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I believe the Theory of Evolution by Natural Selection is the best theory we have so far that explain the facts of similarities and differences between species when taking into account their environment, anatomy and genome.

A theory is not a fact, but an explanation of facts. For it to be a fact, it needs to go through the empirical scientific method; observation. Since evolution takes an incredible amount of time, we have yet to observe an species evolve before our own eyes. That said, the Theory of Evolution by Natural selection is probably the strongest theory there is thanks to the great amount of evidence that supports it. At this point, I think the only thing preventing it of being a fact is a technicality