Ball And Brindley

Summary of The Power without the glory: Multiple roles of hydrogen peroxide in mediating the origins of life (Rowena Ball and John Brindley, 2017)




Rowena Ball Paper notes


Ball and Brindley note that natural power cycling thought to be essential bc you need thermocycling for processes such as polymerisation in the absence of cellular machinery. Several citations for this, but are we blinded by our own bias? Later on I suggest a bootstrapping mechanism that doesn't require occilations but it seems very weak.

In the literature several mechanisms for thermal cycling on the primordial Earth have been proposed: day/night and seasonal cycles [37], tidal inflows and outflows activating and dampening natural nuclear reactors [38], periodic entrainment by hot geothermal streams [39] and thermoconvective cycling between hot and cold sides of rock pores [40].

Oh! TPH occillations as an origin of the proton motive force.

Considering that in a bounded, spatially extended system thermo-pH oscillations manifest as travelling waves and patterns, and in view of the known dependence of all life on trans-membrane proton gradients, we felt justified in adding a new dimension to the HP crucible hypothesis: The gradients of a travelling thermo-pH wave provide a proton motive force that may have driven metabolic processes in the RNA world.

That said, you could argue that the universal nature of the proton motive force is just because it is so fundamental; it is the right answer. Is a gradient of larger ions inherently more difficult (surely not, could you have a mineral gradient driven by minerals leeching into an aqueous medium? I think that would be too slow tho. you could have a mineral gradient around a geothermal vent) Are the processes that harness proton motive forces ultimately monophyletic? (Probably it doesn't matter, the first organism to develop one would outcompete those latecomers who develop crappy ones)

Such pH cycling also provides a possible resolution of the ‘replication versus ribozyme activity’ paradox [42], which is that • folded structures are necessary for ribozyme activity, but replication requires unfolded sequences.

That does seem to require some kind of cycling? Algernately you could imagine a contemporaneous bootstrapping process, where things are constantly being replicated, then folding irreversibly, so only nascent RNA is used for templating. That seems very fragile and expensive and the whole system collapses if you ever stop replicating, tho, because you lose your templates. Wait, no, this is probably wrong; it's based on me thinking of these ribozymes as static rather than dynamic.

There is growing understanding of the necesssity of a far-from-equilibrium environment to create and maintain life, and for good reasons [5]. Chemists and biochemists typically carry out experiments designed to elucidate aspects of pre-biotic chemistry in batch systems, where reagents are added to a stirred reactor which ultimately equilibrates. Although valid measurements can be made during the early phases of such experiments, the system is progressing towards equilibrium and thus does not mimic the strongly nonequilibrium conditions necessary for life to persist, grow and morph.

I don't understand a lot of the math in section four, but this jumps out at me:

Thirdly, we can see why a gamma distribution simply won’t do for the origin of life. Under a gamma distribution of output temperature fluctuations, figure 1(b), a high activation energy reaction would undergo its low activation energy reverse with greater probability, and development of a more complex prebiotic world would be impossible. Even worse, it would favour degeneration to a simple, dead system.

then

Indirect effects involve disruption of RNA structure. Since hydrogen peroxide is a stronger proton donor than water, it may displace other proton donors (intra- or intermolecular) enantiospecifically at the -hydroxyl group, disrupting RNA structural motifs. L-chains are are more destabilized by this chiral interaction than D-chains, because the mean L-chain length is shorter, and thus more likely to occur as single strands and the L-20-hydroxyl group is more likely to be exposed and less protected structurally

Ok but why are L chains inherently shorter? Is there a chemically distinct reason? Otherwise this just seems to be an argument from our own bias.

The existence of microbial “shadow biospheres” that arose from independent origins has been proposed by Davies et al. [28,58], who suggest that maybe we have not observed them because we have not looked hard enough. Surely a shadow biosphere could coexist with the known biosphere — after all, the three domains of life, Bacteria, Archaea and Eukarya, rub along in more-or-less peaceful, often interdependent, coexistence to this day. Could there even exist a remnant RNA world ecosystem in some niche on Earth?

Evolution can be thought of as burning a succession of small bridges: the results of a transformational evolutionary step usually destroy the preconditions for its own occurrence. Equivalently, Bains & Schulze-Makuch [61] describe this propensity as “pulling up the ladder”, highlighting the example of the acquisition of endosymbiotic organelles by eukaryotes.

This relates to the discussion we had earlier about single origin events (eg: endosymbiosis of the mitochondrion).

Finally, I wonder if there's anything in the inherent resistance of canonical amino acids to oxidation? Or do amino acids and polypeptides arrive too far after the HP crucible? The cannonical amino acids (ie: the ones earthlife uses in protein synthesis) are all chemically quite resistant to oxidation for variety of chemical reasons that I don't really remember right now.


Evolution can be thought of as burning a succession of small bridges: the results of a transformational evolutionary step usually destroy the preconditions for its own occurrence.