When it comes to neo-Darwinian evolution, the question isn’t whether Darwin’s proposed mechanism of biological change is true – we know it is because we observe it in nature. The question is whether it can explain what Darwin thought it explained: the diversity of life.
While the process of natural selection working on random mutations (NS+RM) is too slow to observe in mammals, we can observe the equivalent of millions of years of mammalian evolution in mere decades using microbial life and viruses. Experimental data over the last ~20 years has shown that while natural selection working on random mutations does produce change and variation within microbial species, it does not create new species.
The creation of a new species requires biological novelty: new proteins, organs, systems, and gene regulatory networks. Nothing of the sort has ever been observed. Instead of building something new, we observe NS+RM degrading what is already present (devolution rather than evolution). Sometimes such degradations can aid an organism’s survival (similar to how blowing up a bridge in wartime can help save people from enemy attack), but this survival benefit comes at the price of breaking existing genes or cellular machinery, not by creating something new. While mutational degradations may help an organism survive in the short term, it cannot produce a new species in the long term any more than a merchant who loses a penny on every sale can make up for his loss by simply selling more volume. Evolution is a tinkerer, not an inventive force. It can explain how a species can adapt to a changing environment, but not the origin of new species.
Biological novelty requires an infusion of new information, not the degrading of existing information. We know from our repeated and uniform experience that information always and only comes from an intelligent source, not a random process like Darwin proposed. Just like computer code, random changes are much more likely to degrade the existing information rather than create new information.
While Darwinian processes can explain the survival of the fittest, they cannot explain the arrival of the fittest. For that, we need new biological information, and that requires an intelligent source. So while Darwin’s mechanism of NS+RM has been demonstrated to be true, his claim that it can explain the origin of biological diversity has proven false.
I recognize that “species” is notoriously difficult to define, with many different definitions offered by biologists. The most commonly accepted definition, however, understands a species to be a group of reproductively isolated organisms; i.e. organisms that are capable of reproducing with each other. If we accept this definition, then we actually have observed NS+RM producing new species. It should be noted, however, that while the two groups may no longer be capable of interbreeding, they still appear to be nearly identical. Often, the reasons for their inability to mate with each other are practical rather than biological in nature, and in no case is the inability to breed due to the creation of new genes, organs, or systems. So while it is technically accurate to say we have observed speciation given this definition of the word, this is not the kind of speciation Darwinism is purported to account for. It needs to explain how we got cats and dogs, not how we got tiny variations among cats or dogs that prevent one group of cats from mating with another group of cats.