One of the alleged flaws is that the rod and cone cells in the retina face backward rather than forward which would seem to minimize the amount of light that reaches them.
As such, the eye seems to be sub-optimally engineered, and, the argument goes, since sub-optimal structures are what we would expect given that naturalistic evolution is a blind, rather haphazard, process, they're the very opposite of what we would expect were the structure intelligently constructed by a competent designer.
As the short video below illustrates, however, the backward facing cells are actually an ingenious way to optimize vision and not a defective design at all.
The video also makes short work of the claim that complex eyes evolved over very long periods of evolutionary time by numerous successive short steps. In fact, the very earliest eyes found in the fossil record are just as complex as are the eyes found in organisms today. If eyes did evolve the process must have been very rapid and thus, it's reasonable to suspect, somehow intelligently directed.
Indeed, the only basis there can be for ruling out an intelligent agent guiding the process is an a priori commitment to metaphysical naturalism, but why privilege naturalism in such a way if there's evidence to suggest it may be wrong? Yet people do it all the time as this famous quote from geneticist Richard Lewontin reveals:
Our willingness to accept scientific claims that are against common sense is the key to an understanding of the real struggle between science and the supernatural. We take the side of science in spite of the patent absurdity of some of its constructs, in spite of its failure to fulfill many of its extravagant promises of health and life, in spite of the tolerance of the scientific community for unsubstantiated just-so stories, because we have a prior commitment, a commitment to materialism [i.e. naturalism].As Lewontin's declaration of fealty to naturalism illustrates, it's not science as such that conflicts with the notion of intelligent agency at work in biology. The conflict is between two metaphysical worldviews, naturalism and theism.
It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated.
Moreover, that materialism is absolute, for we cannot allow a Divine Foot in the door.
Lewontin is acknowledging that his choice to embrace naturalism is a subjective philosophical preference, a preference akin to a personal taste and not based on any empirical evidence at all.
He embraces naturalism for no reason other than that he has a deep metaphysical, and perhaps psychological, aversion to theism.
Anyway, give the video a look:
