The ID Report

By Robert Deyes
ARN Correspondent

Evolution through natural selection as an all-encompassing theory of how life evolved is considered by school boards across the United States as a strictly non-negotiable part of the teaching of biology (Ref 1). This was biochemist Michael Behe's assessment when he wrote in 1999 of the 'hysteria and intolerance' against those who dared question evolution. Perhaps the most notable challenge to the Darwinian camp's exclusionary stance has come from the latest discoveries in biochemistry and cell biology which, as theoretical biologist Stuart Kauffman remarked, have revealed a cellular world replete with interacting, molecular machines. Stuart Kauffman's brief review of the cell is telling

"A cell is...a rich tapestry of molecular happenings...There is, after all, all of metabolism, the busy building of cell membranes and organelles. There is the business of DNA to RNA to protein, where the code itself is mediated by the very aminoacyl transferase charging enzymes that load the proper transfer RNA molecules with the right amino acids to translate the code that creates, among other things, the aminoacyl transferase enzymes themselves. There is the swishing of energy flowing in and through the multiplexed highways and byways, labyrinthine in their details...The simplest free-living systems, pleuromonia (PPLO), a simplified bacterial species that haunts the lungs of sheep, still has a membrane, DNA, a code, perhaps 300 assorted genes, the machinery of transcription and translation" (Ref 2, pp.29-30).

Labyrinthine indeed. Peering across the fence that was the limited knowledge of biochemistry at the time, Darwin must have hoped that the black box that so characterized the cell would not upset his grand theory of evolution. He was able fill in the gaps of knowledge with the apparent power of natural selection. As he wrote in his autobiography

"The old argument of design in nature, as given by Paley, which formerly seemed to me so conclusive, fails, now that the law of natural selection has been discovered....There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows" (Ref 3, p.87).

Unfortunately for Darwin, we now know that such generalities regarding his grand theory were not only premature but wrong. Indeed, famous amongst the molecular machines that defy Darwin's assertion of a design-less world is the enzyme H+ ATP Synthase that, as Princeton molecular biologist Steven Block brought to the world's attention, is responsible for manufacturing ATP in our cells (Ref 4). The remarkable feature of this enzyme is that it has the ability to rotate much like a man-made rotary motor (Ref 4). The catalytic subunits of the H+ ATP Synthase enzyme are tiny nine-protein complexes, having a characteristic 'flattened sphere' shape with a dimensional area of only 10nm across and 8nm high (Ref 4). The synthase enzyme is a veritable achievement of molecular engineering, coupling protons with subsequent rotational movement in the same way that a combustion engine couples the flow of gas and oxygen with the ensuing movement of the car. As the protons are pumped across a membrane, an electro-chemical gradient is generated that provides the energy to drive the H+ ATP Synthase motor (Ref 4). The catalytic subunits of the H+ ATP Synthase enzyme rotate around a channel, rather like a rotary motor turns around a central shaft (Ref 5). The ATP Synthase, with its precision design, thus provides an elegant illustration of a highly-efficient motor.

One can but wonder what Darwin would have made of minuscule engines with rotating propellers that generate ATP- the energy source of the cell. But the story does not end there. In fact the mechanisms used for eliminating waste proteins from the cell are likewise revealing of a world that contravenes Darwin's premature dismissal. The proteasome, a protein complex that functions as a cellular 'garbage disposal unit', for example degrades redundant proteins by shredding them into smaller parts. In their studies using X-ray crystallography, Michael Groll and his colleagues from the Max Planck Institute in Germany brought the functioning of the proteasome complex to life by elucidating much of its molecular structure (Ref 6). Their analysis of the yeast version of the proteasome provided some valuable insights into its function demonstrating a structure that is ideally suited for breaking up redundant or toxic proteins (Ref 6). According to Sherwin Wilk from Mount Sinai School of Medicine, there is now strong evidence for the proteasome's involvement in the mammalian immune response (Ref 7). Indeed what really distinguishes the proteasome from any other protein complex is the multitude of catalytic activities that it exhibits.

One recent review, described the proteasome in the broader context of the cell's own "sophisticated inventory control program" that ultimately tells cells when to divide and when to die (Ref 8). While proteasomes break proteins down other molecular machines fold proteins up into their functional conformations. These machines are called chaperonins for, just like the chaperones of old that escorted young unmarried women to protect them from harm, they attach themselves to newly synthesized proteins (Ref 9). Like a master of origami that folds paper into exquisite shapes, chaperonins ensure that proteins are folded into their correct conformations for specific functions within the cell (Ref 9). With as many as 24 subunits in a chaperonin complex, we see an elegant co-operativity between the different parts of this protein folding machine (Ref 9).

ATP generation, protein folding and waste disposal are all critical processes for the healthy maintenance of a living cell. Perhaps paradoxically we find that much of how the body eliminates and destroys a cell at the end of its life is also heavily bound up in machines that parallel those discussed above. Until recently, the molecular mechanism of cell death was not well characterized and certainly somewhat of an enigma for most biologists. One type of cell death called apoptosis is a natural process that serves for removing cells that are either threatening or simply unnecessary for an organism (Ref 10). It is a form of controlled cellular suicide that ensures the well being of the organism as a whole. Merck scientists Donald Nicholson and Nancy Thornberry reviewed one aspect of this rather complex process in a landmark paper (Ref 10). Notably, the apoptosis pathway involves inactive precursor molecules that are activated by other proteins.

The core steps of the apoptotic pathway are governed by a family of enzymes called Caspases (Ref 10). What is most fascinating about these enzymes is that their activation carries all the hallmarks of a carefully planned military campaign (Ref 10). Caspases exist as inactive precursors that are cut at specific points by other caspases in a carefully orchestrated cascade of molecular events (Refs 10, 11). Indeed a 1999 study headed by Gerald Cohen at the UK MRC and Douglas Green at the La Jolla Institute in San Diego provided much of the detail of the apoptotic cascade (Ref 12). The overall picture seemingly epitomized much of Behe's irreducible complexity hypothesis, revealing how all the caspases involved required conversion from their precursor (inactive) to their active forms through the activity of other caspases further up the cascade before they could function. A highly controlled activation of caspases is necessary if animals are to ensure that cell death occurs only when it is required.

Writing over a century ago, Darwin could have stood confidently behind his assertion that there was no more design in the make up of life than in the direction of the wind. Little did he know of the molecular biology revolution that would reveal amongst other things the cell's capacity to not only fold proteins but also dispose of them when no longer needed. Drawing much needed energy from the ATP that it generates and commiting suicide whenever its internal processes threaten the well-being of the greater organism, the cell is the masterful 'disarmer' that has taken the wind out of the sails of Darwinism. With such discoveries as those outlined in this paper the involvement of intelligent design is quite simply the best causally specific inference that can be made.

References
1. Michael Behe (1999), Darwin's Hostages: A decision in Kansas to question evolution dogma has given rise to hysteria and intolerance American Spectator December 1, 1999. Article can be accessed at http://www.arn.org/docs/behe/mb_darwinshostages.htm

2. Stuart Kauffman (2000), Investigations, Published by Oxford University Press, New York

3. Charles Darwin, The autobiography of Charles Darwin, Copyright held by Nora Barlow in 1958, W.W. Norton and Company Inc, New York

4. Steven Block (1997), Real engines of Creation, Nature, Vol 386, pp. 217-219

5. T. M Duncan, V V Bulygin, Y Zhou, M L Hutcheon, and R L Cross, Rotation of subunits during catalysis by Escherichia coli F1-ATPase, Proc Natl Acad Sci U S A. 1995 November 21; 92(24), pp.10964–10968

6. Michael Groll, Lara Ditzel, Jan Lowe, Daniel Stock, Matthias Bochtler, Hans D. Bartunik, Robert Huber (1997), Structure of 20S proteosome from yeast at 2.4A resolution, Nature Vol 386 pp463-471

7. Sherwin Wilk (2003), "The Search For Neuropeptidases And The Discovery Of The Proteasome". Seminar held at Promega Corporation, Madison WI on the 19th of November, 2003

8. Kenneth Chang (2004), Study of Cell Breakdown Captures Nobel, New York Times, October 7, 2004

9. Tatsuro Shimamura, Ayumi Koike-Takeshita, Ken Yokoyama, Ryoji Masui, Noriyuki Murai, Masasuke Yoshida, Hideke Taguchi, So Iwata (2004), Structure Vol 12 pp. 1471-1480

10. Donald W Nicholson and Nancy Thorneberry (1997), Caspases: killer proteases, Trends In Biological Sciences Vol 22 pp 299-306

11. Pascale Villa, Scott H. Kauffmann, William C. Earnshaw (1997), Caspase and caspase inhibitors Trends in Biological Sciences Volume 22 pp 388-393

12. Xiao-Ming Sun, Marion MacFarlane, Jianguo Zhuang, Beni B. Wolf, Douglas R. Green, and Gerald M. Cohen (1999), Distinct Caspase Cascades Are Initiated in Receptor-mediated and Chemical-induced Apoptosis, J Biol Chem, Volume. 274, 5053-5060

Copyright(c), 2008, Robert Deyes