Likewise, changes that are beneficial will be selected for, but these helpful changes are close to nonexistent, indicating that the genome was optimal from the beginning.
The conclusion does not follow from the statement. If the genome was optimal from the beginning, then why did the age of reptiles end, and the age of mammals begin? Why are plants, and animals constantly going extinct? They go extinct if their genome does not adapt to environmental changes.
Natural selection operating on mutations may in some cases optimize survival if acting on an existing functional gene, but mutations cannot build-up the code in the first place.
He hasn't stated where he is getting this. Mutations most certainly can build up the code. Anemia is a defense against malaria. The sickle cell variant is deadly. Anemia was a mutation. It is hereditary. Not all humans have it. If not a mutation, then where did it come from?
A preliminary analysis of the DNA finds that the proportion of amino acids existing in genes, introns, and other DNA are not what would be expected by natural selection. When DNA that has no known function, (excluding DNA used for regulatory purposes, for centromeres, for telomeres, and for the production of RNA or tRNA) is examined, the patterns found are clearly in contrast to expected random mutational patterns shown in Table I. This shows that random changes have had only a small role in producing the genome, both in its protein coding and noncoding sections.
Again, it does not follow. He is confusing natural selection with random mutation. Natural selection is not always random. If anemia is a defense against malaria, and it was a random mutation, then why is it only endemic to populations in areas with high levels of malarial mosquitoes? Why is sickle cell anemia not found anywhere else?
Part of the reason is that mechanisms that function to resist change in the DNA genome exist. But these repair mechanisms would not have existed in primitive cells, which would mean that rapid genomic degeneration would have occurred before the repair system had evolved.
Why would they not have existed in primitive cells? He hasn't shown facts to back this up, and that invalidates the conclusion.
One thing that is difficult to follow is that he is using "mutation", "random mutation", and "natural selection" interchangeably. They are not the same thing. He does this throughout the paper. It is not an accident. I don't think that he understands it.