It takes a village to write a scientific paper

Every scientist I know (myself included) underestimates how long it will take to write, edit, and submit a paper.  Despite having 22 publications to date, I still set laughably-high expectations for my writing deadlines.  Even though scientists go into a project with a defined hypothesis, objectives, and workflow, by the end of data analysis we often find ourselves surprised.  Perhaps your assumptions were not supported by the actual observations, sometimes what you thought would be insignificant becomes a fascinating result.  Either way, by the time you have finished most of the data analysis and exploration, you face the difficult task of compiling the results into a meaningful paper.  You can’t simply report your data without giving them context and interpretation.  I’ve already discussed the portions of scientific manuscripts and how one is composed, and here I want to focus on the support network that goes into this process, which can help shape that context that you provide to your data.

One of the best ways in which we can promote rigorous, thoughtful science is through peer-review, which can take a number of forms.  It is worth noting, that peer-review also allows for professional bullying, and can be swayed by current theories and “common knowledge”.  It is the journal editor’s job to select and referee reviewers (usually 2 – 4), to compile their comments, and to make the final recommendation for the disposition of the manuscript (accept, modify, reject).  Reputation, and personal demographics such as gender, race, or institutional pedigree can also play a role in the quality and tone of the peer-review you receive. Nevertheless, getting an outside opinion of your work is critical, and a number of procedural changes to improve transparency and accountability have been proposed and implemented.  For example, many journals now publish reviews names online with the article after it has been accepted, such that the review does not stay blind forever.

Thorough reading and editing of a manuscript takes time.  Yet peer-reviewers for scientific journals almost unanimously do not receive compensation.  It is an expected service of academics, and theoretically if we are all acting as peer-reviewers for each other then there should be no shortage.  Unfortunately, due to the pressures of the publish-or-perish race to be awarded tenure, many non-tenured scientists (graduate students, post-docs, non-tenure track faculty, and pre-tenured tenure-track faculty) are reluctant to spend precious time on any activity which will not land them tenure, particularly reviewing.  Moreover, tenured faculty also tend to find themselves without enough time to review, particularly if they are serving on a large number of committees or in an administrative capacity.  On top of that, you are not allowed to accept a review if you have a conflict of interest, including current or recent collaboration with the authors, personal relationships with authors, a financial stake in the manuscript or results, etc.  The peer-review process commonly gets delayed when editors are unable to find enough reviewers able to accept a manuscript, or when reviewers cannot complete the review in a timely manner (typically 2 – 4 weeks).

I have recently tried to solicit peer-review from friends and colleagues who are not part of the project before I submit to a journal.  If you regularly follow my blog, you’ll probably guess that one of the reasons I do this is to catch spelling and grammatical mistakes, which I pick out of other works with hawk-like vision and miss in my own with mole-like vision.  More importantly, trying to communicate my work to someone who is not already involved in the project is a great way to improve my ability to effectively and specifically communicate my work.  Technical jargon, colloquial phrasing, sentence construction, and writing tone can all affect the information and data interpretation that a reader can glean from your work, and this will be modulated by the knowledge background of the reader.

I’ve learned that I write like an animal microbiologist, and when writing make assumptions about which information is common knowledge and doesn’t need a citation or to be included at all because it can be assumed.  However, anyone besides animal microbiologists who have been raised on different field-specific common knowledge may not be familiar with the abbreviations, techniques, or terms I use.  It may seem self-explanatory to me, but I would rather have to reword my manuscript that have readers confuse the message from my article.  Even better, internal review from colleagues who are not involved with the project or who are in a different field can provide valuable interdisciplinary perspective.  I have been able to apply my knowledge of animal science to my work in the built environment, and insights from my collaborators in plant ecology have helped me broaden my approach towards both animals and buildings.

No scientific article would be published without the help of the journal editorial team, either, who proof the final manuscript, verify certain information, curate figures and tables, and type-set the final version.  But working backwards from submission and journal staff, before peer-review and internal peer-review, there are a lot of people that contribute to a scientific article who aren’t necessarily considered when contemplating the amount of personnel needed to compose a scientific article.  In fact, that one article represents just the tip of the iceberg of people involved in that science in some way; there are database curators, people developing and maintaining open-source software or free analysis programs, laboratory technicians, or equipment and consumables suppliers.  Broadening our definition of science support network further includes human resources personnel, sponsored projects staff who manage grants, building operational personnel who maintain the building services for the laboratory, and administrative staff who handle many of the logistical details to running a lab.  It takes a village to run a research institution, to publish a scientific article, to provide jobs and educational opportunities, and to support the research and development which fuels economic growth.  When it comes time to set federal and state budgets, it bears remembering that that science village requires financial support.

 

Featured Image Credit: Kriegeskorte, 2012

Finding the write words

Recently, a colleague recommended using Voyant Tools to analyze texts, so I thought I would give it a try.  Language metrics can give a fascinating look into a text, and in this example, into what my most commonly used words are, how verbose I can be, and how diverse my written vocabulary is.  It’s important to note that these metrics are sensitive to citation style, the use of text in legends or tables, and other bits of text in manuscripts or webpages that may get incorporated which aren’t part of the text, strictly speaking.  When possible, I uploaded just the written portion of the manuscript.

My first publication

Insight into the bacterial gut microbiome of the North American moose (Alces alces), was written in 2012 and published in BMC Microbiology, which does not have a word limit.  According to Voyant, the document contains 5,904 total words and 1,489 unique word forms. Vocabulary Density, the ratio of the number of words in the document to the number of unique words in the document, is 0.252.  A lower vocabulary density indicates complex text with lots of unique words, and a higher ratio indicates simpler text with words reused. Average Words Per Sentence is 27.1, and Most frequent words are: rumen (80); otus (68); samples (67);  moose (54); colon (50)..

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My latest first-authored publication

An investigation into rumen fungal and protozoal diversity in three rumen fractions, during high-fiber or grain-induced sub-acute ruminal acidosis conditions, with or without active dry yeast supplementation, was written in 2017 and published in Frontiers in Microbiology, which also doesn’t have a word limit.  For this one, I altered the citation style first.  As Frontiers uses a verbose citation style (Author et al., year), my top words were “et” and “al” in the published version of the paper.  In the modified version, there are 7,580 total words and 2,067 unique word forms. Vocabulary Density: 0.273, Average Words Per Sentence: 12.7, Most frequent words: rumen (111); diversity (69); diet (56); fungal (47); protozoa (46).

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My dissertation

My dissertation, written in 2015, contains 75,859 total words and 8,958 unique word forms. Vocabulary Density: 0.118, Average Words Per Sentence: 12.9, Most frequent words are: rumen (632); moose (411); sequences (323); using (304); samples (284).

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Summary

To look at all my first authored research publications to date, I put all the text from the word documents together, excluding figure and table legends, as well as reference lists. Across these 8 documents, there were 40,860 total words and 5,059 unique word forms, Vocabulary Density: 0.124, Average Words Per Sentence: 26.6, Most frequent words: rumen (304); samples (301); sequences (275); using (265); moose (226).

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Word cloud from 8 publications.

 

 

Where does the time go?

As we rapidly approach the end of both the fall semester and 2017, it’s a great time to  reflect about the year’s accomplishments (update your C.V.) and look forward to what 2018 will bring (panic about all the things you haven’t finished yet that need to be completed by the end of the year).

Time management is a reoccurring theme in academia, and with so many items on one’s to-do list, it’s not hard to see why.  Everyone has their own advice about how to be more effective; which was the very first meeting in this year’s Faculty Organizing for Success professional development workshop series, which I attended in October.  I compiled some of the suggestions made there, along with advice I’ve picked up over the years, and strategies I use which I’ve found to be effective.

One of the major questions that came up at the FOS meeting was time management in the face of academic duties, namely service.  Academics have a requirement to provide service or outreach to their university, the community, and their field, and as I’ve previously discussed, these amorphous responsibilities can be time-consuming and under-appreciated.  Sometimes, turning off your ringer, closing your email application, or saying “no” isn’t enough or isn’t possible.  So, how can you make the most of your time while navigating the constraints of a fractured schedule?

Lists

  1. I find lists to be extremely helpful in keeping track of everything I need to do, and it really helps me focus on what I need to get done TODAY.  
  2. Lists help me organize my thoughts
    1. by adding notes for each particular item
    2. and ordering the steps I need to take to finish each item.
  3. Being able to cross tasks off a physical list is also a great visual reminder that you are, in fact, being productive.  
  1.  And, at the end of the day, the remaining items form a new list, so I know where to begin tomorrow.  This saves me a lot of time which would otherwise be spent trying to remember where and how I left off.

Calendars

Don’t like lists?  I also heavily rely on my calendar and will schedule appointments for everything, especially the little things that I’m liable to forget, including catching up on emails, lunch, reading articles, writing posts, etc.  I utilize color-coding and multiple calendars within a calendar, like shared calendars from research labs or online applications.  I have learned to schedule small blocks of time after meetings, especially project development or brainstorming meetings, during which I can write notes, look up deadlines, send emails, or any other action items that came up during the meeting while it’s still fresh in my mind.  I even schedule appointments for my personal events, like hiking, movies, or buying cheese at the farmer’s market.  Having them in my calendar keeps me from scheduling work-related things into my personal time.  Academics, myself included, have a habit of working more than 40 hours a week: “Let me just send this email real quick” can easily transform into “Well, there went my Saturday”.

I’ve been known to schedule reminders months or a year in advance, perhaps to catch up with someone about a project, to have a certain portion of a project completed by a soft deadline, or look up a grant RFA that will be made available approximately three months from now.  Making good use of my calendar has been particularly important for tracking my time for reporting (or billing) purposes. BioBE and ESBL use the Intervals tracking program, and it’s much easier to report my time if I have a detailed account of it in my calendar.  Even better- it’s great for retrospective reports:

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The categorical break-down of how I have spent my time from June to November.

 

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That time has been used for a number of different projects.

Perhaps the best use of my calendar has been to schedule themed time-blocks spanning several hours, such as “catching up on projects” or “data analysis”, specifically on a shared or public calendar to prevent time fractionation.  These events are marked as tentative, so I can be scheduled during those times as needed, but I find that I get fewer requests for my time when I don’t have unclaimed space on the calendar.  And, I can focus on a specific project for several hours, which I prefer to a “30 min here, 60 min there” approach.  If possible, I also try to concatenate meetings, seminars, training and workshops, or other short but disruptive events.  One or two stand-alone events can be a nice way to break up the day, but too many can fracture my time into small blocks and make it very difficult to effectively perform the research portion of my work which is best accomplished when I can puzzle out problems at my own pace.  So, I categorize the day as “administrative”, “social media“, or “project management”, and spend the day taking care of all the other responsibilities I have that are tangential (but important) to my research.

Emails

Prioritizing my emails with flags is also really helpful, especially if you can color-code by importance.  I get dozens of emails every day, from six different email accounts, but I keep my inboxes to less than 10 items each, almost every day.  I spend a few minutes to prioritize them for later, I archive old emails into other folders for future reference, and I dedicate time to deal with my emails on a daily basis.  I also liberally use the “unsubscribe” link.  

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Actual screenshot from one of my inboxes.

Caution: Work Zone Ahead

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Cueva de las Manos, Perito Moreno, Argentina.

Academics love to work outside the office- most often because the office is where everyone goes to find you for some reason.  Coffee shops, parks, airports, and homes are popular locations for “writing caves” (I’m writing this from home right now).  Being in a distraction-free, or distraction-specific (i.e. white noise of cafe chatter) location helps me focus on things without interruption.  When I’m analyzing data or writing up results, I have multiple computer application windows open and am collating information from multiple sources, so I need to focus or else I waste a lot of time trying to pick up where I left off after every interruption.

 

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Monty Python

When I’m stuck on something, sometimes I’ll take a walk- usually to go get coffee.  Ok, always to go get coffee.  Exercise stimulates blood flow and lattes are full of glucose, so it’s a perfect way for me to recharge.  Often, that change of pace is all I need to accomplish in 2 min what I was struggling to put together earlier.  My best ideas often coalesce while hiking or biking home, so I started taking pens and notepaper with me so I can write them down on the fly before I forget.

When possible, I also try not to force myself to work to continue working on specific things past the point where I can make progress on it (you know, for all those times I’m not up against a deadline- haha).  Of course, this flexibility in my schedule during business hours is a privilege that most people don’t enjoy.  It also takes a great deal of self-motivation to enforce, but it can be very effective for me.  Instead, I set that project aside and  focus on something else entirely.  Often, this leads to procrastinating work with other work, but it’s productive nonetheless.  But for me, it also leads to more effective work-life balance. Late afternoons are not a particularly productive time for me; it’s better if I leave early and go grocery shopping, and then work for a few hours in the evening or on Saturday mornings, when I can get an extremely productive hour or two in after I’ve had time to mull things over.  Having down time built into your day has been shown to improve productivity.

Conversely, when I get new data, start writing a new grant, or acquire a novel task, my interest and enthusiasm are high and I’m tempted to drop everything else to start working on it. Following that passion for a day or a week gives me a great start in which to outline what I’ll do for the next few weeks or months.  Then, as my enthusiasm ebbs, my thoughts wander, and other deadlines become more pressing, I can set it aside and pick that outline up later after I’ve thought it over.  Collectively, these strategies allow me to be productive without reallocating time that I would otherwise use for sleeping, and without racing against the clock to submit something.

Find a system you like and stick to it

Everyone uses different technology and productivity applications, and everyone has a different style of organization, so you may have to try different things to find a method you like.  But once you find something that works for you, stick with it.  Too often I see people abandon a time management strategy because they don’t have time to invest in adapting to it.  Maybe you have several hundred unread emails you don’t want to sort, maybe you are having syncing issues across multiple device operating systems, or maybe you keep forgetting to use your strategy because it hasn’t become habit.  I encourage you to devote time to becoming comfortable with some time management strategy, as I can personally attest that it will pay off later.

Featured Image.

How is manuscript editing like roulette?

Because you play another round until your number wins!

Manuscript writing seems like it should be a straightforward ordeal. You explain the current body of research on the subject and identify the knowledge gap that your hypothesis fills, explain the rationale and objectives for the study, describe all the methods you used, present the data results, and then interpret them in the discussion. Oh and don’t forget the bibliography. Simple!

Oh contraire. Many manuscripts grow and then end up splitting into two or more, or you add a collaborative project on after the fact using the samples you’ve already collected. Sometimes you just say “let’s test these and see what happens”, and you don’t have a specific hypothesis except for “it could be cool”. Moreover, when you work in a very novel, difficult, unpopular, or boring field, there often isn’t a lot of previous research for you to read up on.  It makes it more challenging to write what should be the easiest section, the Introduction, because you don’t have much background to introduce.  While this does justify your work and the need for more research, it also makes it difficult to plan an experiment because you don’t know what outcomes or problems will crop up, and it can make your interpretation of the data problematic.

Methods: probably the worst section.

Sometimes you end up with more or less data than you planned. And most often, you didn’t just use commercial kit instructionDSCN1272s, you probably had to piece together methods from two to ten different journal articles, many of which were not verbosely described to maintain a sort of proprietary hold on the procedures, until you end up with a heavily-citationed Frankenstein’s monster of a Methods section. Not to mention that you probably had to mess around with procedures to find just the right settings on your equipment, so you have to go back through your lab notebook and try to tease apart what you did months or years ago. My suggestion: write the Methods while you are running the experiment. Whenever you finish a procedure that worked, type it up, especially if you are stuck waiting for something to process or grow anyway.

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In 2015, I worked on the DNA sequencing section of a project that had begun four years earlier when the original animal feeding trials were run, and which had been sequenced nearly a year prior to my taking over the data. Not only did the original Principal Investigator (PI) have trouble digging up the project files from four years ago, but the technician who had sequenced the data was no longer a member of the lab. Between the two, it was very difficult to track down what had been done, and which sequencing file name corresponded to which sheep sample. Even if you think the project will never be published, TAKE GOOD NOTES. Really specific, legible ones, trust me- you’ll thank me later.

 

Results and Discussion: Let’s be honest, the only two sections anyone actually reads.

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Exopolysaccharide production (white) prevents colonies from being ctained by red dye in the media.

Results is the easiest section to write, but possibly the most difficult to make appealing and understandable to a general scientific audience. Naturally, you need to know how to properly summarize your data and how to graph it. Seems easy: something about means and standard deviations, liberally sprinkle in some p-values…  But in reality, there are lots of ways to statistically validate or measure something, and most of these are minor variations on each other to accommodate slightly different data or situations. Maybe your data has a bell-curve normal distribution like people’s height in North America; maybe it’s heavily skewed to one side, like my preference for maple-frosted donuts over celery. Or you need an ordination plot that takes non-Euclidean distance samples and graphs their relationship to each other by plotting one point, then rotating the axis and plotting another until you’ve plotted all your points. No matter how sophisticated your presentation techniques, if someone can’t look at your graph and the graph summary out of context and understand what you are measuring, you haven’t done your job well. I’ve heard many scientific authors complain that a reviewer demanded changes to the manuscript because they did not under the results or statistical analysis. That can be frustrating, and sometimes it feels like the reviewer is just being obtuse, but as scientific authors it’s our job to properly explain what we did.

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Acid production from different carbohydrates by Streptococcus gallolyticus shown by a pink color change.

The Discussion section is always my favorite, because now you interpret your results into the context of other findings and speculations- in short, you finally get to tell the story of what is happening and why in a more interesting way.

The rest is just details. The Conflict of Interest section is always very interesting. Here you must disclose any conflicts you have, anything from a funding source that paid for your work and may or may not have had input in the experimental design (sometimes commercial companies will contract researchers to do a specific experiment that they more-or-less designed), or that the commercial lab you sent your samples to be tested at has you on the payroll. The Conflict of Interest is usually blank for studies coming out of academic universities, but it’s a good way to track down researchers who might be biased towards or against something.

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You have an acknowledgements section where you can thank personnel that may have assisted you in some small way, someone who you bounced ideas off of in planning and interpretation, someone who gave you samples to work with free of charge. In my case, I most often thanked the hunters who had dutifully collected a jar of rumen (stomach) contents, and sometimes colon contents, from moose while they were field dressing. Or the numerous undergrads that helped feed my newborn lambs five times a day until they were weaned.

Last but not least, the Bibliography or References Cited. Sounds easy enough. But you’d be surprised how pesky it can be. Different journals often want different formatting for your submission, some want authors lists to look like “Last, First; Last, First”, or maybe “Last, F., Last, F.”, or even “Last F, Last F”. Some want years in parentheses, others don’t. Some want issue number, or the journal name to be abbreviated, or a certain part of the reference to be bolded. Trying to reformat 50-100 references for submission to a different journal can be a nightmare. Luckily, there are plenty of citation managers that will create a digital library for your references, and allow you to search for citations while you are writing. Then, you hit “Insert Bibliography” and it numbers or alphabetizes it, and puts them into the desired format. That is, assuming you had put all the correct bibliographic information in. I like Mendeley because I can import references from my web browser; however, on older PDFs sometimes it can’t pick up the info it needs and you have to do it manually. I’ve gotten some interesting inputs for authors’ names when it gets confused.

Manuscript writing can take months, especially with complicated projects or those with many co-authors, as all co-authors need to approve the final version before it can be submitted. Once submitted, a Journal Editor will send the manuscript out to two or three Journal Reviewers, who are researchers in academia or industry that are in that field of expertise and can opt to volunteer to read and review the article. Nearly always, the authors do not know who the reviewers are, and in many cases the reviewers do not know who the authors are, although it is helpful for reviewers to see the authors’ names. If they have a conflict of interest with the author, such as they  don’t get along personally, they might be married, or they are currently working on another project together (anything that might bias them for or against), the reviewers are supposed to decline to review. Reviewers have two to four weeks, depending on the journal, but some will submit their reviews late. The Editor considers all the reviews and makes their final decision to accept as is, accept with minor revisions, accept with major revisions, decline with major revisions (authors may edit and submit a new manuscript for consideration), or decline.  It takes a few weeks to find reviewers, several more to get the revisions in, and another one or two for the editor to make a decision, so this can take anywhere from six weeks to four months.

Often journals will decline without reviewing if they are not interested in the subject material or feel it is outside the scope of the journal. If you have revisions, some journals request that you submit two new versions of the manuscript- one with the changes highlighted. Additionally, you need to address each reviewer comment by explaining what you did. For spelling mistakes, this is as simple as writing “corrected” after the comment. For more complex things, you need to explain the change along with quoting the new text, or explain why you aren’t changing things. If the Editor and Reviewers do not feel that you made all the changes, they may reject the re-submission or send you more edits. Usually they send you more edits that they didn’t notice the first time.

Eventually, a journal might accept your manuscript, and then you only have to approve the author proofs – unless your figures don’t have 18746_603831005730_3060064_na high enough resolution, and then you need to remake them or figure out how to increase your dpi.  Typically it takes between six months to a year to complete the whole peer-review process, depending on the study results and the journal’s internal process.

While tedious and arduous, the manuscript peer-reviewing procedure works very well. Experts in your field can assess the validity of your work, and experts in related fields can give you an outside perspective, especially when you have gotten used to using a very specific jargon or not completely explaining things. Most importantly, it improves the quality of the writing and presentation, and it maintains a standard of integrity and excellence. By the end of the submission process, you are dizzy and you want to get off the ride. But by the time you get through the next project, or eat a soft pretzel, you’ll be ready to climb back on that carousel horse.