scientific writing aug2013

7/30/2019 Scientific Writing Aug2013

1/42

NAARM

1

Writing and Publishing a Scientific Paper:General Principles

NH Rao

National Academy of Ag r icul tu ral Research Management,

Rajend ranagar, Hyderabad
http://www.icar.org.in/http://www.icar.org.in/


2/42

NAARMOutline

why write papers and publish ?

status of scientific writing in India

principles of good scientific writing

scientific paper structure, organization, style

guarding against plagiarism

authorship

review and revision
http://www.icar.org.in/


3/42

NAARM


4/42

NAARM

4

understand cause and effect (discover laws and causes)

understand relationships

develop theories (explain behaviour, make predictions, drive new research)

solve problems

Scientific research

.. by application of the scientific method

particular method for acquiring knowledge about the world to:


5/42

NAARM

5

Characteristics

generated by a question

requires planned programme ofwork

requires reasoned argument to

support conclusions

is open to rigorous objective

testing by others

is reiterative

The Scientific Method

Process

Problem identification

Hypothesis formulation (context/review)

Controlled experiments to get data to

test hypothesis : Systemat ic , r igorou s,

repl icable

Analysis interaction between data and

theory

Reporting/Publishing Interaction with peers peer review

Acceptance/Rejection of theory/

solution - publication

Next question

is within an accepted research paradigm

A paradigm is essent ial to scient i f ic inquiry fo rselection, evaluation, and criticism (Kuhn)

sets of assumptions, laws, theories, methods and applications that form a scientific

research tradition (framework for scientific thinking)

procedures, methods and techniques that have been tested for their validity and

reliability and accepted by the scientific community in the specific area


6/42

NAARM

6

Scientific research is not complete until the results are published. Therefore, a scientific

paper is an essentialpart of the research process. Therefore, the writing of an accurate,understandable paper is just as important as the research itself.

Day, 1989


7/42

NAARM

7

Writing papers is a central part of research. If your research does not

generate papers, it might just as well not have been done. interestingand unpublished is equivalent to non-existent.

Your objective in research is to formulate and test hypotheses, to draw

conclusions from the tests and to teach these conclusions to others.

Your objective is not to collect data

A paper is not just an archival device for storing a completed researchprogram. It is also a structure for your research in progress. If you

clearly understand the purpose and form of research it can be immensely

useful to you in organizing and conducting your research

(Whitesides, 2004; > 1100 papers; 124 patents, h index >100)

If I have seen further it is by standing on ye shoulders of Giants

(Isaac Newton in a letter to Robert Hooke dated February 5, 1676)

Writing papers integral to the Research Process


8/42

NAARM

8

India: MS submissions and acceptance rates

global

Indias share of submissions has increased by 2 % (next only to Chinas 5.5%)

but, < 20% of submissions were accepted in 2010 (among lowest 3 countries)

acceptance rates are coming downSource: Thomson-Reuters, April 2012, Feb 2013

Global Share of Research

Output by Field


9/42

NAARMIndia: Scientific paper quality

Agricultural Science (2006-2010):

Relative Impact factor: 0.55

Non-cited-ness: 61% (% papers

not cited even once)

Source:

Thomson-Reuters, Feb 2013

DST: July 2012


10/42

NAARM

10

Reasons for rejection

1. Unoriginal work no new or useful

knowledge; previously published;

duplication

2. Unsound work weak hypothesis,

logical/design/methodological/anal

ysis errors

3. Not suited to journal

4. Slicing squeezing too manypublications into a limited work

5. Incorrect format for journal

6. Plagiarism (= copying)

7. Unready work: more research

needed

8. Poor writing: language,

presentation (figs/tables), style

The most common reason for

rejection is a lack of new

knowledge.

Errors in research

methodology, data analysis,

and language are flaws that

can be salvaged to some

extent.

Errors in manuscript

organization, including

methods, results, figures,

tables, graphs, and

references, are correctable

Source: Reasons for Rejection of Manuscripts

Submitted toAJRby International Authors


11/42

NAARM

11

A scientific paper must be written in a certain way and it must be

published in a certain way, as defined by three centuries of developing

tradition, editorial practice, scientific ethics, and the interplay of printing

and publishing procedures

Day, 1988


12/42

NAARM

12

General principles - definition of research paper

The first publication describing original research results

In a form whereby peers of the author can:

assess observations

repeat the experiments and test the conclusions

evaluate the intellectual processes

In a journal or other source document readily available in the scientificcommunity

Source: How to Write and Publish a Scientific Paper,

6th edition, by Robert A. Day and Barbara Gastel

(Greenwood Press/Cambridge University Press, 2006)


13/42

NAARM

13

General principles - Organization

Writing a scientific paper is largely a matter of organization structure - to meetthe needs of valid publication

Highly stylized with distinctive component parts

The front matter Title, Authors, Abstract, key words

Title: fewest possible words to adequately indicate contents; Important inliterature searching

Authors: those with important intellectual contributions to the work

Abstract/Summary: paper in miniature, complete within itself

Main body: Standard IMRAD Format for Scientific Papers:

1. Introduction: What was the question?

2. Methods: How did you try to answer it?

3. Results: What did you find?

4. Discussion: What does it mean?

People read sections in various orders; and tables and figures independently of text

Each section needs to be independent; and all sections must form an integrated unit


14/42

NAARM

14

key to scientific writing is clarity, particularly since it is a first

communication of original work contributing to new knowledge

the best English is that which gives the sense in the fewest short words

no room for ornamentation

most important requirement is reproducibility this is what makes scientific

writing unique

poor writing prevents or delays the publication of good science and affects

the growth of science

General principles - clarity


15/42

NAARM

15

Scientific paper structure - Title

A succinct, informative but also tempting title is essential, and is the first

of the key features in a manuscript to come under editorial scrutiny.

fewest possible words that accurately describe the content

Omit waste words such as "A study of ...", "Investigations of ...",

"Observations on ...", etc.

Indexing and abstracting services depend on the accuracy of the title to

extract keywords

useful in cross-referencing and computer searching

be specific: if the study is of a particular species or chemical, name it in

the title. If the study has been limited to a particular region or system, and

the inferences it contains are similarly limited, name the region or system

in the title

Adapted from : www.nature.com/naturephysics

An improperly titled paper may never reach the

audience for which it was intended


16/42

NAARM

16

snapshot of the complete paper

comprises four distinct components:

problem studied significance, hypothesis, objectives

(What problem did you study and why is it important ?)

methods/approach used

(What methods did you use?)

principal results obtained

(What were your principal results?)

summary of the conclusions reached

(What conclusions can you draw from your results about the problem you studied?)

Scientific paper structure - Abstract

Short abstract ?

one sentence answers

Longer abstract ?

several sentence answers

One page abstract ?

One paragraph answers

make sentences as specific and as quantitative as possible

Write the abstract afterfinishing the paper, as writing is an evolutionary

process, and the focus or emphasis of a paper may change during the writing

Source: Effective Abstracts, Celia M. Elliott, 2012


17/42

NAARM

17

Dryland Grain Sorghum Water Use, Light Interception, and Growth Responses to Planting Geometry

J.L. Steiner*

ABSTRACT

Problem/

Rationale

Crop yields are primarily water-limited under dryland production systems in semiarid

regions.

Object ives /

hypothes is

This study was conducted to determine whether the growing-season water balance could

be manipulated through planting geometry.

Method The effects of row spacing, row direction, and plant population on the water use, light

interception, and growth of grain sorghum [Sorghum bico lor(L.) Moench] wereinvestigated at Bushland, TX, on a Pullman clay loam (fine, mixed, superactive thermic

Torrertic Paleustoll).

Results In 1983, which had a dry growing season, narrow-row spacing and higher population

increased seasonal evapotranspiration (ET) by 7 and 9%, respectively, and shifted the

partitioning of ET to the vegetative period. Medium population crops yielded 6.2 and 2.3

Mg ha1 of dry matter and grain, respectively. High population resulted in high dry matter

(6.1 Mg ha1) and low grain yield (1.6 Mg ha1), whereas low population resulted in low drymatter (5.4 Mg ha1) and high grain yield (2.3 Mg ha1). Row direction did not affect water

use or yield. In 1984, dry matter production for a given amount of ET and light interception

was higher in the narrow-row crops. Evapotranspiration was less for a given amount of

light interception in the narrow-row crops and in the northsouth row crops.

conclus ion Narrow-row planting geometry appears to increase the partitioning of ET to the

transpiration component and may improve the efficiency of dryland cropping systems.

Structure of Abstract

(model abstract- ASA-CSSA-SSAA Style Guide)


18/42

NAARM

18

How to construct a Naturesummary paragraph

Annotated example taken from Nature435, 114-118 (5 May 2005).

One or two sentences providing a basicintroduct ionto the field,comprehensible to a scientist inany discipline.

Two to three sentences ofmore deta i led backgroun d, comprehensible toscientists in related disciplines.

One sentence clearly stating the generalproblembeing addressed by this

particular study.

One sentence summarising the mainresult (with the words here we show or theirequivalent).

Two or three sentences explaining whatthe main resul treveals in directcomparison to what was thought to be the case

previously, or how the main result adds toprevious knowledge.

One or two sentences to put the results

into a more general context.

Two or three sentences to provide a broaderperspect ive, readily comprehensible to ascientist in any discipline, may beincluded in the first paragraph if theeditor considers that the accessibility of the

paper is significantly enhanced by theirinclusion. Under these circumstances, thelength of the paragraph can be up to 300 words. (The above example is 190 words without the finalsection, and 250 words with it).

During cell division, mitotic spindles are assembled by

microtubule-based motor proteins1, 2

.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 'pushpull mitotic

muscle' model, in which kinesin-5 and opposing motor proteins

act between overlapping microtubules2, 4, 5

. However, the

precise roles of kinesin-5 during this process are unknown.Here we show that the vertebrate kinesin-5 Eg5 drives the

sliding of microtubules depending on their relative orientation.

We found in controlled in vitroassays that Eg5 has theremarkable 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. 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. We anticipate our assay to be a

starting point for more sophisticated in vitromodels of mitoticspindles. 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.

ABSTRACT/

SUMMARY


19/42

NAARM

19

Scientific paper structure - Introduction

In effect, a roadmap from

problem to solution

should be very clear wherebackground ends and new work

begins

should be fairly short: typically 3

paragraphs; range: 2 to 5

Background

Knowledge gap

Hypothesis

Approach

proposedsolution

Provide background needed to understand the

paper and appreciate its importance

not an exhaustive review - should focus on

hypothesis/purpose of study

1. Backgroundknown information - nature

and scope of problem - (why the work was

done: importance),

2. knowledge gap - Review pertinent literature

3. identify Hypothesis, purpose, research

question

4. Approach: Method of investigation

including reasons

5. State the principal results and conclusion

6. present only information relevant to

experiment

Typically funnel-shaped -

general to specific

Ref: Suggested rules (Day, 1988); Elliott, 2012; Stanford on line- writing in the Sciences, 2012


20/42

NAARM

20

the most important paragraph of the whole paper. Even if it is a

work of expositional genius, few among a broad audience are likely to

read beyond it. So it is vital that this paragraph tells the central story of

the paper, and makes clear why this story deserves to be told. Dont

launch into technical details, or merely list what you did. Set the scene,explain the background that will give the non-specialist reader a

context in which to understand the significance of the work, but fellow

specialists will also appreciate your telling them what you consider to be

the relevant questions in the field.

www.nature.com/naturephysics

Introduction the first paragraph


21/42

NAARM


22/42

NAARMScientific paper structure - Method

Purpose: provide a clear overview of work to allow others

to replicate and evaluate (validity of the results is judged)

Should describe the study design, materials, tests,measurements

Should identify (if applicable)

Equipment, organisms, reagents, etc used (sources)

Approval of human/animal research by an appropriate

committeeHow measurements were made and calculations were

done

Statistical methods/tests

May include tables and figures

An issue: level of detail in which to describe Well-known methods

Methods previously described but not well known

Methods that you yourself devised

Source: Writing a Scientific Paper: Basics of Content andOrganization Barbara Gastel, Elliott, 2012)

Break into smaller

sections with

subheadings

Report methods in

past tense (we

measured),

Use present tense to

describe how data are

presented in the paper

(data are summarized

as means SD)

Cite a reference for

commonly used

methods


23/42

NAARM

23

Scientific paper structure - Results

Purpose: Objectively present key results without any interpretation; (foundation for

Discussion) needs discrimination

Summarize what the data show - Point out simple relationships; big-picture trends

Present in an orderly, logical sequence with text, tables & figures

Figures: create visual impact; show trends and patterns; tell a quick story

Tables: Give precise values; display many values/variables

Design tables and figures to be understandable without the text

Use the same formats for all tables of a series

Avoid including too much information in one figure

Source: Writing a Scientific Paper: Basics of Content and Organization, Barbara Gastel: Elliott 2012)


24/42

NAARMResults (contd.)

Source: Stanford on line writing in the sciences , 2012

Organize in sections around tables/figures

Introduce a Table or Figure in the text beforeyou show it

Complement the information that is already in tables and figures

Report important negative results; gives the basis for a good discussion section

Give precise values that are not available in the figure

Repeat/highlight only the most important numbers, negative and control results

Reserve the term significant for statistically significant

Do not include rationale for statistical analyses within the Results section

Should present results but not comment on them

Use past tense for completed actions

Reserve comments on the meaning of your results for the discussion section

An issue: how much the information in text should overlap with that in tables and

figures minimize overlap


25/42

NAARM

Purpose: state interpretations of results and

opinions, compare with existing work, anddiscuss the implications of Results.

Gives the most freedom to display good

writing skills

Most challenging to write

Should begin with a brief summary of the mainfindings

Should answer the question stated in the

introduction

Support the conclusion (your data, others

data)

Defend the conclusion (anticipate criticisms)

Scientific paper structure - Discussion

Typically should move fromspecific to general (opposite of

introduction)

Invert the funnel !

big-picture

take- home

message

what the results mean

and why shouldanyone care



26/42

NAARM

26

Discussion (contd..)

Some items/questions commonly addressed:

What are the major patterns that arose out of the results?

What are the relationship, trends, and generalizations among the results, and

what are the exceptions to these?

What are likely mechanisms, and why?

Is there agreement / disagreement with previous works?

How does the discussion relate to Results and Background?

What are the implications of the results? discuss theoretical and practical

implications

Give all possible (reasonable) interpretations, dont ignore any possibilities

What do we understand now that we did not understand before this work?

What is the significance of this work.

Limitations of the study exceptions, unsettled points; other research needed

Source: Writing a Scientific Paper: Basics of Content and Organization Barbara Gastel,


27/42

NAARM

Source: Stanford on line

writing in the sciences ,

2012

Discussion (contd..)


28/42

NAARM

J.L. Steiner* - Dryland Grain So rgh um Water Use, Ligh t Interception, and

Growth Respon ses to Plant ing Geometry, Agro nom y Jou rnal

Conclusion - example

NAARM


29/42

NAARM

29

Scientific paper structure - References

Purpose:

To give credit

To add credibility

To help readers find further information

Important to be accurate

reference formats vary with journals

Source: Writing a Scientific Paper:

Basics of Content and Organization

Barbara Gastel; Elliott, 2012

NAARM


30/42

NAARM

30

writing should be clear, concise, and complete

Clear writing: short, active sentences; simple tenses; active voice.

Concise writing: frugal use of words; shorter, simpler words.

Complete writing: difficult in technical work; fine line between writing

everything an article needs to be logically complete and writing more

than is necessary; definitions of symbols, notations and effective use of

citations help

Style (3 Cs)

The best writing in science, as elsewhere, is simple, clear,

precise, and vigorous. Decide what you want to say and say it assimply, informatively, and directly as possible.

Writ ing Successfu l ly in Science

by Maeve O'Connor

NAARM


31/42

NAARM

31

Good writing starts with good structure (sections (IMRAD) ; subsections, paragraphs

List the main points that are relevant to the section/subsection - topic sentences

arrange topic sentences in a sequence so that each successive point is related to and

builds on the previous point

the topic sentences provide the framework for each section

construct the paragraph

Rule: one topic sentence - one paragraph

begin each paragraph with the topic sentence (note: readers pay the

most attention to the beginning sentences of paragraphs)

explain and expand on the idea in the topic sentence; give examples

summarize such that it leads logically to the next paragraph

write short paragraphs ( 8 - 10 sentences)

ensure balance in paragraph structure

Style constructing effective paragraphs

Source: CM Elliott, 2012; http://online.physics.uiuc.edu/courses/Phys496/Spring12/Lectures/

NAARM


32/42

NAARM

32

Suggested reading:

Robert Barass: Scientists must write

There is a definite rhythm in sentences. Read what you have written, and

change the wording if it does not flow smoothly.

If the proof of the pudding is in the eating, then the proof of the writing is in the

reading. Follow this rule above all.

Style: Writing is a creative process

good quality scientific papers require:

good quality research, with good quality experimental design

good quality data to analyze and interpret!

patience to revise, revise, revise

NAARM


33/42

NAARM

33

if somebody reads your conclusions before reading the rest

of your paper, will they fully understand them? If the answer is yes,

theres probably something wrong.

A good conclusion says things that become significant after the

paper has been read. A good conclusion gives perspective to sights

that havent yet been seen at the introduction. A conclusion is about

the implications of what the reader has learned.

And so to conclude... good writing not only serves your audience but

improves the chances of the research being noticed and read, and of

it stimulating further progress.

And neither will it hurt your citations ..

Heres a simple test:

www.nature.com/naturephysics

NAARMG d i t Pl i i


34/42

NAARM

34

Plagiarism is scientific dishonesty

What constitutes plagiarism:

Submitting anothers published or unpublished work, in whole, in part, or inparaphrase, as ones own without properly crediting the author by footnotes,

citations, or bibliographical reference

Submitting material that has been produced through unacknowledged

collaboration with others as ones own original work without written release from

collaborators

Submitting material obtained from an individual or agency as ones own originalwork without reference to the person or agency as the source of the material

Guard against Plagiarism

Tips for avoiding plagiarism:

Study the original text until you fu l lyunderstand its meaning

Set aside the original and write a summary of the text i n your own words

Check your version with the original to ensure that the meaning has been retained

Enclose any text or phrase that you have reproduced exactly in quotation marks

Cite the source!

Source: Cooper SL and Elliott CM, 2012; Avoiding plagiarism, University of Illinois:

http://online.physics.uiuc.edu/courses/Phys496/Spring12/Lectures/Plagiarism.pdf

NAARMA th hi (ICMJE)


35/42

NAARM

35

Authorship credit should be based on

1) substantial contributions to conception and design, acquisition of data, or

analysis and interpretation of data

2) drafting the article or revising it critically for important intellectual content; and

3) final approval of the version to be published

Authors should meet conditions 1, 2, and 3.

When a large, multicenter group has conducted the work, the group should identifythe individuals who accept direct responsibility for the manuscript. These individuals

should fully meet the criteria for authorship (journals may ask individuals to complete

journal-specific author and conflict-of-interest disclosure forms).

Acquisition of funding, collection of data, or general supervision of the research group

alone does not constitute authorship.

All persons designated as authors should qualify for authorship, and all those who

qualify should be listed.

Each author should have participated sufficiently in the work to take public

responsibility for appropriate portions of the content.

Authorship (ICMJE)

Source: http://www.icmje.org/ethical_1author.html

NAARM


36/42

NAARM

36

NAARMChoosing a Journal


37/42

NAARM

37

Choosing a Journal

Depends on significance of the work must be evident from the Introduction:

Global/Interdisciplinary: big international multidisciplinary journal like: Nature,Science, PNAS

Global but Disciplinary: international discipline specialty journals like: LeadingProfessional Society journals; oth er leading jou rnals

Work is of regional significance : regional specialty journals like: Asian Journalof

Work is of local significance : national level journals

Confirmation or Repeat study (me too): high acceptance rate journals some on

line; and author-pays journals like PLoSONE, Nature Communications, .

Adopted from: IB Consulting; http://www.ianbeecroftconsulting.com

NAARMP R i


38/42

NAARM

38

Peer Review process

anonymous - double blind

editor chooses reviewers increasingly authors are being asked to suggest a few names

decision on publication is editors

vast majority of papers are advised to be revised major revision, minor revision (great

opportunity; needs to be handled correctly)

respond quickly but not immediately sleep over it; discuss with co-authors

prepare responses carefully (Reviewer can be wrong! Be tactful and enthusiasticthank the reviewers)

consult co-authors, statistician if necessary

provide a cover letter, point by point response and highlight (identify) responses

specifically (eg page no, para no.)

editor and reviewers are usually on your side trying to help you to publish goodscience they are not usually paid for this service; make their job easy

rejection rates of good journals are high (> 50%)

NAARMResponse to Review


39/42

NAARMResponse to Review

Initial responses

a judgment of Major Revisions (or worse, a rejection) can lead to a variety of emotions

- disappointment/resentment, question self-worth .

remember that comments are not personal and adopt a positive attitude for response

10 Principles of response

decide whether to resubmit to same journal or change journal depending on

comments

contact editor on unresolved issues before revising

prioritize reviewers comments

view the reviewer as consultant/collaborator in preparing responses

deal with comments you do not agree

disagree without being disagreeable

develop a strategy for addressing divergent comments

put in the work and show all that has been done

if suggested, shorten the MS

review literature before submission

Source: Provenzale (2010): Revising a Manuscript: Ten Principlesto Guide Success for Publication; AJR, 195, 382-387

NAARMDoing a Review


40/42

NAARMDoing a Review

Peer Review: Tone

Assume there is some poor student on the other end who did all the work, and

whose confidence and career depend on your critique.

Tone matters! eg. The authors should delete table 5; not only is it completely

irrelevant, but it also reveals their utter lack of statistical understanding.

vs. Table 5 contains unnecessary information (for example), and a Pearsons

correlation coefficient may not be appropriate here. The authors should consider

revising or omitting the table.

Avoid criticizing the authors! Criticize the work.

Avoid generalizations; point out specific errors.

Use positive instead of negative language where possible: The paper is poorly

written. vs. The writing and presentation could be improved. For example

Avoid lecturing to the authors.


NAARM


41/42

NAARM

41

Scientific research is not complete until the results are published.

Therefore, a scientific paper is an essentialpart of the research

process. Therefore, the writing of an accurate, understandable

paper is just as important as the research itself. Therefore, the

words in the paper should be weighed as carefully as the reagents

in the laboratory. Therefore, the scientist must know how to use

words. Therefore, the education of the scientist is not complete untilthe ability to publish has been established

Day, 1989

Easy reading is damn hard writing (Hawthorne)

NAARM


42/42

NAARM

Thank You
http://www.icar.org.in/

scientific writing aug2013

Documents