As for the original article: There's no talk of inheritance or generations. So they're describing the same fish two years apart. If you were required to climb a ladder every day for your food, you'd have stronger arms and legs after two years and you would probably move more efficiently up that ladder. I saw no reference at all to DNA changes. As far as I can see, the point to doing the experiment was to demonstrate that changing environment can change physical structures without needing mutation to cause the change.