Methods

Authorship

Nature: The list of authors should accurately illustrate who contributed to the work and how. All those listed as authors should qualify for authorship according to the following criteria:

  1. Have made substantial contributions to conception and design, or acquisition of data, or analysis and interpretation of data

  2. Been involved in drafting the manuscript or revising it critically for important intellectual content

  3. Given final approval of the version to be published. Each author should have participated sufficiently in the work to take public responsibility for appropriate portions of the content

  4. Agreed to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved

contributions from anyone who does not meet the criteria for authorship should be listed, with permission from the contributor in an Acknowledgments section

First author: associate you with the finding

Ghost authorship, Guest/gift/honorific authorship/orphan authorship, forged authorship

First author: typically the person who did the most work on the experiments and did the bulk of the writing

last author is usually the senior scientist in the lab (e.g. supervisor)

middle authorship: most to least work

When everyone contributes equally, consider listing the authors in alphabetical order

Lab Books

  • complete record of experiments, reagents, data, results, and thoughts

  • can be written in any person or tense

  • passed on to other researchers

  • legal document (can be used for patent applications etc.)

  • discipline dependent

    • waterproof for field work

    • hard cover or electronic for lab work

  • meant to keep up to date

    • complete as you get data

    • include everything (even experiments that don’t work)

    • details are discipline-dependent (include location for field work but not for molecular biology)

  • if a physical book, must include a table of contents on the first couple of pages

    • include all protocols, results, figures

  • electronic books can contain hyperlinks

  • each page should be numbered

  • all entries must be dated

  • all entries require a detailed title, figures and tables need a legend

    • the protocol of …

  • we use Benchling (digital lab book)

Each entry needs:

  • detailed title (e.g. restriction digest of plasmid P blue script with eco R1)

    • this technique of this with this

  • date

  • protocols require a statement of purpose (1 sentence) above them

    • shows why we are performing technique (ligation, transformation

  • results require a BRIEF analysis (1-2 sentences)

  • entries will be checked weekly

Field work Unit

  • notes can become damaged or lost

    • take photos of notes as electronic backups

  • you will embed your photos in a word file and submit your lab notes as a pdf

  • will do this 3 times (each worth 1%)

  • each entry needs:

    • date and detailed location of sampling

    • methods of sample collection

    • notes about weather and time of day

    • results require a BRIEF analysis (1-2 sentences)

    • entries will be checked weekly

    • does not require purpose

Structure of a research paper

  • scientific papers are published in journals

  • thousands of scientific papers published every year, in thousands of different scientific journals

  • it is not possible for a scientist to read every paper every year, so it is important to make your paper grab the audience’s attention so it DOES get read

    • emphasize the title and abstract

  • papers have different structures

  • The Journal of Experimental Biology: use as referring format as it has a paper structure most common in scientific research

    • no references and no statistics in abstract

    • references appear alphabetically by last name of first author

  • article numbers are similar to page numbers (for fully online texts)

  • journals’ decision to follow different formats

Paper Structure

  • Title, Abstract, Introduction, Materials and Methods, Results, Discussion, Acknowledgements, References

will be writing a review paper based on papers we have read

Poster Structure does not include abstract (includes everything else)

General notes

  • when referring to a species, use its common name with its scientific name on first usage within the text

    • after, can use its common name throughout

    • italicize the scientific name

  • use the scientific name in the title, abstract, and on first usage in the introduction

    • title and abstract need to be able to stand alone, because many readers read no further

  • Example: “We studied this in bluegill (Lepomis macrochirus). In bluegill…”

    • use scientific name (binomial nomenclature with uppercase first letter in genus only)

    • use scientific name in title & abstract (better for search)

  • Paragraph structure

    • editors find it easy to help writers improve their work when the ideas are easy to follow

      1. Topic sentence that provides context

      2. content that is all related (use transition words)

      3. conclusion that summarizes the main idea

        • each paragraph should have only one idea!

  • develop a skeleton of your paper before filling it in with details

    • write a topic sentence for each paragraph, then list bullet points supporting that topic sentence with what will be the content of the paragraph

      • helps recognize how ideas fit together

Title: clear and interesting, avoid long titles, witty (can be effective, but not everyone will get it, play on words work well), include a key result or list the hypothesis tested

Abstract: short summary of the paper

  • typically includes sections from each section in the body of the paper

  • give context of the paper’s research questions (why do scientists care, or what remains to be learned) - introduction

  • give the research question or hypothesis - introduction

  • briefly describe the approach to addressing the question - methods

    • general approach

    • don’t need to go into as much detail

  • describe the findings of the experiment - results

    • do not give statistics; only state in words what the experiment found

  • put the findings into context: how does this address the hypothesis, advance the field, resolve an unanswered question, or how can these findings be applied by scientists/policymakers/doctors/engineers - discussion

  • most of the time, the abstract does not have references

    • there are some exceptions (different journals with different formats, or if the paper is being written to criticize or re-test one paper’s results)

      • those exceptions are unlikely to come up during your undergrad

Nature is one of the top journals in science: they have an outline for an abstract

  • abstracts are longer than other journals, but the general idea is correct

Introduction

  1. give the context for the research question and what is already known — takes several paragraphs

  2. give the objective of the research, including the research question — the reader might be able to guess your research question after having read all the context

  3. state the hypothesis — 1-2 sentences

  4. state the predictions — 1-2 sentences, fitting with the hypothesis and the experimental design

  • start: broad, end of intro: narrow

    • broad: discuss the field as a whole, drawing on theory

    • narrower: describe what is already known from other species

    • more specific: what remains to be learned, and justify your choices of study species, what category of treatments you are using, location, timing

    • most specific: give your hypothesis and predictions

Materials and Methods

  • describe what you did in a way that a reader understands what you did and could repeat the experiment

  • mention where the uniquely important equipment was acquired

  • describe your statistical methods, including what the dependent and independent variables are

  • do not give statistics until the results section

  • if you excluded any data, explain why here

  • might include references to studies that used methods similar to your own

    • references help support your choices and may mean that you do not have to repeat every detail

Results

  • discuss what you found in your experiment

  • typically includes a sentence that describes the results of a statistical test, then the result of the test in brackets

  • avoid interpreting the biological meaning of the results here — such interpretation belongs in the Discussion

    • you can interpret if the statistics are significant

  • claim (t = ??, df = ??, P = ???; Fig. 1)

  • list sample sizes here

  • try to include a narrative for your results

    • becomes more important once you have several tests to report on within a single study

    • easier to write if you put tests for similar questions together in the same paragraph

      • if you had a set of experiments on the effect of temperature and another set of experiments on the effect of moisture levels, report them in different paragraphs

  • present your results as a table or a figure (don’t do both for one thing)

    • reference figure in text

    • figure captions should appear BELOW the graph, not above

    • table captions appear ABOVE the table

Discussion

  • do the results support the hypothesis or not?

    • explain why

    • use biological explanations rather than criticizing your own methodology

    • perhaps there is something different about the population you studied than what you had used to set up your hypothesis

  • compare to other studies (with references) that found something similar or different

  • do not include any statistics in your Discussion

  • why should we care about these results

    • did this experiment lead to more questions? we can use those to think of future directions

  • why we should care about these results

    • how would other scientists, policymakers, doctors, or engineers use this information

Acknowledgements

  • list the people & organizations that supported your work, and briefly describe how they helped

  • consider listing the TA’s and technicians

    • it is your responsibility to learn their names!

References

  • different journals have different referencing formats

    • key idea is that the reader is able to look up other research that is relevant to your paper

    • Journal of Experimental Biology: references are listed alphabetically by last name of first author

Within-text References

  • include the reference once after the first sentence, and then word the subsequent sentences to make it clear that you are still referring to the study

    • EX: “Hain and colleagues (2017) found that guppies recognize relatives. In that study, they found that guppies like to hang out with related fish. Those fish were happy.”