In this case it's not about the order of the words, but your interpretation of the meaning of "alone." Read the headline as it is, a news headline (rather than a scientific conclusion), and it might make more sense.
The meaning of sentences is also influenced by the space of what they might possibly mean. While you're correct that the headline, interpreted according to the normal rules of English, implies that nothing other than physical force can affect gene expression, this interpretation is easily ruled out by the fact that it's impossible. It's not a long stretch to the intended meaning.