Of Big Meetings and Me

As I am clearly entering the last four months before giving in my Ph.D. thesis …
I crawl under an unprecedented amount of data and possible projects to put into papers. BUT, the summer 2016 was the perfect timing to present my recent findings at international conferences and I chose to attend The Ecological Society of America Annual Meeting in Fort Lauderdale (ESA2016).

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Here I give you my advices when attending such big meetings:

  • Field trips are awesome especially when you get to see alligators


  • Arrive early to follow a workshop or organize one 

This year I was contacted by a fellow R instructor to help teach a workshop on How to build functions in R. It was a great experience and I definitely want to organize one myself in the future.


  • Get involved as a volunteer

It was a great way to get involved and meet people from outside my specific field of research but I recommend making sure that you don’t miss a key session because of your involvement.

  • Contribute to a section

This year I got involved in the Open Science Section. Since the beginning of my Ph.D., my director Steve Kembel has emphasized the importance of Open Science in our lab. We have published our first two papers in Open Access journal, with links to the data, metadata and code. I believe that making your science available improves its quality and holds you accountable to your work. “Open science is a no-barrier approach to scientific research.”


  • Choose well your talk’s session

This year I was ambivalent between emphasizing the plant or microbial ecology parts of my talk. I ended up choosing to put the microbial ecology forward put after the meeting I reflected on it and decides I should have gone with plant ecology because the talks in this section were much more attended…

  • Be bold, don’t be scared to ask questions, meet people and introduce yourself

Next year’s meeting is in Portland, and I definitely hope to be there!


Pursuing a Ph.D. is a privilege and a test of character


Yesterday I was reading a blog post on the “unspoken dark side” of getting a Ph.D. In the article, the author shared his struggle during his post-graduate studies and described how academia is a hotspot for depression and poor mental health (based on scientific surveys).

I fully agree that getting a Ph.D. (or a Master) can carry you down a road filled with tests and pitfalls. Indeed, the possible issues during post-graduate studies are numerous:

  • Unsupportive/absent adviser
  • Minimal/absent social interactions at work
  • Uncertainty about the future
  • Daily/frequent/obnoxious (self-)doubt
  • Roller-coaster productivity/motivation
  • Academic experience falling short of expectations

I did see people not enjoying post-graduate studies and I did experiment first hand some of the above. Indeed, my jaw blocked shut because I processed my stress grinding my teeth in my sleep. Pursuing post-graduate studies is definitely a test of how you address being stressed. However, I don’t think we should “accept depression as part of the course” and I disagree with saying that there is a psychological cost to a Ph.D. You might as well just say there is a psychological cost to life; depression, isolation or struggle is not reserved to highly trained brainy isolated Ph.D. candidates. You might lose someone close to you; fall ill to some terrible sickness; or just stop seeing the light in a perfectly balanced life. Such is the faith of humans, the brain equilibrium is probably our greatest Achilles’ heel.

I can’t speak for all domains, but I thought we were forgetting a massive thing here:

Having the possibility of pursuing a Ph.D. degree is a great PRIVILEGE one should acknowledge and celebrate.

Featured image

Art created by vinaquero@gmail.com, https://www.instagram.com/vinaquero/.

What should you celebrate?

  • Work in a field or on a subject that you chose
  • Realize yourself through your work
  • Keep learning
  • Make your own schedule
  • Be in contact with curious, educated, informed human beings
  • Have the opportunity to travel and meet people around the world
  • Have an easy access to further training
  • Make a contribution to society, as tinny as it might be
  • Be paid for all the above (at least in Biology)

As I enter the last part of my post-graduate training, I realize the luck (which I also earned through hard work and discipline #earnednotgiven) I had in the last three years and how I enjoyed it. I also plan to keep remembering this every day until the defense, through good and bad days.

Here is what I am grateful for:

  • A great adviser and co-adviser that complement each other well.
  • An outstanding support system, both at home and with my family and friends.
  • A research center that provides priceless professional services.
  • Healthy finances.
  • Loving what I do: learning, research, analyses, coding, teaching, EVERYTHING!
  • Being disciplined with a flexible schedule.
  • Sleeping easily, always.

You’re starting a Ph.D.? Here are some advices.

Yes, sometimes I shiver contemplating all the uncertainty my future holds. But then I remember the vastness of opportunity tomorrow offers me and I fill electrified and thrilled.

Do you?


I love to listen to elders. Their wisdom, their experience, and the differences between their life and ours; they always initiate a rich reflection in me. Things inside and outside of Science have changed so much for the last 100 years and most of us aren’t able to grasp the implications of these changes.

Not so long ago, I had the pleasure to listen to a great conference by a seasoned researcher that shaped and transformed the field of plant ecology. He started to teach and do research at a time where there were no computers, when reviewing articles was done by hand on paper and transmitted by post.


He told us about the time when you took your time to write a manuscript, a time when you would spend your Friday afternoon reading the last interesting paper in your field of research (and didn’t have to pick between 500 hundreds). A time when you could still disconnect from anything when you were in vacation. A time when publishing was at a much more slow pace.

Then he switched to talking about the challenges of Science with the new technologies:

  • The amount of papers being published every year;
  • Trying to keep track of the interesting papers published in your domain;
  • The difficulty of publishing with the increased competition from other countries;
  • The struggle of Journals to select which papers should be published;
  • The issues to find good (and fair) reviewers;
  • The closed (capitalist) access to Science;
  • The limits and burdens of social presence online (blogs, twitter, etc.);
  • Etc.

And then the conference switched from “mighty interesting” to “monumentally depressing”.

I acknowledge the actual limits and pitfalls of Science and the publication system. I know the challenges that await someone that wants to do research in a world where funding comes with profit (especially for the last years in Canada). However, if I only focus on the challenges and the issues that I’ll have to tackle, I might as well stay in bed every morning and never get up.

Yes it will be harder; yes it will require more work. But I won’t be discouraged by the negativity of an elder not able to adapt to a fast changing system. And someone who didn’t achieve his dream job or is frustrated by the challenges encountered along the way won’t dishearten me either.

The key resides in being more strategic and knowing yourself. The first question my supervisor asked me when I started my Ph.D. was: “What do you want to do after your Ph.D.?” After identifying everything I had to do to put the odds in my favor, I have worked (and I am still working) on every aspect of our strategy:

  • I tweet, professionally.
  • I write a blog, occasionally, to practice my writing.
  • I have a personal web site to be present online when a future employer looks for it.
  • I am present on LinkedIn, on Research Gate, and I have a profile on Google scholar.
  • And I work hard to produce good papers.

But I won’t stop to love what I do because it is harder then yesterday.

I’ll try to remember that when I’ll be older and when I’ll get scared of the challenges of the youth.


Writing about my Ph.D. experience, I can’t leave by my horrible great story with scholarship demands. Each September, I go through the same loop: I write not really effectively the never-ending list of documents needed to apply for scholarships. Scholarships from my University. From Companies. From banks. From the provincial and federal govern. And this is how I felt when waiting for answers at the beginning of my Ph.D.:


Pulling together a great scholarship application is tricky. You need to hit the buzzwords real quick and be solid at all levels. Here are the fields you will usually be judged on:

  • Past grades as an undergraduate or master student
  • Research aptitudes and experiences
  • Project quality (scientific and economical)
  • Social implication, leadership and communication abilities

I applied many times to multiple scholarships and “YES” didn’t come too often my way. Every time I got a “NO”, I felt really disappointed and disgusted at the amount of work put in for nothing.


Time passed. I published a paper. I got more experiences in research and gave plenty of talks everywhere. And then one day, it started raining scholarships on me. Thus, here are my advices on how to vanquish Sauron the scholarship committees:

First, identify clearly what are the points you’ll be judged on for each scholarships.

For your grades:

  • I wish I could go back in the past and make myself work harder to get better grades but since this is not possible… yet… if you are still getting grades, make it count!

For your research aptitudes and experiences:

  • You already know this one: try to publish papers. No surprise here…
  • Get involved in many small research projects with your director or fellow students.
  • Offer to give a hand on ongoing projects so that you can learn from this and add it to your curriculum.
  • If you can be the manager of a small intern team during sampling season, this adds definitely to your attractiveness!

For your project:

  • Sadly, these days, scholarships goes with profit, for someone, somewhere. So identify the economical attractiveness of your project and make sure that you make it pop.
  • Make it short, clear, and sound.
  • Identify clearly WHY someone should study that. If you are not able to sell your project and make it sexy, you ain’t trying hard enough.

For your social implication:

  • Get involved in organizations around you. The key here is to find the right amount of time to give. Give too much and it will lessen the energy you’ll have to give on your project.
  • Offer to give conferences at citizen meetings or in schools. This will make you practice your synthesis skills and will improve your quality as a speaker.
  • Use any opportunity to give talks at national or international meetings close-by.

For all your application:

  • Find yourself a good friend (from outside your field of research), that knows you well, and go through your application together. This person will help you proofread your text and can tell you if your project is clear. This person will also be key to add activities or experiences to your curriculum that you could have forgotten.

Armed with all these advices, you can now feel like that when sending your application next fall. Good luck!


The Eleven Commandments of Conference and Stress Management


As the conference season is coming or has already started for Ph.D. students, stress management and slide preparation invade our schedule. So here I give you my best advices for lessening your stress level and achieving the best version possible of your presentation.

  1. PRACTICE: Practice before, and if possible, practice in front of an audience that cares so they can give you feedback. You will be more confident after your test run and the quality of your presentation will be improved by their comments.
  1. RHYTHM: (This one is especially important if you have a dense presentation) Insert a rhythm breaker into your presentation to refocus and recuperate the attention of people that could have gotten lost along the way.
  1. NINJA SLIDES: Imagine what could be the questions someone could ask you and prepare “ninja slides” at the end of your slideshow to support your answer. This will impress your audience and make you look prepared and professional.
  1. AUDIENCE: Know your audience and personalize your presentation to fit their requirements. You will increase your success by hitting the buzzword they want to hear and avoiding spending a lot of time explaining things they know a lot about.
  1. GRAPHS: If you show a graph in your conference, make sure to take the time to explain it’s meaning, the axes and the statistics used. If you don’t plan to explain it don’t show it.
  1. TEXT: Please, you are giving a presentation; not making your audience read your thesis on a big screen. AVOID big sentences, use key words and phrase out loud the theory rather than loading your slides with long pieces of text. Nobody reads them.
  1. WATER: Have a bottle of water with you so you can stop and take a sip. It will give your audience a break and help you to pace yourself.
  1. BREATH: Before the presentation: steady your breath, inspire slowly and keep calm. The first words are always harder, then your voice will steady and you just need to make sure that you will keep breathing!
  1. AAAAAaaaa: Don’t put an “aaaaaaa” sound at each pause between your sentences. It is the most annoying thing in a presentation and shows your lack of control. Just take the time to shape a full sentence and think before talking.
  1. EYE CONTACT: Make sure to make eye contact with your audience, you will be able to see if they are following you or if they are lost and you need to spend more time explaining something. You also engage more with the audience and they are more drawn to your presentation by your energy.
  1. ACCENT: For those of us that don’t speak English as a first language, remember that your accent can get in the way of your presentation and that you need to ARTICULATE and talk SLOWER. It’s already hard to keep focused on a long day of conferences, if your audience can’t understand what you are saying it’s over.

I hope this can be useful to you. What are your advices to give the best presentation?

Making the Best of a Three Months Internship in the West Coast

2015 started with a professional challenge for me: I was to do a three-months international internship at UC Davis, in Jonathan Eisen’s lab (https://phylogenomics.wordpress.com/). I found the Eisen lab extremely interesting because of their presence on social media and the variety of their projects. Most of their lab members are twitting, writing blogs, creating awesome scientific board games (http://microbe.net/gutcheck/) and they have many outreach and citizen science projects. As I remember leaving Montreal, I was excited but also stressed for the coming change of routine and environment. BUT with challenges come improvement.

As I aim to be present in the science world for a long time, I am highly conscious that great Science come from collaboration, not only from single researchers doing their own thing. Thus, I planned to take advantage of advance researchers experience and I contacted many different professors related to my field. On my list were:


OSU, Oregon:

Thomas Sharpton (http://lab.sharpton.org/)

U. Of Oregon, Oregon:

Jessica Green (http://pages.uoregon.edu/green/)

Brendan Bohannan (http://pages.uoregon.edu/bohannanlab/)

UC Berkeley, California:

Steve Lindow (http://icelab.berkeley.edu/lindow-lab-1)

Paul Fine https://ib.berkeley.edu/labs/fine/Site/home.html)

David Ackerly (http://www.ackerlylab.org/)

Ellen Sims (https://ib.berkeley.edu/people/faculty/simmse)

UC Davis, California

Johan Leveau (http://plantpathology.ucdavis.edu/faculty/Leveau_Johan_HJ/)

Jonathan Eisen (https://phylogenomics.wordpress.com/)

UBC Okanagan Campus, British Colombia

John Klironomos (http://johnklironomos.com/)

This also meant that I would have to cover a lot of ground in a short time. However, the encounters with the PIs and their lab compensated greatly for the traveling length. Meeting great and welcoming human beings all over the west coast of USA and Canada that also happen to do research greatly motivated and inspired me to continue doing my best in my field. There are some crazy inspiring projects out there! It was also reassuring to see that the challenges are mostly the same in every lab, especially when working with Next-Generation Sequencing.

Another of my goals was to help teach two workshops, one given by Titus Brown (http://ged.msu.edu/) at UC Davis on mRNA (http://dib-training.readthedocs.org/en/pub/2015-03-04-mRNAseq-semimodel.html) and a Software Carpentry (http://software-carpentry.org/index.html) workshop at U. of Arkansas. These two workshops were great in the sense that teaching boosted my energy and I got great feedback from our attendees. From the RNA workshop I learned a lot; widened my horizon of knowledge and at the same time met the great Titus Brown while broadcasting my skills (http://ivory.idyll.org/blog/2015-a-first-workshop.html). The great people of Rkansas were absolutely amazing, welcoming and most importantly, truly interested.

So this concludes three months of international internship, visits, workshops, meetings, but more importantly three months of growing my network and creating connections with great people all along the west coast.

I would advise any Ph.D. student to take advantage of the scholarships provided by their University (if there are some) to mix traveling and Science.

The Eternal Generalist/Specialist Dilemma

Often I feel torn between being even better at what I am already good at (which is so fun!) and achieving more at all the other (scary) skills. It seems to be a long lasting struggle for all workers across all spheres:

when developing skills in our domain, is it better to diversify our spectrum of knowledge or should we become eminent experts in one area?



The advantages of being highly competent at a single skill might be tremendous in the short term. However, this strategy is also extremely risky, as specialists thrive only when the conditions are perfect. The specialist must choose wisely the ability at which he becomes an expert because if it were to be unnecessary tomorrow, he might lose all the hard work he has done. However, if the choice is right, the specialist could become a crucial asset for any employer, therefore increasing exponentially the possibility of employment.


UnknownOn the other end, diversifying our domains of skills is expensive in time, energy and in memory space (if only we could have more than one brain…). The generalist might always feel like he needs to improve at all levels, that he is not THE best at anything. However, the generalist becomes highly independent, needing only inputs from experts once in a while, and he is never “out of the game” when the conditions change. In the long term, being a generalist is safer since he will always have a base to build on.


Optimus-Prime-optimus-prime-15529314-488-710-2To be the go-to person in at least one skill/domain in your field is necessary. This way you become essential to this area, contributing significantly to the work being done. In a curriculum, showing outstanding specific skills is the most appealing part for employers. However, these specialist skills must not be achieved at the expenses of a well-rounded background. The autonomy and resourcefulness of a generalist are essential to be successful in the long-term, especially in Science. If you aim for the best compromise long-term/short term, you should try to get the best of both worlds. I never said it would be easy, though.

My strategy is therefore spread in two guidelines:

  • Pick a few tactical skills, that should be in high demand in the next years, in which to become as much as an expert as I can.
  • Make sure that I am knowledgeable or at least introduced to for all other domains/skills/areas that could be of interest in my work.

Here are some of my specialist vs. generalist skills:






Vegetal Ecology

Vegetal Physiology

Predictive Models

Plant-microbe interactions


I’ll tell you in 30 years if it worked!

My Actualized Version of Stearns & Huey 1987 : Some modest advices to graduate students

Be strategic


Think about the next 2 years (master) or 4 years (Ph.D.) but also about the aftermath of your graduate studies. What do you want to do after, and at what rhythm? Where do you want to work? What motivates you in life? When you have the answers (or an idea) for all these questions (and it should be in the first month of your studies), play your cards well to get to your life objective. What do you need to do to achieve your goal? Does your director know your goal? Is he acting for you to get it? What can he do to help you? Always be strategic about any training, collaboration and project you set so that when you finish your studies, you will have a full set of arms to shoot for your dream job and life. No regrets.

Learn other languages


If you don’t already speak, read and write in english, get to it soon. You are already late. You’ll go nowhere if you keep using translators to read papers or to write your own manuscript. On the other hand, if you speak only English, know that people that learn many languages stimulate constantly their brain and create patterns of thinking and synapse routes that improve their cognitive efficiency plus help them to keep a healthy memory longer. Thus, get your lazy brain working and learn another language. It will enrich your personality and open your mind.

Select your director(s) carefully


It might be easier to find a director that already has a busy-well-crowded student group. Although some advantages might come of the knowledge and support you can get from colleague students, your director will be really busy and won’t take you by the hand through all steps and challenges. If you are the independent type, this can fit perfectly with you, but if you are rather the dependent type, go with a director that has a smaller group or is beginning he’s professor assignment, for he will be much more present along the way to give you good advices and support you through challenges.

Know when to ask for help


It is always good to solve problems by yourself, or at least try to work the first steps towards a solution. However, if it’s been more than 2 weeks that you are stuck and you feel depress, tired, you want to quit your studies, please ask for help either directly to your adviser or to a supportive post-doc or university professor. Pride and stubbornness will only bring you to exhaustion and will impede you to advance your project. Don’t be scared to look stupid by asking questions, to lose one month over something you could have solved in one week with help makes you look foolish and immature.

E-mails = Short


If you want your message to get through to a busy colleague, don’t write a novel. Go straight to the point. If you have more than one question, consider if a meeting is needed, and if not, make sure to organize your text into paragraph/idea to facilitate your correspondent’s life.

Use your fellow students


The people that are already working in the lab when you arrive are full of knowledge and advices that will definitely be useful to you. You shall treat them well so they will want to support you when time will come. If they look focused or angry with their computer, don’t bother asking now. You should either wait when they get up to do something or ask them to tell you when they would have time for you. In the lab, if you get support from a colleague, you should try to give them a similar favor, for them to see the advantage of having helped you and increase their willingness to support you in the future. Remember, your lab is your home for the next years, so your lab buddies are your family and resources.

Use, acquire & conquer


If your center offers resources to students, make sure to use them to learn more and get more independent with your project every time. Take notes, ask questions, and inquire so that afterward you will be a resourceful researcher. The more useful you are as a colleague the more you will be included in projects and the more you could publish.

Have a healthy life


Make sure to move during your work day, take an activity brake every hour for ten minutes if you can, so that the toxin that accumulate in your body and in your brain get washed away and you can regain focus and energy. Eat well and often (small portions). Your brain needs good protein, stable sugar flow, vitamins, minerals, enzymes and A LOT OF WATER. Sleep as well as you can and try to establish a working routine so that you work and rest enough throughout the week. Find your equilibrium and use it to your advantage.

Organize your day


Find the period in the day during which your brain works to its fullest strength. Then, always plan your brainy tasks to be done at that moment and keep other less cerebral tasks for other moments when you feel more tired. You will feel that your days are more productive and easier to go through because you won’t be fighting all the time to get the job done. Sometimes it will be impossible and you will have to force yourself but the increased energy you will get from this strategic schedule will translate in all spheres of your life.

Do what you love & love what you do


If you feel unhappy about your work, if every morning feels like the hardest day of your life and you struggle to go through it without smile and laughter, then you might consider changing your study path. You have just one life, and though I almost never leave a project incomplete, sometimes if you made a mistake in your life choices, you better fix it soon than too late. Make sure you know yourself well enough to know what you don’t want to do and focus on what intrigues and inspires you, whatever it is.



You should always read papers in your domain, but also of satellites domains to keep in touch with what is being done and what is trendy now. Create a work method that will work for you so that you can take notes whenever reading a paper. A good notes document could be the best thing to have when starting to write. Since writing is something you should do quite often, to already have a bank of insightful notes will give your work a strong baseline.