While I don't agree with all of the author's arguments, he does make some good points. He argues that "Scientism claims that science has already resolved questions that are inherently beyond its ability to answer", and discusses this overreach of science in the areas of metaphysics, epistemology, and ethics. For example, with regard to metaphysics, he writes, "Though physicists might once have been dismissive of metaphysics as mere speculation, they would also have characterized such questions as inherently speculative and so beyond their own realm of expertise". However, recently some scientists have gone further by claiming that metaphysical questions (such as "What is the nature of reality? Where did all this come from? Did the universe need a creator?") are better answered by science.
With regard to the question of "Why should anything exist at all?", Hughes brings up "Physicist Lee Smolin, in his 1997 book The Life of the Cosmos, goes one step further by applying the principles of natural selection to a multiverse model", and then criticizes the multiverse explanation for the origin of our universe, and its being finely-tuned for life to arise:
"...any particular universe may follow from the existence of a multiverse, but the existence of the multiverse remains to be explained. In particular, the universe-generating process assumed by some multiverse theories is itself contingent because it depends on the action of laws assumed by the theory. The latter might be called meta-laws, since they form the basis for the origin of the individual universes, each with its own individual set of laws. So what determines the meta-laws? Either we must introduce meta-meta-laws, and so on in infinite regression, or we must hold that the meta-laws themselves are necessary - and so we have in effect just changed our understanding of what the fundamental universe is to one that contains many universes. In that case, we are still left without ultimate explanations as to why that universe exists or has the characteristics it does."
As I said, I'm not sure I agree completely with Hughes, but he does make some interesting arguments. If I were criticizing scientism, I probably would have instead discussed consciousness and our inability to understand its nature or origin via the conventional scientific method. To my way of thinking, that is where the limits of knowledge gained via empirical (i.e., sensory) observation is most apparent.