BIO 801 Scientific Literature & Writing - Biology Lecture NotesInstructor: Gary Ritchison E-mail: gary.ritchison@eku.

edu 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: is a SKILL that must be developed through practice. Good writers never cease learning. should inform the reader. The writer must present research in a way that your audience can understand. What is the 'audience' for a scientific writer?instructor of a class advisor & committee seminar audience attendees at scientific meeting: state, regional, national, or international readers of theses readers of scientific journals: state, regional, national, or international educated public Before writing a scientific paper, determine: 1. Who is going to read this paper? 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: 1) state, regional, national, & international professional journals 2) conference proceedings (if edited or peer-reviewed) 3) annual reviews 4) some books (if edited & containing original results) 5) theses & dissertations 6) technical reports of government agencies or private organizations 7) on-line journals (if edited or peer-reviewed), e.g., PLoS ONE 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:1) the 1st publication of original research results, 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 There is also a secondary literature (more general works that are based on primary sources):1) textbooks & lab manuals (not original results), 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: 1) Nature & Science 2) "Top" national/international journals in particular fields 3) "Lesser" national journals in particular fields 4) Regional journals (e.g., Southeastern Naturalist) 5) State journals (e.g., Journal of the Kentucky Academy of Science) 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: accept the manuscript for publication with few or no changes ask the author(s) to make certain changes (ranging from minor to substantial) &, after resubmission, decides whether or not to publish decide that he or she likes the study (or the data) but the changes needed are so substantial that, upon resubmission, the manuscript must once again be sent to reviewers reject the manuscript 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?' examine how other scientists write (by studying their publications) become familiar with the basic 'rules' submit your work for review! 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': 1) will not actually be conducted, but will be based on data (unpublished) obtained from me, your advisor, or some other faculty member. In the real world, of course, a study is proposed, then conducted (and data are collected). However, because one semester simply isn't enough time to propose a study and actually conduct the research, you will 'propose' a study that has already been conducted. 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). 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:Google Scholar FirstSEARCH BioOne Other databases available via EKU's library To obtain books and journal articles that the EKU library doesn't have, use InterLibrary Loan. Reading & Citing the Scientific Literature Research is published as journal articles or papers Articles are factual & explanatory but, often, are also persuasive. Authors attempt to persuade readers that what they've done is valid & useful. Common format consists of 4 standard sections (IMRAD): 1 Introduction 2 Methods 3 Results 4 Discussion 5 plus a Literature Cited section Each section plays a part in supporting the larger argument of the whole paper Papers written using the IMRAD format consist of 2 sections that describe the study (Methods & Results) framed by 2 sections that place the work in the context of previous knowledge (Introduction & Discussion). FRAMING SECTIONS and DESCRIBING SECTIONS use different verb tenses:

 Framing - often use present tense if reporting common knowledge or an important, well-known, and agreed upon principle (e.g., "The availability of suitable nest sites is known to influence screech-owl populations.") BUT use past tense if referring to findings of particular researchers (e.g., "Ritchison (1992) suggested that screech-owl populations may be limited by the availability of suitable nest sites.") Describing - typically use past tense to describe actions already taken and data already collected (e.g., "We located nests by observing the behavior of female chats." or "Adult chats fed nestlings at an average rate of 3.5 times per hour.") Reading Scientific Papers 1 - Acquire some background knowledge Papers are written for a relatively specialized audience & assume some knowledge of the subject matter & vocabulary. So, you may wish to start by reading appropriate sections in texts, scientific encyclopedias, popular science magazines (e.g., Scientific American) & books (i.e., books on specific topics written for a non-specialized audience), or review papers. 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). 2 - Read the abstract firstProvides a summary of the paper & should help you decide whether to read the rest of the paper. 3- Understand the basic aims of the studyRead the Introduction. Why was the study conducted? What hypotheses were being tested (i.e., what were the objectives)? 4 - Unless your research requires it, don't focus too closely on METHODSUnderstand the experimental design, use of controls, sampling techniques, or other methods related to specific objectives. Generally, you need not understand the precise details. If necessary, go back to the Methods section after you understand the major findings and conclusions. 5 - Read, and perhaps re-read, the Results carefully.Don't panic if you don't understand some of the details (e.g., the statistical analyses). Focus on main qualitative findings, them move on to more difficult material. It may be helpful to read through the Discussion & then return to the Results. Don't overlook Figures & Tables. 6 - Understand the DiscussionDo the data support the conclusions? What does the author believe is the primary contribution of the study? How do the conclusions relate to your research interests or to your particular study? Specifically, do the author's conclusions in any way agree or disagree with yours? 7 - Plan on rereading important papersYou may miss important details with a single reading. You may gain new insight into a paper if you come back to it at a later date & after becoming more familiar with the subject. 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:copying

an author's exact words & putting them in your paper without quotation marks using wording that is very similar to that of the original source, but passing it off as entirely your own (the most common type of 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: Bibliographic management software, e.g.: 1 Manuscript Manager (Pergamon Software, Maxwell House, Fairview Park, Elmsford, NY 10523) 2 ProCite (Personal Bibliographic Software, Inc., P.O. Box 4250, Ann Arbor, MI 48106) 3 EndNote (Niles and Associates, 2200 Powell, Suite 765, Emeryville, CA 946081809) GUIDELINES FOR BETTER SCIENTIFIC WRITING 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) Passive: Most seedlings were eaten by rabbits. Active: Rabbits ate most seedlings. Passive: Territory size was found to vary with population density. Active: Territory size varied with population density. Passive: From field observations, it was found that all radio-tagged 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. Unclear: Northern Cardinals have been studied by ornithologists for several years. They typically initiate breeding behavior in March. Better: Studies by ornithologists have revealed that Northern Cardinals typically initiate breeding behavior in March. Even better: Northern Cardinals typically initiate breeding behavior in March. Faulty: Farrar and Smith (1998) examined the foraging behavior of House Sparrows. They reported that their diet consisted primarily of seeds. 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). 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:The size of all territories was [not were] reduced at high population densities. 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: In Cupp's study, he found that temperature had no effect on display rates (Cupp 1993). Concise: Temperature had no effect on display rates (Cupp 1993). Wordy: The opossum is of moderate economic importance according to Hamilton (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 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: Many doves exhibited 'nest-calling' behavior. They assumed a position with the tail

and body axis pointing slightly upwards. In this posture, they flicked their wings. This behavior was observed in both sexes. It was especially common in males. I saw it performed both on and off the nest. By combining related sentences, this paragraph becomes more readable:Many doves, especially males, exhibited 'nest-calling' behavior both on and off the nest. During this display, doves assumed a position with the tail and body axis pointed slightly upwards and flicked their wings. Be careful about using nouns as adjectives: Beginning writers frequently use nouns (sometimes proper nouns) as adjectives. For example: Gray (1997) found that Red-winged Blackbird females were less vocal during the pair-formation period. This would be better as: Gray (1998) found that female Red-winged Blackbirds were less vocal during pair formation. 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 Xi 2 - American Museum of Natural History (behavioral & ecological research) 3 - Kentucky Academy of Science 4 - American Society of Plant Taxonomists Before preparing and submitting a proposal to a particular funding source, be sure you know the answers to these questions: 1 - Do they fund research in my area? 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: Is it an original idea? Would it cause a reviewer to say to themselves 'Why didn't I think of that?' Does the author demonstrate a thorough knowledge of the field? Is the study well-designed with appropriate methodologies? Does the description of Methods demonstrate the technical competence needed to successfully carry out the project? Is the proposal well-written? Does it look good? From NIH guidelines - " . . . applications with typos & grammatical errors create a negative impression of the author's competence & attention to detail."Who reviews proposals? Varies among granting agencies, but always involves peer review. Proposals are often sent out for review to experts in the field (but may undergo initial review by 'generalists' before going to experts). Some agencies (e.g., NSF) use panels of experts that collectively evaluate proposals (although grants may be reviewed before going to the panel). What's included in a typical proposal? This varies among agencies but proposals must often include:abstract or summary table of contents body of proposal (introduction & methods) complete budget (&, sometimes, budget detail sheets) biographical information about investigator approval form or letter from an institution's animal care committee Is a proposal's title important?

The BODY (Introduction & Methods) of the proposal remains rather consistent: Explain the background & rationale for the project by surveying the literature, summarizing the current state of the field's knowledge on the topic, & showing how the proposed work will further that knowledge Explain the purpose, significance, & specific objectives of the proposed research Describe, in detail, the methodology to be used and, if necessary, explain the rationale behind these methodological choices 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; proposed research methods; the relationship of hypothesis with data to be gathered; and previous work on the topic." Introducing the research problem & objectives A proposal's introduction will be similar in structure & content to the introduction of a research paper, i.e.: 1) Summarize the current state of knowledge 2) Identify gap, question, or problem that motivates study 3) Provide objective(s) of study However, a proposal generally provides a more detailed introduction to the topic because:1) proposal readers may represent a more diverse group (including 'generalists' as well as specialists) & 'generalists' may need to be 'educated' about the topic &, specifically, about the significance of your research. 2) you are asking readers not just to 'entertain' your ideas but to invest in them. 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?"depends on goals & priorities of funding source depends on individual reviewers 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: letting readers know how familiar you are with current literature letting readers know how well you understand issues & constraints involved in conducting research in this area For example, here is some advice for those submitting to proposals to NIH:"Refer to the literature thoroughly and thoughtfully. Explain what gaps in the literature would be filled by your project. In the past, research proposals have not been funded when applicants seemed to be unaware of relevant published work or when the proposed research or study design had already been tried and judged inadequate." 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. AVOID USE a large number of several (or many) a small number of few a majority of most of importance important smaller in size smaller has the ability to can lacks the ability to cannot make changes in change give consideration to consider utilize use it is often the case that often as a consequence of because as a result of because due to the fact that because in view of the fact that because since* because in the interest of to in order to to *unless related to time (e.g., The focal bird had been observed since 14 May.) Unnecessary words or phrases Needless to say for your information it goes without saying that it is important to note that it is of interest to note that it appears that it should be noted that it stands to reason that it was demonstrated that it was found that the field of, the area of, the idea of, the concept of very, rather, quite

 actually, definitely, completely fortunately, unfortunately ongoing, upcoming, existing, actual