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).

Graduate School Part III: Money!

When you're admitted to graduate school, the university will send you a package describing your degree requirements and the details of your stipend. On average, a Canadian graduate student will make 19,000 per year (sometimes less, sometimes more). Your stipend summary will be broken down into teaching assistantship, research assistantship  and departmental scholarships. Having a stipend is great. I am ecstatic that I get paid to do Science. But, depending on your student fees, stipends can be eaten up pretty quickly. What can you do about it?

It seems obvious but the best solution is to apply for a lot of scholarships. All universities have an awards and/or financial aid office. You can usually request information on available scholarships or log on to their webpage. In Canada, most, if not all, science graduate students will be applying for funding from the National Science and Engineering Research Council (NSERC; http://www.nserc-crsng.gc.ca/) (for the social sciences there is SSHRC, for the medical sciences there is CIHR). NSERC awards are competitive and applications take a lot of time, so check the deadlines at your institution and start preparing early. Always ask your supervisor for feedback on your research proposal and request reference letters as early as possible (if you request letters the day before they're due, you're liable to annoy your supervisor).

Other Canadian awards include the Queen Elizabeth II graduate scholarships. At some (maybe most?) institutions these applications are reviewed internally so check with your awards office. Many provinces also offer provincial scholarships (Alberta Innovates, Ontario Graduate Scholarship) and most universities offer a suite of internal awards. Your awards office should have information on available provincial and internal awards.

There are also numerous small (and some large) awards available through professional societies including, but not limited to, the Society for the Study of Evolution (http://www.evolutionsociety.org/awards.asp), Society of Vertebrate Paleontology (http://www.vertpaleo.info/Awards.htm), and the Canadian Society of Zoologists (http://www.csz-scz.ca/awards/research_grant/description.html). All major societies offer grants and scholarships but you usually have to be a member. The good news is most student memberships don't cost more then $60 per year.

My biggest piece of advice is to apply for everything for which you are eligible. I have heard many graduate students say they won't apply for certain awards because "they won't get it anyway." Well, you CERTAINLY won't if you don't apply! The more scholarships you apply for (successfully or not), the more experience you gain and the better your applications become. I applied for NSERC three times before I was successful. My proposal improved a million fold from the first application to the third. My experience with scholarship applications has now earned me several competitive scholarships including a Fulbright Scholarship. So keep writing those applications! You're never wasting your time!

Graduate School Part II: Choosing a Supervisor

In a previous post I covered the characteristics that are important for success in graduate school (http://evolbiology.blogspot.com/2012/10/graduate-school-part-i.html). However, deciding to attend graduate school is only the first step.

It is of paramount importance that you be interested in your graduate research project. Hopefully, you will have some idea of the area(s) that interest you from your undergraduate courses. As a fourth year undergraduate, I knew I was interested in functional morphology and evolution (thanks to some of the really awesome zoology courses at the University of Calgary). But it can be difficult to judge whether or not you will enjoy scientific research. It is therefore important for most fourth year undergraduates to undertake a research project. Usually, undergraduate research projects last two semesters and can give you a taste of your future in graduate school. You can also volunteer for different labs in your department. Most PhD or MSc students would be excited to have a helper (it gives them more time to drink their precious coffee!). Ask to volunteer for a variety of labs doing different types of research. In Canada, you can also apply for summer internships through the National Science and Engineering Research Council of Canada (NSERC; deadlines for undergraduate applications are usually around December so check with your department). These scholarships look excellent on a CV and provide you with unparalleled research experience. It is also important to peruse the recent scientific literature and/or join a discussion group or club.

Solidifying your interest in science might seem like a lot of work. But doing the work is worth it. Graduate school requires a lot of time and mental energy. Being interested in what you do, makes your job fun. Hating what you do, can make graduate school a bitter experience.

Once you're certain that you definitely want to attend graduate school, you need to find an appropriate supervisor. The best first step is to ask professors with whom you are familiar about potential supervisors in the field. They likely know many people and can point you in the right direction. You can also search university websites. Most professors will publish a description of their research online along with a list of recent (hopefully!) publications. I recommend reading some of their publications. This will give you a good idea of their research interests and make you look keen when it comes time for meetings/interviews.

If you can, it is also a good idea to speak to graduate students. Most graduate students will give you their honest opinion about their adviser. After all, you don't want to end up working for someone who is never around or treats their students poorly. You'll be working under your adviser for years (2-5 depending on your degree level) so it's important to at least get along with them.

The next step is to contact potential supervisors. To get the ball rolling, an email is usually best. Be sure to make your email sound professional. Avoid spelling mistakes and don't use "LOLspeak" ("I can haz masters degree?" = BAD). Also, DO NOT send mass emails to professors. Many profs receive hundreds of mass emails from prospective students every year and yours is liable to be ignored.

I  also urge you to start contacting people EARLY. If you're emailing professors 2 weeks before the application deadline, you are likely to miss it. Professors are busy people! That being said, I would give them 2 weeks to respond before emailing them again (others might have different rules, so ask around). It is okay to remind a professor of your inquiry. It's possible that they tucked the email away for later and forgot about it. I'd forget emails too if I had several graduate students vying for my time, was teaching courses, and serving on departmental committees (among other things!). It doesn't mean that aren't interested!

Once initial contact has been made there are a few options for how to proceed. If they are at a nearby university, you can suggest a one-on-one meeting. These are great because you can often meet lab members and tour the facilities. If they are far away, it's a good idea to arrange for a phone meeting. They are less personal but will show that you're serious about applying. The professor will usually indicate during the one-on-one or phone interview whether they encourage you to apply.

In the event of a positive response, it's time to apply! University websites usually have good instructions and administrative staff that would be happy to help out.

Professional Development and Networking

Most of us know that the network we build will determine (at least in part) the success of our academic careers. The more people we know, both formally and informally, the more likely we are to be considered for post doctoral and other academic positions (assuming your interactions have been positive). Additionally, a larger network affords us more opportunity for collaboration (something that is very important to have on your academic CV when applying for positions). But how can we build a large and targeted academic network? I am far from an expert in this area and I hope this post will be a learning experience for me as well as other graduate students.

There are numerous resources for academics interested in learning how to build a network (websites, books, blogs). Most universities will also hold at least one seminar every year on the subject. I recommend you attend. Seminar coordinators will often invite people with varying levels of academic experience (professors, post docs, and graduate students) to speak on networking. There is usually something for both new and returning graduate students. I have attended a few seminars on networking and there are some recurring themes.

1) Attend conferences and other academic events.

The only way to meet other scientists in your field is to meet them on common ground. This seems really obvious but to some it isn't. Attending conferences can be expensive, especially if you have limited funding, and some graduate students opt out. However, most societies offer travel grants. I received one from the Society of Vertebrate Paleontology to attend the 2009 conference in Bristol, England. Many universities also offer funding for attending conferences and/or professional development. Make sure to check with your Graduate Student's Association and faculty office. Even if you don't have a lot of funding, attending conferences is the best way to build your network and I recommend going anyway (even if that means giving up your daily cup of coffee to save!). I try to attend 2-3 conferences per year and to present something at every one. There is an added benefit of building the "presentations" section of your CV.

2) Introduce yourself or have someone else introduce you to more senior researchers in your field

In my opinion, this is the most difficult part of the networking process. It is really tough to walk up to a famous researcher (or a not so famous one) especially if they are surrounded by other adoring fans. In fact, I find conferences super awkward and stressful for these reasons. It is a lot easier to hang out with your friends at conferences because it's comfortable (I call it my "safety zone"). But you have to force yourself to do it. It will get slightly (very slightly) easier with time. As your network grows and you know more and more people, it is also easier to set up introductions, which is considerably less difficult than approaching a famous researcher at random. Your adviser is also a good resource. Most advisers are happy to set up introductions. The graduate students of said famous researcher are also good resources. They can set up introductions and help reduce any ensuing awkwardness. I had some help from other graduate students when I was applying for PhD positions (and it worked!).

3) Get your research out there

This follows from point 1. If you don't advertise your research through presentations and publications, you are a lot less likely to be noticed. I love giving presentations at conferences, even if they sometimes go badly (usually because I didn't practice!). I also find publications to be a huge motivating factor when I am sitting in the lab or office. There is nothing like a "shiny" reprint with your name on it! Of course, presenting and publishing is only the first step. Emailing your new papers to colleagues or acquaintances will help them remember you and generate feedback on your work. Publishing titles and links to your papers on your website will also help alert the online community to your work. You should also bring reprints and abstract copies to conferences. This will help people remember you when they get home!

4) Get business cards

It might seem like something out of the movie American Psycho (it's up to you whether your business cards sport a fancy water mark!) but business cards are really important tools. As above, they can help people remember you when they return home from a long and stressful conference. However, I have definitely gone home with business cards and had absolutely no recollection of why I had them. I (and others) recommend writing what you talked about or the title of your poster/talk on the back of your business card before handing it off. I have recently started doing this and it REALLY helps. We can't all remember every face and conversation.

5) Online or email networking

Emailing other researchers is an obvious first step! We have all had "missed connections" at conferences. A well-worded email can help maintain or initiate relationships. There are also numerous other means of online networking including blogging, twitter, and websites such as Linked In. Of course, you should keep all of your online activity as professional as possible. Inappropriate online content can prevent you from building a successful network. You should also be prepared to get feedback from the online community! Not everyone will agree with your blogs or tweets (but you should have a thick skin if you want to succeed in academia!).

This is a very brief introduction to academic networking. I suggest you also speak to other graduate students as well as your adviser. We have all been there!

Professional Development

Dr. Sora Kim gave an excellent seminar on professional development in academia today and you can view the PDF on her website at the following link - http://geofaculty.uwyo.edu/skim11/Updates/Entries/2012/10/11_Building_a_Professional_Network.html.

I'll write a more extensive post about this soon!

Graduate School Part I

I have had a few inquiries from some undergraduate friends about applying for graduate school. I thought I would publish some advice here but also open up the comments to anyone who has further advice or competing views.

Many undergraduates are concerned about the fact that they don't have straight A's. Well, it's no big secret, but neither did I (at least for my entire program)! I did "okay" in first year but just scraped by in my second (by the skin of my teeth! Okay, teeth don't have skin, but you know what I mean). The good news is that biology programs normally only consider your last two years (or equivalent number of courses). You should always check with the program you're interested in, but many seem comparable. So if you're entering your third year and a little disappointed with your first two, you'll be just fine.

I also don't think straight A's necessarily make a good researcher. Does the ability to memorize thousands of facts make you a critical thinker? It might get you good grades but it won't help you design a relevant and interesting research project. This is not to say that all people with straight A's merely memorize facts (please, no angry comments!). All I am saying is that the person with the B+ average and the person with the A+ average may not be so different when it comes time for grad school. It all depends on personal characteristics that are at least partially independent of grades. Some important qualities that successful students possess are self motivation, competitiveness (healthy competitiveness!), and passion (not like a romance novel!).

Firstly, self motivation is important because no one is going to be there prodding you to finish your experiment. When your yearly committee meeting rolls around and you haven't made any progress, there will be no one to blame but yourself. You have to be good at setting goals and meeting them. I use two levels of goal setting. The first are long-term goals. For example, "I will submit paper A by January." The second are short-term goals. For example, "Today, I will write three paragraphs of paper A." Because I am self motivated I usually meet my goals (or at least come close).

Secondly, I want to be clear about what I mean by competitiveness. I define this as the desire to excel when your goals for excellence are set by the people around you. This means feeling motivated by how well others are doing and working hard to match their successes (or maybe to do a bit better!). I am only talking about hard work and not about immoral means of competing with others (purposely scooping their research, "bad mouthing" them, or sabotaging experiments). These are all unacceptable and place you into the category of ruthless rather than competitive.

I suspect there is a near linear relationship of healthy competitiveness with number of publications and number of scholarships. Publications and scholarships (in addition to experience and interesting research) are good determinants of future success (jobs, more scholarships) assuming they are of good quality. Of course, there may be exceptions to this "rule."

Finally, you have to be passionate about your research. If you are passionate you are most likely also self motivated and competitive. I think very positively about my research and am always generating new ideas. I wake up in the morning and immediately start thinking about science. But I don't want to be unrealistic. Every day will not be positive! Experiments fail and equipment breaks, but if it doesn't stop you from wanting to pursue research, then you're on the right track!

Part II will cover choosing a supervisor and a university.

A Brief Introduction to Testing for Phylogenetic Signal in Comparative Data

Phylogenetic comparative methods (PCMs) were the subject of my last post. You can read it here (http://evolbiology.blogspot.ca/2012/09/phylogenetic-comparative-methods-some.html). It was a VERY brief description of two commonly employed PCMs (Phylogenetically Independent Contrasts and Phylogenetic Generalized Least Squares Regression). However, it is important to note that PCMs should not be applied unless their use is justified. It's true that the availability of phylogenies and the array of methods for reconstructing phylogenies has skyrocketed. As a result, reviewers are suggesting PCMs more and more. But it is important to consider whether PCMs are necessary and whether they add to your analysis or aid in the interpretation of your data. But how can you determine if your study needs PCMs?

One of the questions to ask is whether your data (rather the residuals; Revell 2010) are phylogenetically structured. In other words, do your data show phylogenetic signal? Two common methods are the K statistics of Blomberg et al. (2003) and Pagel's lambda (Pagel, 1999). The K statistic compares the observed and expected variance for calculated independent contrasts (Blomberg et al. 2009; Glor, 2009). Pagel's lambda is a multiplier of the off diagonal elements of the covariance matrix that varies between 0 and 1. Lambda transforms the phylogenetic tree with the purpose of comparing a complete lack of phylogenetic structure (lambda = 0; star phylogeny) to the untransformed topology and branch lengths of your original tree (lambda = 1) (Pagel, 1999; Gor, 2009). In other words, Pagel's lambda determines which situation, a star or structured phylogeny, fits your data best.

Here is some basic R code for using Blomberg et al.'s K:

require(picante)

# Help file http://127.0.0.1:17385/library/picante/html/phylosignal.html

kstat<-phylosignal(data,tree) 

# Your data must have matching taxon names or be sorted in the same order as the tip labels of the phylogeny

# This will return the K statistics and p value (as well as the variance of the independent contrasts and the associated z value)

Here is some basic R code for using Pagel's lambda:

require(phytools)
# Help file http://127.0.0.1:17385/library/phytools/html/phylosig.html
lamb<- phylosig(tree,data,method="lambda")
# Your data also require names that match the tip labels on the tree
# This will return a lambda value and log likelihood, values of lambda closer to 1 indicate singificant phylogenetic signal

Using the K statistic and Pagel's lambda, you can justify the use of PCMs or demonstrate that they are not necessary. Although I feel strongly that PCMs are powerful tools in comparative studies, I also feel they should only be used when it is statistically justifiable to do so.

You can follow the instructions of Glor (2009) to further understand Pagel's lambda. There are also other methods for testing for phylogenetic signal that I have not covered here.

References

Blomberg, S. P., T. Garland, Jr., and A. R. Ives. 2003. Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution 57:717-745.

Glor. 2009. IV. Testing Phylogenetic Signal in R. Bodega Phylogenetics Wiki.

Pagel, M. 1999. Inferring the historical patterns of biological evolution. Nature, 401, 877–884.

Revell, L. J. 2010. Phylogenetic signal and linear regression on species data. Methods in Ecology and Evolution 1:319-329.

Phylogenetic Comparative Methods: Some Generalities

The comparative method, in one form or another, has been of paramount importance in biology since its inception. It is the basis for understanding how and why organisms differ. Prior to the 1980's the comparative method most often involved simple statistics (regression, correlation). There are several problems with this approach when comparing different taxa (species, genera etc.). Firstly, taxa do not have completely independent evolutionary histories. This is not a new concept. Even Linnaeus' hierarchical classification system indirectly represents the non-independence of species. Secondly, simple statistics such as correlation assume complete independence and the evolutionary process inherently violates this assumption. But comparative biologists need not despair!

There are a few methods for dealing with the issue of phylogenetic non-independence. These include (but are not limited to) Phylogenetically Independent Contrasts (PIC) (Felsenstein 1985) and Phylogenetic Generalized Least Squares Regression (PGLS) (Grafen 1989). The most commonly used method has been PIC.

PIC involves the calculation of contrasts (branch length calibrated differences) between sister taxa. Regressions are then carried out on the contrasts (through the origin) as opposed to the raw data, which effectively removes the influence of relatedness (Felsenstein 1985). PIC can be used for the comparison of one continuous with one categorical trait and for two continuous traits.

R code:
require(ape) # Paradis (2006)
tree <- read.nexus("tree.nex") # A tree with branch lengths
data <- read.csv("data.csv", header=T,row.names=1) # Data with row names as taxon names and two traits
pic1 <-pic(trait1,tree) # Calculate contrasts for each trait
pic2 <-pic(trait2,tree)
piclm <- lm(pic1~pic2 -1) # Regress contrasts through the origin

On the other hand, PGLS is very similar to statistics employed by ecologists concerned about spatial autocorrelation (localities closer to each other are likely to be more similar). PGLS constructs a correlation matrix based on the distance of taxa on the tree. The matrix is then incorporated into a generalized linear model (Grafen, 1989). One advantage of PGLS over PIC is that it can accomodate several models of evolution (e.g. changes in evolutionary rate, stabilizing selection). In contrast, PIC assumes a Brownian Motion (stochastic; BM) process of trait evolution (Felsenstein, 1985). Although PIC and PGLS may be equivalent under a BM model (Blomberg et al. 2012), the comparison cannot be made under other evolutionary models (evolutionary models will be the subject of a coming post). PGLS can be used to compare two continuous traits (for the comparison of a continuous and categorical traits, Phylogenetic Generalized Estimating Equations (Paradis and Claude (2002)) function similarly to PGLS).

R code:
# PGLS assuming BM

require(ape)
tree <- read.nexus("tree.nex")

data <- read.csv("data.csv", header=T,row.names=1) 

gls1<- gls(trait1~trait2,data=data,correlation=corBrownian(phy=tree),method="ML")
# Using the maximum likelihood method enables the comparison of evolutionary models using AIC

This post has been rather brief but I intend to continue posts on this topic.

References

Blomberg, S.P., J.G. Lefevre, J.A. Wells, and M. Waterhouse. 2012. Independent contrasts and PGLS estimators are equivalent. Systematic Biology 61: 1-61.

Felsenstein, J. 1985. Phylogenies and the Comparative Method. The American Naturalist 125:1-15.

Grafen, A. 1989. The Phylogenetic Regression. Philosophical Transactions of the Royal Society of London B 326:119-157.

Paradis, E. and J. Claude. 2002. Analysis of Comparative Data Using Generalized Estimating Equations. Journal of theoretical biology 218:175–185.

Paradis, E. 2006. Analysis of Phylogenetics and Evolution with R. Springer Science+Business Media, LLC, New York.

Scientific Politics Part II

Scientific progress is built on testing hypotheses and refining our ideas about the world. We test and re-test hypotheses until we are satisfied that they are supported (or not). An inner belief or intuition is not enough to convince any scientist that a particular hypothesis is true. In other words, the words "I believe in evolution" are meaningless. It's the bountiful evidence for evolution that has convinced every biologist that it is a fact. The greatest thing about the majority of scientists is also that they're willing to discard even their most beloved hypotheses in the wake of new evidence.

However, I think it is sometimes easy to get involved in personal rivalry over competing hypotheses. I have seen people at conferences very nearly yelling at each other and even heard stories about death threats! This is not appropriate conduct for anyone, let alone an educated scientist. In my opinion, you should never take a disagreement with your hypothesis (no matter how awesome!) personally. It's not an insult. It is on disagreement that scientific progress is built! Every time a reviewer or fellow conference attendee disagrees with me, I take time to remind myself that they are enabling science to move forward. After all, if each of us stuck with our respective hypotheses and worked only to find support for them, we would not know that the earth revolves around the sun or that the big bang really happened!

But how should we disagree with each other in a productive way? If someone disagrees with you, it is their responsibility to demonstrate convincingly that your hypothesis is not supported and not to call you names (the reverse is also true). Probably the best outlet for debate is in the scientific literature. Firstly, publication avoids name calling and death threats (usually!). It is important to avoid personal slurs in print. This does not reflect on the person you are refuting, only on you. It doesn't do anyone any good to gain a reputation as a whiner. But if you are scientific and careful in presenting your evidence, you will gain a reputation as a respectable scientist. Secondly, publication involves other scientists in the debate. Broadening your audience will always bring unexpected insight.

Most importantly, if it is demonstrated that your beloved hypothesis is not supported, you should discard it. There is no merit in clinging to debunked ideas. Of course, I think the VAST majority of us scientists find new hypotheses exhilarating and are therefore unlikely to marry any particular one. That's what I love about science!!!

Scientific Politics Part I

I thought I would write about a very touchy subject tonight! That topic is politics. What I include in the term politics are things like authorship, how to deal with disagreements, and what to publish and when (especially when someone disagrees with you or works on a similar or even the same topic). Of course, being a PhD candidate and not a seasoned professor, I am far from an expert but I have some opinions that may or may not be the same ones that others hold.

I'll start with the subject of authorship. Who should be included on your papers, in what order, and why? These are difficult questions, especially when you're a budding scientist. I definitely want to collaborate and share authorship with people that I admire. For me, it has always been a relatively easy process but I usually have a frank discussion with collaborators about who should be included and in what order. It might seem like a subject that is uncomfortable to talk about, especially if you're worried about upsetting someone. But I guarantee that it is less uncomfortable than having a disagreement when it comes time to submit a publication or even after the paper has been published.

It is important to determine what the contributions of individuals will be to the paper. In my opinion, all authors must make an intellectual contribution. Acceptable contributions usually include analyses, writing, or data collection (or all of the above). There are some cases, however, when it is unclear if someone should be included on the paper. For example, if an individual has given you advice or ideas, do you include them on the paper? I think this depends on the gravity of the advice. Did they simply suggest you use a particular analysis? I would not include this person as an author. Did they come up with the idea? I would include this person. Whenever you feel an individual's contribution might merit inclusion on the paper, you should always proceed by asking them if they wish to be. If they decline, then you've done your political duty and made sure that there will be no hurt feelings. If they say yes, the next step is to determine the order of authorship.

For me, author order has always been obvious. The person who writes the paper and does most of the analyses is first author, the person who did some of the analyses or contributed some data is second author and so on. But I have never been involved in a project with more than three or four authors. Once the number of authors starts to grow, I think an explicit agreement should be made prior to any paper submission. Don't leave the discussion until it is too late or until someone is put off. Ask them outright! "Shall I include you as second/third/fourth/fifth author?"

The situation is a bit different when it comes to your supervisor. Different supervisors have different policies when it comes to authorship. Some prefer to be included on all papers and others make this judgement on a case by case basis. Sometimes supervisors prefer to be included as the last author (this is sometimes reserved for the PI) while others are open to any position depending on their contribution. Regardless, when you move on to a new supervisor you should always ask! That way no one will have any excuse to be angry. You'll also avoid pissing off the person that controls your funding!

I have only heard of people having major problems with authorship. I can imagine there have been situations when someone originally agreed to contribute but then failed to uphold their obligation. This can be politically difficult if this person is an office or lab mate but especially if they are a seasoned professor or famous researcher. I can't offer solid advice on this front but if you have made every effort to elicit a contribution, I think you would be justified in excluding them. A well worded email or phone call is likely to smooth things over.

Unfortunately, graduate students are often afraid to have these conversations or exclude authors that haven't contributed. All I can say is that, you're not at the bottom of the ladder. If you're going to put the effort into a project then you should be satisfied with everyone's contribution.

Leaving Ottawa in Ten Days!

I'm officially leaving Ottawa in ten days to study at the University of Wyoming for 9 months! I recently received a Fulbright Scholarship (http://www.fulbright.ca/ if you're interested in applying) to study under Dr. Mark Clementz. I will be investigating isotopic signatures in the hard tissues of pronghorn (Antilocapra americana) from the USA and Canada. I have to say that I am excited.

I applied to Dr. Clementz' and Dr. Rybczynski's labs in 2010 to start a PhD program. It was a difficult decision but I decided to pursue my PhD at Carleton and the Canadian Museum of Nature with Dr. Rybczynski. Now that I have received the Fulbright scholarship it feels like I am getting the best of both worlds. So in a couple of weeks I will be saying a temporary goodbye to Ottawa and will be heading to Laramie, Wyoming.

Laramie is about 2 hours northwest of Denver, Colorado. According to Wikipedia, Laramie is home to only 31,000 people and the University of Wyoming has approximately 14,000 students. At the University of Wyoming I will have access to a stable isotope laboratory, which is something that Carleton does not have. I hope that the experience will broaden my skill set and, let's face it, get me some more publications!

Aside from research, Laramie is located near several national parks and there is ample opportunity for enjoying the great outdoors. There is even a nearby ski hill (although I can't speak for it's quality, yet). I have been missing snowboarding since moving to Ontario. Skiing in the west is significantly better than in the east and I refuse to lower my standards.

It will be a challenge to be away from Canada for so long. It is somewhat difficult to travel into or out of Laramie as the nearest international airport is in Denver. But I am up for the challenge and look forward to interacting with the students in Laramie!

My new blog is a work in progress

I am (as it says to the right) a current PhD candidate at Carleton University and the Canadian Museum of Nature in beautiful Ottawa, Canada. My dissertation is primarily focused on the effects of climate change on Cenozoic mammals (primarily hoofed mammals). I have traditionally worked in the areas of ungulate dietary morphology and tooth wear but over the last two years or maybe more, I have been dabbling in the areas of macroevolution and phylogenetics. I think my interests are generally broad but I have tended focus on morphology and its effects on macroevolutionary patterns. I'm also interested in the successful combination of fossil and extant animals in studies of both macroevolution and climate change. As with most PhD students, I have a long way to go and want to document the process of discovery!