Instructor: Gary Ritchison
Course syllabus: Click here!
Writing a Scientific Paper | Abstract | Introduction | Methods | Results | Discussion | Literature Cited | Useful Links
Scientific writing is NOT a science. There are no proven theories or testable hypotheses.
Before writing a scientific paper, determine:
2. Why are they going to read it?
The audience influences style!! For example, how would research on avian mating strategies be presented to an ornithological journal, to a departmental seminar audience, & to a local bird club??
This course will focus primarily on writing for others in the profession, i.e., on writing publications for the primary literature. The primary literature includes:
2) in a form in which peers can repeat the experiments & test the conclusions (i.e., methods & results included),
3) in a journal or other form readily available within the scientific community
2) review papers that summarize & interpret primary literature,
3) some books (unedited or not containing original results),
4) articles in popular magazines (e.g., Natural History, Audubon, & Scientific American)
5) scientific encyclopedias & dictionaries
The relative ‘prestige' of journals in the primary literature varies:
The format of publications in these various journals varies but, wherever a paper is submitted, an author should strive to write the best paper possible. How do you get a paper published?
1) Submit your manuscript to the editor of a journal (making sure
followed the journal's
2) The editor has the manuscritp reviewed by 2 - 4 reviewers
3) The editor reads the manuscript, evaluates the reviews, & may then:
5) Editor assigns manuscript to particular volume &, at the appropriate time, sends it to the publisher.
6) Several weeks before that volume is to be published, the author receives page proofs (manuscript in form that it will appear in the journal). The author carefully reviews proofs to make sure there are no typos or other problems. A limited number of changes can be made in the manscript at this point but the authors must pay for any changes not the fault of the publisher. The author is also informed about page charges at this point & the availability of reprints.
7) Manuscript is finally published.
Is good writing important?
Active biologists write papers for the primary literature, but they also write lots of other things such as lectures, poster presentations, grant proposals, resumes (or vitae), letters (e.g., of application & recommendations), memos, & progress reports.
Others who read these make judgements about you based on the quality
of your writing. How does a poorly written letter of application affect
your chances of getting a position? What chance does a poorly written
have of getting funded? What chance does a poorly written manuscript
of being accepted for publication? Obviously, good writing is very
How does one become a good 'scientific writer?'
In BIO 801, you'll be writing a research proposal, a research paper, an oral presentation, and a poster. You'll also be reviewing several manuscripts. Your proposal, paper, presentation, and poster will be based on a 'study' of your choosing. This 'study':
2) will be the focus of most of your writing in this course. And, you'll be reading and writing (and re-writing) about it all semester!! So, it's very important that you choose a topic of interest to you. I'd be happy to provide some ideas and I'd also encourage you to discuss ideas with your advisor or other faculty members (or other graduate students).
To obtain books and journal articles that the EKU library doesn't have, use InterLibrary Loan.
Reading & Citing the Scientific Literature
Reading Scientific Papers
1 - Acquire some background knowledge
Review papers provide historical perspective, summarize contributions of influential researchers, & often point out where additional work is needed. The Literature Cited sections of reviews are an excellent introduction to the primary literature of a particular field. Reviews may occasionally appear in many journals and some publications specialize in review papers (e.g., the Annual Review series).
9 - Develop a system for keeping track of all your references. For example:
GUIDELINES FOR BETTER SCIENTIFIC WRITING
1) Omit unneeded words; shorten wordy phrases. Here are some examples of sentences with unneeded words; edit to make them more concise.
There is now a method, which was developed by Jones (1973), for analyzing the growth of rotifer populations.
It has been reported by Smith (1988) that the majority of birds are insectivorous.
It should be noted that most nests were in close proximity to the forest edge.
Singing was monitored in order to determine if older males have the ability to produce more complex songs.
Traps were checked on a daily basis.
Increased levels of nitrogen gave rise to quite a few changes in leaf morphology.
It was demonstrated that juvenile sparrows lack the ability to forage as efficiently as adults.
The eggs were blue in color, and they were covered with a large
of black spots.
HINT: Modifiers such as very, quite, & rather are meaningless in scientific writing (so, in other words, don't use them!).
ADDITIONAL HINTS: Useful information about word choice.
2) Use active voice (but not excessively)
Passive: Territory size was found to vary with population
Active: Territory size varied with population density.
Passive: From field observations, it was found that all
individuals remained on the study area.
Active: Field observations revealed that all radio-tagged individuals remained on the study area.
Passive: Several marking techniques were used on the birds.
Active: I used several marking techniques on the birds.
Pronoun Reference (identification of a pronoun with its intended antecedent). Make sure all pronouns can be easily identified.
Faulty: Farrar and Smith (1998) examined the foraging
of House Sparrows. They reported that their diet consisted primarily of
Better: Farrar and Smith (1998) examined the foraging behavior of House Sparrows, and found that sparrows fed primarily on seeds.
Even better: House Sparrows fed primarily on seeds (Farrar and Smith 1998).
The dominant male, along with his subordinates, defends [not defend] the den site.
The color and shape of the beak are [not is an] important taxonomic features [not feature].
Avoid repetition - Some sentences or paragraphs are wordy because the writer includes the same information twice. For example:
Wordy: The opossum is of moderate economic importance according to
(1988), who reviewed the importance of the opossum in detail.
Concise: Opossums are of moderate economic importance (Hamilton 1988).
Make sure paragraphs are coherent units of thought.
Paragraphs should be logically constructed passages organized around
a central idea often expressed as a topic sentence. A writer
orders, and connects paragraphs as a means of guiding the reader from
topic to the next, along a logical train of thought. Topic sentences
occur at the beginning of a paragraph, followed by material that
illustrates, or supports the main point.
Vary your sentences.
Pay attention to the structure, length, and rhythm of your sentences. If your writing is unvarying and one-dimensional, you will not get your message across as effectively. For example, the following paragraph is dominated by short, choppy sentences:
Be careful about using nouns as adjectives:
This would be better as:
Use commas and hyphens correctly, use numerals correctly, & use the correct tense.
WRITING RESEARCH PROPOSALS
Most research requires some funding! Cost and quality are not necessarily correlated; low-budget research can be high-quality research! But, it's nice to get some financial assistance even for low-budget projects.
Requests for funding are called GRANT PROPOSALS. Research can also be supported by CONTRACTS, e.g., USDA Forest Service or the Kentucky Department of Fish & Wildlife Resources may provide funds to perform work that they specify. The researcher is contracted to perform specific work. Grants are usually awarded on a competitive basis, whereas contracts often are not.
A grant proposal must convince readers that the work will be valid AND that the granting agency should pay for it! Grantsmanship is the 'art' of getting financial support for your research.
Some possible sources of funding for Master's students:
1 - Sigma
2 - American Museum of Natural History (behavioral & ecological research)
3 - Kentucky Academy of Science
4 - Kentucky Society of Natural History
5- Kentucky Ornithological Society
6 - American Society of Plant Taxonomists
7 - Raptor Research Foundation
8 - Wilson Ornithological Society
Before preparing and submitting a proposal to a particular funding source, be sure you know the answers to these questions:
2 - If so, what is the duration of funding and how much will they provide?
3 - Who can apply (i.e., are you eligible?)
4 - What is the deadline for receipt of proposals?
5 - What is the required format? (Formats do vary among funding sources.)
Factors important in writing a quality proposal:
Who reviews proposals?
Is a proposal's title important?
The BODY (Introduction & Methods) of the proposal remains rather consistent:
"The main body of the proposal should be a clear statement of the work to to undertaken and should include: objectives for the period of the proposed work and expected significance; relation to longer-term goals of the primary investigator's (PI) project; and relation to the present state of knowledge in the field, to work in progress by the PI under other support and to work in progress elsewhere. The statement should outline the general plan of work, including the broad design of activities to be undertaken, an adequate description of experimental methods and procedures and, if appropriate, plans for preservation, documentation, and sharing of data, samples, physical collections and other related research products."
Sigma Xi - "Good proposals address an explicit research hypothesis
in the context of a larger theory or model."
Introducing the research problem & objectives
A proposal's introduction will be similar in structure & content to the introduction of a research paper, i.e.:
2) you are asking readers not just to 'entertain' your ideas but to invest in them.
Examples of Introductions: Example 1, Example 2, Example 3, Example 4, Example 5 -- Example 6, Example 7, Example 8, Example 9, Example 10, Example 11,
Specific Aims: All other things being equal, a proposal that is hypothesis-driven is likely to be more favorably received than one that is not. "Fishing expeditions" and primarily "descriptive" proposals are unlikely to be funded. A proposal whose primary aim is to develop a new method will probably not be funded unless subsequent aims within the proposal involve using the method once it is developed. Be sure that you understand--and delineate for the reviewer--the difference between broad, long-term objectives and specific aims.
Providing background information in the Introduction is important in:
Background and Significance: In addition to describing the background for the proposal, you must critically evaluate the existing knowledge in the field. To justify the need for the proposed research, you should identify the specific gaps the project is intended to fill and state the importance of the research by relating the specific aims to the broad, long-term objectives. Make it clear which previous work was done by others and which by you, the principal investigator. The citations you choose to include in this section will give the reviewer a sense of your knowledge of the field.
Describing proposed methods
Compared to a journal article, the methods section of a proposal may include fewer details but more explanation of rationale (that is, why this approach, & not others, was chosen).
As a result, the methods section of a proposal should be
(i.e., use references where possible to lend support to your choices).
Explaining your methods helps 'generalist' readers understand what's
to accomplish the project & helps 'specialists' determine whether
understand what's needed to carry out the project.
NIH (1993) guidelines:
When in doubt about what to include in the Methods section of your proposal, it's almost certainly better to provide 'too much' detail than 'too little.'
Examples of Methods sections - Example 1, Example 2, Example 3, Example 4, Example 5
The Research Proposal Abstract or Summary
"It should not be an abstract of the proposal, but rather a self-contained description of the activity that would result if the proposal were funded. The summary should be written in the third person and include a statement of objectives, methods to be employed and the significance of the proposed activity to the advancement of knowledge. It should be informative to other persons working in the same or related fields and, insofar as possible, understandable to a scientifically or technically literate lay reader."
What about the budget? (Also: see Sigma Xi guidelines)
The proposal review process exerts substantial influence on the 'direction' of research. For example:
Possible concerns about the review process for proposals:
2 - May discourage research that's out of the 'mainstream' (or, for national funding agencies like NIH & NSF, research that may be considered unpopular with, or even ridiculed by, members of Congress or their staffs or by the media)
3 - Possible misappropriation of ideas
4 - Possible loss of confidentiality
Proposal guidelines may include a list of criteria to be used by reviewers:
How important is the proposed activity to advancing knowledge and understanding within its
own field or across different fields? How well qualified is the proposer (individual or team) to
conduct the project? (If appropriate, the reviewer will comment on the quality of prior work.) To
what extent does the proposed activity suggest and explore creative and original concepts?
How well conceived and organized is the proposed activity? Is there sufficient access to
How well does the activity advance discovery and understanding while promoting teaching,
training, and learning? How well does the proposed activity broaden the participation of
underrepresented groups (e.g., gender, ethnicity, disability, geographic, etc.)? To what extent
will it enhance the infrastructure for research and education, such as facilities, instrumentation,
networks, and partnerships? Will the results be disseminated broadly to enhance scientific and
technological understanding? What may be the benefits of the proposed activity to society?
2) Sigma Xi - general significance and degree to which the project will advance the field is probably most important
3) Many small grants - no specific guidelines presented
In general, the most important criteria include:
2) professional competence of researcher(s)
3) relevance of the work to agency's goals
Top reasons why proposals are not funded (from a survey of NIH reviewers):
NIH reviewers must officially assign a score to each of five criteria (Significance, Approach, Innovation, Investigator, and Environment) before coming to a decision on an overall score.
See How to Write a Losing Proposal,
Why Proposals are Rejected, & Research Proposal - Common Mistakes
Guide for Writing a Funding Proposal
Proposal Writer's Guide
Writing successful science proposals (pdf)
Accessing the Biological Literature - Traditional
Biological Abstracts & the Zoological Record:
Zoological Record - Search Guide
Each section - 5 indexes: Author, Subject, Geographical, Paleontological, & Systematic:
Writing a Scientific Paper
Discussion - describes the 'new' state of the field's knowledge; now that the new results are known
BUT Adaptive Significance of Territoriality in Iguanid Lizards
Be concise & make every word count.
Omit unnecessary words, e.g., "Studies on . . .", "Observations of . . .", "Investigations of . . .", or "Preliminary Studies on . . .". Words like 'a', 'the', & 'an' are often unnecessary.
Include appropriate taxonomic information.
If your work focuses on a particular species or larger taxonomic group, specify this clearly in the title.
BUT Effect of Vitamin B on Gametophyte Development in the Moss, Pylaisiella
The abstract is a concise summary of a paper's most important points, and must be able to stand alone (e.g., abstracting services may only provide the title and the abstract). Abstracts must be brief (typically no more than about 5% of the length of the entire paper or, in other words, usually no more than about 250 words). A good abstract should:
Abstract examples: JKAS1, JKAS2, JKAS3, Condor1, Condor2, Condor3
2- Prepare for present research by indicating a gap in previous research or by raising a question about previous research
3- Introduce the present research by stating the objective(s)
These components are sometimes in a different order, one or more may be only implied, some may be made more than once, & some may overlap (e.g., authors may cite previous research while announcing the topic).
Despite variation in length & organization, effective Introductions share the same goal:
2) reviews pertinent literature (which helps establish the author's credibility)
3) sets up argument for significance that is a goal of the
section (i.e., creates a 'desire' for a solution!)
Information is usually presented in past tense, either active voice (I observed focal animals daily . . .) or passive (Focal animals were observed daily . . .). Passive writing has traditionally been used in scientific writing, but active writing is now preferred by many editors.
Check "Instructions to Authors" to determine if active writing is recommended in a particular journal.
When writing with an active voice, avoid using 'I' or 'we' too often. Well-written Methods sections use both active and passive writing.
Include enough information so that the study could be repeated:
1 - Materials:
Use past tense!
Evidence is presented to address the gap or question noted in the Introduction.
Summarize data & generalize from data! Generalize with explanatory details, statistics, tables, & figures. Point out trends in the data so the readers will see why you drew the conclusions that you did. Relationships between data & generalizations are apparent by observing how tables & figures are referred to:
Integrating quantitative data with the text:
2 - When reporting results of statistical analyses, provide the test statistic (e.g., F value, z value, t value, or chi square value), degrees of freedom, and probability level (P value).
3 - Use accepted abbreviations & symbols. These may vary somewhat among disciplines.
4 - Do not begin sentences with numbers. Either write out the number or, better, revise the sentence.
5 - Use the word significant only when reporting statistical significance. Use the word correlated only when two variables are statistically correlated. When results are statistically significant, it is not necessary to use the word significant. And, when not significant, it is not necessary to say results were not significant or did not differ significantly. For example:
Singing rates did not vary among breeding stages (F3, 14 = 1.1, P = 0.35).
Examples of Results sections: WJO-1, WJO-2, WJO-3
Tables & figures - Which should be used to present data? (Useful sources: Tables vs. Graphs & Almost Everything You Wanted to Know About Making Tables and Figures)
Figures (graphs) - highlight trends & patterns. Of course, not all figures are graphs. Other types of figures include diagrams, cross-sections, maps, photographs, & flow charts (Examples of figures: Figure 1, Figure 2, Figure 3, Figure 4, Figure 5, Figure 6).
General guidelines include:
Constructing a table:
2 - Words in a column are lined up on the left; numbers on the right (or on the decimal point).
3 - Horizontal lines may (should) be used, but rarely are vertical lines used.
4 - Column headings must be brief and precise.
5 - Footnotes may be used for clarification, but should not unnecessarily repeat details provided in Methods section. Tables must be self-explanatory, but need not present details needed to repeat experiment(s).
6 - Table legends go above the table.
Constructing a figure:
The purposes of the Introduction & Discussion are inversely related. An Introduction introduces the research question & reviews state of knowledge in the field that motivated the question, while the Discussion explains how the question has been answered (at least in part) by the new research & shows how the field's knowledge is changed with the addition of this new knowledge. Interpret your results, & support conclusions with evidence. Tell the readers what your findings mean. Do the data support the original hypothesis? Why or why not? Refer to your data, citing tables or figures where necessary (BUT do not repeat the data!). Discuss the work of other investigators. Are your findings consistent with theirs? How do your results fit into the bigger picture?
Do not present every conceivable explanation. Too much speculation weakens a discussion. Based on your data, pick & support the most plausible interpretations.
Recognize the importance of negative results. Negative results require an explanation, & may provide new insight!
Proceed from the specific to the general (but not too general).
Start by pointing out your major finding(s) (without excessively repeating results). Focus the reader's attention on the most important findings, patterns, or trends.
If there are conflicting or unexpected results, suggest explanations.
Compare your findings with the work of other investigators. Are your results similar? Supplement your own evidence with relevant material from other studies. If other investigators obtained results different from yours, suggest possible explanations for the differences.
End with more general interpretations & conclusions. Can you generalize from your findings to other situations? How does your work contribute to an understanding of the broader topic? Try to end the Discussion with a strong concluding statement.
How do scientists phrase their claims & conclusions in a Discussion? To illustrate, fill in an appropriate word or phrase:
1. Eleven of the trials have shown the treatments to be ineffective, yielding an overall response rate of 4/278 (1.4%). These data ________ that the minimal response rate of interest should be 0.15.
2. These observations ________ that (1) fertilized soils tend to attain apparent equilibrium with orthophosphate solid phases and (2) soils with moderate to high P-fixing capacity tend to have limited movement of P when fertilized with inorganic P sources.
3. Statistical analysis ________ that corn yields were not influenced by the rate of application of nitrogen fertilizer in 1990, but were in 1991 (Table 1). The lack of influence of fertilizer in 1990 was attributed to high levels of native nitrogen in the soil and climatic conditions unconducive to high corn yields (Fig. 2).
4. More recent studies of modern thickly sedimented convergent margins _________ that the Washington margin is anomalous. For example, the Makran (Platt et al. 1985) and Barbados (Westbrook 1982) convergent margins are thickly sedimented and have convergent rates similar to the Washington margin (about 5 cm/yr). However, only the Washington margin is dominated by landward-verging structures.
5. Results of this study __________ that significant genetic divergence has occurred among geographically separated groups of raccoons. The average differentiation among the 14 localities examined (37.4%) is similar to the value obtained among populations of pocket gophers (41.0%; Patton and Yang 1977).
As the above examples probably illustrate, the verbs suggest, indicate, show, & demonstrate are commonly used in scientific writing to make claims and draw conclusions. Such terms carry particular, agreed-upon meanings among scientists, i.e., that an investigator is drawing a conclusion or interpretation of the facts but that the conclusion is not a fact.
Scientists also use other 'qualifiers' to convey the interpretative nature of their claims. For example, adverbs & adverbial phrases are often used to note limitations or special conditions, e.g., possibly, probably, necessarily, presumably, maybe, & as far as we can determine. Such qualifiers indicate the strength or extent of the claim being made. Verbs like may, might, would, could, should, must, & can are also used to indicate qualifying conditions.
Qualifying verbs & adverbs can be used anywhere in the text of a
paper where an author needs to qualify or limit their claims.
use them to acknowledge the limitations of their work & to
and head off questions & counterarguments that readers might pose.
Examples of Discussion sections: 01, 02, 03, 04, 05, 06, 07
A short acknowledgments section usually comes between the Discussion
& the Literature Cited sections. In this section, the author(s)
anyone or any agency that assisted with the research or writing.
List all references cited in the paper.
Citing sources in the text:
House sparrows were first observed in Madison County in 1905 (Farrar 1906).
Some journals require a comma between the author and date (Farrar,
but most do not.
Snow geese consumed all corn east of the Mississippi River during
winter of 1995 (Frederick and Hill 1996).
Crayfish were largely consumed by rednecks (Homo kentuckiensis)
during the period from March - June (Farrar et al. 1997).
The intellectual capacity of salamanders and George W. is similar
Global warming will be beneficial because heating bills will be
every winter (Limbaugh 1999a, b).
When citing in the text, put references where they make the most sense. Put each citation close to the information you wish to acknowledge. Do not always include citations at the end of sentences, e.g.:
Don't overuse citations. Citing a large number of papers may be more confusing than enlightening. Decide which references are most important & use them.
Use correct format in Literature Cited section. Check the Instructions for Authors because different journals use different formats in their Literature Cited sections.
Always check & double-check the Literature Cited section for accuracy, completeness, and consistency!!
Papers: 01 02 03
Writing Exercises for Engineers and Scientists
Writing Resources on the World Wide Web
Back to BIO 801 syllabus