I have lost count of how many protocols I've seen, including those supposed to be professionally written (such as manuals that come with kits from well known brands, or methods sections of papers in respected journals), that outright fail to give unambiguous instructions. Some common examples are:

  • Give centrifuge speed in RPM instead of RCF, and not say what rotor or centrifuge it is.
  • Say to spin a sample at "maximum speed".
  • Use subjective time periods, e.g. "incubate briefly" (is one minute brief enough or does it have to be five seconds?)
  • Subjective quantities, such as "get a good amount of cells" (!!!)
  • Give time ranges without explaining the consequences of the choice, such as "5-10 minutes" (is it 5 or 10? which one???).
  • Say "mix well", without specifying if vortexing is okay.
  • Say "mix well, don't vortex", and don't explain what mixing technique I'm supposed to use.
  • Give urgent-sounding warnings, such as "don't touch the pellet!", without explaining what happens if I do it or how to fix it (do I need to start over? will I just get 5% lower yield?).
  • Give urgent-sounding warning, without explaining how to actually heed the warning ("dry the pellet, but do not over-dry it!")

It is in fact extremely rare that I ever see a protocol that has none of these issues. It almost never happens.

It is extremely important that scientific results be reproducible, and it seems like you are opening yourself up to a lot of trouble with an ambiguous protocol. What if somebody fails to reproduce your results, not because your experiment wasn't legitimate, but simply because you left out some crucial detail from the protocol you gave them? You would look bad, and for no good reason.

So why is it so common for protocols to be ambiguous? Is there some nuance to this that escapes me, or do people just not care? How do you follow a protocol that left out crucial information so as to be impossible to follow? Or are you supposed to have amassed a sufficiently vast reservoir of practical knowledge that you can draw on it to "fill in the blanks" on the fly?

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    $\begingroup$ As a counter argument to the hold: I am specifically interested in the personal experiences of researcher who have encountered this problem far more often than I have (perhaps I have failed to communicate this adequately). I am hoping that these anecdotes will be useful to me, and other novice experimentalists like me. As such, I think it can qualify (perhaps with some revisions) as a good subjective question. $\endgroup$ – Superbest Dec 8 '14 at 15:45
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    $\begingroup$ I agree. This is more a meta question for biology research, so I don't think it's completely off-topic. $\endgroup$ – Karolas Dec 11 '14 at 10:55
  • $\begingroup$ @Karolas Incidentally, the "boring lab questions" have always been a bit of an unclear case as to whether they fit. I believe a Meta discussion concluded that it's best to include them here, as opposed to say Academia@SE or a separate SE site. That said, the hold appears to be not for topicality, but subjectivity (and to be honest I don't understand how it's opinion based, but that's another matter). $\endgroup$ – Superbest Dec 11 '14 at 18:23

This is too long for a comment, so I post my thoughts about this here:

This falls into different important parts here: One is an insufficient understanding of the techniques on which the method is based. This makes it hard to decide which steps are important and which are not. One prominent example would be the use of EDTA in DNA gel running buffers. This recipe originated from RNA research (where you need the EDTA) which where then simply used for DNA as well. Since it worked somehow, it was never really changed.I have seen enough people in the lab clinging to old photocopies of protocols without knowing why they do certain steps.

And the other (connected) issue is that protocols are usually passed down through labs. Things are then done in a certain way because they have always done in this way (with some changes in the protocol probably not even documented) and are not changed. People are even told to use the exact routine, even if this makes absolutely no sense.

In publications there may also be another thing which comes into play: The fear that someone uses the own methods and will then be faster than the own group. At least some groups only publish incomplete and vague methods because of this reason. Then it's a thing of space: There are character limitations in publications and when you need to save a few hundred characters when the article is too long, it's much easier to shave the methods than the discussion.

  • $\begingroup$ Thanks, this a quite informative comment/answer. The EDTA example is a very good one that I had noticed myself. I'll wait for other answers, since the question is probably more useful as "What do you do if a protocol is vague?" rather than "What is the reason for protocols being vague?". $\endgroup$ – Superbest Dec 7 '14 at 23:46
  • $\begingroup$ @Superbest As I said, it's more like a comment, but too long for it. $\endgroup$ – Chris Dec 8 '14 at 6:41

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