And that is exactly the problem with feedback online. Instead of assuming something is the way it is for a reason, people assume it is that way because the author, who spent who knows how much time thinking about things, was too selfish to cover my own particular need.
I think selfish is the right word for how people view it. If it was just incompetent, people would be more willing to help. But people take it personally, and that implies people see open hostility.
On the other hand, when competence in the author and humility in ourselves is assumed, the dialog is much more interesting and useful. Instead of just shredding the work, helpful language and reasons for the concern are used.
1. I have no idea if this is the author's actual thought process, but when I viewed the page, I immediately thought, "Wait, it makes sense for the video to be at the bottom. Anywhere else would be highly distracting to the article."
Is it really an either-or situation here? If it's not right for the video to be at top (which would go against a lot of other user-studies showing how important it is to have imagery leading the text, and how especially important it is to have assets close to where they are referred to in the text) then there should be a link. This is how the web was meant to work. If the readers end up clicking through (there's no reason you can't just have it anchor to the bottom instead of going externally) and never come back to the text, then that is an issue of the author not fulfilling his first rule of advice: "I like the first line to be funny right away" (replace "funny" with "compelling").
And you may be right, just because the author did it this way doesn't mean that he is "selfish". But it's hard to have any sympathy for him when he rips on someone for being ad hominem with an ad hominem attack.
(Also, it's worth pointing out that if the OP author had explicitly made the argument that it's good SEO practice to put the source material at the bottom and force the reader to discover it at the bottom, the OP would never have been upvoted to the front page. I don't think that's a design philosophy shared by many at HN)
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Having read your original post on HN, I noticed you didn't actually fix the problem that the rude user complains about. The rude user is definitely out of line, but are you really much better by just dismissing their point as simply "sheer mind-numbing stupidity"? Is the user wrong because he/she was an asshole or just wrong period? Because I think the user had a good point: you refer to an off-site video that you don't show until the very end, and you don't even link to the indepth NYT article that includes the video, which would be common courtesy for any SEO specialist.