rainbow wrote:

Calilasseia wrote:

rainbow wrote:I simply asked a question.

If you can't answer my question, then just say so.

For now we'll accept that you don't have any hypothesis that can be backed up by laboratory evidence.
OK?

So you're going to pretend that those papers I cited don't exist?

No. Why would I?

Are you going to pretend that any one of those papers actually contains compelling evidence to support at least one Hypothesis of Abiogenesis?

GenesForLife wrote:Errr, no, Will, the Urey-Miller experiment showed that amino acids can emerge in prebiotic conditions. I don't know how you are defining "organic" but precursors like methane are considered organic molecules. A protein is a polypeptide of more than 10,000 daltons in molecular weight, and as far as I am aware they were not produced in the Urey-Miller experiment.

GenesForLife wrote:Errr, no, Will, the Urey-Miller experiment showed that amino acids can emerge in prebiotic conditions. I don't know how you are defining "organic" but precursors like methane are considered organic molecules. A protein is a polypeptide of more than 10,000 daltons in molecular weight, and as far as I am aware they were not produced in the Urey-Miller experiment.

Calilasseia wrote:

GenesForLife wrote:Errr, no, Will, the Urey-Miller experiment showed that amino acids can emerge in prebiotic conditions. I don't know how you are defining "organic" but precursors like methane are considered organic molecules. A protein is a polypeptide of more than 10,000 daltons in molecular weight, and as far as I am aware they were not produced in the Urey-Miller experiment.

However, even oligopeptides can be biologically important. See, for example, oxytocin and vasopressin, both of which contain just nine amino acids. Amanitin is a cyclic oligopeptide comprising just eight amino acids, which is most definitely biologically active, as anyone who makes the mistake of eating Death Cap mushrooms will quickly find out. There are numerous other mycotoxins, namely the Phallotoxins, that comprise just seven amino acids, and which are extremely hepatotoxic. Glutathione is a tripeptide (just three amino acids) whose function as an antioxidant is important to aerobic life forms, and is critical in regulating the nitric acid cycle in more derived metazoans.

The point of this being, of course, that one of the papers in my collection deals with the formation of oligopeptides under carbonyl sulphide catalysis. Which provides a starting point for more complex peptide chemistry. All that is needed once an oligopeptide synthesis route exists, is some means of coupling that to RNA, and any minimal protocells have from that point on a means of acquiring ever greater emergent complexity.

Sure, no qualms with oligopeptides being functionally useful and vital, you just cannot call them proteins, however.

Calilasseia wrote:

GenesForLife wrote:Errr, no, Will, the Urey-Miller experiment showed that amino acids can emerge in prebiotic conditions. I don't know how you are defining "organic" but precursors like methane are considered organic molecules. A protein is a polypeptide of more than 10,000 daltons in molecular weight, and as far as I am aware they were not produced in the Urey-Miller experiment.

However, even oligopeptides can be biologically important.

rainbow wrote:

Calilasseia wrote:

GenesForLife wrote:Errr, no, Will, the Urey-Miller experiment showed that amino acids can emerge in prebiotic conditions. I don't know how you are defining "organic" but precursors like methane are considered organic molecules. A protein is a polypeptide of more than 10,000 daltons in molecular weight, and as far as I am aware they were not produced in the Urey-Miller experiment.

However, even oligopeptides can be biologically important.

There is no evidence that oligopeptites were produced in the Miller-Urey experiments.
Not a one.

rainbow wrote:There is no evidence that oligopeptites were produced in the Miller-Urey experiments.
Not a one.

rainbow wrote:

Calilasseia wrote:

GenesForLife wrote:Errr, no, Will, the Urey-Miller experiment showed that amino acids can emerge in prebiotic conditions. I don't know how you are defining "organic" but precursors like methane are considered organic molecules. A protein is a polypeptide of more than 10,000 daltons in molecular weight, and as far as I am aware they were not produced in the Urey-Miller experiment.

However, even oligopeptides can be biologically important.

There is no evidence that oligopeptites were produced in the Miller-Urey experiments.
Not a one.

Geoscientists today doubt that the primitive atmosphere had the highly reducing composition Miller used. However, the volcanic apparatus experiment suggests that, even if the overall atmosphere was not reducing, localized prebiotic synthesis could have been effective. Reduced gases and lightning associated with volcanic eruptions in hot spots or island arc–type systems could have been prevalent on the early Earth before extensive continents formed (8). In these volcanic plumes, HCN, aldehydes, and ketones may have been produced, which, after washing out of the atmosphere, could have become involved in the synthesis of organic molecules (3, 4, 8). Amino acids formed in volcanic island systems could have accumulated in tidal areas, where they could be polymerized by carbonyl sulfide, a simple volcanic gas that has been shown to form peptides under mild conditions (9).

byofrcs wrote:

rainbow wrote:

Calilasseia wrote:

However, even oligopeptides can be biologically important.

There is no evidence that oligopeptites were produced in the Miller-Urey experiments.
Not a one.

I don't think that was ever the intent of Miller-Urey. On the other hand, this here, Carbonyl Sulfide-Mediated Prebiotic Formation of Peptides..., has that intent.

GenesForLife wrote:They report that that the Urey-Miller process using simulated volcanic atmospheres can produce amino acids which can form oligopeptides in the presence of carbonyl sulphide which can also be found in volcanic conditions.

rainbow wrote:

GenesForLife wrote:They report that that the Urey-Miller process using simulated volcanic atmospheres can produce amino acids which can form oligopeptides in the presence of carbonyl sulphide which can also be found in volcanic conditions.

Fair enough. However we'd expect volcanic conditions to disperse the amino acids rather than concentrate them. I can't get the paper, so I don't understand how the amino acids get to a concentration that would allow them to polymerise.

Present-day levels of COS in volcanic gases have been reported up to 0.09 mol % (14). Because the gas hydrolyzes rapidly on a geological time scale, it is unlikely to have accumulated to a high concentration in the atmosphere. Thus, if COS was important in prebiotic chemistry, it is likely to have functioned in localized regions close to its volcanic sources. Although it may be unlikely that a substantial proportion of any amino acids present would have been converted to thiocarbamates, this would have been no obstacle to a “polymerization on the rocks” scenario (15, 16) in which peptides long enough to be irreversibly adsorbed near the source of the COS were subject to slow chain elongation.

Abstract
It is difficult if not impossible to synthesize long polymers of amino acids, nucleotides, etc., in homogeneous aqueous solution. We suggest that long polymers were synthesized on the surface of minerals in a prebiotic process analogous to solid-phase synthesis. Provided that the affinity of a mineral for an oligomer increases with the length of the oligomer, adsorption must become essentially irreversible for sufficiently long oligomers. Irreversibly adsorbed oligomers may be elongated indefinitely by repeated cycles in which the mineral with its adsorbed oligomers is first incubated with activated monomers and then washed free of deactivated monomer and side-products. We discuss in some detail the formation of oligomers of negatively-charged amino acids such as glutamic acid on anion-exchange minerals such as hydroxylapatite or illite. We show that the average length of adsorbed oligomers at steady state, n, depends on the balance between the rate of chain elongation and the rate of hydrolysis, and we derive a very approximate formula for n.

Abstract
Oligomers of the negatively-charged amino acids, glutamic acid, aspartic acid, and O-phospho-L-serine are adsorbed by hydroxylapatite and illite with affinities that increase with oligomer length. In the case of oligo-glutamic acids adsorbed on hydroxylapatite, addition of an extra residue results in an approximately four-fold increase in the strength of adsorption. Oligomers much longer than the 7-mer are retained tenaciously by the mineral. Repeated incubation of short oligo-glutamic acids adsorbed on hydroxylapatite or illite with activated monomer leads to the accumulation of oligomers at least 45 units long. The corresponding reactions of aspartic acid and O-phospho-L-serine on hydroxylapatite are less effective in generating long oligomers, while illite fails to accumulate substantial amounts of long oligomers of aspartic acid or of O-phospho-L-serine.

Rumraket wrote:The concentration and oligomerization of amino-acids on rock surfaces simply isn't imagined to be the biggest problem.

rainbow wrote:

Rumraket wrote:The concentration and oligomerization of amino-acids on rock surfaces simply isn't imagined to be the biggest problem.

Absolutely. I can imagine far bigger problems, but lets deal with this one first.
Besides amino-acids, the Miller-Urey reactions will also form simple carboxylic acids and amines. These will terminate any peptide and stop it growing. How is this overcome?

Abstract
A review of the most significant contributions on the early phases of genetic code origin is presented. After stressing the importance of the key intermediary role played in protein synthesis, by peptidyl-tRNA, which is attributed with a primary function in ancestral catalysis, the general lines leading to the codification of the first amino acids in the genetic code are discussed. This is achieved by means of a model of protoribosome evolution which sees protoribosome as the central organiser of ancestral biosynthesis and the mediator of the encounter between compounds (metabolite-pre-tRNAs) and catalysts (peptidyl-pre-tRNAs). The encounter between peptidyl-pre-tRNA catalysts in protoribosome is favoured by metabolic pre-mRNAs and later resulted (given the high temperature at which this evolution is supposed to have taken place) in the evolution of mRNAs with codons of the type GNS. These mRNAs codified only for those amino acids that the coevolution theory of genetic code origin sees as the precursors of all other amino acids. Some aspects of the model here discussed might be rendered real by the transfer-messenger RNA molecule (tmRNA) which is here considered a molecular fossil of ancestral protein synthesis.

byofrcs wrote:Heck we're only just two emergent layers up from elements and now we hit fatty acids.