By Alex Lincoln-Dodgson
On the 5/7, I-DEEL from UNSW and the Beta-Cell Regeneration Group from the Garvan Institute went out for the first of hopefully many outings together. The night's activity was bowling, where skill was seen across the board. Notable mention goes to Dr Daniel Hesselson with his winning score of 115, and David Nguyen with the close second of 114. However the highlight of the night was A/prof Shinichi Nakagawa with 53 points, getting absolutely smashed by his children with astonishing scores of 72 and 82.
We’re looking forward to a rematch!
By Fonti Kar
Have you ever had a lull in productivity? Days where you feel like you are not achieving very much? You are not alone. In my first year of my PhD, the thing the stressed me most was not knowing whether I was productive enough. How do I track my progress? A few weeks ago, I went to a workshop on ‘A novel framework for research productivity’ run by post-doc Khandis Blake from the Sex Lab, UNSW. Inspired by Khandis’ productivity (she completed 16 studies during her PhD in 2.5 years!), I decided to blog about this and hope someone will find this helpful with their own project management as well.
Khandis has a background of business coaching. In her workshop, she drew parallels between sales pipelines and research projects (Fig. 1). She discussed one can increase customers, revenue and profits or in research terms – the number of completed studies, submitted manuscripts and publications by working on factors that affect these key things.
For example, a business can work on converting people that walk in the store (‘leads’) into paying customers, which will ultimately increase store revenue/profits. Think store promotions or sale assistant greetings as you walk in. You can do the same with the number of completed projects by working on your leads. This can be the number of collaborations you have or own ideas you’ve identified from reading. You can focus on converting these ideas into completed projects by recruiting help with data collection (e.g. interns and student volunteers), or use a more efficient way to test your idea (e.g. theoretical models), or perhaps the data already exists and all you need to do is to put these together (e.g. meta-analyses).
Now, once a business has converted a lead to paying customer, one can increase the number transactions per sale, which will increase revenue. Think “Would you like to have fries with that?”, a line we are all too familiar with. The research equivalent of this is the idea of publication frames i.e. number of manuscripts one can address in a single project. Can you partition your data in multiple ways to test multiple hypotheses? Can you collect just a little bit more data (with minimal effort) so you can address another interesting question? Depending on the of results, can you segment these to tell more than one cohesiveness story?
Finally, to ultimately increase the number of publications– your manuscripts need to be submitted. Your success rate depends on a range of factors, some of which are not in your control (e.g. time in review) but you can increase your chances by making sure the story is clear, concise and well written; stick to journal guidelines; a fast turnaround with revisions or resubmissions to another journal.
But there is a catch with the research pipeline…
The lag in research
Khandis emphasised that the research pipeline is long one. The time from a conceived idea to data collection, to manuscript submission and submitted and acceptance is LONG. For example, I started the data collection in early December 2014 for a paper that was accepted earlier this month (3-year pipeline!!!). This means that there is always a lag in productivity and in order to avoid lulls, here are some tips:
Research projects – especially PhDs – can be long and demanding journeys, but with a clear pipeline in mind, one can hopefully navigate this path with a bit more ease and come out on the other side with a few more papers under your belt. Good luck!
Six years ago, I wrote a course manual for biology students learning statistics using R. I wanted to publish this manual as a book, but 6 years passed since that resolution. Two months ago, I finally decided to accomplish this aim, and I am actually writing the book. I have already finished the first 2 chapters!
I did not want to create yet another textbook for stats (there are already a lot of good R stats books). Rather, the main reason for writing this book was my desire to join great English playwrights, like Bill Shakespeare. Yes, my stats book is a play! It is structured as conversations between 6 people. I give you an excerpt here:
Originally, I was planning 12 chapters (my original course manual had 7 chapters), but now I plan to have 15 chapters (and maybe plus 5 appendix chapters...). I have to update the 7 already written chapters, because R has moved on a lot. Now, we have many new super-nice packages (e.g., the tidyverse family). So, in the updated version of the book, I use ggplot2, dplyr, tidyr and readr instead of the base functions from the basic packages. I am learning so much on the way! I just found a package called ‘GGally’ (the ally of ggplot2) - it is so great! I have redrawn the original scatterplot matrix (house sparrow morphological data) with ‘ggpairs’ function instead of the ‘pairs’ function. Doesn’t it just look stunning?
When will I finish? I’ve told my publisher that I want to finish the whole book by the end of year... Let me aim for that – still 13 chapters to go!
by Losia Lagisz
We had a very special Saturday on 22 of April 2017, with two special events. In the morning, we took part in March for Science organised in Sydney. In the afternoon, we watched an AFL (Australian Football League) game, which seems to have nothing to do with science, but it has a link to our group.
March for Science felt like a good place to go. It was a colourful and peaceful gathering of people who recognise and appreciate science,who are concerned about politicians ignoring science, and who see the need for evidence-based decision making. No need to mention, members of our lab attended this important gathering.
Photos: Marching for science
The AFL game was important to us for a different reason. It was not that Sydney Swans played against the Giants – we did not particularly favour any of these two teams. It was our first live AFL game. And it was mostly about watching Rose. Rose is an Umpire (a judge), she is one of only 4 female Umpires in AFL, and she also is a member of our group, doing a PhD at UNSW. We are very proud of her!
Photos: Rose in action. Watching the game.
We hope that what we did on Saturday matters. And the big thanks for the AFL tickets go to Rose!
Celebrating my final day with I-DEEL – thank you for an amazing year!
On the first day of March, 2016, I was invited to meet the I-DEEL team. Nervously prepared for an interview, I was instead greeted by a smiling Shinichi, Losia, Rose, and Dan, who immediately welcomed me to their group and their first lab meeting of the year. Throw in a lunch date with Rose, and I knew I had stumbled across a very special group of people, who have been nothing but inclusive and encouraging, and have continued to impress me with their skill, knowledge and determination for the following twelve months.
The past year has been somewhat of a whirlwind for me. I remember my induction at the Garvan Institute of Medical Research. I remember meeting Daniel Hesselson and his lab group, claiming my desk, and feeling slightly overwhelmed. I remember being shown around the Biological Testing Facilities (BTF), struggling to catch my first zebrafish, and feeling at peace the first time I saw their developing embryos. I remember meeting the BTF team, and being shown an empty room that was full of potential and eager optimism.
Our laboratory, May 2016 – After a quick tidy up and sourcing some new equipment.
That empty room quickly engulfed my time spent at Garvan. When I wasn’t helping Rose maintain her growing zebrafish collection, or learning the fragility of molecular work the hard way, my time was spent transforming that room into a fully-functional laboratory. Designing floor plans, negotiating with suppliers and liaising with engineers. Enduring the frustration of incorrect, delayed, or completely absent deliveries. Remedied by my enthusiasm to organise, colour coordinate and ‘go label-maker crazy’. It was a big project. Exasperating at times, but overall gratifying. And I feel honoured that I could have contributed to it.
Our laboratory, November 2016 – Our room is now fit with incubators to control the developmental temperature of our zebrafish, a new desk and equipment to measure zebrafish larvae activity, a respirometer to measure zebrafish metabolism, and a custom built filming platform (thanks to the engineering department at Garvan) to quantify adult zebrafish behaviour.
With a background in animal behavioural studies, my research contributions were focused on developing a high-throughput behavioural screening assay that we could use to rapidly quantify zebrafish behaviour and personality. My interests in information technology, video editing and computer animation meant I was completely in my element. Hours upon hours were spent compiling digital assays, rendering videos, troubleshooting tablets and familiarising myself with the finer details of EthoVision. By October, the methods were finalised and Rose was applying them to her PhD.
Throughout the year we have welcomed many new faces. Fonti, who is conducting her PhD, Takuji and Harry, our two interns, and Marissa, who we were lucky to have helping us over the past summer. We have also been blessed to meet and work with the staff at The Garvan Institute. A special thank you to BTF members Jennifer Brand and Michael Pickering, and engineers Mark Irons and Myall Quint, to whom our laboratory would not have been completed without – your contributions and continuous support were deeply appreciated.
Finally, I wanted to say thank you to everyone at I-DEEL, for welcoming me into your group and giving me this opportunity. I’m going to miss being a part of the team! I wish all of you the best of luck with your future endeavours.
While my time working at The Garvan Institute has come to an end, my contributions to I-DEEL are not yet over. From here, I am going to write and publish a paper detailing our novel approach to rapidly quantifying adult zebrafish personality – so stay tuned for more!
At the end of every year (or the beginning of a new year), it has been a tradition in our group to write a blog summarizing a whole passing year.
As usual, 2016 has been a really busy year. Good news is that Bene finished his PhD with his thesis being on the Dean’s list (top 5% PhD theses at the Otago University); he has already published papers in Molecular Ecology and Functional Ecology from this thesis, and more to come. Carlos visited me in Sydney, in December; he has made great progress, and plans to finish his PhD in July 2017.
Our group is expanding. Rose has officially started her PhD on zebrafish, and Fonti on lizards,. We are extremely lucky to have Melissa working on the behaviour system for our experiments on zebrafish and Takuji have joined us later in the year to help us on various projects. We have been very productive, often working with many scientists around the world. We have had several good papers accepted and being published, for example, in BMC Biology and Molecular Ecology, with Dan and Losia involved. Notably, Joel not only published in Current Biology but also co-authored a son with his wife!
We finished the year with a group BBQ at the Coogee Beach (25 min walk from our office at UNSW). We were planning to do that a year earlier, but it was rainy. This year we were lucky with the weather. It was sunny, almost too hot, and some of us event went snorkeling. Thanks to everybody for contributing by bringing food and other stuff for the BBQ! Hopefully, next year we can repeat this.
I have been told it takes 2 years to build up a new lab and it is getting to be 2 years since our relocation to Sydney. We are finally feeling that we are settling down as a group. We are now getting a lot of good data from the fish and lizard study systems, so we have a lot to look forward to in 2017!
By Fonti Kar
Writing is the bread and butter to all researchers. It is the main form through which our findings are communicated to the scientific community as well as to the general public – so, its important to do it well. But how does one do that? Do researchers just have a natural flair for writing?
A few weeks ago, I went to a workshop run by my supervisor, A/Prof Shinichi Nakagawa on "How to write a lot and (well)”. A/Prof Russell Boundriansky and Prof Rob Brooks were also there to contribute their tips too. Thankfully, all three academics admitted that writing is HARD, but stressed how important it is, if you want to strive in academia.
Shinichi firmly believes that there is no such thing as 'writing talent', which is very reassuring. He emphasised that through 'deliberate practice', everyone can write well. Deliberate practice in a nutshell, is about having a clear goal of what you want to improve and working towards this goal consistently with feedback and repetition. Below, I have summarised the key tips from the workshop, which form the basic ‘writer’s toolkit’ and hope this will be helpful to those that need some inspiration in their workflow. Remember - tips that work well for some, may not work well for others - but everything is worth a try!
According to Shinichi, one can only deliberately practice something for no more than 4 hours. If you have trouble focussing, give Pomadoro timers a go! Do 25 minutes of completely focussed work - no emails, no distractions. Then have a 5 minute break where you can indulge in a bit of Facebook or whatever takes your fancy. Rob reckons 10 Pomadoro cycles is considered really productive day!
No reading means no writing
One of the challenges I often face is that I don't know what to write and this is usually because I haven't done enough reading. So it is crucial to read regularly and engage with the literature.
Tip 1. Shinichi showed us The Old Reader - an RSS subscriber that keeps ALL your alerts in one place. This is my new favourite thing! It keeps you updated to all the relevant journals and it also eliminates the 'Table of Contents' emails - BONUS. He recommends reading everyday, particularly influential or 'Trends' journals.
Tip 2. The trick is to read efficiently. Read the abstract, the last paragraph of the introduction, the first and last paragraph of the discussion to get the sense of the paper first. Then dig deeper if you need the details.
Tip 3. Find a reference manager and become a master of it. This will organise your reading. Highlight and take notes as you read. I find the functions in Papers3 very handy for this because your notes and highlights become searchable!
Tip 4. Don't like reading? Why not try an audiobook or podcast? You can listen faster than you read!
Mastery of mind maps and outlines
*You need to read enough before you can make a map
Tip 5. Put your ideas/themes/questions/hypotheses/key papers/anything on a mind map. Maps will really help you organise your thoughts and actually make you think about how ideas are linked. I use VUE, it has a simple interface and a few core functions – that’s all you need! I've also used it to make figures for presentations/papers too.
Tip 6. Translate this mind map into an outline. The main 'bubbles' basically form the major headings of a skeletal outline. 'Sub-bubbles' become subheadings within the major headings. This allows you to make sure ideas flow nicely, starting from broad ideas and then honing down to specifics.
Tip 7. Transfer your notes to your outline. If some headings are low on substance, you can then go back to target your reading for those sections! EFFICIENCY!
Writing clarifies thinking
Now with your outline and notes, you can begin to write. Having your ideas chopped in sections and subsections should make workflow more manageable too, because you can work in bite-size bits. The next few tips were Russell's contribution
Tip 8. Write for a target audience. Are you targeting specialists or to the wider field? Tailor your examples and terms you use to appeal to your audience. Use this particularly in your title.
Tip 9. Keep it simple, really. Clearly written papers have the most impact. Avoid long, vague, complex sentences. Explain your idea out loud to someone out of your field and write that down.
Tip 10. Good writing is an iterative process. Re-read your writing with fresh eyes (after a week or so) and rework those paragraphs.
Tip 11. FEEDBACK FEEDBACK FEEDBACK. Ask your writing group, your lab group and supervisors. Give people enough time to review and do the same for them. Really THINK about their edits and recommendations. Don't just click 'Accept all changes'.
The work and effort that goes into writing a scientific article can be overwhelming. I really think, with the right sort of tools and habits and plenty of deliberate practice, everyone can improve and write well!
For more info on deliberate practice, check out the book: “Peak: Secrets from the New Science of Expertise” by Anders Ericsson – we are currently reading it as a lab!
By Rose O'Dea
What is the best book you’ve read recently? When I was an undergrad, two PhD students told me they didn’t have one, because they were too busy reading papers. I found this alarming because I loved reading books, and disliked reading papers. Would I need to sacrifice reading for fun to stay in science?
Recently, my co-supervisor Michael Jennions sent me a book that has alleviated these fears: The Sense of Style: The Thinking Peron’s Guide to Writing in the 21st Century, by Steven Pinker. Steven Pinker is a psychology Professor and the chair of the American Heritage Dictionary Usage Panel. He thinks academia is rife with bad writing. This makes papers tedious to read, even for professors in the same field. In The Sense of Style, Pinker uses linguistics and cognitive science to explain the style of writing we should be aiming for, and why it is so hard to achieve.
Why Writing Well is Hard
“Man has an instinctive tendency to speak, as we see in the babble of our young children, whereas no child has an instinctive tendency to bake, brew, or write.” – Charles Darwin, as quoted in The Sense of Style (p. 50)
Writing translates the web of ideas in our mind into a string of words. The reader then parses the sentence into a tree of syntax, after first holding the beginning of the sentence in her working memory. Cognitive science tells us that our working memories are prohibitively small, so Pinker details a number of tricks to help readers parse sentences more easily and avoid ambiguity. But, as Pinker points out, “it’s hard enough to formulate a thought that is interesting and true” (p. 137), let alone write these thoughts coherently. Style guides are therefore guides on how to revise, rather than on how to write.
“Most writers polish draft after draft. I rework every sentence a few times before going on to the next, and revise the whole chapter two or three times before I show it to anyone. Then, with feedback in hand, I revise each chapter twice more before circling back and giving the entire book at least two complete passes of polishing. Only then does it go to the copy editor, who starts another couple of rounds of tweaking.” – Steven Pinker, reminding us that writing is hard, even for best-selling authors (p. 136 – 137).
Pinker thinks that academia is filled with opaque writing because of a failure to appreciate the depths of other people’s ignorance. He refers to this phenomenon as “The Curse of Knowledge”, and it is backed up by experimental psychology (and the experience of helping your elderly relatives with their computers). When we are familiar with a topic, we package information into chunks and forget what it was like before we consolidated this information. We then fail to explain ourselves properly and, as a result, our reader is left bewildered by jargon. Sometimes I thought The Sense of Style provided an unintended demonstration of this problem: the middle of the book is filled with technical terms, and diagrammed sentences, that were completely absent from my Australian education in the late 90s and early 2000s (I have asked around to make sure I am not merely forgetting my formal education). I therefore grew frustrated by having to frequent the glossary. Pinker admits that the curse of knowledge is very difficult to overcome, so showing your drafts to people that are unfamiliar with your topic is the best safeguard.
What We Should Aspire To
“My task, which I am trying to achieve is, by the power of the written word, to make you hear, to make you feel – it is, above all, to make you see.” (Joseph Conrad, 1897)
Pinker thinks that academic writing is opaque because it is written in self-conscious, rather than classic, style. Classic style directs the reader’s gaze, like the director of a film, to tell a story about a subject, allowing the reader to reach the same conclusion as the writer. It avoids unnecessary use of meta-concepts (concepts about concepts, such as “frameworks” and “level”), because the reader cannot picture them. It also limits the use of hedging words (e.g. “almost”, “apparently”, “perhaps”), because they distract the reader from the subject. Pinker thinks these words are so over-used in science that they have become a tic.
Classic style aims to both create pictures in the reader’s mind, and present them in a coherent order. Advice to “avoid the passive voice” is simplistic because it focuses on the first aim but neglects the second; passive voice removes characters (i.e. pictures) from a scene, but sometimes this is necessary. By starting the sentence with the done-to, rather than the doer, passive voice changes the order in which events are presented to the reader. Good writers will therefore use both active and passive voice to write clear and coherent prose.
I highly recommend The Sense of Style. Through its 500 pages, Pinker sprinkles enough jokes, amusing examples, and interesting science to keep the reader engaged. There are many practical tips for improving your writing (e.g. read your drafts aloud). Reading this book will not turn you into a good writer, because knowing what you should do is easier than actually doing it. But it will make you a better editor, by providing diagnostic tools for clumsy sentences and incoherent prose. Pinker provides a compelling case for how we should aspire to write, which is far clearer than the accepted standard in science. On the downside, the middle of the book gets bogged down in more technical detail than I required; the longest chapter is devoted to the rules of grammar, most of which I had never heard of, and are subsequently dismissed as unimportant anyway. If most careful writers ignore a rule then it is not a rule at all, and you will not lose the trust of readers by ignoring the sticklers who tell you otherwise. Pinker says that trying to memorise all the idiosyncrasies of the English language is neither the most effective nor the most enjoyable way to improve your own writing. What does he suggest? Read for pleasure, and pay attention to how careful writers write.
So, what is the best book you’ve read recently?* Let me know, and we could choose it for book club.
1. Pinker, S. (2014). The Sense of Style: The Thinking Person's Guide to Writing in the 21st Century. New York, NY: Penguin.
*mine is We Are All Completely Beside Ourselves, by Karen Fowler.
By Melissa Fangmeier
For my first I-DEEL blog, I wanted to introduce to you one of the main projects I have been delegated. This year, I will be setting up a behavioural ecology laboratory at The Garvan Institute of Medical Research. This lab, our ‘phenotyping room’, will be used by Rose O’dea as she explores behavioural syndromes in zebrafish. But until then, it is my job to get everything ready – from preparing the behavioural assays, to designing the layout of the room (with some help along the way, of course).
We were given a (nearly) empty room within the Biological Testing Facilities (BTF) at Garvan (already fit with two fish racks and a sink). It has since been up to us to furnish the room according to our needs. We have achieved a lot over the past four months. The room is almost finished, and I’ve learned a lot along the way. So, I wanted to use this blog to share some insight on four key things that you will need to transform a room into a laboratory:
2. Organisational skills
My background in graphic design and veterinary nursing has meant that I have been ‘blessed’ with a somewhat dangerous combination of “Visually motivated” and “Total clean freak”.
The pros: Give me a label maker and a day and I can guarantee everything will have a place and nothing will ever get lost.
The cons: I am constantly faced with the battles of tidying up after those who don’t share the same enthusiasm in ‘storage solutions’ as I do, and the way I feel whenever I see the nest of wires presently hovering over our respirometer station.
The key to keeping your lab organised is finding a balance between ‘functional’ and ‘tidy’. Delegate a purpose to every corner of the room, and link every corner to the next to create a flowing floor plan. Embrace your label maker and simple (easy-to-access) storage solutions, and make the most out of the space that you have.
Be prepared to manage a lot of orders, and be prepared for a lot of mess-ups. One of the biggest fiascos we dealt with was ordering our modular shelves and work-bench: what should have arrived in one delivery took no less than three (ten, frustrating days). We were left dealing with missing parts and mystery gifts with every order, managing refunds where we were overcharged and making many, many phone calls (by my last phone call, I actually heard someone in the background ask if it was me calling again). Be flexible and plan ahead.
When things don’t go as planned, it’s time to get creative. This is more than just problem solving (which, at some times, may also require a bit of creativity). This is the ability to turn a problem into a solution. Here’s an example:
We recently ordered a fancy, new, three-tray trolley for our lab. It was delivered fast (with a complimentary packet of biscuits – score), but one of the trays had cracked during transit. The shop quickly sent us a replacement, but we were now stuck with a broken trolley. Instead of throwing the trolley away, I asked a member of engineering to create a miniature, two-tray trolley for us. What did we end up with? A trolley that fits perfectly under the sink, and which also perfectly stores all of the tanks for our behavioural assays (needless to say, I was excited by that unlikely storage solution).
For our lab, limited space was our greatest restriction, so being able to plan, organise and create space where there wasn’t space before has been the most useful skillset. Whether this was laying a plank over the sink to create another desk, or asking Garvan engineering to build us some more shelves, we took what we had and we made it work.
So, where to from here? I will continue developing our behavioural assays (which I will talk about in my next blog), and engineering will build us a fancy new filming platform for our behaviour arenas. I can’t wait to see how it all turns out!
by Losia Lagisz
SRSM stands for the Society for Research Synthesis Methodology. The 11th annual meeting of the Society was held from 11th to 13th July 2016 in Florence, Italy.
I was able to attend the meeting as a guest, together with Shinichi, who is a member of the Society. It was a rather small and very collegial gathering, with around 40 people attending. The attendees represented a very broad spectrum of research fields and approaches to research synthesis, from theoretical to applied. Everybody was giving a talk and there were ample opportunities to chat and to get to know other people. On the first evening we a lovely banquet at the conference venue, on a hill overlooking Florence, wrapped in a Tuscan landscape. The second day ended with a guided city tour of Florence and a dinner at a local restaurant. And I had my talk on the third day, which was the last one and was packed with interesting and very interdisciplinary talks.
The real highlight of the meeting, for me, was being able to meet authors of the seminal papers and books on research synthesis methods (basically, the fathers and mothers of meta-analysis). It was also good to very enjoy nice food, and warm Italian summer, while escaping a bit of the chilly Sydney winter.