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.
In the first place, Random Mutation is called "random" because it is the result of copying errors, radiation, etc. none of which are deterministic as to time or place or effect.
Natural Selection is dependent on selective pressures which are all random processes; weather, climate, predation, natural causes, catatrophic events, cosmic events, geography arrangements.
The combination of Random mutation and Natural selection being totally random somehow generates a biased
result defined as survival of the fittest, meaning producing more offspring as an affected subpopulation of a species is a very nice hunch, but where is the evidence for it ?
Just what percentage of the 3 billion base pairs in the genome do you think affect the anemia ? You seem to call that building up a genome informationally....I can't see how.
If you think the DNA repair machinery and its coordination systematically with the cell replication process was a part of a primitive cell, I suggest you rethink this paradigm because I don't think it makes sense at all.
We can demonstrate this phenomenon quite readily even today. Take your average chicken ~ this is a very successful species that numbers in the billions. These critters have even managed to enslave humanity to their purposes ~ we feed them, breed them, house them, etc.
However, as successful as their genome might be in bringing them all the benefits of an easy life, if you take but one chicken and cook him, he's dead Jim!
Successful adaptation to one's environment does not guarantee long life!