When one ask of certain questions relating to the origin of matter, energy or intervening space of the early universe, or to its organization or distribution, one is appealing to a highly specialized branch of physics called cosmogony.  It may very well be that such questions, while arising from common sense and everyday experience, are too simplistic and may be unsuitable and inappropriate for understanding the origin of the universe.

In his famous equation E=mc2, Albert Einstein demonstrated that matter and energy are equivalent and interchangeable, and that neither is capable of being destroyed or created, that they only change form.  This powerful discovery of the real nature of matter/energy led to the development of atomic energy (and weapons).

But we as non-physicists have a very difficult time grasping the concepts of particle physics, general relativity, and, especially, quantum mechanics-- incredibly complex subjects that are necessary for understanding cosmogony.  The mathematics needed to perform the calculations are far beyond what most people are familiar with, and require at least a dozen years of higher education.  According to cosmologist Timothy Ferris, resolving the origin of the universe entails a shift "from a classical [relativistic] to a quantum paradigm."  He goes on to say: "Living in a macroscopic world where quantum phenomena are rarely manifest, we humans came upon classical physics first, and tend to think of quantum physics as a special case.  Nevertheless it's beginning to look like the universe is fundamentally a quantum system."

There are at least three paradoxes associated with the beginning of the universe.

1) First Cause, which states that there can be no effect without a cause.  Each event must have been caused by some prior event.

This completely logical sounding argument, which fully agrees with everyday experience, was the basis of Thomas Aquinas's "cosmological proof" of the existence of God.  But today we understand the nature of causation a little differently than in the 13th century.

Timothy Ferris, in his book "The Whole Shebang: a State of the Universe Report", says: "The doctrine of causation erodes considerably when applied to the subatomic realm of quantum physics, and therefore seems a dubious tool for understanding the early universe, when virtually all particles were subatomic.  (To construct even an atom in the big bang would have been like building a house of cards in a firestorm.)"

Strict causation, (if A then B), is not a concept applied in quantum mechanics (there is a 50% chance of A, and therefore a 50% of B), where the probabilities are said to be inherent in nature and not merely a reflection of our limited knowledge.

"Strictly speaking there seems to be, for instance, no such thing as a "cause" of the radioactive decay of a radium atom.... Similarly, there is in quantum mechanics no such thing as a strict cause of a particular vacuum fluctuation, such as the fluctuation that some versions of inflation theory postulate as the agency of creation... So strict causation may break down both in quantum physics and in considering the origin of the universe.  Possibly this is not a coincidence, but a clue that the quantum principle holds the key to understanding genesis."

2) Getting Something from Nothing, which states that you can't create the universe out of nothing, and therefore there can be no logical explanation of the genesis of the universe.

Again, appealing to our common sense and experience, we find this to be the case in the everyday world.  But why should our notions of the everyday world be applied to the world of high energy subatomic particles?

The whole argument of "you can't get something from nothing" is a plain English statement of the law of conservation of energy- that a zero-energy system to which no energy is added must remain in a zero-energy state.  This would apply to the universe if indeed it has an energy content of zero.  As the physicist Edward Tryon proposed, gravitation is a purely attractive force and so should be entered into the negative side of the total energy ledger.  When it is calculated against all the matter and energy in the universe, the result, remarkably, is zero.   If these observations are correct, then the origin of the universe is not a matter of getting something from nothing, but of getting one zero-energy system from another zero-energy system.

There is a quantum mechanism called tunneling that could have generated the universe from a zero-energy balloon from a preexisting space.  In noted cosmologist Andre Linde's theory of inflation, he proposes quantum tunneling, as does Alexander Vilenkin of Tufts University.

Quantum mechanics permits genesis through the tunneling concept of many sorts of zero-energy ballooning universes, and can resolve the something-from-nothing paradox.

3) Infinite Regress, which states that regardless of the energy, the universe must have originated from another system, and it must have likewise originated in an earlier system, and so on; we are caught in an infinite regress.

There are two types of infinite regress.

The first is temporal, (time) based on the assumption that time is infinitely divisible.  In this case, scientists might propose theory after theory, getting closer and closer to the moment of generation, but never quite reach it.

But quantum physics suggest that time is not infinitely divisible.

"If the very early universe- during the Planck epoch- comprised a quantum space-time foam, then time as well as space was fragmented.  In these conditions there was no "arrow of time," so it would be meaningless to talk of something as having come "before."  Hence no problem of infinite temporal regress arises."

The second is logical regress.

"The problem of logical regress is more robust.  Certainly it is very difficult to imagine a theory in which the universe originates out of absolutely nothing... As we have seen, some versions of inflation theory postulate cosmic expansion as having arisen from a chaotic array of scalar fields, but one may always ask where the chaotic fields came from.  String theory makes everything from ten-dimensional space- but what selected that particular geometry for primordial space?  Either [the fundamental constants of nature] are inevitable, like the statement 1+1=2, or they are the random result of phase transitions or other chance occurrences... So there's potential regress either way.

"Ultimately, logical regress may turn out to be a bedrock paradox, but it's just too soon to say.  In any event, progress would be made if science were to demonstrate that the universe emerged from some quite different state, regardless of whether future generations were able to explain that state's origin.  The big bang is itself a theory of that kind.  It depicts our universe as having emerged from a quantum state, the particulars of which may be investigated experimentally.  It remains to be seen whether such investigations will lead to a new scientific paradigm capable of resolving the paradox of logical regress."

There are two kinds of physics available for us to choose from- classical and quantum, and classical physics, as Alex Vilenkin points out, "fails to describe the beginning of the universe."  The three paradoxes detailed above compel us to use the quantum approach.  Quantum mechanics is not something humans made up to explain away difficult problems.  It is the way the universe works.  It is why, for example, we have television sets.

The problem is that we, as human beings, gain comfort from the idea of "concrete" knowledge- knowing something in absolute terms.  Questions such as "Where did all the matter/energy/space for the universe come from?" reflect that craving for absolute knowledge.  The bible, and creationism, seem to satisfy this longing.

But if you begin your quest for origins and truth with the outcome already firmly (and irrevocably) established, then you have painted yourself into a philosophical corner.  As someone once said:

When the evidence conflicts with the theory, the scientist rejects the theory.  The theologian rejects the evidence.

Or, as I say:

Science deals with questions that may never be answered.
Religion is based on answers that may never be questioned.

Science is a search for truth that does not assume its own infallability, and as such, yields the purest results, and in the end is the only real method for discovering empirical truths.

Truth is the degree with which a thing corresponds to reality.

Reality is limited to that which is directly perceptible through our physical senses and scientific instruments or indirectly ascertained through the proper use reason.  (If you disagree with this statement, please prove an instance of an empirical reality that is imperceptible).

Reason is a tool of critical thought that limits the truth of a statement according to the strict tests of the scientific method.

The Scientific Method states that for a statement to be considered true, it must be testable (what evidence or repeatable experiments confirm it?), falsifiable (what, in theory, would disprove it, and have all attempts to disprove it failed?)  parsimonious (is it the simplest explanation, requiring the fewest assumptions?), and logical (free of contradictions and non sequitors).

Scientific knowledge is tentative.  Many people have a problem with that.  Others do not, realizing that as our observations, technology and calculations improve, our understanding of the universe comes into sharper focus.  Science is the best tool we have.  We, as a species, have only just begun to explore the origin of the universe, and it is unrealistic to expect such deep mysteries to be solved in a few short decades.

The world's most famous cosmologist, Professor Stephen Hawking, speaking at a 1983 General Relativity conference in Padua Italy, stated:

"Today I want to make a proposal for the quantum state of the universe... This proposal incorporates the idea that the universe is completely self-contained, and that there is nothing outside the universe.  In a way, you could say that the boundary conditions of the universe are that there is no boundary."

In his film, "A Brief History of Time", Hawking says:
"So long as the universe had a beginning, we could suppose it had a creator.  But if the universe is completely self-contained, having no boundary or edge, it would neither be created nor destroyed… it would simply be.  What place, then, for a creator?"

In his book "Black Holes & Baby Universes", he writes:
"One does not have to appeal to God to set the initial conditions for the creation of the universe, but if one does He would have to act through the laws of physics."

Albert Einstein (1879-1955) had this to say:

“I do not believe in the immortality of the individual, and I consider ethics to be an exclusively human concern with no supernatural human authority behind it.”

"A man’s ethical behavior should be based effectually on sympathy, education, and social ties; no religious basis is necessary. Man would indeed be in a poor way if he had to be restrained by fear of punishment and hope of reward after death."

“No idea is divinely inspired.”

If you are seriously interested in pursuing cosmology, you might start your quest here.