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Guide to the study

• introduction
• research paper
• homeostasis
• feedback inhibition

Lab part 1

• tutorial/specimens
• Paramecium
• Chlamydomonas
• fixing/observingflagella
• Chaos (Pelomyxa) carolinensis
• Naegleria gruberi
• the five kingdoms

Lab part 2

• experiment introduction
• microtubules
• amputating flagella
• experimental design
• data collection
• class data

Flagella Regeneration – Data Analysis and Research Paper

You are not expected to write up your microscopic studies of biological models, conducted the first week. This paper will cover the experiments of the second week of the course. At least skim through this section as part of your preparation for the laboratory work, so that you are fully aware of the objectives of the study and what will be expected of you.

You are asked to write and submit this paper in parts, starting with the materials and methods and results sections. Shortly afterwards you will submit the discussion, abstract, and introduction. You will receive direct instructor feedback on all parts of your paper except for the results sections, which we will assess using Calibrated Peer Review. We provide explicit instructions for this first paper. For later papers you will increasingly be expected to apply the principles and practices that you learn through guidelines, examples, practice, and instructor comments on your previous work.

Honor code – giving/receiving/sharing information

Every part of every paper that you write for this course must be your own original work, including all text, all tables, and all figures. You may not consult a paper written by another student for this assignment in this or any previous semester. You absolutely may NOT copy written text from any source. Paraphrasing large sections of text also consitutes plagiarism.

On the other hand, you are encouraged to seek advice, share data files, share responsibilities for data analysis such as calculating means and standard errors, and to discuss findings and possible explanations with fellow students, provided that you share in such efforts and do not merely take it all in passively.

Professionalism

A major objective of the writing assignments is development of a professional approach to writing. These papers are not "lab reports." Your hypothetical role is that of an investigator, preparing a publishable manuscript on your original research. Your paper is to be read by other scientists working in the same field and/or other professionals and/or students who conduct scholarly research, such as a literature review. Your anticipated readership is well versed in basic biological science and experimental design.

A scientist does not introduce a paper with a broad generalization, such as the statement, "this study will advance our knowledge of cell biology," or "the purpose of a scientific investigation is to collect data to uncover truths about nature." Of course an investigator will not refer to a learning experience, instructor, classroom, the "lab manual," teams of students, etc. Play the role of scientist as you write your research papers.

Materials and methods

A materials and methods section serves to document the methodology that was employed for a laboratory study. Our general guidelines advise that this documentation serves two major purposes.

1. It provides sufficient information with which to permit a reader to reproduce all or any part of the methodology that was applied to the research project.
2. It permits a reader to judge the scientific merit of the methodology that was employed.

What a materials and methods section does NOT do include the following.

1. It does not describe what you did in the laboratory, step by step. That is, it describes only the methods, not exactly how you applied them.
2. It does not present methodology in the form of instructions.
3. It does not provide explanation or justification for methods that were used.

For the first paper your materials and methods should include the following information, clearly and accurately described.

• Species used for the study, its source, and the source of any specialized reagents or uncommonly used supplies or instrumentation
• Culture conditions for growing the organism and the method used for amputation of flagella, including separation of cells from amputated flagella and their resuspension in media
• Composition of media (including concentrations of colchicine, cycloheximide), composition of the fixative/stain
• Conditions for maintaining the experimental and control cultures during the experiment (time, temperature, volume, lighting, etc.)
• Method of sampling cultures and mounting them for microscopy
• Methods for selecting cells randomly, observing and measuring flagella (including magnification, optics)

Some things that we do not include are the following.

• Informal lists of any kind
• Reference to students, instructor, classroom, etc.; we write these papers from the perspective of a scientist publishing original work
• Descriptions of commonly used materials such as pipets, beakers, inorganic chemicals, etc.
• Descriptions of instruments used when their use is implicit in the methodology described; in particular we only report brand names of instruments or supplies when a specific source must be used to ensure the success of an experiment
• Explanatory material of any kind
• Any sort of chronological account of procedures that you conducted

The documentation must be written using normal prose and paragraph organization. Use complete sentences, including articles ("a," "the," etc.), but otherwise try to keep it succinct. Publishing costs are high and people do not have time to wade through a lot of verbiage, so we try to consolidate information while remaining clear and grammatically correct. Needless to say, we avoid redundancy. Even if you apply the same methodology to several treatment groups, for example, you only describe it once.

Results

As you should have figured out by now, each section of a typical research paper serves a specific purpose, allowing an individual to read selectively. A results section serves to present the findings themselves. We use three elements to present findings in a results section. A text write-up is essential. The text should summarize and illustrate the findings. One or more tables serve to present information that would be tedious and cumbersome to report in text form, such as large amounts of quantitative information or even verbal material of a repetitive nature. One or more figures serve to present information that is best visualized rather than described verbally. A graph is the most common type of figure, used to illustrate important patterns, trends, or relationships. Figures can also be used for images such as cropped and labeled gel images.

Neither tables nor figures are essential elements in all write-ups, however for this first paper some of the findings are presented most effectively in the form of a graph (figure) and others are best presented in the form of a table. Our "rules for submitting manuscripts" call for figures (with captions) and tables to be submitted on one or more pages following your text, not to be incorporated into your text. Your results section is to include the following elements.

• Text, describing observations that are not summarized in table or figure form
• Although the focus is on the findings you should provide context by very briefly describing the overall objectives of the study.
• In a logical order describe observations that are not readily apparent from looking at the figure or table. For example, was the amputation 100% successful? Were there complications that might have compromised the data? Was there evidence of broken flagella, for example? These are just examples. Use your judgment when deciding what to report
• Again in a logical order, summarize the information to be gleaned from the figure. For example, were there recognizable trends among cultures that regenerated flagella? Did regeneration reach some limit and then stop? Are there obvious differences between the control and experimental cultures?
• Summarize what should be learned from the tabled information.
• Figure, presenting the experimental findings
• Plot data only from cultures that showed changing flagella length with time; it makes no sense to plot something that does not change.
• Prepare your figure so that the reader can readily appreciate the differences in regeneration patterns between experimental and control cultures.
• Prepare a well-edited figure as described in the graphing tutorial.
• Remember that your figure should be sufficiently informative that it can stand apart from text.
• Table, presenting the results from control experiments
• For each of the three controls in which flagella were not removed, use "Student's t test to determine if there was a difference in mean length at the end of the experiment compared to the start.
• Use the simple form that is typical of a published table (see the writing text and/or portfolio of examples)
• Include sufficient information so that the table can stand apart from text
• Remember to report only converted data (summary data), not raw data such as individual measurements
• Present the outcome of your statistical analysis, and of course the method used for analysis

As with other sections of a paper, use normal prose, proper English grammar, and paragraph organization. Here are some more "rules" for writing an effective results section.

• Present converted data only (summary data such as means ± standard deviations, statistical outcomes, etc.), no raw data such as tables of individual measurements.
• Present each set of findings in the single, most effective way that you can; if you plot data, do not list the individual data points in a table. If you place data in a table, do not repeat the exact same information in text – text should complement figures and tables, not duplicate the information.
• Use past tense to refer to specific findings – it is almost certain that someone conducting this same study would obtain at least slightly different quantitative findings. Using present tense implies that your specific observations are common knowledge, already generally accepted by the scientific community.
• Use precise and informative language – avoid making vague statements or convoluted statements that are not clear.
• When you report any quantitative finding that is based upon measured quantities, round the numbers consistently to reflect the uncertainty in the measurments. This "rule" applies to error estimates such as standard deviations, not just to sample means.
• Avoid presenting background information and avoid interpreting the findings; interpretation is for the discussion; report conclusions that can be drawn directly from the data (e.g., there was a 20 min delay before start of regeneration; elongation rate was linear).
• Avoid incorporating subjectivity into your writing, such as the use of hyperbole. One doesn't write, for example, that "the cells regenerated flagella at a furious rate," or "the cultures looked terrrible." You can describe the same observations by writing, "the cells regenerated complete flagella within one hour," or "the presence of clumps of cells, noncellular debris, and damaged cells complicated observations of the cultures."

Criteria for evaluating your results sections

The following statements describe criteria that you and your peers will use to evaluate your papers. See the presentation on CPR criteria for more details.

Organization

• The paper includes a significant text portion.
• Figs and/or tables submitted separately, not placed within the text.
• Author presented converted data, not raw data.
• Quantitative data are rounded to reflect precision of the measurements.
• Figures and/or tables are used, if appropriate, to present new findings.
• Page breaks used well – no split tables or orphaned headings.

Text

• Complements figs/tables rather than merely describing/introducing them.
• Uses specific, informative, clear language.
• Focuses on observations and results, not background information.
• Presents facts only, with little or no interpretation.
• Professional style, appropriate for a research paper (not a "lab report").
• Author consistently used past tense to refer to the findings.
• Author used paragraph form and wrote in normal prose.
• Author consistently used good grammar and accurate spelling.

Figures

• Neat, appropriately labeled, with properly placed, informative captions.
• Plot types are appropriate for the data presented.
• Plots are simple, black and white, without "computer clutter."
• Plots include error bars representing s.e.m. if appropriate.
• Used trend lines effectively.
• Plot areas are well proportioned.
• A single graph is used when comparing two or more sets of data.

Tables

• Table can stand apart from text (informative title/description, summary data, units, categories, species, name/outcome of statistical test if used).
• Summary data include error estimate (e.g., means ± standard deviations).
• Headings used correctly – data in rows, data headings in columns.
• Table uses no vertical lines, minimum necessary horizontal lines.

Discussion

Here is where you report what you think your findings mean, keeping the overall objectives of the research in mind. An obvious starting point is to address the question, "did the findings support the original hypothesis?". As you interpret the findings, refer to your data (in past tense), without dwelling on the data. You already presented the data in the results, so now need refer to the findings only when it is necessary in order to make a point.

It is important here to try to explain the findings, being as clear, accurate, and specific as you can. It is important to explain all of the findings, not just the major finding. Use a logical organization. A good approach is to address the most important conclusions and explanations first, then deal with interpretation that is less important and/or peripheral to the objectives of the study.

For a study of this sort it is absolutely critical that you discuss possible intracellular mechanisms that could explain your observations. Be confident when you offer an explanation. For example, one doesn't write, "it is possible that...," "maybe this is what happened...," or "the data seem to show..." Do be open to alternative explanations, though. We use phrases such as, "the data strongly suggest," or "the findings are consistent with the following explanation." Do not speculate wildly, but do offer less likely alternative explanations if they are reasonable.

Here are some specific suggestions for this particular discussion.

• Was the hypothesis supported? Were there significant differences between the experimental and positive control cultures?
• Consider how feedback inhibition of tubulin synthesis and/or a dynamic equilibrium between free and assembled tubulin and/or some other mechanism(s) might explain specific observations, including
• onset of flagellar regeneration, including any delay in onset
• pattern of regeneration (length versus time)
• cesssation of regeneration
• findings from control cultures with intact flagella (non-deflagellated cultures0
• Clearly distinguish among tubulin subunits and their synthesis, microtubules and their assembly, and the major underlying concepts of feedback inhibition on tubulin synthesis. spontaneous assembly of tubulin into microtubules, and dynamic equilibrium
• Cover all of the observations, including results from control groups; offer explanations for all of the trends
• Finish your discussion with some kind of summary paragraph, such as summarizing the major conclusions and/or suggesting a direction for future research in this area

The BIGGEST MISTAKE that many students make in this particular paper (and to some extent in others) is to be vague when expressing concepts. If you explain an outcome, make it clear which treatment group you are discussing. When you explain theoretical basis for a finding, describe the concept explicitly, and make it clear what specific finding you are discussing.

Abstract

An abstract is a concise summary of the findings, most often presented as a single paragraph. Our "rules" require that you write a single paragraph summary. It should summarize the major elements of the paper, focusing primarily on the findings. A reader should be able to read only the abstract and know your objectives, how you accomplished them, what findings you obtained, and what conclusions you drew.

• Present all of the relevant findings including (for a study this focused) a complete summary of quantitative and qualitative findings; support your statements with statistics if applicable
• Address the objectives at the beginning of the abstract, but briefly; revisit the objectives with a summary statement at the end

Two of the biggest mistakes that students make are

• failure to summarize specific findings, especially quantitative findings
• including excessive background information

Remember, the abstract is to be a concise summary. We avoid presenting rationale, detailed explanations, speculation, and excessive details on methodology. As a general rule for starting out, devote no more than a sentence or two to presenting the objective and the design of the experiment itself. Go quickly into a thorough summary of the quantitative and qualitative findings, omitting none of the major results. Finish with no more than a sentence or two, summarizing major conclusions.

Introduction

An introduction should present the rationale behind the study. There are all sorts of ways in which to write a good introduction. Some authors write a manuscript page or more (that's four double spaced typed pages), while some limit the introduction to just a couple of paragraphs. For your introduction, simply make sure that all of the information you include is relevant to the goal of fully acquainting the reader with the reasoning behind your choices – overall research, specific hypothesis, experimental model, methods. Here are some elements of a good introduction, not necessarily to be presented in this order. The items in this list are neither exclusive nor absolutely necessary for every paper.

• What is the overall objective of the research that includes this particular study?
• What was this study specifically designed to accomplish?
• What was the basis for choosing the species, tissue, or cell type used as a biological model?
• How, in somewhat general terms, was the experiment conducted?
• How did the experimental design accomplish its objectives?
• How did you intend to use the findings?

We don't generally describe the results in an introduction to a paper, although some authors will summarize the outcome. As for context, keep in mind that when you submit the introduction for publication, all of the work will have been completed. The study is in the past, and so any reference to the experiment, specific findings, decisions made, conclusions drawn, etc. should be made in past tense.