charles darwin

Charles Darwin

Scientific Writing

A naturalist’s life would be a happy one if he had only

to observe, and never to write

jean

80-90% of all the scientists who have ever lived, are alive today... and trying to publish papersThe number of papers published doubles every 10 yearsYou need to use every availble tool to enhance your chances of publishing your work in the best possible journal

Even the most successful scientists usually would rather conduct new research than write a new draft to report their work.

Yet, research is of little value unless it is reported in written form to the greater scientific community.

Published work creates a historic record of scientific advances and provides a permanent resource for all future scientific inquiry.

The scientific community has long emphasized the quantity and quality of scholarly publications as a way to judge the reputation of scientists.

Why Publish?

Choosing A Journal - Considerations Journals that commonly publish work in this area. Impact factor. Speed of review and publication. Page charges. Will your colleagues see your paper if you publish here? Is the expected size (length) of the paper appropriate for this journal? When in doubt, email, write or call the editor of the journal and ask whether they will consider a manuscript of the type (research or review article), general subject area, and length that yours is expected to be. While it helps to know what journal you will be submitting to, it is not required to begin the writing process. When you choose a journal, use Instructions to Authors (ITA) to guide your writing. If you have not settled on a specific journal, write based on generally accepted scientific style. You can fine tune the article later for a specific journal.

Impact FactorThe Journal Impact Factor measures how frequently the average article in a journal has been cited in a particular year.

The Impact Factor is calculated by dividing the number of current citations to items published in the two previous years by the total number of articles & reviews published in the two previous years.

Getting OrganizedCopy or print at least the abstract of every article that you think you might need.Develop an organization system for these articles.Take notes… write your notes directly on the article or on a separate piece of paper.It is helpful to write key points of relevance at the top of the front page of each article.Write the full journal source on each copied article if it is not visible on the front page.

Patterns for Organizing Material Pattern BasisChronological Sequence in which something happensGeographical or spatial Physical arrangement of entitiesFunctional How parts workImportance Usually with elements of decreasing importancePossible Solutions From least to most likely/best, or building to a climaxSpecificity General to particular or particular to generalComplexity Usually from simple to complexPro and Con Presenting both sides of an issue or decisionCausality Cause and effect

Define the Question and the Answer:

Scientific Writing Begins Where Research Does, With a Question

Ask yourself what a reader needs to know to understand the study.

Show the reader why the work is important – telling them isn’t enough.

You should be able to state the question addressed by your work in one clear sentence. Similarly, the answer you have found should be stated in one clear sentence.

Writing is a process of coding the thoughts in your mind into words. The reader must then decode the words back into thoughts. The trick is to ensure that the thoughts created in the reader’s mind are the same thoughts that were in your mind.

General Principles

Need to be able to explain your work to people outside the field.

Make the story as simple as possible, make it easy to read and understand.

Remove pompous language, extra words, and empty sentences.

In all sections of the paper:

Organize from most important to least important when useful.

Use topic sentences to state the overview whenever possible.

Reading the first sentence or two of every paragraph should reveal the story.

Make sentences, paragraphs, and each section of the paper concise.

Remove any unnecessary information or repetition. "The more noise, the less message"

All information in the text and in the figures and tables should closely relate to the question and answer.

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The Story consists of four main parts:1) the question2) the experiments done to answer the question3) the results obtained that answer the question4) the answer

In addition, the story includes: how the question and answer fit in with previous work why the question and answer are important

The Goal:The goal of any scientific publication is to state a clear message and tell the story of the

paper while simultaneously presenting all the necessary details.

The reader must be able to see both the forest (the big picture) and the trees (the details)

The Message (Answer):You must be able to state the message of the paper (the answer to the question) in a single sentence

A Scientific Manuscript Tells a Story

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Parts of a Scientific Manuscript


A short phrase. Rarely a complete sentence.

Purpose: The title conveys the key points of your study to a reader glancing through a citation index, database, table of contents, or references page.

Should accurately, completely and specifically reflect the paper.

Should be clear, informative, and detailed, but not contain unnecessary details.

Most journals prefer titles that are no more than 100 characters, including spaces.

Should contain key words that define your topic.

Should emphasize subjects or findings that are unique to your study.

Many readers will decide whether to read the paper based only on the title.

Avoid humor (intended or unintended), two-part titles, trivial phrases (“Notes

on…” or “A Study of…”).

Capitalize each “significant” word in the title. Generally, do not capitalize

words like (a, an, the, and, but, if, at, in, on, of, between, because, after).

When writing the first draft any title will suffice, you can revise it later.

The Title



Too Vague: Effects of pH on the Growth of Bacteria

Revision: Effects of pH Variance on Growth of Pseudomonas aeroginosa

Too Detailed: Effects of pH Variance from 4.0 to 9.0 on the Growth of Prokaryotic Pseudomonas aeroginosa Bacteria (strain142) in Minimal Media under Aerobic Conditions

Revision: Acidic pH Increases the Growth Rate of Pseudomonas aeroginosa

Examples of Titles


Titles – Keywords, Emphasis and Impact!

• Effects of the Novel Drug Blancamycin on Tumor Growth in vivo

• Tumor Growth Arrest by the Angiogenesis Inhibitor Blancamycin

• Tumor Arrest by the Angiogenesis Inhibitor Blancamycin




A condensed version of your paper, written for people who may never read the complete version.

Purpose: The abstract conveys the relevance of the topic to the reader, and summarizes the approach to answering the question, the major supporting data, and the major conclusions reached by performing the study. It should entice the reader to read further.

Must stand on its own, without the text.

Avoid abbreviations and reference to figures or other information in the text. In most cases, avoid citation of other literature.

Can be roughly constructed by rewording topic sentences from each section to flow well in one paragraph. The abstract should never repeat sentences from your text.

Generally 100 – 250 words in length, one paragraph, check ITA for specific rules.

The Abstract



To provide clear continuity throughout the abstract:

Repeat key terms.

Use consistent order for details.

Keep the same point of view in the question and the answer.

Use parallel or consistent point of view for comparisons and other parallel ideas.

Signal the parts of an abstract both visually (by starting a new sentence) and verbally (by using a signal word or phrase) at the beginning of the sentence.

Continuity in the Abstract



Abstract - Overall Organization Topic Signal Phrase

Background (if any)

Question To determine whether… We…

Experimental Approach Therefore, we asked whether…. To answer this question we.... To test this hypothesis we….

Results We found…

Answer We conclude that…. Therefore….

Implication-Speculation-Significance These results suggest that….

The question and the experiment done may be presented in the same sentence, in which case only the question needs to be signaled.


Example Abstract

Background

Question

Experimental Approach

Results

Answer

Significance


Nearly all journal articles have introductions that present background information, the gap in knowledge, a rationale for the current study and the purpose/question addressed in the current study. However, not all articles are organized precisely this way. Some will not contain each section, and some will present the information in different order. Use this information as a tool to ensure that you include all information necessary to put your study into the broader context of scientific knowledge. As in the abstract, specific words and phrases should be used to indicate the purpose of the section.

Importantly- the Introduction should not contain a statement of the answer.

Introduction

Topic SentenceThe topic sentence is usually the first sentence of the paragraph. It introduces the topic of the paragraph.

The topic sentence of the first paragraph begins your paper on general terms and engages your reader’s interest.



One or more paragraphs provide a brief, condensed history of the previous studies that your work challenges or develops. Do not exhaustively review the literature, but do discuss and reference relevant previous work.

Purpose: To show that you are well-versed in the topic and have appropriately studied the literature before performing your experiments. Also to provide a context for your work.

Introduction - Previous Studies

…

…



Introduction - Gap in Existing KnowledgeA few sentences between history and background states the gap in existing knowledge of the topic and relate the context to your work.

Purpose: To smooth the movement of your introduction from the general history to information specific to your study. To connect the context directly to your work.


Any background information essential to understand your study should be stated now. Terms unknown to the scientific community are defined here, and information is cited.

Purpose: To help the reader understand and interpret the contents of the paper.

Introduction - Background of Study


Introduction - Hypothesis or Overall ConclusionsThe last sentence is nearly always your hypothesis, which is the main objective, prediction, or question you hope to answer. The introduction may also end with a statement of the overall significance of the paper. A “mapping” section may also be included to inform the reader of what they will find in the rest of the paper.

Purpose: To pose the question or problem that your study addresses; also to show the reader what to expect in the rest of the paper.



Materials and MethodsThe major challenge in writing the Methods section is deciding how much detail to include.

Purpose:Readers use the Methods section to determine whether sufficient analytical methods were used to make the results meaningful.

Serves as a historical marker, denoting the technology available at the time.

Provides readers with a way to test your results; they should be able to reproduce the results you obtained by following your methods.

What Should Be Included in the Methods?Names of chemicals, instruments, and special equipment used. Should provide a step-by-step procedure. Sometimes a diagram of an apparatus or a flowchart of the procedure can be used to clarify complicated methods. Omit details of well known methods that have already been reported; cite a reference.Briefly describe methods that have been reported but are less well known, and cite a reference.



Unnecessary Information:Omit unnecessary details that distract the reader and waste space. These include names that are vague, unofficial, or names of typical laboratory equipment (gloves, stirrers, pipettes, balances).

Measurements of amounts where concentrations suffice are unnecessary.

Descriptions of items or procedures that are common knowledge are also unnecessary.

Necessary Information:There should be enough detail that a scientist in the same field could reproduce the

experiment or study and obtain the same results.

Names Measurements DescriptionsChemicalsProceduresSpecial equipmentEquationsInstruments: Model # Manufacturer

ConcentrationspH

TemperatureWavelength

Time intervals Number of samples

VolumesWeights

ProceduresStatistical analysis

InstrumentsStudy Sites:

Topography Vegetation

Climate Ecology

Information to Include in Methods Section



Materials and Methods

For every piece of data (Tables and Figures) and every result in the Results section there should be a method in the Methods section.

Use subheadings to separate sections of the Methods.

Use transition phrases such as: To prepare the enzyme solution….

To separate collagenase-resistant fragments from intact surfactant protein A…

State the purpose or reason for any method whose relation to the question may not be obvious to the reader. For example: Bovine serum albumin (0.1%, fraction V) was included in the binding buffer because albumin reduced adherence of protein A to microcentrifuge tubes but did not alter the binding of surfactant protein A to human lymphocytes.



Purpose: The results section is where you present the data and develop a convincing case that the results answer the question posed by your study.

Subheadings signal topics of subsections visually. Topic sentences and transition phrases or clauses at the beginning of subsections and paragraphs signal topics verbally.

Words such as 'We found' signal the results.

Most figures and tables are used in the Results.

Refer to specific Figures and portions of Figures.

As much as possible, do not discuss the implications of data in the Results section.

Results



For studies in which the results of one experiment determine what the next experiment will be, the story consists of a repeated four-part pattern:

• Subheading

• Question• Experiments• Results• Answer

Results



• Transition/Background

• Question• Experiments• Results• Answer

• Interpretation/Transition

Results



The figures and tables together should tell the story of the paper.

Omit nonessential figures and tables and nonessential data.

Do not present the same data in both a figure and a table.

Each figure and table should be simple, with a clear point.

Figures and tables should be as parallel as possible in design.

When appropriate, show the main story of the paper in figures and background information in tables.

Figure legends and footnotes of tables should contain sufficient information to make the figure or table understandable without reference to the text.

Use large size fonts that will be legible when reduced to publication size, but minimize the use of text in figures.

Optimize the layout and space requirements of each figure.

Figures and Tables

Presenting Data EffectivelyFlow Diagram – pathways, procedures Emphasizes concepts Eliminates unnecessary words

Tables – quantitative data Use a title No figure legend

Line Graphs – shows trends Many points for one variable often used for concentration or time dependence Symbols must be clearly distinguishable from the line and from each other May use different colors if comparing multiple relationships (but check whether journal accepts color figures and what costs are) Use different colors if comparing multiple relationships

Histograms – testing only a few conditions Compares different conditions

Visual Data – autoradiograms, gels, photographs (cells, EM, in situ hybridization) Models



Which Figure is the Most Useful?


Optimize Spatial Organization of Figures

sc35 Tax Merge

No

Stre

ssSt

ress

CB

FED

A

sc35 Tax Merge

No Stress

Stress

CB

FED

A


00K503

3356

33R

34tS-11

346/85

44F

44A5969

MAb 4G1/FMAb 8F7/FMG strains

Assay scores (range 0-4)

The same Table modified to fit one side of a double-column layout

4 3 3 03 3 3 0

43

4 44 4

8F7/F4G1/F

tS-11 R S6 K5036/85A5969 F MAb

Assay scores (range 0--4) determined for various MG strains

Wide table that would fit on a single-column page

Format your Tables to Fit Available Space


The Discussion has three parts:The beginning states the answer to the question and provides evidence to support the answer.

Do not begin with a summary of the results.Do not begin by repeating the Introduction or writing a new Introduction.

The middle explains the answer, thus indicating how the answer fits in with previous work.

The end states recommendations, applications, implications, or speculations, thus indicating the importance of the answer.

In General:The discussion should include alternative explanations of results.

Topic sentences at the beginning of every paragraph, either alone or in combination with transition words, phrases, or clauses, repeated key terms, and other techniques of continuity, tell the story in the Discussion.

The answer should be clearly identifiable at both the beginning and end of the Discussion.

In each paragraph, supporting sentences should be organized to support the topic sentence.

Do not include tangential topics.

Discussion


Every reference in the text must be in the reference list.

Every reference in the reference list must be in the text.

Every reference must say what you claim it says.

Have a sufficient number of references to accurately give credit to the work of others and to direct readers to sources of further information.

Keep the number of references to a minimum.

All discussion of previous work or ideas of others MUST be referenced.

References must be formatted as described in the ITA.

References


There should be:• no loose ends in the text.• no answer in the Discussion without a question in the Introduction.• no answer in the Discussion without a result in Results. • no result in Results without a method in Methods.

Key terms and abbreviations should be consistent throughout the paper.

The figures and tables should agree with the text and key terms should be consistent.

References to specific data in a figure (lanes, markers, units of measurement, etc.) should be stated clearly in the text and exactly as shown in the figure.

Each figure and table should show what the text says it shows.

Make all statements of the answer the same.

Make all statements of the question the same.

Make sure that the answer answers the question asked: use the same key terms, the same verb, and the same point of view.

Continuity of the Parts

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