When Edwin Hubble discovered that the universe is expanding, it gave strong scientific support that the universe had an ultimate beginning. This left atheists with the impossible task of explaining in natural terms how matter, energy, and the laws of physics came into existence out of nothing. Their options are to either deny cause and effect by saying the universe popped into existence without a cause, or engage in circular reasoning by saying the material universe had a material cause. Because both options are problematic, atheists usually avoid the challenge by responding in the following ways:

They change the subject. 

Some atheists avoid the problem by changing the subject and saying God is a worse explanation for the universe. This was the approach Dawkins took in his book 'The God Delusion', where he tried to affirm atheism by saying God is a less probable explanation. However, even if God is a bad explanation, the atheistic explanation is still circular. Changing the subject or attacking another person's position doesn't make the challenge go away. They must address this fundamental flaw in their logic before naturalism can be seriously considered. 

They shut down conversation. 

Some atheists avoid the problem by shutting down conversation. Stephen Hawking says it's meaningless to ask what happened before the Big Bang, while Dawkins says scientists are "working on it" and will come up with a natural explanation someday. In the meantime we're supposed to adopt their circular logic uncritically. However, even if they succeed in silencing opposition, it can't take away the problems built into their naturalistic presuppositions. Anyone seeking truth should be willing to have their deepest held beliefs challenged in order to identify weak points in their thinking. Open inquiry is vital for the effectiveness of both philosophy and science.

They redefine the word "nothing".

Some deal with the problem of a universe appearing out of nothing by redefining the word "nothing". Lawrence Krauss redefines it as empty space or a quantum vacuum. But these things cannot be called "nothing". All Krauss has done is changed the definition of a word and pushed the problem back another step. 

They invoke a multiverse. 

Some respond by imagining a hypothetical cluster of many universes. The thought is that if trillions of randomly generated universes exist with different sets of physics, then one of them is likely to be a fine-tuned life permitting universe. This explanation fails because it doesn't provide a universe creating mechanism and multiplies the problem by assuming trillions of unexplained universes just to explain the existence of one. We're still stuck with the problem of where energy, matter, and physics came from. All the multiverse does is push the problem back another step and make it infinitely more complex.

They tell a story.

Atheists often respond with hypothetical stories about life spontaneously arising from a primordial pond of amino acids. However, stories are not scientific evidence no matter how probable we think they are. The abiogenesis hypothesis can't be observed and has yet to be tested. Leading scientists are unable to create life in the lab even under ideal circumstances. This is powerful evidence against the idea that life can randomly arise without guidance.

They change the subject to avoid the challenge.

Atheists often avoid the question of life's origin by attacking God as a "less probable" explanation. Their argument is that God is such a ridiculous explanation, it makes abiogenesis credible by comparison. But even if we were to agree God is improbable, the idea of life spontaneously arising from matter remains irrational and unscientific. Attacking a "less probable" idea doesn't make the challenge go away.

They push the problem back another step.

Those who acknowledge the impossibility of life spontaneously arising from non-living matter, postulate a hypothesis known as Panspermia. It's the idea that microorganisms came to earth from a meteor or extraterrestrial and evolved. But this explanation simply pushes the problem back another step. The question of how life arose in the universe still remains regardless of which planet it came from.

They site the Miller-Urey experiment.

Most atheist authors and bloggers site the Miller-Urey experiment as evidence that life can spontaneously arise out of non-living matter. The fact that this experiment is so heavily relied upon reflects the poor state of evidence for abiogenesis. Miller's experiment was based on a speculative reconstruction of earth's early conditions and only resulted in the creation of simple amino acids. The experiment didn't even touch on how molecules might be able to organize themselves into living matter. Explaining how basic molecules could come about is much different than explaining how they became complex, organized, self replicating cells.