Hi All,

A quick question for anyone who is writing up/has submitted, especially if you're from a science background - I've had a lot of problems with experiments failing and have spent a lot of time optimising assays before I could get any results. As a result, my supervisor has recommended that I write up my results chapters by explaining the optimisation stages followed by the final results.

So, the question - in my methods chapter, would it be better just to write up the final methods that were used for each assay? And then in each results chapter, explain how the assay conditions changed over time and final results etc.? It doesn't make sense to me to repeat all the optimisation bits in the methods chapter as well.

Apologies if this sounds like an obvious question. I've asked my supervisor for advice and he refuses to help, instead he tells me not to worry about writing up yet 'in case I make myself ill' even though I'm only 9 months away from my funding running out! (I have a long term health condition but that's another story...) Any advice on the writing up would be great, cheers!

Tulip

Hi Tulip,

I would say the last thing you should be worried about right now is your methods chapter. In my thesis, that was by far the shortest chapter and more to avoid repeating more straightforward bits in my experimental chapters, i.e. something to refer back to. It mostly contained detail about such things as sourcing and preparing tissue, and how I came up with a model against which I prepared much of my data later on.

If you've spent a lot of time fiddling with methods, then there's always a bit of a grey area between balancing methods and results within chapters. You could describe all the parameters used in the methods and then the results would describe how it panned out. That's probably the best way here. If you have chapters dedicated entirely to method optimisation, then your description of that process needs to be restricted to that chapter in my opinion. Then if you use the optimised/"perfected" method in a later chapter, refer back to that one.

I'm no fan of PhD supervisors: though I accept there are good and bad, most are far from good and mine was a dick-head. However though it sounds like yours has made some characteristically glib "supervisory" remarks to you re worrying about writing up - the sooner the better, surely? - I do tend to side with him here in "refusing to help", inasmuch as it really is up to you. It is YOUR thesis, and entirely YOUR intellectual property after completion. So in a sense, you will get more satisfaction out of having resolved the issue independently... as PhDs generally should. At your stage, my thoughts were tangled with worry about all manner of things. Have faith that you will iron all these things out as you go along, and you'll wonder why you were so concerned as you approach the end. It will come together. Promise.

Hi Tulip,

I usually write everything I 've done, at first as a very " honest" first draft, and then I let it cool down and come back to it formatting.

Since you ve done a lot of work on optimising the assays IMO it would be a waste not to write them down. Even if you only include them in the Appendix.

Try not to get stressed (which is what possibly worries your sup); my generic advice for writing up is "confident and in control of the process". What I experienced in my first draft was that it felt more like a primary school essay, than a scientific contribution. It is kind of normal that everything seems trivial after working on a project for 3-4 years day in day out.

Good luck

I think you should do what you suggested and put the final method in the 'methods' chapter and add the optimisation of it in your results.

The reason I think this is because 1) it seems logical and 2) if someone ever refers to your thesis for a method, they will look for it in the methods section and if there's lots of different methods in there for the same thing it will be confusing 3) optimising a method is a result

Hi guys,

Thank you for the comments.

SimonG - You're right, I have loads of other things to work on besides my methods chapter. I was hoping that by writing up some easier bits, I'd feel like I'm making progress. I need to write up as much as I can before September really (while finishing experiments, etc.). I appreciate that it probably is much better to sort these things out without the supervisor's input, it's just I'm at a point where it's hard to see that things will come together. Thank you for the support!

Dr Jeckyll - I probably should have rephrased - my supervisor isn't concerned that I'm stressed, I'm actually surprisingly calm. He has basically told me not to bother writing anything until my experiments are finished, by which time my funding will have run out. The big cynic in me reckons it's because he wants experiments done for a paper so doesn't want me 'wasting my time' on writing, but I could be wrong. But I will definitely take your advice and write up the optimisation stuff, the experiments were so time consuming that I would be a bit sad to have to leave it all out.

TreeofLife - Thanks, I agree with your reasons. I'll go with my original plan to include optimisation as part of the results chapters, it will save a lot of repetition too! How's your final year going? Hope everything is going well!

Cheers,
Tulip

Hey Tulip,

I'm slowly getting there. I'm waiting for a reply from my UK supervisors about whether they think the next stage of my research is a good idea or not. I think they are just really busy and don't have time to look at my suggestions in detail, which is understandable, but not helpful when I only have 9 months of funding left!

Hopefully they will reply soon... In the meantime I still have plenty of other things to keep me busy but they don't make me feel like any progress is being made!