It’s something we have to accept early on, or go mad. And a liberal arts education acts perfectly as an antidote to the madness.
In geology, we really have very limited information, in both time and space. In time, because most environments do not leave a geologic record of any kind, and those that do leave only detritus. Fossilization is an extremely rare event. In space, because we are limited to what we can see on the surface, or from the pin-pricks of drill holes, or the bounced shadows of geophysics.
Exploration and discovery are every bit as much an art as they are a science. We utilize a Multiple Working Hypotheses approach, encouraging new models that fit the data and provide predictive results.
Years ago I had mentor who wrote abstracts in iambic pentameter, applied Sun Tsu’s writings to the practice of discovering ore, and played the bagpipes in the desert. Me, I prefer artistic scientists and scientific artists. I’m sure you know who said, “Specialization is for insects.”
As far as the article goes: what a cry-baby. Just because you finish a doctorate in any field doesn't grant you a tenure position at a top notch University. (And, you'll note, the author does have a job at a University.) Back when I was working on my Master's degree I saw first-hand how difficult it was to get all the way to a tenured position. Nothing’s changed all that much except the author finally experienced it. I know brilliant geologists who fought through the post-doc swamp to find their way in the world, and that was decades ago. Very few get there. It's just math. One prof can crank out dozens of replacements, but only one will end up with the job.