Tag: academia

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Public service announcement: How not to email a professor

Mr.rudeface

Quite regularly you get emails that annoy you… often they are flippant emails, and sometimes from students. Harmless or probably naïve that they are, they do get up some peoples’ noses.

But every once in a while you get one that really gets your goat. Several months after some media coverage of a research paper from my group (as it happens one of my favourite papers I’ve been involved with of all time) I got a real gem of an email.

“Woah!!! Who the F*%K is this guy and why is a CEO of an internet security company sticking his nose into what at this stage is an old press release for a research paper?” was my first impression. This guy just doesn’t get it was what I settled on in the end… but here is what played out.

Turns out Luke Latham has published 4 research papers with a modelling angle. He seems to have a bee in his bonnet though. He also has a knack for writing a totally rude and irritating email that only incited me to reply mirroring his rudeness – a subtlety of irony apparently lost on him. I have posted all the emails, along with some pointers as to how he managed to stuff up a perfectly reasonable email in the first instance. In the end I ignored this for my own sanity, and only now got around to writing up this blog post without getting too annoyed. My advice on how not to write like a [insert derogatory word of your choice] is in italics.

The icing on the cake was that he wrote to one of my colleagues (not my line manager) and told them they shouldn’t give me tenure because I was rude! I just don’t think this guy does social interactions very well. Needless to say he was told that it was totally inappropriate for him to try to influence decisions like that, and in any case, the Irish system is not like the USA one, and as it happens, I am tenured!

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On 8 September 2014 15:51, Luke Latham <luke@guardrex.com> wrote:

Subject: Major FAIL on one of your press releases [oh man.. before he has even begun this has annoyed me. “Major FAIL” is confrontational to say the least… I’m really hacked off already.]

Hello, [uh oh… the bad start continues… Dear Sirs/Madams/Prof/Andrew would have been better. This doesn’t bode well… ‘who is this dude’ I’m thinking]

Referring to: http://www.tcd.ie/Communications/news/pressreleases/pressRelease.php?headerID=2424&pressReleaseArchive=2012

The passage:

“Scientists have discovered proof that the evolution of intelligence and larger brain sizes can be driven by cooperation and teamwork, shedding new light on the origins of what it means to be human. ”

There is no such thing as “proof” in empirical science based on statistical models. Whomever wrote that summary of the research in your office is a scientific ignoramus. Scientists are not in the business of “proving” things. It is true that with an overwhelming amount of statistical and observational data, we lift a hypothesis to the level of calling it a “theory” and give it a special place as a scientific principle, but no single study can ever provide enough information to make a theory … and even theories are falsifiable in principle.

[Entirely correct about falsifiability of hypotheses.. but I stand by this statement…. “intelligence… can be driven by cooperation…” is the key finding… with emphasis on “can”. People have speculated for ages that it should drive it, and we showed, I think for the first time, that it can. Whether other selection pressures exist in place or tandem with this is beyond the scope of our paper. We did not say we proved that intelligence in humans was driven by cooperation, but that it could be. I see nothing at all wrong with this statement, no matter how pedantic one wants to get]

Next, you’re way, way off base claiming that this sheds new light on “what it means to be human.” The researchers’ 50 brain computer models that were run through a series of computer games (also vastly simplified over real-life interactions) were so simplistic and unlike real brains that its virtually impossible to draw any conclusions about such a correlation in real organisms. There is nothing wrong with computer simulation per se, as they can be quite helpful in research, but let’s put simulations in context: Simulations can point you in the direction of possible real-life biological relationships but never be used to draw firm conclusions about biological organisms. Simulations are just too vastly oversimplified to guarantee that the phenomenon under study will yield the same results when experiments are carried out on real organisms. Only empirical research on organisms themselves can be used to draw conclusions about organisms.

[I disagree, but I’m not getting into this here. This is a perfectly reasonable question, and one I would have been more than happy to engage with had Luke Latham, CEO not been such a jerk]

Educators (at least here in the US) have utterly failed to teach people what science is and how science works, and you jumped right on the bandwagon spreading misinformation. I think you should release a retraction on those statements in a new press release. In the future, I hope you will run your press releases that deal with scientific subjects past a REAL scientist before publication.

[I’m rather proud about how I, and my group communicate science to the discipline and to the wider public. We have a good track record of public engagement. This is just insulting, but again, I don’t think he gets it. He has also implied that we have “utterly failed” which is just inflammatory. And worst of all…. I was the “REAL scientist” that helped to write and ultimately signed off on that press release… so “[insert expletive of your choice here] you Luke Latham, CEO”]

 

Luke Latham, CEO

GuardRex Corporation

Cheyenne, Wyoming, USA

 

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So… in spite of my better judgement, I replied… and hastily… (though I don’t regret anything)

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Date: Mon, 8 Sep 2014 16:09:24 +0100

Subject: Re: Major FAIL on one of your press releases

From: a.jackson@tcd.ie

To: luke@guardrex.com

hello to you too [this was me being ironic and parodying his own choice of impersonal address… he didn’t get this… but maybe one can start to build up a picture about how this guy thinks and deals with people]

yeah, thanks for this. I feel enlightened. [ok… so straight up sarcasm]

maybe next time you could proof all our press releases? You seem to have a special grasp [of] things. [parodying his “In the future, I hope you will run your press releases that deal with scientific subjects past a REAL scientist before publication.”]

I think you should read things a bit more carefully and put some thought and maybe even a hint of decency and politeness into your missives. [this is me parodying his “I think you should release a retraction” bit, but again he seemed to miss this irony]

In the future, I hope you will stick to whatever it is you might be good at. [and a return to his “in the future I hope you will….”]

Andrew

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He replied. But also apparently wrote to a colleague behind my back in a vain (both narcissistic and pointless) attempt to have my tenure blocked… nice guy eh?

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Subject:  Major FAIL on one of your press releases

Dr. Jackson,

 

My comments have nothing to do with the quality of your research or institution. I happen to be a great supporter of computer simulations of biological phenomenon (see http://www.bioone.org/doi/abs/10.1662/0002-7685%282008%2970%5B30%3ACARSFT%5D2.0.CO%3B2 ). My comments were directed to your Communications Office regarding their comments about your research … their inappropriate statements regarding “scientific proof” and the extrapolation of the results to “what it means to be human,” which you well know are inappropriate.

[well Luke… had you taken some time and being vaguely more polite you would have discovered that I wrote that press release with my co-authors, and signed off on it too. So actually your comments do have relevance to me and my research. Also… by your logic, you were not being a rude ass to me, but to my communications office? It’s not ok to write emails like this to anyone, and as it turns out, your ire was directed at me]

If your study drew conclusions on differences in simulated brains with a statistical model, then I doubt that your P-value was 0 (zero)! I don’t understand your hostility to my remarks. You should be just as upset as I am that non-technical, non-scientists constantly speak about scientists “proving” things, when that is utterly impossible and not really the point of advancing our knowledge of biological phenomena.

[he doesn’t get it. I seriously wonder about this guy’s social skills]

“Read things a bit more carefully”? What do you mean? … that was a direct quote from your institution’s press release. It is abhorrent to the process of science and to the education of a public that is scientifically illiterate (here in the US … I know things are much better in your country, where education is taken more seriously). As for “stick to whatever it is you might be good at,” I really don’t think that’s a fair remark given that you really didn’t explain how my original argument is false. In regard to “decency and politeness,” I don’t understand that attack either: I don’t make a single statement that can be taken as a personal attack on anyone. I’m talking about scientific incompetence … I’m sure the fellow or lady who wrote that press release is a perfectly nice person. My differences with the press release are professional … and respectful insofar as one can be when I see a daily misrepresentation of the process of science (here in the US, again, I know these matters are handled better in the UK).

[nope. Doesn’t get it. Also Luke… Ireland is not in the UK, we are a sovereign independent country. It really is difficult to endear oneself to this guy.]

I’m sorry that you are offended by my concerns, but we’re losing the battle over here in the US. The press release was taken out of context by a popular blog writer here and used to inappropriately support his arguments about cooperation in business organizations. We really don’t need scientific results misused in this way. I’m just attempting to call attention to a serious general problem in the dissemination of scientific information. If you don’t want to take the matter up with your Communications Office, if you feel their statements were perfectly acceptable, then just forget the matter. But if you do, then don’t cringe the next time someone says that evolution is “only a theory” or that climate change is not a heavily man-made/man-caused problem.

[I think I finally see where he is coming from. He has a bee in his bonnet about how science is treated by some corners of the media. You can’t get bent out of shape with the free press for how they report on findings. Some will be better than others, and some will mis-quote. But having a free press is better than trying to impose control over them. We could have had a civil discussion, but Luke Latham, CEO stuffed it up from the very first subject line. Sorry Luke, im not going to engage with you.]

Luke

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There you go. This whole thing really annoyed me and had me seething for days. Nice to be able to right this up now without feeling my blood boiling though.

Author: Andrew Jackson @yodacomplex

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

Photo credit: http://mrmen.wikia.com/wiki/Mr._Rude

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The Allure of Couzins: Self-organising collective groups

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Every now and then you stumble on a paper that changes everything for you. Typically something of a personal zeitgeist moment, it opens your eyes to a whole new world of potential and can spin your own research out in new directions, or encourage a complete re-orientation of your goals. In this new series, we are going to profile some of our favourite papers and maybe share the inspiration a little wider.

I don’t get out from behind my computer much, but when I do, my favourite engagement with real animals is to watch swirling flocks of starlings or trails of ants in search of food.

During my PhD I was working on the evolution of behaviours in social groups when I stumbled on a paper as I was searching through my supervisor Prof Graeme Ruxton’s publications. This was one of the first collective behaviour papers I read, and it was a huge eye-opener for me, pandering to both my love of biology and computers. Collective memory and spatial sorting in animal groups by Couzin, Krause, James & Ruxton brought home for the link between individual behaviour, self organisiation, emergent behaviour, complex biological pattern formation and how evolution could exploit this system and shortcut adaptive strategies without the need for invoking complex cognitive processes.

The concept itself wasn’t new: Craig Reynolds in 1986 demonstrated that interacting individual computer animals, which he termed boids, following three basic rules of separation, alignment and cohesion could generate a variety of complex group level patterns akin to biological swarming, shoaling and flocking. This simple computer simulation showed how the interactions themselves could create coordinated group-level behaviour without a need for centralized control, or for agents to possess any knowledge of their surroundings beyond their nearest neighbours. Instead, the patterns are an emergent property of the system of interacting agents that arise through a process of self-organisation. Craig Reynolds went further, and showed that information could be transmitted through the group so that obstacles (or predators) could be avoided by individuals responding to their neigbours avoidance, without having to actual see the obstacle or threat for themselves. Such characteristics have clear selection benefits in an evolutionary sense whereby there are cheap, effective ways to gain benefits of living in large collective groups.

What Couzin et al did was to show in even more detail the ecological and evolutionary relevance of these systems. They described in detail how subtle changes to individuals’ behaviours, manifested in adjustments to the radii that define whether they avoid, align or cohere with their neighbours, could arise in abrupt changes to the group-level pattern. A system dominated by attraction and avoidance tends to produce swarming behaviour around a relatively stationary point whereas one dominated by alignment produces shoals that move in a rather rigid, elongated diamond-like formation. In between there exists an intermediate state in which the group spontaneously starts to rotate in a torus (ring-doughnut) structure. The key point here is that no-one in these groups knows what a torus is, never mind how to achieve it, and nor is there a leader telling them to swim in a circle – rather, it is an inevitable consequence of the aggregation of the interactions between individuals with a mid-range tendency for alignment. An extra quirk to the system is that though the individuals are completely bereft of any brain or memory, the system shows evidence of memory – or hysteresis as physicists would refer to it. Individuals starting in a swarming pattern and increasing alignment will move through the rotating torus and on to the rigid diamond-like structure with individuals locked into a particular place in the group. However, if you start with the rigid structure, and reduce individuals’ tendency for alignment, they skip the torus structure and revert straight to swarming. In this manner, the group has memory of what it was doing in previous states, even though the individuals have no such memory. This is surely a rather cheap way for interacting ants, fish, birds, or maybe even the neurons of our brain to encode a sense of memory or history without having to explicitly encode and record the details of past states.

Perhaps most relevant from a behavioural ecology perspective, Couzin et al went further and explored how changes to an individuals behaviour relative to the group could alter its location. Increasing speed, decreasing turning rate or increasing one’s tendency for alignment would see an individual end up towards the front of the group. Reducing ones tendency for avoidance would see an individual move to the centre of the group. This is beautifully simple. Without any knowledge of the group structure, or where one is in the group, simple behavioural rules linked to internal state can now allow an individual to navigate the group. For example, if hungry, simply speed up and you will be at the front with first access to food. Once sated, you can seek out the relative safety of the middle by reducing your how much ‘personal space’ you require.

Prof Iain Couzin has gone on to show myriad intricacies of collective groups in terms of how they can make decisions as a group, and how locust swarms are driven by similar properties. During my PhD I had the pleasure to meet with Iain Couzin, study under the tutelage of Graeme Ruxton, share code with Richard James, and collaborate with Jens Krause (I didn’t get to meet the last author Nigel Franks, but now that I’m back on the conference tour there is still hope!)

Author

Andrew Jackson

Photo credit

wikimedia commons

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Internal Affairs

Internal-Affairs

So for various reasons, one of which was being unsure of whether a PhD was for me, I found myself asking to work as an Intern with the good people in the Zoology Department at TCD. To give you a bit of background, I am a Zoology graduate with an MSc in Marine Biology, so not just some random bloke who happens to like animals and fancied chancing his arm. Anyway, I approached Dr. Ian Donohue whose research group interested me and thus began a 9 month Internship as a Research Assistant.

minion!

With a little trepidation and a great deal of excitement I began my stint as a minion with a site inspection for a proposed project looking at community structure in a rocky shore ecosystem. (Note to anyone who is interested in rocky shore ecology, I would advise not severely spraining your ankle the day before, it’s incredibly frustrating trying to navigate a boulder field while being unable to walk). Over the following weeks, I assisted in the field work required to set the project up. I thoroughly enjoy being outdoors so this suited me perfectly, although I must admit how lucky we were weather wise, it rained on only one day of 9 or 10 days we had out there so perhaps my love of the outdoors will diminish as soon as I’ve encountered some proper Irish weather!! Since then I have been involved in a range of projects from pilot studies on coevolution and trophic complexity of bacterial communities to feeding and respiration rates in Mysid shrimp, encompassing a range of laboratory and field techniques.

The learning doesn’t stop at the practical side of science either, merely by being involved in a working department I have learned more in the last 7 or 8 months about the ways of forging a career in science than I have done in my entire career to date. Our weekly journal club, NERD club was a bit of a revelation if I’m honest. Seeing how a collective of brilliant minds can come together and interact to assist with, develop and fine tune current and future work was an eye opener. It’s also an extremely beneficial way of encompassing different working groups/departments. The sharing of ideas, new techniques and sometimes just a different perspective can lead to a well-rounded project and/or person and is something I would definitely recommend in any institution.

I’ve also begun to build a network, something crucial to succeeding in science (and any workplace I guess!), and definitely not one of my strongest attributes. I was fortunate enough to attend the BES Macroecology conference in Nottingham in July and to display our work to the public during the Discover Research event in September, both of which were thoroughly enjoyable and valuable to furthering my development. I am an avid supporter of outreach programmes so to participate in what was an extremely successful night was most rewarding.

To anyone who is in a similar position to the one I was I would highly recommend contacting a Professor or otherwise and asking is there a job you can do for them. If like me, you are willing to do it for nothing other than your own benefit then there is no reason why they would not accept the offer. I have learned so much during my time here, added considerably to my skill set and most of all I now know that a) I would like to continue to work in an academic environment and b) that I am fully capable of doing a PhD. Whether I do or not depends on a number of factors, but that is for another day.

Author: Alain Finn, alfinn@tcd.ie, @finchyirl

Image Credit: http://nassauso.com/internal-affairs/, https://twitter.com/DM_Minions

 

 

 

 

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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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A Spark of Science

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Why are some snakes more venomous than others? When did plate tectonics begin? What geological mysteries await our discovery on Mars? How do organisms build their own bodies? How do businesses manage biodiversity?

These are just some of the interesting and diverse Lightning Talks which were presented at a recent event in the School of Natural Sciences. Researchers from the disciplines of Botany, Geology, Geography and Zoology had just two minutes to present their work to colleagues and friends. The strict format created an interesting evening filled with bite-size chunks of science.

We were very lucky to have a great judging panel comprised of Professor Fraser Mitchell (Head of School), Donal Daly (Senior Scientific Officer at the EPA), Thomas Deane (Press Officer for Engineering, Maths and Science), Aoibheann Bird (Education and Outreach manager, Insight Centre for Data Analytics) and Diane McSweeney (Education team at the Science Gallery). The speakers were judged on their content, delivery and use of props. Prizes were kindly sponsored by the Trinity Foundation, the Science Gallery, the Botanical Society of Britain and Ireland and the Graduate Student’s Union.

Botany PhD student, Brian Murphy, won first prize for his talk “A hidden force that will feed the world”. Brian’s research focuses on endophytes: fungi that live in the roots of plants that have great commercial potential for increasing crop yield in an eco-friendly and sustainable way. There were two runner up prizes: Kevin Healy for his talk on the evolution of snake venom (which also featured as part of the Science Gallery’s recent event, Dead Beats) and I won a prize for story about how looks can be deceiving in tenrecs. Other prize winners from the evening included Alwynne McGeever, Hannah Hamilton, Gary O’Sullivan and Mike Williams.

It was a great evening filled with lots of interesting talks and a good chance to find out about the diverse research in the School. Thanks to the fantastic organising committee: Jane Stout, Maria Long, Frances Leogue, Rachel Kavanagh, Tara Kelly, Clare Stead and Alwynne McGeever for making everything run so smoothly!

Videos of all the prizewinning talks can be found on the School’s YouTube channel.

Author: Sive Finlay, @SiveFinlay

Photo credit: wikimedia commons

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Are you Shutting Up and Writing?

Smiling_boy_seating_at_a_table_writing,_China,_ca._1918-1938_(MFB-LS0248A)Inspired by the awesome blog, the Thesis Whisperer and under the constant reminder that we must publish or perish, post docs from the School of Natural Sciences have been meeting on a weekly basis, on and off for the past year to sit down, shut up and write. Here is a bit of background on the Shut Up and Write ‘movement’, a little bit of what we’ve learned along the way and a big invite to any post grads, post docs and PIs in TCD’s School of Natural Sciences to come along and join us.

The post docs shutting up and writing. It’s that simple!
The post docs shutting up and writing. It’s that simple!

One of the most fun things to do while procrastinating on the internet is to read productivity hacks. There is a treasure trove of resources out there telling you how much better you would be at your job if you ate better, slept better, exercised more and bought their productivity app. Funnily enough, none of them tell you to just close the browser window and get on with it. On one of these jaunts through the internet I stumbled upon Dr Inger Mewburn’s, ‘The Thesis Whisperer’ blog and while I have spent longer than I should have trawling through her blog’s archives, it is such a great resource that I now annoy all the post grads in our lab with recommendations to do the same. One of the great ideas I found while procrastinating reading was that of setting up a Shut Up and Write group. These do exactly what they say on the tin, providing a place for interested people to come together and write. For some, this may seem counter-intuitive, going somewhere to meet takes time that could be better spent just getting on with the project in question. However, as Mewburn and fellow Shut Up and Write enthusiasts find, the problem with staying at your desk is one of continued interruption by email and requests for time by those who assume that because you are at your desk, you are ‘free’. Having a dedicated time to write also means that you are less likely to schedule other meetings/activities over it.

So, having met a couple of the School’s post docs and recognising in each other a desire to organise ourselves and meet with some sort of regularity, I proposed that we try out Shut Up and Write. What better group to sell the idea of regular writing sessions to, than post docs? Our group is small and we try to meet every week. We’ve tried the busy coffee house, but as our campus is in the city centre, busy is definitely too busy for our tastes, and we now meet on campus (in very close vicinity to tea and coffee facilities!!). We have also been derailed at times by the changes to our schedules that the switch between term time and holidays can bring. However, having regrouped recently after a bit of a break, I think the key is not to stress out about having spent time away from the group, or from writing and to just get on with it.

Once we’ve all come together, the session works something like this; we all grab a cup of tea/coffee and have a good natter. After about 15 minutes we sit down to our computers/notebooks and write for 25 minutes. We then have a quick breather (maybe 5 minutes) and then work for another uninterrupted 25 minutes (yes, that is the Pomodoro Technique). We currently tend to work on our own writing projects, but new collaborations and assistance with reading and editing manuscripts are all part of the potential a Shut Up and Write group has. Over the year we’ve worked on journal articles, grant proposals, blog posts, book chapters, technical reports and project management reports and the fact that we are still making time in our schedules suggests that it’s been a pretty productive experience all ’round. If you’re a post grad, post doc or PI in the School and would like to know more, please let us know in the comments!

Author: Caroline Wynne (@wynne_caroline)

Photo credit: wikimedia commons

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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

 

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On the writing of a PhD thesis

writing“Writing a [thesis] is an adventure. To begin with it is a toy and an amusement. Then it becomes a mistress, then it becomes a master, then it becomes a tyrant. The last phase is that just as you are about to be reconciled to your servitude, you kill the monster and fling him to the public.” Winston Churchill

I’ve just finished my PhD thesis and thought I’d share some of my opinions on how best to go about writing one. But before we get there I’d like to express my skepticism of the value of writing a thesis as a means to evaluate a budding scientist. I don’t know of any papers in journals that run over a 100 pages but classically this is what was expected of us at PhD level. It’s rare that a scientist writes a monograph. Instead we compose pieces of research that can be explained in around 10 pages. Scientists use mathematics and statistics to make our points, in that way our numbers do the talking so we can afford to be succinct. This is in contrast to students of the arts who typically draw on argument and rhetoric in their works building to a singular point or thesis! But that’s irrelevant to this topic because you still have to write one and many departments are quite flexible with their definition of thesis.

So my first piece of advice is write chapters with the aim of publishing them. You’re training to be a scientist and papers are your currency so keep that in mind. Three or four data chapters with a general introduction and discussion seem to be the way to go. If you have this approach you’ll be able to finish up parts long before the deadline. If you can get papers published, all the better, a peer-reviewed chapter looks very well and will be an improved piece of work for having gone through the process. The final body should be a coherent whole but these are not book chapters in a story. That said be aware of how you want to frame the whole thing.

Try to be concise; it’ll be easier for you to write, easier for your examiners to correct and more attractive to anyone else who wants to read it. There may be some work you did over the course of your PhD that has to get the chop to achieve this.

There’s no problem in seeking help. Science is meant to be collaborative, even more so today. In 2012 only 11% of all papers were single authored. You’ll be able to get much better chapters if you include people who can add a bulwark to any of your weaknesses. Just make sure you do the bulk of the work and properly credit your collaborators where necessary.

Give some thought to the program you’ll use to write up the project. MS Word isn’t the only way. I found assembling the whole thing in LaTeX went quite smoothly because it’s specifically made for writing technical documents. The downside was it was difficult for others to comment on it. There are ways to do this but I was a novice at the time.

Step back from the cult of the busy too. I found giving myself a break from the write up helped me come up with a much better frame for my discussion.

Start early, don’t write much, aim for papers, and use LaTeX. Simple. How’s that for concise?

(The contents of this post are subject to change after my thesis defence)

Author: Adam Kane, @P1zPalu, kanead[at]tcd.ie
Photo credit: http://centrum.org/2014/08/creative-nonfiction-workshop-nov-6-9/