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This question was formulated after there was an extensive amount of commenting on the following question:

How can action potentials be generated through thoughts?

Basically what happened was that the question was kind of vague and nearly all sub-questions were duplicates of existing questions. However, after extensive commenting with the PO it actually matured into an excellent question (from my point of view at least).

Anyway, what I did was deleting most of the comments on my end, leaving a few key comments in place that more or less contained the most important comments. However, a set of answers of the PO to my comments were still left in place. These comments on my comments were therefore also obsolte, as they basically answered a question that was deleted.

I decided to do remove my obsolete questions based on my previous question on Meta: what to do with obsolete comments

However, @CRags later commented to me that I perhaps should have flagged the PO's questions for being obsolete, as they make no sense with the deleted corresponding question-comments from my side. However, my reasoning is that folks (PO in this case) should be aware of their commenting and remove them themselves.

So my question boils down to:

After deleting my own obsolete comments, should I flag obsolete comments from others (e.g. PO), thereby promoting a clean Bio.SE but placing burden on the moderators?"

On a side note: somehow all of the comments were deleted in the end -- Was this moderator's work?!

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If comments are obsolete, just flag them. You don't need to worry about moderator workload on a site as small as this.

I saw the flags and removed most of the comments. This specific question would also have attracted moderator attention anyway as it was automatically flagged for having more than 20 comments in a short time.

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