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Users with 3,500 rep (or 15,000 if when we get a site-design) can protect challenges. This makes it so that users who have not earned 10 rep on the site can not answer.

As a user with this privilege, I have no idea when it would be appropriate to use. This is because the idea of "protecting questions" makes perfect sense for a Q&A site with a popular question attracting non-answers or low-quality answers. But we're not a Q&A site! Nobody posts challenges here because they need help with a problem, only because they enjoy coming up with programming tasks and challenging other users to solve them. So pretty much all of the guidelines for when to protect don't make sense on our site. For example, the original announcement says:

So, in the future, if you see a question that is attracting a lot of drive-by noise answers, please flag it for moderator attention. We'll turn on protection.

But that never (or at least very rarely) happens here. I can find lots of old challenges that are protected, (1, 2, 3, 4, 5, etc.). But "drive-by noise" is not the problem. The "auto-protection" is being triggered by self-deletions.

So my question is pretty much when does it make sense to protect questions and prevent new-users from participating on these challenges, specifically in the context of our site? Should we un-protect challenges that were automatically protected by community? Does it ever make sense to protect a challenge that is not attracting low-quality "drive-by noise"?

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Other SE sites have questions that already got a satisfying answer, and new answers will likely be thank you posts or other kinds of noise. In these situation, protecting questions is the way to go. However, our challenges are never really over; protecting rarely ever makes sense on PPCG.

The challenges that usually wind up protected either manually or automatically have attracted a couple of bad answers, but this is usually because it's an entry level challenge that is appealing to newcomers. Protecting the challenge is the last thing we should do in this situation.

Should we un-protect challenges that were automatically protected by community?

I do that regularly. I've had to unprotect Is this number a prime? three times so far. If I hadn't done it, the creator of this answer (new user, hasn't written another post before or after that one) wouldn't have been able to post his stellar Hexagony primality tester which earned 90 upvotes and a juicy +500 bounty. Yes, this is a rare gem, but it surely was worth the 22 answers that had to be dealt with without protection.

Does it ever make sense to protect a challenge that is not attracting low-quality "drive-by noise"?

Protecting challenges should be done rarely. Longest common substring in linear time earned its protection for being insanely difficult and attracting 11 invalid answers without a single valid one. At least in my opinion, the five ones you linked to didn't.

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    \$\begingroup\$ I like this answer. I especially agree that it rarely makes sense to prevent new users from answering. However, there's one more detail I'd like to hear. Is it ever appropriate to protect? If not, should we systematically go through old challenges and un-protect them? \$\endgroup\$ – DJMcMayhem Oct 26 '16 at 3:25
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    \$\begingroup\$ Very rarely. This question earned its protection for being insanely difficult and attracting 11 invalid answers without a single valid one. At least in my opinion, the five ones you linked to didn't (although some answers to the first one really got on my nerves). \$\endgroup\$ – Dennis Oct 26 '16 at 3:37
  • \$\begingroup\$ I think that's worth adding into the answer - challenges that get way more invalid answers or non-answers than valid ones should probably be protected. That's what the system is made for, at least. Once the wave of invalid answers (likely coming from HNQ) slows down, then it can be unprotected. \$\endgroup\$ – Mego Oct 26 '16 at 5:16

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