I've said before that in the view of many, there are three profound questions that pose a fundamental challenge to scientific inference. I think that only two of them really count however.
The first I discussed last time. We've been able to deduce approximately when the universe came into existence and how it has evolved since. But it is not apparent what path of scientific inquiry could explain why that happened when it did (if "when" even means anything before there was time), and why it has the observed laws and physical parameters, To put the problem in an epistemological nutshell, the answer to these questions must lie outside the universe, and by definition the universe consists of what we can directly observe or deduce from observation. Again, saying "God did it" is the intellectual equivalent of saying "OogaBooga!" It's completely meaningless. Nevertheless this is frustrating.
Note that deep mysteries we just haven't solved yet, such as the nature of the Dark Matter and Dark Energy (if it exists, which has been called into question) are not in this category. They are answerable in principle, we just haven't done it yet.
The second hard question, and probably the hardest, is the nature and origin of consciousness. Something is going on inside our heads that no-one else can directly observe. We can only assume that other people experience something roughly like it, though certainly not exactly the same, but how do we really know that? Maybe everyone else in the world is a zombie. And how about dogs, lizards, fish and octopi and earthworms? How does the physical system of neurons give rise to this thing we call experience, which apparently exists outside the physical world and is as far as we can tell undetectable and immeasurable by any material means. We just have to take each other's word for it that we all have it. This is the one so far irreducible challenge to scientific materialism.
Many people have intuitive ideas about this, which I won't go into, but that's all they are. So far no way to test any of them.
The third question I do not personally consider to be in the hard category at all. That is the origin of life -- that is life on earth, which is the only place we know it to have happened so far. It happened so long ago that the evidence needed to figure out exactly how it happened is may just be lost, and no investigation, even with as yet undiscovered technology, will ever suffice to answer it. But in principle it's pretty simple. At some time from 3.6 to maybe 4.3 billion years ago, a molecule or assemblage of molecules happened to appear that could catalyze its own reproduction, but not always perfectly. That's all you need. It only had to happen once, and given the vastness of the oceans and the uncountable chemical entities that existed within them, it doesn't seem improbable, it seems inevitable.
Once that happened, quickly there were 2 of them and then 8 and 16 and soon enough 4,294,967,296 (minus however many fell apart along the way). At some point some of them were slightly different, because replication wasn't always perfect, and then you had various kinds of which some may have lasted longer and reproduced more often than others, and we were off to the evolutionary races. I personally don't consider this difficult to understand. We've had more than 3.6 billion years of the process and in that amount of time it has produced an extraordinary diversity of complicated products, each of which may seem improbable in and of themselves but the existence of which as a whole -- however different it might have been in the specific -- is inevitable. That it all derives from a single ancestor (known as the Last Common Ancestor, LCA) is evident because it all uses the same basic machinery of DNA, RNA, and amino acids. (DNA probably came along last.)
However unsatisfying it may seem, there is no need whatsoever for God in this story.
Update: If hundreds of people with many years each of hard-won expertise have spent their careers thinking about a difficult question, and you don't understand the answer they come up with, the most likely conclusion is not "they are really stupid because what they say doesn't make sense to me." The likely conclusion is that you need to work hard and study to try to understand them, and if you don't want to do that, go and argue about something else.
The basic molecular building blocks for life evidently existed in the oceans of early earth. Biochemists have a number of hypothesis about how the first self-replicating system may have arisen, although they can't prove any one of them. But none of their hypotheses consist of "yadda yadda," the actual meaning of which is "I'm not listening."
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Your post reminds me of my dear departed friend, Betty, who had (has) a son-in-law who's a philosophy professor in Iowa. About 25 years ago, she and I were talking and she mentioned that her grandson--about six years old at the time--had to tell his class, as did all the other kids, what his parents did for a living, or whether they were stay-at-home parents, etc. (my mother joked this could be referred to as "domestic supervisor").
Anyway, Colin gave a six-word description about what it is that philosophers do that is--to my mind--still the single-greatest definition of what his dad did, and what exactly it means to be a philosopher:
"He thinks hard about hard things."
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