Functionality for junk DNA is prevalent, and was successfully predicted by intelligent design.
The re-usage of highly similar and complex parts in widely different organisms in non-treelike patterns is best explained by the action of an intelligent agent.
The dominant pattern in the fossil record is explosions of new biological forms. The Cambrian explosion is a prime example.
“Evolution” in its deepest sense is a foundational metaphysical commitment, not a scientific theory that one could test.
The paper could cause a stir, since it has violated an “implicit agreement” that mainstream academics should never criticize public advocates of evolution.