I can see your frustration with this article. I think the point is that we need to come up with new methods to predict and learn from. Just like we came up with a system of linking cause and effect, we need to come up with a system that links multiple causes and effects easily.

Making the article relevant to this point, Pfizer spent tons of money developing a drug and bet it would work simply because (at the time) lowering HDL = better cholesterol. No one asked what does HDL do in the body? What does LDL do in the body? What depends on cholesterol?

It's kind of like when you come up with a really cool idea but forget to look at the target market to see if it's actually viable.