# A Guide To Writing Experimental Reports

> Colby College - [BI279L Genetics Lab](https://moodle.colby.edu/my/)
> Updated 20 November 2020 - [Dave Angelini](mailto:[e-mail])

### <a name="sciwriting"></a>Science writing

Experimental reports published in scientific journals allow the dissemination of new results to the community. This is how new knowledge is introduced to the world. The format and style of scientific writing emerges from the philosophy of empiricism that underlies science. This traditionally minimizes the voice of the author and does not valorize other people. The focus is on the subject: living things and the data describing them. Your goals as a scientific writer are to clearly present the purpose, results and interpretations of experiments, and to connect those elements with past knowledge in a way that's meaningful to an audience of your peers.

> **Tips**
>
> * Avoid sentences that pack in too many ideas.
> * Never say anything is "complicated" in a scientific paper.
> * Be succinct. If you can make a point in 10 words, don’t use 20.
> * Don't let the tone of your writing to be too conversational.
> * Avoid vague and cliched "SAT words" like "plethora", "myriad"
> * Avoid wordy phrases that don't add anything to the meaning of your text: "It has long been known that..."

Good science writing requires knowledge of your subject. In an advanced Spanish course, you need to know your verbs and sentence structures, before you can write about a visit to Madrid. Similarly, you will need to understand some background information, many terms and experimental methods before you can write effectively in science.

> **Tip**
>
> Our target DNA is regulatory sequence. Therefore unlike DNA from an exon, it doesn’t encode a protein or anything else. Be careful about where you use the words “code” or “encode”.

### <a name="audience"></a>Who is your audience?

The goal of your writing should be to persuade a reader of your conclusions. What you should ask yourself as you write is, does this make a convincing case for my idea? Has each logical step from the purpose of the experiment, through its conclusions been made clear to a reader?

Remember that you are practicing to write for a scientific audience. Do not write with your lab instructor in mind as the audience. Your lab instructor has been in on each of the steps of your project and has a very clear idea of what you've done. Instead, you need to practice writing for an audience that isn't so familiar with the everyday events in your lab. If it helps to imagine specific readers, imagine you are writing for students who've just completed the genetics course at Bowdoin or Bates. They'll be familar with core concepts of genetics, but maybe not with the genes you're using or the experiments you've conducted.

> **<a name="writingcenter"></a>Tips**
>
> * Consider visiting Colby's [Farnham Writing Center](http://web.colby.edu/farnham-writerscenter/) for advice and support with writing.
> * English isn't your first language? Consider meeting with Colby’s Multilingual Writing Specialist, [Ghada Gherwash](mailto:[e-mail]).

## <a name="format"></a>The format of an experimental report

Your experimental reports for BI279 will follow the format of most scientific journals.

### <a name="title"></a>Title

A concise **Title** should convey the most important conclusions. Titles should state the variable being manipulated, what is being measured, and the biological context of the experiment. The best titles will actually convey the conclusions of the study. Here are some good examples:

> **Good Examples**
> - The *Drosophila* proboscis is specified by two Hox genes, *proboscipedia* and *Sex combs reduced*, via repression of leg and antennal appendage genes
> - Targeted gene expression as a means of altering cell fates and generating dominant phenotypes
> - Ectopic activation of *torpedo/Egfr*, a *Drosophila* receptor tyrosine kinase, dorsalizes both the eggshell and the embryo

A title should not be vague. A title should also not mention your drivers. It also can't include everything!

> **Bad Examples**
> - Wing development in flies
> - Crosses of flies to misexpress proteins
> - Misexpressing *decapentaplegic* and *hedgehog* in the intervein areas and margin of the wing in *Drosophila* using Gal4/UAS causes some flies to die as pupae and transforms the bristle cells in other flies into naked cuticle

### <a name="abstract"></a>**Abstract**

An abstract is a paragraph-length summary of the entire report. The abstract should be no more than 250 words. Write it last and include the most important points from each of the later sections of the paper. Typically, the abstract summarizes the paper in the same order as the section headings, covering the important points from the introduction, methods, results, and then discussion. The abstract does not need to cite sources.

> **Tip**
>
> * If you mention the drivers or other transgenes in the first few sentences, it is usually a sign of an abstract that is not highlighting the key things.

### <a name="intro"></a>**Introduction**

The Introduction provides your readers with the background information that will be necessary for them to understand the purpose and interpretation of your experiment. You want to describe the issue or question being addressed by your study. You will need to provide background from the published literature for this assignment. At a minimum, you will need to provide primary literature citations that describe where each gene in your study is normally expressed and what kind of protein the gene encodes (e.g. transcription factor, cell surface receptor, secreted ligand) and what role that protein normally plays in wing development.

An important part of that background is making it clear ehy your work in important. The Introduction should start with a very broad statement for the significance of your question or the findings your report will share.

#### <a name="Hypothesis">Hypothesis</a>

Present a hypothesis to explain the issue. ("The wing veins carry nerves. Notch signaling is involved neuronal development, therefore we wanted to test whether misexpression of Notch in the wing could induce vein development.") Remember, your hypothesis should be a general statement about what your pathway does. It should not reference your transgenes. After stating your hypothesis, you should describe how it will be tested, briefly outlining the key parts of your experiment (such as misexpressing proteins using Gal4/UAS).

After you've described the misexpression experiment, then you should state your <a name="predictions"></a> predictions for the outcome. ("We expect that driving N^intra^ in the wing should lead to extra vein development, while misexpression of a dominant negative form of the Notch receptor should prevent vein formation.")

> **Tips**
> * A common pitfall is that students present predictions as though they were a hypothesis. But a hypothesis is meant to be a general statement about the process or pathway being studied. Your predictions are the results you expect from the experiment, if your hypothesis is actually true.
> * When you state your hypothesis, try to avoid using "hypothesize" as a verb. It's not wrong, but it is inelegant.

It is not necessary for your results to support your hypothesis. It is possible for you to write an excellent report, in which you present a hypothesis whose predictions are not met by your results. Scientific articles get a lot of attention if they challenge or overturn convential thinking in their field. So authors will often pose their hypothesis based on that conventionial thinking (and supported by the background they present in the Intro). If the results don’t match the predictions, the Discussion can then speculate on how and why everyone’s previous understanding was incomplete. In some cases people even pose a hypothesis that’s so weak, a skeptical reader might call it a “strawman” – one that’s easily knocked down. It’s okay to do this in our class if you need to!

### <a name="results"></a>**Results**

Results should be reported in their own section. Sub-section headings should communicate results in a short phrase, just like the title of the paper. The actual, observed results should be clearly organized and summarized in writing for a reader to judge. Provide the details that are necessary to reach conclusions later in the Discussion. One part of this will be stating the expected results, such as the band size you expect from your PCR product.

Talk through the logic that brings a reader to your conclusion. For example, explain what you expect from the restriction digest of your plasmids, then describe the pattern you actually observed. Point out the bands that indicate the presence of your intended insert. Or if those expected bands are absent, make that point plainly.

> **Tips**
>
> * Reference your figures parenthetically, like this (Fig. 1).
> * In a reference to a figure or source, never include the word “See”. -- Don't do this (See Fig. 1).
> * Don't ignore results just because they don't match what you expect or want to see.
> * You should never write a sentence that is simply a list of things. For example, it's not adequate to simply list in your text the samples in each lanbe of a gel. You need to explain why those samples were included, what was expected and what was observed.

For each step of the experiment, you should explain its purpose and the 'samples' tested. Provide enough of an explanation to allow the readers to understand the experiment and interpret (by themselves) the results that will be described, without actually stating the interpretation or conclusion in this section.

> **Good Example - Note that this describes an experiment different from the one our class does.**
> The timing and expression pattern of *twist* in early *Drosophila* embryos was examined using a probe created to detect *twist* mRNA through *in situ* hybridization. A 1597-bp fragment of the *twist* coding sequence (*twist* PCR product) was amplified from purified *w^1118^* genomic DNA. Forward and reverse PCR primers contained EcoRI and HindIII sites, respectively, to facilitate cloning. The concentration of the 1576-bp *twist* PCR product produced after digestion was determined by agarose gel electrophoresis. To control for restriction enzyme activity…

Keep in mind that procedural details would be covered in a <a name="methods"></a> **Materials and Methods** section. For BI279 you are not required to include a Materials and Methods section. So don't include details such as volumes or concentrations of reagents in your paper. The example above does an appropriate job of mentioning her methods (PCR; in situ hybridization; cloning; electrophoresis) and key details (genomic DNA was purified; PCR product size; name of the RE cut sites in the primers).

In your paper be sure to briefly describe how your putative regulatory sequence was selected. Give the primer sequences and explain the presence and purpose of *attB* sequences.

> #### Tip
> Do you know what "putative" means? And why we might use it in biology?
>
> **pu·ta·tive** *adjective*
> [/ˈpyo͞odədiv/](https://www.youtube.com/watch?v=qXO0Mtvnf5g)
> *synonyms:* supposed, assumed, presumed, presumptive, alleged
> Something that is putative is not confirmed, but only assumed to be the thing mentioned. A "putative regulatory element" is DNA that is provisionally considered to be a regulatory element, but that fact has not yet been fully verified.

The Results section *should* mention <a name="controls"></a>controls, whenever appropriate. Remember, that just calling something a "control", doesn't say much. You must explain what experimental variable is being controlled. For example, running genomic DNA on a gel with your PCR product controls for the assumption your PCR reaction contained template DNA.

> #### **Tip**
>
> * [Gateway cloning](https://www.thermofisher.com/us/en/home/life-science/cloning/gateway-cloning.html) is based on site-specific recombination. The clonase enzymes **do not cut** DNA. Gateway accomplishes the same thing as [traditional RE-based cloning](https://blog.addgene.org/plasmids-101-restriction-cloning) (insertion of your PCR product into a plasmid), but it is faster and more efficient. So, don’t refer to our cloning methods with terms like “cutting” or “ligating”.

> #### Miscellaneous
>
> * Ever wonder what the "LB" in LB broth stand for? This standard culture media for *E. coli* is a solution of amino acids, salt and an enzymatic digestion of dried yeast. The recipe can be used in liquid form, or added to agarose to make plates. LB was originally developed in 1951 by [Guiseppi Bertani](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4588218/) for work on bacteriophage. It was called [lysogeny broth](https://en.wikipedia.org/wiki/Lysogeny_broth), which is where the "LB" comes from. However, the initials of Bertani and his collaborator, [Salvator Luria](https://en.wikipedia.org/wiki/Salvador_Luria) became conflated with the name over time. -- So, why did two Italians name their reagent in English? Bertaini worked at the University of Illinois, and Luria was a professor at [Indiana University](https://biology.indiana.edu/research/faculty-awards.html).

### <a name="quant"></a>**Quantitative data**

For BI279, your experimental report must include quantitative data of some kind. Depending on the pathway you're manipulating, you might measure different things. Some possibilities:
* the number of flies from each cross
* the number of males and females from each cross
* the number of flies from a cross that carry parental markers, perhaps indicating that you had non-virgin female parents
* the number of flies from a cross with mild, moderate or severe phenotypes
* the number of flies with a particular kind of abnormality
* the width or length of wings, relative to some other body part like the legs

Your results section should include at least one set of quantitative data on some aspect of your project. Use an appropriate statistical test to make comparisons. Whenever you want to say two things are different, that assertion should be supported by a test. Our Moodle page has a guide to statistics, which includes detailed instructions for performing tests in R. You can also talk to your lab instructor!

> **Tips**
> * <a name="jargon"></a>Don't refer to your crosses by short-hand numbers: 1a, 1b, 2a, 2b, etc. They are meaningless outside our lab, and do not help a reader.
> * If you say something is a control, what is it a control for? Why do we run genomic DNA beside the PCR products? Why do we run undigested plasmids on the RE gels? Why did we make crosses of *w^1118^* x *w^1118^*? What are these actions controlling for? (Answers: Including genomic DNA verifies that you had genomic DNA as template in your PCR. Undigested plasmids control for the presence of plasmid and its different isoforms; the *w* crosses control for the potential lethality, reduced offspring numbers, or sex effects produced by misexpression. – Try to communicate these ideas in your own words.)
> * "Data" are plural. So you should write, "Our data show..." rather than "Our data shows..." (The singular form of "data" is "datum.")

### <a name="figures"></a>**Figures**

Figures should be used to present images or graphical data. Think carefully about how best to organize the visual impact of image data. Label the important parts of gels or anatomical pictures. Summary diagrams in the Discussion can also help you make your point visually. Think about graphic design for the best communication of your data. For example, crop blank space from the top, bottom, and sides of your gels. Images that need to be compared to one another should be included as separate panels within the same figure. In figures with fly wings, it helps to keep them all oriented the same way!

Many students find PowerPoint a convenient program in which to compose figures. [ImageJ](http://rsbweb.nih.gov/ij/) is free software that can be used to crop or rotate images, adjust brightness and contrast, along with many other image manipulations.

Always include a **legend** for figures and tables that gives a brief sentence summarizing the figure's meaning—not its content. Think of this as the title to the figure. ("Figure 1. *engrailed* is expressed in the posterior compartment of the *Drosophila* wing.") Individual panels within the figure should be lettered, and important content should be labeled. Since space may be tight, abbreviations are okay, but define them in the figure legend. After the figure title, explain the content of each panel. Be as specific and detailed as possible to help a reader. ("(B) Fluorescent micrograph from a 2-h old wing of a *en-Gal4; UAS-EGFP* female fly. Anterior is up; distal is right. The bright spot near the wing hinge is an autofluorescent artifact from damaged tissue.") Figure legends should appear below the figure. The legend for a table should be above the table. (Notice that this how the lab protocols are formatted.)

> #### Tips
>
> * <a name="#figure1shows"></a>Don’t make figures or tables the actors in your writing. (For example, avoid statements like "Figure 1 shows that our PCR was successful." or "Our results are shown in Table 1.") Just cite results parenthetically. (e.g. "PCR produced the intended 1kb product and a ~400 bp off-target product (Fig. 1)." or "Misexpression of human *FoxP2* in the fly brain resulted in increased language ability (Table 2).")
> * Include the GFP expression images of both drivers used in your misexpression crosses. Remember, you don’t need to use just “your” images.
> * You can and should consider all the images from past semesters as your data too. Just add mention of this fact in the Acknowledgements.

### <a name="tables"></a>**Tables**

Tables can be a convenient place to report numerical data like counts of offspring from each cross, the number of offspring with a certain phenotype, etc. Use a Table if conveying all of this information directly in the text would be tedious and difficult to interpret. Alternatively, if the data could be easier to interpret as a figure, considering reporting them that way. Be sure to give headings to each column and include units were appropriate. Lastly, avoid allowing tables (or figures) to break across a page or column in the final version of your report.

> #### **Tip**
>
> * Tables are okay, but bulleted lists are not.

### <a name="discussion"></a>**Discussion**

The Discussion provides your interpretation of the results of the study. What do the results mean? State your conclusions and then follow it with a convincing argument. Don't repeat all the results in the Discussion section, although you should parenthetically refer to your data figures to point out key bits of data. You should state how your results answer (or fail to answer) the question you raised in the Introduction. Importantly, the Discussion should also put your study in a broader context and point out the significance of your work. Conclude the Discussion by returning to the issues raised in the Intro and give overall conclusions.

If your experiment was unable to adequately address the question, you can offer an explanation of why that might be so. If needed, discuss what might be done in the future to better accomplish your goal. However, you should not present a litany of problems or ascribe unexpected results to human error. And don't undersell your results! If any of your crosses produced a wing that is not normal, then you just used transgenic manipulation to reveal something about how an organ is constructed. It's not necessary that all (or even most) of your crosses had dramatic effects. Just one clear phenotype can be informative, and you should base your conclusions on your positive results, without apologies for parts of the project that didn't work.

> Appreciate that what you've done in this lab was inconceivable just 25 years ago!

### <a name="acknowledgements"></a>**Acknowledgements**

In the Acknowledgements you give credit to anyone who may have helped you, such as your lab partner, tutor, or a particularly helpful person at the writing center.

### <a name="refs"></a>**References**

A section of References should list the full citations of any source referenced in the text. More details on this below.

## Advice

### <a name="outline"></a>Start by outlining

Don't just sit down and let words tumble out. This will result in a disjointed mess. Start by making an outline. You should decide how to organize your writing within each section (Intro, Results and Discussion). When outlining, your goal is to organize ideas without worrying yet about the choice of words. Each section should be divided into sub-sections that describe each step of the study. Bullets within each subsection should note the individual points that you want to make. If this is done well, you should be able to revise each bullet into a sentence or phrase to produce a good preliminary draft of your paper.

### <a name="resultsfirst"></a>Write the Results section before the Intro

Don't start writing at the beginning. (This is true even when you are outlining.) You may not fully appreciate all the implications of your data until you get organized. In an experimental report, the Introduction should support the Discussion and its conclusions. So you need to organize the facts of the Results section first.

1. Start by organizing your data into figures and tables.
2. Then write the text of the results. You may find that this leads you to change your figures. Try to make your figures convey the important parts of your data in a clear and well-organized way.
3. Next write the Discussion and conclusions that follow from your results. Discuss the experiments with other people. Often drawing a summarizing figure can be helpful to organize your thoughts, and it may be helpful to readers too!
4. Now write an Introduction that provides the background a reader will need to understand your discussion. Add references to your paper as you write.
5. Once you're comfortable that you won't need to add any more citations, format the reference list.
6. Finally, choose a good title and write an abstract that highlights the most important parts of each section of the document.

### <a name="litsearch"></a>Finding sources from the published literature

As you develop your outline, search the literature for articles that provide background information on your topic. In a busy field this can be daunting, but it is essential. The good news is that it's not necessary to read everything! (At least while you're in college.) For any topic you will probably find hundreds of articles. Choose your search terms carefully to provide a focused, manageable number of titles. Use titles and abstracts to filter down to the articles that are most useful to you. For example, scan the titles of about 25 articles. Choose the most relevant and carefully read the abstracts of about 10. From those, read only a handful of articles in detail. If what you're writing touches on multiple topics, you should repeat this process for each search-able set of terms you have in mind. As you read, be open to searching more if the articles you read suggest there are other areas you should think about.

<a name="searchtools"></a>Many search tools exist for the literature on genetics. [Google Scholar](https://scholar.google.com/) will provide fast results, but search fields are not very customizable and links to journals may require payment for access. Colby subscribes to several databases that allow you to search for keywords, journals, authors, years, etc. The links below will provide you access to all journals to which the college has active subscriptions.

> **Literature Search Tools**
>
> * [PubMed](https://colby.idm.oclc.org/login?url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi) - The US public database of biomedically releavant literature.
> * [SCOPUS](https://colby.idm.oclc.org/login?url=https://www.scopus.com/) - A commercial search engine for academic and scholarlyu literature.
> * [JStor](https://colby.idm.oclc.org/login?url=https://www.jstor.org) - A database covering less medically-oriented sciences, including ecology and organismal biology, as well as the humanities and social sciences.
> * [ILL](https://colby-illiad-oclc-org.colby.idm.oclc.org/illiad/illiad.dll) - If you have difficulty getting access to an article, you can request an "inter-library loan". Complete the form, and library staff at Colby will find the article or book any where in the world and provide you with a PDF (for articles) or a hard copy (for books).

<a name="annotatedbib"></a>As you search, keep notes for yourself on the ways you might use these articles in your paper. While the words "annotated bibliography" might make you grown, thinking back to high schools English. In our class, these notes are not graded. This is just good practice, and it can help you stay organized and ultimately save you time.

> **Good Example**
>
> Your notes might look like this. You can also paste URLs into your notes to link back to the articles.
>
> * Carroll 1995 *Nature*. [https://www.ncbi.nlm.nih.gov/pubmed/7637779](https://www.ncbi.nlm.nih.gov/pubmed/7637779) -- This is a review that explains how homeotic genes are conserved across animals. Clusters of them may evolve through gene duplication. Good ref for these background facts.
> * Halder, Callaerts & Gehring 1995 *Science* [https://www.ncbi.nlm.nih.gov/pubmed/7892602](https://www.ncbi.nlm.nih.gov/pubmed/7892602) -- Using Gal4/UAS they ecotopically expressed *eyeless/Pax6* in the legs of flies and got eyes to develop on the leg! A good ref for the importance of *Pax6* in eye development: necessary and sufficient. Might also serve as a ref showing the power of Gal4/UAS misexpression.
> * Yamamoto, et al. 2004 *Nature* [https://www.ncbi.nlm.nih.gov/pubmed/15483612](https://www.ncbi.nlm.nih.gov/pubmed/15483612) -- Cite this one to show Hedgehog is important for eye development in vertebrates. Cool experiment showing that applying a drug to inhibit Hh partly rescues development of eyes in "eyeless" cave fish.

One important way to find useful articles is to search "backwards" and "forwards". Go backward in time by looking at the references within articles to find other useful ones. Then search forward in time by using citation databases to find [later articles that cite](https://www.ncbi.nlm.nih.gov/pubmed?linkname=pubmed_pubmed_citedin&from_uid=15483612) those you've already found. A professor or the [science librarians](http://www.colby.edu/olin/) can help you use these databases.

### <a name="integrity"></a>Academic Integrity

The scientific community and the Colby community value [intellectual honesty](http://www.colby.edu/academicintegrity/the-colby-affirmation/). The written work you present must be your own, and you should always give credit when information or ideas were developed by others. Plagiarism includes misrepresenting any part of a written document as your own if it isn't. Writing services (paper mills) are not allowed. Uncredited text of any length (cutting and pasting as well as paraphrasing) also violates academic integrity.

You may be tempted to think that a source you read says something better than you ever could. But you are writing *your* ideas about their work. So, describe it in *your* words and give them credit for the idea or information with a citation. Colby's libraries have more resources for [avoiding plagiarism](http://libguides.colby.edu/avoidingplagiarism).

The only circumstances where citations aren't necessary, are for "common knowledge" in your field. It's typically not necessary to cite [Darwin (1859)](https://www.gutenberg.org/files/1228/1228-h/1228-h.htm) for the theory of natural selection or credit [Watson and Crick (1953)](http://www.sns.ias.edu/~tlusty/courses/landmark/WatsonCrick1953.pdf) for the structure of DNA. However, if you're uncertain, it's always best to be cautious and err on the side of making unnecessary citations rather than being called out for plagiarism.

> <a name="directquotes"></a>**Tip**
>
> * Experimental reports should never include direct quotes from your sources, even if they *are* cited. Why? This practice reflects the philosophy that we should value the information, independent of the personality of its authors. We credit them, but directly quoting is seen as too reverent.

### <a name="citationformat"></a>How to cite your sources in BI279

The natural sciences deal differently with citations than the humanities and many social sciences. In the text of biology articles, when an idea or fact is stated, an in-text citation is given at the end of that phrase or sentence, like this (Darwin 1859). If several sentences are obviously discussing the same source, only provide a reference to the first and last sentences that cover that source. If you devote a large amount of text to one source, you may choose to name the authors in the text. For example, you could easily spend a paragraph discussing the major work of Charles Darwin, in which case you only need to give the year of the source as an in-text citation (1859). Then, all sources mentioned in the text must have a complete, detailed citation given at the end of your document.

In BI279 we will use the [citation format of the journal *Genetics*](http://www.genetics.org/content/prep-manuscript#references). Citations in the text of your paper include the authors' last names and the year of publication. If the paper has more than two authors, list only the first, then the Latin abbreviation "*et al*.", which means "and others" (e.g. Angelini *et al*. 2012). The full reference then appears at the end of the report in the Literature Cited section. Lab protocols from BI279 may be cited in the text too (BI279L Protocols 2018). The full citation, including title must then appear in your reference list.

> **Examples**
> Angelini D. R., Smith F. W., Aspiras A. C., Kikuchi M., Jockusch E. L., 2012 Patterning of the Adult Mandibulate Mouthparts in the Red Flour Beetle, *Tribolium castaneum*. Genetics **190** : 639–654.
>
> BI279L Protocols, 2018 *Drosophila Wing Development*. Colby College, Waterville, Maine.
>
> Darwin C., 1859 On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. John Murray, London.

### <a name="proofreading"></a>Proofreading

After you have a draft, proofread your paper—twice! First, read it over to look at the narrative flow. Do ideas flow logically from one point to the next? Do you have sensible headings? Someone else may be better for this purpose. You may be emotionally attached to your own words. So ask a friend to be merciless, and take her advice when she says to cut that sentence. Next, edit for grammar, spelling, and the formatting of references, chemical symbols, or mathematically notation. (Don't get bogged down in these details early, just to have them cut or overhauled later because the sentence makes no sense.) Give yourself the time to write. Life is always busy. But when you use time to work on writing, it will improve.

> **Tip**
>
>* Use the [checklist](#checklist) at the end of this document to help proofread!

### <a name="voice"></a>Voice and tense

In the Introduction you'll present background information that is mostly accepted as true. These facts should be conveyed in the present tense. ("Frogs accomplish gas exchange via diffusion across the skin.") The results of your experiment should be written in the past tense. Avoid the [passive voice](https://webapps.towson.edu/ows/activepass.htm). ("Cells were cultured overnight." -- This point of grammar has seen a lot of [debate](http://advice.writing.utoronto.ca/types-of-writing/active-voice-in-science/) in the last several decades, but most people now favor the use of a clearer, active voice.)

Scientific writing does not emphasize the author, so avoid personal pronouns like "I" or "we". These pronouns can still be used, but only sparingly. ("We have conduced a detailed study of acorns, and our results reveal...")

> **Tips**
>
> * Avoid using vague words like "properly". Students often write "...properly inserted..." or "...properly sequenced..." Something is either inserted into a plasmid or not. The question is whether the inserted DNA is the expected sequence. Sanger sequencing data either has a high percentage of quality base calls, or not. (And reporting the exact percentage is preferably to simply writing "it didn't work".)
> * Gender is a human idea that's irrelevant to fruit flies. Biologically speaking, "sex" is their status as male or female. (While [intersex phenotypes](https://en.wikipedia.org/wiki/Gynandromorphism#As_a_research_tool) are possible in fruit flies, they are too rare in our populations to be relevant.)

### <a name="terms"></a>Terminology

Proper use of terminology conveys your understanding of the subject. "Heterozygotes have two loci for each allele." – That statement is not quite right, and it suggests the author is either being sloppy or doesn't really understand genetics. Be careful that you are using your terms properly. This can be difficult in a new or unfamiliar subject, but if you're uncertain of using a term, check its biological meaning first. The most common misuse of terms comes from confusion around DNA, RNA and proteins. (e.g. "Pax6 encodes eye development." That's not quite right.)

> **Tips**
>
> * [Gateway cloning](https://www.thermofisher.com/us/en/home/life-science/cloning/gateway-cloning.html) is based on site-specific recombination. The clonase enzymes **do not cut** DNA. Gateway accomplishes the same thing as [traditional RE-based cloning](https://blog.addgene.org/plasmids-101-restriction-cloning) (insertion of your PCR product into a plasmid), but it is faster and more efficient. So, don’t refer to our cloning methods with terms like “cutting” or “ligating”.
> * If any of your transgenes encode constitutively active (CA) or dominant negative (DN) versions of proteins, then be aware that these are not the wildtype forms of those proteins. They are mutant versions that alter the protein's function or regulation. You'll need to briefly explain these facts to your readers.
> * If one of your transgenes is [balanced](https://en.wikipedia.org/wiki/Balancer_chromosome) (e.g. *UAS-ras1^CA^/CyO*), that's its genotype. The "*/CyO*" indicates the homologous chromosome that does not carry the transgene. So the name of the transgene is just "*UAS-ras^CA^*".

### <a name="speciesnames"></a>Species names

Species names always appear in italics, such as the fruit fly *Drosophila melanogaster*. The first mention of a species in an article should use the full name (genus and specific epithet). Properly, subsequent mention of the same species should abbreviate the genus and use the specific epithet, as in *D. melanogaster*. While it is not strictly correct, molecular biologists often simply use the genus name for subsequent mentions of the same organism, for example referring again to *Drosophila*. Authors may also interchange the scientific and common names (flies and *Drosophila*).

Higher taxonomic groups, like family and phylum are treated as proper names and capitalized. However, the names can often be used as non-italics non-Latin names. ("Diptera is the order containing flies." vs. "Insecta is the class containing dipterans.") Taxonomists will insist that only "natural groups" (monophyletic groups) be given Latin names. Since it is now accepted that protists are not monophyletic, "Protista" should no longer be used. Some group names can also be used as adjectives. ("Heteroptera includes the cicadas, seed bugs and bed bugs. These insects share a specialized heteropteran mouthpart anatomy.")

> **Tips**
>
> * *E. coli* is a species name too, and should follow these conventions. The "*E.*" stands for *[Escherichia](https://www.cdc.gov/ecoli/general/index.html)*.
> * For more info and stories related to scientific names check out the blog [*Scientist Sees Squirrel*](https://scientistseessquirrel.wordpress.com/category/latin-names/).

### <a name="genenames"></a>Genes and protein names

Genes and gene products (e.g. proteins, microRNAs, and other non-coding RNAs) also have a convention when their names appear in print. When referring to any DNA sequence, such as a gene or regulatory element, the name should appear in italics, as with *Pax6*. Capitalization refers to whether the first mutant allele to be isolated for the gene was dominant or recessive. ([*abdominal-A*](http://beta.flybase.org/reports/FBgn0000014) was discovered as a recessive mutation, while [*Abdominal-B*](http://beta.flybase.org/reports/FBgn0000015) was first identified from a dominant mutation.) Italics are also used when referring to RNAs, for example the *Pax6* mRNA. However, proteins are never italicized and always start with a capital letter, as in Pax6.

> **Tip**
>
> * The case-sensitivity of gene names applies even when they start a sentence. For example the following sentence is grammatically and typographically correct. *rde-4* is recessive. That information can be conveyed easily if lowercase is maintained.

Just applying the rules regarding italics, it becomes much more clear when you are referring to a protein versus the gene encoding it. So you can write "Pax6 activates *dachshund*," and it is clear you mean that the protein Pax6 is responsible for activating expression of the gene *dachshund*. For more details, and some links to the rules specific to other model species, refer to the [WikiPedia entry for gene nomenclature](http://en.wikipedia.org/wiki/Gene_nomenclature).

### <a name="abbreviations"></a>Abbreviations

Overuse of abbreviations and uncommon jargon can annoy readers. If something will be referred to many times and it has an abbreviation or technical (jargon) term, you are entitled to use it, but define it at your first use. ("The occurrence of adults in some insect species with long and short wings is known as brachyptery." "The enzyme $\beta$-galactosidase ($\beta$-gal) can break-down the organic substrate molecule 5-bromo-4-chloro-indolyl-$\beta$-D-galactopyranoside (X-Gal).") Some abbreviations are so common that no definition is needed, like DNA or PCR. If you're uncertain, ask yourself if friends in the biology major would be sure to know the abbreviation.

> **Tip**
>
> * Abbreviations should never begin a sentence. It helps readability to avoid starting a sentence with an uncommon abbreviation.

There are some common abbreviations and foreign phrases that appear in science that deserve to be defined (Table 1).

**Table 1: Common abbreviations and Latin phrases used in biology.**

| **Notation** | **Definition** |
| ------------------------ | ------------------------------------------------------------ |
| e.g. | "for example"; don't use with "etc." since it's redundant |
| etc. | "and the rest" |
| et al. | "and others"; usually meaning "and coworkers" in an author list |
| in vivo | "in life"; in a live organism |
| in vitro | "in glass"; in an artificial system |
| in silico | "in a computer simulation" |
| i.e. | "that is"; used to start a complete list; incomplete lists start with "e.g." |
| senu stricto | "in the strictest sense"; the narrowest definition of the subject |
| senu lato | "in the loose sense"; the broadest definition of the subject |
| locus (plural: loci) | In genetics, a locus refers to a position on a chromosome. It can refer to a gene, or any other large genetic element, like a transposon. People tend not to use the term when you get down to the level of nucleotide sequences. Don't confuse the singular (locus) and plural (loci -- pronounced "low sigh") |
| milieu | A French word meaning "surroundings". Often used by chemists to mean other compounds in solution, or by cell biologists to refer to other things in a cell, which are not immediately under consideration. |
| anlage (plural: anlagen) | From German, most literally meaning "primordium". However, it can be used to refer to any "developmental field" or "territory" at any stage of development. |

These guidelines include the basics, and some of the relatively easy things you can do to give your writing more polish. The best thing you can do to develop your skills in science writing is to practice and keep reading the primary scientific literature.

------

## <a name="checklist"></a>Appendix A: Proofreading checklist

#### Higher-order concerns

* Adopt a tone and style appropriate to an [audience](#audience) of peer scientists
* Write concisely, avoiding extraneous words or phrases
* Write with scientific accuracy, especially for [terminology](#terminology) and essential biological concepts
+ Write to emphasize the biological entities [rather than figures](#figure1shows) or citations
* Structure an argument in a logical progression
* Demonstrate an understanding of the scientific method
+ Distinguish among [hypotheses](#hypothesis) and predictions
+ Qualify speculations and interpretations as such
+ Support assertions with evidence
* Present [results](#results) precisely and accurately
+ Explain the purpose or significance of experiments
+ Effectively convey information [visually](#figures) (e.g. choice of figure type, clear labels)
* Analyze results
+ Summarize patterns in the data that support or refute a [hypothesis](#hypothesis)
+ Use of [statistical tools](#quant), as appropriate, to identify patterns or differences among groups
* [Discuss](#discussion) findings in a way that considers alternative explanations (i.e. avoid confirmation bias)
* Synthesize results with prior knowledge

#### Format

* [Title](#title) is appropriate for the paper
* [Abstract](#abstract) summarizes key points from all sections
* [Introduction](#intro) explains the importance and purpose of the study
* Introduction provides necessary background
* Introduction states [hypotheses](#hypothesis)
* [Results](#results) section includes all data necessary to reach conclusions
* Includes a figure showing the locations targetted by PCR primers within the locus
* Includes a table listing PCR primer names, DNA sequences, location within the locus (e.g. "upstream", "intron 2"), and expected PCR product size
* Results section mentions procedures, but not details of methods
* Results section contains minimal interpretation
* [Figures](#figures) and [tables](#tables) are well-designed to communicate the data
* Figures and tables are numbered in the order in which they're discussed in the text
* All figures and tables are discussed in the text
* Figures and tables have descriptive legends
* Columns and rows in tables are labeled
* Values in tables have units
* [Discussion](#discussion) does not reiterate the results
* Discussion interprets the results
* Discussion connects to the background information to highlight broader significance
* [Acknowledgements](#acknowledgements) section is included
* [Citations](#citationformat) are given wherever appropriate, throughout the paper
* Reference list gives full information for all citations
* Reference list is properly [formatted](#citationformat)
* All listed citations are referenced in the text

#### Style

* Correct grammar [throughout](#proofreading)
* Consult with the [Writing Center](#writingcenter) or [Multilingual Writing Specialist](mailto:[e-mail])?
* Limited use of first-person pronouns ("I" or "we")
* Background in the Intro is written with the present verb tense
* Results are written with the past verb tense
* Discussion and conclusions are present tense
* [Species names](#speciesnames) are italics
* [Gene names](#genenames) are italics
* [Proteins names](#genenames) are Roman and capitalized
* [Terminology](#terminology) is used properly
* [Jargon](#jargon) is avoided or defined
* Uncommon [abbreviations](#abbreviations) are define before use
* Measured values have units (including DNA sizes in bp)
* Avoid citing sources that are not peer-reviewed (e.g. web pages)
* No [direct quotes](#directquotes) from sources, even when cited

#### [Figures](#figures)

* Descriptive legends
* Panels are labeled
* Appropriate lighting in photographs
* Consistent, appropriate framing
* Consistent, appropriate orientation
* Important results are clearly evident
* Gel figures are inverted (black bands on white background), cropped to the bands, accurately label ladder band sizes, and label lanes descriptively (not letters or numbers refering to a list)

#### Type-setting

- Acceptable file formats: [MS Word](http://www.colby.edu/its/microsoft-home-use-program/), [Google Docs](https://www.google.com/docs/about/), [markdown](https://en.wikipedia.org/wiki/Markdown). (Please do not submit [PDF](https://en.wikipedia.org/wiki/PDF) or [Pages](https://www.apple.com/pages/) documents)
- Font is Times New Roman, 12 point
- Single line spacing
- All margins are 0.7-1 inch
- Tables and figures do not break across pages