“The functional sequences of amino acids within amino acid ¬sequence space should be extremely rare rather than common.”
The final prediction listed in this appendix relates directly to the research work done by Doug Axe in the BioLogic Institute. The argument is that the arrangement of amino acids in functional molecules like proteins should be rare, that is, the protein’s function is very sensitive to changes in the amino acid sequence. The inference is that it could not have been achieved by chance mutations of individual amino acids and therefore could only have been arranged by an intelligent designer. Axe has reported on a significant amount of work that shows the arrangement of amino acids is indeed highly tuned and specific to its function.
The question is not whether such a sequence is rare, but whether this truly reflects the work of an intelligent agent rather than natural selection operating on a large population of possibilities. The ID claim builds on Dembski’s explanatory filter and relies on probability calculations to show that no random event could achieve such a configuration in the lifespan of the universe.
However, the great difficulty of all probability calculations for living molecules is that neither the intermediate steps nor the process mechanisms are adequately known to calculate a trustworthy probability. The history of biochemistry has been that transformations from one state to another that seem incredibly improbable, turn out to be highly probable when we understand the details of the process. One example of that was discussed in a previous post, namely the antibody example. The transition from a state of a population of identical pre-B cells to a state of highly specified complex B cells with high affinity to relevant antigens would be calculated to have impossible odds of occurring if we knew nothing about the mechanisms driving that transition. Now that the details have been elucidated over the last few decades, we see how random rearrangement processes and natural selection make that transition highly probable.
I would suggest that all of Meyer’s probability calculations in this book, as well as any others relating to the development of biomolecules, suffer from this deficiency. A proper probability calculation requires detailed knowledge of the initial state and the process by which the system moves to the next state. It must also reflect the size of the population of the initial state. Instead, Meyer makes calculations of the type that assume the initial state is a set of disconnected nucleotides which then inexplicably and randomly assemble themselves into a functional protein. It is no wonder the result is impossibly low. Nature doesn’t work that way. Most origin of life researchers are not looking for evidence of the incredibly improbable event. Rather, they seek the understanding of the precursor populations that could predictably migrate to the next step. At the present time, no one knows enough about the intermediate steps to either claim understanding of such evolution or of claiming that such evolution could not have occurred.
Axe may well find that the sequences are rare with respect to sensitivity to changes in individual amino acids but that still doesn’t give us much information about the probability of its evolution. Larger scale mixing, matching, and borrowing of sections of amino acids are known to occur in many processes that form proteins. This means that the opportunity space for generating new proteins is enormous, making it extremely difficult to ascertain what actually happened in the evolutionary past. But it makes it even more difficult to show that such evolutionary changes couldn’t have happened. In light of current evolutionary thought of how proteins evolved, one might even predict that many, if not most, amino acid sequences in proteins are rare. They were unlikely to have evolved by changes in one amino acid at a time. This prediction does not seem to be fruitful in elucidating a unique prediction of ID.