Philosophical Naturalism makes the claim that empirical and rational science is the only sure path to true knowledge. Yet in recent years the findings of science are making Naturalism increasingly implausible.
Einstein’s theories about the expanding Universe confirmed through observations of red-shift in light from stars point to an origin of time and space and matter at the time of the “Big Bang” – most likely around 13.8 billion years ago (https://en.wikipedia.org/wiki/Big_Bang). This theory contradicts the idea of an eternally existing Universe and points to a transcendent cause of the Universe outside of Nature – strongly suggesting a Divine Creator.
The “Fine Tuning of the Universe” (see https://www.youtube.com/watch?v=X3d0zC3G3b8) is acknowledged as fact by physicists today, and Professors Jonathan Borwein and David Bailey acknowledge that “We physicists need to confront the crisis facing us.” (http://phys.org/news/2014-04-science-philosophy-collide-fine-tuned-universe.html)
Of course, it is only a crisis because in order to remain committed to Naturalism in the face of the evidence for a Designer, they find the need to speculate about things they can never use Science to test, like 10^500 or more Universes we can’t possibly access. In other words, Naturalism needs naked philosophical speculation untestable by Science in order to remain plausible.
Naturalism is also under siege from theorists such as William Dembski (Information theory), Michael Behe with his work on irreducable complexity of biological systems and others.