Technical Writing Skills For science and engineering PhD students

D.P. Shepherd and R.W. Eason10th March 2014

Introduction

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I can write so why would I need your advice?• English Language and Literature O-levels and bad

speller

• Author of >100 journal papers, never (quite) had one rejected

• Supervisor of 12 PhD students

• Technical writing for 27 years

• Topical Editor for Optical Society of America journal, Applied Optics, for 9 years

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• Also have English Language and English Literature O-levels, and I can spell just fine!

• Author or >300 papers, (but several rejected…)

• Supervisor of 32 PhD students so far (and no failures)

• Technical writing for 37 years

• Editor of 2 textbooks in 1993 and 2007

• Editor of University ‘Viewpoint’ magazine

• Written a novel (that has not been published!)

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I’m a researcher, why should I worry about writing skills?

• If you don’t communicate your research results properly you may as well not bother in the first place

• You will be required to write progression reports and a thesis to get a PhD

• Your research career will be judged by the impact you make. Academic impact largely arises from your publications.

• The act of writing up your results forces you into thinking carefully about your results and will help you understand their significance and how they might be improved.

Structure of a Journal Paper Suggestions please…….

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Structure of a Paper• Title

• Authors

• Affiliation

• Abstract

• Introduction

• Main Body (theory, experiments, results, analysis)

• Conclusions

• Acknowledgments

• References

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Abstracts

“The abstract should be limited to approximately 100 words. It should be an explicit summary of the paper that states the problem, the methods used, and the major results and conclusions……. Note that the combination of abstract and title must be an adequate indicator of the content of the paper, since it will stand alone in electronic bibliographic databases and printed abstracting journals.”

OSA Author style guide

“The Abstract should be limited to about 100 words and should be self-contained (contain no footnotes). It should be adequate as an index (giving all subjects, major and minor, about which new information is given), and as a summary (giving the conclusions and all results of general interest in the article). The abstract should be written as one paragraph and should not contain displayed mathematical equations or tabular material.”

Applied Physics Letters Information for Contributors

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• Example of a good abstract:

• A range of high-quality crystalline garnet multilayer structures have been fabricated via multi-beam, multi-target PLD in conjunction with a system of mechanical shutters. Structures grown consisted of alternating Gd3Ga5O12 (GGG) and Gd3Sc2Ga3O12 (GSGG) layers on Y3Al5O12 (YAG) substrates, with both simple and chirped designs. Distinct layers are observed where layer thickness is around 2 nm or greater, although some layering may also be present at a sub-unit cell level. These structures demonstrate the viability of the shutter technique as a quick, simple fabrication method for a variety of optical multilayer structures.

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• Example of a bad abstract:

• We grew some crystal layers that were quite complicated really and also they had structure. In fact we used several different materials (which you can read more about in the actual paper if you want) and then we measured things about them. From our results, which we were very pleased with, we now know that we can grow even more complicated things, including chirping designs. Basically this is what we found.

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• Example of an abstract this is much too brief:

• Crystal multilayer growth was performed and measured, showing the capability for complex garnet superlattice fabrication.

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• …and finally much too long

• Thin film multilayers are of interest in a wide variety of applications, from microwave devices to photovoltaics. They are used extensively in optics; Bragg reflectors, laser diodes and planar waveguides and waveguide lasers are just a few examples. While a range of fabrication techniques may be employed to create such structures, many processes can be slow, costly or limited to simple materials, and often require harmful precursors or solvents. Pulsed Laser Deposition (PLD) compares favorably in many situations; in particular, it is suitable for depositing multi-component materials with complex stoichiometries at potentially high growth rates (up to 10 μm per hour). Combinatorial PLD extends the basic PLD setup to include multiple lasers and targets, increasing the number of controllable growth parameters and making the technique even more versatile. It is already making headway in precision materials engineering; strain and stoichiometry control [1,2] have already been demonstrated, as has material mixing to obtain specific physical properties [3]. However, investigation into the significant promise for structural engineering (multilayers, graded layers, composite crystals etc.) has only just begun. Some inter-layer mixing in a multilayer system is unavoidable, due to indiffusion, particulates and the potential for island crystal growth. There hence exists a minimum thickness of growth required to obtain distinct layers. We have fabricated a series of multilayer structures with varying layer thicknesses in order to determine at what point the transition from mixed crystal to distinct layering occurs. We have concluded that in order to obtain fully mixed layers, the thickness of material deposited per target must be less than one unit cell and subsequently we have demonstrated further proof of principle via growth of more sophisticated chirped structures. We have achieved this via a shutter technique that will allow us to exploit the advantages of combinatorial PLD to grow crystalline multilayer structures quickly and easily. Garnets are excellent laser hosts that have been grown well in both single film and multilayer geometries [4,5]. Different garnets can be easily mixed to give high quality films with tailored average properties, such as defined lattice constant or refractive index [3]. Gd3Ga5O12 (GGG) and Gd3Sc2Ga3O12 (GSGG) are two such garnets; they are known to grow well under the same conditions as both single and mixed layers [1], and hence are ideal as tester materials for multilayer and graded growth.

Group Exercise 1

What Makes a Good Introduction?

Read these Nature Letters introductions

What is their common structure?

What is the purpose of these introductions?

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During cell division, mitotic spindles are assembled by microtubule-based motor proteins1,2.

How to Construct a Nature Summary ParagraphAnnoted example taken from Nature 435, 114-118 (5 May 2005)

One or two sentences providing a basic introduction to the field, comprehensible to a scientist in any discipline.

Two to three sentences of more detailed background, comprehensible to scientists in related disciplines.

The bipolar organization of spindles is essential for proper segregation of chromosomes, and requires plus-end-directed homotetrameric motor proteins of the widely conserved kinesin-5 (BimC) family3. Hypotheses for bipolar spindle formation include the ‘push−pull mitotic muscle’ model, in which kinesin-5 and opposing motor proteins act between overlapping microtubules 2,4,5.

However, the precise roles of kinesin-5 during this process are unknown.

One sentence clearly stating the general problem being addressed by this particular study.

One sentence summarizing the main result (with the words “here we show” or their equivalent).

Two or three sentences explaining what the main result reveals in direct comparison to what was thought to be the case previously, or how the main result adds to previous knowledge.

We found in controlled in vitro assays that Eg5 has the remarkable capability of simultaneously moving at ~20 nm s–1 towards the plus-ends of each of the two microtubules it crosslinks. For anti-parallel microtubules, this results in relative sliding at ~40 nm s–1, comparable to spindle pole separation rates in vivo6. Furthermore, we found that Eg5 can tether microtubule plus-ends, suggesting an additional microtubule-binding mode for Eg5.

Here we show that the vertebrate kinesin-5 Eg5 drives the sliding of microtubules depending on their relative orientation.

Our results demonstrate how members of the kinesin-5 family are likely to function in mitosis, pushing apart interpolar microtubules as well as recruiting microtubules into bundles that are subsequently polarized by relative sliding.

One or two sentences to put the results into a more general context.

Two or three sentences to provide a broader perspective, readily comprehensible to a scientist in any discipline, may be included in the first paragraph if the editor considers that the accessibility of the paper is significantly enhanced by their inclusion.

We anticipate our assay to be a starting point for more sophisticated in vitro models of mitotic spindles. For example, the individual and combined action of multiple mitotic motors could be tested, including minus-end-directed motors opposing Eg5 motility. Furthermore, Eg5 inhibition is a major target of anti-cancer drug development, and a well-defined and quantitative assay for motor function will be relevant for such developments.

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What about one of your papers?One or two sentences providing a basic introductionTwo to three sentences of more detailed background

Once sentence stating the general problem

One sentence summarizing the main result

Two or three sentences explaining what the main result reveals or how it adds to previous knowledge

Two or three sentences to provide a broader perspective

Tea / Coffee

Technical Style

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Active vs. Passive Voice

Voice is determined by whether the subject of the sentence is the agent or the receiver of the action of a transitive verb. (A transitive verb is one that takes a direct object.)

• Traditional science writing uses the passive voice

“ A power of 1W was measured” rather than “I/We measured a power of 1W”.

Why - impersonal, seems more objective, the measurement is believed to be more important than who did it, it shows the reader you’re a proper scientist, convention

But it can be obscure and dull and is going out of fashion, especially with American scientists.

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Active vs Passive Voice

• Nature journals encourage authors to write in the active voice

For more discussion on this topic look at http://www.nature.com/authors/author_services/how_write.html

• You can often use an active voice and maintain an impersonal style

e.g. “The device delivered a power of 1W” (active, impersonal)

“A power of 1W was delivered by the device” (passive)

• In practice many papers mix passive and active constructions. Certainly many introductions/conclusions include phrases such as “Here, we demonstrate…..”., “we have shown that….”

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Tenses

• Science papers report results that happened in the past and should be referred to in the past tense

“The laser power was 1W”

• However, the conclusions drawn from the results are true now and should be referred to in the present tense

“The results show that Yb:YAG is a highly efficient laser system”

• Also accepted facts that might be presented in the introduction are present tense

“Yb:YAG is a highly efficient laser system, [1],”

Tenses

• It is good practice to use the present tense for an abstract as it describes the paper that exists in the present.

“ An ultrashort-pulse waveguide laser is demonstrated with an output power of 1W. The laser self-starts and uses a saturable Bragg reflector for mode-locking.”

Sometimes logic dictates that tenses are mixed but in general it’s better to keep sentences, paragraphs, and sections in one tense if at all possible.

You will find that a huge number of papers don’t follow these guidelines

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Some minor irritations• That/Which

– use “which” when the words following are an aside that could otherwise be put in brackets

“I constructed a laser, which had a wavelength of 633 nm, to measure the distance to the moon”

means I constructed a laser to measure the distance to the moon and by the way it had a wavelength of 633nm

- Use “that” when the words following it restrict the definition

“I constructed a laser that had a wavelength of 633 nm to measure the distance to the moon”

means I specifically constructed a 633-nm laser to measure the distance to the moon

Some minor irritations

So which of these are correct?

“Cars which produce carbon dioxide are bad for the environment”

“Cars, which produce carbon dioxide, are bad for the environment”

“Cars that produce carbon dioxide are bad for the environment”

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Some minor irritations• Compound adjectives

Use a hyphen between two words that proceed a noun to modify it, if the words are not adverbs ending in “ly”

e.g. “the laser is a highly useful device”

and if it would otherwise lead to confusion

e.g. “a nuclear-free zone” is not a place where you can get nuclear stuff for free

For numbers and units the rules are the same

“A 10-Watt laser has a power of 10 Watts”

More compound adjectives: right or wrong?• The laser assisted process was…• Photonics is the driving force behind…• End polished waveguides can be…• Pulses in the nanosecond regime are…• Laser direct write processes…• Bandpass filters can be used• Single crystal substrates can be…• Surface profiling will show that…• Analysis showed well defined regions…• High quality measurements show that…• Non contact measurements are beneficial…

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Some Examples – right or wrong?

"Diode‐pumped solid‐state lasers," Journal of Applied Physics , vol.44, no.1, pp.230-237, Jan 1973

“Scalable Concept for Diode-Pumped High-Power Solid-State Lasers,” Appl. Phys. B 58, 365-372 (1994)

"115-W Tm:YAG diode-pumped solid-state laser," Quantum Electronics, IEEE Journal of , vol.33, no.9, pp.1592-1600, Sep 1997

“Diode Laser—Pumped Solid-State Lasers” Science 12 February 1988: Vol. 239 no. 4841 pp. 742-747

“Directly diode-laser-pumped Ti:sapphire laser” Optics Letters, Vol. 34, Issue 21, pp. 3334-3336 (2009) 

Group Exercise 2

Active/Passive Voice and Tenses?

In pairs, read each others work and identify where active or passive voice is used and what tenses are used.

Discuss with each other if they have been used appropriately.

What did you find?

Writing Coherently

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Where do I start?First think of the story you are wanting to tell your

readers.

• Write down the main points that you want to put across.

• Work out a logical order for the points.

• Decide how much detail you need to include in the text.

• Decide how much information you can assume that your readers know?

• What is relevant or irrelevant?

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Building up a report

• Each paragraph can develop a point.

• When you move on to a new point then try to start a new paragraph.

• You may even need to start a new section or a new chapter.

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Paragraphs in coherent text• Your points are developed in chunks of text –

paragraphs

• Subsequent paragraphs take your topics and points further so that your arguments are developed

• Paragraphs should not contain just one sentence.

Build logical bridges between new ideas

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Use link words across a sentence to improve cohesion.

• However,

• In addition to,

• Nevertheless,

• Despite…….,

• Firstly, secondly, …..

• Afterwards,

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Paragraphs set up reader expectations

• Each sentence will have a topic and point.

• The first few sentences of a paragraph indicate the topic and point you want to develop within that paragraph.

• You may be able to skim read an article by just reading the first two sentences of each paragraph.

The same concepts can be used for constructing paragraphs as are used for sentences.

Group Exercise 3

How Coherent are your Paragraphs?

In pairs -

Read first sentence of a paragraph from your partner’s work – hide the remainder of the paragraph

Guess what the next sentence will be about

Read what comes next and discuss whether it was as you guessed

Move to next paragraph and repeat

Swap over roles at half time.

Academic Integrity

Background

Why this is important

The Power of the Web• With the rise of the internet, the World Wide Web,

and search engines such as Google, anyone with access to a computer has an unprecedented amount of information available to them “at their fingertips”

• This is good news to you when researching your essays, reports, and projects

• But with power comes responsibility

• And the increased need for academic integrity

Definitions (taken from the OED)Academic

• Of or belonging to an academy or institution for higher learning; hence, collegiate, scholarly

Integrity

• Soundness of moral principle; the character of uncorrupted virtue, especially in relation to truth and fair dealing; uprightness, honesty, sincerity

Our Expectations • We expect you to

– be honest and balanced in evaluating the strengths and weaknesses of your own work, and that of others

– respect the intellectual property of others, their moral rights, and copyright

– conduct yourself according to the standards and conventions of your discipline

– avoid taking unfair advantage of others

Important GuidelinesSome details of what you have to know

University Policy• The University has adopted policy and procedures

regarding the standards we expect from our students, and what should be done in cases where students fall short of these standards

– “breaches” of academic integrity

• See the Calendar and the QA handbook (both available on-line via SUSSED)

Summary of Policy

• You must ensure you avoid

– plagiarism

• copying or paraphrasing without acknowledgement material attributable to, or the intellectual property of, someone else

– cheating

• gaining unfair advantage for yourself or another– falsification

• fictitious or distorted data, false claims– re-cycling

• re-using your own work without declaring you have done so

Range of Penalties• Your studies may be terminated

• You may be deprived of a degree

– even after it has been awarded

Where, in the panel's view, it is established that a breach of academic integrity has been committed, the panel will prescribe a penalty. Penalties that may be applied in cases where it is established that a breach of academic integrity has been committed shall include:

a requirement to make amendments to the thesis within a specified timescale;

failure in the thesis and permission to re-submit a revised thesis within a specified timescale;

failure in the thesis and termination of course with no right to re-submit.

Plagiarism

What it is, and how to avoid it

What is Plagiarism?

• In some countries/cultures students may expect to copy

• Teachers may want students to repeat exactly what is in text books or lecture notes.

• At the University of Southampton, however, all work you submit for marking must be your own original creation

Plagiarism is using someone else’s work…

…without indicating that it is not your own

…without crediting the original author

How to Avoid Plagiarism1. Quote any material copied from elsewhere

• it may be appropriate to paraphrase rather than copy and quote, as discussed below

2. Follow the quotation (or paraphrased material) with a citation such as [3] which clearly identifies an item in your bibliography

3. Put the bibliography at the end of your report

• this must give bibliographic details such as title, author, and year for each source you have cited

4. You must do this for all sources

How to Quote• The easiest and clearest way to identify a quotation is with

quote marks “…”

– for example “the other pre-eminent name in British Computing, Maurice Wilkes, arguably contributed rather more than Turing, certainly in practical terms, but is much less prominent in the popular perception”

• An alternative is to indent, or display, the quoted material, which is usually in italics

The other pre-eminent name in British Computing, Maurice Wilkes, arguably contributed rather more than Turing, certainly in practical terms, but is much less prominent in the popular perception

How and When to Paraphrase• Copyright law only allows you to copy small amounts of text

(one or two lines)

– longer quotes require the author to give permission

• In such cases you should paraphrase the source by putting the material in your own words

– Wilkes, though not as famous as Turing, perhaps made greater practical contribution

• You should also paraphrase to make sure your report flows smoothly and reads well

– a sequence of quotations can confuse your reader

Paraphrasing vs Plagiarism• It could be plagiarism if you

– take too much from one source,

– only replace some words with synonyms, or

– simply swap words or phrases round to make the sentence look different

• Instead you should

– summarise the key points from your source

– use your own words and phrases

– comment on and evaluate your source

How to Cite• Immediately after each quotation, or piece of paraphrased

material, include a citation tag

• This is a number, year, or other identifier in square brackets […]

– different styles exist, but you must use the same style throughout each essay or report

• For example

– “the other pre-eminent name … in the popular perception” [Halley 2005]

– Wilkes, though not as famous as Turing, perhaps made greater practical contribution [3]

Why Do We Cite Our Sources?• We are legally obliged to respect the author’s

moral right to be acknowledged as the source

•And also to support the scientific process:- new results are published- leading to new claims being made- these results and claims may be challenged - or they may be supported by further findings

• And the process requires a clear audit trail

• This is how scientific understanding develops

A “Victimless Crime”?• If you plagiarise

– you deny the true author the credit, and

– undermine the scientific publication process

• All breaches of academic integrity– divert staff from more

constructive activities, and– undermine the reputation of University of

Southampton degrees

Please Remember• Academic Integrity is important

• Breaches include plagiarism, cheating, falsification, and re-cycling

• We use automatic plagiarism detection software to help us identify breaches

• Students have been caught, and some have failed their degree as a result

• Make sure you quote (or paraphrase) and cite all your sources in a clear and standard way

The Process of Writing a Journal Paper

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Academic Integrity

• Before writing a paper discuss the idea with all your co-workers and especially your supervisor.

• Discuss who should write the paper and who should contribute various parts of it.

• Discuss the author list and order. This may change but you can normally decide who should be first author and the first author would normally write the first draft of the paper.

• Do not use anyone’s results without first obtaining their permission and discussing authorship with them.

Academic Integrity• Do not copy parts of other peoples papers even if “you can’t

think of a better way of putting it”.

• Always try to acknowledge the relevant previous work of others (and yourself) fairly through references.

• Acknowledge the work of others who have contributed to the work but who are not co-authors (e.g. for useful discussions, or for fabricating a certain fibre) in the Acknowledgements section.

• Acknowledge your sponsors – e.g. if the work was carried out under a certain grant or if your studentship is funded by a certain body.

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Which Journal?• Is it appropriate for your work – subject matter, where

has this sort of work previously been published, length of paper

• What is the quality of the journal – impact factors - and what is the quality of your work? Go for the highest feasible impact rather than the easiest ride, but don’t submit routine papers to Nature / Science.

• How fast is the journal’s submission to publication time?

• How much does it cost to publish in this journal?

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Follow the Journal Instructions• Most journals will give detailed instructions on the style and

structure of the papers that they will publish.

• They will ask for reviewer suggestions – choose people who have the expertise to do the job well, choose someone who would find your work interesting, don’t choose your (or your supervisors) enemies, don’t choose your close collaborators, choosing people that you have referenced in the paper is normally a good choice. If your choices look fair the editor will often use them as assigning appropriate and willing reviewers can be a tricky process.

• Follow the mechanical submission instructions exactly.

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Writing• Follow the suggestions we have already discussed for

coherent writing

• Once written – spell check

• Read you paper, correct it, re-read it, correct it, re-read it….until it’s as good as you can get it.

• Send a first draft to all co-authors for their comments. Do not submit your paper until all co-authors have acknowledged that they are happy with the final version.

• Make sure any figures are readable when shrunk to the size they will appear in the journal.

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Typical Peer Review Process• The editor will probably ask 3 or 4 anonymous reviews from

the relevant scientific community

• Once 2 or 3 are received the editor will make a first decision – publish as is, publish with optional revisions, publish with mandatory revisions, manuscript requires major revisions, rejected

• If you are asked for revisions, whether optional or not, always consider each change in a positive manner. In your response make clear your response to each and every comment, and change your manuscript accordingly. If a reviewer did not understand a part of your paper it is likely that other readers won’t understand it too. This is your chance to improve your paper. If you choose not to agree with a particular comment (avoid if at all possible) make your reasons very clear to the editor.

Typical Peer Review Process• You can normally appeal a reject decision but only

do so if you are very confident. You’re probably better off submitting an amended paper to a lower impact factor journal.

• Always give your co-authors the opportunity to comment on what revisions can be made

• Return your revisions within the allowed timescale

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…and Finally• In a 100 years time, or maybe in just 4 years time it is likely that:

Your experimental apparatus will be dismantled

Your lovingly created samples and devices will be lost

Your log books will be collecting dust on a shelf

Your thesis may be read – but mainly by your supervisor’s new students

But your Journal Papers will still be there as a permanent contribution to the world’s knowledge, they will be read and referenced by people from all over the world, they will inspire and be the foundation of new work, and act as a record of your personal achievements. So take great pride in your papers!

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World Map of My Citations – how else will you influence this spread of people in your life?

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World Map of My Citations – how else will you influence this spread of people in your life?