Chris, I very much appreciate the thought - I recognize all of that in theory, but my observation is simply that, at some point, some proteins had to mutate to take on a categorically new function that was not itself facilitated by a step-by-step incremental process. The protein that transports oxygen, for instance, either does or doesn't bond/adhere to the oxygen molecule. It can grow better or worse at doing so, but at some point it either has that function or it doesn't. And unless that function existed in the earliest ancestor to all life on earth (and my understanding is that it did not), then at some point that "leap" had to be made.
Now, I recognize that this leap may have happened 1) because some protein, doing another function, started doing double-duty by mutating, still accomplishing its original function, and coincidentally it happened to be able to bond oxygen as well. The argument from the ID folks, (I am guessing, I don't recall reading this specifically) would be that the design/structural specifications requirements to hold an O2 molecule are so specific that it is unlkely that anything that could do so could really be very functional at anything else (someone correct me if I am mistaken).
or 2) the other alternative (as Curtis recently educated me about above) is that the gene for a protein was erroneously copied in the code, but was not being transcribed, and therefore over generations was susceptible to all manner of random mutations - thus the intermediate forms did not require any functionality. Then, fortuitously, at some point, the exact code was stumbled upon that would allow O2 transport, and, fortuitously, that part of the code was then activated (allowing transcription).
Now, I am trying to study and understand this better, so please, someone who knows better than I, please let me know if I have mischaracterized anything above.
But all that being said, the pure mathematics of it boggle my mind. In my limited understanding, the requirement of designing an amino acid chain, both the sequence and the folding, that will function to hold even a single O2 molecule are so remarkably specific that the idea of a pseudogene just popping one out after various generations of random mutation seem utterly crazy.
But alternatively, if there is no selective pressure (i.e., benefit to the organism) pushing an active protein to take on oxygen transport function, I cannot imagine all the mutations necessary to allow it to take on that function leaving the original function of the protein intact. So many changes would have to occur before said molecule could begin to carry the O2 molecule that it would almost certainly destroy whatever the original function was before it could take up the new one, no?
Hence, at core, one of my many reasons I remain so skeptical of random mutation working alongside the various natural forces to accomplish these things. But I am always open to being corrected if I have missed, misunderstood, or misconstrued anything above.