I'm not so sure. Gradient Descent refers to reaching the best solution available. Xkcd seems to be referring to more like the Bonferroni principle where you are looking for patterns without a hypothesis and post facto justifying it.
I'm guessing that, in the sciences, that is a big no-no. Imagine if doctors, seeing that a new drug being trialled is failing to cure a disease, simply started chucking out the sick subjects until all the ones that were left where healthy, declaring the sick ones to be "noise" and the trial a success. Somehow, I don't think that would fly...
Data manipulation is different from data transformation. Manipulation changes the nature of data, transformation does not change the nature of data. PCA is data transformation, not data manipulation.