[ableChair]

"Am I to assume that you have no objection then to evolution or natural selection, and that in fact your issues involve only abiogenesis? "

The focus of my reply was to explain the orginal point made by the author; i.e., that he is referring to a process preceeding natural selection and the improbability of sufficiently complex genetic information appearing at that stage. I thought you misunderstood his point as you were focusing on processes occuring in the context of natural selection; where he wasn't.

As for your broader question above, a theory can be internally consistent, agree with all known observable phenomena, and still be incomplete. An elegant example is General Relativity. While it explains the vast majority of gravitational phenomenon, it fails to describe, for example, what happens to the fundamental metric tensor of G.R. (the meat and potatoes of G.R.) at the center of a black hole: The eigenvalue of the tensor approaches infinity as the singularity is approached, a physically meaningless result. It seems to me that if evolution is supposed to be the theory of genetic change over time, then the theory of evolution is incomplete if it cannot explain the origin of biologically meaningful b.p. sequences. Ergo, I do not have any reason to not believe that the process of natural selection is a reasonable mechanism for explaining some genetic change over time. But I have little or no evidence to convince me that it is sufficient to explain the genetic changes that occured from beginning to the present. So, I'm not sure I agree with your use of the term 'abiogenesis' as I'm not sure you can so safely decouple the emergence of biologically meaningful b.p. sequences from biology. Indeed, a process other than natural selection would have been necessary for that initial sequence, but whatever it was, by definition, it must have had distinctly biological implications in order that it:

1.) Be responsive to the selection pressures that were later levied upon it.

2.) Provide information sufficiently complex to guide the formation of some biological organism (before it existed!).

Your point is valid that we can debate how complex that organism must have been at its' simplest. That would, of course, drive the probability analysis.

I suspect, for the reasons alluded to above and for many other reasons, that evolution is largely correct in some of its' most basic assumptions, but that it fails as a complete theory of genetic change over time. That is, of course, stated with the qualifications of any honest amateur in the subject.

I've reviewed the mathematics the author is using and, formally speaking, his usage is valid. But what isn't clear is his application of it to physical systems. That requires a lot more brain power than math alone but I'll look at it this weekend (could take a while!).

[general_re]

Ah, we are making progress ;)

As for your broader question above, a theory can be internally consistent, agree with all known observable phenomena, and still be incomplete.
...
It seems to me that if evolution is supposed to be the theory of genetic change over time, then the theory of evolution is incomplete if it cannot explain the origin of biologically meaningful b.p. sequences.

Agreed. I do not think that any honest student of evolution would describe the theory as "complete". For instance, although you object to the separate consideration of abiogenesis versus the evolutionary process, it is hardly a secret that the mechanisms and pathways of abiogenesis are not currently well-understood. While the separation of the two is admittedly inelegant from a theoretical standpoint - everyone wants a theory of "everything", after all - it allows one to do other things like examine and trace the development of the diversity of species we have arrayed before us. Yes, that requires a certain amount of bootstrapping away from the discussion of where and how those first self-replicating organisms came about, but as possible mechanisms for such a thing are investigated further, I have little doubt that more compelling theories will arise.

And already, many theories exist as to how biological structures could have arisen from non-biological sources. As a single example, simple amino acids have been discovered riding on comets, so perhaps abiogenesis got something of a head start from otherworldly sources. If this is a subject that interests you, a good place to start would probably be the talk.origins FAQ on the state of abiogenesis. It is fairly open about the current shortcomings of scientific knowledge about this subject, I think, although I am sure that someone who wishes to dispel evolution will be able to provide you with other counterarguments as well. Ultimately, you are, of course, free to evaluate for yourself where you think the bulk of evidence currently lies.

Your point is valid that we can debate how complex that organism must have been at its' simplest. That would, of course, drive the probability analysis.

Exactly - one of the most obvious responses to this type of statistical analysis. They tend to be predicated on the assumption that the first organisms were akin to what we see today, with membranes and cytoplasm and all sorts of complicated internal structures. But if we can imagine a simple naked molecule that is capable of self-replicating by grabbing bits of material from around it, then that will blow this analysis straight out of the water in short order. Membranes, et cetera, are not necessarily a requirement for self-replication in early biotic systems.

I've reviewed the mathematics the author is using and, formally speaking, his usage is valid. But what isn't clear is his application of it to physical systems.

And that is, as I am sure you are aware by now, the crux of objections to this article. I have no problem with the arithmetic on display. What I object to are some of the assumptions that the arithmetic is based on. So, if you're going to spend a weekend with this puppy anyway, you might consider evaluating it in light of this rather general critique of such statistical approaches.

In any case, the field is still wide open, with lots of room for thoughtful questions from interested amateurs like you and I ;)