Cook also ran into some conflicts with the scientific community over his religion. Cook was asked by Elder Joseph Fielding Smith, then an Apostle in the LDS Church's Quorum of the Twelve, to write an introduction to his book "Man: His Origins and Destiny." But criticism of the book among the scientific community led to become more deeply involved in Science and Religion issues.

In a well-publicized seminar at the University of Utah, Cook publicly claimed that evolution violated the second law of thermodynamics. The assertion gained him notariety, with the press carrying an article about the seminar nationwide. The next year the American Association for the Advancement of Science carried a vigorous debate on the issue in a conference in Switzerland, and a formal conference was held at Philadelphia's Wistar Institute to debate the subject.