The article conflates two very different types of science. One is experimental: cigarettes cause cancer. That's a testable, provable (and proven) hypothesis. The scientific method can be used. Alternate explanations can be systematically disproven.
Then there's the science that says, "because X and Y are true, it makes sense that Z is true". Note that it does NOT say "therefore Z MUST be true", which is what the article is implying. Z is something like the story of the universe from Big Bang through inflation up to today, or the story of manmade global warming. "Science" can project itself in those directions and come up with some answers, but there is no scientific method on a narrative. There are no controlled experiments. Every alternate hypothesis cannot be evaluated. They are at best projections, models. They're not "truth" without faith.