Intelligent Design

To avoid begging the question, Coyne must provide a justification, independent of the predictions of evolutionary theory, for believing that (a) an organism much simpler than M. genitalium is viable; (b) that complex enzymes could have evolved gradually from simpler proteins; and (c) that enzymes and coenzymes could have coevolved via rudimentary precursors.

This is the sort of recurring pattern that one might expect to see in designed systems, but it is more surprising in stochastically evolved systems. It therefore suggests that operon regulation is best understood as the product of engineering rather than blind, unguided processes.

The design logic is the same. And yet, these two systems are not evolutionarily related to one another — as evidenced by the fact that the enzymes encoded by these two operons do not share sequence homology, indicating distinct evolutionary origins.

The headline that prompted me to read this paper claimed that the study “shows how bacteria evolved powered-up propellers.” But the paper does not do this at all. All it shows is another example of a flagellar protein that bears homology to a non-flagellar protein.

The origin of spliceosomal introns represents a significant challenge to an evolutionary account of their origins. While the hypothesis that group II introns from bacterial endosymbionts gave rise to eukaryotic introns is the prevailing explanation, it faces a series of substantial obstacles.

Recurring design logic across multiple unrelated systems is surprising in an evolutionary perspective, whereas on the hypothesis of design it is what might be reasonably predicted. Examples like this, therefore, suggest the existence of a master-architect behind biological systems — particularly when we find many different examples of design logic that are found recurrently throughout life.

By an unguided process of tinkering, it seems quite implausible that the genes would be appropriately arranged along the chromosome in a manner that corresponds to the timing of their expression. Not only must the necessary genes be organized into a hierarchical transcriptional cascade to ensure proper timing and coordination of assembly, but the specific order of the genes along their respective operons is also significant.