Science published their 125th Aniversary Issue that listed a 125 big questions in science. Here's a selection of my thoughts on those.

What Is the Universe Made Of?

This article tells about the questions that scientists have about their observations of the cosmos. It mentions dark matter, dark energy, and how the universe is expanding at a faster and faster rate. Here's a quote I want to nitpick:

But even this mysterious entity pales by comparison to another mystery: dark energy. In the late 1990s, scientists examining distant supernovae discovered that the universe is expanding faster and faster, instead of slowing down as the laws of physics would imply. Is there some sort of antigravity force blowing the universe up?

My answer is no. If you take the right point of view you imagine that galaxies are getting smaller relative to each other. I haven't really worked it out mathematically, but this is how I picture it. The math would rest on the fact that the projected size of something is inversely proportional to how far away it is. So if something is moving away from you it will get smaller and smaller linearly. But if something is truely getting smaller, ie: shrinking, at a constant rate then it'll not only appear to be going farther and farther away but it'll do so at a non-linear rate.

That could all be demonstrated with a computer simulation, and I suspect it'll be correct. The question then remains whether that matches up with observations such as red-shift, the rotation of galaxies, and everything else I haven't researched.

This is a radical idea and hopefully avoids such answers as dark energy.

What Is the Biological Basis of Consciousness?

The quote from this one is:

Experiments under way at present generally address only pieces of the consciousness puzzle, and very few directly address the most enigmatic aspect of the conscious human mind: the sense of self. Yet the experimental work has begun, and if the results don't provide a blinding insight into how consciousness arises from tangles of neurons, they should at least refine the next round of questions.

Ultimately, scientists would like to understand not just the biological basis of consciousness but also why it exists. What selection pressure led to its development, and how many of our fellow creatures share it?

I think all of these questions have been addressed by Gerald Edelman, and he's either right or on the right track. Read some of his books and think about it. For a very basic introduction read Wider Than the Sky, but his best writing on the subject is A Universe of Consciousness.

So don't try to answer the question of "what is the basis for consciousness?". Just try to understand the answer.

How Did Cooperative Behavior Evolve?

Simply put: sex.

My basis is that you're out in the wild without much company. When you see two hairless arms wailing about in the water you're hoping for a beautiful young lady so you dive in. Maybe you hoped right and got laid, but even if you hoped wrong you could still get something out of it. Remember, you were pretty lonely.

On a non-human level though this probably is the reason. Give a few evolutionary iterations, I suspect this will eventually become the meme to cooperate, but it all originated from an entity's desire to at least survive and hopefully to have glorious sex.

Do Deeper Principles Underlie Quantum Uncertainty and Nonlocality?

My quote from this one is: "Some physicists in the second group are busy trying to design experiments that can get to the heart of the weirdness of quantum theory. They are slowly testing what causes quantum superpositions to 'collapse'."

That only shows that people need to stop overthinking quantum mechanics. No the atom cannot be on both the left and right side of the box. It can only be on one. Quantum mechanics only says that YOU DON'T KNOW and have to find out by taking a peek.

It's mathematics from the real world for the real world, get over it.