The EZ way to write a prospectus, thesis,

publishable paper

John M. Hoenig, Ph.D.

Department of Fisheries Science
The EZ Way to Write a Prospectus

All you need to do is

1) Define the problem
2) Say what youre going to do
3) Say what you need

4) Show youve reviewed the literature, but

only in context of 1, 2, & 3
11 - 15 pages, MAX!

(but check with your committee)

Can you believe its so simple?

Think of the purpose of the prospectus: your

committee wants to know
1) Do you understand the problem and its
complexities? Will your approach work? Are you
reinventing the wheel?
2) You have no business going in the lab or the
field if you dont know what youre going to do.
Are you familiar with the procedures?
3) Are you going to be able to get the data,
specimens, equipment youll need?
 What if you dont stick to the plan
in the prospectus?
Its an action plan, not a contract. Unforseeable
problems arise. Plans change. Get over it. Youll be
judged on whether you did good work, not on
whether you stuck to the plan.

Unforseeable problems happen. A good prospectus

has a back-up plan.

The prospectus is to help you. Done after the fact

its a waste of time. Do you want to waste your
committees time?
Writing a thesis or dissertation

chapter vs manuscript format

Writing a thesis or dissertation

Chapter format the old way to do it

Introduction (review of literature)

All Materials and Methods
All Results
All Discussion
Complete rewrite to publish this!
 Manuscript format the modern way
Short(er) Introduction (define the problem)
Manuscript 1 (in format for journal 1)
Introduction
Materials & Methods
Results & Discussion
Manuscript 2 (in format for journal 2)
Introduction
etc.
Concluding chapter (pull things together)
 Some things in the thesis wont go in the
published version (maybe put them in an
appendix)

Use this to your advantage: things you dont

want in the publication but that need
documenting can go in the thesis (e.g.,
negative results)
Example: youre interested in how growth of clams varies with
depth, temperature and salinity but you measure 15 other
environmental variables just to eliminate the possibility that theyre
influencing growth. None of the correlations are significant.
Including all of these data would take up a lot of space and be
tedious. So, put the results in your thesis or a technical report and
simply refer to it in your journal article.
So the secret to writing a thesis is to write
manuscripts. OK.

So whats the secret to writing manuscripts?

Cardinal Rule: Write the paper before you do
the research.

! ??? !!!!
 Write the Materials and Methods first.

Its easy.
And you need to know what to do (preferably
before you do it!)

(Hopefully, you can lift this from your prospectus)

 Next, write the Introduction

EZ Formula:
1) Whats the problem?
2) Why is it of interest?
3) How does your work contribute to an
understanding of the problem?

There are other ways to write the introduction but

the EZ formula works every time
Also write the Results section

! ??? !!!!
Make up plausible results
I might see this, or this, or maybe this

How are you going to graph the data?

How are you going to analyze the data?
How are you going to interpret the data?
Is it unethical to write the results before you do
the research?

No. Its good practice. You get to

- review your design
- think about assumptions
- anticipate problems
- plan your analysis
For the discussion section, just list points you
want to remember to discuss
After the research

Update everything
Insert results

Now, a major portion of your thesis is already

done. (This is important sitting down to write
a 100 page thesis is intimidating. Having it half
done makes it MUCH easier.)
Generally, its easier to combine results
& discussion into one section, and most
journals will let you do this.
The sphaghetti problem: sometimes the ideas are
all tangled up and its hard to find the start and
end of the story you want to discuss

make a list of the points you want to make, in any

order. Then try to put them in sequence. Then fill
in with more detail. Then make an outline, & keep
adding detail
If youre still having problems, say your
discussion instead of writing it. Do it again and
again until it stabilizes. Typically, the first time
itll take you 20 minutes to explain your findings,
the second time it will take 10 minutes, then 5.
Then write it down.
When youre too tired to think but still want to
make progress

Type up the bibliography, title page, etc.

(Its got to be done sometime).
Congratulations, you now have 8 of your 100
pages finished. Just 92 left to go
Common Errors (thought police)

Results occurring in introduction

Results in methods section
Methods in results section
 EZ Publishing
Pick a journal before you start writing, and type
manuscript (especially references) in the right style
from the start

NOTE: its i.e., e.g., (get it right the first time)

Generally, no more than 35 pages per manuscript

Figures & tables must be able to stand alone

 Submit papers as early as possible for publication.
Dont wait until youre about to defend.

If a paper is a done deal (i.e., in press) your

committee probably wont give you a hard time
about the paper (e.g., making you work on
organization, style, etc. After all, why bother if its
already in press.)
Its nice to get the ms back from the journal while
youre still at VIMS because it will be easier to
revise at home than in your new surroundings
after you leave VIMS.
Suggest reviewers when you submit ms

When ms is returned by the journal

- respond to all reviewers comments
- make all changes you can live with
- always take the high road

If your ms is rejected
- rebut reviewers errors
- take your lumps if its a matter of opinion
Baseball Rule: strike 3 and youre out!

If your paper is rejected, try another journal. If

its rejected again, try again. If its rejected a
3rd time, throw it in the garbage. But dont give
up until youve tried 3 times.

(Rejections by Science and Nature dont count.

Those are badges of honor.)