by Samantha Burke

From July 12th to July 14th, many members of I-DEEL attended the first ever SORTEE Conference. You may remember, from Rose’s blog post in February, SORTEE as a society committed to increasing awareness and opportunities to make ecology and evolutionary biology research more open, reliable, and transparent  (see SORTEE.org). This inaugural conference hosted plenaries, presentations, workshops, unconferences, and hackathons all related to providing resources, gathering feedback, and actively pursuing SORTEE’s missions. Its success was reflected by its large attendance with over 700 participants from over 60 countries. It occurred continuously for 48 hours, actively engaging participants across all time zones.

Members of I-DEEL organized many events for the conference:

• Shinichi facilitated an unconference on facilitating pre-registration
• Patrice organized a hackathon for contacting journals to include options for registered reports
• Losia and Sammy facilitated an unconference alongside SORTEE’s Education Outreach Committee to discuss SORTEE member’s perspectives on open science
• Rose and Sammy facilitated an unconference with members of SORTEE’s Executive Committee on SORTEE’s positions on advocacy for initiatives and policies in open science
• Losia, Szymek, and Sammy organized a hackathon for creating infographics to educate others on different topics relating to open, reliable, and transparent research

Many members of I-DEEL attended these events as well as other workshops, unconferences, hackathons, presentations, and plenaries, and learned a great deal about the importance and avenues for conducting open, reproducible, and transparent research. I look forward to the future of SORTEE and how the ideas shared at the conference can shape the future of ecology.

by Losia Lagisz and Shinichi Nakagawa

Have you received and email from GitHub titled “[GitHub] Deprecation Notice“? Or you are still creating a new repositories on GitHub using https links to clone repositories into RStudio and your local computer? If so, it is time to change how you access GitHub from RStudio (and from your computer in general).
 
From August 13, 2021, using a password with GitHub will no longer work and token (or SSH key) authentication will be used for GitHub operations (if you are already using two-factor authentication for GotHub, you do not need to change anything). You can read official information about this change here: https://github.blog/2020-12-15-token-authentication-requirements-for-git-operations/ .

It may seem quite daunting to go through all the details and options. So, below we present two main ways of switching to SSH when using GiTHUB with RStudio. First, setting public SSH key(pair) for your computer. Second, switching remote URLs from HTTPS to SSH for your existing repositories.
​

​Note: This set up needs to be done for each of computers (and accounts) you are using to access GitHub, i.e. each computer (account) should have its own SSH key. More detailed description of SSH and alternative ways of setting up and troubleshooting are available from: https://happygitwithr.com/ssh-keys.html.

1.1. Open RStudio and go to Preferences from the top menu. [for all Windows users, it is Tools -> Global Options (?)]

1.2. Options box appears. Press on GIV/SVN icon in the left side menu.

1.3. Press the "Create SSH Key..." button.

​1.4. Enter Passphrase and Confirm it (optional). Press "Create" button.

1.8. Press "New SSH Key" green button.

1.9. In Title box, type e.g. name of your current computer. In Key box, paste your public key copied from RStudio. Press on "Add SSH key" green button below. Confirm access change by entering your GitHub password (if prompted).

.
1.10. You should get an email from [GitHub] notifying you that a new public key was added to your account
1.11. Restart RStudio.
1.12. From now, when creating a new repository in GitHub use SSH code to create connect your project to your GitHub account (see https://happygitwithr.com/rstudio-git-github.html, just use SSH not https).

2.1. For each repository: open related R project in RStudio. Display current url link used to fetch and push to GotHub for this project by entering in the Terminal pane:
​
git remote -v

You should get output similar to this (with your own USERNAME/REPONAME, where USERNAME is your GitHub username and REPONAME is the name of your GitHub repository):
​
origin https://github.com/USERNAME/REPONAME.git (fetch)
origin https://github.com/USERNAME/REPOSITORY.git (push)

This output shows what sort of url link you are currently using to connect to GitHub.

2.3. Verify that the remote URL has changed by repeating the code from step 2.1.:

git remote -v 

The output should look like this:

origin git@github.com:USERNAME/REPOSITORY.git (fetch)
origin git@github.com:USERNAME/REPOSITORY.git (push)

2.4. In RStudio Git pane, try pulling and pushing to GitHub (first time, you will get a message that new key was permanently added).
 
If this approach does not work, the simple way around is to delete a local project folder from your computer and cloning it from GitHub using SSH. If you have any files and sub-folders that are not tracked by git within that folder, remember to store/archive these elsewhere before deleting the folder.
 
You can read more about managing remote repositories using git via Terminal here: 
https://docs.github.com/en/get-started/getting-started-with-git/managing-remote-repositories

By Patrice Pottier

In a recent tweet, Sir Richard Evans shared the acceptance rates in the Journal of Contemporary History. Besides the low acceptance rate, a comment raised a public debate: the main reason for rejection was “poor English”. Tweeter users from all over the world highly criticised his opinion, highlighting that non-native English speakers are thus disadvantaged in the academic publication process, and that solutions exist to limit this bias.  

​Yet, Evans was not convinced, posting a second provoking tweet suggesting that “authors whose English is poor don’t of course realise it’s poor, otherwise they would have corrected it.”  Unsurprisingly, this second tweet generated another set of critics over Evans’ opinions.

Although I do not share his opinions, these tweets highlight a sad reality – publishing is hard, and it may be even harder for those whose English is not their primary language. Although Evans focuses on Contemporary History, I believe this applies to all fields in academia.  

In this assay, I share my journey at learning English and the language-related difficulties I faced in academia. The purpose of this assay is not to criticise Evans’ views directly, but to show a different perspective to his argument.

I am a white male who grew up in France, a highly developed country. English is taught at school from a young age, which provides an environment to learn and progress in English. France is a touristic country, and English is sometimes the only way to communicate with tourists. Travelling, if one’s economic situation is suitable, is also relatively easy within Europe, and English is once again, the gold standard for communicating in other countries. All the above reasons combined, one may expect French people to have a high proficiency in English, but the reality is different. Learning a new language is hard, and, although the reader of this assay may have learned a new language relatively easily, this does not apply to everyone. Financial barriers are also major constraints for travelling in English-speaking countries, which is the most efficient way at learning English.

Now, can you imagine how hard it would be to learn English when you grow up in a country where English is not the primary language, is not or hardly taught, with a difficult economic situation, and limited travelling opportunities? I cannot. I am deeply privileged by the country I was born in, the opportunities I had to travel, the fantastic pedagogy of my English-teachers, the similarities between English and French, and my learning facilities. I cannot imagine how hard it would be to learn English without these privileges. Yet, even with these privileges, I faced major barriers when I had to use English during my studies in Biological Sciences.

All my undergraduate studies and experiences of the natural world were taught in French. When I had to use English for academic purposes – I had to learn everything again. All the scientific terms, things as simple as the name of common animals – everything had to be translated. Fortunately, French has a Latin origin, which facilitate the translation. Still, this represents a major challenge that, I believe, many have faced when learning a new language and applying it to their studies.

At the end of my master’s degree, I had the unmatched opportunity to travel to the United States for six months. That was it. That was my opportunity at getting better in English - but I was terrified. I was terrified by my proficiency in English at the time, and how hard it would be to communicate my thoughts. Worse, I thought I would not be able to understand others. Hence, I prepared for my trip. Again, my privileges living in France allowed me to have a personal computer on which I could watch countless videos to improve my English. This “training” was helpful and I felt confident that, although not perfect, my English would be good enough to be understood and understand others.  

The reality was different. My first few weeks in the States showed me how unprepared I was. Even though I worked hard to learn English, I was not quite there yet. I could understand most of the conversations, but it required a high level of concentration. I could not understand most jokes, which made me feel socially awkward, and my communication skills were lagging. My flow of words was probably halved relative to French, and I would sometimes get stuck – unable to communicate what I intended to. Communication with your supervisors and peers is a crucial part of academic work. We generate ideas, discuss them with others, challenge them. We also raise issues and solve complicated problems. All of this represent a substantial part of a job in academia. Difficulties to communicate not only slow down the progress on those parts, but also delay progress on others. Again, I was privileged to be surrounded by supervisors and peers who were compassionate and supportive. I cannot imagine how hard it would be to navigate in such environment without support.

Besides oral communication, I quickly faced another barrier that relates to Evans’ tweets – writing. Writing in another language is exceptionally hard. Again, all my previous trainings were done in French and I did not know how to write in English. Academic writing also relies on references from the literature, which are mostly in English and require extra reading time. Eventually, I produced a piece I am proud of. Yet, I would have produced the same piece in significantly less time, and perhaps of higher quality in my native language.

Slowly, but surely, my English got better. I now have been communicating in English daily for nearly two years and most of my personal and professional writing is done in English. Yet, I still face some issues. In my view, the most troublesome is how different my personality is in English vs. French. I realised that there are some things one cannot translate from a language to the other, some things need to be adjusted more deeply. It is an ongoing challenge that needs to be acknowledged.

In summary, privileges can shape our success at learning a new language. Given that academia is English-centred, people whose English is their secondary language are disadvantaged in many ways, both at the professional and personal level. Facing language barriers not only slow one’s progress in the workplace, but also act as a burden on mood, well-being, and confidence – which may easily feedback on working performance. For every part of an academic journey, language barriers add an extra layer of difficulty and stress. The extent to which these barriers will act on one’s feelings is variable, but some factors like the economic situation of the country or family of origin, the geographical situation, or the similarities with the primary language, are non-exhaustive examples that are important to acknowledge.

Rather than filtering the writing performance of English vs. non-English native speakers, providing an environment where everyone can thrive would be more profitable. In a world where some inequalities are finally brought to light, it appears crucial to me to acknowledge our privileges, learn from other’s experience, and embrace, rather than excluding, diversity in academia and beyond.

by Hamza Anwer
As an undergraduate, I used to be fascinated reading journal articles. Seeing not only the amount of effort that went into doing science but also the writing and publishing for the world to see. There would have been a lot going on behind the scenes. It was something I aspired to do but even then, I knew it was going to be a long tough climb.

I started my PhD feeling a little overwhelmed. Looking up at the mountain I had to conquer, I started the climb with a monkey on my back, constantly reminding me that publishing was something I had not yet achieved despite completing my Honours.

I always had pride in my persistence. As an athlete, and competitive one at that, I always set myself goals with an end goal in sight: to win. Prior to winning my first football championship, I had played in several others…and lost. It made the feeling of victory that much sweeter. I had got the monkey off my back. My next championship victory followed not long after. It was a recipe I believed in: conquer the initial climb, enjoy the view at the top, and everything else will follow so as long as you continue to work hard.

Fast forward to the final year of my PhD. Not only had I made great strides in my climb, but the weight of that monkey on my back was getting lighter. I had learnt to carry it with me not as a burden, but as a reminder. Learning the ins and outs of what was required to plan my research, conduct it, write, and publish for the first time was exciting and something I will always value. It was not without challenges, however.

Working as part of a team, we first had to rigorously plan out the experiment and conduct it successfully. Following, we had to plan the analysis and put together reproducible code to ensure transparency. Writing up the manuscript seemed simple enough once we had mapped out our narrative and goals, however it took many sets of eyes and edits to ensure it was a worthy document to submit. Following submission, I was warned there was a decent chance at being rejected, however we received the manuscript back with positive comments, although a lot needed to be changed for it to be considered for publication. Putting together the reply for the editor was very time consuming but we knew it made our manuscript much stronger. After submitting with our edits, I had received a reply about a month later that it had been accepted for publication and was available online on my birthday, a pleasant surprise. Something I need to stress is that while this is my first published paper as first author, I could not have gotten here without the support of my lab members and supervisors who were with me every step of the way.

For now, that monkey is gone, but not forgotten.

My first published paper as first author is on measuring zebrafish anxiety with a new efficient assay that can better detect between-individual differences. Check it out here.

by Rose O'Dea

Peruse the website of the Inter-Disciplinary Ecology and Evolution Lab, and you will read that one of Shinichi’s mottos for this group is ‘Think like a scientist and act like one too.’ The way you interpret this motto probably depends on the way you conceptualise a scientist.
 
Perhaps you picture a scientist as someone one who uses critical thinking and rigorous methods to advance human understanding of the way the universe works. This idealised scientist works hard to form reasoned conclusions, trying to avoid the many cognitive biases and logical fallacies that they know they are susceptible to. They are intellectually humble, honest, and value constructive criticism from their peers. They do not hold tightly onto their beliefs, for they are always seeking disconfirming evidence. They are skeptical of authority and anecdote. Nullius in verba — take nobody’s word for it.
 
Or perhaps you have seen how scientists work.
 
Here at I-DEEL we think fondly of that ideal scientist. But our recent lab discussions have focussed on the messy reality of science in practice.
 
For lab meetings we’ve been reading* stories of scientists behaving badly: chasing metrics over answers, using sloppy or unvalidated methods, and ignoring inconvenient evidence. In our idealised vision of science, errors would be quickly caught and corrected. In reality, too many errors go unchecked, and too few rewards are offered for finding them. All this results in a lot of published research that is unreliable and cannot be reproduced.
 
It doesn’t have to be this way. Most scientists want to produce reliable work. They just need the training and the incentives to do so.
 
That’s why, over the last year, myself and other members of I-DEEL have been helping to from the Society for Open, Reliable, and Transparent Ecology and Evolutionary Biology. ‘SORTEE’ was launched last December, as a community-driven effort to improve the way ecological and evolutionary research is done and change the way researchers are evaluated.
 
Work is already underway to hold a virtual SORTEE meeting later this year, and you can join the growing community of nearly 500 SORTEE members by going to https://www.sortee.org/join/.
 
This brings us back to the moto ‘Think like a scientist and act like one too.’ I asked Shinichi why he chose this motto for his lab at the University of Otago, and what he originally meant by it. The answer? He wanted to capture the leap that students take when they first join a research lab: they go from memorising facts prescribed in textbooks, to generating and testing their own ideas, and finding answers to unsolved problems.
 
Now, I-DEEL is trying to use those skills to bring the messy reality of science in practice a little closer to our ideals.

*Recent lab meeting readings:
 
Rigor Mortis: How Sloppy Science Creates Worthless Cures, Crushes Hope, And Wastes Billions
By Richard Harris
https://richardharriswrites.com/
 
The Matter of Facts: Skepticism, Persuasion, and Evidence in Science
By Gareth Leng and Rhodri Ivor Leng
https://www.penguin.com.au/books/the-matter-of-facts-9780262043885
 
The Art of Statistics: Learning from Data
By David Spiegelhalter
https://www.penguin.com.au/books/the-art-of-statistics-9780241258767

Hanging on to the Edges:Essays on Science, Society and the Academic Life
By Daniel Nettle
https://www.openbookpublishers.com/product/842
​

by Cat Vendl

To Sydney for the whales (well, that was at least one of the reasons)
In 2016, I moved to Sydney to start my PhD at the University of New South Wales. My PhD investigated the airway bacteria in whales and dolphins. Sydney is the perfect place to study whales as every year between June and October thousands of majestic humpback whales roam its coastal waters migrating to and from their breeding grounds. I have always been fascinated by whales and the elegant way they move in the water. The whales and I certainly share the excitement for their fluid habitat.

The dark side of whale research
I was quite curious to learn that the population of currently around 30,000 humpback whales passing by Sydney every year was once severely depleted. In the 1970s and 1980s only a few hundred individuals remained. The culprit was easy to spot as the industrial whaling fleets of the 20th century were infamous. However, the more I learned about the issue the more intrigued I became. It wasn’t ‘just whaling’ that almost wiped out the entire population of east Australian humpback whales. What happened there was a brutal yet surprising event in modern history that a world-leading whale expert once called ‘one of the greatest environmental crimes of the 20th century’. The culprits are long dead, but the memory of their crimes lives on.

The text below was originally published in German in Wissenschaft' (Springer Nature, German version of Scientific American). The photos are reproduced with permission from their current owner.
​

References:
Clapham, P. and Ivashchenko, Y., 2009. A whale of a deception. Marine Fisheries Review, 71, pp.44-52.
Clapham, P., Mikhalev, Y., Franklin, W., Paton, D., Baker, C.S., Ivashchenko, Y.V. and Brownell Jr, R.L., 2009. Catches of humpback whales, Megaptera novaeangliae, by the Soviet Union and other nations in the Southern Ocean, 1947–1973.
Ivashchenko, Y.V., Clapham, P.J. and Brownell Jr, R.L., 2011. Soviet illegal whaling: the devil and the details. Marine Fisheries Review, 73, pp.1-19.
Ivashchenko, Y.V. and Clapham, P.J., 2014. Too much is never enough: the cautionary tale of Soviet illegal whaling. Marine Fisheries Review, 76, pp.1-22.
Rocha, R.C., Clapham, P.J. and Ivashchenko, Y.V., 2014. Emptying the oceans: a summary of industrial whaling catches in the 20th century. Marine Fisheries Review, 76, pp.37-48.

by Losia Lagisz

After months of complete or semi-isolation, we were finally able to hold a proper i-deel lab get-together. 

We were super lucky with great wether, food and company and a new fantastic place near the campus – a small, but fancy, park near the new apartments at Newmarket. Some lab members even managed to sneak out to test a giant double super-slide in the playground behind the BBQ spot.

Thanks to Cat and Shinichi for organising, and to everybody for showing up and sharing food, drinks and stories!
​

by Erin Macartney

My first experience of academic related stress was at 13 when I was studying for my first high school exams. Unfortunately, I got so stressed that I couldn’t sit my exams at all. Since then, I have developed a pretty substantial toolbox of stress management techniques that I use almost on a daily basis. These were particularly useful for getting through my PhD mostly stress free. 

While some of these tools may sounds cliché, they have helped me a lot and hopefully they can help you too. 

1) Spend time on time management 

A PhD can seem like an insurmountable task, and even individual chapters can feel like a steep slope to climb. One of my main ways to make big tasks feel less overwhelming is making mountains into molehills. One way to do this is to set goals at different scales. Firstly, break your large goals (e.g., complete a PhD) down into what you want to achieve in a year (e.g., collect data for a chapter and publish a nearly complete one). The next step is to break these goals into a set of smaller milestones. For example, plan out when you want to have a finalised plan for data collection, when you expect data collection to be done by, and set a predicted date to have submitted your manuscript to a journal. After this, it is much easier to break down your days and weeks into small tasks that will help you get you to your milestones and ultimately achieve your bigger goals. 

I have found that setting these daily and weekly goals really helps me switch off at the end of the day or for the weekend by quieting that nagging back-of-the-mind voice telling me that I should be working. 

Note: Ensure that you set realistic goals otherwise you risk increasing stress. Also, life can get in the way sometimes, so don’t be afraid to be flexible and shuffle things around. 

A couple of helpful tools that can help you plan out your time: 

• Todoist lets you plan your week as well as create to-do lists for different projects
• Google Calendar (or any calendar): Use a calendar to plan out your milestones
• A workflow pipeline (see Fonti’s blog post on research pipelines). Your pipeline should have tasks in each quadrant to prevent a ‘blockage’ so that you have a consistent ‘flow’ of chapters/publications

2) Work out when you work best

One of the benefits of doing a PhD is that you can work whenever works for you. Getting to know when you work best and prioritising that time is so helpful in getting the most out of your day (or night) and prevents you from forcing yourself to work hours that aren’t right for you. For example, I concentrate the best as soon as I wake up. Instead of spending my most productive hours getting ready for the day, I make a coffee and generally do some writing or analysis first thing in the morning. After lunch, my brain slows down, so this time is best for lab work. I enjoy reading in the evenings, so this is often a good time to read papers, proofread some writing, or review manuscripts. As you can see, my day doesn’t fit into standard working hours and is broken up into three segments where I can take breaks in the middle to exercise, cook meals, sit in the sun etc. This timeline won’t work for everyone, but my point is to figure out what works best for you and plan your work around that. This will hopefully prevent those hours sitting at your desk being unproductive and feeling guilty. 

3) Find what helps you relax

Everyone needs time in their day to switch off and relax without feeling guilty. Find something that helps you wind down and try to fit that into your daily schedule. This may be doing some cardio to burn off energy, spending time outdoors, watching a trashy TV show, reading a book, having a glass of wine, or mediating etc. This is important for giving yourself a chance to wind-down so you can return to work feeling refreshed. 

If you struggle to turn your brain off, try to make your space as relaxing as possible. I find using an oil burner/candle, dim lighting, and attempting to stay away from screens before bed is helpful (staying away from screens is easier said than done but using ‘bedtime’ mode is quite helpful).

These are some apps and youtube channels that you may find helpful: 

• https://www.youtube.com/user/yogawithadriene
• http://www.c25k.com/
• https://zombiesrungame.com/
• https://www.headspace.com/

4) Talk it out

Having a support network is really important for talking through problems and providing a respite from ruminating thoughts. It’s good to have a balance of friends within academia that understand what you are going through as well as friends and/or family outside of academia that can give you a different perspective. Try to make time for these relationships. 

If you feel like you want professional help or a completely objective ear, these are some options you could use: 

• UNSW counselling service for students
• Benestar UNSW counselling service for staff
• Medicare covers up to 20 free sessions for a majority of psychological practitioners
• PSS may also be an option if you meet the criteria

Just remember that stress is a normal part of life. Figuring out what tools work for you will hopefully make navigating a PhD (and life) a little bit less stressful.  

by Dony Indiarto

Research that you do interests a wider range of people than those who read research journals. - David Lindsay

In a world of short attention span, three-minute thesis (3-MT) is one way of communicating science. Scientists are expected to share their cutting-edge research into a three minutes long talk in plain language so that everyone can understand. This may seem trivial, yet preparing a 3-MT can be a journey to think and reflect on the essence of our work.

At our School (BEES), doing a 3-MT talk is compulsory for every third-year PhD student. I used to think this is as a joke. Most of us have come up with sophisticated analysis and exciting findings to share on the third year, and the School only gives us 3 minutes?!? But I was wrong! Spending a lot of time studying some niche-topics within our discipline could turn us into a 'caveman'. We may have no idea how some concepts that seem intuitive for us can make someone's forehead furrowed.

While some scientists are naturally good at sharing their research to their high-school mates at a local pub, most of us need some considerable preparation. Plus, in this unprecedented time, we have to deliver the talk virtually. Giving a 3-MT talk online may not be as exciting as standing in front of crowds, I believe there are several things we can do to spice up the talk. Here is the short-list I've gathered so far:

1. Narration*
   1. Prepare a video-audio script (as many film students do!)
   2. Identify the highlight of your research.
   3. Tell the audience how you did it!
   4. Plan a storyline; identify the at the hook at the beginning, maybe a joke in the middle, and a punchline at the end.
   5. Identify uncommon words/jargons and replace them with layman's terms whenever possible.
2. Voice
   1. Clear pronunciation has never been this important. Rehearse, rehearse, rehearse!
   2. Adjust your microphone (adjust the freq/pitch), and do a test video call.
   3. Speak like you are in a real conversation. Humans can read better than SIRI!
3. Slides
   1. Be comic sans' ish only when you do it by purpose, otherwise, your slides are ugly.
   2. Sync your slide with the spoken narration
   3. Cut down texts, images/animation should be self-explanatory.
4. Presence**
   1. Maintain eye contact makes the conversation a bit more natural.
   2. Body language remains (e.g. posture and gestures)
   3. Position your camera accordingly, adjust the lighting and the background (again, a test call with friends/colleague can be helpful).

*The utmost important aspect IMHO; **Turned out to be unimportant for the judges in the previous 3-MT Aug 12, 2020.
​
PS: I don't claim any of the point listed above as mine. I've collected these wise suggestions from random chats with friends and colleagues, as well as tips from the judges. All of the suggestions, of course, are subject to criticism.