November 24, 2005 | David F. Coppedge

Nature Cover Exploits Intelligent Design While Inside Attacks It

The 11/24 issue of Nature included two very caustic letters attacking intelligent design, yet its cover story highlighted the promising new field of Synthetic Biology.  In one of the leading papers,1 David Sprinzak and Michael B. Elowiz of Caltech (see 06/25/2005 entry) described the synthetic approach in terms reminiscent of William Paley’s old Divine Watchmaker:

By taking apart an old clock, you could probably come up with a pretty good guess at how it works.  But a more concrete understanding of the clock mechanism might be obtained by designing and building one’s own clock out of similar parts.  Contemporary biology presents us with similar reverse-engineering problems.  For example, Drosophila [fruit fly] cells contain a circadian clock that oscillates with a 24-h rhythm and self-synchronizes to the day/night cycle.  Using genetic and biochemical techniques, researchers have isolated genes and proteins involved in interlocked feedback loops of gene expression…that are necessary for clock function.  However, many fundamental questions remain difficult to answer: what sets the period of the oscillation, how does the clock operate reliably in diverse cellular conditions, and what features of its design are responsible for its reliable operation?  To gain insight into such questions one could design and build new clock circuits, using similar genes and proteins, and study their dynamics in the organism.  In fact, several synthetic genetic clocks have now been constructed in bacteria…. These circuits are much simpler than the Drosophila clock.  They fail to operate as reliably, but they provide a proof of principle for a synthetic approach to understanding genetic circuits. (Emphasis added in all quotes.)

Their article is an attempt to show how “synthetic biology can address biological questions at the level of genetic circuits,” and how tools being developed for synthetic biology are being used to “answer fundamental biological questions.”  One topic of great interest is how biological circuits remain stable in the face of noisy and dynamic environments, and how they achieve high-fidelity outputs in a sea of random Brownian motions.
    One such mechanism was elucidated by a team from Yale and Howard Hughes Medical Institute.  Writing in the same issue,2 they found that charged transfer-RNAs (tRNAs) undergo precision changes in shape when entering the active site of the ribosome.  These induced conformational changes, including 90° swings of one of the components, impel the substrate into the inner sanctum of the active site and simultaneously protect it from destruction by water molecules (hydrolysis).  When an incorrectly-charged intruder is present or a “stop-code” element enters, the water molecule is able to get in and destroy the intruder or end the completed translation.
    In another example in the same issue of Nature,3 a team from Stanford, Berkeley and U. of Wisconsin achieved the highest-resolution images yet of RNA Polymerase (RNAP) transcribing DNA.  They found that the motor channels the noisy motion in the interior of the nucleus into a “Brownian ratchet” that takes discrete steps along the DNA track.  These steps are exactly the distance down one base pair.  Interestingly, a clutch mechanism can release the ratchet if the enzyme needs to back up and fix a typo.
    In keeping with the implied-design theme of synthetic biology, a German team titled their article, “Design principles of a bacterial signalling network.”4  The design theme was ubiquitous, while references to evolution were merely assumed and seemed forced: i.e., “Our results suggest that this pathway has evolved to show an optimal chemotactic performance while minimizing the cost of resources associated with high levels of protein expression” (cf. 10/04/2005 story).  Ironically, the article investigated such topics as the regulation of the flagellar motor, a molecular machine the intelligent design movement considers their mascot.
  Another review article in the issue by Drew Endy has the design-friendly title, “Foundations for engineering biology.”5  A word search for evolution turns up some interesting hits.  Consider the mixed metaphors in this sentence: “Furthermore, it is possible that the designs of natural biological systems are not optimized by evolution for the purposes of human understanding and engineering.”  One can envision Dawkins and Behe scrambling for control of the ball on that pass.  Another hit is even more revealing:

Today, four challenges that greatly limit the engineering of biology are (1) an inability to avoid or manage biological complexity, (2) the tedious and unreliable construction and characterization of synthetic biological systems, (3) the apparent spontaneous physical variation of biological system behaviour, and (4) evolution.  In considering how best to address these engineering challenges, one practical starting point is to consider past lessons from when other engineering disciplines emerged from the natural sciences.  Are any past lessons relevant to the engineering of biology today?  For example, could we usefully consider adapting or extending ideas from structural engineering to synthetic biology?6

By evolution, Endy is talking about the ability of engineers to design synthetic biological systems that can reproduce and adapt to change.  That may be the biggest challenge.  “At present, we do not have a practical theory that supports the design of reproducing biological machines,” he says, “despite great progress in understanding how natural biological systems couple and tune error detection and correction during machine replication to organism fitness.”  That sounds again more like design than evolution, especially when he adds, “Once developed, many of these foundational technologies will take the form of ideas or information….”
    But now, back to Sprinzak and Elowitz with their Paley-like similes.  Their article ends comparing the superiority of natural engineering to synthetic attempts: “Even the most optimistic synthetic biologist would expect such circuits to be less functional than their natural counterparts.  However, perhaps at this stage one can learn more by putting together a simple, if inaccurate, pendulum clock than one can by disassembling the finest Swiss timepiece.
    To top it off, Erika Check reported on an exciting competition to “to build functioning devices out of biological parts.”7  Scientists and students from around the world competed at the first “Intercollegiate Genetically Engineered Machine competition” in fun and challenging efforts to make molecular switches, oscillators, transistors and other items as intriguing as “bacterial Etch-a-Sketches, photosensitive t-shirts, thermometers and sensors” from E. coli parts.  One especially notable achievement was a “the world’s first bacterial photography system,” teasing bacteria to respond to light and forming an image with 100 megapixels – per square inch.  They described their achievement in a separate article.8  Another team rewired bacteria to run a relay race.  Great fun was had by all; one geneticist commented, “The competition is essentially stimulating every level, from graduate and undergraduate to senior people.”
    In the midst of all this enthusiasm about reverse-engineering biology and the stampede to imitate nature’s designs, Nature printed two vitriolic letters against intelligent design.  Dr. A. Richard Palmer (U of Alberta) mocked and ridiculed the actions in Kansas9 by elaborating on a hypothetical question, “Is the ID debate proof of an intelligent deceiver?”  And newly-graduated PhD in biology Jason Underwood (UCLA) received a prominent page accusing intelligent design people of bringing science to a halt by giving up on the need for evidence (see Nature Graduate Journal).  Bristling with anger and irony, he wrote about how he felt when the state of his alma mater “voted to change the science curriculum so that it casts doubt on evolution and includes the teaching of ‘intelligent design’.9
    Nature rarely if ever prints any letters from qualified intelligent design spokespersons.  Dembski or Nelson or Meyer might have pointed out that it is precisely the evidence that eliminates chance and natural law, and justifies the design inference only after all natural explanations fail.  They might have explained how complex specified information (such as irreducible complexity) can provide positive evidence of an intelligent cause according to standard scientific practice, with formalized algorithms based on mathematically sound principles.  They might have also countered with a litany of the sweeping evolutionary speculations offered by Darwinists, in the absence of scientific rigor, when confronted by complex biological machines.  As a coup de grace, they might have pointed to this very issue of Nature as an example of the possibilities for fruitful research conducted from a design perspective.  Without opportunity to hear such rebuttals, however, readers may just have to put these two letters alongside all the other articles on synthetic biology, and draw their own conclusions.

1David Sprinzak and Michael B. Elowitz, “Reconstruction of Genetic Circuits,” Nature 438, 443-448 (24 November 2005) | doi:10.1038/nature04335.
2Schmeing et al., “An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA,” Nature 438, 520-524 (24 November 2005) | doi:10.1038/nature04152.
3Abbondanzieri et al., “Direct observation of base-pair stepping by RNA polymerase,” Nature 438, 460-465 (24 November 2005) | doi:10.1038/nature04268.
4Kollman et al., “Design principles of a bacterial signalling network,” Nature 438, 504-507 (24 November 2005) | doi:10.1038/nature04228.
5Drew Endy, “Foundations for engineering biology,” Nature 438, 449-453 (24 November 2005) | doi:10.1038/nature04342.
6For historical examples of engineering disciplines emerging from natural science, see our biographies of Faraday or Kelvin.
7Erika Check, “Synthetic biology: Designs on life,” Nature 438, 417-418 (24 November 2005) | doi:10.1038/438417a.
8Levskaya et al., “Synthetic biology: Engineering Escherichia coli to see light,” Nature 438, 441-442 (24 November 2005) | doi:10.1038/nature04405.
9It should be noted that the Kansas school board did not require teaching intelligent design, but specifically excluded it; they only allowed for scientific criticisms of evolution to be heard, and actually increased the teaching of evolution.  They also removed methodological naturalism from the definition of science, as do all other states.  See 11/08/2005

Let’s do a little thought experiment (pardon the oxymoron).  Let’s say a grad student at the Federal Institute of Technology in Zurich succeeds in remodeling some E. coli such that the colony swarms into a photograph image of whatever shadow falls on them.  Let’s also imagine that she surreptitiously watermarked her invention by encoding her name in the DNA of the new synthetically-engineered species.  Question: How would an independent researcher detect the intelligent design of the student?  Let’s proceed further in our story.  A biologist ignorant of the history of this bacterial species discovers it, and writes it up with a brief Darwinian just-so story about how the bacterium evolved this capability, and how the function might confer fitness.  Another scientist suspects the engineering and writes a paper rigorously defending his reasons for inferring this particular species was modified by an intelligent agent.  Question 2: which paper would Nature publish?
    This entry is extremely important to comprehend.  It basically illustrates that intelligent design is the future of biology.  Oh, they may not use the loaded words “intelligent” and “design” together, but the authors saturated these articles with de facto ID principles.  We might call it Lab-Implied Intelligent Design (LIMPID) or Virtual in vivo Intelligent Design (VIVID).  Enthusiasm will grow when AVID (Ardent Voices for Intelligent Design) stimulate a new generation of Fit, Energetic Researchers Vindicating Intelligent Design (FERVID).  When synthetically engineered biological products hit the market some day, we might call them Canned Intelligent Design (CANDID).  Most will think this is splendID, except for the remaining critics who will be seen for what they are: miserable, ornery, rancid badmouthers of ID (MORBID).  Like slobbering drunks, they have nothing to offer but froth and spit (11/21/2005).  Get them off the tracks before they get hurt by the new bullet train of design-inspired science.

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