They also assert that what evolved biochemical and molecular systems actually exhibit is "redundant complexity"—a kind of complexity that is the product of an evolved biochemical process. They claim that Behe overestimated the significance of irreducible complexity because of his simple, linear view of biochemical reactions, resulting in his taking snapshots of selective features of biological systems, structures and processes, while ignoring the redundant complexity of the context in which those features are naturally embedded.

An example we will pursue later is that of the species of Darwin's finches that diverged in the Galapagos from a common ancestor. The beaks of some species are large and nutcracker-like, and those of others are small and forceps-like. As Darwin did, we too might imagine that many small heritable beak variations accrued slowly in the different species to create large observable differences. Small variations are arguably the only viable and selectable ones, because they would allow the upper and lower beaks, the adjacent skull bones, and head muscles to coevolve with each other in small selected steps, thereby maintaining viable intermediate beaks along the paths to the nutcracker and forceps forms. Repeated selections would be needed to coordinate the numerous, small, independent beak and head changes, all requiring genetic change. Is this an accurate appraisal of the paths of change? Or might the finch's own means of beak development coordinate many changes, allowing larger viable variations and a simpler, more rapid beak evolution?

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Weak regulatory linkage is important in developmental plasticity, which West-Eberhard has persuasively argued is a frequent substrate for heritable regulatory cooption (14). This plasticity entails the choosing of alternative developmental pathways according to environmental inputs. Examples include male–female differences, learning, and alternate jaw structures. In her view, if the capacity to develop large phenotypic differences already exists in the organism as self-inhibited alternate states, and these can be elicited by simple signals (weak linkage), then large evolutionary steps can be made with a modicum of genetic change. In such cases, the distinction blurs between evolutionary gradualism and saltation (the generation of significant traits by single mutations). As an example, sex in some vertebrates (fish and reptiles) is determined environmentally (temperature, crowding, or social interactions) but in others, heritably (sex chromosomes). The underlying mechanisms for sex determination are similar in all vertebrates. It is just that an environmental stimulus (acting via weak linkage) has been replaced by a genetic one in the sex chromosome case.

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Adaptable robust processes can support nonlethal phenotypic variation in other processes, a situation called “accommodation” by West-Eberhard (14). A specific example is the evolution of the tetrapod forelimb to a bird or bat wing. Not only did the length and thickness of bones change, but also the associated musculature, nerve connections, and vasculature. Did many regulatory changes occur in parallel, coordinated by selection, to achieve the coevolution of all these tissues in the limb evolving to a wing? The answer comes from studies of limb development showing that muscle, nerve, and vascular founder cells originate in the embryonic trunk and migrate into the developing limb bud, which initially contains only bone and dermis precursors. Muscle precursors are adaptable; they receive signals from developing dermis and bone (17) and take positions relative to them, wherever they are. Then, as noted previously, axons in large numbers extend into the bud from the nerve cord; some fortuitously contact muscle targets and are stabilized, and the rest shrink back. Finally, vascular progenitors enter. Wherever limb cells are hypoxic, they secrete signals that trigger nearby blood vessels to grow into their vicinity (18). This self-regulating vasculogenesis operates not just in the limb but throughout the body, accommodating to growing tissues, to exceptional demands such as pregnancy, and alas to growing tumors. The adaptability and robustness of normal muscle, nerve, and vascular development have significant implications for evolution, for these processes accommodate to evolutionary change as well. In the case of the evolving wing, if bones undergo regulatory change (driven by genetic change) in length and thickness, the muscles, nerves and vasculature will accommodate to those changes without requiring independent regulatory change. Coevolution is avoided. Selection does not have to coordinate multiple independently varying parts. Hence, less genetic change is needed, lethality is reduced, larger phenotypic changes are viable, and phenotypic variation is facilitated.

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The theory predicts that developmental biologists will continue to find (i) more examples of core processes used in diverse developmental and physiological traits in different combinations, amounts, and states, and (ii) in each new case a few small regulatory changes sufficing to redeploy core processes, which are themselves robust and adaptable. When introduced experimentally, such regulatory changes should significantly alter the phenotype, and other processes should accommodate to the directly altered ones, giving viable outcomes. Furthermore, it predicts that, as comparative experimental studies uncover the history of evolutionary innovation in animals, regulatory types of changes will predominate. Indeed, as is already clear, altered cis-regulation of gene expression and altered production of secreted signals lie behind specific phenotypic changes in stickle back fish and Drosophila (34–36).

A recent example of bone morphogenetic protein (Bmp) and calmodulin signaling supports facilitated variation via robust adaptable processes. As described in the Introduction, Darwin noted the rapid divergence of beak morphologies by Galapagos finches. If we think mostly about selection and not phenotypic variation, we might imagine that selection acted repeatedly on many small changes occurring independently in the upper and lower beaks, adjacent skull, and head muscles to coordinate and order them into viable intermediate beaks throughout divergence. Many regulatory changes and many selections would be needed for this detailed coevolution of parts. Recent results, however, make a different impression. Tabin's group has compared two Galapagos finches, one with a large nutcracker-like beak and another with a small forceps-like beak (37). In beak development, neural crest cells migrate from the neural plate to five primordia around the mouth. The primordia of the large-beaked finch express Bmp earlier and at higher levels than do those of the small-beaked finch. To test the importance of this difference, they introduced Bmp protein into the primordia of a chicken embryo, which normally develops a small pointed beak. The experimental chick developed a deep, broad beak, like the large-beaked finch. The beak was not monstrous; its parts fit together and properly adjoined the head. Recently the same group demonstrated that elevated levels of calmodulin, a ubiquitous calcium signaling protein, correlate with increased beak length, and experimental increases of this protein in the developing chick beak caused coordinated increases in beak length (38). Thus, two highly conserved factors quantitatively control much of the overall anatomy of the beak and adjacent head, producing a functional structure. Much coordination of parts is inherent in beak development; selection need not direct a detailed coevolution of parts; larger beak variations may be viable and selectable. Similarly the exuberant radiation of jaws in cichlid fishes of Lake Malawi is now attributed to changes at a small number of quantitative trait loci (39), including for Bmp. These results imply quantitative adjustments on robust, adaptable processes due to a few regulatory changes rather than many small independent changes coordinated by repeated selections.

Weak regulatory linkage is important in developmental plasticity, which West-Eberhard has persuasively argued is a frequent substrate for heritable regulatory cooption (14). This plasticity entails the choosing of alternative developmental pathways according to environmental inputs. Examples include male–female differences, learning, and alternate jaw structures. In her view, if the capacity to develop large phenotypic differences already exists in the organism as self-inhibited alternate states, and these can be elicited by simple signals (weak linkage), then large evolutionary steps can be made with a modicum of genetic change. In such cases, the distinction blurs between evolutionary gradualism and saltation (the generation of significant traits by single mutations). As an example, sex in some vertebrates (fish and reptiles) is determined environmentally (temperature, crowding, or social interactions) but in others, heritably (sex chromosomes). The underlying mechanisms for sex determination are similar in all vertebrates. It is just that an environmental stimulus (acting via weak linkage) has been replaced by a genetic one in the sex chromosome case.

some conserved core processes appear to search and find targets in large spaces or molecular populations. Specific connections are eventually made between the source and target. These processes display great robustness and adaptability and, we think, have been very important in the evolution of complex animal anatomy and physiology. Examples include the formation of microtubule structures, the connecting of axons and target organs in development, synapse elimination, muscle patterning, vasculogenesis, vertebrate adaptive immunity, and even behavioral strategies like ant foraging. All are based on physiological variation and selection. In the variation step, the core process generates not just two output states, but an enormous number, often at random and at great energetic expense. In the selective step, separate agents stabilize one or a few outputs, and the rest disappear. Although that agent seems to signal the distant process to direct outputs to it, it actually only selects locally via weak linkage among the many outputs independently generated by the process. Components of the variation and selection steps of the process are highly conserved.