When I first began to immerse myself in philosophic writings and abandon faith, my father shared with me a story that took place between one of the European Rabbonim (I forget the name) and his student.
In short, The Rov sees that a former Talmid of his is no longer observant, and inquires as to why he left the fold. The student responds with an ardent philosophic erudition refuting Torah m’Sinai, etc. The Rov responded by asking him: Did you first find philosophy, and then go off the derech? Or, did you first go off the derech, and then find philosophy?
The Mumar l’Teavon is an old and depressing character throughout Jewish history.
In regards to OP’s friend, since science is based on inductive reasoning, as opposed to deductive reasoning, his belief that science refutes the Torah is not a very strong one to make. Science, by its very nature, is prone to substantial error. Besides, most of science does not conflict with the Torah at all, and those areas that do, may be reconcilable.
Just remember, the great scientist/philosopher Aristotle believed that objects fell to the ground because they were drawn to the center of the earth. It was only millennia later that gravity was discovered, and Aristotle’s beliefs were dismissed.
In all the time that science has made great errors, and faced great revisions, observant Jews stuck to their guns and observed the Torah as per their mesorah.
Alas, I’m a kofer too, only my arguments are quite solid. 😉