Big Mountain, Whitefish MT

Prof T's Science Writing, Reading, Presenting thoughts and info...

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First and foremost, with todays modern word processing software (including email clients), there is no need for a double space after a period!

Some points and thoughts for each section of a manuscript, thesis, or article:

—Note the info below include many great points by Rachel Dresbeck at OHSU.


The goal of a paper's central hypothesis and individual experimental hypotheses might be based on a prediction of a physiological mechanism that governs some initial observation(s). It's often a great starting place to consider a hypothesis based on an “If-then” statement where the “If” portion states a physiological mechanism that you are proposing might be taking place, and the “then” part of the sentence will state a plausible outcome of an experiment designed to test the mechanism.

For example: "If calcium is required for synaptic vesicle fusion and neurotransmitter release, then focal application of calcium just inside the pre-synaptic terminal will cause an increase in neurotransmission."

This PDF is an excellent resource for learning how to craft a hypothesis that relies on a plausible mechanism and not just stating some predicted experimental outcome (that would result from a hypothesized mechanism).

Here are some informative websites that also nicely describe scientific hypotheses:


Determines/identifies the what and where. The more broad it is, the more vague it is.


Written for a broad audience. States the problem/research question. May include research importance. Ends with results and conclusions. Abstract template:

Important, big picture sentence. Follow-up sentence that ties big picture into more focused picture that includes your research area. Sentence that ties your research area to your research question. Another sentence or two that explains how your research is well-suited to answering the research question. Ideally a hypothesis is mentioned in the preceding or this sentence. A few sentences on your findings and how cool they are. A final sentence that ties your findings to the hypothesis and hope it answered the question and will improve understanding of the big picture.

The research should be motivated by a longstanding problem or an important question. There should be a hypothesis that governs the study and the intro should mention how the specific experiment(s) will test the hypothesis or predictions based on the hypothesis.

• Should be audience appropriate • Should get to the research question right away (first paragraph) • State what is not known • Why is it important to study/address this problem/question • Orient the reader with necessary and sufficient background • Often will end with what was found and broad conclusions.

Materials and Methods

This section should be in the past tense and written in the passive voice. Clear and concise. Enough information that someone could replicate your experiments. E.g.,

Bacterial cultures were transferred into 96-well plates following overnight incubation.


This section should start with a couple sentences to remind the reader what the goal of the study was and then segue into the first experiment.
Written in the past tense and in the active voice. Each subsequent experiment should be motivated by previous results and/or test a new/novel hypothesis. 

• Descriptive—what was done and what was found • Good results sections will motivate experiments with hypotheses • Usually written for experts • Should state what was found including values and means/errors etc • Presents data and analyses of data within figures and tables

Figures and Figure Legends

Every figure must have a legend. Show relationships / give data context • When values are important—-use a table • When patterns are important—-create a figure • The Legend describes what is in the picture • The legend points out important features if necessary. The legend should never make conclusions, save that for the text.

Consider the following programs for plotting your data:

  • Microscoft Excel, Apple Numbers, or Google Sheets are all decent for making simple plots but sadly they're not very good at analyzing data, running statistics, nor making aesthetically pleasing plots
  • Graphpad Prism is a robust plotting and analysis program with great statistics built into it. They offer a trial period to demo the full-functioning software.
  • Igor Pro is a powerful data plotting and analysis program with great statistics. They offer a trial period to demo the full-functioning software.
  • The Anaconda version of Python is an excellent open-source option for making plots and performing data analysis. It has a steep learning curve but is well worth the investment of learning this powerful coding environment.
  • The R project is an excellent open-source option for statistical analysis as well as making plots and performing data analysis.
  • Desmos is another cool online program for plotting functions.
  • There are many other great options including MatLab, Origin, SigmaPlot and others.

Are you making your own figures and want free, open-source software? Check out these great programs:


This section should initially summarize your overall findings and whether they support or reject the specific hypothesis you were testing. It should also include potential problems and sources of error with the study. It should also include future directions or possible experiments and then end with a nice overall summary statement.

• Goal of section is persuasion • It should make sense of data/evidence and give it context • “We found this and this and conclude this.” • In the first paragraph: summarize what was found and learned and use the next paragraph or two to summarize each of the experimental findings • Make comparisons with other findings (accords and disagreements) • Provide potential sources of error, alternative explanations/interpretations, anomalies and unsettled points (limitations)• Provide examples for future follow-up studies • It's super important to discuss the physiological importance of the findings • End the Discussion with why your findings are valuable to the field and what they contribute • Last sentence: Theoretical and practical implications of the work and how cool it is!

Citations and Bibliography

Citations are within the text and usually found within parentheses or superscripted numbers. Citations point to the references that are found in the Bibliography • Format for both citations and the reference list is particular to a given journal.

  • There should always be a space between a number and its units:

2 mM or 4 kg (not 2mm or 1inch)

  • If you use the em dash—do not use spaces on either side of it. (And please don't overuse it!) (the em dash is the width of an "m")

For example (note the use of hyphens (-), em dashes (—), and en dashes (–):

"... 'Can I start you off with a cocktail? Say yes, because I will not stop talking about cocktails until you order a cocktail. Have you had cocktails before? Cocktail, cocktail, cocktail, cocktail...'

'Yes. I think so. No. I'm going to say no. No, we have not.'

'That's correct. Because we do cocktails a little differently. Our mixologist takes artisanal moonshine, adds an ice cube larger than the glass it is in, mixes with something you'd never want in your cocktail—lighter fluid, wood chips, tears of nineteen-eighties Romanian Olympic gymnasts—and then, in the manner of an offended female character in a nineteen-thirties film, the mixologist will toss it right in your face. It's a really refreshing way to start your meal. He pitched AAA ball in Rochester for a while, so you'll really feel the face splash' ..."

Joel Stein. I will be your server. The New Yorker, July 9–16, 2012

  • Don’t start a sentence with it or this, without a word or two more clarifying what it or this is! Especially when there are multiple nouns in the preceding sentence.  
  • “This blank shows ...” (instead of "This shows...")

  • Again, add a space between a number and its units: 1 mM/min
  • avoid colloquial words (conversational): like, so, kinds, etc..
  • know the difference between affect (verb) vs effect (noun)
  • use a semicolon between two or more references in a citation: (Einstein, 1905; Trapani et al., 2011) (oh to be cited in the same sentence as Einstein...)
  • if you’re citing an article that you didn't read directly but that you found in a review paper you read, then you must state that:
  • (as reviewed in Trapani and Einstein, 2012)

  • If you identify an author within a sentence, then add the publication year to the end of sentence:
  • Trapani et al. said put the year at the end of the sentence (2015).

  • the editorial comment, awk = awkward sentence
  • the editorial comment, pilcrow (¶) = start a new paragraph

How to Read a Scientific Research Paper

a four-step guide for students

Ann McNeal, Professor Emeritus

School of Natural Science, Hampshire College, Amherst MA 01002


Reading research papers ("primary articles") is partly a matter of experience and skill, and partly learning the specific vocabulary of a field. First of all, DON'T PANIC! If you approach it step by step, even an impossible-looking paper can be understood.

1. Skimming. Skim the paper quickly, noting basics like headings, figures and the like. This takes just a few minutes. You're not trying to understand it yet, but just to get an overview.

2. Vocabulary. Go through the paper word by word and line by line, underlining or highlighting every word and phrase you don't understand. Don't worry if there are a lot of underlinings; you're still not trying to make sense of the article.

Now you have several things you might do with these vocabulary and concept questions, depending upon the kind of question each is. You can

  • Look up simple words and phrases. Often the question is simply vocabulary--what's a lateral malleolus, or a christa, or the semilunar valve. A medical or biological dictionary is a good place to look for definitions. A textbook of physiology or anatomy may be a good source, because it give more complete explanations. Your ordinary shelf dictionary is not a good source, because the definitions may not be precise enough or may not reflect the way in which scientists use a word (for example "efficiency" has a common definition, but the physical definition is much more restricted.)
  • Get an understanding from the context in which it is used. Often words that are used to describe the procedures used in an experiment can be understood from the context, and may be very specific to the paper you are reading. Examples are the "lithium-free control group" in a rat experiment or the "carotene extraction procedure" in a biochemical experiment. Of course, you should be careful when deciding that you understand a word from its context, because it might not mean what you think.
  • Flag this phrase as belonging to one of the major concepts of the paper--it's bigger than a vocabulary question. For example, a paper about diet and cancer might refer to "risk reduction," which you would need to understand in context and in some depth.

3. Comprehension, section by section. Try to deal with all the words and phrases, although a few technical terms in the Methods section might remain. Now go back and read the whole paper, section by section, for comprehension.

In the Introduction, note how the context is set. What larger question is this a part of? The author should summarize and comment on previous research, and you should distinguish between previous research and the actual current study. What is the hypothesis of the paper and the ways this will be tested?

In the Methods, try to get a clear picture of what was done at each step. What was actually measured? It is a good idea to make an outline and/or sketch of the procedures and instruments. Keep notes of your questions; some of them may be simply technical, but others may point to more fundamental considerations that you will use for reflection and criticism below.

In Results look carefully at the figures and tables, as they are the heart of most papers. A scientist will often read the figures and tables before deciding whether it is worthwhile to read the rest of the article! What does it mean to "understand" a figure? You understand a figure when you can redraw it and explain it in plain English words.

The Discussion contains the conclusions that the author would like to draw from the data. In some papers, this section has a lot of interpretation and is very important. In any case, this is usually where the author reflects on the work and its meaning in relation to other findings and to the field in general.

4. Reflection and criticism. After you understand the article and can summarize it, then you can return to broader questions and draw your own conclusions. It is very useful to keep track of your questions as you go along, returning to see whether they have been answered. Often, the simple questions may contain the seeds of very deep thoughts about the work--for example, "Why did the authors use a questionnaire at the end of the month to find out about premenstrual tension? Wouldn't subjects forget or have trouble recalling?"


Here are some questions that may be useful in analyzing various kinds of research papers:


What is the overall purpose of the research?

How does the research fit into the context of its field? Is it, for example, attempting to settle a controversy? show the validity of a new technique? open up a new field of inquiry?

Do you agree with the author's rationale for studying the question in this way?


Were the measurements appropriate for the questions the researcher was approaching?

Often, researchers need to use "indicators" because they cannot measure something directly--for example, using babies' birthweight to indicate nutritional status. Were the measures in this research clearly related to the variables in which the researchers (or you) were interested?

If human subjects were studied, do they fairly represent the populations under study?


What is the one major finding?

Were enough of the data presented so that you feel you can judge for yourself how the experiment turned out?

Did you see patterns or trends in the data that the author did not mention? Were there problems that were not addressed?


Do you agree with the conclusions drawn from the data?

Are these conclusions over-generalized or appropriately careful?

Are there other factors that could have influenced, or accounted for, the results?

What further experiments would you think of, to continue the research or to answer remaining questions?

—all the above is taken from Ann McNeal's document.

Must see Poster Session video on Youtube:

How to create a better research poster in less time (including templates)

Barth’s Random Tips for Scientific Presentations

Daniel S. Barth | University of Colorado, Boulder

Never assume your audience CARES AT ALL about the subject you are about to present. It is completely up to you to get them interested up front before they glaze over and/or fall asleep, then keep their interest throughout.

Assume your audience is intelligent but KNOWS NOTHING about your subject, including jargon and tiresome abbreviations (i.e. GB2T5alpha receptors, etc.).

Don’t lecture to those in the room whom you think are experts in your field (i.e. members of your own lab, etc.). Instead, explain your subject simply and elegantly to the non-experts in the audience. Experts in the room always love a simple, well crafted, general explanation. Non-experts always hate being lost up front and are not impressed or humbled by their own lack of knowledge. Instead, they glaze over and/or fall asleep.

Create generous, clearly labeled, simple graphics. Your graphics should tell the story for you well enough that even if you are off in some corner having an anxiety attack, the message should get across clearly if someone is willing to advance the slides for you.

NEVER write whole sentences in your graphics, even for bulleted statements. This inevitably leads to a speaker-audience read along. This is perhaps one of the most boring experiences on earth for those in the audience who already have mastered reading.

If you use PowerPoint (nice), try desperately to limit the use of bells, whistles, fades, background vistas, and other idiotic things. This makes you seem more like a sales person than a scientist, and gives the impression that your actual data is pretty insignificant and boring. However, some PowerPoint features are useful for drawing attention to data or concepts.

If you use a laser pointer, don’t wave it around the screen or point it into the eyes of your audience to get their attention. Turn it on and use it only to slowly circle or underline what you want to highlight.

Always get to some actual data within about 15-20 minutes for a one hour talk, 10 minutes for a half hour talk, and 1 minute for a 15 minute talk. If you take any longer than this, you probably will either over run your time limit (THE ULIMATE SIN), and/or you really don’t have much of a scientific nature to present.

NEVER over run your time limit (THE ULIMATE SIN). One hour talks should only go for 50 MINUTES. Half hour talks for 20-25 MINUTES. To avoid the ultimate sin, try the following:

  • Be realistic in what you want to accomplish during your allotted time.
  • Practice your talk slowly, standing up and pointing, speaking out loud, in the privacy of your home. If it times out right slowly at home, it will probably work in public.
  • Keep an eye on your watch, or preferably a clock at the back of the room, during your talk, and plan in advance which slides can just be amputated, and the talk still make sense, if you start running out of time. Don’t just speed up your presentation. That is really silly.
  • Practice your talk!

NEVER use notes when you give a talk. You will end up reading them, looking really shabby, and the audience will glaze over and/or fall asleep. Instead, practice your talk sufficiently so that your graphics serve as your reminders and notes (that is NOT to say that your graphics should actually contain notes). If you make notes, fold them up, put them in your pocket, and know they are with you to provide comfort and security.

Never take your eyes off your audience for even a second unless it is to briefly turn toward a screen to make a point. Do not lecture to the screen. It does not care what you have to say and neither will the audience if they only get to know your back side.

On the flipside, don’t ignore or fail to describe any slides.

Try to be animate (or animated as the case may be). Use hand gestures and such for evidence, but don’t twitch, run around, or stand like a statue.

Always answer questions at the slightest hint of an interrogative twitch from your audience. Questions are more important than anything you have to say. But answer questions with humility (i.e. your are not being attacked), brevity, and try not to perseverate with run-on answers to questions that were not asked. “That brings up a very interesting subject of...” is usually a sign that you are about to launch into something that is boring even to the person who asked the question, and they will be tortured with looking interested until you mercifully release them. The rest of the audience will glaze over and/or fall asleep.

Anticipate questions your audience may have. Have backup slides at the end of the talk if necessary to assist with explanation.

It is nice to start a talk by telling the audience what you are going to say (after you get them INTERESTED or course), then say it, then tell them what you said at the end. tell the audience a story. This provides structure and organization to the talk and generates audience interest (Point #1). Here is a nice example of the structure of a talk:


  • Introduction:
  • - Conflict in literature to be resolved
  • - What you did to resolve it


  • What did you do
  • What did you get


  • Summarize what you got
  • How does the new information you got resolve the conflict - Conclusion

The best talks are the ones that are so interesting and clearly presented that the “take home message” actually arrives to an alert and interested audience for delivery, makes it past the door of the lecture hall, maybe actually gets taken home by the audience, and maybe, just maybe, gets mentioned to a spouse or loved one over dinner.

Good talks are like good text. With good writing, one sentence flows logically from the last, one paragraph flows from the previous one with some reason for existing as a separate paragraph. In talks, slides are somewhat like short paragraphs. Try to arrange your slides with the same smoothness and logic. Also, think hard about appropriate segues from one slide to the next. A bad segue is “So this next slide shows... etc.”

If you present work done collaboratively with others (i.e. your lab), it is nice to show a slide with their names. THAT’S ALL! The dripping biographies and personal anecdotes will cause your audience (except those in it who you are referring to) to, yes, glaze over and ... This usually also comes at the end of a talk when your audience wishes you would knock off. The only exception to this rule is the classic “job talk”, where all the warm and fuzzy discussion of members of your lab impresses the audience (your colleagues) that you are a real nice collaborative person running a big lab, and thus deserve employment/promotion. In job talks, it is also nice to note all your funding sources so the audience (your colleagues) recognize how financially important you are to the department.

Submitting a poster abstract for a conference or meeting? Consider the important parts of the abstract as depicted in this template abstract:

Important, big picture sentence. Follow-up sentence that ties big picture into more focused picture that includes your research area. Sentence that ties your research area to your research question. Another sentence or two that explains how your research is well-suited to answering the research question. Ideally a hypothesis is mentioned in the preceding or this sentence. A few sentences on your findings and how cool they are. A final sentence that ties your findings to the hypothesis and hope it answered the question and will improve understanding of the big picture.

Must see Poster Session video on Youtube:
How to create a better research poster in less time (including templates)

Two other useful Poster creation links:

Using Zotero to manage in-text citations and references is a massive time saver and a great way to organize your paper from the very beginning of writing. It can be used to cite sources in your papers and generate the References section (aka Bibliography) at the end of them.

Goal: The best way to effectively use Zotero is to install the Desktop app onto your computer, install the Zotero Add-in into Microsoft Word for in-text citations and bibliography management when writing your papers, and then add the appropriate Zotero Connector to your web browser to automatically add references from the Pubmed website.

To accomplish this goal, follow these instructions:

  • Download and install the Zotero Desktop App:
  • Within Zotero Preferences select the Cite tab and click the Word Processors subtab and then click the "Install Microsoft Word Add-in" button. If you use Apple Pages or Google Docs, there are options to integrate into those word processing programs as well. More details here:
  • There are two useful ways to quickly add references into Zotero so that they will be available for citing in your manuscript/paper:

  • OPTION 1: While browsing for papers on PubMed (, click the "Cite" button and choose the "Download .nbib" file. Next open Zotero and select Import and choose the .nbib file to import the reference into your library.
  • Option 2:Install the Zotero Connector for your web browser of choice: Now when you visit PubMed and are viewing an individual reference (like this one: you can now click on the button for your Zotero Connector and the reference details will automatically be added to your Zotero library.
  • To add citations to your paper, be sure to first install Zotero in your word processing program (e.g., Microsoft Word or the plugin also installs in Open Office and other word processing programs: You can add citations and references automatically. See these directions for Word specific details:

  • Finally add and format your Bibliography/References section of your paper. I personally use the Journal of Neuroscience style, but many can be found in the Zotero repository:
    Instructions for installing a downloaded style can be found here: