Some of those “new atheist” authors that write books such as God: The Failed Hypothesis. How Science Shows That God Does Not Exist, where they claim science actually demonstrates there is no God, are actually engaged in a loose form of reductio ad absurdum, that is; an argument that leads to contradiction. This is because while operating under the assumed worldview atheism gives them of man and his intellect, they also expect science and the human intellect to give a real account and explanation of the ultimate Reality. And there are other new atheist writers such as Richard Dawkins who pin their hopes on science finding a “Theory of Everything”, which would supposedly explain not only exactly how the universe operates and exists, but even why the laws of nature demand it’s existence. It supposedly would explain everything, (even the old “why is there something and not nothing?” question), and in these atheist’s minds finally riding the world of God.
The problem is, under the worldview of atheism, man’s mind is merely an end product of natural selection, different merely in degree, not kind, from all the other little critters natural selection has produced. This little critter we call man builds a better dam than a beaver does, and he’s much more clever than a beaver, but that’s all, he has no more right to make pronouncements on the ultimate nature of reality than the beaver does. Because in the atheist view of man this little guy’s mind was constructed through the blind machinations of natural selection, a process which selected for attributes that would help him catch his next meal, avoid the next predator, and then live to mate and pass on his “selfish genes”. Thus, under this assumption there's no reason to believe these minds that unguided natural selection cobbled together piecemeal are capable of constructing reliable abstract inferences or a true understanding of the ultimate structure of reality, they weren’t “designed” for that. This critter known as man is good at recognizing patterns in his day to day world, through fallible inductive reasoning, which allows him to construct useful gadgets like campfires, dams, lasers, and MRI machines. But once he steps beyond this into the realm of unfalsifiable and untestable abstract inferences on the ultimate nature of Reality he’s overstepped what his brain was constructed for.
On top of that, man takes in all he knows of “the world” through a mere five senses, senses that were selected for solely to help him survive, they helped him hear the approach of a wild boar and see the tree to which it would be a good place to climb to safety. We can only perceive the part of the world that these senses give us access to. Just consider if we ever met a race of beings with brains similar to ours but with just three senses, missing the senses of sight and sound. Would anyone expect those beings to ever form a complete description of Reality, or even know some of the things we do through our sense of sight and hearing? It’s likely some being with seven senses would know even more about the world than us, I believe Kant made this point about our inability to grasp the "noumenon" world, or what he called the "thing-in-itself". Thus, both our senses and intellectual faculties evolved in a context concerned mainly with survival and reproduction. And the powers that such clever little critters may possess are wholly inadequate to picture Reality itself, which belongs to an order that utterly transcends our daily concerns.
The Nobel laureate Eugene Wigner published in 1960 what’s become a pretty famous and much quoted essay titled; “The Unreasonable Effectiveness of Mathematics in the Natural Sciences”. Wigner pointed out the near miraculous “fit” between mathematics and physical Laws in describing the workings of our universe. He observed that the mathematical structure of our laws of physics often point the way to further advances in theory, and he argued that this is can not be just a coincidence and therefore must reflect some deeper truth about both mathematics and physics. This all has to do with the mystery of the rational intelligibility of the universe, why are human minds able to figure out the workings of the universe and why does mathematics “work” as such an effective tool in describing the universe? Since Wigner first published his paper physicists and philosophers of a theistic bent have pointed out that it’s really not surprising that the universe is intelligible to us, since both the universe and human minds were created by the same God, that is, both the laws of physics and mathematics are traceable to the mind of the same God who created both the universe and the human mind. Therefore it’s not surprising when mathematical theories produced by human minds match the workings of the actually Laws of the universe.
But not so fast, say other physicists and philosophers of a more atheistic view of the world. They say that the reason the Laws of the Universe follow mathematical rules is simply because humans first invented mathematics and then started looking at the universe through their “mathematical colored glasses”. They’ve merely “projected” their man-made invention of mathematics onto the universe, the universe doesn’t really follow laws based on mathematics. In other words, Wigner’s "mystery" that mathematics actually describes the Laws that the Universe follows is about as significant as the “mystery” that English is the language that plays are written in. The philosopher Thomas Kuhn has even gone so far as to say that if we ever met a race of aliens from another planet, they would likely have completely different “Laws” for describing the workings of the universe that have nothing in common with our “Laws”. Remember that the next time a Dawkins tells you that once we “discover” the Theory of Everything we’ll have no room left for God.