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Over the last maybe 6 months or so (I haven't really been keeping track), I've noticed a number of questions either nominated for closure or actually closed with some variant of this custom close reason:

I'm voting to close this question as off-topic because it is based on a faulty presupposition.

sometimes with more info, sometimes not. Now, I haven't been following meta too closely lately, so I may have missed this discussion, but since when is this a valid close reason?

Science is based on presuppositions (we generally call them hypotheses), then attempting to provide an experimental basis for them, or disproving them. I go into an experiment with an idea in mind, then use the results to reevaluate my idea should they be different from what I expect.

I don't see anything wrong with someone asking a question based on faulty information (their own thinking, a conversation with a friend, a random website, whatever), as we can use the answers to show how their idea is incorrect, then provide data and references to show what the current state of the field is.

A recent example is here (I don't want to throw anyone under the bus, but I think a concrete example is necessary). A new user asked a question based on two incorrect assumptions - that a "neutral" allele should be present in 50% of the population, and that the condition being referred to doesn't have any negative selection pressures on it. Two answers were provided (one by me), the first one showing why a neutral polymorphism wouldn't necessarily be present in 50% of the population. The other one (mine) showed that the condition isn't really "neutral" at all, as there have been several medical conditions associated with the phenotype in question, one of which leads to infertility, which definitely would lead to negative selection.

Both answers helped address the OP's question, and showed why they were incorrect in their initial thinking. However, some time after both answers were posted, a user voted to close based on the "faulty presupposition" reason, and within nine hours, four other users agreed, and as of now the question is on hold. I have nominated the question for reopening, so we'll see where that goes, but in the meantime I would like to have a discussion on the merits of the faulty presupposition argument.

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    $\begingroup$ Agree. Also this is in my opinion not good for the overall atmosphere of Biology.SE. I mean, recently >80% of the incoming questions were going through a close vote for a reason or another. I agree some of them were poorly asked but I think we should also be a bit more laxist. Same applies to answers. Some recent ones were of bad quality indeed but a downvote should suffice. Flagging them for deletion seems a bit extreme in my opinion (+ we need more answers per questions anyway...). $\endgroup$ – cagliari2005 Apr 3 '15 at 17:28
  • $\begingroup$ The close reason for the question is that it isn't in the scope of bio. The faulty presumption was a comment. That is, the majority could have felt it isn't in the scope not it was faulty. I don't know but it may be helpful to ask the closers since they may provide insight to what case it is. $\endgroup$ – dustin Apr 3 '15 at 18:14
  • $\begingroup$ @dustin I assume you're talking about the example in my question. How exactly was that question not in our scope? $\endgroup$ – MattDMo Apr 3 '15 at 18:15
  • $\begingroup$ I didn't vote on the question, I just read the close reason and the comments so I don't know if the closers felt one way or the other. $\endgroup$ – dustin Apr 3 '15 at 18:16
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    $\begingroup$ @dustin When you vote to close for a custom reason, that reason appears as a comment, even though the banner that appears when the question is put on hold gives the generic "not in scope of Biology" statement. When someone agrees with that custom close reason and uses it for their closure vote, the comment gets upvoted. If all 4 subsequent close-voters agree with the initial reason, the comment should have 4 upvotes. It has 5 because someone else just upvoted it on their own, without voting to close. $\endgroup$ – MattDMo Apr 3 '15 at 18:20
  • $\begingroup$ @dustin The custom close reason appears in the comment thread when it was added - it's not moved to the top. $\endgroup$ – MattDMo Apr 3 '15 at 18:25
  • $\begingroup$ @dustin Generally. Most full sites have populated their off-topic close reasons with enough specific options that custom reasons are rarely used. But, I think that if a custom reason is used, it's just added to the comment thread, it doesn't appear in the on-hold banner $\endgroup$ – MattDMo Apr 3 '15 at 18:28
  • $\begingroup$ Okay, I will pay more attention next time as well so I can test the hypothesis. I shouldn't ask that question here since it might get closed as a faulty premise. Just a joke for levity. $\endgroup$ – dustin Apr 3 '15 at 18:31
  • $\begingroup$ This answer to a question about our custom close reasons is relevant to this discussion (I now see that you were also part of that exchange). $\endgroup$ – fileunderwater Apr 3 '15 at 23:09
  • $\begingroup$ I have previously also posted a question at Meta StackExchange which is relevant: Need for factual errors as a close reason?. $\endgroup$ – fileunderwater Apr 3 '15 at 23:15
  • $\begingroup$ I had previously posted a question and it was immediately closed. later i commented that people who cannot contribute to an answer should leave a question alone and not term it has off topic and close it. If you don't know the answer, don't comment, why would you close it.. Let someone else see it and comment. And it did happen with my question. Someone had the answer. Later they opened the question. But whatever, this shouldn't be the attitude... $\endgroup$ – girl101 Apr 6 '15 at 4:15
  • $\begingroup$ @MattDMo - Thanks for posting this question. It made me think, and I believe you're right. I'll not use it as a close reason again. I do still feel, though, that some questions based on faulty presuppositions should be closed. I'm pretty sure someone asking a question based on creationism would be closed very quickly. $\endgroup$ – anongoodnurse Apr 15 '15 at 6:29
  • $\begingroup$ @anongoodnurse I agree with your point about creationism/other mythology-based questions - here is a good Meta discussion on the topic. Such questions should be closed as Primarily Opinion-Based. $\endgroup$ – MattDMo Apr 15 '15 at 15:04
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I agree entirely. Oftentimes questions come from not understanding the material entirely, which often is related to faulty presumptions. The whole point of this site is to help people learn, and if someone asks a question with a faulty presumption, I think the correct thing to do would be to answer the question while addressing the faulty presumption so as to help the asker, and anyone else reading the question, learn. Basically, I think questions based on faulty presumptions are still valid questions, and indeed a good chunk of questions people have are based on faulty presumptions. If we outright removed all such questions, we would have far fewer questions left.

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