How does a scientist come up with the theory?

By reviewing extensive amounts of evidence that support a scientific explanation of phenomena. For example, Darwin's Theory of Evolution is supported because of the evidence and research of the finches in the galapagos islands that make sense in a scientific world that evolution does indeed exist.

Explanation:

the calvin cycle has three stages. in stage 1, the enzyme rubisco incorporates carbon dioxide into an organic molecule. in stage 2, the organic molecule is reduced. in stage 3, rubp, the molecule that starts the cycle, is regenerated so that the cycle can continue

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