Jeff Dougan has brought an interesting new paper to my attention: evidence against intelligent design from chemistry. It begins,

Disagreements among proponents of intelligent design and evolution continue (1). We wish to put forward an argument in favor of imperfect or unfinished evolution based on some metabolic pathways in which it seems that intelligent design would have done better.
In teaching metabolic pathways, every instructor emphasizes the chemical logic of the transformations wherever possible. In cases such as those to be described here, the lecturer is reduced to impotent hand-waving.

It then lists half a dozen chemical detours and inefficiencies in metabolism that just don't make sense, including:

• Unnecessary inversions
• Unnecessary pathways
• Duplicate pathways
• Unnecessary waste
• Unnecessary connections
• Unnecessary editing

As everyone who has gone through biochemistry (there was a year when my bathroom and bedroom were papered with charts I was struggling to memorize) would appreciate, it sure would have been nice of the Intelligent Designer to have pared down the complexity a little bit.

I will predict that the two classes of replies ID creationists would make to this are 1) the mind of the Designer is ineffable, and 2) we are corrupt and in decline. The point is, however, that the historical accumulation of 'good-enough' chemistry and chance is a better, more parsimonious explanation than inventing an invisible super-being who is mucking about with earthly biochemistry.

One last point that I find more convincing than lists of apparent flaws is the recent evidence that random mutation and selection is a good strategy for developing effective enzymes.

Finally, we note that in recent years, “directed evolution” (or in vitro evolution or molecular evolution) has been used to obtain proteins, often enzymes, with modified properties. In brief, this work involves random mutations in DNA followed by a selection process for the best-fitted. Such work has provided new enzymes with altered substrate specificity, specific activity, topology, enantioselectivity, thermal stability, and resistance to organic solvents. There is an extensive literature. To cite two recent papers (2003) in The Proceedings of the National Academy of Sciences, Williams and coworkers modified the stereochemistry of an aldolase (8) and Leong and co-workers optimized the expression and specific activity of an interleukin, IL-12 (9). We also cite the classic work of Hartley (10), a recent book (11), and a short review (12).

In case anyone wants to chase down those references, here they are:

8. Williams, G. J.; Domann, S.; Nelson, A.; Berry, A. Proc. Nat. Acad. Sci. USA 2003, 100, 3143–3148.
9. Leong, S. R.; Chang, J. C.; Ong, R.; Dawes, G.; Stemmer, W. P. ; Punnonen, J. Proc. Nat. Acad. Sci. USA 2003, 100, 1163–1168.
10. Hartley, B. S. Proc. R. Soc. Lond. B 1979, 205, 443–452.
11. Directed Molecular Evolution of Proteins; Brakmann, S., Johnsson, K., Eds.; Wiley-VCH: Weinheim, Germany, 2002.
12. Alexeeva, M.; Carr, R.; Turner, N. J. Org. Biomol. Chem. 2003, 1, 4133–4137.

Behrman EJ, Marzluf GA, Bentley R (2004) Evidence from Biochemical Pathways in Favor of Unfinished Evolution rather than Intelligent Design. J Chem Ed 81(7):1051-1052.