Literature

Who can ever cease to be amazed at the complexity of cells and genetic systems? A Perspective essay in today's Science, concerned with "gene regulatory networks for development", confirms yet again the reality of complexity. The authors bring out the role of subcircuits in the gene regulatory network. These are "often of elegant and sometimes counterintuitive design, even more so, the ways they are combined in the overall network." The authors add: "Among the most fascinating aspects of gene regulatory networks are their design principles, for these are often interestingly different from what would seem the "simplest" solution."
The modular construction of these subcircuits is fascinating because it is at a much deeper level than the feedback circuitry we are more familiar with. "Thus, although subcircuits are indeed the modular functional components of developmental gene regulatory networks, they are to be distinguished from simpler "building blocks" or "motifs" that are used for many diverse developmental functions (e.g., feedforward or feedback elements, per se)."
The complexity goes even deeper: "As we have come to understand developmental gene regulatory networks, there arises an impression of "overlayered" circuit design--or more precisely, deployment of multiple subcircuits--that in different ways support the same end result."
What are we to make of the inter-dependent modular nature of regulatory networks? Is this the 'tinkering' model of Darwinism, or do we have the 'exquisite design' model of ID? "We may interpret this as we like--as overengineering; or as design deluxe, replete with bells and whistles; or as the expected result of an evolutionary process in which individual regulatory modules have been added in and overlain at different times." The authors plump for the 'tinkering' model. But even they appear to concede that what we have before us are irreducibly complex systems: "once integrated into the regulatory system, they are there to stay, barring evolutionary redirection". All I can say is that the hallmarks of 'tinkering' are noticeable by their absence! I'll go for the 'design deluxe' option!

Built to Run, Not Fail
Paola Oliveri and Eric H. Davidson
Science 315, 16 March 2007: 1510-1511.

On first encounter, gene regulatory networks for development often seem so complicated as to defy intuitive understanding. But the overall maze of gene interactions that they represent is actually composed of subcircuits that perform separate functions. The subcircuits are often of elegant and sometimes counterintuitive design, even more so, the ways they are combined in the overall network. As the underlying subcircuit structure is clarified, we see that gene regulatory networks in fact provide a direct and simply organized bridge from the phenomena of development to the detailed genomic programs that encode it. Among the most fascinating aspects of gene regulatory networks are their design principles, for these are often interestingly different from what would seem the "simplest" solution. Gene regulatory networks for development are the direct product of evolution, and the character of their design both illuminates evolution and is illuminated by it.

[snip]

Last para: We may interpret this as we like--as overengineering; or as design deluxe, replete with bells and whistles; or as the expected result of an evolutionary process in which individual regulatory modules have been added in and overlain at different times, so that some are more ancient and others more new (1). However, once integrated into the regulatory system, they are there to stay, barring evolutionary redirection. But the generality of this quality of developmental gene regulatory networks is emerging as a fact of life--it is what we see in modern animals. The consequences of evolutionary history determine the shape of the control apparatus that determines life processes. Perhaps in current system design we are seeing something of the grim pressures that modern lineages survived in past evolutionary bottlenecks--of the absolute necessity for lineage survival of genomic regulatory systems built to run and not to fail.