So, I decided to take a crack at that article BibleStudent linked. I will let my conclusions speak for themselves.
Life is not a naturalistic phenomenon with unlimited evolutionary potential as Darwin proposed. It is intelligently designed, ruled by immutable laws, and survives only because it has a built-in facilitated variation mechanism for continually adapting to internal and external challenges and changes. The essential components are: functional molecular architecture and machinery, modular switching cascades that control the machinery and a signal network that coordinates everything. All three are required for survival, so they must have been present from the beginning—a conclusion that demands intelligent design. Life’s built-in ability to adapt and diversify looks like Darwinian evolution, but it is not. Darwin’s theory of speciation via natural selection of natural variation is correct in principle, but it cannot be extrapolated to universal ancestry. What we see instead is different kinds of organisms having been designed for different kinds of lifestyles, with enormous potential for diversification built-in at the beginning, but with time this potential for diversification has become depleted by selection and degraded by mutations so that we are now rapidly heading towards extinction. Intelligent design and rapid decay point to recent Creation and Fall, as the Bible tells us.
First off, just this initial paragraph makes it extremely clear that the author considers intelligent design to point straight to Christian religious beliefs, specifically young-earth creationism, evidenced by his reference to a recent Creation and Fall. He makes not even the slightest effort to include any other possible interpretation of intelligent design except for the one that he personally believes in, which comes straight from his own religious beliefs.
There are also other problems. For example, he has a classic example of circular logic - he presumes that life is intelligently designed from the start, states that it survives because of facilitated variation and that the components of this must have been present from the beginning, and concludes that this requires intelligent design. No evidence, just a circular chain of logic. He goes on to state that facilitated variation mimics the process of evolution, but that it actually proceeds from different kinds of organisms designed for different lifestyles, and that the potential diversity of organisms has diminished greatly over time (due to selection and mutation), meaning life is rapidly headed towards extinction. I can only assume this is based on the usual misunderstanding of mutations being only negative and detrimental, and the belief that life cannot diversity beyond its initial starting point. Again, no evidence to back any of this up as far as I can tell.
He goes on to discuss various "laws", such as biogenesis, Darwinian evolution, irreducible structure, survival, facilitated variation, inverse variation, code variation, signals, modules, and degeneration. The problem is, these are not laws in any sense. It may be convenient to describe them as such, but that is no excuse in something which presumes to explain "how life works". At best, they are theories which have been verified experientially. For example, biogenesis is a refutation of the long-held belief of spontaneous generation, but to describe it as a law is to overstate its conclusions. Similarly, "Darwinian" evolution is incorrectly described as a law, and Williams simply declares without evidence that evolution cannot be extrapolated beyond the various ancestral species.
Next, we come to irreducible structure, a statement (made by a polymath named Michael Polanyi) that the physical and chemical properties of biological molecules are constrained by ordering principles, which is true enough as far as it goes. However, Polanyi did not speculate on the precise nature of these ordering principles, which Williams calls "coded information". He then states that according to biogenesis, there is no source for DNA except previous DNA, a conclusion which is only appealing in its seeming simplicity. Following that is survival, in which he again declares his theological explanation of the Fall being why life eventually dies, which he incorrectly attributes to biological mutation. He then declares that an intelligent designer would naturally give organisms self-repair and self-maintenance mechanisms, and would also build in a reproductive capacity to cope with the eventual breakdown of the first two. Leaving aside the circular logic which led him to conclude that there had to have been an intelligent designer in the first place, it is in no way guaranteed the way he assumes that such systems had to have been built in before life happened. It is not particularly likely either, as the first organisms could have developed a reproductive capacity first to take advantage of the lack of competition, and developed the other two later in order to facilitate being able to reproduce.
He then follows with the statement that environments have changed dramatically during Earth's history, and thus life would have had to continually vary in order to survive. Except that he ignores the fact that environments do not necessarily change all that much, and an organism which has developed in such a way to be able to survive with little change across a broad range of environments would have no need to continually vary itself. He considers such organisms to be on the verge of extinction specifically because they do not show much variation, based on his flawed idea that variation can only be exhausted by selection and depleted by mutation.
He then goes on to talk about facilitated variation, where he again makes the mistaken declaration that mutations only create defects and monsters. If he had actually studied what mutations really are, he would understand that most mutations are benign - they do not noticeably affect an organism, or affect it positively. In any case, he gives a description of facilitated variation which I will grant is a fairly accurate layman's understanding of the science involved, even if the terms he uses are questionable. However, he ignores the fact that, since most mutations are benign, such a mutation can easily increase the number of variations possible, so these organisms do not need to have all of their variations "programmed in" from the start. They can gain new variations from such mutations, which outweigh the damage caused by harmful mutations. And even some harmful mutations can generate unintended side benefits, such as sickle-cell anemia's ability to resist malaria - a variation that could not have happened without the harmful mutation of red blood cells.
He then discusses inverse causality, which he claims is necessary because facilitated variation requires the "basic processes" described earlier in order for life to happen at all. This is an assumption, which I have already demonstrated is not a valid one; self-repair and self-maintenance can have developed as the need arose (an organism without those will not instantly die), and reproduction can happen due to external processes rather than internal ones. It does not need to be present in an organism
[1]. He further describes the development of characteristics in a zygote which are only "useful" in an adult as being inverse causality, which is incorrect. The true cause of those developing characteristics is their usefulness in the adult, passed down through genes into offspring. The "future need" that Williams talks about is a red herring; in actual fact, a zygote does not "prepare" against future or anticipated need, it reacts to past need, expressed in its parents. That is how traits are passed down, and it is how traits that are not present in the adult can be in the offspring, because the pressures of the environment facilitate variation in the adult's gametes in order to increase the likelihood of those future offspring surviving.
His discussion of code variation is little more than an elaboration on facilitated variation which he barely acknowledges by referring to "Kirschner-Gerhart properties", which are actually part of facilitated variation. In essence, he takes facilitated variation, adds on his invalid assumption of inverse causality, and then claims that code variation expresses this inverse causality, when in fact there is no inversion of causality in the first place. The variation of genes in a zygote depends on the genes passed down by its parents; the causality is from the parents to the child, not from "future need" back to the child. His discussion of signals is basically the same thing, an elaboration on part of the facilitated variation theory which he mistakenly assumes is a "law" because of prior "laws" which are not necessary.
And finally, he discusses degeneration. While Williams is correct that DNA accumulates damage over time, he is emphatically not correct in his claim that variation which is not expressed through reproduction simply vanishes. This is again because of his prior assumption about mutations and his failure to recognize the benign nature of most of them. So while degeneration within a single organism is inexorable, it is anything but within life itself. This goes for what he describes as epigenetic degeneration as well, which can much more accurately be described as epigenetic changes. The fact that genes change as they are passed down in no way means that those changes are only negative. So his belief that extinction is inevitable simply because total possible variations are reduced is incorrect, and it ignores most of the effects of natural selection which also incorporate into the process
So, to conclude, Williams's entire article is based on faulty premises, faulty assumptions, and faulty conclusions. It contains enough genuine information to seem compelling, but breaks down very quickly upon examination by someone reasonably competent in that particular field. In other words, he depends on the credulousness of his readers to accept his argument without skepticism; a reader who did not come in with a similar preconception of Biblical truth would not be convinced by this article, simply because they would expect more compelling evidence to support Williams's conclusions.
