The foundational rule for biology, Genetic Entropy, which can draw its foundation in science from the twin pillars of the Second Law of Thermodynamics and from the Law of Conservation of Information (Dembski, Marks) (Abel - Null Hypothesis), can be stated something like this:
"All beneficial adaptations away from a parent species for a sub-species, which increase fitness to a particular environment, will always come at a loss of the optimal functional information that was originally created in the parent species genome."
_ Genetic Entropy is the true rule for all biological adaptations -
The malaria parasite, due to its comparatively enormous population size, has in 1 year more mutation/duplication/selection events than all mammal lineages have had in the entire +100 million years they have been in the fossil record. Moreover, since single cell organisms and viruses replicate, and mutate/duplicate, far more quickly than multi-cellular life-forms can, scientists can do experiments on single celled organisms and viruses to see what we can actually expect to happen over millions of years for mammals with far smaller population sizes.
Malaria and AIDS are among the largest real world tests that can be performed to see if evolutionary presumptions are true.
"Indeed, the work on malaria and AIDS demonstrates that after all possible unintelligent processes in the cell--both ones we've discovered so far and ones we haven't--at best extremely limited benefit, since no such process was able to do much of anything. It's critical to notice that no artificial limitations were placed on the kinds of mutations or processes the microorganisms could undergo in nature. Nothing--neither point mutation, deletion, insertion, gene duplication, transposition, genome duplication, self-organization nor any other process yet undiscovered--was of much use." Michael Behe, The Edge of Evolution, pg. 162 Swine Flu, Viruses, and the Edge of Evolution
A review of The Edge of Evolution: The Search for the Limits of Darwinism by Michael J. Behe
The numbers of Plasmodium and HIV in the last 50 years greatly exceeds the total number of mammals since their supposed evolutionary origin (several hundred million years ago), yet little has been achieved by evolution. This suggests that mammals could have "invented" little in their time frame. Behe: Our experience with HIV gives good reason to think that Darwinism doesnt do much—even with billions of years and all the cells in that world at its disposal (p. 155).
Behe and Snoke go even further in addressing the Gene Duplication scenario in this following study:
Simulating evolution by gene duplication of protein features that require multiple amino acid residues: Michael J. Behe and David W. Snoke
Excerpt: Gene duplication is thought to be a major source of evolutionary innovation because it allows one copy of a gene to mutate and explore genetic space while the other copy continues to fulfill the original function. (However), At smaller population sizes, the time to fixation varies linearly with 1/N and exceeds the inverse of the point mutation rate. We conclude that, in general, to be fixed in 10^8 generations, the production of novel protein features that require the participation of two or more amino acid residues simply by multiple point mutations in duplicated genes would entail population sizes of no less than 10^9.
Intelligent Design - The Anthropic Hypothesis