# Guidelines for Final Project Written Reports

> Colby College - [BI332 Developmental Biology](http://web.colby.edu/devbio/)
> Updated 20 November 2019 - [Dave Angelini](mailto:[e-mail])

This document will serve as a guide as you prepare your final project's written report for Developmental Biology. It will begin with general considerations for science writing, then provide specific guidance on this assignment. You will notice indented "tips" throughout the document. These tips point out common mistakes students make in scientific writing. A supplemental [guide to statistical analysis](https://hackmd.io/@dts8RULgQqi0n0PPDKh7JQ/rJmbl8Q2S) should also be consulted for analysis of your data.

## General considerations

### The purpose of scientific 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 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.
> * Don't use too many fancy words. Science has many specific terms because they are useful in their specificity, not simply because big or unfamilar words are better!
> * Some words in biology are taken from standard English, but have specific meanings in our field. For example, be careful about your use of words like "code" or "encode".

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 background information, terms and experimental methods before you can write effectively.

> **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]).

### Who is your audience?

The goal of your writing should be to inform your reader about the subject and to persuade them of your experimental conclusions. Ask yourself, does my text make a convincing case for my idea? Has each logical step, from the purpose of the experiment to 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 developmental biology course at Bowdoin or Bates. They'll be familar with basic concepts of development, but maybe not with your topic., and definitely not with the specifics of your experiment.

> **Tip**
>
> * Whenever you write, don't use phrases that distance yourself from the field. You are a biologist. Own it!

## The format of the BI332 Final Report

For this class you will follow the format of scientific journals such as *Current Biology* or *eLife*, which report experimental results, but are written for an audience with a wide range of expertise in the life sciences. Because you've had limited time in the lab this semester, you will have less data to report than the article that actually appear in these journals. Therefore, I ask that you skew the content of your articles to have more background relative to the amount of data you'll report.

The format of your report will include the following sections, in this order:

- Title
- Author list
- Summary
- Graphical abstract
- Introduction
- Results & Discussion
- Conclusions
- Materials & Methods
- Acknowledgements
- Literature cited

### Title

A concise **Title** should convey the most important conclusions of your study. 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
> - Human-specific gene *ARHGAP11B* promotes basal progenitor amplification and neocortex expansion
> - Induction of Pluripotent Stem Cells from Adult Human Fibroblasts by Defined Factors

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

> **Bad Examples**
> - Wing development in flies
> - 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

### Author list

Hopefully this is obvious, but please include your names.

As an aside, this is sometimes a more profound choice than you may initally think. Once your name appears on a published article in your professional field, that will become the most important search term for people to locate your work. Choose the inclusion of middle names carefully. For people with common names, there is a danger of confusion. Also, if your name comes from a culture where the [surname comes first](https://en.wikipedia.org/wiki/Surname#Order_of_names), will that be obvious to readers? A trend in the sciences is to couple names with a unique identiying number such as [ORCID](https://orcid.org/). (e.g. [0000-0002-2776-2158](https://orcid.org/0000-0002-2776-2158)).

### Summary

A Summary (or abstract) should begin your paper 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.

### Graphical Abstract

A graphical abstract is an image that summarizes your experiment and its conclusions. It should employ the best practices in graphical design and help a naive reader appreciate your study. It should be 10 cm by 10 cm (4 inches by 4 inches) on the page. The imagery must be original, but it can be generated in any way, including R, Abode Illustrator, PowerPoint objects, scanned freehand drawing, or any combination of these methods.

Cell Publishing has an excellent [guide](https://www.cell.com/pb/assets/raw/shared/figureguidelines/GA_guide.pdf) to graphical abstracts.

### Introduction

The Introduction provides 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. You may use sub-headings within the Introduction or not.

The Introduction should be organized so that it moves from general information to more specific information. It should begin by emphasizing the importances of the topic you're studying. Details related to your specific study system and experiments should come later in the Intro.

#### Hypothesis

At some point in your Introduction, you should make clear what hypothesis your experiment will test. Ideally, this is done early, such as the end of the first paragraph. Remember, a hypothesis is a general statement about the process you predict to explain a previously observed pattern. After stating your hypothesis, you should describe how it will be tested, briefly outlining the key parts of your experiment. After you've described the experiment, then you should state your predictions for the outcome.

> **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. Some readers (including your instructor) find it grating.

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.

### Results & Discussion

For this assignment you are welcome to combine results and their interpretation into one section, but you may also choose to keep them separated. 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 a conclusion. One part of this will be stating the expected results. If you are combining Results & Discussion, talk through the logic that brings a reader to your conclusion.

> **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.

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 the results.

Keep in mind that procedural details would be covered in the Materials & Methods section. However, it will be necessary here to mention the techniques you used (e.g. PCR; in situ hybridization; cloning; electrophoresis) and key details (e.g. "We purified RNA from young adults").

The Results section *should* mention controls, whenever appropriate. Remember, that just calling something a "control", doesn't say much. You must explain what experimental variable is being controlled.

In each sub-section (or in a distinct Discussion section) provide your interpretation of the results of the experiment. What do the results mean?

#### Quantitative data

Your experimental report should include quantitative data of some kind. Depending on your experiment, you might measure different things. Some possibilities:
* the number of individuals surviving to a particular stage
* the number of males and females
* the number of days it took individuals to reach a certain stage, like hatchling or adult
* the number of some structure on an individual or on some part of an individual (e.g. number of melanocytes on a zebrafish hatchling; number of legs on an adult bug; number off feather papillae in 1 mm^2^ of a chick embryo's flank)
* the size of a structure -- this usually needs to be measured along with some measure of overall body size and with reference to sex, since males and females of most species different in average size
* gene expression -- usually in comparison to a reference gene
* gene copy number

Report your raw data in a table. Typically it is best to also report quantitative data in some sort of graph. Whenever you want to say two things are different, that assertion should be supported by an appropriate [statistical test](https://hackmd.io/@dts8RULgQqi0n0PPDKh7JQ/rJmbl8Q2S), unless there is [complete separation](https://en.wikipedia.org/wiki/Separation_(statistics)) (no overlap) in the data. Our Moodle page has a [guide to statistics](https://hackmd.io/@dts8RULgQqi0n0PPDKh7JQ/rJmbl8Q2S), which includes detailed instructions for performing tests in R. You can also talk to your lab instructor!

> **Tips**
> * Don't refer to your samples by short-hand numbers: 1a, 1b, 2a, 2b, etc. They are meaningless outside your lab group, and do not help a reader.
> * If you say something is a control, what is it a control for?
> * "Data" are plural. So you should write, "Our data show..." rather than "Our data shows..." (The singular form of "data" is "datum.")

#### 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. Think about graphic design for the best communication of your data. For example, crop blank space from the periphery of gels or pictures of animals. Images that need to be compared to one another should be included as separate panels within the same figure.

Many students find PowerPoint a convenient program in which to compose figures. [ImageJ](https://imagej.net/Welcome) 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**
>
> * Keep multiple specimens oriented in the same direction!
> * 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. "Misexpression of human *FoxP2* in the fly brain resulted in increased language ability (Fig. 2).")

#### Tables

Use tables to report numerical data. Be sure to give headings to each column and include units where appropriate. 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.

### Conclusions

Use the last main section of your text to report to your hypothesis and state the overall conclusions unambiguously. You should also put your study in a broader context and point out the significance of your work. 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.

> **Tips**
>
> * Don't undersell your results!
> * Don't present a litany of problems.
> * Don't ascribe unexpected results to human error. If needed be specific about unexpected problems that prevented you from getting a clear result.

### Materials & Methods

This section should describe each phase of your experiments. You should be succinct, but give enough detail that a knowledge developmental biologists could replicate your experiment. State the origin of all living animals used in the experiment. If your procedures are based on course protocols or previously published studies, be sure to include references to those sources. You do not need to include details such as volumes used, since concentrations are adequate. If you used molecular reagents, such as sgRNAs and [PCR primers](https://hackmd.io/@dts8RULgQqi0n0PPDKh7JQ/Hk1mwb1hS), be sure to list those in the text (if you have only 2) or a table.

### Acknowledgements

In the Acknowledgements you give credit to anyone who may have helped you with experiments. It is also appropriate to thank anyone who provided significant help with your writing process.

### Literature Cited

A section of references should list the full citations of any source referenced in the text. BI332 will follow the citation format used in the journal *[Development](https://dev.biologists.org/content/manuscript-prep#3.3.)*.

-----

## Advice

### 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.

### 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.

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).

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.

### 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.

> **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.

### 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!

### 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. But you will probably still use personal pronouns like "I" or "we", but be sparing. ("We have conduced a detailed study of acorns, and our results reveal...")

> **Tip**
>
> * Gender is a human idea that's irrelevant to other organisms. Biologically speaking, you should refer to their status as male or female as their sex. Don't use the word gender in reference to animals.

### 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.)

### 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.")

For more info and stories related to scientific names check out the blog [*Scientist Sees Squirrel*](https://scientistseessquirrel.wordpress.com/category/latin-names/).

### 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).

### 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.

------

## Checklist & Rubric

#### Higher-order concerns

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

#### Format

* Title is appropriate for the paper
* Author list is included
* Summary summarizes key points from all sections
* Graphical Abstract summarizes most important aspects of the study
* Introduction explains the importance and purpose of the study
* Introduction provides necessary background
* Introduction states a hypothesis
* Results & Discussion section mentions procedures, but not details of methods
* Figures and 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 interprets the results
* Discussion / Conclusions connects to the background information to highlight broader significance
* Materials & Methods section succinctly describes key components of experiments procedures
* Materials & Methods section includes citations to sources of the procedures used
* Acknowledgements section is included
* Citations are given wherever appropriate, throughout the paper
* Reference list gives full information for all citations
* Reference list is properly formatted
* All listed citations are referenced in the text

#### Style

* Correct grammar throughout
* Consult with the Writing Center 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 described with the past verb tense
* Discussion and conclusions are present tense
* Species names are italics
* Gene names are italics
* Proteins names are Roman and capitalized
* Terminology is used properly
* Jargon is avoided or defined
* Uncommon abbreviations are define before use
* Measurable values have units (including DNA sizes in bp)
* Avoid citing sources that are not peer-reviewed (e.g. web pages)
* No direct quotes from sources, even when cited

#### Figures

* Descriptive legends
* Panels are labeled
* Appropriate lighting in photographs
* Consistent, appropriate framing
* Consistent, appropriate orientation
* Important results are clearly evident

#### 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
- Line spacing is 1.5
- All margins are either 1 inch or 2 cm
- Tables and figures do not break across pages

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