PNAS: Evolution of complexity in signaling pathways

PNAS has published an article by Soyer and BonHoeffer titled Evolution of complexity in signaling pathways

Abstract: It is not clear how biological pathways evolve to mediate a certain physiological response and why they show a level of complexity that is generally above the minimum required to achieve such a response. One possibility is that pathway complexity increases due to the nature of evolutionary mechanisms. Here, we analyze this possibility by using mathematical models of biological pathways and evolutionary simulations. Starting with a population of small pathways of three proteins, we let the population evolve with mutations that affect pathway structure through duplication or deletion of existing proteins, deletion or creation of interactions among them, or addition of new proteins. Our simulations show that such mutational events, coupled with a selective pressure, leads to growth of pathways. These results indicate that pathways could be driven toward complexity via simple evolutionary mechanisms and that complexity can arise without any specific selective pressure for it. Furthermore, we find that the level of complexity that pathways evolve toward depends on the selection criteria. In general, we find that final pathway size tends to be lower when pathways evolve under stringent selection criteria. This leads to the counterintuitive conclusion that simple response requirements on a pathway would facilitate its evolution toward higher complexity.

Read on for some of my thoughts. First of all, the research once again shows how science can very well explain the functional complexity in biology, and thus contradicting some of the basic creationist claims. My focus is on the following claim about neutrality.

The intuitive view for the emergence of complexity is that it is due to increasing fitness, a view that has found support from studies on digital organisms (13). However, this study suggests that an imbalance in the effects of size-decreasing and -increasing mutations on function could lead to increase in complexity, supporting a mechanistic or neutral explanation (15). Hence, as long as there is selection acting on a system, even neutral processes that do not cause any immediate fitness benefit would force the system toward higher complexity.

and how the results tie in nicely with the concept of robustness. As others have already shown, the concept of selection, gene duplication can help explain such concepts as modularity, robustness, evolvability and complexity. Remind me again how Intelligent Design explains all this?...