BIO 801
Scientific Literature & Writing - Biology
Lecture Notes

Instructor: Gary Ritchison
Course syllabus: Click here!

Reading & Citing Scientific Literature | Guidelines for Better Writing | Writing Proposals | Accessing the Literature

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.

Scientific writing:

The writer must present research in a way that your audience can understand. What is the 'audience' for a scientific writer?

Before writing a scientific paper, determine:

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:

The primary literature is indexed in such forms as Biological Abstracts, Zoological Record, Science Citation Index, & Dissertation Abstracts. Primary literature contains primary publications. A primary publication is: There is also a secondary literature (more general works that are based on primary sources):

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 you've followed the journal's guidelines)
2) The editor has the manuscritp reviewed by 2 - 4 reviewers
3) The editor reads the manuscript, evaluates the reviews, & may then:

4) Once accepted, the author(s) must submit a 'clean' version of the manuscript (i.e., proper format with any problems corrected) along with original figures.

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 proposal have of getting funded? What chance does a poorly written manuscript have of being accepted for publication? Obviously, good writing is very important!

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':

Once you've selected a topic, of course, your next step is to find all relevant references. Some good places to begin this search include:

Reading & Citing the Scientific Literature

Reading Scientific Papers

1 - Acquire some background knowledge

2 - Read the abstract first 3- Understand the basic aims of the study 4 - Unless your research requires it, don't focus too closely on METHODS 5 - Read, and perhaps re-read, the Results carefully. 6 - Understand the Discussion 7 - Plan on rereading important papers 8 - If aspects of a paper are relevant to your work, summarize that material, for future reference, in your own words. It's very important to avoid plagiarism: It takes additional time to summarize in your own words because, to do so, you must have a clear understanding of the work you're summarizing, but you will avoid plagiarism and, perhaps, will better understand the material.

9 - Develop a system for keeping track of all your references. For example:


Avoid wordiness

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 number 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)

Pronoun Reference (identification of a pronoun with its intended antecedent). Make sure all pronouns can be easily identified.

Make sure each verb agrees with its subject. Do not lose sight of the subject in a sentence by focusing on modifying words, such as prepositional phrases, occurring between the subject and verb. For example:

Avoid repetition - Some sentences or paragraphs are wordy because the writer includes the same information twice. For example:

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 constructs, orders, and connects paragraphs as a means of guiding the reader from one topic to the next, along a logical train of thought. Topic sentences often occur at the beginning of a paragraph, followed by material that develops, 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:

By combining related sentences, this paragraph becomes more readable:

Be careful about using nouns as adjectives:

Use commas and hyphens correctly, use numerals correctly, & use the correct tense.


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:

Before preparing and submitting a proposal to a particular funding source, be sure you know the answers to these questions:

Factors important in writing a quality proposal:

From NIH guidelines - " . . . applications with typos & grammatical errors create a negative impression of the author's competence & attention to detail."

Who reviews proposals?

What's included in a typical proposal? This varies among agencies but proposals must often include:

Is a proposal's title important?

The BODY (Introduction & Methods) of the proposal remains rather consistent:

For example - PROJECT DESCRIPTION from NSF Grant Proposal Guide (1995):

"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 set 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.:

However, a proposal generally provides a more detailed introduction to the topic because: The primary goal of a proposal is to convince readers of the significance of the proposed work; it's not enough to assert that a problem exists or that a question has not been answered. What is "significant?"

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,

Example 12

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:

For example, here is some advice for those submitting to proposals to NIH: Keep in mind that you are reviewing research to introduce your study & how it will further the field's knowledge (and, perhaps, the funding agency's goals).

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 well-documented (i.e., use references where possible to lend support to your choices). Explaining your methods helps 'generalist' readers understand what's needed to accomplish the project & helps 'specialists' determine whether you understand what's needed to carry out the project.

NIH (1993) guidelines:

Writing hints for the Methods section of a proposal:

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

What about the budget?  (Also: see Sigma Xi guidelines)

How are proposals evaluated?

The proposal review process exerts substantial influence on the 'direction' of research. For example:

Possible concerns about the review process for proposals:

In sum, the proposal review process is imperfect, but continues to be evaluated.

Proposal guidelines may include a list of criteria to be used by reviewers:

In general, the most important criteria include:

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.

The hard part may be trying to balance feasibility with innovation, says Gerald Greenhouse, scientific review administrator for NIH's Cell Biology and Physiology. His advice? "Try to submit an application that includes both solid science and more risky stuff."

See How to Write a Losing Proposal,

Why Proposals are Rejected, & Research Proposal - Common Mistakes

Useful links:

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:

Biological Abstracts:

Zoological Record:

Zoological Record - Search Guide

Each section - 5 indexes: Author, Subject, Geographical, Paleontological, & Systematic:


Writing a Scientific Paper

Published papers:

IMRAD - two sections in which the study is described (Methods & Results), framed by two sections that place the work within the context of previous knowledge (Introduction & Discussion):

The Title

    For example:

    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.


    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


Components of a typical introduction:

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:

So, the Introduction serves several functions: Methods

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:

If information about any materials (e.g., the 'recipe' for one of your solutions) has been provided in previous publications, refer readers to that source (as long as it's a readily available source) to save space. Make sure information is presented in an organized, logical manner:


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:

Do not interpret the data or draw conclusions in the Results.

Integrating quantitative data with the text:

Singing rates varied among breeding stages (F3, 14 = 21.6, P = 0.001).


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)

Specific guidelines for tables & figures can be found in Instructions for Authors of each journal.

General guidelines include:

Designing Tables:

Constructing a 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. Scientists use them to acknowledge the limitations of their work & to anticipate 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) thank(s) anyone or any agency that assisted with the research or writing.

Literature Cited

List all references cited in the paper.

Citing sources in the text:

When two or more papers by different authors are cited at the same time, list the references in chronological order with the earliest first.

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

Useful links:

Writing Exercises for Engineers and Scientists

Writing Resources on the World Wide Web

Back to BIO 801 syllabus