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					        Writing an essay;


         A guide for the perplexed




                                         Pete Smith

A set of notes for those starting to write essays, reports
                        or theses.

                      Let's face it; it’s terrifying.


                                1
        That's a normal reaction. We all feel it. Feeling either frightened or overwhelmed
is a standard reaction when faced with a new task and for most young scientists,
producing an extended piece of writing is a completely new task.
        Welcome to the world of avoidance behaviours. As the deadline approaches you
will be surprised to find how attractive watching a video, doing the washing-up,
cleaning your shoes or in fact anything other than actual writing can become. This is to
say nothing about your mobile or the pub.
        Don't worry; avoidance behaviour is normal. We all do it (I have just taken a
break to record the serial number of my printer!). Avoiding actual writing is part of the
writing process. So you have to accept it. Later I will come back to this issue and argue
that 'not writing' is a critically important activity that is totally necessary to the process
of producing a document.


        These notes are designed to help you through the rocky road to the production of
          essays, reports or the introduction and discussion sections in theses.


                             They attempt to meet three big problems.


                     They are designed to help you get HIGHER MARKS
          In order to do this they will start with an analysis of what examiners
                                 actually award marks for.


                 The second is that they should make writing EASIER
                They divide the job of writing into ten separate activities
                   and provide instructions on how to do each task.


            They are designed to help you avoid the PERFECTION TRAP
          They suggest you should always remember that you are writing drafts
                                you intend to improve.




                                              2
                                                   CONTENTS

Perfection .....................................................................................................................3

What the examiner will be marking. ........................................................................4

Sequence of tasks in writing an essay .......................................................................7

Expansion of tasks ......................................................................................................8

           GROUP 1. Getting started .............................................................................8

                      1.1. General reading ............................................................................8

                      1.2. Make bibliography entries ..........................................................10
                      1.3. Make a structural skeleton. .........................................................10

           GROUP 2 The actual writing ........................................................................13

                      2.1 Goal directed reading ...................................................................13

                      2.2 Flesh out the skeleton....................................................................13

           GROUP 3. Editing ..........................................................................................15

                      3.1. Produce a first draft and restructure. ........................................15

                      3.2. Check content by paragraph and sub-section. ..........................16

                      3.3. Check links ...................................................................................16

                      3.4. Proof read .....................................................................................16

                      3.5. Produce final document. ..............................................................17

Appendix 1 Web based searching…………………………………………………18
Appendix 2 Using a word processor………………………………………………21

Appendix 3 Using the Net ..........................................................................................22




                                                                 3
                                       Perfection

                           Perfection is your biggest enemy.

   It is a cunning foe that traps you with a number of apparently reasonable phrases.


                     "I must do my best. The best is perfection.
                          What I am writing is not perfect.
                             So I won't write anything."


                   "I can't write anything perfect until I am ready.
                                   I'm not ready yet.
                              So I won't write anything."

These notes are designed to help you overcome these gumption traps but, paradoxically,
            they may also present you with a chance to develop a new trap.


   " These notes tell me how to write, if I follow them I will produce perfection.
  But, the notes are overwhelming, they outline too much work, following them
                                would be impossible.
           As I can't follow them, I won't be able to produce perfection.
                              So I won't write anything."

        Don't worry, nobody has ever written anything by doing everything that is
outlined here. The notes provide guides to progress not rules for perfection. You don't
have to follow them slavishly, nobody could. Read them, think about them, but use
them only if they seem to make sense to you.
        Just in case you miss it, let's repeat the central theme of the approach taken in
these notes. Always be aware that you are writing drafts. Drafts aren't perfect; they are
things written to be improved, later. The only time you stop working on drafts is after
the final stage of editing. What the guidelines recommend is;


 "Write drafts, get something, anything down. You can improve it later but you
                   can't improve something that doesn't exist."




                      What the examiner will be marking.

                                             4
        Examiners are people. This is true, really. Each examiner has their own pet
obsessions, their particular demands and their particular areas of knowledge. Always
respect that when you prepare work for a particular examiner. This section, however,
outlines seven general criteria that all examiners will use to evaluate your work.
Knowing these criteria will help you produce work that will get MARKS.


Presentation
        Presentation is important to the examiner at both the conscious and unconscious
levels. At the conscious level the examiner will be looking at the extent to which you
have presented your work in the format that was requested. As in all examinations it is,
therefore, essential that, before you start, you read whatever instructions are given.
Different examiners have their pet hates. Some focus on spelling, some on punctuation,
some on referencing and bibliographies. As you often do not know the nature of the
examiners obsessions in advance, the only thing you can do is pay attention to them all.
       All examiners are unconsciously affected by the appearance of a piece of work.
Make the final product look good. It really is worth marks.


Quantity
       Quantity refers to the length of the written material relative to the amount
requested. You should always find out how long any piece of work is expected to be.
You have a right to this information. If the essay is too short the examiner will assume
that you haven't tried or you don't have the ability. Writing too much can also lose you
marks. The examiners may have set a short word limit in order to force you to think and
to write concisely. Writing concisely is a skill that requires you to work out exactly what
you think are necessary and to eliminate material that is not really relevant. It’s not as
easy as it sounds. As Oscar Wilde said "I'm sorry for the length of this letter but I didn't
have time to write a shorter one."


Relevance
        Examiners will check whether everything you have written is relevant to your
topic. Don't ramble. They will also look to see if you have left out anything that they
think is relevant. A further aspect of relevance is balance. Balance refers to the relative
amount of time you spend on each aspect of the topic.
       If you are aware that there is an aspect that you could have covered but didn't, or
one that you spent less time on than it might appear to have deserved, always give an
explanation, in the essay, why you made your decision. The examiner may not agree
with your decision but at least he/she will know that your were aware of the issue.



                                             5
Coherence
       This is one of the central things an examiner is influenced by. Is there a narrative
flow? is there a structure? Is it clear why one section follows another? Can somebody
read the piece without getting lost?
                 Big rule; an examiner should never get lost.
        If they get lost, if they have to keep turning back to see where they are or where
they are going, they will get pissed off and they assume it is your fault. Always have a
structure, tell the reader what is going on, where they are in that structure. Always make
sure that you provide links from one section to another. Pay real attention to headings
and titles. If examiners find a good structure, they will always assume that this implies
that you are in command of your material - that you understand it. This is what they will
reward.


Language
       In terms of scientific writing, language can refer to either general or specific
aspects of the language used. Here, general refers to the principles of English syntax
and specific refers to the particular jargon associated with a scientific area. An
examiner will be influenced by the extent to which a piece of writing adheres to the
common standards of both these aspects of language. Both these aspects of language
should be addressed at the editing stage.


Creativity
        This is the one all examiners love to see. Evidence that they are looking at a
mind that is working creatively gives an examiner pleasure, and giving an examiner
pleasure mean more marks, a lot more marks. A little bit of creativity can even earn you
forgiveness for many other deficiencies in your work.
        Remember, marking is always boring and often depressing for the examiner. The
sight of a pile of essays or even of a big fat thesis does not bring instant thoughts of joy.
Coming across evidence of a little originality is like the sun shining on a cloudy day.
Let me tell you evidence of creativity is rare. It is worth striving for.


Depth
        Depth here refers both to the type of references you have consulted and the detail
of the arguments you have described. The depth of any essay must be appropriate to the
level of the course for which the written material has been required. If in doubt, ASK.
Reference material is divided up into primary and secondary sources.
        Primary sources are the actual peer-reviewed papers in which original results,
together with the methods used to obtain them, are presented and discussed



                                             6
       Secondary sources are reviews or book which summaries and discuss the
material presented in primary sources.
       Examiners will always be positively influenced by the use of up-to-date, primary
references. However, whether you use primary or secondary sources often depends on
how important the particular argument you are presenting is to the overall structure of
your essay. The more important the issue the more you should be using primary
sources. For advanced level work you are expected to have used a significant proportion
of primary sources. (See APPENDIX 1 Web based searches and APPENDIX 3 Using the
Net)


Originality
      Although you are expected to derive most of the facts and many of the opinions
you write about from the published literature, it will be expected that all the actual
words you use will be your own. This may seem a little weird at first. If a senior
researcher has already described something well, why do you have to re-describe it in
your own words, why not use theirs? However, it is a very strong rule of academic
writing that it is not acceptable to copy chunks out of other people's work. There are
rules for quoting other people's work. If you include more than a single phrase of
another author's work, you must acknowledge the source and put the words you have
borrowed in inverted commas. If you don't obey these rules, YOU WILL LOSE
MARKS.
         Copying other peoples work, either their words or ideas, without
acknowledgement is called plagiarism but the examiner might call it cheating. Don't be
tempted to try it. Remember, even if the examiner has not read the paper they will,
almost certainly, recognize a change in style and use of language.


Appropriate referencing
        One of the major requirements of academic writing is that you are expected to
give the source of all the facts you incorporate in your essay, report or thesis. The idea
here is that the reader should be given the information that would allow them to check
the originals. If you want to get the hang of this, just look at the referencing in any well-
written published paper.
        Occasionally, in undergraduate essays, the strict rules of referencing might be
relaxed. However, unless this is specifically part of the instructions given to you, you
will be expected to obey the rules.
        Remember, most examiners will deduct marks from an essay if it is poorly
referenced.




                                              7
Sequence of tasks in writing an essay

GROUP 1. GETTING STARTED


1.1. General reading
This is the first step. It is where you collect and quickly scan the papers, reviews and
books you will be using as source material.
1.2. Make bibliography entries (in final form)
Make a complete bibliographic entry for every source you read when you first read it.
1.3. Make a structural skeleton
Produce a provisional structural outline of the essay to the level of sections and sub-
sections.

GROUP 2 THE ACTUAL WRITING


2.1. Detailed, goal directed reading
This is when you go back to your sources with specific questions that have been
generated by your structure.
2.2. Flesh out the skeleton
This is what most people call writing. Fill in the skeleton sub-section by sub-section,
always starting at the one you find easiest. Remember, what you are writing in this task
is a draft text not a final polished document.

GROUP 3. EDITING

3.1. Produce a first draft and restructure.
Put all the bits you have written together in the right order and rethink the structural
skeleton
3.2. Check content by paragraph and sub-section.
Go through the work checking that each part says what it is supposed to say and doesn't
contain anything unnecessary.
3.3. Check links
Check that you have sentences or short paragraphs that explicitly link the sections or
sub-section into a whole.
3.4. Proof read
Eliminate errors in spelling, syntax and typing. Also do a final check for meaning and
coherence.
3.5. Produce final document.
Check final layout against instruction, and beautify.


                                             8
                                  Expansion of tasks

GROUP 1. GETTING STARTED


1.1. General reading
       The first step in writing is reading. There are various styles of reading and it is
important to understand, at any time, why you are reading. At different stages of the
writing process you will be reading for different reasons. In producing any serious piece
of work you might as well accept that you will read the same articles more than once,
each time for a different reason.


            Scientific writing is dense. It is not possible to make all the notes
                               you will need at one reading


        It might appear diligent when you first read a paper to take detailed notes but
experience suggests that it is normally a waste of time. At this stage you rarely know
what details you will want from that paper and often, if you do take detailed notes, you
will find that, in the end, they contain much that you will never use and little of what
you will ultimately return to that paper to find.


 You cannot take good detailed notes until you have worked out what question you are
                                       asking.


        The first reading is primarily aimed at developing an understanding of the shape
of the territory in front of you. Who are the players and what are they on about? An
important outcome of a first reading is a list of more papers to read. On a first reading
any note you take should just describe the general properties of that material.

What to read
        In general reading you almost never read a paper from beginning to end. At this
stage, the most important part of a paper to read is the Abstract, after all this is what the
author thinks the paper is all about. The references in the bibliography are also
important. They may indicate what you should read next. At this level, these two might
be all you read or you might also have a look at the Introduction as well. Introductions
sometimes provide short and concise summaries of the field.


How to find stuff to read
        If you can find a good, detailed and recent review of the field, God loves you. It
will be a wonderful source of, and introduction to, the primary references you will need

                                              9
but be careful not to copy this review into your own work It is nearly certain that the
examiner knows the review as well.
       Wandering up and down the library shelves is a poor way to look for
information. Nearly certainly you will be using electronic databases to search the
available literature. A guide to the use of these is given in Appendix 1.



When to stop
         When have you read enough or collected enough papers or reprints? The simple
answer is never. There never will be any stage in your life when you have read all that
you could. What you need here is a functional limit. Two guides can be offered. The
first is when you find that you recognize the majority of the authors cited in the
bibliography of a paper you start to read. At this point you can be reasonably certain that
you have got somewhere. The second is when you yourself are beginning to get 'a feel'
for the topic.


1.2. Make bibliography entries
       The most important note you can take during a first reading is the correct
bibliographic details of the paper you are reading. If you are working on a computer you
should, at the first reading of all papers, enter the full accurate and appropriate
bibliographical details either into a text document or into a bibliographic software
package like Endnote™.
        If you are writing by hand, make a card file and enter all the correct details of
everything you read. Keep each citation on an individual card. It will make sorting them
easier.
                                 THIS IS IMPORTANT.

         The amount of time and frustration that you will experience in trying to find a
reference during the final editing of a text is enormous. Having to spend, as a deadline
approaches, the best part of a day trying to find the number of pages in a book you read
in a library two months ago, is a rapid way to panic and madness.
         The details of the style required in any bibliography are normally available
before you start to write. Massive time will be spent if you record the details in this
format correctly the first time. Treat the nit-picking, pedantic details that are given in the
instructions very seriously. Are the years supposed to be in brackets? Are they followed
by a full stop? Time taken to get this right at the beginning is time well spent.




                                             10
1.3. Make a structural skeleton.

         This is one of the most important parts of the process of writing.


         Nearly all scientific writing can be broken down into a number of sequential
sections. It is possibly, in its use of clearly delineated sections, that scientific essays
differ from those essays your English teachers tried to get you to write. With anything
that is between 5 -50 pages long there will be a limited number of these sections.
Somewhere between 4 and 6 would be common.


What is a skeleton?
       A skeleton is simply the layout of the major sections of your work and the
divisions of these sections into their sub-sections.
       Figure 1 gives an example of part of a structural skeleton. Have a look at it.
The major sections used (Step 1) in this example do not, of course, represent the only
skeleton that could be arrived at. It may not even be the final structure that will be used.
BUT IT IS A START
Figure 1       Example of a skeleton
       In an essay on vaccination against influenza the following provisional
       structural skeleton might be adopted.


Step 1
                1. The nature of influenza
                2. The nature of the virus
                3. Vaccination strategies and laboratory trials
                4. Vaccinations in the field and their consequences.
                5. Possible future strategies.
Step 2
       Start sub-dividing each section, for example, section 1 might contain sub-
sections       on;
               1.1 The history of the disease
               1.2 The symptoms of the disease,
                1.3 The transmission of the disease
                1.4 Susceptibility by age, genetics and income.




                                             11
       Once you have the major sections of a provisional skeleton (Step 1) it is a good
idea to take a clean sheet of paper for each section. Write the section heading on the top
of each sheet and pin them up in front of you wherever you are working. Now you can
proceed to break down each major section into its component sections (Step 2). Now
write the sub-sections on your master sheets.


                    THIS IS YOUR PROVISIONAL SKELETON

Why make a skeleton?
     Skeletons and their master sheets have three great advantages.


       1. They guarantee that anything you write will have a structural narrative, it will
flow and it will be easy to read.


    If the reader finds your work easy to read, they will tend to assume that you are
              intelligent and understand the material you are writing about.


       2. They help you get round the problem of the first sentence. Once you have the
skeleton you can start anywhere!


             ALWAYS START WITH THE BIT YOU FIND EASIEST

       3. Once you have a skeleton you can plan your work. You will always know
where you are and you will know where what you are writing is going to be in the final
document. It will also help you see that, despite all appearances, you are actually making
progress.


        4. A structural skeleton will help you avoid writing one of the worst types of
essay or review. These are the ones where the author appears to have made a pile of the
papers he/she will use. The author starts by taking a paper, discusses its contents, then
proceeds to the next paper, discusses that and then proceeds ad infinitum. Not only does
this approach to writing produce a very boring product, it will also fail to provide an
examiner with any evidence that you understood the material you were reading.




                                            12
How to get a skeleton
         Have faith. You are a human being and human beings are pattern makers. A
structural skeleton is a pattern and making one is as natural as breathing. A number of
things can, however, get in the way. Fear is the biggy. With its friends, anxiety and
self-doubt, fear, in any of its major disguises, is the real enemy. So what's new?
         The other problem is that because pattern making is a natural and often an
unconscious activity few of us know how to do it. I'll let you into a secret. You can't do
it by trying. It’s not like studying or reading or working. The steps to pattern making
are;


       1. Load the system.
              Do your general reading. Get the stuff sloshing around inside your mind.
Work hard at this but at this stage you should not be trying to write anything more than
very general notes to yourself.


        2. Take a break; stop trying.
                 This stage can take days and it can feel as if you are dossing, not working
and definitely not writing. Rest assured, if you have put a load of stuff into your mind
the poor thing has no option but to try to make something out of it. This is the time
where not writing is an essential part of writing. Go play football, fall in love, go down
the pub saying to yourself all the time this is how I write, wow, how weird. Don't feel
guilty. If guilt turns up uninvited, work on something else. Don't worry; it won't get in
the way of patterning. If you're working on a thesis, now might be a good time to work
on polishing up the layout of some tables or graphs.


        3. Make your skeleton
                There is an art in knowing when to go back and ask your mind for its best
shot at a pattern. Personally I often find that going for a walk is a good idea or
sometimes talking to another person - conversation requires a structure too. One of the
best times is the morning after you have spent the night failing to come up with a pattern
that pleases you. You might be asleep but the poor old pattern making function of your
mind gets no rest. Whatever, one day try doodling on a piece of paper.


                REMEMBER AVOID THE PERFECTION TRAP

        You are only trying for a provisional skeleton you can always change it later (see
task 3.1).




                                            13
GROUP 2 THE ACTUAL WRITING

       The two tasks in this group Goal directed reading and Fleshing out the
skeleton are not really separate. You will find yourself switching between reading for a
sub-section and writing it. Or you might do the detailed reading for more than one sub-
section before you start to write. Again go with the flow. If your head is ready to write,
do some writing. If you feel like reading, read. If you don't feel like doing either, go
back and re-read and edit something you wrote recently.


      There is one most important thing to bear in mind when you start to put words
down on paper or on screen. Your first version is not supposed to be the final version.


                              YOU ARE WRITING A DRAFT

        Always remember that you are not trying to get it right. At this stage you are just
trying to get something down. You can go back, change it, improve it, or even discard it.


                                 WRITE SOMETHING,


                      ANYTHING YOU WRITE IS PROGRESS



 2.1 Goal directed reading
         When you have your structural skeleton now is the time to read again. This time
you are reading for detail. Again, you will not be reading all of a paper or of a review
article. You will go in to get specifically what you want for that sub-section you are
working on.
         Choose a sub-section that you feel most at ease with and make a pile of the
relevant papers. Your general reading should help you understand which papers or
review articles you need to read and your structural skeleton will tell you what you want
from each of them.
         Any time you read a paper, you should be able to see where you are going to use
the information it contains. Remember any single paper may turn up in a number of
sections or sub-sections and you may have to go back again and again to find the
specific bits of information you need for each of your sub-sections. It is a good idea to
make notes on your master sheets of the references that you will be using in each sub-
section. This is a continuing process and papers can be continually added or taken out as
you carry on writing.


                                            14
 2.2 Flesh out the skeleton
        Once you have a skeleton, it is now the time to start filling in the flesh. This is
the task that most people think of as writing.
         The important thing here is to start with the sub-section you are happiest with or
think you will find easiest, continue on, always choosing to work on the easiest of the
remaining sub-sections. This way when you get to the really difficult bits you will have
the confidence of a load of work behind you.
        Remember this is a draft not the final version so don't be perfectionist,
concentrate on getting stuff down on paper or on the screen. One big help here is to be
prepared to write a bit of garbage into your text. It can happen that when, at last, a bit of
writing is going well, a sub-section is really getting filled in, you come to a bit that stops
you. It might be the name of an author, it might be a specific number or set of numbers
or it might just be a word or phrase that won't come right. At this point, don't interrupt
your flow by trying to solve the problem or look up the information, moments when the
writing is flowing are too valuable. Just write BLAH or something and carry on. If you
are writing on screen put it in BOLD, if you are writing by hand put it in CAPITALS. In
my first drafts a surprising number of papers seem to have been written by Fred (19XX)
and a lot of numbers appear as XX. Later you can go back and fill these details in later.
Filling in these bold bits does not take the same kind of energy as writing. You can do
them one at a time when the mood is right. If you are writing directly onto a computer
just scan for BLAH or Fred or XX using the ‘find’ option.
        Writing takes time and concentration. Importantly, in each session of actual
writing it takes time to get into the swing of getting words down on paper. It is an old
saying that if you spend one hour at your desk you produce 5 min of actual writing. If
you spend two hours you get 35 min writing done and if you spend three hours you get
an hour and a half's production. So, if you haven't got the time don't start on a new
section of writing. You will only end up feeling frustrated and defeated. Do something
that can be fitted into smaller time slots like editing or reading. Short time periods can
be productively used to go back and check all the bits you have left in BOLD or
CAPITALS.
        An important point about this task is that you never throw anything away. Often
you will find you have written something that you don't like. Don't scrap it. If you are
working on-screen, open a 'rejects' file and put it there. It is surprising how often you
will go back to this file and recycle a bit of this rejected writing in another part of the
essay.




                                             15
GROUP 3. EDITING

       Now is the time to see what you have got. From now on you will be involved in
what can generally be termed editing your text. If you have never done this job before,
then there is one enormously important fact you need to know,


     EDITING TAKE MUCH MORE TIME THAN YOU EVER IMAGINED

                               another way of stating this is


                   EDITING TAKES LONGER THAN WRITING

        Editing is, however, very important. In the end the quality of your editing will
have a real influence on how the examiner feels about having to read your work.
Reading poorly designed work with a clumsy layout that contains typographical errors
and bad spelling will put any examiner in a bad mood. They will start looking for errors
in content and will be preparing themselves to give a low mark. A well-produced piece
of work automatically gives the impression of competence and ability. The examiner
will prepare himself to be impressed by the content and will be ready to award high
marks.
        It is just like getting ready for a date. First impressions matter. You may be a
very nice person but if you clothes are dirty, your fingernails filthy and you have bad
breath and BO you are reducing your chances that anybody will notice how attractive
you really are underneath.



3.1. Produce a first draft and restructure.
        Print out your text, collect all your sheets of paper and put them in the right
order. This is your first draft. At this stage you do not have to have finished filling in all
the sub-sections but it is better not to start this task until you have something written in
the majority of them.
        Once you have a first draft it is time to re-look at the structural skeleton you have
been using. The idea here is to make sure that each section and each sub-section is in the
right place. This is when you can decide to change the overall skeleton.
        It is practically impossible to do this kind of editing on-screen and few people
have the kind of mind that allows them to look at the structure in a vertical pile of sheets
of paper. A trick here is to find a large flat surface and to lay the work out horizontally.



                                             16
You can then walk up and down your essay thinking about the structure and moving bits
around. Try using scissors and Sellotape.


3.2. Check content by paragraph and sub-section.
        There are unique sets of errors that are associated with editing on a computer. I
call then orphans and ghosts. They are the residues left behind after using the cut and
paste functions. Orphans are sentences, or occasionally a group of sentences, that are
meaningful in themselves but are now in the completely wrong part of the document.
Ghost are parts of sentences or sometimes just single words that got left behind. An
important type of ghost is the invisible ghost. The most common form of invisible ghost
is the presence of a double space, rather than a single space, between words. These
double spaces detract from the appearance of your work and should be eliminated.
Luckily this is easy. Just go to the replace function in the word processing package and
ask it to replace all double spaces with single spaces. Hey presto, all invisible ghost
gone in a second.
           There is a really good technique for getting rid of more substantial ghosts and
orphans that also has the advantage of seriously improving the quality of your writing.
This time it is wise to start at a place where you had real problems writing because this
is where you will have been most involved in cutting and pasting. Focus on a paragraph.
Read it quickly to see what it is trying to say. On a separate sheet write down, in note
form, the points you are trying to make in that paragraph. Return to the document and
see if each sentence is consistent with the aims of the paragraph. Cut out those that are
not necessary or don't fit. Carry on with each successive paragraph until you have
completed a whole section or sub-section.
        I know this sounds laborious but if you do it properly it will be worthwhile. Your
writing will flow and reading it will be easy. Remember your main job is to keep the
examiner in a positive frame of mind. If the reading is easy, because each sentence is in
the right place, the examiner will enjoy his/her work, will assume you are in compete
command of your material and will award you HIGH MARKS.
        If you cannot face the prospect of checking each paragraph in your work, you
should, as a minimum, check those parts where you know you did a lot of cutting and
pasting.


3.3. Check links
        When you write in sections and subsections, as is recommended here, the one
disadvantage is that you can end up with a slightly disjointed text. A disjointed text will
leave the reader/examiner lost as you force them to jump from topic to topic. Now is the
time to put in a sentence or two to lead the reader gently from one section to the next or



                                            17
from one sub-section to the next. These links can either be at the end of a section or
more commonly at the beginning of the new one.




                                            18
3.4. Proof read
        The first step here is to use the facilities provided by your word processing
software. Always do a spell check and a grammar check before getting down to serious
proof reading. However, you should remember that computers are morons and can
occasionally become corrupted morons. Custom dictionaries are particularly susceptible
to corruption. As a result a spell check may accept incorrectly spelt words or, more
often, words that are correctly spelt but that are not the ones that you intended to write.
        Nothing will replace a careful reading of the text. This is where you need your
friends.


            NOBODY CAN PROOF READ HIS OR HER OWN WORK

       There is an overwhelming tendency to read what you meant to write rather than
the words that are actually on the page in front of you. It is a good idea to use more than
one proofreader, each person has the errors they see well and the errors they don't see at
all.


3.5. Produce final document.
        Read the instructions to authors. Take everything they say seriously. Check your
layout. A good layout should not only make your work look attractive but it can also be
used to help the reader know where they are in the text. Again it is a good idea to lay
your work out horizontally on a large table when you are examining its layout.
         Are the page breaks in the right places? You can use page breaks to help the
reader. Don't, for example, start a new section at the bottom of the last page of a
previous section. If you start a new section at the top of a new page you are telling the
reader that you have changed the topic under discussion.
         Are the headings all in the correct typeface, For example, if you are using 14 pt
bold for section headings and 12 pt italic for sub-section headings, are all the headings
in this format?
       When you think you have finished, do a final spell chuck.

       Remember editing is never finished. The best time for seeing serious mistakes in
your manuscript is five minutes after you have submitted it!


                     PERFECTION IS AN IMPOSSIBLE GOAL




                                            19
                         Appendix 1 Web base searching

NB This information is also on the Departmental Web site. Remeber the hard copy
will only be updated every year but the Web version will be continually up-dated.

There are three basic strategies for web-based searching.


1. Start at the College Library home page www.library.nuigalway.ie/
2. Start at the Departmental Web site www.nuigalway.ie/microbiology
3. Go direct to a particular site on the Web



1. IF YOU START AT THE LIBRARY HOME PAGE

       You can straight to Science direct. www.sciencedirect.com
Covers 1,200 journals with links to 10,000 journal titles, and, at any one time, 1.5
million articles. Elsevier journals only. Full text available with articles available from
400 journals as PDF files. Search using subject keywords, author, title of journal etc.
Demonstration available on-line.
OR
       Go to the dialog box a left hand side of library homepage and pick a database
from there.
OR
        Click on Science icon on top of the home page. This gives you further options to
click on.
        Books: link gives location of science textbooks and links to other university
        libraries
        Journals: link to list of online journals available in library. The full
        text of some journals are available online, but only if the library
        subscribes to them.
        Databases: This gives you links to some of the most commonly used databases
                these databases can also be accessed from the library home page, from
        the dialogue box called resource index on left side of screen. The most
       useful databases available here are;


Web of Science
      Allows access to 5, 700 journals in 150 disciplines. Updated daily. Gives citation
      and abstract only. Does not provide full text of articles. Can perform cited
      reference searching. Search using subject keywords, author, title of journal etc.

                                              20
       Tutorial available on-line, or alternatively contact science librarian Rosie Dunne
       who organises training sessions at the beginning of academic term.


Medline. Bibliographic and abstract coverage of biomedical, dental, and medical
      literature. Access to 3, 900 journals, but abstract available only. Database covers
      articles from 1966 onwards.



2. IF YOU WANT TO GO VIA THE DEPARTMENTAL WEB SITE

From the NUI, Galway home page click on Faculties and Departments found on the
navigation bar at the left hand side of the page. Then click on Microbiology which will
appear on the main part of the page under the Departments heading. The Microbiology
Dept. website will then appear. On the front page, right hand side, click on the link that
reads Microbiology Online. This will take you directly to the page which contains links
to a wide variety of useful sites.


3. IF YOU WANT TO GO DIRECTLY TO A USEFUL DATA BASE

Here are a list of some that are frequently used by postgrads in the Department.


2.1 For finding peer-reviewed papers.
Science Direct (use groupwide login)
       http://www.sciencedirect.com/
Web of Science
      http://wos.heanet.ie/
Medline/PubMed
      http://www.ncbi.nlm.nih.gov/PubMedOld/

American Society for Microbiology. Access to all ASM journals, mainly abstracts.
      www.journals.asm.org



2.2 Data bases for molecular biology
The National Center for Biotechnology Information (NCBI) homepage
http://www.ncbi.nlm.nih.gov/
Click the entrez link. NCBI homepage provides a literature search engine, Pubmed,
and the Entrez browser which searches the GenBank DNA database. Another useful




                                            21
tool is the BLAST (Basic Local Alignment Search Tool) program which compares user
inputted DNA sequences to the GenBank database.
European Bioinformatics Institute (EBI) homepage
http;//www.ncbi.nlm.nih.goc/
The EBI is the European centre for genomics and bioinformatics services and is based in
the UK. Its location means it is often easier and faster to access than its american
counterpart, the NCBI (especially after lunchtime). In particular, the Tools and
Databases links are comprehensive and user friendly.
The Ribosomal Database Project
http://rdp.cme.msu.edu/html/
This is a specialist database for small and large subunit ribosomal RNA analysis.
Allows user to perform on-line DNA sequence similarity searches, sequence alignment
and basic phylogenetic analysis
Pedro’s Biomolecular Research Tools.
http://www.public.iastate.edu/~pedro/research_tools.html.
This web site contains links to a host of resources covering a wide range of topics in
molecular biology. Also contains links to many major journals in biology.


2.3 Reputable agencies

UK Public Health Laboratory Service The web site for the public health laboratory
service in the UK. Facts, news, publications and information on various notifiable
pathogens.
www.phls.co.uk


Centers for Disease Control, US. Great site for information on the epidemiology of
diseases
http://www.cdc.gov/


US Food and Drug Administration. Great site for reports on disease and food safety
issues.
 http://www.fda.gov/.


World Health Organisation. Fund of information about current state of diseases and
epidemics all over the world. Some data is a little politically tainted
http://www.who.int/home-page/

Bandolier. A UK database on evidence based medicine. Reviews the evidence that
therapies do or do not, work.


                                           22
http://www.jr2.ox.ac.uk/bandolier




                                    23
                      Appendix 2 Using a word processor.

         If you are not fluent in the use of a word processing package you will find that
you want to write your first drafts by hand. If this is what is easiest for you then maybe it
is the right thing to do. Writing on-screen is like sending a rather large text message and
most people master the art of texting their friends quite quickly. Writing drafts by hand
is only postponing the moment when you have to come to terms with the computer. In
making your decision as to when to start working on-screen you should remember;


1.     In the big, bad world outside, everybody, except the very old, composes directly
on-screen. In employment it is a skill you will be expected to have. Your colleagues at
work will see writing first by hand and then copying the words into a computer as rather
like using your fingers to count on.


2.    Your document will have to be printed and so you will have to get it into a
computer sometime.


3.      However you write your first drafts, it is certain that, before you produce your
final copy, you will have to get involved in editing a document, which is in a computer.
Editing is an inherently finicky, nit picking and frustrating activity. Trying to learn how
to edit and how to use a word processing package at the same time will normally result
in your giving up too early. The result will be poor editing, poor layout and lower marks
than you deserve for the effort you put into the reading and writing.


4.      As the deadline approaches you will, if you are normal, start to panic. Mild
panic makes learning very difficult. Full-blow, serious, the deadline-is-coming panic
makes learning impossible.

        My advice to you is to get used to word processing as soon as possible and
definitely before the pressure is really on. When you do start to work on-screen there are
two words you need to know;


       BACK UP, BACK UP, BACK UP, BACK UP, BACK UP, BACK UP,

   If you wish to avoid the suicidal panic the can be engendered by the simple phrase;


                                Unrecoverable disc error

       BACK UP, BACK UP, BACK UP, BACK UP, BACK UP, BACK UP,

                                             24
                             Appendix 3 Using the Net

         The Net was designed to disseminate information. When approaching a new
topic it has obvious attractions. It is fast and organized by key words. No frustrating
searches for journals the library doesn't have, or for issues that are 'missing'. No waiting
for expensive inter-library loans. The Net can, however, be used in two ways. The first
is to use databases to search the published literature. This is totally legitimate and
nobody has any problems with it. The second is to use a search engine to find any
information that is 'out there' on a particular topic. This is where the problems really lie
and it is this use of the Net that will be discussed here.
         As a general rule examiners react badly (i.e. give low marks) if they think a piece
of writing is "just downloaded from the Net". This is not just because examiners are
geriatric stick-in-the-muds who are just not able to keep up with progress. There are real
reasons for concern about the quality of the information that is available on the Net. As
anybody who has carried out a key-word search knows, the majority of the sites that turn
up are rubbish. The problem is that in amongst the dross are some valuable gems. How
do we discriminate? What are the rules or guidelines here?
        What this note will attempt to do is to outline the main argument about the use
of the Net, discuss some of the theoretical background to these arguments and then to
suggest some guidelines for the use of the Net as an information source in scientific
writing.
        Before we attempt to illustrate where the rules might lie, however, it is probably
valuable to remind ourselves of what examiners are looking for when they mark any
piece of writing. What lies behind that dismissive comment "just downloaded from the
Net"? Of primary importance to the examiner is that any writing you submit is meant to
be yours. It is meant to be the result of your thinking about material you have read. It is
meant to be a critical evaluation and synthesis of many different sources of information
(how many depends on the level of the exam but in general the more sources the higher
the marks). At one level, the disparaging comment "just downloaded from the Net",
refers not to the quality of the information sources but to the absence of critical thought
in the writing.
        Here, however, we are not concerned with the degree of critical thought in your
writing, which has been dealt with elsewhere, but rather with the legitimacy of the use
of the Net as a source of the information. The issues surrounding the legitimacy of the
use, in scientific writing, of information collected from the Net is still unresolved and
unfortunately no firm and absolute rules can be given. What we can do is to outline the
arguments and suggest some guidelines.



                                            25
The arguments
        Traditionally the issue of legitimacy of data has been established by reference to
peer-reviewed journals. Simply stated the position was that, if information appeared in
an article in a peer-reviewed journal, it was, thereby, considered legitimate. Information
that was disseminated by any other means, if it had not originally appeared in a peer-
reviewed journal, was considered suspect.


Those who defend this reliance on peer-reviewed journals generally rely on three
main arguments.
       1. Any article in such a journal has been subject to critical review by at least one
and normally more, leading scientists in the field before being accepted by the editor for
publication. This, it is argued, maintains standards and eliminates crap.
        2. The standard of these journals ensures that data are never presented without
the full details of the methods used to obtain them and the conditions under which they
were obtained.
        3. These journals are in the public domain and are, therefore, at least in theory,
available to everybody.


On the other hand, those who advocate the use of the Net would argue;
        1. Traditional journals are very slow. It can take a year or more to get a paper
published this way. In contrast the Net represents instant communication that can be
rapidly updated.
        2. Journals are expensive and many have only a small circulation and are
virtually inaccessible. In contrast, anybody can get on the Net and access a much wider
range of material.
        3. The process of peer-review itself is deeply conservative. The so-called 'leading
scientists' use their position to prevent publication of genuinely new or radical material.


Those who argue against the use of the Net as a source of scientific data tend to
argue;
       1. Information on the Net is ephemeral. It can change over time or even
disappear totally. You cannot rely on its being there if you wish to check it.
       2. The total absence of any editorial control, peer-review or any editorial
standards means that material can be published on the Net that meets none of the criteria
traditionally associated with empirical science. Data can frequently be separated from
method. You have no way of knowing whether what you are reading is total crap.

           The real problem is that all these arguments are essentially
                                 correct.

                                            26
Theoretical background to the arguments
         Underlying the arguments outlined above are issues of the nature of the
scientific enterprise. Both those who basically oppose the use of the Net and those who
support it would argue that they are preserving science. Thus, in order to think our way
through these issues we have to think about what science is. Science's claim to authority
is based on two of its central properties. It is empirical, in that its facts are derived from
experimental observation and it is objective in that these observations are independent
of the opinions of the observer.
        As the facts that science deals with are those that have been established by
experimental observations, their validity is directly dependent on the quality of the
experiments used to establish them. From this it follows that information cannot be
considered to be of the highest quality unless the methods that were used to obtain it are
also presented. This gives us the primary rule governing the legitimacy of data;
        It does not matter if the information is on the Net, on the back of an envelope or
in a reputable journal, if the method is not given the data are not a legitimate part of
science.
        Another approach to the discussion of the legitimacy can be based on Science's
claim to be an objective body of wisdom. This is more controversial than its claim to be
empirical. Many analysts would now claim that Science is a sociological and cultural
activity and that the manner in which it approaches the world is not value-free. Thus,
science, to the extent that it derives its values from the society it operates in, cannot be
truly objective. Others, using historical analysis have also argued that Science is not
objective but is actually deeply conservative and that at most times it is remarkably
closed to new ideas. The consequence of the development of these ideas is that we have
now less confidence in judging what is legitimate Science and what is not. Peer-review,
which many claim is the mechanism by which illegitimate ideas are eliminated from
Science, can also be seen as a mechanism that promotes a conservative Science, one that
eliminates creativity. The Net introduced a way by which information can be published
and disseminated which bypasses peer-review. Thus, it represents a medium through
which new creative, original and heterodox ideas can be freed from the oppression of
the conventional thought of the scientific establishment. Of course, it equally represent
a medium through which every lunatic and obsessive can disseminate their ravings.
        So, if we are to use the Net as a source of information, the question is how can
we tell the difference between creative novelty and arrant rubbish. It is not easy, one
person's creative genius is another one's raving lunatic. In some cases, time will sort the
issue out but for the moment we are, inevitably, in the area of value judgments.




                                             27
So what are the guidelines for using the Net.
       So the background is heavy-duty, theoretical stuff. Major philosophical players
are wrestling with these fundamental issues. We are not going to solve them here.
Luckily we don't have to. What we have to decide is to what extent you can use the Net?
and what for? As this involves value judgments, the issue becomes, whose values.
Yours or your examiner.
       What follows is a reasonable synopsis of the conventional positions that will be
taken by most examiners;


Totally acceptable uses
        1. The use of the Net to access articles in peer-reviewed journals on-line is
clearly totally acceptable. In this case you bibliographic citation should be to the journal
and not to the web site.
       2. We have to accept that with respect to data of certain types the only source is
the Net. This is, for example particularly true of data bases associated with DNA
sequencing. In this use, as the contents of these sites are continually changing, it is
important to record the day you accessed them.


Acceptable uses
        The acceptability, for the purposes of scientific writing, of material on the Net is
often related to the reputation of the agency or person that produced it. There is a clear
difference for example, between citing a report from an international, inter-
governmental agency like the World Health Organization and citing one from the
Cloonboo Health Action Group. The discrimination between different origins of web
sites is, of course, another value judgment. No absolute guidelines can be provided but
if you are in doubt talk to your supervisor.
         We are not arguing here that the material from one source is correct and that
from a source, that might be considered less authoritative, is necessarily wrong. What
we are arguing about is how an examiner will react to the use of these information
sources. In the end it is the examiner's value judgments that will influence the marking
of your work. In general it will be safer, if slightly more conservative, to limit yourself
to material placed on the Net by agencies that represent some recognized authority.
         One way to achieve this is to adopt a surfing strategy that focuses on agencies
rather than on key words. Entering keywords into a search engine is a rapid way of
generating a large number of site addresses many of which will be either irrelevant or of
questionable authority. If, on the other hand, you go first to the sites of reputable
agencies, like the FDA, the Centre for Disease Control or the World Health
Organization and then search for the topic you are interested in, you will at least be
accessing sites that the examiner will, in all probability, be happy with.


                                             28
       A large number of national and international agencies publish documents on the
Net. Sometimes, but not always, these are simultaneously published in hard copy. These
documents frequently contain valuable information and nobody would to prohibit their
citation just because they were accessed via the Net. ( Note; If you accessed these
reports via the Net then your citation should be to the web site, even if you are also
aware that there is also a legitimate hard copy reference.) These reports can be
considered as falling into three categories.


        1. Those where the data is associated with full details of the methods employed
to generate the data. These can be treated as primary sources of data.
       2. Those where the methods are not given but reference to the primary sources
are provided. These can be treated as secondary sources.
       3. Those where no methods or references to primary sources are provided. These
can only be treated as evidence of the attitudes or opinions of the agencies themselves.
When you are using these reports in this way you should make this explicit in your text.


        Remember, there is nothing intrinsically wrong about using some secondary
sources or occasionally reporting the opinions of reputable agencies but if an examiner
thinks your writing relies too heavily on secondary sources, it will not gain high marks.


Totally unacceptable uses
       Net sites that sell essays are now in existence. It is, however, totally
unacceptable to download a whole essay or even parts of one, from the Net and then to
present it as your own work.
        This is CHEATING and will be viewed very seriously. If it is proved that an
essay was, in whole or in part, downloaded from a Net site, the candidate submitting
that essay will be reported to the University Disciplinary Committee. The consequences
of this will be severe. In this context you should be aware of three things;


       i) In response to the appearance of Net sites that sell essays, software has been
developed that allows an examiner to enter an essay or parts of an essay into his
computer and to search the Net for the original source.
       ii) The vast majority of essays have been produced for downloading by
American secondary school students. They are therefore, written in American and not to
a very high academic standard.
        iii) Those marking essays have many years experience. They know the standards
and the style to expect. They are very likely to detect 'downloaded' essays from their
style and use of language.



                                             29
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