As a self-proclaimed metaphysician (student of metaphysics–the branch of philosophy which explores the nature of reality) as well as a physician, I was pleased to read Jim Holt's piece in the New York Times http://www.nytimes.com/2012/06/10/opinion/sunday/what-physics-learns-from-philosophy.html?pag He addresses some of the nastiness that has passed between philosophers and scientists in recent publications. Although scientists often consider their approach (the scientific method) to uncovering the nature of reality to be superior to those of philosophers, in truth, they have been exploring philosophical questions since the first "scientist" lifted up a rock or starred into the starry night sky.
It does seem that much of contemporary physics such as quantum theory, string theory, ,dark matter and energy, multiple universe theory is philosophically "frustrating". By that I mean the scientific theories are not easily supported by scientific evidence. They make mathematical and theoretical sense but have yet to be "proved" in the more traditional, standard methods of scientific experimentation. Even more unsettling is a belief among some scientists that certain theories (such as the multiverse) may be inherently untestable!
Also, the theories mentioned seem contrary to what is referred to as common sense. They lead us into a universe that makes science fiction seem tame. Quantum theorists have been known to admit that if anyone claims to truly understand it and its metaphysical implications they are kidding themselves.
An interesting graph placing scientific knowledge over time with a comprehensive understanding of the universe would lead to a strange paradox. Until the beginning of the 20th century, scientific explanations seemed to reduce the mystery of how the universe worked. There was a level of logic that the average individual could follow. But beginning with the 20th century and extending into the 21st century, science is deep into theories that are producing more mystery, not less.
Ultimately we may or may not be capable of wrapping our minds around where science is leading us, but recognizing their own frustration, some scientists would rather NOT explore the philosophical implications of their work.
Still, as human beings with human awareness, we cannot help but try make sense of the universe around us. As Nietzsche is quoted in the piece, "As the circle of science grows larger, it touches paradox at more places."
Attempting to deal with the paradox is philosophy. The two disciplines are interconnected. Turf battles merely reflect human egocentric nonsense. The mysteries that exist are fodder for both scientific and philosophical exploration. They should be joint ventures.