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The (historical) question that must be asked about biological origins is not "Which materialistic scenario will prove adequate?" but "How did life as we know it actually arise on earth?" And that is for me both a religious question, and a science question.
Our creationist friends begin by saying that one of the logically appropriate answers to this latter question is that "Life was designed by an intelligent agent that existed before the advent of humans."
Indeed it is true that creation - creation of life and perhaps more basic - creation of the universe - is not explained by science - except when science itself becomes a faith as in string theory.
But the RNA world is not in dispute as far as I know - RNAs can't reproduce like animals or plants, but given the right materials, they can make copies of themselves that are more or less identical.
Then we say with only a little faith that less-identical reproduction is the path (we can show that a path exists that leads to RNA better able to put carbon and nitrogen together - or render it completely useless - and indeed we can get a group of RNAs that are really good at sticking the atoms together).
And for some reason creationist folks find the intelligent intervention in the synthesis of the randomized RNA; then again in the selection of a few functional RNA molecules out of that mixture; then, finally, in the amplification of those few functional RNA molecules, to be a problem with evolution - WHY?
I do not find that to be a problem. The problems of "prebiotic soup" and "self-assembly" phases of the scenario will be solved, IMHO.
Problematic Chemical Postulates of the RNA World Scenario
Postulate 1: There was a prebiotic pool of beta-D-ribonucleotides.
Beta-D-ribonucleotides (see Figure 2) are compounds made up of a purine (adenine or guanine) or a pyrimidine (uracil or cytosine) linked to the 1'-position of ribose in the beta-configuration.
There is, in addition, a phosphate group attached to the 5'-position of the ribose. For the four different ribonucleotides in this prebiotic scenario, there would be hundreds of other possible isomers.
But each of these four ribonucleotides is built up of three components: a purine or pyrimidine, a sugar (ribose), and phosphate. It is highly unlikely that any of the necessary subunits would have accumulated in any more than trace amounts on the primitive Earth. Consider ribose. The proposed prebiotic pathway leading to this sugar, the formose reaction, is especially problematic9. If various nitrogenous substances thought to have been present in the primitive ocean are included in the reaction mixture, the reaction would not proceed. The nitrogenous substances react with formaldehyde, the intermediates in the pathways to sugars, and with sugars themselves to form non-biological materials10. Furthermore, as Stanley Miller and his colleagues recently reported, "ribose and other sugars have suprisingly short half-lives for decomposition at neutral pH, making it very unlikely that sugars were available as prebiotic reagents."11
Or consider adenine. Reaction pathways proposed for the prebiotic synthesis of this building block start with HCN in alkaline (pH 9.2) solutions of NH4OH.12 These reactions give small yields of adenine (e.g., 0.04%) and other nitrogenous bases provided the HCN concentration is greater than 0.01 M. However, the reaction mixtures contain a great variety of nitrogenous substances that would interfere with the formose reaction. Therefore, the conditions proposed for the prebiotic synthesis of purines and pyrimidines are clearly incompatible with those proposed for the synthesis of ribose. Moreover, adenine is susceptible to deamination and ring-opening reactions (with half-lives of about 80 years and 200 years respectively at 37º C and neutral pH), making its prebiotic accumulation highly improbable13. This makes it difficult to see how any appreciable quantities of nucleosides and nucleotides could have accumulated on the primitive Earth. If the key components of nucleotides (the correct purines and pyrimidines, ribose, and phosphate) were not present, the possibility of obtaining a pool of the four beta-D-ribonucleotides with correct linkages would be remote indeed.
If this postulate, the first and most crucial assumption, is not valid, however, then the entire hypothesis of an RNA World formed by natural processes becomes meaningless.
Postulate 2: Beta-D ribonucleotides spontaneously form polymers linked together by 3', 5'-phosphodiester linkages (i.e., they link to form molecules of RNA; see figure 2).
Joyce and Orgel discuss candidly the problems with this postulate14. They note that nucleotides do not link unless there is some type of activation of the phosphate group. The only effective activating groups for the nucleotide phosphate group (imidazolides, etc.), however, are those that are totally implausible in any prebiotic scenario. In living organisms today, adenosine-5'-triphosphate (ATP) is used for activation of nucleoside phosphate groups, but ATP would not be available for prebiotic syntheses. Joyce and Orgel note the possible use of minerals for polymerization reactions, but then express their doubts about this possibility15:
WHY SHOULD ANYONE GET UPSET THAT whenever a problem in prebiotic synthesis seems intractable, it is possible to postulate the existence of a mineral that catalyzes the reaction ...AND...such claims cannot easily be refuted.
In other words, if one postulates an unknown mineral catalyst that is not readily testable, it is difficult to refute the hypothesis.
Postulate 3: A polyribonucleotide (i.e. RNA molecule), once formed, would have the catalytic activity to replicate itself, and a population of such self-replicating molecules could arise.
The difficulty with this postulate is evident in the following quotation from Joyce and Orgel:
...it is assumed...that a magic catalyst existed to convert the activated nucleotides to a random ensemble of polynucleotide sequences, a subset of which had the ability to replicate. It seems to be implicit that such sequences replicate themselves but, for whatever reason, do not replicate unrelated neighbors.17
They refer to this as a component of "The Molecular Biologists Dream," and discuss the difficulties inherent in such a view. In order for a stable population of self-replicating RNA molecules to arise -- a prerequisite for further evolution -- the RNA molecules must be able to replicate themselves with high fidelity, or the sequence specificity which makes self-replication possible at all will be lost. While "it is difficult to state with certainty the minimum possible size of an RNA replicase ribozyme," Joyce and Orgel note, it seems unlikely that a structure with fewer than 40 nucleotides would be sufficient. Suppose, then, that "there is some 50-mer ," Joyce and Orgel speculate, that "replicates with 90% fidelity. ... Would such a molecule be expected to occur within a population of random RNAs?"
Perhaps: but one such self-replicating molecule will not suffice.
"Unless the molecule can literally copy itself," Joyce and Orgel note, "that is, act simultaneously as both template and catalyst, it must encounter another copy of itself that it can use as a template." Copying any given RNA in its vicinity will lead to an error catastrophe, as the population of RNAs will decay into a collection of random sequences. But to find another copy of itself, the self-replicating RNA would need (Joyce and Orgel calculate) a library of RNA that "far exceeds the mass of the earth."
I do not see why one must reject self-replicating RNA molecule arising de novo from a soup of random polynucleotides.
Postulate 4: Self-replicating RNA molecules wouild have all of the catalytic activities necessary to sustain a ribo-organism.
S.A. Benner et al. note20:
...one is forced to conclude that the last ribo-organism had a relatively complex metabolism that included oxidation and reduction reactions, aldol and Claison condensations, transmethylations, porphyrin biosynthesis, and an energy metabolism based on nucleoside phosphates, all catalyzed by riboenzymes...It should be noted that this reconstruction cannot be weakened without losing much of the logical and explanatory force of the RNA World model.
Although Benner et al. speak of the last "ribo-organism," surely the first ribo-organism would have required nearly all of the same metabolic capabilities in order to survive. It is also apparent that the scenario of Benner et al. would surely include enclosing the ribozymes within a membrane with the ability to transport ions and organic molecules across that membrane.
Granted it would take hundreds of different ribozymes, each with a particular catalytic activity, to carry out the metabolic processes described above. And that it is apparent that most of these metabolic capabilities would have to be functional within a short period of time (certainly not hundreds of years), in the same microscopic region, or the ribo-organism would never survive.
But why do creationist folks reject this as a possible path is beyond my ability to understand their thinking.
We have more to learn about RNA, both in vivo (as used by organisms) and in vitro, in terms of its chemistry generally and functional properties in particular. RNA is a remarkable molecule.
But then I also do not understand the idea that RNA world folks put out that if design exists at all, it is a matter of subjective intuition.
What in the world is not subjective ? :-)
In the end GOD is by faith alone -and evolution is good science.
At least in my opinion.
:-)
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