Scientific expertise is problematic is three fundamental ways: its basic assumptions, its method and its social support structures. The basic assumptions of science are: (a) All of reality that exists is subject to human sensory perception and mathematical reason; anything outside this is "supernatural" and either does not exist or isn't worth investigating; (b) The universe, including human evolution, runs by arbitrary chance and blind necessity and is essentially meaningless and dead; (c) In spite of this, humans can manipulate and master nature, creating their own future in a history of evolutionary progress; (d) Human beings are the arbiters of ultimate value; (e) Objective reality is value free; (f) Nature is expendable; and (g) There is meaningful order in the cosmos.
The scientific method is problematic, if for no other reason than its dominance over other methods. It has had its successes but it is viewed as the only 'right' method. Reductionism, that is reducing the object under study into smaller and smaller components whether it be the human body, a crystal or the Earth is central to science. One adverse side-effect is that research is fragmented into specialties and sub-specialties which become insular, jealous and parochial. Another side-effect is the separation of science from nature. The scientific method is rational and thereby linear, precluding non-linear and intuitive thinking.