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The Professional Literature
Other examples of irreducible complexity abound in the cell, including aspects of protein transport, the bacterial flagellum, electron transport, telomeres, photosynthesis, transcription regulation, and much more. Examples of irreducible complexity can be found on virtually every page of a biochemistry textbook. But if these things cannot be explained by Darwinian evolution, how has the scientific community regarded these phenomena of the past forty years? A good place to look for an answer to that question is in the Journal of Molecular Evolution. JME is a journal that was begun specifically to deal with the topic of how evolution occurs on the molecular level. It has high scientific standards, and is edited by prominent figures in the field. In a recent issue of JME there were published eleven articles; of these, all eleven were concerned simply with the comparison of protein or DNA sequences. A sequence comparison is an amino acid-by-amino acid comparison of two different proteins, or a nucleotide-by-nucleotide comparison of two different pieces of DNA, noting the positions at which they are identical or similar, and the places where they are not. Although useful for determining possible lines of descent, which is an interesting question in its own right, comparing sequences cannot show how a complex biochemical system achieved its function; the question that most concerns us here. By way of analogy, the instruction manuals for two different models of computer putout by the same company might have many identical words, sentences, and even paragraphs, suggesting a common ancestry (perhaps the same author wrote both manuals), but comparing the sequences of letters in the instruction manuals will never tell us if a computer can be produced step by step starting from a typewriter.

None of the papers discussed detailed models for intermediates in the development of complex biomolecular structures. In the past ten years JME has published over a thousand papers. Of these, about one hundred discussed the chemical synthesis of molecules thought to be necessary for the origin of life, about 50 proposed mathematical models to improve sequence analysis, and about 800 were analyses of sequences. There were ZERO papers discussing detailed models for intermediates in the development of complex biomolecular structures. This is not a peculiarity of JME. No papers are to be found that discuss detailed models for intermediates in the development of complex biomolecular structures in the Proceedings of the National Academy of Science, Nature, Science, the Journal of Molecular Biology or, to my knowledge, any science journal whatsoever.

"Publish or perish" is a proverb that academicians take seriously. If you do not publish your work for the rest of the community to evaluate, then you have no business in academia and, if you don't already have tenure, you will be banished. But the saying can be applied to theories as well. If a theory claims to be able to explain some phenomenon but does not generate even an attempt at an explanation, then it should be banished. Despite comparing sequences, molecular evolution has never addressed the question of how complex structures came to be. In effect, the theory of Darwinian molecular evolution has not published, and so it should perish.