The author states, "Can mutations produce real evolutionary changes?"
"Do they produce evolutionary changes? Do they really produce new traits?"
Yes, They can. E. Coli bacteria require 2 mutations in order to utilize salicin. In a lab, these two mutations were observed to occur and produce a strain of E. Coli that utilized Salicin. In a more impressive case, a gene duplication is responsible for creating an antifreeze protein in a species of Antarctic fish. There are other cases of things like this happening as well.
The author goes on to talk about how three or four mutations occuring simultaneously would be so unlikely as to be impossible. He does not give any examples of things that would require this many mutations.
"So even by the wildest “guesstimates,” the universe isn’t old enough or big enough to reach odds like the 1 in 103,000,000 that Huxley, an evolutionist, estimated as the odds against the evolution of the horse."
Richard Carrier has written an essay about the odds of evolution, and this is, he writes, a misquote. Huxley calculated these odds based on pure chance, leaving out the effects of Natural Selection.
"Way back in 1967, a prestigious group of internationally known biologists and mathematicians gathered at the Wistar Institute to consider Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution.10 All present were evolutionists, and they agreed, as the preface clearly states, that no one would be questioning evolution itself. The only question was, could mutations serve as the basis—with natural selection—as a mechanism for evolutionary change? The answer of the mathematicians: no. Just plain no!"
I will again rely on Carrier for the answer to this one:
"Only one paper comes anywhere near proposing that the origin of life and subsequent evolution is improbable: Murray Eden, "Inadequacies of Neo-Darwinian Evolution as a Scientific Theory" (pp. 5-20). He does not really argue that evolution is improbable, but rather that no present theory accounts for certain peculiarities of life on earth, especially the fact that all living organisms are composed of a very tiny fraction of all the possible proteins."
"Among the huge flaws in Eden's paper, pointed out by his critics, is that he somehow calculates, without explanation, that 120 point mutations would require 2,700,000 generations (among other things, he assumes a ridiculously low mutation rate of 1 in 1 million offspring). But in reality, even if only 1 mutation dominates a population every 20 generations, it will only take 2400 generations to complete a 120-point change--and that even assumes only 1 point mutation per generation, yet chromosome mixing and gene-pool variation will naturally produce many at a time, and mix and match as mating proceeds."
The AiG author then begins to quote Michael Denton:
"If complex computer programs cannot be changed by random mechanisms, then surely the same must apply to the genetic programs of living organisms. The fact that systems in every way analogous to living organisms cannot undergo evolution by pure trial and error [i.e., by mutation and selection] and that their functional distribution invariably conforms to an improbable discontinuum comes, in my opinion, very close to a formal disproof of the whole Darwinian paradigm of nature. By what strange capacity do living organisms defy the laws of chance which are apparently obeyed by all analogous complex systems?"
I think we can all see the major flaw in this analogy. Non-living entities like computer programs cannot mutate and reproduce the way living things do, so this is a false analogy.
The author then begins talking about genetic burden:
"Thanks to our accumulated genetic burden, serious hereditary defects are present in perhaps 5% of all human births, and that percentage greatly increases among the children of closely related parents."
What he is forgetting is that human beings live in an unnatural situation nowadays, thanks to medicine. The mutation that causes Diabetes would not be so prominent in a natural situation because people born with that condition would not survive or produce offspring, and it would be eliminated from society. And while it is true that there is a "genetic burden" that all populations carry, it is balanced out by natural selection.
"Natural selection cannot save us from this awful situation either. Selection can and does eliminate or reduce the worst mutations—but only when these mutants come to visible (phenotypic) expression. Most mutations “hide” as recessives, “invisible” to selection, and continue to build up in secret at multiple loci, somewhat like a “genetic cancer” slowly but steadily eating away at genetic quality."
These recessive traits are subject to genetic drift, and can be corrected as time passes. They are also subject to being "drowned" by good genes in a large population. This is one reason that the number of blondes is decreasing - the gene for it is recessive (it probably arose in a small isolated population).
(Note: the article I cited about the blondes debunks the myth that blondes will one day go extinct, but states in the conclusion:
"Most scientists asked to comment on the faux study in recent years have opined that although the proportion of blondes in the population might decrease a bit in the coming years, it likely won't drop to nothing anytime in the forseeable future.")
