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Writing a Scientific Paper: General Principles

NH Rao National Academy of Agricultural Research Management, Rajendranagar, Hyderabad

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India: MS submissions and acceptance rates

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global

Indias share of submissions has increased by 2.2% (next only to Chinas 5.5%) < 20% of submissions were accepted in 2005-10 (lowest 3 countries) acceptance rates are coming down

Source: Thomson-Reuters, April 2012

General principles - Purpose

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Writing papers is a central part of research. If your research does not generate papers, it might just as well not have been done. interesting and unpublished is equivalent to non-existent.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 research program. 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)

The goal of scientific research is publication

(Robert Day, 1988)

General principles - definition

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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 scientific community

Source: How to Write and Publish a Scientific Paper, 6th edition, by Robert A. Day and Barbara Gastel (Greenwood Press/Cambridge University Press, 2006)

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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

General principles - Organization

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Writing a scientific paper is largely a matter of organization structure - to meet the 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 in literature 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 (Introduction, Methods, Research [and] Discussion)

1. 2. 3.

Introduction: What was the question? Methods: Results: How did you try to answer it? What did you find?

4.

Discussion: What does it mean?

Note : People read sections in various orders; and tables and figures independently of text (each section needs to be independent and at the same time all sections must form an integrated unit)

General principles - clarity

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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

Abstract
snapshot of the complete paper comprises four distinct components:

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problem studied significance, hypothesis, objectives (What problem did you study and why is it important ?)
methods/approach used (What methods did you use?)

Short abstract ? one sentence answers Longer abstract ? several sentence answers One page abstract ? One paragraph answers

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?) make sentences as specific and as quantitative as possible Write the abstract after youve finished 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
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Structure of Abstract
(model abstract- ASA-CSSA-SSAA Style Guide)

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Dryland Grain Sorghum Water Use, Light Interception, and Growth Responses to Planting Geometry J.L. Steiner* ABSTRACT Problem/ Rationale Objectives / hypothesis Method Crop yields are primarily water-limited under dryland production systems in semiarid regions. This study was conducted to determine whether the growing-season water balance could be manipulated through planting geometry. The effects of row spacing, row direction, and plant population on the water use, light interception, and growth of grain sorghum [Sorghum bicolor (L.) Moench] were investigated at Bushland, TX, on a Pullman clay loam (fine, mixed, superactive thermic Torrertic Paleustoll). 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 dry matter (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. Narrow-row planting geometry appears to increase the partitioning of ET to the transpiration component and may improve the efficiency of dryland cropping systems.
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Results

conclusion

How to construct a Nature summary paragraph

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Annotated 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.

ABSTRACT/ SUMMARY

One sentence clearly stating the general problem being addressed by this particular study. One sentence summarising 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. 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. Under these circumstances, the length of the paragraph can be up to 300 words. (The above example is 190 words without the final section, 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 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. 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 vitro models of mitotic spindles. For example, the individual and combined action of multiple mitotic motors could be tested, including minus-enddirected 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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Introduction

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Purpose: introduce the paper by providing background needed to understand the paper and appreciate its importance (In general, should be fairly short) Suggested rules (Day, 1988; Elliott, 2012):

Give background so that reader can understand the nature and scope of problem (why did you do the work: motivations/importance),
Review pertinent literature; back all statements of fact with a reference State the method of investigation including reasons State the principal results State the principal conclusion present only information that is relevant to the experiment It should be very clear where the background ends and your new work begins this is important

In effect, a roadmap from problem to solution

Typically should be funnel-shaped, moving from general to specific

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Methods

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Purpose: description of your work to allow others to replicate and to evaluate what you did (crucial as this is where the validity of the results is judged) Should describe the study design, materials, measurements, tests

Should identify (if applicable)

Equipment, organisms, reagents, etc used (and sources thereof) Approval of human or animal research by an appropriate committee How 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

use papers published in the same journal as models

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

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Results

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Purpose: Objectively present key results without any interpretation; (foundation for Discussion) needs discrimination Present in an orderly, logical sequence with text, and tables & figures, or both

Organize sections around tables/figures

Introduce a Table or Figure in the text before you show it Important negative results must be reported; gives the basis for a good discussion section

An issue: how much the information in the text should overlap with that in the tables and figures minimize overlap
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 Should present results but not comment on them Combine with Discussion ?

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

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Purpose: state your interpretations of results and opinions, compare to existing work, and discuss the implications of your Results. Should begin with a brief summary of the main findings Should answer the question stated in the introduction Some other 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 your Results and Background? What are the implications of your 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
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Typically should move from specific to general (opposite of introduction)

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

References

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Functions:

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, MD, MPH

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Style (3 Cs)
writing should be clear, concise, and complete

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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; effective use of citations help

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Style constructing effective paragraphs

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Good writing starts with good structure (sections (IMRAD) ; subsections, paragraphs List of 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
Source: CM Elliott, 2012; http://online.physics.uiuc.edu/courses/Phys496/Spring12/Lectures/
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Writing is a creative process

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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. Suggested reading:

Robert Barass: Scientists must write

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Peer Review process

anonymous - double blind

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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 provide a point by point response on resubmission rejection rates of good journals are high (> 50%) editor and reviewers are usually on your side trying to help you to publish good science reviews can be used to advantage by the authors in revising scripts/work

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Guard against Plagiarism

Plagiarism is scientific dishonesty What constitutes plagiarism:

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Submitting anothers published or unpublished work, in whole, in part, or in paraphrase, 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 original work without reference to the person or agency as the source of the material Tips for avoiding plagiarism: Study the original text until you fully understand its meaning Set aside the original and write a summary of the text in 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/L ectures/Plagiarism.pdf
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Guard against plagiarism

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Using another authors ideas or words without proper documentation; representing someone elses creative work (ideas, words, images, etc.) as

ones own, whether intentional or not

Tips for avoiding plagiarism: Study the original text until you fully understand its meaning Set aside the original and write a summary of the text in 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/L ectures/Plagiarism.pdf
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Scientific research is not complete until the results are published. Therefore, a scientific paper is an essential part 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 until the ability to publish has been established
Day, 1989

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Thank You

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