Tag: PhD students

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3 years as a PhD student

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I arrived in Ireland October 2012 with the purpose of undertaking a PhD supervised by Natalie Cooper on Primates evolution. Looking back, the start of the whole endeavour seemed really stressful to me (new country, new customs, new language) and the project just as frightening (what do I do?, where do I start?, will I be able to do it?)… What happened after was way below my expectations: these three years were anything but stressful and frightening!
OK, even though not everything went smoothly and it had to take the best of the personalities (that are thankfully common sights in Trinity College’s Zoology Department) for dealing with some ups and downs, here is my top 5 list of personal thoughts that always improved the two aspects of my PhD: the working aspect (the research) and the “social” aspect (feeling relaxed and enjoying it).

Be ready to change your PhD

As I mentioned in the first line, my PhD was supposed to be on Primates evolution. In the end, the world “Primates” is mentioned only once (and that is, buried in a sentence about several other mammalian orders). Of course, sometimes the PhD is a Long Quiet River if everything goes well and you keep your highest interest in the original topic. However, sometimes it changes completely! And this should never be a problem! The PhD should be allowed to evolve just as much as yourself (or more pragmatically: your field) evolves into these three or four years.

Failure happens to everyone

Another major part about the PhD (and about the scientific endeavour itself!) is that it will fail. More or less often and more or less dramatically in each case but failure should just be part of the process. As a early career researcher, you can learn a lot from the mistakes and the success of others. However, I found that there is nothing much more personally instructing than the trial and error. I already mentioned how my biggest PhD disaster led to my most positive development.

Stay open-minded and curious

Writing the thesis or even just doing the lab/computer work for the PhD can narrow your mind and highly decrease your sanity. I found that the best way to avoid that was to try as much as possible to make the PhD only priority number two and put all the other things (seminars, meeting speakers, chatting/helping colleagues, etc…) before it. It has two advantages for the PhD: (1) you don’t work on it 24/7 and (2) everything you learn outside of it will actually be super useful for the PhD. In the Zoology Derpartment, we were only a couple of people doing macroevolution surrounded by ecologists. Yet, I think my work benefited heavily from the influence from these people.

Don’t rush

One thing I found nice with the PhD is that before you even start – before day one! – you already know the final deadline. OK, at day one, the handing in date seems far away (3 or 4 years away actually!) but that leaves you plenty of time for doing awesome research, writing it down as papers/chapters (and even trying to publish them before the deadline) and going to the pub or to other non-PhD recreational events…

Chat with your colleagues

Finally, I found that I gained so much just by chatting with my colleagues. And by colleagues I mean my fellow PhD students of course but also with the post-docs and the staff. I always found a long term benefit to both PhD aspects, whether it was talking about the latests video games during working time (I’m not only looking at you @yodacomplex) or having heated debates about species selection during coffee time.
I know much of these tips worked for me but might not apply to other people. In the end their is only one ultimate tip: make your PhD a hell of a good time!
Photo Credit: Thomas Guillerme
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The Skeleton in the Closet

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After a few ups and downs, everything you always wanted to know about the effect of missing data on recovering topology using a Total Evidence approach is now available online (Open Access)!

This paper also treats many different questions that people might be interested in (Bayesian vs. ML; how to compare tree topologies; comparing entire distributions, not only their means and variance; and many more!) but I’ll leave it to you to discover it…

Back on track, more than one an a half CPU centuries of calculation ago, Natalie and myself wanted to build a Total Evidence tip-dated primates tree. The Total Evidence method is the method that allows you to combine both living and fossil species (or actually, read “both molecular and morphological data”) into the same phylogenies. The tip-dating method, is an additional method that uses the age of the tips rather than the age of the nodes for dating such a tree. But I’m not going to talk about that in this post.

At the start of the project, we were both confident about the idea behind it and that primates would be the ideal group for such work since they are so well studied. A study that I described in a former post also came out around the same time, encouraging us and comforting us in this project.

However, as you might guess, something went wrong, horribly wrong! For the Total Evidence method, we need molecular data for living species (check) morphological data for fossils species (check) and also for living species (che… No, wait)! After looking at the available data, we quickly found out that there was a crucial lack of living taxa with available morphological data (check our preprint to be submitted to Biology Letters putting the actual numbers on the problem). From that problem, rose the idea of actually testing how that would influence our analysis. And funnily enough, this problem become one of the two major parts of my PhD!

Running thorough (and loooooong) simulations, we assessed the impact of missing data on topology when using a Total Evidence method. We looked at three parameters where data would be missing:

  1. The first one, was obviously the one I introduced above: the number of living taxa with no available morphological data (at all!).
  2. The second one, was the amount of available data in the fossil record (because yes, fossils can be a bit patchy).
  3. And the third one, the overall amount of morphological characters.

 

We then compared the effect of different levels of available data for each parameter individually and and their combination on recovering the correct topology, using both Maximum Likelihood and Bayesian Inference. For the correct topology, we used the tree that had no missing data in our simulations. For each parameter combination, we measured the clades in common between the correct topology and the trees with missing data as well as the placement of wild-card taxa (typically fossils jumping everywhere).

Unsurprisingly, we found that the number of living taxa with no available morphological data was the most important parameter for recovering a good topology. In fact, once you go past 50% living taxa with no morphological data, the two other parameters have no effect at all, even if you have a perfect or a really bad fossil record or many or really few characters. This is kind of intuitive when you think about it because the only way to branch the fossils to living taxa is to use the morphological data. Therefore, if there are no morphological data for the living taxa, the fossils cannot branch with them regardless of the quality of the data. Therefore, in this paper, we argue that to improve our topologies in Total Evidence, we should visit more Natural History museums. And not only the exciting fossil collections but the well curated collections of living species as well!

All the code for this paper is available on GitHub.

Check out the latest presentation about both papers.

Paper 1: Guillerme & Cooper 2015 – Effects of missing data on topological inference using a Total Evidence approach – Molecular Phylogenetic and Evolution (doi:10.1016/j.ympev.2015.08.023).

Paper 2 (preprint):  Guillerme & Cooper 2015 – Assessment of cladistic data availability for living mammals – bioRxiv (doi: http://dx.doi.org/10.1101/022970).

 

Author: Thomas Guillerme, guillert[at]tcd.ie, @TGuillerme

Photo credit: Thomas Guillerme (AMNH collections)

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A Day in the Life of a PhD Student

nine_to_fiveWe thought it might be interesting to share what the daily life of a PhD student actually looks like. So here are three perspectives on the average day.

Adam

A typical day for me begins between 8 and 9. I start out by checking my emails for correspondence and any interesting new papers that have been published. You typically have content alerts set up to send directly to your email account. As the blog administrator, I often upload new posts to our site in the morning.

I’ll usually be in the middle of composing a paper given that this is the main part of a PhD student’s work. This has three aspects to it, reading, writing and coding. I don’t adhere to a rigid timetable day by day, instead I’ll just pick one of the three that I’m interested in doing at the time.

I take a break at 11 and 1 where I talk to my friends about work as well as shooting the breeze. I work until 5 or 6 most days and if I begin to flag in the afternoon with doing research I’ll try my hand at writing a blog post. I share my office with four other people so the idea of the lonely academic is definitely not applicable in my case.

Thomas

Fortunately my day does not only consist of writing papers and analysing data! In fact I spend also a good amount of time doing rather chilled out stuff (such as drinking coffee, reading/writing sciency blogs, checking conferences or trendy papers on twitter or reading/writing emails). I also spend some nice hours chatting with my colleagues, whether it is at lunch break or in the office and whether it is about the last Hobbit movie or the simplest algorithm to match names in a phylogeny.

The “purely productive” aspects that can lead to a publications are actually constantly fed by the “less productive” ones (such as chatting around or reading stuff) and I’m always glad that these are not mutually exclusive parts of my day to day PhD life.

Deirdre

My typical day is very similar to those of Adam and Thomas above but, as my PhD is very empirically based I also have bursts of field, outdoor and lab based experiment days so, to be different, here is what a day in the field (doing freshwater work) for me is like:

Typically I get up sinfully early, pile on as many layers as I can and head out in the (hopefully preloaded) van for a long drive to the field site with my field buddy of the day.

We’d spend anything from 2- 4 hours at the different sites collecting algae and invertebrate samples from our cages, usually pausing for a slightly soggy cheese sandwich in the middle or to chat to curious a passer-by. On clear weather days this can be lovely and you see all sorts of beautiful country and wildlife but the rain makes everything take twice as long- especially when you need to see below the water surface. Not all bad though, on one of these rainy cold days our bedraggled selves were invited in for tea and scones to one of the lakeside houses. Then it’s a long drive back, trying to do some water filtering and sample sorting on the winding country roads. Usually, depending how late we get back, then there is the unloading of the van and lugging all of the samples to the cold room for storage.  Fieldwork is great fun though; it lets you see the country and bump into all kinds of creatures and characters.

Authors: Adam Kane, Thomas Guillerme, Deirdre McClean

Photo credit: http://www.blogmarketingacademy.com/which-is-more-secure-the-9-5-job-or-self-employment/

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Badgery Fieldwork

cuddle time

One of the best things about my PhD has got to be the fieldwork. My project involves analysing the GPS data of a population of badgers to find out where they forage, how big their territories are, who lives with whom and how they disperse. This means putting GPS collars on them twice a year. Badgers have a bit of a bad rep, one they really don’t deserve. Contrary to popular opinion they are not vicious beasts that, once clamped on to your foot, won’t let go until they hear the bones crack (people say this to me a lot). They are in fact quite timid and very cute with it! Continue reading “Badgery Fieldwork”

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Pathway to PhD: should I do a masters degree or an internship?

charlieWith deadlines looming for attractive PhD scholarships such as the Irish Research Council, current undergraduates often realise that the path to a PhD is somewhat opaque, with many different ways to get there.

Finding a PhD is something we have covered already, but a question I often get asked is: do I need a MSc or can I go straight in, or what about an internship?

There is nothing stopping you going straight into a PhD from your undergraduate degree, but it can be difficult to be competitive unless you have a flawless academic track record, or have been singled out by a supervisor as an ideal candidate and its pretty much your PhD from the start. More usually, whether you are applying for an open post that has been advertised, or your own funding through a scholarships scheme, you need to out-compete your peers. To do so requires some non-algorithmic compilation of your academic grades, degrees, and academic experiences. Opting for a taught MSc is one obvious way to lengthen your academic training on your CV, as well as hopefully improving on your track-record. Its also a useful way for you to highlight your new skills and explain how they will make you a better PhD student than the rest.

It is important to remember that simply listing your modules or new skills in bullet-points is not the way to do this. You need to elaborate, and explain how your modules improved you as an academic, and how you interacted with the course to better yourself. Don’t just say “I took a course on linear mixed effects modelling”, tell us about how you realise now that this tool is important in ecology as a hierarchical data structure is a very common feature of research in this domain, and that you can now tease apart effects that manifest within and among groups. Give an example of how you applied this tool to answer an ecological question. The MSc projects are typically larger than your undergraduate ones, and ideally you would conduct a novel enough piece of research to allow you to write it up as a research paper – this is a great way to rubber-stamp your CV for PhD applications.

Of course, MSc courses tend to cost money, and last up to one year (or some are even two years these days). Another option is to volunteer as an intern in a research group. With the right match to your supervisor, and a bit of luck, this approach can be just as good as a MSc or even better  (at least in my opinion). You might intern as a research assistant helping to run experiments or collect field data for on-going projects. Such teams are often in need of extra hands, and being involved can mean you learn lots of new skills and techniques. Ideally though you want to make sure you are involved enough, and have the chance to put enough academic input to the project to deserve and be rewarded with authorship on a research paper.

Alternatively, you might intern more as an individual in a group, and work on your own project much like doing a MSc project but without the actual degree. Again, you are looking to develop new skills, learn new techniques and apply them to ecologically or evolutionarily relevant questions. The not guaranteed, and by no means necessary, icing on the cake would be a research publication.

Ultimately, some post-graduate experience will really help your CV when applying for PhDs but only if you can articulate how your efforts have improved you as an academic. A research paper (or several!) would be the ideal outcome from whatever path you take as it is nearly indisputable evidence of your ability to do science as part of a team, to a high standard and to convey your findings to an audience.

I took a research assistant position after my undergraduate degree, and used that to explain how the overall experience had convinced me of my desire to pursue academic research, as well as providing me with new skills. I am therefore quite keen on the idea of internships or research assistant positions in place of the more formal and structured MSc courses, so it’s rather a personal thing for me. Take some advice from others though, as maybe the MSc route carries more weight for different people.

Author: Andrew Jackson @yodacomplex

http://www.tcd.ie/Zoology/research/research/theoretical/andrewjackson.php

Photo credit: http://www.quickmeme.com/Condescending-Wonka/page/1826/

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Career planning for PhD students

6a00d8341c761a53ef0120a6330c87970b-piThe Royal Society has published a new set of guidelines for managing the career expectations of PhD students in STEMM subjects (science, engineering, technology, maths and medicine). The publication was the result of a series of roundtable discussions held at the Royal Society with PhD students, supervisory teams and University careers professionals.

This blog post from the British Ecological Society provides a good overview of the document and discussion of how it fits into existing career development opportunities for PhD students.

With ever increasing numbers of PhD graduates and restricted academic jobs, academic careers are becoming the exception rather than the rule in many STEMM disciplines. The report highlights the need for PhD students to be realistic about their career expectations and goals and the importance of continuous professional development during their studies.

The document contains guidelines and recommendations for students, supervisors, career professionals and higher education institutions. It’s very encouraging to see that the training and mentoring of ecology and evolutionary graduate students at TCD already follows many of the principles.

This is mainly due to the success of NERD club, our weekly meeting of ecology and evolution researchers. The primary purpose of this group is to develop research projects and encourage new collaborations but many sessions are also devoted to career development. We have discussed academic careers advice and application tips but also non-academic careers and the transferrable skills such as public communication and teaching that can be applied to any career choice.  As students, we’re very lucky to benefit from the mentoring and advice of enthusiastic and dedicated staff members.

One aspect of the Royal Society guidelines which I hadn’t considered previously is the recommendation that PhD students should seek a mentor who is not their supervisor for career advice. It’s an interesting suggestion, especially since many supervisors have limited personal experience of non-academic careers, and a good thing to consider for any PhD student.

Hopefully these new guidelines will encourage more students, supervisors and institutions to make broad career planning an integral part of every PhD student’s experience.

Author: Sive Finlay, @SiveFinlay

Photo credit: http://sironaconsulting.com/2009/10/29/my-top-10-funny-job-interview-cartoons/

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‘By live voice’ – how to plan for and get through your viva

VE Day

“Make big plans; aim high in hope and work, remembering that a noble, logical diagram once recorded will not die, but long after we are gone be a living thing, asserting itself with ever-growing insistence.” Daniel Burnham

The viva or thesis defence is a daunting obstacle. It’s built up so much that you feel as if your previous three years of work hinge on how you perform for one morning/afternoon. Despite all the reassurances I was offered I was hugely nervous before it. That said, some of the advice I received meant I wasn’t flying blind and could anticipate some of the questions.

It really is a help to have had some of your chapters published. It means two or three other academics have evaluated your ideas and thought them good enough for publication. This is not to say your examiners will ignore these parts, but remember they’re making sure you could perform as an academic and this is strong proof that you could.

Before the day, make a copy of the thesis you submitted and bring it with you to the viva. Have the pages with your figures on it highlighted. These sections are typically big discussion points because they capture the essence of your results. Read over it a couple of days beforehand too, but not the day before, keep that as a buffer to relax.

In terms of structure, the viva panel consists of an external examiner, an internal examiner and the chair. The extern is someone in your field but outside of your university. It is typically stipulated that they cannot have published with you or your supervisor so as to avoid bias. The intern comes from your department and has some knowledge of your field and again has not published with you. The extern takes the lead in asking the questions. The chair is there to make sure everyone keeps a civil tongue in their mouths and the whole event comes to a close after a reasonable time. A typical viva will last three hours.

The aim of the viva is to ensure you are capable of functioning as an academic, I’ve heard it being described as the ‘gateway into the scholarly community’. The expectation is firstly, that the work is mostly your own and secondly, that you have an appreciation of where your thesis fits in with the field at large. This means the questions you’re asked come at two levels, the specific and the general. You are the author so you’re best placed to know the specifics. If you have been helped with some aspect, such as the statistics, make sure you’ve an understanding of why it was done. The general questions are posed to test that you’re widely read in the area. So one question I had was ‘If I could ask God any question about vulture biology what would it be?’The tone of the viva should one of a scholarly discussion. Your examiners are not there to chew you up and spit you out again.

Recognise that your thesis is not the final word on the subject, admit to its shortcomings, and realise it could be improved upon. You can engage in civil debate if there’s a point of difference but don’t get argumentative. You may be asked, in hindsight what would you have done differently?

A good thesis supervisor will know that your work is good enough to get you through a viva with relative ease. Any significant problems will likely have been flagged well in advance. So despite all of your fears coming up to it, you’ll know you’re good enough to walk through those scholarly gates.

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This post drew on my own experience and the advice offered by the presenters of the BES Webinar ‘Surviving the viva’.

Author: Adam Kane, @P1zPalu, kanead[at]tcd.ie

Photo credit: dailymail.co.uk

 

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Demonstrating: getting the most out of undergraduate teaching

demonstratingOne of the benefits of doing research in an academic institution is the opportunity to interact with undergraduate students. Students benefit from being taught by leading researchers while staff have the opportunity to inspire the next generation of scientists. Practical lab classes are usually a focal point of this direct interaction between student and researcher. However, due to the logistics and practicalities of managing large class sizes, PhD students are playing an increasingly important role as teaching assistants or lab demonstrators. In one of our recent NERD club sessions, Jane Stout led an interesting discussion about the importance of practical classes, the role of postgraduate students and best practice for what makes a good demonstrator. Here’s a compilation of our thoughts.

Why do we teach undergraduate practical classes?

Lab practicals can be expensive, time consuming and difficult to manage so why bother including them in the undergraduate curriculum? We think that the main reasons are to engage students in the subject and to teach them how to become scientists. Every student has a different learning style and practical classes can help to address this issue. For many people, sitting in a large lecture theatre can be a rather passive and ineffective learning experience. Practical classes offer an opportunity for active learning and hands on experience. Students can deepen their understanding of a topic and go beyond lecture content to form their own questions. They also learn the skills and techniques necessary for future employment, whether that is in a research environment or not. From the lecturer’s point of view, practical classes are useful opportunities to interact with students and to assess their level of understanding.

Why demonstrate? What are the benefits for a postgraduate student?

Large practical classes would not be possible without a team of demonstrators, so lecturers rely on their help. But there are also many benefits for postgraduate students. Demonstrating is excellent teaching experience and a good way to improve your own understanding of a subject. Demonstrators learn how to explain concepts to non-specialists and how to handle large groups of people; essential skills for any career. Challenging and unexpected questions from students also teach you to think on your feet (I’m a zoologist but at various stages I have feigned expertise in biochemistry, plant sciences and microbiology). It’s all too easy for postgraduates to get stuck in a very narrow focus of their particular research area but demonstrating is a great way to broaden and develop your skills. Furthermore, if you’re stuck on a particular research problem, demonstrating can be a fun and rewarding moral boost: you may be stuck in your project but at least you know enough to help somebody else! Overall, demonstrating is fun, rewarding and a good skills/CV boost. The pay isn’t bad either…

Why do we need postgraduate demonstrators? What are the benefits for undergraduate students?

Demonstrators bridge the gap between undergraduates and lecturers. Postgrads are less intimidating than lecturers and direct interactions with demonstrators can help students to feel more involved in a class. Interacting with demonstrators also gives undergrads an insight into what it’s like to work in research and academia. Chatting to your demonstrator helps to put a human face on science and to break down the mystiques of academia. We all agreed that it’s important to remind undergraduates that demonstrators (and lecturers) are not just teachers: they are the ones doing the research that ends up in the text books.

What makes a good demonstrator?
We’ve all had good (and not so good) demonstrators so what are the characteristics that one should try to develop? The two most important things are preparation and enthusiasm. Demonstrating is a professional commitment so it should be treated as such.  Make sure to read the manual beforehand, understand what you are teaching and be prepared for students’ questions. The best way to keep a class engaged and interested is to show some of those qualities yourself.  Be approachable, friendly and willing to help. It’s important to be confident in your explanations and behaviour but also don’t be afraid to say “I don’t know” swiftly followed by “but I can find out” or “this is how you can find out”. Try to explain concepts without too much jargon but don’t patronise by over-simplifying.

Combining all of the advice and pointers from above, here’s our best practice guide on how to be a good demonstrator.

  1. Be cheerful and positive, not grumpy and negative: there’s always something that can be taken from any practical session no matter how boring it may appear.
  2. Encourage students to work as a group and to help each other.
  3. Ask questions and be proactive: don’t just wait for students to come to you with their problems, engage them in discussions instead.
  4. Try to pre-empt common problems and mistakes but don’t just give students the answer: explain things in a clear and logical way and talk students through the steps they need to get to an answer.
  5. Be fair: give an equal amount of attention and help to all students on your bench, not just the ones who ask the most questions.
  6. Be patient and empathetic. You may get frustrated explaining the same concept for the umpteenth time but try to remember what it was like when you were a novice yourself. Pass on any tips or skills that helped you to learn a particularly tricky concept.
  7. Interact with other demonstrators and provide constructive feedback to lecturers.
  8. Be inspirational! Remember that you are an ambassador for your subject and undergrads will look to you to see what life is like as a researcher. You should be an enthusiastic and positive representative for your subject and inspire the researchers of tomorrow!

Author: Sive Finlay, @SiveFinlay

Photo credit: http://www.w5coaching.com/meet-john-nieuwenburg/

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PhD – Positive, Happy, Developments

RightOrWrong1921

When wrong is right part 2

This post follows on directly from my previous discussion of my PhD going wrong. As a brief summary of the previous episode: I ran time consuming simulations that took me around 6 month to design and another 6 months to run. The simulation failed in the end because of a bug in some of the software I was using. Therefore, I had to run them all over again!  That took me one day (at least to relaunch it, the simulations are actually still running). In this post I’d like to focus on the importance of starting to enforce good habits in using computers from the start of your PhD, whether you’re doing bioinformatics or field ecology.

Coding facilitates life. A lot. If I could only offer two tricks to remember they would be:

–Writing function-based scripts: which involves isolating functions (the bits that are actually doing stuff) from scripts in order to be able to reuse/modify them easily for further/new analysis.

–Using version control: which involves saving your work as you modify it and keeping a good track of the history so that when something goes wrong you know exactly which one was the last version that worked and which is the version that bugs.

There are loads of other good tips and many excellent blogs about how to start good coding habits (for example, this one or that one) so I am not going to develop the point here.

I’ll just try to make the point by using a philosophical-historical-dodgy example that convinced me to start coding. Coding is like using a printing press vs. a pencil to write a sentence: I can write this sentence of 71 characters in approximately 16 seconds. And that is, with a pencil. If I had to use a printing press, it would take me one second to input each character in the press (assuming I trained a lot) plus one seconds for actually pressing the sentence. So that’s 16 seconds with a pencil and 72 seconds using the printing press (4.5 times longer). If you’re not that old-school, you will use a computer to analyse your data and what often happens is that it will take you less time to do things “by hand” (e.g. modifying column names, removing rows with NAs, etc…) than to write fancy functions. So why bother?

Well it’s the same as using the printing press, if you just want to write the sentence once, then, sure, don’t bother, but if you need to write it 10 times? The writing would take 160 seconds and the printing takes only 81! Also you’re likely to make typos when copying the sentence with a pencil, but you won’t make any with the press!

And the same applies to your computer analysis. If you’re removing columns with NAs “by hand” it will probably take you less time than writing a function. But what if you have more tables? How can you be sure you didn’t miss any? And on the plus side, if you write function-based scripts, chances are that you already have a function that does remove the columns with NAs from a former analysis.

To follow up with my previous post, applied, to me, this happened to be a salvation! Because I spent 6 months trying to apply bioinformatics good practice, it only took me one day to relaunch the whole analysis! I just had to change the name of the version of the software that was bugged and press enter…

            The process of doing actual science (i.e. from coming up with an interesting idea to submitting the paper) is not a continuous and straight process and it can drastically change at every step and is more about trial and error than about succeeding straight off.

Author: Thomas Guillerme, guillert[at]tcd.ie, @TGuillerme

Photo credit: wikimedia commons