Generic structure of a PhD thesis in neuroscience (and perhaps mathemathical and natural sciences in general)

If you are wondering how your PhD thesis should be structured, here is a 

line of thoughts that helped me building mine and that is helping me right now 

in writing the content of the different parts.

Just think of a poster presentation in an important meeting. You are 

standing  there, a bunch of visitors with different backgrounds show-up at your poster asking you to present your work.

Professor - Hi, I'm Prof. X. I heard you just obtained your PhD degree. 

Congratulations! Now tell me what you have done.

You - Hello Sir, I'm <name>, I work in <institute>, with <name> and 

<name>. My work has been to develop a model of <something> to explain <evidences> and 

Give hints about <other problems>. We used <method> and tried <other thing>, 

and we found that <best> is the best way to do it.

Other professor - Oh wow! Interesting, I worked on the exact same field! 

Why did you choose this problem?

Y - Because <this and that>.

O - But isn't this useless?

Y - No because if you look at <fact> you might wonder whether it has a

relationship with <other fact> and this work might help understanding this

issue.

O - I see. But I heard <people> solving <similar problem> with <methods 

Different  from your>. Isn't also Michael <last name> in <lab in the US> doing the 

same?

Y - True, we might have tried that, but their method doesn't fullfill <some

requirement> and can't explain <some cool aspect>.

As you have seen, we just went through our Titlepage (introducing yourself 

And your institution), the abstract (a short, sounding summary) and the 

Introduction. The content of the Introduction chapter is needed to justify your work and identify it in light of other labs' research. As you see, it's not a summary of what you have done.

P - Ok, we got it, so how did you solve <problem> and what is your model

about?

Y - Ok, here is what I have done. First I developed <tools> by using <some

software> to interface to <some hardware>. Then I...

P - Wait a sec! Wouldn't it been easier to just use <this>?

Y - No for <this and that reason>. This new tool can be used also for 

<this and that>.

P - Alright, go on.

As you see, in the Methods you should always provide a little discussion 

for each of the important aspects of your research. We will skip the other 

parts of the thesis because I think you got the point.

Y - That's it!

P - Ok, interesting! We got the story. And... so what?

Y - Well, first of all our work shows that while <this> has revealed to be

true, <that> has revealed unimportant and <this other> is not true. It's 

like <analogy>, right? That's why probably the work of <authors> I told you in 

the beginning didn't lead to <some result>. Isn't this exciting?

Annoying professor - Oh, right, and would your model work in <other 

condition>?

Y - Well.. We tried something similar. we tried doing <this>, which we 

didn't put in the results, and the preliminary results suggest that it <does/doesnt> 

work.

A tall professor - If it does, will it be better than my model?

Y - Certain <yes/no>... We compared <this measure> with your model and the 

result <is/is not> in favor of our model.

Kind professor - Cool, so what do you think, is it better to follow now 

<this line of research> or <this other>?

Y - From my experience, both have interesting aspects...

This is the Discussion. It's a... discussion. People want to understand 

what's the benefit of your research, what are the insights they can gain on the 

field  from your research.

P - Ok guys, I have to catch a train soon, so now please summarize your 

work so I can remember you in the future.

Y - Alright. The field is <field>. The main issue of existing models is

<issue>. We thought "Well, why don't we <action> in <this way>". The 

Results are <results>. In the future it would be interesting to go in <some 

direction> to improve <aspect>.

And here we go, our Conclusion chapter is done! But before leaving the 

meeting, we need the most important chapter: Acknowledgments. Let's say the poster

session is over. You meet a friend and he proposes to have a drink.

Your friend - Do you want a drink? Let's leave this boring room and have a

drink on the balcony.

Y - Alright!

Your friend - So, how do you feel now that is over?

Y - Relieved but also excited, there is a lot to do!

Your friend - What do you think was the best part of your stay in

<institution>?

Y - Well I think <person> and <colleague> have been very important for all 

the drinks and stuff. The fun I had doing <this funny activity> helped me in

releasing  the tension. But also the inspirational conversations I had with

<friend> and <professor> have been very important for this work. It's been

difficult to always deal with my <girl/boy>friend and explain her that 

playing <sport> once a week is not wasting time for the thesis but it is a way to

improve productivity on the coming week. In conclusion, I think I should be

thankful to my family.

Friend - ...why??

Y - I don't know, but this is how acknowledgments always end.

- F. Stefanini