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Today, I was shown this concept which further stoked my fires. A few simple rules and a simple building block can create vast complex variation. Maybe this all-pervasive god-particle has only a few rules... created by an intelligent designer?

Ah, old news . Several yaers ago this Wolfram guy mounted a nice PR campaign announcing his new book on Life, the Universe and Everything, claiming that it contained 42. It pretty much fizzled.

As for 'only a few rules', they are generally known as 'fundamental constants'. If things like light speed, Planck's constant, elemenatary charge, rest mass of elementary particles were a tiny bit different, we wouldn't be here. There are generally two school of thought about this: Someone made sure the Universe is compatible with and leads to evolution of intelligent life, or there are many (infinite number of) universes, and some of them are life-friendly (relatively speaking). Or Someone made sure there is an infinite number of universes, in which case He could just sit back and enjoy - life would be bound to appear somewhere. See Anthropic Principle. (BTW, accidentally making a brand new Universe in one's laboratory is a favorite topic for physicists turned SF authors.)

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Science ultimately boils down to faith. You have to believe that this deep science is actually true because it has gotten just to complex to handle.

You mean, can I personally verify that COBE indeed did corroborate Big Bang theory, and was not just a part of a complex conspiracy? Well, I can't...

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What if one of the equations is slightly wrong? Then every equation based on that is wrong. What if subatomic particles are actually shattered fragments of protons, neutrons, and electrons? What if gravity and magnetism are actually forces from higher order dimensions which are physically impossible for humans to observe?

I don't mean to chastise my own kind, but maybe the scientists are padding science to support their desired result: their faith in the existing equations and laws.

The good thing is, in science one doesn't get 'rich and famous' (OK, make it just famous) by upholding existing worldview, but tearing it down, or at least improving on it. There is no shortage of cosmological conjectures that avoid dark matter or dark energy you linked to (the one quite popular now draws from apparent anomaly in Pioneer spacecraft trayectory). The trouble is, none of them is rafined or corroborated enough as yet to be a simpler explanation for the observed universe than cludges we currently use.

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How arrogant are we, thinking that we have the capacity to _really_ understand what happened at the beginning of time?

Exactly! While I really hope humanity does figure EVERYthing out, I can't trust that they're right due to our limited observational ability. Maybe there really are the 26 dimensions suggested by string theory, but those higher order dimensions are likely just beyond our observational ability. Yes, awfully proud chains of carbon we are.

You don't have to go to cosmology to venture past intuitive understanding (take, for example, functioning of a tunneling diode or a Josephson junction). As Doug said, intuitive thought evolved to solve everyday problems of getting food and avoiding predators. To reach further, we had to invent things like mathematics. We describe and model the deeper, more exotic layers of reality using it, but I think nobody expect us to be able to visualize them (except as crude analogies, which often are obstacle, rather than aids, in understanding).
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