The author of this piece makes some real doozies of logical fallacies here, but dresses them up in language of his choosing. For example, he makes the argument that because worldview is tied to emotional attachments, the atheist worldview must be flawed because it is based on an emotional attachment to the belief that there is no god. He ignores the converse argument that he himself is arguing from an emotional connection to the belief in the existence of a god.
Next, he argues that because a skeptic is skeptical, they must be open to the possibility that the supernatural is possible. This is both a leap, and incorrect. Such a person who believes in a nature-only viewpoint, when confronted with a true 'miracle' or the like, would simply be compelled (assuming it was truly genuine) to expand their definition of natural.
He then ties the atheist belief to what he defines as a skeptic, and lumps them together in order to select which party he refers to at any given time. He does this in order to make the point that atheists violate their own worldview, but all he's argued is that the atheist violates the worldview that he has assigned to his definition of skeptic. It's a straw man argument.
He then goes on to basically say, that because there is no observed (although he says observable, which is another leap, as we simply may not have observed it YET) cause to the beginning of the universe that there must be a god. This ignores all of human history where the unexplained or as of yet unobserved were attributed to deities until they were finally able to be explained through more advanced observation techniques or by a scientific approach. For example, the sun was once Apollo riding his chariot through the sky, and evidence to the contrary was unobservable. Does that mean that the sun MUST then be Apollo riding his chariot through the sky? No, it is far more likely that there is a natural explanation.
The argument of the REASON for the belief in naturalism is left completely out. Based on all historical discovery of knowledge, the skeptic and the atheist both can note that a natural explanation has been found in every case. This makes the likelihood that other phenomena have a natural explanation much higher than the various 'supernatural' theories that have EVERY TIME been found to be false. They hang their hat on the numbers, as a skeptic should. The numbers are completely on the side of a natural explanation being the likely cause for any particular phenomenon including the beginning of the observed universe.
In Part 2, he goes completely off the logical reservation immediately. He starts by stating that he won't support his assertions with evidence for the sake of brevity. That's a red flag right there. He even says that because we know more about the conditions at the beginning of the universe, that said knowledge is indirect evidence that a super-intelligent Agent designed it. This is the first of many naked preferences of the Creationist worldview. This is almost exactly like saying that the universe is so complex, that it must have been created.
Now we're in familiar territory and it's time for a thought experiment.
If the universe's complexity can only be explained by a more complex creator, (The argument that the universe is a painting and must have had a painter) In this case the argument is that complexity can only rise from something more complex than itself. This alone means that God was created by a more complex and, how else can I put it, more omnipotent God. Essentially, it's turtles all the way down. This alone logically disproves the Christian god, but let's not stop there.
It has already been observed that more complex structures can and do form from less complex ones. For example, the more complex Helium atom is created when Hydrogen is consumed in our sun. More complex from less complex. Archeology has shown that the history of life becomes, on a macro scale, less complex the further you go back into the Earth's history. This continues all the way back to algae and viruses, and to amino acids. Once again, less complex becomes more complex. Even in a tangential sense, it holds. Diamonds, which are harder and more structured than coal, are the end product, and not the coal or graphite states of carbon.
Now ask yourself, if things tend to become more complex from less, why would it seem more likely that something as complex as the universe would spring from something more complex than itself?
The argument as a whole that Mr. Deem is making, is that because a cause for many newly discovered phenomenon has not yet been observed or discovered, that they are evidence in favor of not only a god, but the Christian one. All the while, he says that it is only because of an emotional attachment to an existing belief that prevents the reader from accepting the Christian god as the scientifically proven truth. This is precisely the kind of careless and intentionally flawed logic that propagates the idea that “Intelligent Design” should be taught AS SCIENCE in US schools. It makes haphazard references to some discoveries and theories, while ignoring others, and ignoring the obvious. All quadrilaterals are not squares, and it is not turtles all the way down.