the mathematics assumes what chemistry has to supply.  Short peptides do not have the sequence-specific catalytic discrimination the proofs silently require.  His question and answer:  "Would one expect similar discrimination in the catalytic potential of peptides of length ten or less?  The answer is clearly 'no,' and it is this conclusion that ultimately undermines the peptide cycle theory."1

The best modern computational result contains its own limit.  Joana Xavier, with Wim Hordijk who built the formalism, plus Kauffman, Steel and Martin, searched modern microbial metabolism for self-sustaining autocatalytic networks.  Given inorganic food plus small-molecule catalysts, a large network appears, generating "acetyl-CoA as well as amino acids and bases."  Run it the other way, supplying the amino acids and bases but no organic catalysts, and it "only produces a minute RAF with 33 reactions."14  Catalysts, not monomers, are the bottleneck.  Two limits the article states plainly:  it is an analysis of a database of modern metabolism, not an experiment, and the cofactors that make it work were placed in the food set by hand.14

A second, independent objection comes from theoretical biology and it is about inheritance.  Vasas, Szathmáry and Santos found that replication of compositional information "is so inaccurate that fitter compositional genomes cannot be maintained by selection and, therefore, the system lacks evolvability."15  Orgel says the chemistry will not stay on course.  Szathmáry says that even if it does, it cannot inherit.

The clay hypothesis, and a cautionary tale

Graham Cairns-Smith proposed that the first genes were clay crystals, whose defects replicate as the crystal grows, with organic chemistry later taking over.  It is the most-cited alternative in popular writing about this field, and its experimental basis collapsed.

The evidence was Armin Weiss's 1981 claim that clays replicate their layer charge through generations.  Nobody reproduced it.  The methods were never published in usable detail and cited references turned out to be untraceable or irrelevant.  Arrhenius, Cairns-Smith, Hartman, Miller and Orgel jointly published a letter saying so.  Hyman Hartman, writing as co-author of the review that tells the story first-hand, "was furious that he had invested time and NASA money in what had turned out to be a fraud."16

Do not over-read that.  Clay as genetic material collapsed.  Clay as catalyst did not.  Ferris's montmorillonite oligomerisation of nucleotides stands, and montmorillonite is the same mineral that converts fatty-acid micelles into vesicles in Szostak's laboratory.  The collapse of one claim about a mineral is not the collapse of the mineral.

Three camps, three unanswered objections

The most useful thing this literature offers a reader is that its mainstream camps attack each other, and each attack is made by a specialist.

Deamer against vents.  "Self-assembly of membranes composed of amphiphiles has not been demonstrated in hydrothermal vents, either in situ or in laboratory simulations."17  He and Bruce Damer add that a proton gradient across a barrier a thousand times too thick leaves "almost no energy available."18

Lane's group answered the membrane half in 2019, and the answer is good.  Mixtures of ten- to fifteen-carbon fatty acids and alkanols form vesicles at seawater ionic strength, 50 millimolar magnesium, and 70 °C.19  Damer and Deamer cite the result and do not dispute it;  they answer that a prebiotic source of such mixtures remains uncertain.

Russell against hot springs.  The hot-spring camp needs dry land, and Russell denies there was any:  the early Earth's "all-enveloping ocean was never less than 4 km deep," with no Icelands and no Hawaiis.20

Mulkidjanian against both.  This third camp is the one most often left out, and it argues from what cells are made of rather than from where they might have formed.  "All cells contain much more potassium, phosphate, and transition metals than modern (or reconstructed primeval) oceans, lakes, or rivers," and the universal, and so probably primordial, protein systems "show affinity to and functional requirement for K+, Zn2+, Mn2+, and phosphate."  His conclusion:  "protocells must have evolved in habitats with a high K+/Na+ ratio," which he places in terrestrial anoxic geothermal fields, neither in the sea nor at a vent.8

Set the three side by side.  Deamer's objection to vents was answered.  Jackson's was partly answered and partly not.  Mulkidjanian's has no published answer this research could find.  That is the honest state of the field, and it is more useful to a reader than any one camp's press release.

The claims, audited

Claim Verdict
"You cannot get organic molecules from CO2 abiotically" Dead. Formate at 200 mM over ordinary minerals
"Core metabolism cannot run without enzymes" Dead. Nine of eleven Krebs intermediates from iron in water
"Orgel refuted hydrothermal origin-of-life chemistry" Misuse. He attacked self-organising cycles and said vent chemistry "would have many attractive features"
"Jackson showed life could not start in vents" Misuse, and Lane says so in print. The geometry objection is answered; what stands is narrower
"No self-sustaining autocatalytic cycle has been demonstrated" Sound. Nearly forty years on, the demonstrated chemistry is linear reactions and open networks
"The proton gradient is doing the work" Not supported by the yields. The largest results use no gradient at all
"Autocatalytic sets solve the problem" Overstated. A database analysis with cofactors supplied by hand, and a published proof that such systems cannot evolve

Objections

1. You are quoting Orgel against a theory he did not attack

That is the danger and this article names it before making the argument.  Orgel attacked self-organising metabolic cycles.  He explicitly allowed that hydrothermal sulfide chemistry might supply the molecules a genetic system needs.  The section above quotes the allowance as prominently as the attack.

2. Low yields are what you would expect from a first attempt

Fair, and the trend is upward.  The counter is not that the yields are low but that they are lowest in the apparatus the theory requires and highest without it.  If proton gradients were doing the work the theory says they do, the gradient reactors should not be the worst performers by five orders of magnitude.

3. Muchowska's experiment starts from pyruvate, which is cheating

Half right.  Pyruvate and glyoxylate are described by the authors as products of abiotic carbon dioxide reduction, and Preiner's minerals do make pyruvate from carbon dioxide and hydrogen, at 10 micromolar.  The two halves have not been joined in one experiment, and that is the accurate way to state it rather than calling the starting material implausible.

4. A network is as good as a cycle

It is not, and the distinction is Orgel's.  A cycle regenerates its own catalyst and grows;  a network runs downhill from whatever is fed in.  Muchowska's authors say a steady state would need continuous input.  That is a flow reactor, not a self-sustaining cycle, and calling it one blurs exactly the point in dispute.

5. This is all just god-of-the-gaps

The article makes no inference from the gap.  It reports what runs and what does not, mostly in the words of the researchers who did the work.  The parent article on the origin of life states the position in full.

6. Metabolism-first is a fringe position

It is not.  Its critics are Orgel and Szathmáry, its proponents include Martin, Lane, Russell, Moran and Kauffman, and its experiments appear in Nature and Nature Ecology & Evolution.  What is true is that the field has three incompatible camps and the disagreements between them are geographical:  the sea floor, a hot spring, or a geothermal field.  They cannot all be right, and each has a specialist's objection to the other two.

What this article claims, and what it does not

It claims that non-enzymatic reactions from core metabolism run in water at modest temperatures, that minerals fix carbon dioxide at millimolar concentrations, and that these results should be conceded rather than disputed.  It claims that no closed, self-sustaining, side-reaction-resistant cycle has been demonstrated, that Orgel's specificity objection has been worked around rather than answered, that the proton gradient carries little experimental weight, and that the field's three camps hold mutually unanswered objections.

It does not claim that vent chemistry is refuted, that Orgel refuted it, or that Jackson refuted it.  Lane's replies are quoted at length because they are good.  It has not opened Preiner 2020 beyond its abstract, nor Vasas 2010 beyond its abstract, nor Kauffman's original proofs, and it prints no number resting on those alone.  Those gaps are listed in the literature review.

Sources


  1. 1.

    Orgel.  “The Implausibility of Metabolic Cycles on the Prebiotic Earth.”  PLoS Biology 6(1):e18.  2008.  An essay by Orgel arguing that metabolic cycles are implausible on the prebiotic Earth, because a cycle needs catalysts specific enough to avoid the side reactions that drain it.  It attacks the peptide cycle theory of Stuart Kauffman.  The article uses it for the strongest objection to abiotic cycles, which concerns specificity rather than probability.

    1. 1a.

      “Lack of specificity rather than inadequate efficiency may be the predominant barrier to the existence of complex autocatalytic cycles of almost any kind.” ↩ ↩ ↩

    2. 1b.

      On hydrothermal chemistry as distinct from cycles, the essay says that a theory in which.  “metal sulfide–catalyzed reactions provided some or all of the organic molecules needed for the formation of a primitive genetic system would have many attractive features.”  Page 5:  The methodological sentence:  “It must be recognized that assessment of the feasibility of any particular proposed prebiotic cycle must depend on arguments about chemical plausibility, rather than on a decision about logical possibility.  Any reaction sequence that is allowed by thermodynamics could, in principle, be realized, given a sufficiently active and specific family of catalysts.” ↩ ↩ ↩

    3. 1c.

      From the closing paragraph, the full sentence:  “However, solutions offered by supporters of geneticist or metabolist scenarios that are dependent on 'if pigs could fly' hypothetical chemistry are unlikely to help.”  Orgel spent his career on the genetic side, so the line indicts his own camp as well. ↩ ↩

    4. 1d.

      On Kauffman's autocatalytic peptide sets, the essay says that enzymes.  “discriminate between potential substrates that differ very slightly in structure.  Would one expect similar discrimination in the catalytic potential of peptides of length ten or less?  The answer is clearly 'no,' and it is this conclusion that ultimately undermines the peptide cycle theory.” ↩

  2. 2.

    Muchowska, Kamila B. et al.  “Synthesis and breakdown of universal metabolic precursors promoted by iron.”  Nature 569:104–107.  2019.  The conditions were 70 °C under an inert atmosphere, which the authors describe as.  “to simulate a mild hydrothermal environment”.  Within three hours the mixture contained acetate, pyruvate, malate, fumarate, succinate, α-ketoglutarate, isocitrate and aconitate.  The amino acids appear within an hour of adding hydroxylamine and iron metal.  Section Abstract:  “nine of the eleven Krebs (tricarboxylic acid, TCA) cycle intermediates, including all five universal metabolic precursors”.  “The intermediates simultaneously break down to CO2 in a life-like regime resembling biological anabolism and catabolism.”  “produces four biological amino acids in a manner paralleling biosynthesis”.  A laboratory study in which pyruvate and glyoxylate, two products of abiotic carbon dioxide reduction, react in iron-rich water with no enzymes and no ATP.  The reaction builds a network that overlaps the Krebs and glyoxylate cycles, and the intermediates break down again.  The article concedes that this is real chemistry, and that iron alone builds nine of the eleven Krebs intermediates. ↩ ↩

    1. 2a.

      “The observed non-enzymatic reaction network bears some remarkable similarities to the TCA cycle, encompassing seven of its eleven reactions and nine of its eleven intermediates (only oxalosuccinate and citrate are missing).”  The authors also note that the citrate-aconitate interconversion has been achieved with chromium(III).  “albeit under more extreme conditions (1 M HCl, 140 °C) that are incompatible with the current study.”  Citrate is one of the two missing intermediates, and it is the molecule Orgel singled out, which is why the article says the specificity problem is reduced rather than removed. ↩

  3. 3.

    Preiner, Martina et al.  “A hydrogen-dependent geochemical analogue of primordial carbon and energy metabolism.”  Nature Ecology & Evolution 4:534–542.  2020.  Section Abstract:  “Here we show that three hydrothermal minerals—greigite (Fe3S4), magnetite (Fe3O4) and awaruite (Ni3Fe)—catalyse the fixation of CO2 with H2 at 100 °C under alkaline aqueous conditions.  The product spectrum includes formate (up to 200 mM), acetate (up to 100 µM), pyruvate (up to 10 µM), methanol (up to 100 µM) and methane.”  A laboratory study that tested three hydrothermal minerals as catalysts for making simple carbon compounds from hydrogen and carbon dioxide at 100 °C in alkaline water.  The article calls its formate yield the largest in this literature. ↩

  4. 4.

    Herschy, Barry et al.  “An Origin-of-Life Reactor to Simulate Alkaline Hydrothermal Vents.”  Journal of Molecular Evolution 79:213–227.  2014.  “We established the presence of formate in low micromolar quantities using a head-space GC–MS analysis…  We also detected formaldehyde in samples, again by head-space GC–MS analysis, in low nanomolar quantities…  While these preliminary findings are encouraging, the formation of formaldehyde, especially, is variable and inconsistent between runs, and these methods are still being optimised.”  The figure captions give "Estimated concentration is 50 µM" for formate and "Estimated concentration is 100 nM" for formaldehyde, both "based on extrapolation from calibration data."  The 50 µM in the caption and "low micromolar" in the text do not agree, so no single formate number from this paper should be quoted without saying so.  On sugars, the paper says:  “Sugars identified by this process include ribose and deoxyribose, albeit at low yield (~0.06 % of formaldehyde was converted to ribose).”  That step was run at 0.5 M formaldehyde, about five million times the concentration the reactor itself produced.  A laboratory paper describing a small electrochemical reactor built to copy alkaline hydrothermal vents, and what the reactor made.  It formed thin-walled structures containing nickel-doped mackinawite, a catalytic iron-nickel sulfide mineral, and these simulated vent structures gave low yields of simple organic molecules.  The authors include Nick Lane, so the test comes from the vent camp itself.  The article uses it for the formaldehyde yield and for the warning that the yield changes from run to run.  Mirror:  PMC ↩

  5. 5.

    Hudson, Reuben et al.  “CO2 reduction driven by a pH gradient.”  Proceedings of the National Academy of Sciences 117:22873–22879.  2020.  Removing H2, removing the precipitate, acidifying the vent side or alkalinising the ocean side each killed the product completely, and formate rose monotonically with vent-side pH: undetected, then below 0.37, 0.9, 1.5 and 1.8 µM.  That is a dose-response curve, and the article says the controls are good.  The "no carbon–carbon bond" statement in the body of this article is about this class of pH-gradient reactor as a whole, not a negative result reported in this paper alone.  A laboratory study in which a microfluidic pH gradient across iron-nickel sulfide precipitates drove hydrogen to reduce carbon dioxide to formate, a simple carbon compound, at room temperature and 1.5 bar.  Carbon-13 labelling confirmed the formate production.  The article uses its formate yield of 1.5 micromolar, and its controls. ↩ ↩

  6. 6.

    Jackson, J. Baz.  “Natural pH Gradients in Hydrothermal Alkali Vents Were Unlikely to Have Played a Role in the Origin of Life.”  Journal of Molecular Evolution 83:1–11.  2016.  Section Abstract:  “There is as yet no evidence for thin inorganic membranes holding sharp pH gradients in modern hydrothermal alkali vents at Lost City”.  A review by a bioenergeticist at the University of Birmingham that tests the natural pH gradient hypothesis against the physics of molecular machines.  It argues that there is no evidence for thin inorganic membranes holding sharp pH gradients at the Lost City vents, and that small motors could not work across the thick barriers the hypothesis uses.  The article prefers it to any creationist critique of the same model, because its author is no origin-of-life partisan and thanks Lane and Martin in the acknowledgments. ↩

    1. 6a.

      Figure 4b:  “the DpH across the machine is much less than that between the bulk aqueous phases, only about 0.004 units…  this amounts to an insignificant 24 J mol-1 protons transferred across the machine.”  Section Abstract:  “Small molecular motors comprising a few hundred atoms would have been unable to function in the relatively thick (>1 μm) inorganic membranes that have hitherto been used as descriptive models for the natural pH gradient hypothesis.”  The arithmetic is the argument; it does not depend on any view about design. ↩ ↩

  7. 7.

    Lane, Nick.  “Proton gradients at the origin of life.”  BioEssays 39(6):1600217.  2017.  The central rebuttal:  “The biggest problem is that Jackson conflates thin inorganic barriers with organic membranes (lipid bilayers) throughout his article…  Jackson argues that proton gradients could not have driven the origin of life because he envisages some kind of proton-driven machine – analogous to the proteins found today in lipid membranes – embedded in these inorganic barriers.  But that is not what is claimed.”  He then quotes his own 2010 paper:  “We do not envisage the ancestral ATPase as embedded in the inorganic walls, but rather in organic lipids lining the walls.”  His framing sentence, from the abstract:  Section Abstract:  “Unfortunately, Jackson mainly criticized his own interpretations of the theory, not what the literature says.  This counterpoint is intended to set the record straight.”  A counterpoint by Nick Lane of University College London, replying to Jackson's critique of the alkaline vent hypothesis.  Lane argues that Jackson attacked a machine embedded in inorganic rock, which the theory does not claim, and he concedes where the models are weakest.  William Martin was a co-author of an earlier draft and asked to be removed, which the acknowledgements state.  The article uses it for Lane's reply on the membrane question and for the concessions Lane makes himself. ↩ ↩

    1. 7a.

      “Contrary to Jackson's claims, there is no requirement for ΔpH-utilizing molecular machines, just an inorganic barrier containing spontaneously precipitated FeS minerals.  Electrons, not protons, are transferred across this barrier from H2 to CO2…  Critically, this process does not depend on proton transfer across barriers, and the thickness of the barriers is practically irrelevant, dispelling much of Jackson's argument.  The barriers need to be semi-conducting for electrons, not protons.”  His evidence that this is not a stringent requirement: equivalent iron-sulfide minerals.  “conduct electrical currents across entire chimneys up to 10 cm thick”.  in black smoker vents. ↩

    2. 7b.

      “pH units are not equal and opposite, as Jackson depicts them, but a log scale representing the concentration of protons and hydroxide ions…  The concentration of protons at pH 7 is 10-7M (0.1 µM).  The concentration of OH- ions at pH 10 is 10-4M (100 µM), a 1000-fold difference…  Therefore the pH gradient across the ocean side is much steeper (nearly 3 pH units) than the pH gradient across the vent side (about 0.2 units).” ↩

    3. 7c.

      He concedes the modelling assumptions:  “Our computational modelling shows that natural proton gradients could indeed have driven carbon and energy metabolism in LUCA, but only if the lipid membranes were highly permeable to protons, with a permeability equivalent to fatty acid vesicles.  The model assumes steep pH gradients across vent pores, which is plainly a best-case scenario.”  His closing claim:  “there is little doubt that natural proton gradients in alkaline hydrothermal vents could in principle have helped power the origins of life.” ↩

    4. 7d.

      Lane says that Jackson's paper.  “is already being cited as evidence that life could not have started in alkaline hydrothermal vents.  That is not sustained in his paper.” ↩

  8. 8.

    Mulkidjanian, Armen Y. et al.  “Origin of first cells at terrestrial, anoxic geothermal fields.”  Proceedings of the National Academy of Sciences 109:E821–E830.  2012.  The weakness with it: the argument runs from the composition of modern cells back to their setting, so it inherits whatever is wrong with treating universal components as primordial.  Gogarten makes the same methodological point about LUCA reconstructions elsewhere in this article.  Section Abstract:  “All cells contain much more potassium, phosphate, and transition metals than modern (or reconstructed primeval) oceans, lakes, or rivers.”  “show affinity to and functional requirement for K+, Zn2+, Mn2+, and phosphate.”  “protocells must have evolved in habitats with a high K+/Na+ ratio”.  A paper that tries to reconstruct where the first cells lived by comparing the ion needs of universal components of modern cells with the chemistry of geothermal fields.  Its authors conclude that the ion mix the first cells needed could not have existed in marine settings, but fits the vapor-dominated zones of inland geothermal systems.  The article uses it as the third camp, which argues from what cells are made of rather than from where life might have formed. ↩ ↩

  9. 9.

    Wächtershäuser, Günter.  “Before enzymes and templates: theory of surface metabolism.”  Microbiological Reviews 52:452–484.  1988.  Section Central thesis:  “at an early stage of evolution, there are precursor organisms drastically different from anything we know.”  “These organisms are acellular and lack a mechanism for division, yet they can grow.  They possess neither enzymes nor a mechanism for translation, but they do have an autocatalytic metabolism.  They do not have nucleic acids or any other template, yet they have inheritance and selection.”  “Although they can barely be called living, they have a capacity for evolution.”  “an autocatalytic metabolism confined to an essentially two-dimensional monomolecular organic layer”.  “anionically bonded to positively charged surfaces (e.g., pyrite).”  A review by Günter Wächtershäuser, who set out a theory that life began as a two-dimensional chemical network on the surface of a mineral such as pyrite, before enzymes or genetic templates existed.  It is a theory, not an experiment.  The article uses it for the theory itself and for its thermodynamic numbers. ↩

    1. 9a.

      The thermodynamics section gives these reactions:  “FeS + H2S(aqueous) → FeS2 + H2  ΔG0 = -41.9 kJ/mol”.  “CO2(aqueous) + H2 → HCOOH (aqueous)  ΔG0 = +30.2 kJ/mol”.  The two sum to a net −11.7 kJ/mol.  His laboratory later delivered part of the programme: Huber and Wächtershäuser, Science 276 (1997) and 281 (1998), made an activated thioester and then peptides on nickel-iron sulfide.  Note the inputs in those experiments: carbon monoxide and methanethiol, not the CO2 and H2 the 1988 theory runs on. ↩

  10. 10.

    Huber, Claudia, and Günter Wächtershäuser.  “Activated acetic acid by carbon fixation on (Fe,Ni)S under primordial conditions.”  Science 276:245–247.  1997.  Section Abstract:  “In experiments modeling the reactions of the reductive acetyl-coenzyme A pathway at hydrothermal temperatures, it was found that an aqueous slurry of coprecipitated NiS and FeS converted CO and CH3SH into the activated thioester CH3-CO-SCH3, which hydrolyzed to acetic acid…  When NiS-FeS was modified with catalytic amounts of selenium, acetic acid and CH3SH were formed from CO and H2S alone.  The reaction can be considered as the primordial initiation reaction for a chemoautotrophic origin of life.”  The inputs are carbon monoxide and methanethiol, not carbon dioxide and hydrogen.  Popular accounts drop that distinction.  A laboratory paper in Science that tested a step of the reductive acetyl-CoA pathway, a way some microbes fix carbon, using a mineral slurry under hydrothermal conditions.  The slurry turned carbon monoxide and methanethiol into acetic acid, which the authors call the primordial initiation reaction for a chemoautotrophic origin of life.  The article credits it as a real demonstration of carbon fixation on minerals. ↩

  11. 11.

    Huber, Claudia, and Günter Wächtershäuser.  “Peptides by activation of amino acids with CO on (Ni,Fe)S surfaces: implications for the origin of life.”  Science 281:670–672.  1998.  Section Abstract:  “In experiments modeling volcanic or hydrothermal settings amino acids were converted into their peptides by use of coprecipitated (Ni,Fe)S and CO in conjunction with H2S (or CH3SH) as a catalyst and condensation agent at 100 degreesC and pH 7 to 10 under anaerobic, aqueous conditions.”  The amino acids are supplied.  A laboratory paper in Science that tested whether amino acids, the building blocks of proteins, can link into peptides on a nickel-iron sulfide surface with carbon monoxide as the activator.  The reaction ran at 100 degrees C and pH 7 to 10.  The article credits it as a second result from the same pair, although the amino acids were supplied rather than made. ↩

  12. 12.

    Martin, William, and Michael J. Russell.  “On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells.”  Philosophical Transactions of the Royal Society B 358:59–85.  2003.  Section Abstract:  “We propose that life evolved in structured iron monosulphide precipitates in a seepage site hydrothermal mound at a redox, pH and temperature gradient between sulphide-rich hydrothermal fluid and iron(II)-containing waters of the Hadean ocean floor.”  Their picture of the ancestor is stronger than most summaries report:  “The universal ancestor we infer was not a free-living cell, but rather was confined to the naturally chemiosmotic, FeS compartments within which the synthesis of its constituents occurred.”  A hypothesis paper proposing that life began inside structured iron monosulphide precipitates on the Hadean ocean floor, where sulphide-rich hydrothermal fluid met iron(II)-containing waters.  The authors argue that the ancestor of all cells was confined to these natural compartments.  The article uses it as the leading version of the alkaline vent theory. ↩

  13. 13.

    Jackson, J. Baz.  “Ancient Living Organisms Escaping from, or Imprisoned in, the Vents?”  Life 7(3):36.  2017.  A third Jackson paper, in J. Mol. Evol. 85 (2017): 1-7, arguing that Herschy's formate was an equilibrium artefact, is the specific charge that Hudson et al. 2020 answers.  He is explicit about scope:  Section Abstract:  “Our arguments apply to three of the four concurrent models employed by the proponents of the natural pH gradient hypothesis.  A fourth model is exempt from these arguments but has other intrinsic difficulties.”  A follow-up to Jackson's 2016 critique, by the same author, asking what would have happened to organisms that used a natural pH gradient.  It argues that they would have been trapped in the vents rather than becoming free-living, a consequence about selection rather than chemistry.  The article uses it for that consequence. ↩

  14. 14.

    Xavier, Joana C. et al.  “Autocatalytic chemical networks at the origin of metabolism.”  Proceedings of the Royal Society B 287:20192377.  2020.  Section Abstract:  “acetyl-CoA as well as amino acids and bases”.  A computational study, not an experiment, that searched a database of modern microbial metabolism for self-sustaining networks of reactions, called RAFs, in which every reaction is catalysed by a molecule from within the network.  The networks it finds lie in the metabolism of ancient anaerobic autotrophs, which live from hydrogen and carbon dioxide.  The article uses it to show that catalysts, not monomers, are the bottleneck. ↩

    1. 14a.

      The database limit is theirs, stated plainly:  “no reactions in KEGG have RNA catalysts assigned in Uniprot, an observation concerning both the nature of catalysis in microbial metabolism and the limitations inherent to current databases.”  So the analysis cannot see an RNA-catalysed network even if one existed.  Anyone citing this paper against the RNA world is citing it past its own caveat. ↩

  15. 15.

    Vasas, Vera et al.  “Lack of evolvability in self-sustaining autocatalytic networks constraints metabolism-first scenarios for the origin of life.”  Proceedings of the National Academy of Sciences 107:1470–1475.  2010.  Section Abstract:  “In sharp contrast with template-dependent replication dynamics, we demonstrate here that replication of compositional information is so inaccurate that fitter compositional genomes cannot be maintained by selection and, therefore, the system lacks evolvability (i.e., it cannot substantially depart from the asymptotic steady-state solution already built-in in the dynamical equations).  We conclude that this fundamental limitation of ensemble replicators cautions against metabolism-first theories of the origin of life, although ancient metabolic systems could have provided a stable habitat within which polymer replicators later evolved.”  Note the last clause, which is not a rejection of metabolism-first chemistry, only of its heredity.  A theoretical study that models how well a self-sustaining network of chemicals can copy its own composition, and whether selection can improve that copying.  It is a hostile result from the centre of mainstream evolutionary theory, and Szathmáry co-wrote The Major Transitions in Evolution with John Maynard Smith.  The article uses it as an objection from theoretical biology about inheritance: even if the chemistry stays on course, it cannot pass on improvements.  Mirror:  PMC ↩

  16. 16.

    Kloprogge, J. Theo, and Hyman Hartman.  “Clays and the Origin of Life: The Experiments.”  Life 12(2):259.  2022.  A review of experiments on clay minerals and the origin of life, written by a researcher at the University of Queensland and by Hyman Hartman of MIT.  Hartman is a co-author writing about his own part in the story, so the account is a participant's and should be read as one.  The review also reports a joint correction letter by Arrhenius, Cairns-Smith, Hartman, Miller and Orgel, Angew. Chem. 25 (1986): 605-606, which is known here only through this review.  Nothing in the article is a quotation of Cairns-Smith, whose own papers and 1982 book were not read.  The one direct experimental test of crystal inheritance, Bullard et al., Faraday Discussions 136 (2007): 231-245, was read only as an abstract that states no result, and the article does not claim it falsified anything.  The article uses it for the history of Armin Weiss's 1981 claim that clays copy their layer charge through generations, and for the collapse of that claim. ↩

  17. 17.

    Deamer, David, and Bruce Damer.  “Can Life Begin on Enceladus? A Perspective from Hydrothermal Chemistry.”  Astrobiology 17:834–839.  2017.  “Self-assembly of membranes composed of amphiphiles has not been demonstrated in hydrothermal vents, either in situ or in laboratory simulations.  In contrast, hydrothermal fields are supplied by what is essentially distilled water with ionic solutes in millimolar ranges that are more conducive to the self-assembly of amphiphiles into vesicles.”  The article quotes only the first sentence.  The second sets the contrast: hydrothermal fields, not vents, are supplied with nearly distilled water and dilute ions, which favour vesicles.  A second objection in the same paper does not depend on ionic strength and is harder for the vent camp to answer:  “Because hydrothermal vents cannot undergo such [dehydration-rehydration] cycles, how protocells with encapsulated polymers could assemble is an open question.”  The bracketed words are the article's gloss on "such cycles."  The supporting experiment is Milshteyn, Daniel, Bruce Damer, Jeff Havig, and David Deamer, "Amphiphilic Compounds Assemble into Membranous Vesicles in Hydrothermal Hot Spring Water but Not in Seawater," Life 8, no. 2 (2018): 11.  A perspective article that compares two proposed sites for life's origin, hydrothermal vents on the ocean floor and hydrothermal fields on land, and asks whether either could work on Enceladus.  The Cassini probe found a long-lived ocean there, laced with organic compounds.  The article uses it for Deamer's objection that membranes have never been shown to self-assemble at vents. ↩

  18. 18.

    Damer, Bruce, and David Deamer.  “The Hot Spring Hypothesis for an Origin of Life.”  Astrobiology 20:429–452.  2020.  The authors say a three-pH-unit gradient can drive an ATP synthase.  “only if the ATP synthase operates within a membrane that is 5 nm thick and relatively impermeable to proton flux.  All the energy of the proton gradient is concentrated in that 5 nm thickness.  However, the pH gradient of 3 pH units between alkaline vent fluid and an acidic ocean is proposed to lie across a mineral membrane three orders of magnitude thicker than a lipid bilayer, with dimensions of micrometers rather than nanometers.  There would be almost no energy available to an ATP synthase embedded in such a thick membrane.”  They credit the point to Gogarten and Deamer 2016.  This is the same objection Jackson makes, from the rival camp, and Lane's reply about lipid membranes lining the walls applies to it equally.  A hypothesis article that proposes life began in fluctuating volcanic hot spring pools on land, and compares that idea with the seafloor vent scenario.  The authors set out laboratory and field experiments that test the first steps of the idea.  The article uses it for the objection that a proton gradient across a barrier a thousand times too thick leaves "almost no energy available." ↩

  19. 19.

    Jordan, Sean F. et al.  “Promotion of protocell self-assembly from mixed amphiphiles at the origin of life.”  Nature Ecology & Evolution 3:1705–1714.  2019.  Damer and Deamer cite the result and do not dispute it.  Their answer, in Damer, Bruce, and David Deamer, "The Hot Spring Hypothesis for an Origin of Life," Astrobiology 20 (2020): 429–452, is that a plausible prebiotic source of such mixtures.  “remains uncertain”.  One catch neither camp stresses: the result needs pH 11-12, and Jordan et al. report.  “very few”.  vesicles below pH 9, and RNA does not survive pH 11-12.  The alkaline hydroxide complexation that removes the divalent cations and the RNA-hostile pH are the same fact.  A laboratory study that mixed twelve fatty acids and 1-alkanols of 10 to 15 carbons, the kind that hydrothermal Fischer-Tropsch chemistry makes, and tested whether they form vesicles.  The mixture forms vesicles at 600 mM NaCl, 50 mM Mg2+, 10 mM Ca2+, pH 11-12 and 70 °C, which is modern seawater ionic strength under alkaline vent chemistry.  The critical bilayer concentration falls thirtyfold, from 39 mM for pure decanoic acid to 1.3 mM for the mixture.  The authors are Nick Lane's group at University College London, and the article uses the result as the vent camp's answer to the membrane objection. ↩

  20. 20.

    Russell, Michael J.  “The 'Water Problem' (sic), the Illusory Pond and Life's Submarine Emergence — A Review.”  Life 11:429.  2021.  “the evidence refuting the warm little pond scheme is overwhelming given the facts that (i) the early Earth was a water world, (ii) its all-enveloping ocean was never less than 4 km deep, (iii) there were no figurative 'Icelands' or 'Hawaiis', nor even an 'Ontong Java' then because (iv) the solidifying magma ocean beneath was still too mushy to support such salient loadings on the oceanic crust.”  This is a geological claim about the Hadean, and the hot-spring camp contests it.  A review by Michael Russell, a proponent of the alkaline vent theory, arguing that the evidence against the warm little pond is overwhelming.  The article uses it as Russell's answer to the hot-spring camp, which needs dry land. ↩