A proponent of the human-orangutan clade, Jeffrey Schwartz argues, in this paper , that molecular phylogenetics is largely based on a baseless assumption. To sum up, according to him:
- this type of phylogenetics relies on overall similarity, rather than cladistic considerations, to infer relationships. He claims that even parsimony algorithms (albeit traditionally contrasted with distance-based methods) group taxa on the basis of overall similarity.
- this reliance on overall similarity is based on the baseless and questionable assumption that sequence evolution is gradual and continuous.
Could you tell me if his objections and paper hold water, and how valid they are?
 Schwartz & Maresca, 2006, "Do Molecular Clocks Run at All? A Critique of Molecular Systematics", Biological Theory, Springer.