Understanding the diversification of phenotypes through time—“descent with modification”—has been the focus of evolutionary biology for 150 years.
And next for the statement that reveals how evolutionists handle contradictions. They don’t consider the possibility that evolution may not be a fact. Rather, they search for evolutionary explanations:
If, contrary to expectations, similarity evolves in unrelated taxa, researchers are guided to uncover the genetic and developmental mechanisms responsible.
And while that might seem reasonable, one problem is that while the search is on there is no acknowledgment that evolutionary theory has problems. Evolution racks up problem after problem, and still no such acknowledgment. For those problems are interpreted as research problems which deal with the theory of evolution and have no influence on the fact of evolution. Such research is taken as a sign of good science at work.
So while there is nothing wrong with doing research, the years pass by with no acknowledgment of the actual state of the science. This brings us to the second problem, which is that evolution is sufficiently malleable that it always seems to have at least some sort of explanation, albeit unlikely, to service the contradictions. To wit, the paper continues:
Similar phenotypes may be retained from common ancestry (homology), but a phylogenetic context may instead reveal that they are independently derived, due to convergence or parallel evolution, or less likely, that they experienced reversal.
In this case, the contradictions can be explained by various combinations of common ancestry, convergence, parallel evolution and reversal, to name a few. They could have included unique selection scenarios, accelerated evolution, and other mechanisms to account for those profound differences found amongst otherwise allied species.
In any case, one way or the other the contradictions will be explained by some mechanisms, no matter how speculative or unlikely. And the whole exercise will be cast as an investigation of how evolution really works.
Such examples of homoplasy present opportunities to discover the foundations of morphological traits. A common underlying mechanism may exist, and components may have been redeployed in a way that produces the “same” phenotype. New, robust phylogenetic hypotheses and molecular, genomic, and developmental techniques enable integrated exploration of the mechanisms by which similarity arises.
Components may have been redeployed? Evolutionists will try hard to explain the findings, but don’t expect an objective, theory-neutral, scientific evaluation of their idea.