I think you have a misconception of science. Scientific Inquiry is a process grounded in reason where by contributions of many we eliminate bias and come to a conclusion that is good enough for action. Though this, we accumulate and build upon concrete knowledge laid down by previous luminaries...
I use Scrivener to write my manuscript and Scrivener + OneNote to store my notes & scribbles. (names have been expunged.)
My notes are divided between : Manuscript, Outline, Trivia; Characters, Organizations, Laws, Bestiary, Timeline, Locations.
I read your story and it's quite well written. The folk & fairy tale style of narration was quite enjoyable to read. As for what you've said about Pullman, I am on hiatus with his book 'On Stories and Storytelling' but I think I've come across what you've mention. I don't agree with his theory...
Screenwriting 101: Mastering the Art of Story
WonderWorks: The 25 Most Powerful Inventions in the History of Literature
The Elements of Style by William Strunk
Even if there is no ultimate purpose to the cosmos, that doesn't actually invalidate any of our human pursuits. It's the wrong way to think about it, because we don't tie our life's hope to something as abstract as the ultimate purpose of the cosmos. Our lives are ruled by smaller scale and...
Highly-incompetent enemies, because the trope doesn't have its intended effect on me: which is to make the mc appear highly skilled and proficient on one thing or the other.
And many more tropes too, but I don't think its the tropes that makes a story bad. If a story does nothing new or...