Chromatography and fractionation.

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Chromatography and fractionation.

Postby Derek Potter » Sun Mar 11, 2007 12:03 pm

One problem with imagining the processes that lead up to the first replicators is that of dilution: the supposed ingredients for RNA are likely to be present in parts per billion in the average puddle, making reaction times so long that the product will be lost before it has a chance to do anything sensible like evolve a bit...

Enter, stage left, two simple processes from the chemistry lab, fractionation and chromatography, both superb methods of separating chemicals from a mixture. My question: what is the role of natural physical processes that concentrate biotic chemicals in current models of ambiogenesis. Case in point: trace earth elements are concentrated by fractional crystallisation until enormous, and quite pure, crystals of, say an erbium ore, form in a pegmatite. What about processes that depend on absorbtion - like running a column in chemistry? Is it likely that vast amounts of dilute solutions could end up concentrated by soaking through porous rock and then the adsorbed product being eluted by a solution with, say, a different pH later on? If nature can put together a couple of nuclear reactors and many many stills, why not a chromatography column? Why stop at clays just being a substrate for catalysis? What about their bulk properties? Just a thought.

Answers in words of one syllable please, not a list of URLs entitled "Primitive modified natural zeololites show negative temperature-dependent chiral asymmetry in partially reduced oligosaccharide adsorbtion dynamics model." :)
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Postby tubataxidriver » Sun Mar 11, 2007 10:01 pm

The likely mechanism for this is chemical action at solid surfaces or liquid interfaces.

Surfaces are known to bind quite tightly (but reversably) to many active chemicals, increasing the rate of collision with other chemical species moving around in solution. Surfaces also demonstrate in some cases a catalytic effect on reactions, increasing the rate of reaction per collision.

Chromatography and crystal building are both surface effects.

When solutions come into contact with a surface or penetrate a porous solid the active chemicals present would form a mono-layer on the surface, bound by relatively weak forces. Once one component in a reaction is immobolised in this way, the statistics on meeting the other component diffusing at random through a solution are improved significantly.

There are also well-known physical surface effects seen with long chain type chemicals which can result in bi-layer membrane structures emerging from surfaces.

I would suggest that surfaces had a significant role in early chemical evolution of macromolecular substances.

Jeremy Hodge
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Postby Derek Potter » Mon Mar 12, 2007 12:45 am

tubataxidriver wrote:The likely mechanism for this is chemical action at solid surfaces or liquid interfaces.

Surfaces are known to bind quite tightly (but reversably) to many active chemicals, increasing the rate of collision with other chemical species moving around in solution. Surfaces also demonstrate in some cases a catalytic effect on reactions, increasing the rate of reaction per collision.

Chromatography and crystal building are both surface effects.

When solutions come into contact with a surface or penetrate a porous solid the active chemicals present would form a mono-layer on the surface, bound by relatively weak forces. Once one component in a reaction is immobolised in this way, the statistics on meeting the other component diffusing at random through a solution are improved significantly.

There are also well-known physical surface effects seen with long chain type chemicals which can result in bi-layer membrane structures emerging from surfaces.

I would suggest that surfaces had a significant role in early chemical evolution of macromolecular substances.

Jeremy Hodge

Yes, but even with a fortuitously effective catalyst, replicating molecules would probably have had a very difficult time, since the precursors would very likely be in short supply and, even more importantly, destructive chemicals would be all over the place.

Separating and concentrating the precursors could occur through simple physical processes and would hugely shorten the odds. That's why I was asking whether that sort of thing was considered in modern theories of ambiogenesis.
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Postby Timothy Chase » Mon Mar 12, 2007 5:18 am

I don't think I have heard of the chromatography column idea before, however, I know that evaporation has its problems since it generally means exposure of intermediate products to the destructive effects of the energy source - although this can be mitigated by salts.(1) Alternatively, freezing was proposed as far back as 1966 by Sanchez, et al. as a means of concentrating intermediates.(2) The onset of freezing dehydrates and separates intermediate products, with periodic freezing and thawing further increasing the concentrations, and while low temperatures slow down the rates at which most reactions take place, the actual onset of freezing will increase the rates of some reactions - including the ligation of some ribozymes.(3)

With regard to concentrations, what you are looking for are reaction vessels at some point which will perform the role of cells in maintaining high concentrations. I know that this is something which Ferry and others have certainly been looking into. I myself probably wouldn't be thinking in terms of trying to cook up nucleic acid right away, though, but metabolism first. Once you have an autocatalytic chemical reaction along those lines, given the appropriate environment - a porous mineral, oil, lipids - you could concentrate the intermediates. (See for example (4).) Montemorillite catalyzes the formation of linear, chiral RNA. Then once you have ribozymes - unlike protein enzymes, water actually enhances catalytic activity.

Derek Potter wrote:If nature can put together a couple of nuclear reactors...

They were actually left by ET. He needed the energy to perform certain failed experiments intended to hybridize early archaea and bacteria.


1. The search for traces of life: the protective effect of salt on biological macromolecules. Moeava Tehei, Bruno Franzetti, Marie-Christine Maurel, Jacques Vergne, Codjo Hountondji, Giuseppe Zaccai, Extremophiles. 2002 Oct ;6 (5):427-30
2. Conditions for Purine Synthesis: Did Prebiotic Synthesis Occur at Low Temperatures? R. Sanchez 1, J. Ferris, and L. E. Orgel, Science 1 July 1966: Vol. 153. no. 3731, pp. 72 - 73
3. Ligation of the hairpin ribozyme in cis induced by freezing and dehydration, Sergei A. Kazakov, Svetlana V. Balatskia, and Brian H. Johnston, RNA (2006), 12:446-456.
4. On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells. William Martin, Michael J. Russell, Phil. Trans. R. Soc. Lond. B (2003) 358, 59–85
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Postby Timothy Chase » Wed Mar 14, 2007 5:46 am

Quick note:

I have been looking around a bit, and it appears that the same sort of chemistry which House and Ferry proposed for the first metabolism involving acetate, iron sulfide and carbon monoxide may have been conducive to the formation of peptides which through an autocatalytic process would have resulted in the formation of more amino acids. Moreover, they may have fascilitated the formation of longer chains of RNA - which would help to explain how peptides and RNA would have developed a mutually reinforcing chemistry - resulting in natural selection at a much earlier point in prebiotic chemistry. There are other possible paths, but this is actually beginning to look rather promising.

Interesting convergence. Anyway, I should get going.
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