#14. Three Stages of Abiogenesis [evolution, chemistry]

The iconic Miller experiment on the origin of life

Abiogenesis chemistry outside the box

EV    CH    

Red, theory; black, fact

Repair, growth, reproduction

"Abiogenesis" is the term for life originating from non-life.

Self-repair processes will be important in abiogenesis because life is made of metastable molecules that spontaneously break down and have to be continually repaired, which results in continuous energy dissipation. I will assume that self-repair in non-reproducing molecules is what eventually evolved into self-replication and life.

I also assume that the self repair process was fallible, so that it occasionally introduced a mutation. Favorable mutations would have increased the longevity of the self-repairing molecules. Nevertheless, a given cohort of these molecules would relentlessly decrease in numbers, but they would have been continuously replenished in the juvenile form by undirected chemistry on the early Earth. Eventually, at least one of them was able to morph self-repair into self-replication, and life began. I call this process of refinement of non-reproducing molecules "longitudinal evolution" by analogy to a longitudinal cohort study in medical science. The process bears an interesting resemblance to carcinogenesis, where an accumulation of mutations in long-lived cells also leads to an ability to self-replicate autonomously. Carcinogenesis is difficult to prevent, and so must be considered a facile process, suggesting that longitudinal evolution to the threshold of life was also facile.

A simple self-repairing molecule

The "enzyme ring" shown above is an example of a possible self-repairing molecule that I dreamt up. It is a ring of covalently-bonded monomers that are individually large enough to have good potential for catalyzing reactions, like globular proteins, but are small enough to be present in multiple copies like the standardized building blocks that one wants for templated synthesis.

If the covalent bond between a given pair of monomers breaks, the ring is held together by multiple, parallel secondary valence forces and hydrophobic interactions, until the break can be repaired by the ring's catalytic members. With continuing lack of repair, the ring eventually opens completely, and effectively "dies." To bring the necessary catalysts to the break site reliably, no matter where it is, I assume that multiple copies of the repair enzyme are present in the ring, and are randomly distributed. I also assume a temperature cycle like that of the polymerization chain reaction technology that repeatedly makes the ring single-stranded during the warm phase and allows it to collapse into a self-adhering, linear, double-stranded form during the cool phase. This could simply be driven by the day-night cycle. In the linear form, the catalytic sites are brought close to the covalent bond sites, and can repair any that are broken using small-molecule condensing agents such as cyanogen, which are arguably present on the early Earth under Miller-Urey assumptions. When the ring collapses, it does so at randomly selected fold diameters, so that only a few catalytic monomers are needed, since each will eventually land next to all covalent bonds in the ring except those nearby, which it cannot reach because of steric hindrance and/or bond angle restrictions. The other catalytic monomers in the ring will take care of these.

How it would grow

The mutation process of the enzyme ring could result from random ring-expansion and ring-contraction events, the net effect being to replace one kind of monomer with another. Expansion would most likely begin with intercalation of a free monomer between the bound ones at the high-curvature regions at the ends of the linear conformation. The new monomer would be held in place by the multiple, weak parallel bonds alluded to above. It could become incorporated into the ring if it intercalates at a site where the covalent bond is broken. Two bond-repair events would then suffice to sew it into the ring. The ring-contraction process would the the time-reversed version of this. 

In addition, an ability to undergo ring expansion allows the enzyme ring to start small and grow larger. This is important because, on entropy grounds, a long polymer is very unlikely to spontaneously cyclize. The energy-requiring repair process will bias the system to favor net ring expansion. Thus, we see how easily self-repair can become growth.

How it would reproduce

If large rings can split in two while in the linear conformation, the result is reproduction, without even a requirement for templated synthesis. Thus, we see how easily growth can become reproduction.

Onward to the bacterium

To get from reproduction-competent enzyme rings to something like a bacterium, the sequence of steps might have been multiplication, coacervate droplet formation, cooperation within the confines of the droplet, and specialization. The first specialist subtypes may have been archivists, forerunners of the circular genome of bacteria; and gatekeepers, forerunners of the plasma membrane with its sensory and transporter sites. Under these assumptions, DNA would not have evolved from RNA; both would represent independently originated lines of evolution, but forced to develop many chemical similarities by the demands of templated information transfer.

Back to chemistry

During the classic experiment in abiogenesis, the Miller-Urey experiment, amino acids were formed in solution, but no-one has been able to show how these could subsequently have polymerized to functional protein catalysts. The origin of the monomers in my enzyme ring thus needs to be explained. However, the formation of relatively large amounts of insoluble, dark-colored "tars" is apparently facile under the Miller-Urey reaction conditions. The carbon in this tar is not necessarily lost to the system forever, like a coal deposit. In present-day anoxic environments relevant to the early Earth, at least three-quarters of modern biomass returns to the atmosphere as marsh gas. The driving force for these reactions seems to be not enthalpy reduction, but entropy increase.

Seen in the library of the University of Ottawa

Retrofractive synthesis

I therefore propose that if you wait long enough, and a diversity of trace-metal ions is present, then the abiogenesis tar will largely break down again, releasing large, prefab molecular chunks into solution. Reasoning from what is known of coal chemistry, these chunks may look something like asphaltenes, illustrated above, but relatively enriched in hydrophilic functional groups to make them water soluble. Hydrolysis reactions, for example, can simultaneously depolymerize a big network and introduce such groups (e.g., carboxylic acid groups). I propose that these asphaltene analogs are the optimally-sized monomers needed to form the enzyme ring.