Special Thanks to RL friend ErikJ for all the help in creating this series.
The Big Bang Singularity
The first piece of scientific evidence that Craig will appeal to is the Big Bang Singularity Theorem. Note that this is different from the Big Bang Theory. This is because the Big Bang Theory actually says nothing about how the universe came into existence, and only describes how our space-time universe (note the distinction) expanded and evolved after the first “Planck second” (10-43 seconds) of its existence.
The Big Bang Singularity Theorem is an attempt to explain what happened before the first Planck second, assuming that general relativity holds at the scales involved at that point. What results is a mathematical and physical singularity, where many of the physical properties quickly break down into infinities – including temperature, density, and curvature. In an extremely odd philosophical move, Kalam proponents take this to mean that all of the matter and energy described in the Singularity Theorem must have come into being from nothing (more on this in the philosophy section).
Why the Singularity Theory is not evidence to support the Kalam
The first important thing to realize about the Big Bang Singularity Theory is that it is largely disregarded by a majority of cosmologists. This is because the critical assumption that is made, that general relativity holds before the first Planck second, is known to be unsound. At that point in the Big Bang, the scales are so small that quantum mechanical effects become extremely important, and general relativity breaks down.
In fact, singularities are generally a sign that there are missing pieces in a scientific theory. As it turns out, cosmologists already know there is a missing piece to general relativity theory – specifically we do not yet have an understanding of quantum gravity, which is required to marry quantum mechanics with general relativity.
That said, our best attempts at accounting for quantum effects do point to the idea that there was no actual singularity event at the beginning of our space-time universe (more on this in the section on quantum nucleation).
However, in case this was not enough to disabuse the notion that the Singularity Theory does not support the idea of all matter and energy “beginning to exist” – there is one more point that needs to be made. Even if the singularity theory held, there is no way that one could show that any point of infinite density, temperature, and curvature is literally equivalent to “nothing”, which would then expand into incredibly dense quantities at the first Planck second, and then expand into the universe.
Craig’s Philosophical Shenanigans with the Big Bang Singularity
It’s almost as though apologists realize that the science here, even if it were still held as valid, doesn’t imply that all matter and energy simply came into existence by divine fiat. This is true even if one accepts the Big Bang Singularity Theorem. What says that the universe didn’t exist perpetually in this state of infinite density, temperature, and curvature before it started expanding via a natural process? In order to correct this theologically untenable situation, some philosophical sleight of hand is required.
For anyone familiar with the KCA, and in defense of premise two in particular, will remember the main philosophical arguments in support of it is that (supposedly) an actual infinite cannot exist in reality. This is directly at odds with the predictions of the Big Bang Singularity Theorem, which predicts a singularity that is quite literally filled with infinities. 
Normally, one would assume that a person with a strong commitment against the existence of anything that is a completed infinite would mean that such a person would reject the Big Bang Singularity Theory with its infinite temperature, curvature, and density. Never one to disappoint, apologists like William Lane Craig directly try to argue that the singularity being infinite actually means its equivalent to literally nothing:
“This event that marked the beginning of the universe becomes all the more amazing when one reflects on the fact that a state of "infinite density" is synonymous to "nothing." There can be no object that possesses infinite density, for if it had any size at all it could still be even more dense.” 
So rather than agree with the scientists who show that general relativity doesn’t hold at these extremely small scales, and reject the Big Bang Singularity Theorem – apologists must now defy any notion of mathematics and state that infinity equals zero.
This is just plain bad philosophy, as pointed out by philosopher Wes Morrison:
“No one would suppose that it follows from the fact that there can be no round squares, that “round square” is synonymous with “nothing.” But neither should anyone suppose it follows from the fact (assuming it is a fact) that there can be no infinitely dense objects, that “infinite density” is synonymous with “nothing.” 
Still, the problem seems to get worse for apologists trying this argument, because on some reflection it seems they’d have to deny the transitive property of equality (that if a=b, then b=a). Because if an apologist holds that no “actual infinite” can exist, and also states that something with “infinite density” is synonymous with “nothing”, then they cannot claim that we had a creation out of nothing (ex nihilo). This is because if there actually was a state of “nothing” then by the apologists own definition, it is the same as an actual infinite existing.
The Borde, Guth, Vilenkin Theorem
The second piece of scientific evidence cited to support premise two of the KCA is a paper written in 2003 by cosmologists Arvind Borde, Alan Guth, and Alexander Vilenkin. Without getting too technical, it was mathematically proven that for any constantly expanding space-time universe, that universe is geodesically incomplete into the past.
In basic terms, this means that any space-time universe cannot have “always been expanding”, and one thing we know from modern cosmology is that our space-time universe is expanding, like an inflating balloon. This means that the space-time universe that we live in right now has not always existed in its present form, which was a scientific assumption for much of the 19th and 20th centuries.
What makes this theorem so powerful is that it requires only a very basic assumption: that the space-time in question is expanding. This means that it would apply to any theoretical “multiverse” (a collection of space-time universes of which ours is just one) that was expanding, or to a large number of theoretical cosmological models of our own universe.
Why the Borde, Guth, Vilenkin Theorem does not support the Kalam
The most important thing to realize from the Borde, Guth, Vilenkin theorem is that all it states about the universe is that the inflation, or expansion of the space-time universe cannot have been happening infinitely into the past.
This is not to belittle the theory, because it is extraordinary and has had significant impacts on modern cosmology. However, apologists like William Lane Craig make entirely too many metaphysical leaps off of this theory, specifically using it as evidence that all of matter and energy of our physical universe “began to exist” when the theory provides no justification for such a claim.
To illustrate what the theorem does and does not prove, consider the idea that our space-time universe was actually oscillating, with trillions of years expanding, followed by trillions of years collapsing, and then repeating the cycle for infinity. Such a model of the universe would still be compatible with the BGV theorem, as there was always a point where the universe would have a start time of expanding. It needs to be stated that at the time of this writing there is no evidence to think that such an “oscillating universe model” is the case for our space-time universe. This is merely an example of what the BVG theorem does and does not prove.
There is nothing in the Borde, Guth, Vilenkin theorem that shows that all matter and energy must have been created at some point in the finite past. It does imply that our space-time universe did not always exist in the fashion it does now, and that it evolved into its current form of existence a finite time ago, however this is very much distinct from having the matter and energy that make up our universe “pop into existence out of nothing”.
This most certainly does not imply that we need to invoke a god in order to explain what happened when our space-time universe came into being.
What modern science actually says about the origins of the universe
None of these scientists cited here believe in the personal creator god of the apologists that twist the meaning of their theorem. These scientists are working on one of the most promising models for the beginning of our space-time universe: the expansion of the space-time universe from a quantum nucleation event.
For the scientific and philosophical discussions of this paper quantum nucleation means effectively this: Our four dimensional space-time didn’t always exist, however the energy that makes it up has always existed, specifically at the quantum level. It can be shown mathematically that our space-time universe possibly evolved out of a quantum nucleation event that occurred in this energy 13.7 billion years ago.
The details of quantum nucleation are extremely complex, and any description of it even in laymen terms would go well beyond the scope of this paper. For a good popular level explanation of the theory, I recommend reading “A Universe from Nothing: Why There is Something Rather than Nothing” by Lawrence Krauss.  If you are not up for reading a book on the subject, then I suggest spending an hour to watch a free YouTube lecture on the topic by Lawrence Krauss. 
Suffice it to say, this theory of the origin of our space-time universe does not require a deity to get off the ground. In the interests of honesty it should be pointed out that this theory does not disprove the existence of a god, it merely makes the existence of one unnecessary to explain the origins of the universe. Further, it should be pointed out that there are other theories for the origin of the universe besides the quantum nucleation theory that are compatible with the BVG theorem and other evidence, however much like the god theory, this is all still theoretical.
Philosophical and explanatory advantages of Quantum Nucleation
The theistic account of creation presented by the Kalam is based on providing an efficient cause for the universe, specifically avoiding any notion of a material cause in its account. It should be noted that the quantum nucleation theory provides both an efficient (the laws of quantum mechanics) and material cause (the quantum energy itself) for the explanation of the universe. This means that the quantum nucleation theory, or any other scientific theory that assumes something natural has always existed, has more explanatory power than the theistic theory.
The honest answer about the origin of the universe
The most honest answer about the origin of the universe is quite simply that “we do not yet know”. It is quite possible that we may never know. Currently, there are too many parts of physics that have yet to be resolved, most crucially quantum gravity, for us to be able to accurately model what happened before the Big Bang. Though we are rather certain that there was no singularity involved in whatever did occur.
What we have are two different types of theories that speculate about what happened, and a level of probability associated with each theory. There is the theistic theory of divine creation supported by the Kalam, and a scientific explanation that assumes a natural process created the universe (in this case, quantum nucleation).
Both types of theories rest on the assumption that something exists as a necessary or brute fact. For the theistic account, god exists in this fashion. For the atheist’s scientific explanation, the energy that makes up the space-time universe exists in this fashion.
On the surface, this may seem like an even match in terms of the assumptions each theory makes, but the advantage lies with the scientific explanation:
There is a wealth of objective, verifiable evidence that the universe and quantum mechanics actually exists. We also have mathematical models and experimental evidence confirming or at least supporting that it is at least possible for the universe to have evolved this way. We also have the first law of thermodynamics indicating that matter and energy can never be created or destroyed, heavily implying that some form of energy that makes up the matter and fabric of space-time has always existed.
On the theistic side, we currently have no objectively verifiable evidence for the existence of any deity. Further, there is no reason to think that the god implied by the Kalam is a necessary being that must exist. This is why philosophers such as Immanuel Kant stated that any Cosmological Argument is really just the Ontological Argument in disguise.References
1.) This point comes from an excellent video debunking the Kalam Cosmological Argument, made by YouTube user “skydivephil”. It can be accessed here: http://www.youtube.com/watch?v=baZUCc5m8sE
2.) “The Existence of God and the Beginning of the Universe”, by William Lane Craig http://www.leaderu.com/truth/3truth11.html
3.) "Creation ex Nihilo and the Big Bang", by Wes Morriston
4.) “A Universe from Nothing: Why There is Something Rather than Nothing”, by Lawrence Krauss. Available Here
5.) Lecture: “A Universe from Nothing”, by Lawrence Krauss.