Protein Structures Reveal Even More Evidence for Design

Protein Structures Reveal Even More Evidence for Design

Recent structural characterization of three proteins, RNA polymerase II, thioredoxin reductase (from E. coli), and chloroplast F1-F0 ATPase, provides exciting additional evidence for Design at the subcellular level.1-3  These three proteins possess, as part of their architectural make-up, components that are literally machine parts. These new discoveries add to the growing list of molecular motors (enzyme assemblies responsible for cellular movement) and other enzyme systems that are direct analogs to man-made devices.4-6 

A team of researchers from Stanford University has recently solved the structure of the RNA polymerase II backbone at 3.5 Å resolution.7 RNA polymerase II is a 12-protein subunit complex that synthesizes messenger RNA using DNA as a template. Messenger RNA produced this way contains the information needed to direct the synthesis of proteins at subcellular particles called ribosomes. For this reason, RNA polymerase II plays a central role in gene expression.

The structural analysis of RNA polymerase II has been nearly 20 years in the works.8   This has been due to such factors as the small amount of it in the cell, as well as its fragility, its large size, and its complexity. Diligent effort over the years coupled with technological advances has finally allowed the team from Stanford University to visualize the structure of RNA polymerase II.

The results of this work have been well worth the wait. The molecular basis for understanding RNA polymerase II function is now in place. Equally as exciting are the theological implications of this work.

RNA polymerase II has remarkable machine-like character.9 RNA polymerase II subunits form a channel that houses the chain-like DNA template. “Jaws” help grip the DNA template holding it in place during RNA synthesis. The newly formed RNA chain locks into place a hinge clamp as it exits the RNA polymerase II channel. A funnel-like pore delivers the small subunit molecules to the RNA polymerase II channel. Then the small subunit molecules in the channel are added to the growing end of the RNA chain.

In a similar vein, structural characterization at 3.0 Å resolution reveals that thioredoxin reductase function is built around a ball and socket joint.10 This enzyme, isolated from the bacterium E. coli, assists in the transfer of electrons between molecules. During the catalytic cycle, the enzyme undergoes a conformational rearrangement that involves the 67° rotation of one of its domains around a clearly defined swivel surface.

Finally, recent image analysis by a team from Germany and Switzerland using atomic force microscopy has revealed structural information about chloroplast F1-F0 ATPase. On the basis of this work, we can now add this enzyme to the growing list of ATPase enzymes that are rotary motors.11 As with the other rotary motor ATPases, chloroplast ATPase has a rotor, stator, and turbine.

The recent recognition that these three enzymes have machine-like domains, along with previous structural characterization of other enzymes with machine parts (such as F1-F0 ATPase, V1-V0 ATPase, bacterial flagellar proteins and myosin) serve to revitalize the Watchmaker argument.12 Popularized by William Paley in the 18th century, this argument states that as a watch requires a watchmaker, so too, nature requires a Creator.

This simple, yet powerful, argument has been challenged by skeptics like David Hume, who asserts that the necessary conclusion of a Creator, based on analogical reasoning, is only compelling if there is a high degree of similarity between the objects that form the analogy.13 Skeptics have long argued that nature and a watch are sufficiently dissimilar so that the conclusion drawn from the Watchmaker argument is unsound.

The discovery of enzymes with domains that are direct analogs to man-made devices addresses this concern, because of the striking similarity between the machine parts of these enzymes and man-made devices.  Furthermore, as the list of enzymes with machine parts grows, the conclusion of the Watchmaker analogy grows even more certain. Experts in inductive thinking will point out that the more objects taking part in an analogy, the more sound the conclusion arrived at through analogical reasoning.14

  1. Patrick Cramer, et al., “Architecture of RNA Polymerase II and Implications for the Transcription Mechanism,” Science 288 (2000): 640-49.
  2. Brett W. Lennon et al., “Twists in Catalysis: Alternating Conformations of Escherichia coli Thioredoxin Reductase,” Science 289 (2000): 1190-94.
  3. Holger Seelert et al., “Proton-Powered Turbine of a Plant,” Nature 405 (2000): 418-19.
  4. Michael Behe, Darwin’s Black Box: The Biochemical Challenge To Evolution (New York: The Free Press, 1996), 69-72.
  5. Hugh Ross, “Small Scale Evidence of Grand-Scale Design,” Facts and Faith 4, no. 2 (1997): 1.
  6. Fazale Rana and Micah Lott, “Hume vs. Paley: These ‘Motors’ Settle the Debate,” Facts for Faith 1, No. 2 (2000): 34-39.
  7. Patrick Cramer et al., 640-49.
  8. Joan Weliky Conaway and Ronald C. Conaway, “Light at the End of the Channel,” Science 288 (2000): 632-33.
  9. Conaway and Conaway, 632-33.
  10. Lennon et al., 1190-94.
  11. Holger Seelert et al., 418-19.
  12. Rana and Lott, 34-39.
  13. Rana and Lott, 34-39.
  14. Patrick J. Hurley, A Concise Introduction To Logic, 6th ed. (Belmont, CA: Wadsworth Publishing,1997), 494-96.