The Ghost of Paley
Posts: 1703
Joined: Oct. 2005
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Faid:
| Quote | From what I've read, this book does not give any valid, fundamental reasons why abiogenesis cannot possibly work: Its author presents the thermodynamic hurdles, spending quite some time in them, and concludes that a "coupling mechanism" is needed -something accepted by scientists already (see here for instance). In fact, this mechanism (mineral catalysis, authocatalysation process, photocatalysis, combinations of those) is the very thing they are looking for.
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Correct. To further the discussion, here are a few of the book's objections:
| Quote | Mineral Catalysis
Mineral catalysis is often suggested as being significant in prebiotic evolution. In the experimental investigations reported in the early 1970's15 mineral catalysis in polymerization reactions was found to operate by adsorption of biomonomers on the surface or between layers of clay. Monomers were effectively concentrated and protected from rehydration so that condensation polymerization could occur. There does not appear to be any additional effect. In considering this catalytic effect of clay, Hulett has advised, "It must be remembered that the surface cannot change the free energy relationships between reactants and products, but only the speed with which equilibrium is reached."16
Is mineral catalysis capable of doing the chemical work and/or thermal entropy work? The answer is a qualified no. While it should assist in doing the thermal entropy work, it is incapable of doing the chemical work since clays do not supply energy. This is why successful mineral catalysis experiments invariably use energy-rich precursors such as aminoacyl adenylates rather than amino acids.17
Is there a real prospect that mineral catalysis may somehow accomplish the configurational entropy work, particularly the coding of polypeptides or polynucleotides? Here the answer is clearly no. In all experimental work to date, only random polymers have been condensed from solutions of selected ingredients. Furthermore, there is no theoretical basis for the notion that mineral catalysis could impart any significant degree of information content to polypeptides or polynucleotides. As has been noted by Wilder-Smith,18 there is really no reason to expect the low-grade order resident on minerals to impart any high degree of coding to polymers that condense while adsorbed on the mineral's surface. To put it another way, one cannot get a complex, aperiodic-sequenced polymer using a very periodic (or crystalline) template.
In summary, mineral catalysis must be rejected as a mechanism for doing either the chemical or configurational entropy work required to polymerize the macromolecules of life. It can only assist in polymerizing short, random chains of polymers from selected high-energy biomonomers by assisting in doing the thermal entropy work.
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| Quote | Chemical Energy (Energy-Rich Precursors)
Because the formation of even random polypeptides from amino acids is so energetically unfavorable (G = 300 kcal/mole for 100 amino acids), some investigators have attempted to begin with energy-rich precursors such as HCN and form polypeptides directly, a scheme which is "downhill" energetically, i.e., G < 0. There are advantages to such an approach; namely, there is no chemical work to be done since the bonding energy actually decreases as the energy-rich precursors react to form more complex molecules. This decrease in bonding energy will drive the reaction forward, effectively doing the thermal entropy work as well. The fly in the ointment, however, is that the configurational entropy work is enormous in going from simple molecules (e.g., HCN) directly to complex polymers in a single step (without forming intermediate biomonomers).
The stepwise scheme of experiments is to react gases such as methane, ammonia, and carbon dioxide to form amino acids and other compounds and then to react these to form polymers in a subsequent experiment. In these experiments the very considerable selecting-work component of the configurational entropy work is essentially done by the investigator who separates, purifies, and concentrates the amino acids before attempting to polymerize them. Matthews39 and co-workers, however, have undertaken experiments where this intermediate step is missing and the investigator has no opportunity to contribute even obliquely to the success of the experiment by assisting in doing the selecting part of the configurational entropy work. In such experiments-undoubtedly more plausible as true prebiotic simulations-the probability of success is, however, further reduced from the already small probabilities previously mentioned. Using HCN as an energy-rich precursor, and ammonia as a catalyst, Matthews and Moser40 have claimed direct synthesis of a large variety of chemicals under anhydrous conditions. After treating the polymer with water, even peptides are said to be among the products obtained. But as Ferris et al.,41 have shown, the HCN polymer does not release amino acids upon treatment with proteolytic (protein splitting) enzymes; nor does it give a positive biuret reaction (color test for peptides). In short, it is very hard to reconcile these results with a peptidic structure.
Ferris42 and Matthews43 have agreed that direct synthesis of polypeptides has not yet been demonstrated. While some peptide bonds may form directly, it would be quite surprising to find them in significant numbers. Since HCN gives rise to other organic compounds, and various kinds of links are possible, the formation of polypeptides with exclusively alpha-links is most unlikely. Furthermore, no sequencing would be expected from this reaction, which is driven forward and "guided" only by chemical energy.
While we do not believe Matthews or others will be successful in demonstrating a single step synthesis of polypeptides from HCN, this approach does involve the least investigator interference, and thus, represents a very plausible prebiotic simulation experiment. The approach of Fox and others, which involves reacting gases to form many organic compounds, separating out amino acids, purifying, and finally polymerizing them, is more successful because it involves a greater measure of investigator interference. The selecting portion of the configurational entropy work is being supplied by the scientist. Matthew's lack of demonstrable success in producing polypeptides is a predictable indication of the enormity of the problem of prebiotic synthesis when it is not overcome by illegitimate investigator interference.
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One note of optimism as far as HCN concentration levels are concerned.
Here's Moritz's summary:
| Quote | In any case, minerals most likely provide the clue to a lot of the answers regarding the origin of life. They have been demonstrated to allow for the prebiotic synthesis of nucleotide precursors that have so far proven elusive, for example, the synthesis of ribose in sufficient purity – borate minerals stabilize ribose (Ricardo, A et al. 2004; see also press release; however, for a possible stereoselective synthesis of D-ribose catalyzed by amino acids, see below). Minerals have also been shown to catalyze polymerization of nucleotide-like molecules (Orgel 2004). Vesicle formation is aided by them as well, and mineral particles could have wound up inside vesicles and there exhibited catalytic properties (Hanczyc et al. 2003, Hanczyc et al. 2006).
In a different putative scenario, minerals also play an interesting role. Instead of in an aqueous "prebiotic soup" on or near the surface of the earth, it has been hypothesized that life may have begun in the depths of the ocean, in the unique environment of deep-sea hydrothermal vents. In high-pressure, high-temperature water as there, organic molecules show a level of (albeit not always particularly specific) chemical reactivity that is usually observed in "normal" aqueous environments only upon speeding-up of reaction rates by enzymes. See for example the review Hazen et al. 2002. For the physico-chemical properties of high-pressure, high-temperature water, see Basset M-P 2003 and Gen-e-sis: 1. Catalysis by minerals, such as those present in deep-sea hydrothermal vents, further enhances chemical reactions in such an aqueous environment. Degradation under these high-temperature and high-pressure conditions of synthesized organic molecules may be prevented by minerals as well – at least this has been shown for amino acids (see Hazen et al. 2002). Fatty acids, as a source of membrane-forming material, might have been synthesized there too (see Orgel 2004).
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The bolded & italicised part doesn't address the book's concerns with configurational entropy. This source seems to agree:
| Quote | Initial studies using thermal energy (heat) to drive the formation of polynucleotides and polypeptides from monomers were only marginally successful even if they were carried out in the absence of water. Polymer formation in the presence of water is a more plausible prebiotic scenario since it is likely that water was prevalent on the primitive Earth. Therefore, the only way to prepare RNA or proteins in the presence of water is to supply the required energy to "active" them (to change the structure by adding a reactive group) thus making polymer bond formation more favorable. While current theories suggest that RNA or protein was involved in early life, scientists have yet to provide a feasible explanation for how the individual activated monomers would have been formed on the early Earth.
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I'm no chemist by any means, so any assistance is appreciated.
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Dey can't 'andle my riddim.
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