It is not clear that the mechanisms we observe are capable of causing the origin of species. What we observe are mechanisms that help species to adapt. Whether or not these mechanisms are capable of the larger-scale change evolution requires is in question.
In fact, the scientific evidence suggests that they don’t. So the fact that we observe adaptations is not proof that evolution is a fact. Such a claim amounts to an equivocation on evolution. It could be that the mechanisms we observe are up to the task, but we don’t know that they are.
The question of how evolution occurred is very much relevant to whether evolution occurred. And after centuries of research, we certainly do not know how evolution could have occurred. Here is how one research paper described the problem:
As encompassed by the ‘Synthetic Theory’ (or ‘Modern Synthesis’) of evolutionary biology, the 20th century has provided a thorough understanding of the mechanisms of microevolution (Dobzhansky, 1937; Mayr, 1942; Simpson, 1944; Mayr and Provine, 1980). It is relatively well known how organisms adapt to their environment and, arguably, even how new species originate. However, whether this knowledge suffices to explain macroevolution, narrowly defined here to describe evolutionary processes that bring about fundamental novelties or changes in body plans (Theissen, 2006), has remained highly controversial.
How fundamental innovations (or novelties) originate in evolution remains one of the most enigmatic questions of biology. According to the proponents of the Synthetic Theory, the gradual process of evolution by natural selection that operates within populations and species also creates the unique traits recognizable at higher taxonomic levels, meaning that macroevolution is just microevolution extended over relatively long periods of time.
However, it has been repeatedly pointed out that innovation is different from adaptation, and that the Synthetic Theory, which is largely based on population genetics, falls short of explaining innovations, novelties, and the evolution of body plans (Riedl, 1977; Gilbert et al., 1996; Bateman et al., 1998; Erwin, 2000; Wagner, 2000; Haag and True, 2001; Wagner and Müller, 2002; Wagner and Laubichler, 2004; Müller and Newman, 2005; Theissen, 2006). These are not the only shortcomings of the Synthetic Theory. It considers evolution as the result of changes in allele frequency due to natural selection that engender subtle modifications of phenotype. According to the Synthetic Theory evolution always occurs gradually, in a countless number of almost infinitesimally small steps. Given sufficient time, these gradual changes accumulate and result in the larger differences that typically separate higher taxa. The fossil record, however, with its often abrupt transitions, provides limited evidence for the gradual evolution of new forms (Gould and Eldredge, 1993). In addition, the branching patterns of higher taxa in both animals and plants, as revealed by cladistics, do not support the view that the major features of body plans and their constituent parts arose in a gradual way (Vergara-Silva, 2003).
How fundamental innovations (or novelties) originate in evolution remains one of the most enigmatic questions of biology. But that is the heart of evolution. When evolutionists say evolution is an undeniable fact, they very much are including innovations and novelties. And in doing so, they damage the reputation of science.
Whether or not evolution occurred is another question entirely. But if we want to speak of facts, the fact of the matter is we do not know how, or even whether, evolution occurred. That is a scientific fact, and to claim otherwise is to harm science. Evolutionists accuse skeptics of doing damage to science. If they are genuinely searching for threats to science they should look closer to home.