Methods in Papers vs Protocol - Thinking aloud about the difficulty of using methods listed in papers (Jul/19/2008 )

Hi people,

I am a newbie to research. I have been tasked to read a couple of papers. Though all the papers have listed the methods they employed during the experiments, I find it hard to understand as they are not really explicit and do not spell out the steps sequentially. I mean I understand that they do not want to overload the paper with specific protocol but I am just wondering if it is possible for other researchers to replicate methods used in the paper just by reading them?

And in the event that I do not understand the methods they have listed in the paper, would it be appropriate for me to email them asking for their step-by-step protocol?

I am just confused over the norms in science over this issue. Please enlighten me. Thanks much.

Generally speaking, methods in Materials and Methods section should not be trusted. Some papers do write detailed and accurate methods, but many do not because probably authors think that this section is not critical to whether their paper can be accepted or not. As a result, the method section tends to be error-prone compared to other sections.

Sometimes you have the imagination that in papers one or another point is missing and/or wrong. Often the really important one, that makes the whole protocol work, and you've to investigate why you cannot repeat the experiment. Time consuming and annoying, but helps to keep the competitors at bay.

I look at the methods section only to be sure of what the authors have done and from where do they get their supplies (for example, I will trust antibodies from diverse vendors, but I usually frown if there is only one antibody and it comes from Santa Cruz).
Suggestions:
- Look it up in a book or in "Current Protocols"
- Posting here helps,
- Writing the corresponding author should help. If you do not get a reply, move a step higher: write the letter and forward it to your tutor, along with the full reference and email of the corresponding author. The point here is that the letter should be well written, so that it will just be forwarded.

good luck

I think most often the problem is that the published method, while accurate, doesn't adequately convey the effort involved. A sentence like "Colonies were screened, and a mutant was isolated..." doesn't say that it took them 15 tries before they found one. There's nothing nefarious in this; it's just they way it's done.