Actually, the way I see it, the intial article proves that the scientific method does work. Through reptition, and vigourous scritiny by peers, the conclusions of these studies did not hold up. Valid theories do stand up to vigourous repition, and close analysis.
Of course the scientific method is flawed, it's a human creation, but what it seeks do to illimate (or keep to the bare minium) bais, and skewing of data to favour the intial out come.
Reading the artical, I felt the author missed the point somehow. You cannot base your entire premise on one study (or even two).
The author forgets that by it's very nature the scientific method breaks things to smaller parts before it can fitted back together to create the bigger picture, and that the picture changes with addition of new data obtained from a slightly different angle.