if the government tries to tell companies what to research, they'll do a half-assed job.
the only way is if the companies are driven by consumers, and therefore profits, to find new energy solutions.
it's difficult, because we can't all just boycot gasoline, or heating fuel, or electricity made from coal.
we need these things to conduct our lives,
and the companies know that in the end we will pay whatever we have to.

using gas as an example, it should be enough for the oil companies to realize that whoever develops the first universally usable fuel cell can control the next generation's energy needs.
instead they'll all wait until the world runs out of oil, some lab assistant working in a hut somewhere discovers the secret, and the world ends up ruled by Nepal (or someone to that effect)

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The government cant and shouldnt tell oil companies what to research or produce, its not their job. If people dont want to use oil anymore than someone should research themselves. Or if the oil companies see that people will buy something else they will start to make it. Energy costs go up and down, just like the economy, in the 70's gas was more expensive (with respect to inflation back then) then it is now. People used to have to line up at gas stations on their designated day during the wonderful carter administration.
Something new will come, till then we have to work with what we have. Drill some where else, and research new energy.

Let capitalism do it's job.

I agree that companies should decide what exactly to research, but I think government funding or tax policy to aid companies pursuing alternative energy can bolster the effect.

The problem with leaving it totally to the market is that you either end up with a patent... making it more difficult to spread and improve on the technology...
or you end up with a company spending resources on necessary technology, only to end up at market disadvantage when competitors take hold of the technology.

The government should allow the fast transfer and diffusion of this technology without giving a market disadvantage to those companies that do all the work!

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"Man lives in the sunlit world of that which he believes to be reality. But unseen by most is an underworld, a place that is just as real... but not as brightly lit... A DARK SIDE!"
-opening from Tales From the Darkside