Preparing a manuscript for publication

Preparing to submit your first manuscript to a peer reviewed scientific journal can be nerve racking, especially without an experienced graduate student or available adviser to guide you. When I began to prepare my first paper for submission, I was surprised by how pain staking and time consuming the process can be (especially, if it's your first time!). I thought I would share my experience in the hopes that it might help guide newer graduate students through their very first submission (Awwwwwww! They're growing up!).

1) Pick a journal in advance (before or during the writing phase!)

I'll admit that I don't always do this and sometimes change my mind part way through the writing process. However, it can help guide your writing. If you're familiar with the aims of your journal of choice, it can be easier to formulate an appropriate paper. That being said, familiarize yourself with the "aims and goals" of journals you may submit to. This is most often posted on the main journal page. You can also access and read several papers from said journal. Are any of the published papers similar to yours? do they have similar goals? If the answer is yes, you have likely chosen an appropriate journal. You may also wish to ask for input from your adviser, they are frequently more familiar with a larger number of journals than their graduate students.

2) Get as much feedback as possible

You'll likely receive comments and feedback from your adviser (let's hope!). But it's also good practice to ask for feedback from others. These people might be other experts in your field (that you feel comfortable asking!) or lab mates. Hopefully, receiving as much feedback as possible will help identify issues with grammar, gaps in logic, and other errors (thus reducing the burden of reviewers!). 

3) Download the author guidelines (preferably during the writing stage) and prepare your manuscript file for submission

Again, I am guilty of writing first and asking questions second (it's not a good habit!). Journal articles can be persnickety about font type, line spacing, line numbering, title page format, reference format etc. (although they may vary in specificity). This stage is usually more time consuming than difficult but follow ALL the guidelines. If you do not follow these guidelines, you risk having your paper returned before it is even sent for review (help your paper succeed!). You'll also save time. I've spent too many hours formatting and re-writing to meet journal requirements. Save yourself!

5) Prepare high quality figures/tables

The author guidelines for all peer reviewed journals should outline the ideal quality of figures including font types, font sizes, line widths, colors, image sizes, and resolutions. Most journals require that figures be submitted at sizes of 1, 1.5, or 2 column widths. Consider how large you wish the final print figure to be (will the detail be visible if the size is too small? does the figure need to be 2 columns width to be understood by the reader?) Similarly, most journals require a minimum of 300 to 600 dpi resolutions for most figures. I use Adobe Photoshop to to edit final image sizes and resolutions although other, cheaper software will also do the trick. Be certain to submit your figures in the preferred format (.jpg, .psd,.gif etc.). Graphic design of figures is beyond the scope of this post. There are numerous online and print sources on graphic design. I also recommend scientific design courses and/or conference workshops.

Journals also usually have a preference regarding table format (where to include and no include lines). As a general rule, vertical lines are not used and horizontal lines are limited to above/below the table contents. Whether the tables can be submitted as .xls files or .doc files also varies from journal to journal. Be sure to check with the journal guidelines.

6) Write a cover letter

A cover letter should address the handling editor for your journal of choice. If you do not know who it is, address it to "Editor, Journal of Unicorn Biology" or the editor of a journal that, you know, actually exists. A good cover letter should VERY BRIEFLY describe what you did, why it is unique, and why the journal should publish your paper. A cover letter probably shouldn't be longer than 1-1.5 pages. If you have never written a cover letter, send it to your adviser for feedback and ask fellow graduate students for samples from their own work. 

7) Create an account and fill out the form

This is self explanatory. Most (all???) journals now have an online submission system that is usually accessed from the main journal page (buttons usually say "submit an article"). Gather all information for co-authors including their emails, affiliations, and institutional addresses or you'll be scrambling to find it at the last minute. The specifics of the online form vary from journal to journal but have some commonalities. You will be required to input author information, the article title, the article abstract, and to upload your cover letter, manuscript file, and figure/table file(s). You are usually also required to declare no conflict of interest (and if there is conflict of interest, to disclose it), to declare that all authors have agreed to submission, and to declare that the article has not been submitted/published elsewhere. Be sure that you can truthfully make these declarations (or terrible things will happen, like being bitten by hundreds of angry ferrets!). In all seriousness, your paper will not be considered for publication. 

Once you upload your files, you will be prompted to build a PDF file (at least this has been the case for all journals I have submitted to, see REJECTION! http://evolbiology.blogspot.ca/2013/08/rejection.html for proof of my experience with submission). You will then have to view and approve the final PDF. Ensure that all figures, tables, and text look as they should. If not, return to the upload page and replace the offending files. Once you're PDF looks acceptable, you usually have to click approve and then submit. Don't get too nervous! 

8) Wait for the results!

Most journal webpages allow you to check the status of your paper. The status will change to "in review" once the manuscript has been sent out for peer review. As a general rule, if the status does not change for three months, I will email the handling editor. I have heard horror stories of some people waiting 8 months to a year. Don't do it! It's in your best interest to make sure your paper is not forgotten or stuck on a reviewer's desk somewhere. A polite email will often get the ball rolling or at least assure you that your paper hasn't been forgotten. 

Any additional advice on paper submission? Post it in the comments.  

Preparing for and attending conferences!

With the annual meeting for the Society of Vertebrate Paleontology coming up and the annual meeting of the Geological Society of American under way, I thought it was the perfect time to post about conferences!

Attending conferences is an important part of academic life. They are opportunities for networking, showing off your work, learning about the work of others, and socializing with your peers. I have posted about networking and selling your work previously.

Selling yourself and your work!
http://evolbiology.blogspot.ca/2013/03/selling-yourself-and-your-work.html

Professional development and networking
http://evolbiology.blogspot.ca/2012/11/professional-development-and-networking.html

I have yet to post about conference preparation strategies and general rules. So here we go!

1) Prepare your poster/talk in advance

We're all often making last minute touch-ups but hopefully we're not analyzing new data the day before our scheduled presentation! If you're not a seasoned scientist, it can be difficult to deliver a polished talk without a lot of practice (I would know!). Making large-scale changes to your presentation at the last minute is a "sure fire" way to embarrassment! My approach has always been to present to a group of peers at least a week before the start of the conference, giving myself plenty of time to make revisions. I also spend time reciting my presentation to myself, ensuring that each part follows logically. Of course, these strategies don't work as well for poster presentations, which must be printed before the conference. But preparing responses to poster session questions is never a bad idea!

2) Pack business cards

Be memorable! I can't speak for everyone but I often talk to dozens of people at conferences and can't remember them all. Especially if you're new to the field, business cards can make you memorable! Collecting business cards and writing notes about your conversation on the back will also help you remember important interactions.

Business cards should be simple. Although hot pink might seem like the perfect choice, it's not. Business cards are not an expression of your inner fashionista. You should (obviously) include your name, affiliation,  area of study (something simple like "Unicorn Ecology"), and email. Do not use an embarrassing email address such as I_love_unicorns@unicornsarepretty.com! Your institutional email (dani@universityofcool.com) or a professional non-institutional email (dani@normalmail.com) make a better impression.

3) Pack appropriate clothing (don't dress like a slob)

Conferences are often unofficial interviews for MSc, PhD, or postdoctoral positions. Looking like a homeless person, as many graduate students often do, will not do you any favors. Although many people wear casual clothing or even what appears to be field attire to conferences, you should not. I am not saying you should wear a tuxedo or an evening gown (but how awesome would that be?!). A pressed shirt and pants should suffice.

4) Don't make a fool of yourself in social situations

Many of us are guilty of this infraction, including myself. But you don't want to be remembered for any alcohol induced antics. Sometimes, we're also remembered for our sober antics such as slipping and falling on the dance floor after attempting a dance move that probably resembled a seizure (which definitely happened to a friend of a friend of mine).

How else should we prepare for conference? Are there any other conference rules?

Rejection!

REJECTION! The word itself sounds menacing but it's a normal part of academic life. Very few of us (maybe none?) have never had a paper rejected from a scientific journal. We're all members, willing or not, of Rejection Club.

I'll start by confessing my "dirty" secret. In the last year, I have received EIGHT rejections from scientific journals! I hope that makes some of you feel a little better. Of course, it' not fair to say that they were eight separate rejections. Six were rejections from very high impact journals that didn't even send the papers out for review (four were actually the same paper). Experiencing rejection on such a scale has taught me some very important lessons.

The first rule of Rejection Club is...it happens to everyone! You know that professor whose work is constantly published in Nature or Science? They've been rejected more times than you will be during your entire MSc or PhD (possibly your entire career). Moreover, all of the graduate students I talk to have had papers rejected from journals with both high and low impact factors. If you're determined to be an academic, you better grow a thick skin and get used to the idea!

The second rule of Rejection Club is...don't take it personally. The first question I asked when my first paper was rejected in 2008 was "Does this mean I am a terrible scientist?" The answer to this question is usually no but my automatic response was to feel upset and embarrassed. Of course, I have experienced several more rejections since and realized that an emotional response is usually unwarranted (although it hasn't stopped me from having one every once in awhile!). Once I started receiving invitations to review manuscripts, I realized that the goals of MOST reviewers are to i) honestly help improve the paper and ii) simply guide the journal in making a publication decision. Although I have seen some manuscripts that needed considerable revision, I have never judged the authors (after all, I've been in their shoes!!!).

The third rule of Rejection Club is...seriously consider all reviewer comments. You might be saying "DUH!" But the fact of the matter is that some reviewer comments can sound utterly inappropriate. I have definitely asked "was that reviewer high when they read my paper?" However, comments that don't make sense or seem unrelated might point to a more serious problem with your paper (e.g., unclear explanation and writing). You should try to clarify any areas of confusion in new versions of the manuscript. After all, you might get the same reviewer(s) on the second round.

The fourth rule of Rejection Club is...balance impact and quick publication. I have only recently come to terms with the fact that the ultimate goal during my PhD should be to publish many papers, quickly (again, DUH, but I was stuck on trying to get that one, life altering Nature paper). It's a matter of fact that journals like Nature and Science reject a very large portion of the submissions they receive without sending them for external review (trust me, I have experience). After such a rejection you're left with very little to work with because they provide very little feedback. After submitting to two other high impact journals (and getting advice from various advisers), I realized that I had nothing to show for months of work, not even constructive reviewer comments. After seeking the advice of several advisers, I realized (rather, they helped me realize) that if I had submitted to a mid-range journal, my paper would be published by now. Ultimately, the success of your PhD is partially measured in the number of good/acceptable (rather than amazing) papers you publish.

The fifth rule of Rejection Club is...rejection makes your paper better. It's confirmed, papers that are rejected and re-submitted are cited more often than papers that aren't (http://www.sciencemag.org/content/338/6110/1065)! Rejection might actually increase the awesomeness of your paper. It's really easy to become myopic when working on a project or paper for a long time. Comments from a diverse array of reviewers and editors will improve the quality and ultimately the reception of your paper by the scientific community. Rejection, although frustrating, can be a good thing. So keep on submittin'.

I am absolutely certain there are more rules of Rejection Club. Post them in the comments!

General Advice on Writing!

Hello! It's been a long time. I am preparing for an epic trip to Barcelona for the International Congress of Vertebrate Morphology (http://icvm2013.com/). I am hurriedly re-analyzing data and putting together my talk. I'm also attempting to submit at least one manuscript before leaving in three weeks (we'll see!), which reminded me of a topic I wanted to post about, writing! Disclaimer: I am not necessarily the world's expert on writing scientific manuscripts but I do have considerable experience and hopefully some useful advice. This is not intended to be an instructional on "how to write an introduction/discussion section." You can consult numerous books and courses on scientific writing.

So, you're part way through your graduate school experience and it's time to start writing your first manuscript for submission to a scientific journal. What's the first step when staring at the awful blinking cursor?

1) Outlining

Yes, since high school we have all been told we should create an outline before starting the writing process. But we're not necessarily taught how to make a good outline. Here are what I consider to be bad and then good outlines. I have used the introduction section as an example but the general advice applies to all sections of the manuscript.

Paper title: Cuteness index for prairie unicorns

Bad:

Write something about unicorns
Write something about cuteness
Unicorns are awesome and breathe rainbow fire

Good:

Unicorns are related to horses

1. Closest relative is extinct Dinohippus (cite Fraser et al. 2013)
2. Possess horns
3. Much cuter than other living equids (cite Equus and Fraser, 2012)

Unicorn cuteness can be measured as the index of horn length to tail length

1. Horn length is a measure of breeding vigor (cite James and Cutie, 1988)
2. Longer tails make unicorns more attractive mates and are proportional to strength of rainbow fire breathing (cite D'ior and Gabbana, 2001)

I won't go on any further. The point I am trying to make here is that a good outline should be detailed and guide your writing on the topic (even if it isn't unicorn cuteness). A good outline will bring together the relevant information and literature.

2) Start "barf writing" (also called stream of consciousness writing, if you prefer something less grotesque)

I don't mean projectile vomiting at your computer screen (although I have had the urge once or twice!). Once I have made an outline, I start filling in the gaps. Importantly, I don't spend much, if any, time editing my writing at this stage. Why? It's better to get your ideas and thoughts on paper and then cut them down or add to them later as needed. Additionally, if you "edit while you write" it will take exponentially longer to write the paper. 

Your "barf writing" will likely be terrible. But that's okay! No one has to see the paper at this stage. I have written some absolutely awful sentences during barf writing but that's what editing is for!

3) Edit like mad (re-write entire sections, if need be)

I am using the word edit very broadly here. I say I am editing even when I am re-structuring paragraphs and moving sentences from one paragraph to another. This is the stage where I asses the flow and structure of the paper. The introduction, for example, should introduce the problem of the study early on and then explain the details of the problem and how it will be solved. I carefully assess the flow of each sentence and it's placement in the paragraph/entire section. Anything that doesn't fit, is cut. The introduction/discussion (at least) should tell a story that flows logically from one element to the next. Resist the urge to tell the reader everything you know about the topic. We don't want to bore them! We want to lead them logically through the problem, convince them it is important/interesting, and tell them how our study is a great way to address it.

I admit this is the most challenging part of writing a scientific paper and it takes the longest. But I find it the most rewarding. As a coherent paper starts to form, I enjoy the sense of accomplishment. 

I wouldn't call this post exhaustive advice on writing scientific papers but it is a start and I consider the points above to be among the most important. If you have any tricks or advice, leave them in the comments!

How to Keep (at least some of) Your Sanity During Graduate School

I have had very little time to update this blog because I have been busily preparing manuscripts and hard tissue samples. But I want to write about a very important topic that MANY graduate students overlook when beginning their careers in academia, their sanity.

Many graduate students think (maybe not consciously) that the path to success in graduate school is working 24 hours a day, seven days a week. In my experience, this approach only leads to exhaustion and resentment. But how can we publish, attend conferences, and finish our theses on time without working 24/7?!

It's all about EFFICIENCY. "Great Dani, all you have given us is a buzz word." But it's true!

1) Make to do lists

This seems really simple but many people don't make useful lists. For example, making a list of things like "write thesis" will not help you become more efficient. These lists are nebulous and not achievable on short timescales. Here is an example of one of my daily "to do" lists.

A) Read So and So et al. 2010
B) Email Dr. Awesome about samples
C) Write two paragraphs of thesis introduction
D) Add acid to samples
E) Create an outline for that upcoming manuscript

I would normally have more on my daily list, but you get the gist.

Note how specific my list is. These are all goals that are achievable in a single day. Using my approach, you will experience an increase in overall productivity and meet your longer term goals sooner.

2) Move on to something else

If you just can't look at your paper anymore, work on something else for awhile (an afternoon or a couple of days). You're doing yourself and your productivity a disservice by paining over one project at a time without making significant progress. A bored mind is an unproductive mind! You'll find it easier to come back to the project after a short break.

3) Don't wait until the day before

Hopefully, most of us learnt this during our undergraduate years. I certainly did! My grades improved a full letter grade once I stopped leaving things to the last minute. So don't wait until the week before your comps to start studying or the day before your proposal to start writing! You won't be able to enjoy points 1) and 2). You will also likely have a miserable experience in graduate school and disappoint your adviser.


So far, I have told you how to maintain efficiency but not necessarily your sanity. Naturally, following the three steps above will help, but there are some very important things that are often overlooked.

Rest, relaxation, and fun are all an integral part of the successful academic life.Working 24/7 will only lead to burn out (even if you're working efficiently). Going to a movie or getting a good night's sleep can actually benefit your research! I am lucky because I have a partner who does not work in academia and he keeps me engaged in non-academic activities like dog walks, barbecues, and date nights. The power of leisure activities cannot be understated!

I recommend a hobby that is not directly related to your research. I am a film fanatic. I also enjoy playing racquetball and walking my dog. I know others who enjoy knitting, role playing games, guitar, hiking, biking, and camping. These activities are not off limits because you're a graduate student.

*Disclaimer* I do not mean that you should spend all of your time in leisure. If you want to be a successful academic, you will need to work long days and long hours (I work between 8 and 10 hours a day because I am efficient but many people work longer). But breaking up your week with fun activities will help you keep at it!

A mentally healthy graduate student is a good graduate student!

Sitka and I at puppy training class, maintaining our collective sanity!

Selling yourself and your work!

It's one thing to know you're awesome, it's another to convince others of it! "Selling yourself" is one of the most important skills you will develop in graduate school. Successfully selling yourself and your work will get you scholarships, fellowships, offers to collaborate, and offers to work in new labs (among many other things). So how do you do it???? I am FAR from an expert and I learn more about selling myself every day, so leave your suggestions/corrections in the comments.

1) Get your name out there

This follows from my previous post on networking (http://evolbiology.blogspot.ca/2012/11/professional-development-and-networking.html). Talk to people, present your work, and take every chance to tell your colleagues about new and exciting things you're working on.

2) Know why your research is exciting

Selling yourself and your work goes beyond presenting at conferences. You need to convince your colleagues that your work is worthwhile and exciting (you might like doing it for the sake of knowledge or because you're "in love" with a particular organism or system but not everyone will agree with you!). Answering the following questions is a good start:

Why should the general public care about your work? In other words, what would you tell your grandma to get her interested?

What are the broader impacts of your work? How will the results affect science and/or society?

How would you pitch your work to a granting committee? Why should they fund your work?

You'll become more comfortable with the answers to these questions the more conferences you attend and grants you apply for (the better you get, the more grants you'll get too!). Keep a 2-3 sentence summary in the back of your mind for impromptu conversations with colleagues.

3) Write a lot of grant/scholarship applications

There's nothing like practice! You might get some money too! Also, see my previous post (http://evolbiology.blogspot.ca/2013/01/graduate-school-part-iii-money.html).

3) Publish

Publishing seems obvious and it is! But it's not as simple as publishing 1000 papers per year in low impact journals. In modern academia you're expected to publish in high(er) impact journals. This doesn't mean you have to publish only in Science and Nature (although I would certainly give anything to do that!). It means finding and telling a compelling story. Papers in Science and Nature tend to have simple but exciting punch lines.

What is the punch line for your work?

You're part way to a high impact paper! Of course, there is a lot more that goes into a Nature paper than a catchy punch line (well-collected data, compelling data analyses etc.) but without one, you're unlikely to be published there. Sometimes it is tempting to get caught up in details and methods. These are important things to consider when designing and performing research. But, unless you're specifically intending to publish a methods paper, they probably shouldn't over shadow your punch line.

4) Have a well organized CV

The following blog is a great guide (http://theprofessorisin.com/2012/01/12/dr-karens-rules-of-the-academic-cv/). If it's difficult to find pertinent information on your CV, you'll be overlooked for grants and jobs!

5) Share your work online

When you publish a new paper or present at a new conference, tell the world wide web about it! You can use Facebook, Twitter, LinkedIn, Academia.edu etc. It's also good practice to email your papers to close colleagues. So much new literature is published every day that your paper might be overlooked by relevant researchers. Don't be afraid to be a little self serving. Some day you'll be judged on the number of times your papers have been cited and you won't ever regret having distributed your work!

Fulbright Fellowship at the University of Wyoming

Since September I have been a Fulbright Fellow at the University of Wyoming. If you're a Canadian interested in doing study or research in the USA, check out the Fulbright Canada webpage (http://www.fulbright.ca/). I've been working in the lab of Dr. Mark Clementz (http://www.uwyo.edu/profiles/faculty-staff/mark-clementz.html), a specialist in the areas of isotope ecology and marine mammal palaeoecology. Dr. Clementz has written some of the seminal papers in marine mammal isotope ecology. I'm also working with Dr. Clementz's recent postdoctoral fellow, Dr. Sora Kim (http://geofaculty.uwyo.edu/skim11/Welcome.html). Dr. Kim is an isotope ecologist and has worked primarily on extant and fossil shark ecology.

My Fulbright project is focused on patterns of oxygen isotopes (from phosphates and carbonates) in the teeth and bone of pronghorns (Antilocapra americana). Pronghorns are "wicked cool" hoofed mammals from the family Antilocapridae. They are not members of the family AntiloCRAPridae, as I once reported in a departmental seminar. They are the only living or extant member of the family but were preceded by a large number of extinct species. I always have to mention the fact that they are the the fastest land mammal in North America (much faster than their current predators). Their speed is usually discussed as a hold over from times when faster predators pursued them.

Besides their coolness, why did I choose to work on pronghorns?

The obvious answer to the question is that UW houses a very large collection of modern and archaeological pronghorn specimens. But I had other motivations. First, pronghorns have an extensive geographic range (northern mexico to southern Alberta). This enables the study of geographic variation in pronghorn isotope values. From this you can create "isoscapes" and compare them to values from rainwater (http://wateriso.eas.purdue.edu/waterisotopes/). Second, because pronghorns are a game animal, they are numerous in collections all over the USA and Canada. These collections span thousands of years, enabling researchers to study temporal changes in pronghorn isotope values, which is relevant to changes in migration and climate change (among other things).

What isotopes am I using and why?

Stable oxygen isotope ratios covary with temperature and rainfall, thus varying with distance from the coast, latitude, and altitude (check out an isoscape of oxygen here http://iamtheweather.com/vveather/wp-content/uploads/2010/07/beverages.jpg). I am now about to describe geographic variation in oxygen isotopes as briefly as possible (so don't expect to become an expert!). Oxygen isotopes change with distance from the coast and with altitude due to the preferential rain out of heavy (18O rather than 16O) isotopes closer to the coast and at lower altitudes. So rainwater isotopes become progressively lighter inland and at higher altitudes. This explains some of the latitudinal variation in oxygen isotopes. Ambient temperature also affects oxygen isotopes in water on the ground. At high temperatures (low latitudes), the light isotope is evaporated from the ground, leaving more of the heavy isotope. At cooler temperatures (high latitudes), less of the light isotope is evaporated. This is an oversimplified explanation of oxygen isotopes but should give you a basic understanding of why oxygen isotopes vary across North America as in the linked map. I'm sure my temporary lab mates are ganging up for attack!

What is the purpose of my research?

My mains goals involve characterizing changes in oxygen isoscapes from mammals under conditions of climate change because these changes can provide indirect evidence for changes in terrestrial rainfall and temperatures on long timescales (thousands to millions of years).