Sometimes, but the example you gave makes perfect sense to me. Why would a NASA scientist waste their time with every crank (not saying Ben is a crank, I know nothing about his claims) they refuted? It would be like asking a car repairman to work on your airplane engine. Sure, it's related, but wouldn't it be better to submit to a journal who's livelihood and profession directly deal with reviewing scientific claims? That's what they do. That's the role of the editor.
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True.
In this particular case, the NASA scientist called out Ben and then refused to review his work.
Does that matter? The burden of proof is on those who are willing to go through scientific peer review. Sounds to me Ben was given good advice. If he thinks his work is above reproach, it should be easy to get published.
He tried to get it published. They told him he had to be peer reviewed first.
In the end he had to get peer reviewed outside of the established community and published that way. Not 6 months later, the established scientific community is releasing similar papers.
Peer review is not a separate thing, it occurs as a part of the submission process and is done by the journal you submit to. It is not done by the researcher. It is a tool for the editor to know whether other experts in the field can find scientific validity in the work. The editor then takes their recommendations into consideration, if the comments are too bad (and the article is hogwash) it's rejected. If the reviewers say ... Well maybe but I want to know "blah" then the reviews are sent back and the author gets a few months to respond, make changes and resubmit. Then the process repeats. Until the reviewers and editor are satisfied in the quality of the work.