A GUIDE TO WRITING SCIENTIFIC PAPERS
Scientific experiments are demanding, exciting endeavors, but, to have an impact, results must be communicated to others. A research paper is a method of communication, an attempt to tell others about some specific data that you have gathered and what you think those data mean in the context of your research. The "rules" of writing a scientific paper are rigid and are different from those that apply when you write an English theme or a library research paper. For clear communication, the paper obviously requires proper usage of the English language and this will be considered in evaluating your reports. Scientific papers must be written clearly and concisely so that readers with backgrounds similar to yours can understand easily what you have done and how you have done it should they want to repeat or extend your work. When writing papers for the biology department, you can assume that your audience will be readers like yourselves with similar knowledge.
Although scientific journals differ somewhat in their specific requirements, a general format that would be acceptable for most biological journals is:
Materials and Methods
The section headings (Abstract, Introduction, etc.) should be centered and the body of each section should follow immediately below the heading. Do not begin each section on a new page. If one section ends part of the way down the page, the next section heading follows immediately on the same page.
One important general rule to keep in mind is that a scientific paper is a report about something that has been done in the past. Most of the paper should be written in the PAST TENSE (was, were). The present tense (is, are) is used when stating generalizations or conclusions. The present tense is most often used in the Introduction, Discussion and Conclusion sections of papers. The paper should read as a narrative in which the author describes what was done and what results were obtained from that work.
Every scientific paper must have a self-explanatory title. By reading the title, the work being reported should be clear to the reader without having to read the paper itself. The title, "A Biology Lab Report", tells the reader nothing. An example of a good, self-explanatory title would be: "The Effects of Light and Temperature on the Growth of Populations of the Bacterium, Escherichia coli ". This title reports exactly what the researcher has done by stating three things:
1. The environmental factors that were manipulated (light, temperature).
2. The parameter that was measured (growth).
3. The specific organism that was studied (the bacterium, Escherichia coli).
If the title had been only "Effects of Light and Temperature on Escherichia coli ", the reader would have to guess which parameters were measured. (That is, were the effects on reproduction, survival, dry weight or something else?) If the title had been "Effect of Environmental Factors on Growth of Escherichia coli ", the reader would not know which environmental factors were manipulated. If the title had been "Effects of Light and Temperature on the Growth of an Organism", then the reader would not know which organism was studied. In any of the above cases, the reader would be forced to read more of the paper to understand what the researcher had done.
Exceptions do occur: If several factors were manipulated, all of them do not have to be listed. Instead, "Effects of Several Environmental Factors on Growth of Populations ofEscherichia coli " (if more than two or three factors were manipulated) would be appropriate. The same applies if more than two or three organisms were studied. For example, "Effects of Light and Temperature on the Growth of Four Species of Bacteria" would be correct. The researcher would then include the names of the bacteria in the Materials and Methods section of the paper.
The abstract section in a scientific paper is a concise digest of the content of the paper. An abstract is more than a summary. A summary is a brief restatement of preceding text that is intended to orient a reader who has studied the preceding text. An abstract is intended to be self-explanatory without reference to the paper, but is not a substitute for the paper.
The abstract should present, in about 250 words, the purpose of the paper, general materials and methods (including, if any, the scientific and common names of organisms), summarized results, and the major conclusions. Do not include any information that is not contained in the body of the paper. Exclude detailed descriptions of organisms, materials and methods. Tables or figures, references to tables or figures, or references to literature cited usually are not included in this section. The abstract is usually written last. An easy way to write the abstract is to extract the most important points from each section of the paper and then use those points to construct a brief description of your study.
The Introduction is the statement of the problem that you investigated. It should give readers enough information to appreciate your specific objectives within a larger theoretical framework. After placing your work in a broader context, you should state the specific question(s) to be answered. This section may also include background information about the problem such as a summary of any research that has been done on the problem in the past and how the present experiment will help to clarify or expand the knowledge in this general area. All background information gathered from other sources must, of course, be appropriately cited. (Proper citation of references will be described later.)
A helpful strategy in this section is to go from the general, theoretical framework to your specific question. However, do not make the Introduction too broad. Remember that you are writing for classmates who have knowledge similar to yours. Present only the most relevant ideas and get quickly to the point of the paper. For examples, see the Appendix.
MATERIALS AND METHODS
This section explains how and, where relevant, when the experiment was done. The researcher describes the experimental design, the apparatus, methods of gathering data and type of control. If any work was done in a natural habitat, the worker describes the study area, states its location and explains when the work was done. If specimens were collected for study, where and when that material was collected are stated. The general rule to remember is that the Materials and Methods section should be detailed and clear enough so that any reader knowledgeable in basic scientific techniques could duplicate the study if she/he wished to do so. For examples, see the Appendix.
DO NOT write this section as though it were directions in a laboratory exercise book. Instead of writing:
First pour agar into six petri plates. Then inoculate the plates with the bacteria. Then put the plates into the incubator . . .
Simply describe how the experiment was done:
Six petri plates were prepared with agar and inoculated with the bacteria. The plates were incubated for ten hours.
Also, DO NOT LIST the equipment used in the experiment. The materials that were used in the research are simply mentioned in the narrative as the experimental procedure is described in detail. If well-known methods were used without changes, simply name the methods (e.g., standard microscopic techniques; standard spectrophotometric techniques). If modified standard techniques were used, describe the changes.
Here the researcher presents summarized data for inspection using narrative text and, where appropriate, tables and figures to display summarized data. Only the results are presented. No interpretation of the data or conclusions about what the data might mean are given in this section. Data assembled in tables and/or figures should supplement the text and present the data in an easily understandable form. Do not present raw data! If tables and/or figures are used, they must be accompanied by narrative text. Do not repeat extensively in the text the data you have presented in tables and figures. But, do not restrict yourself to passing comments either. (For example, only stating that "Results are shown in Table 1." is not appropriate.) The text describes the data presented in the tables and figures and calls attention to the important data that the researcher will discuss in the Discussion section and will use to support Conclusions. (Rules to follow when constructing and presenting figures and tables are presented in a later section of this guide.)
Here, the researcher interprets the data in terms of any patterns that were observed, any relationships among experimental variables that are important and any correlations between variables that are discernible. The author should include any explanations of how the results differed from those hypothesized, or how the results were either different from or similar to those of any related experiments performed by other researchers. Remember that experiments do not always need to show major differences or trends to be important. "Negative" results also need to be explained and may represent something important--perhaps a new or changed focus for your research.
A useful strategy in discussing your experiment is to relate your specific results back to the broad theoretical context presented in the Introduction. Since your Introduction went from the general to a specific question, going from the specific back to the general will help to tie your ideas and arguments together.
This section simply states what the researcher thinks the data mean, and, as such, should relate directly back to the problem/question stated in the introduction. This section should not offer any reasons for those particular conclusions--these should have been presented in the Discussion section. By looking at only the Introduction and Conclusions sections, a reader should have a good idea of what the researcher has investigated and discovered even though the specific details of how the work was done would not be known.
In this section you should give credit to people who have helped you with the research or with writing the paper. If your work has been supported by a grant, you would also give credit for that in this section.
This section lists, in alphabetical order by author, all published information that was referred to anywhere in the text of the paper. It provides the readers with the information needed should they want to refer to the original literature on the general problem. Note that the Literature Cited section includes only those references that were actually mentioned (cited) in the paper. Any other information that the researcher may have read about the problem but did not mention in the paper is not included in this section. This is why the section is called "Literature Cited" instead of "References" or "Bibliography".
The system of citing reference material in scientific journals varies with the particular journal. The method that you will follow is the "author-date" system. Listed below are several examples of how citations should be presented in the text of your paper. The name(s) of the author(s) and year of publication are included in the body of the text. Sentence structure determines the placement of the parentheses.
One author: 'Scott's (1990) model fails to ...' or 'The stream model (Scott 1990) is ...'
Two authors: 'Libby and Libby (1991) show...' or 'Previous moose migration studies (Libby and Libby 1991)...'
Three or more authors: 'Roche et al. (1991) reported that ...' or 'During April, moose sightings increased over those in a previous study (Roche et al. 1991) .....'
Entries in the Literature Cited section are listed alphabetically by author(s) and chronologically for papers by the same author(s). The following citations illustrate the details of punctuation and order of information for a journal article, book, Internet source, and your laboratory packet.
Schneider, M.J., Troxler, R.F. and Voth, P.D. 1967. Occurrence of indoleacetic acid in the bryophytes. Bot. Gaz. 28(3): 174-179.
Stebbins, G.L. 1977. Processes of Organic Evolution. Prentice-Hall, New Jersey. 269 pp.
MSW Scientific Names: Microtus ochrogaster. Online. Smithsonian Institution. Available: http://www.nmnh.si.edu/cgi-bin/wdb/msw/names/query/22128. updated August 8, 1996 [accessed 8/10/98]
Colby Biology Department. 1998. Salt Tolerance in Phaseolus vulgaris. In: Introduction to Biology: Organismal Biology. Waterville, ME: Colby Custom Publishing
Generally, most references will be to the primary literature (i.e., journal articles) and, to a lesser extent, books. Popular literature and the Internet should be used sparingly and with caution. Other sources such as book chapters and pamphlets typically have their own specific citation formats. If necessary, be sure to find out what these formats are and use them appropriately.
For a much more detailed discussion about writing scientific papers, consult: CBE Style Manual Committee. 1983. CBE Style Manual: A Guide for Authors, Editors and Publishers in the Biological Sciences. 5th Edition, revised and expanded. Council of Biology Editors, Inc., Bethesda, Maryland.
This guide is based on a paper by Gubanich, A.A. 1977. Writing the scientific paper in the investigative lab. Amer. Biol. Teacher, 39(1): 27-34.
Examples from the scientific literature that illustrate material in various sections of a scientific paper.
A. Excerpted from: Hasegawa, K., Sakoda, M. and J. Bruinsma. 1989. Revision of the theory of phototropism in plants: a new interpretation of a classical experiment. Planta 178:540-544.
Went's classical experiment on the diffusion of auxin activity from unilaterally illuminated oat coleoptile tips (Went 1928), was repeated as precisely as possible. In agreement with Went's data with the Avena curvature assay, the agar blocks from the illuminated side of oat (Avena sativa L. cv. Victory) coleoptile tips had, on the average, 38% of the auxin activity of those from the shaded side. However, determination of the absolute amounts of indole-3-acetic acid (IAA) in the agar blocks, using a physicochemical assay following purification, showed that the IAA was evenly distributed in the blocks from the illuminated and shaded sides. In the blocks from the shaded and dark-control halves the amounts of IAA were 2.5 times higher than the auxin activity measured by the Avena curvature test, and in those from the illuminated half even 7 times higher. Chromatography of the diffusates prior to the Avena curvature test demonstrated that the amounts of two growth inhibitors, especially of the more polar one, were significantly higher in the agar blocks from the illuminated side than in those from the shaded side and the dark control. These results show that the basic experiment from which the Cholodny-Went theory was derived does not justify this theory. The data rather indicate that phototropism is caused by the light-induced, local accumulation of growth inhibitors against a background of even auxin distribution, the diffusion of auxin being unaffected.
B. Excerpted from: Farmer, E.E. and Ryan, C.A. 1990. Interplant communication: airborne methyl jasmonate induces synthesis of proteinase inhibitors in plant leaves. Proc. Natl. Acad. Sci. 87: 7713-7716.
Inducible defensive responses in plants are known to be activated locally and systematically by signaling molecules that are produced at sites of pathogen or insect attacks, but only one chemical signal, ethylene, is known to travel through the atmosphere to activate plant defensive genes. Methyl jasmonate, a common plant secondary compound, when applied to surfaces of tomato plants, induces the synthesis of defensive proteinase inhibitor proteins in the treated plants and in nearby plants as well. The presence of methyl jasmonate in the atmosphere of chambers containing plants from three species of two families, Solanaceae and Fabaceae, results in the accumulation of proteinase inhibitors in leaves of all three species. When sagebrush, Artemesia tridentata, a plant shown to possess methyl jasmonate in leaf surface structures, is incubated in chambers with tomato plants, proteinase inhibitor accumulation is induced in the tomato leaves, demonstrating that interplant communication can occur from leaves of one species of plant to leaves of another species to activate the expression of defensive genes.
A. Excerpted from: Shukla, A. and Sawhney, V.K. 1992. Cytokinins in a genic male sterile line of Brassica napus. Physiol. Plant. 85:23-29.
The failure or inability of an individual to produce functional gametes under a given set of environmental conditions is known as sterility. Male sterility in plants is generally associated with the lack of production of viable pollen; however its expression can vary (Frankel and Galun 1977, Kaul 1988). In any event, male sterility is of fundamental importance in the production of hybrid seeds and in breeding programs.
Plant growth substances, both exogenously applied and endogenous, have often been implicated in the regulation of male sterility in several plant species (Frankel and Galun 1977, Kaul 1988). Cytokinins, gibberellins, auxins and abscisic acid, as well as polyamines, are all known to affect pollen and stamen development in a number of species (e.g., Sawhney 1974, Ahokas 1982, Saini and Aspinall 1982, Rastogi and Sawhney 1990, Nakajima et al. 1991, Singh et al. 1992).
[Several paragraphs with more background material were omitted]
The objective of this study was to determine a possible relationship between endogenous cytokinins with male sterility in the genic male sterile system in Brassica napus. Thus, an analysis of a number of cytokinins in various organs of the wild type and genic male sterile plants was conducted.
B. Excerpted from: Reader, R.J. and Beisner, B.E. 1991. Species-dependent effects of seed predation and ground cover on seedling emergence of old-field forbs. Am. Midl. Nat. 126: 279-286.
A major goal of plant ecology is to explain spatial variation in a species frequency of occurrence. Spatial variation in seed predation may contribute to spatial variation in plant frequency by reducing seed supply sufficiently to limit seedling emergence more at one location than another (Louda 1982, Anderson 1989). Spatial variation in seed predation is well documented (e.g., Janzen 1971, 1975,; Bertness et al. 1987; Smith 1987), but few investigators tested whether differential seed predation resulted in differential seedling emergence (e.g., Louda 1982, 1983). Since factors such as dense ground cover may suppress seedling emergence regardless of the amount of seed predation (Harper 1977), additional studies are needed to clarify the effect of seed predation on seedling emergence. Therefore, we examined the effects of both seed predation and ground cover (i.e., plant biomass and litter) on seedling emergence of some old-field forbs.
MATERIALS AND METHODS:
A. Extracted from: Sakoda, M., Hasegawa, K. and Ishizuka, K. 1992. Mode of action of natural growth inhibitors in radish hypocotyl elongation -- influence of raphanusanins on auxin-mediated microtubule orientation. Physiol. Plant. 84:509-513.
Seeds of Raphanus sativus L. var. hortensis f. shogoin were sown and germinated in petri dishes on 4 layers of paper-towel (Kimberly-Clark Corp.) moistened with distilled water. After 3 days in darkness at 25oC, 4-mm hypocotyl segments were excised below the hook of the 3 cm long etiolated seedlings. After subapical segments were held for 1 h in darkness at 25oC in distilled water, they were transferred to 1 mM IAA solution or mixed media containing 1 mM IAA and raphanusanin B ( 1 or 3 mM). In other experiments, segments were preincubated for 1 h in small petri dishes containing 1 mM IAA solution, and then raphanusanin B was added to the medium (final concentrations 1 or 3 mM). Segment lengths were measured using a microscope with microgauge. All manipulations were carried out under dim green light (3mW m-2).
[The authors then explained visualization of microtubules by immunofluorescence]
B. Excerpted from: Kanbe, T., Kobayashi, I and Tanaka, K. !992. Dynamics of cytoplasmic organelles in the cell cycle of the fission yeast Schizosaccharomyces pombe: Three-dimensional reconstruction from serial sections. J. Cell Sci.,94: 647-656.
Schizosaccharomyces pombe h90, the homothallic, readily sporing haploid strain, was used. The strain was maintained on malt extract-yeast extract (MY) agar as described by Tanaka and Kanbe (1986). Cells were cultured on a MY slant at 30oC for 48 h, transferred to MY broth and cultures at 30oC overnight. Cells at the exponential phase were spread on a MY plate and further incubated at 30oC for 4 to 6 h before harvesting for microscopy.
Cells were fixed with a solution of 3% paraformaldehyde in a 50mM-phosphate buffer containing 1mM-MgCl2 (pH 6.8) at room temperature for 2 h. After washing with the buffer, cells were treated with Novozyme 234 (Novo Industri A/S, Bagsvaerd, Denmark) for 60 min at 30oC with reciprocal shaking to remove the cell wall. For the staining of F-actin, cells were washed and suspended in Rh-ph solution (Molecular Probes, Inc., Eugene, OR, USA) diluted 20 times in 50 mM-phosphate-buffered saline containing 1mM-MgCl2 (PBS, pH 7.3) at room temperature for 2 h. Nuclei were stained by 4,6-diamidino-2-phenylindole (DAPI) in NS buffer described by Suzuki et al. (1982). Preparations were examined with an Olympus BHS-RFK epifluorescence microscope using a U-G dichroic mirror with excitation filter BP490 for Rh-ph staining and UG1 for DAPI, and were photographed on Kodak Tmax400 film.
[This section continued to describe preparation for electron microscopy and the three-dimensional reconstruction of serial sections.]
A. Excerpted from: Takahashi, H., Scott, T.K. and Suge, H. 1992. Stimulation of root elongation and curvature by calcium. Plant Physiol. 98:246-252.
As shown in Table 1, the growth of roots treated with 10 mM Ca2+ was approximately 30% greater than the controls for a 3.5 h period following Ca2+ application to Alaska pea roots and approximately 80% greater than control for 12 h following the treatment in ageotropum pea. However, the growth of Alaska pea roots did not differ from that of control roots when measured 12 h after Ca2+ treatment. Roots of Silver Queen corn also showed an increase of approximately 70% in growth 3 h following application of 20 mM Ca2+ (Table 1). Such symmetrical treatment of root caps with Ca2+ did not cause curvature of the roots.
[The results section continued for several more paragraphs.]
B. Excerpted from: Sato, S. and Dickinson, H.G. 1991. The RNA content of the nucleolus and nucleolus-like inclusions in the anther of Lilium estimated by an improved RNase-gold labelling method. Jour. Cell Sci. 94:675-683.
Gold particles were predominant over the nuclear nucleolus-like bodies (NLBs) (Fig. 9). Although the distribution histogram of gold particles over the nuclear NLBs showed that labelling varied from 40 to 130 particles mm-2, most of that fell in the range of 80 - 90 particles mm-2 (Fig. 4). The quantitative estimation of labelling, which represented the average number of gold particles per mm2, indicated the labelling over the nuclear NLBs to be twice as strong as that over the loosened chromatin, and four times as strong as that over the condensed chromatin (Table 2).
[The results section continued for several more paragraphs.]
A. Excerpted from: Takahashi, H., Scott, T.K. and Suge, H. 1992. Stimulation of root elongation and curvature by calcium. Plant Physiol. 98:246-252.
The effect of Ca2+ on root elongation has been reported to be both stimulatory and inhibitory (Burstrom 1969, Evans et al. 1990, Hasenstein and Evans 1986). In those initial studies , however, the whole root was treated with Ca2+. Because the site of action for Ca2+ in gravitropism is considered to be the root cap rather than the zone of elongation, we focused on the role of the Ca2+/cap interaction in root growth as well as in gravitropic responses. We found that Ca2+ at 10 or 20 mM applied to the cap end of pea and corn roots mediated elongation growth of roots for at least 3 to 4 h following treatment. Unilateral application of 1 to 20 mM Ca2+ to the root cap always induced unequivocal curvature of roots away from the Ca2+ source in Alaska pea and to a greater extent in the roots of the agravitropic mutant, ageotropum (Figs. 1 and 2). Roots of Merit and Silver Queen corn also always curved away from Ca2+ applied to the cap, although a somewhat higher concentration was required for the response than in the pea roots. [Several sentences were omitted here.] These results show a strong correlation between an increase of Ca2+ levels in the root cap and stimulation of root elongation. The results are in contrast to the previously proposed model that an increased level of Ca2+ in the root cap mediated inhibition of root growth (Hasenstein et al. 1988).
[The discussion continued for several more paragraphs.]
A. Excerpted from: Noguchi, H. and Hasegawa, K. 1987. Phototropism in hypocotyls of radish. III. Influence of unilateral or bilateral illumination of various light intensities on phototropism and distribution of cis- and trans-raphanusanins and raphanusamide. Plant Physiol. 83: 672-675.
The present study demonstrates that phototropism in radish hypocotyls is caused by a gradient of growth inhibition which depends on the light intensity through the amounts of growth inhibitor, and thus strongly supports the Blaauw (Blaauw 1915) hypothesis, explaining phototropism as an effect of local growth inhibition by light.
B. Excerpted from: Nick, P., Bergfeld, R., Schäfer, E. and Schopfer, P. 1990. Unilateral reorientation of microtubules at the outer epidermal wall during photo- and gravitropic curvature of maize coleoptiles and sunflower hypocotyls. Planta 181: 162-168.
The striking agreement between changes in microtubule orientation observed at the outer epidermal wall during tropic bending and during induction or straight growth by external auxin strongly indicates that auxin is, in fact, functionally involved in mediating asymmetric growth leading to organ curvature.
There is no evidence that short-term growth of epidermal cells is controlled through the orientation of microfibrils. Also the data do not prove a causal relationship between auxin action on microtubule orientation and tropic curvature. However, our results do show that microtubule reorientation is a specific auxin-mediated response which can be used as a diagnostic test for an asymmetric distribution of the hormone, correlated with asymmetric growth.