Most of biological ID literature is focused on Irreducible Complexity and Specified Complexity (Specified Improbability) and information theory, no free lunch, critique of OOL, the Cambrian explosion, etc,
But there is another line of argument that is devastating to the claims of mindless evolution that has been underappreciated partly because it is highly technical, and in many cases most biologists will not even learn it in detail, namely that most molecular evolution is non-Darwinian.
Here is the simplest way to understand why evolution is mostly non-Darwinian. The ability to select for or against a trait involves the cost of sacrificing individual lives. When we spend money we have a limited budget to buy things. From our budget we can select to have maintenance done on our houses, cars, computers, our bodies (healthcare) or we can buy other thing to accumulate possessions.
What Darwin and most Darwinists do not realize is that selection for individual traits likewise comes at cost. To select to maintain one part of the genome means that there is no budget to maintain another part of the genome. To select to construct new features of the genome means one must abandon the maintenance budget of another part. This will be true even if the selection process is done by an intelligent agency like a human. The reason most computerized “proofs” of evolutionism like Dawkins Weasel and Avida are invalid is they do not model the problem of cost of maintaining and constructing mutli gigabit complex designs.
To understand things more clearly, here is a hypothetical illustration. If an asexually reproducing species could only have one offspring, selection must necessarily be neutral because there is no reproductive excess, there is zero “money” to carry out selection. If there are harmful mutations along the way, oh well, no “money” of excess reproduction to fix it. This would be an extreme case of Muller’s ratchet where the bad irreversibly just keeps accumulating.
Now if an asexually reproducing species could have two offspring, it now has a little more “money” in the form of reproductive excess to select to maintain one trait that goes bad. Let’s say one of the two offspring develops a bad mutation and the other doesn’t. We can expend him, or dare I say “spend” him to fix the genome. But our selection budget would be blown if each of the kids develop 1 bad mutation each, and it would really be blown if they develop 100 bad mutations each! And at this point we are not even considering the budget needed to build new functional traits.
When we actually do careful accounting of the costs of natural selection envisioned by Darwin and Dawkins versus the available money of reproductive excess, we realize that if evolution happens, it must be mostly free of selection as a matter of principle, and thus mostly neutral. There is simply not enough “money” in the form of reproductive excess to maintain and construct complex designs composed of billions of nucleotide and epigenetic “traits”. There is some selection obviously, because there is some “money” to do a little bit, but not enough.
The accounting of the cost of selection can be done in a number of ways. One way to demonstrate this is through the equations of population genetics, and the other way is a computer simulation that does the accounting. One of the best, if not the best computer accounting simulations is Mendel’s Accountant written by the dream team of creationist population genetics. The irony then is population geneticists, PZ Myers, Larry Moran, the YECs have had a rare moment of agreement where they have all signed the claim, “most molecular evolution is non-Darwinian.”
But if most evolution is non-Darwinian, maintenance much less construction of design cannot be explained by Darwinism, then the case for ID is strengthened.
Now if most evolution had been non-Darwinian, one would rightly argue it would have been a random walk, and thus not much better than a tornado going trough a junkyard. Creationist have seized on this and said, “well we’re not a junkyard, therefore some non-random process must have created designs in nature, hence we are designed”. In contrast, Larry Moran and friends have said “evolution is a random walk and we are obviously junkyards and you’re an IDiot if you think biological organisms are mostly functional.”
[cross posted at CEU IDCS Cost of maintenance and construction of design, neutral theory supports ID and/or creation]