Abiogenesis: Does a Single Mechanism Solve Multiple Problems?

To those of you who say there is no or too little progress in abiogensis research I have a couple of article suggestions for you. Food for thought, and a caution against thinking we now know enough to know that it’s not possible.

In arguments against different models on the origin of life, it is often asserted that one problem that permeates the entire field is that even where scientists can find solutions to one problem, it often contradicts solutions to other problems. A typical example is where scientists may find a way that a natural environment could have overcome one problem with a “step” in the abiotic synthesis of RNA, but the conditions required would be a problem for a later step in the same pathway, or conflict with the conditions required to synthesize other molecules.

Three problems often highlighted against many different models are

  1. The concentration problem:
    If life originated in the oceans or some lake, the sheer volume of these bodies of water would make it unlikely for any two relevant molecules, should they even be synthesized, to ever meet up before they’re lost again to degradation and/or hydrolysis. If monomers were synthesized in the open ocean, even in close proximity to each other, they would normally just tend to diffuse away and become more and more spatially separated with time.
  2. The chirality problem:
    We know life today is exclusively using homochiral sugars and amino acids to produce it’s polymers through the structures of enzymes, but there’s no obvious mechanism that could ensure the enantioselective synthesis of these molecules before enzymes had evolved, so since functional enzymes themselves (presumably) requires homochiral monomers, it is unlikely for random polymerization to assemble a homochiral polymer from a relatively uniform mixture of heterochical monomers.
  3. The hydrolysis/degradation problem:
    The temperatures conducive to the kinds of chemistry that yields the molecules we consider relevant to life as we know it is also known to be relatively problematic for the long-term persistence of those same molecules. Chemical reactions usually proceed faster at higher temperatures, so at increased temperatures lots of relevant molecules could be produced in a short time, but they would also degrade again faster at those same temperatures. In particular RNA polymers is quite temperature sensitive, and at high temperatures RNA strands quickly hydrolyze into it’s monomers again.

Turns out there’s a likely solution to all three of these problems in the same natural microenvironment: Laminar microflows, akin to convection, across a temperature gradient in microscopic mineral pores. As monomers are synthesized deeper in the hotter interior of the mineral matrix, they can propagate out into colder areas and accumulate by thermophoresis in microscopic channels. Amazingly this same mechanism exhibits chiral selection, being able to induce achiral molecules into adopting chiral structures. And continous cycling in the internal convective flows in the pore can assist the process of replication and selection for increasing polymer length against the tendency to hydrolyze.

1: Sun J, Li Y, Yan F, Liu C, Sang Y, Tian F, Feng Q, Duan P, Zhang L, Shi X, Ding B, Liu M. Control over the emerging chirality in supramolecular gels and solutions by chiral microvortices in milliseconds. Nat Commun. 2018 Jul 3;9(1):2599. DOI:


The origin of homochirality in life is a fundamental mystery. Symmetry breaking and subsequent amplification of chiral bias are regarded as one of the underlying mechanisms. However, the selection and control of initial chiral bias in a spontaneous mirror symmetry breaking process remains a great challenge. Here we show experimental evidences that laminar chiral microvortices generated within asymmetric microchambers can lead to a hydrodynamic selection of initial chiral bias of supramolecular systems composed of exclusively achiral molecules within milliseconds. The self-assembled nuclei with the chirality sign affected by the shear force of enantiomorphic microvorticesare subsequently amplified into almost absolutely chirality-controlled supramolecular gels or nanotubes. In contrast, turbulent vortices in stirring cuvettes fail to select the chirality of supramolecular gels. This study reveals that a laminar chiral microflow can induce enantioselection far from equilibrium, and provides an insight on the origin of natural homochirality.

2: Mast CB, Schink S, Gerland U, Braun D. Escalation of polymerization in a thermal gradient. Proc Natl Acad Sci U S A. 2013 May 14;110(20):8030-5. DOI:


For the emergence of early life, the formation of biopolymers such as RNA is essential. However, the addition of nucleotide monomers to existing oligonucleotides requires millimolar concentrations. Even in such optimistic settings, no polymerization of RNA longer than about 20 bases could be demonstrated. How then could self-replicating ribozymes appear, for which recent experiments suggest a minimal length of 200 nt? Here, we demonstrate a mechanism to bridge this gap: the escalated polymerization of nucleotides by a spatially confined thermal gradient. The gradient accumulates monomers by thermophoresis and convection while retaining longer polymers exponentially better. Polymerization and accumulation become mutually self-enhancing and result in a hyperexponential escalation of polymer length. We describe this escalation theoretically under the conservative assumption of reversible polymerization. Taking into account the separately measured thermophoretic properties of RNA, we extrapolate the results for primordial RNA polymerization inside a temperature gradient in pores or fissures of rocks. With a dilute, nanomolar concentration of monomers the model predicts that a pore length of 5 cm and a temperature difference of 10 K suffice to polymerize 200-mers of RNA in micromolar concentrations. The probability to generate these long RNAs is raised by a factor of >10(600) compared with polymerization in a physical equilibrium. We experimentally validate the theory with the reversible polymerization of DNA blocks in a laser-driven thermal trap. The results confirm that a thermal gradient can significantly enlarge the available sequence space for the emergence of catalytically active polymers.

3: Baaske P, Weinert FM, Duhr S, Lemke KH, Russell MJ, Braun D. Extreme accumulation of nucleotides in simulated hydrothermal pore systems. Proc Natl Acad Sci U S A. 2007 May 29;104(22):9346-51. DOI:10.1073/pnas.0609592104


We simulate molecular transport in elongated hydrothermal pore systems influenced by a thermal gradient. We find extreme accumulation of molecules in a wide variety of plugged pores. The mechanism is able to provide highly concentrated single nucleotides, suitable for operations of an RNA world at the origin of life. It is driven solely by the thermal gradient across a pore. On the one hand, the fluid is shuttled by thermal convection along the pore, whereas on the other hand, the molecules drift across the pore, driven by thermodiffusion. As a result, millimeter-sized pores accumulate even single nucleotides more than 10(8)-fold into micrometer-sized regions. The enhanced concentration of molecules is found in the bulk water near the closed bottom end of the pore. Because the accumulation depends exponentially on the porelength and temperature difference, it is considerably robust with respect to changes in the cleft geometry and the molecular dimensions. Whereas thin pores can concentrate only long polynucleotides, thicker pores accumulate short and long polynucleotides equally well and allow various molecular compositions. This setting also provides a temperature oscillation, shown previously to exponentially replicate DNA in the protein-assisted PCR. Our results indicate that, for life to evolve, complicated active membrane transport is not required for the initial steps. We find that interlinked mineral pores in a thermal gradient provide a compelling high-concentration starting point for the molecular evolution of life.

4: Kreysing M, Keil L, Lanzmich S, Braun D. Heat flux across an open pore enables the continuous replication and selection of oligonucleotides towards increasing length. Nat Chem. 2015 Mar;7(3):203-8. DOI: 10.1038/nchem.2155


The replication of nucleic acids is central to the origin of life. On the early Earth, suitable non-equilibrium boundary conditions would have been required to surmount the effects of thermodynamic equilibrium such as the dilution and degradation of oligonucleotides. One particularly intractable experimental finding is that short genetic polymers replicate faster and outcompete longer ones, which leads to ever shorter sequences and the loss of genetic information. Here we show that a heat flux across an open pore in submerged rock concentrates replicating oligonucleotides from a constant feeding flow and selects for longer strands. Our experiments utilize the interplay of molecular thermophoresis and laminar convection, the latter driving strand separation and exponential replication. Strands of 75 nucleotides survive whereas strands half as long die out, which inverts the above dilemma of the survival of the shortest. The combined feeding, thermal cycling and positive length selection opens the door for a stable molecular evolution in the long-term microhabitat of heated porous rock.

5: Budin I, Bruckner RJ, Szostak JW. Formation of protocell-like vesicles in a thermal diffusion column. J Am Chem Soc. 2009 Jul 22;131(28):9628-9. DOI: 10.1021/ja9029818


Many of the properties of bilayer membranes composed of simple single-chain amphiphiles seem to be well-suited for a potential role as primitive cell membranes. However, the spontaneous formation of membranes from such amphiphiles is a concentration-dependent process in which a significant critical aggregate concentration (cac) must be reached. Since most scenarios for the prebiotic synthesis of fatty acids and related amphiphiles would result in dilute solutions well below the cac, the identification of mechanisms that would lead to increased local amphiphile concentrations is an important aspect of defining reasonable conditions for the origin of cellular life. Narrow, vertically oriented channels within the mineral precipitates of hydrothermal vent towers have previously been proposed to act as natural Clusius-Dickel thermaldiffusion columns, in which a strong transverse thermal gradient concentrates dilute molecules through the coupling of thermophoresis and convection. Here we experimentally demonstrate that a microcapillary acting as a thermal diffusion column can concentrate a solution of oleic acid. Upon concentration, self-assembly of large vesicles occurs in regions where the cac is exceeded. We detected vesicle formation by fluorescence microscopy of encapsulated dye cargoes, which simultaneously concentrated in our channels. Our findings suggest a novel means by which simple physical processes could have led to the spontaneous formation of cell-like structures from a dilute prebiotic reservoir.


Really interesting @Rumraket, thanks.

The original title (too long) was:

Does a single physical mechanism in fluid dynamics solve the concentration problem, chirality problem, and replication / degradation / hydrolysis problem of abiogenesis?

The problems here are:

  1. Concentration
  2. Chirality
  3. Replication
  4. Degradation
  5. Hydrolysis

Could anyone have predicted from first principles that a convective flow in a temperature gradient in a long thin mineral pore, could simultaneously effectuate strong chiral aggregation, concentrate biological molecules, drive the replication of genetic polymers in a way reminiscent of PCR, and select for increased length?

Scientists have been hypothesizing about the hydrothermal origin of life now for decades for reasons that have to do with chemistry and bioenergetics, well before this collection of physical effects were known, and the precipitated mineral structures of hydrothermal systems happens to be the kinds of natural environments that are most likely to produce these kinds of mineral micropore systems.

Isn’t that a funny coincidence? Isn’t that a remarkable collection of properties? Could this be a significant clue? Do any of you think we know enough to say that we can rule this out?

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