Regarding the puddle analogy, there are certain situations where the "intelligent" water (puddle dwellers) would wonder about the hole they're in.
A) If the pond were in the shape of a regular jagged circle (i.e., crater-shaped), it would likely be chalked up to the outcome of one of many natural processes and very little thought would be given.
B) If they found they lived in a pond in the shape of, say, a hexagon, they would probably wonder a bit about that, and rightly so. Regular hexagons don't show up in nature a lot. When we found one on Saturn, it was pretty surprising. We still don't know what's causing it.
So the puddle dwellers would be surprised by the shape of their "universe" and want an explanation for it. It would be a "problem" in the sense that it would be an outstanding mystery that they would actively want a naturalistic explanation for. They would assume (as we assume for the Saturn Hexagon), that the hexagon is likely the result as some as-yet-not-understood natural phenomenon.
C) If they found they lived in a pond shaped like 2+2=4 (in their number system) they would find that extremely surprising. Coincidence would be unbelievable. The natural explanation for such a shape forming naturally is only one: a vast series of ponds, all with different shapes formed by a natural process (e.g., erosion, cratering). AND the pond shapes would have to differ. It would do no good for there to be a vast number of ponds, all shaped like 2+2=4.
Absent a vast ensemble of differently shaped ponds, the pond dwellers are going to assume their pond was created by design.
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The question for us is, what kind of pond do we find ourselves in? The cosmologists say it is
prima facia fine-tuned for the possibility of complex structures to arise (molecules, stars, galaxies, etc), and there is not much possibility of life arising without there being complex things like stars, molecules, or nothing but hydrogen atoms. Complexity is a necessary condition for life. Yet if you change the values of constants in the smallest ways, cosmologists tell us you get universes where the necessary conditions for life are absent.
At the very least, we seem to live in a (B) type pond, which creates a minor problem of "fine-tuning". The universe is surprising, but not catastrophically so for natural theories. Some natural explanation, as yet unknown (or unproven), could solve it, but an explanation is required, because we keep finding physical constants whose value seem finely-balanced for complexity.
I think the coincidence explanation went out the window with dark energy and dark matter, the utterly wrong prediction of the cosmological constant's value, and now the discovery of the Higgs Boson (which, surprise surprise, also appears extremely fined-tuned:
"
So, let’s take a birds-eye view of the whole equation. The mass of the Higgs is equal to the theoretical mass plus a monstrously large number multiplied by the fermion/boson sum. Unless the fermion/boson sum is practically zero, the observed mass of the Higgs boson should be huge.
The only way to escape this conclusion is to somehow balance the fermion/boson sum to be exceedingly small. And to have the balance so perfect is utterly unnatural, as if we added up all the monthly paychecks of everyone in the United States and subtracted their monthly bills and those two huge numbers canceled out neatly.
That doesn’t happen in bookkeeping, and it shouldn’t happen in physics, either; unless, that is, there is some new and as-yet-undiscovered physical principle that enforces it. Thus, the small mass of the Higgs boson all but ensures that there is new physics to be discovered. Otherwise, we have to “tune” the masses of these particles to very precise values. Such precise balancing is utterly unnatural in physics theories, leading theoretical physicists to propose a series of ways in which this cancellation could occur naturally.
http://www.pbs.org/wgbh/nova/blogs/physics/2013/02/why-is-the-higgs-so-light/
Absent coincidence, that leaves two options: an as-yet-undiscovered natural theory or a multiverse of universes where the values of the constants differ (the values of the constants would have to differ, otherwise we're in the same situation as the pond-dwellers looking at a vast number of ponds that all have the same hexagon shape (or worse, a 2+4=4 shape), which doesn't explain anything). Since the LHC, the best candidates for a natural explanation that would explain all these precise values (super-symmetry and string theory) took some hits, and with the BICEP2 findings, inflation gained a lot of ground.
Without a good natural theory, we're in a situation of the pond dwellers in (C): we appear to live in a universe that seems vastly improbable, yet one of the few universes where the values of the constants are just right for life. If this is an unnatural universe, the tension then is the probability of the existence of a cosmological fine-tuner + the probability that we might be living in a simulated universe (and the real universe doesn't have this fine-tuning problem) vs. the probability of the values of the constants just randomly being what they are (and cosmologists say the odds of a life-permitting universe arising by chance are extremely unlikely). The odds of the existence of a fine-tuner (or us living in a simulated universe) are simply unknown. Agnosticism trumps extremely unlikely every time.
In other words, if we find we're not in the right kind of multiverse, then either theism or simulation theory wins out.