I have great admiration for scientists and their work, and I understand the philosophy of their methods. I start with that preface since I will do a little bit of scientist bashing here, which is not the same as science bashing. Scientists, just like theologians, often need some correction. To help anyone reading this anticipate my biases (we all have them) I consider myself a believer in progressive creationism.
Theology often takes the easy way out by saying, “God does things in ways that we can’t understand, therefore we don’t need to explain x, y and z.” Atheism on the other hand often takes the easy way out by saying, “We don’t fully understand x and z, but we have mostly figured out y, so it is rational to assume that x and z will have a similar explanation.”
X in this case is the creation of life, which is so far not understood by scientists. They believe (I use that term intentionally) that if the chemical and other conditions are right, and that if enough time has passed, then life will usually or at least often begin after the correct random sequence of events has occurred. But what the required sequence of events are is not understood (“yet” is usually inserted here). So scientifically there is no way to make predictions on how often life is created, or if it even happened anywhere else in the Universe.
However while this fact is usually somewhat acknowledged, at least whenever the topic is publicly discussed, clearly a large number of scientists believe that life has been created elsewhere and extremely often. Evidenced by what seems to be the very surprised reaction within the scientific community to the fact that SETI attempts have been (insert “so far”) unsuccessful. Leading to the now predominant theories of reasons for this, such as they don’t want us to know about them, or they have evolved beyond using radio waves, etc. But less credence seems to be given to the idea that perhaps life, and especially intelligent life, is extremely rare, possibly occurring only in a small percentage of galaxies, or perhaps it doesn’t exist anywhere else at all. And yes many religious people believe this also, using the standard argument that God would not create this massive Universe, but then only put people on one tiny planet. Implying that creating the Universe caused God to break a sweat. And also calling into question the value of people, which I assume was not their intention.
Y is the evolution of life, which is partially explained by Darwin’s theory, although things like how DNA software began and developed to its current level, or how ants with microscopic brains developed the ability to work together in complex ways for the common good, are not (“yet”) understood. And yes I know that there is a semantics argument whether DNA is software, or can be considered computer code in the strictest definition. What I am referring to is the complexity of DNA and its dynamic ability to manage the creation and maintenance of complex biological mechanisms.
Z is the development of human intelligence, emotion, and self-awareness.
Of course x and y are often debated between the two sides, generally falling into the differing opinions on explaining the gaps. The answer to your question is that in the atheistic viewpoint each gap that is explained is further proof of the non-existence of God, or at least the non-existence of supernatural creation of any type. And as you suggested the idea that God is only allowed to use methods that cannot be scientifically explained.
However while they are less discussed, it is the explanation for those last two items of z, emotion and self-awareness, that is in my opinion at the heart (that word intentionally used also) of the difference between at least Judeo-Christian theology and atheism. Yes animals seem to have emotions also, and apparently apes have demonstrated some level of self-awareness. But it seems that humans have these attributes at a much higher level. Love, compassion, and morality are much harder to explain as being just another so far unexplained gap in the atheistic explanation, which is that we are just biological computers running human intelligence and emotion software version 3.21063E+12. In other words the view that our level of love, compassion, and morality, to the extent that it exists, simply comes from being licensed to use a premium version of the cooperation software suite that ants are running.
A straw man argument that is typically tossed up at this point is refuting the idea that only people who believe in God can have real morality. It is certainly true that many Christians, Jews, and I think I can include many Muslims feel this way. As exemplified by the late Jerry Falwell and his “Moral Majority” political organization. A type of thinking that clearly still exists today. But finding fault with Christians is taking the easy way out in the discussion. As is finding fault with atheists. And it leads to a separate topic that all Christians should think about, which is the fact that in the gospels Jesus was the hardest on the religious leaders who felt that they had the moral upper hand. In fact they were the only group that he exhibited what appeared to be no compassion for.
