Can designs be selectively neutral and even deleterious but still functional? Yes. As Allen Orr said:
selection can wreck their exquisite engineering just as surely as it built it. An optic nerve with little or no eye is most assuredly not the sort of design one expects on an engineer’s blueprint, but we find it in Gammarus minus. Whether or not this kind of evolution is common, it betrays the fundamental error in thinking of selection as trading in the currency of Design.
Actually, Orr made a mistake, selection can’t build exquisite engineering design, but it can wreck it!
In a rare moment of honesty, from the most recent Wiki version of Genetic Redundancy, we read how genes can be functional but invisible to selection (neutrally evolving):
Genetic redundancy is a term typically used to describe situations where a given biochemical function is redundantly encoded by two or more genes. In these cases, mutations (or defects) in one of these genes will have a smaller effect on the fitness of the organism than expected from the genes’ function. Characteristic examples of genetic redundancy include (Enns, Kanaoka et al. 2005) and (Pearce, Senis et al. 2004). Many more examples are thoroughly discussed in (Kafri, Levy & Pilpel. 2006).
The main source of genetic redundancy is the process of gene duplication which generates multiplicity in gene copy number. A second and less frequent source of genetic redundancy are convergent evolutionary processes leading to genes that are close in function but unrelated in sequence (Galperin, Walker & Koonin 1998). Genetic redundancy has classically aroused much debate in the context of evolutionary biology (Nowak et al., 1997; Kafri, Springer & Pilpel . 2009).
From an evolutionary standpoint, genes with overlapping functions implies minimal, if any, selective pressures acting on these genes. One therefore expects that the genes participating in such buffering of mutations will be subject to severe mutational drift diverging their functions and/or expression patterns with considerably high rates. Indeed it has been shown that the functional divergence of paralogous pairs in both yeast and human is an extremely rapid process. Taking these notions into account, the very existence of genetic buffering, and the functional redundancies required for it, presents a paradox in light of the evolutionary concepts. On one hand, for genetic buffering to take place there is a necessity for redundancies of gene function, on the other hand such redundancies are clearly unstable in face of natural selection and are therefore unlikely to be found in evolved genomes.
To understand genetic redundancy and biological robustness we must not think in linear terms of single causality where A causes B causes C causes D causes E. Rather it must be appreciate that biological systems operate as in a scale-free network. In a scale-free network the distribution of node linkage follows a power law, in that it contains many nodes with a low number of links, few nodes with many links and very few nodes with a high number of links. A scale-free network is very much like the internet: the major part of the websites makes only a few links, less make an intermediate number of links, whereas a minor part makes the majority of links. Usually hundreds of routers routinely malfunction on the Internet at any moment, but the network rarely suffers major disruptions. As many as 80 percent of randomly selected Internet routers can fail and the remaining ones will still form a compact cluster in which there will still be a path between any two nodes [Barabasi et al, 2003]. Likewise, genes never operate alone but in redundant scale-free networks with an incredible level of buffering capacity.
An interactive network of cooperating proteins that substitute for or by-pass each other’s functions provide the robustness of biological system. It is hard to imagine how selection acts on individual nodes of a scale-free, redundant genetic system. From an evolutionary standpoint, genes with overlapping functions implies minimal, if any, selective pressures acting on these genes. One therefore expects that the genes participating in such buffering of mutations will be subject to severe mutational drift diverging their functions and/or expression patterns with considerably high rates. Although the functional divergence of paralogous gene pairs can be extremely fast, redundant genes do commonly not mutate faster than essential genes (Winzeler EA et al. 1999; Wagner A, 2000; Kitami T, 2002].
Thus entire systems could be knocked out with little effect on the organism’s basic activity. The ability to knock out DNA without compromising basic function is not evidence against the design, and in fact in some cases this would be evidence for design. For further examples, see:
Reductive evolution of complexity — square circle
Why don’t Darwinist models of evolution like Weasel, Avida, Steiner, Ev, Geometric and Cordova’s Remarkable Algorithm model modes of natural selection that destroy design? Direct real time observation in the lab and field show natural selection is much more a Destroyer than a designer. Why is this not prominently modeled? Because Darwin and Dawkins ideas are divorced from biological reality. The only place Darwinism works for creating exquisitely engineered designs is in man-made, make-believe worlds.
In the essay, Dennett’s Strange idea is a bad idea fro recognizing biological function, I pointed out:
However, fitness is hard to define rigorously and even more difficult to measure….An examination of fitness and its robustness alone would thus not yield much insight into the opening questions. Instead, it is necessary to analyze, on all levels of organization, the systems that constitute an organism, and that sustain its life. I define such systems loosely as assemblies of parts that carry out well-defined biological functions.
but Wagner’s definition of “system” sounds hauntingly similar to Michael Behe’s definition of Irreducible Complexity:
A single system composed of several well-matched, interacting parts that contribute to the basic function of the system
Selection is a horrible criteria for determining if something is functional or not. Same with superficial knockout experiments.