It is my understanding the great weakness of evolutionary theory is that the mechanism for evolution has never been found. Random genetic mutations didn't pan out. I don't doubt there have been changes in species. But scientists have not been able to explain how or why. Because they are unwilling to look for any "intelligent design" or reason behind the universe. They want everything to be pure physical chance.
The BASIC mechanism of evolution is well known---mutation PLUS selection. Neither one by itself does the job. Together they are all that is required. The ONLY valid SCIENTIFIC criticism of evolution is that sometimes evolution happens more quickly than "normal" mutation rates (molecular clocks) alone can account for ("punctuated equilibrium").
The "criticisms" in the posted article are mostly strawmen, or valid only in the minds of the "creation science" types.