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Changes to GitHub access for RStudio workflows

22/6/2021

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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.
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1. Setting public SSH key for your compute

​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 (?)]
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1.2. Options box appears. Press on GIV/SVN icon in the left side menu.
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1.3. Press the "Create SSH Key..." button.
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​1.4. Enter Passphrase and Confirm it (optional). Press "Create" button.
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1.5. A a new window with some key info will appear – it confirms that a file with SSH key pair info was created and stored on your computer. Close this window and press "Apply" button at the bottom of the Options window.

1.6. Still in the Options window, press on "View public key" link and copy the content of the new window box to you clipboard.
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1.7. Log into your GitHub account online (via web browser), go to Settings from the top right corner (next to you photo) and select “SSH and CPG keys” from the left-side menu.
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1.8. Press "New SSH Key" green button.
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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).
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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. Switching remote URLs from HTTPS to SSH for your existing repositories

Note: You should have already completed step 1, so that the SSH key is saved in both RStudio and GitHub . Now it is time to point each of your local repositories to its matching SSH link.
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:
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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):
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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.

​2.2. Change your remote's url from https to SSH by typing into the Terminal window (use exactly the same USERNAME/REPONAME as you got in the output of the previous step 2.1.):

git remote set-url origin git@github.com:USERNAME/REPONAME.git

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
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Onto language barriers

19/4/2021

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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.  
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Sir Richard Evans’ first tweet on acceptance rate in the Journal of Contemporary History
​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.
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Sir Richard Evans’ tweet following the heated comments with the Tweeter community

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.

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Getting the monkey off one's back

25/3/2021

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Picturehttps://www.flickr.com/photos/elycefeliz/4537192775
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.

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Join SORTEE: The Society for Open, Reliable, and Transparent Ecology and Evolutionary Biology

23/2/2021

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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.

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*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
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Mass killing for no reason? The paradox of Soviet whaling

24/1/2021

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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.
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Mass killing for no reason? The paradox of Soviet whaling

Japan, Norway and Iceland are the countries we usually associate with whaling. But are they really to blame for the massive decline of whale populations in the 20th century? The truth is much more complicated and includes a secret that was kept for almost 50 years.

The waters surrounding Australia and New Zealand once had thousands of migrating humpback whales. In 1961 this picture changed and all of a sudden the Southern Ocean resembled a vast aquatic desert. The shore whaling stations in NZ and Australia closed down, as most of the whales were gone. Almost 26,000 humpback whales had disappeared within 2 years and at the time the reason was unknown.
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A secret global player in whaling
The secret was revealed only in 1993 and it became public knowledge who the actual perpetrator was. In only 30 years of intensive whaling (about 1948 to 1975) the Soviet Union (USSR) had not only almost destroyed the humpback whale population around NZ and Australia, but had caught about 370,000 whales in total, mainly in the Southern Ocean. At least 180,000 of those catches were illegal.

The USSR entered industrial whaling on a large scale comparably late in 1946, when most whaling nations had already been part of the business for decades. In the same year, 15 countries came together to create the International Convention for the Regulation of Whaling (ICRW) and the International Whaling Commission (IWC). The treaty they all signed (including the USSR), was to end the reckless whaling strategies that had significantly depleted whale populations world-wide. The purpose was not whale conservation as such, but turning commercial whaling into a sustainable industry. The treaty determined catch quotas, introduced minimum sizes for captured animals and completely banned whaling for a few particularly endangered species like the right whale.
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Breaking the treaty in silence
As it turned out, the USSR had little intention to stick to the treaty. Every season the country sent out up to 5 whaling fleets with a large factory ship at its heart. Each populated by up to about 600 crew members, the ships were like floating cities. The processing on board was highly efficient: A whale was taken to pieces within 30 min. Up to 25 smaller catchers and scout boats accompanied each factory ship. What happened to the whale depended on its species: Toothed whales, predominantly sperm whales, were turned into industrial oil and animal food. Only the meat of baleen whales, like blue and humpback whales, was used for human consumption. Their oil provided the base for margarine. A large percentage of all whale carcasses were turned into bone meal and used as fertilizer.

The number of whales killed increased every year. Catcher boats regularly caught more whales than the factory ships could process. Hence the carcasses started rotting while floating behind the catchers. As a result the flensers often stripped off only the blubber of the carcasses and threw the remains back into the ocean.
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The Soviet whaling paradox
Why did the USSR kill so many whales, even though the country had comparatively little use for their products?
The devil lies in the detail of the economic system of the USSR. Being a worker in the Soviet whaling fleet came with many privileges: Salaries were among the highest paid in any industry, due mainly to large performance bonuses. Before the start of every whaling season, the government set monthly and yearly production targets (as they did for every Soviet industry). In whaling this determined the number of whales to be caught. Production targets had to be met. If targets were not met, everyone involved expected punishment. Supervisors reported on the performance of their subordinates and if output was low, employees lost their jobs. On the other hand, if the fleets met or even exceeded the target, the government rewarded employees with generous bonuses. Motivation to meet or even exceed the production target was naturally high. The production output of the previous whaling season often set the target for the upcoming year. Yearly targets inevitably kept increasing at a greater rate. In addition, workers in the whaling industry were well-regarded in the public eye with large celebrations at their home port on their return to the USSR. Newspapers honoured the whaling crews like heroes.

​Soviet whaling was a highly subsidized industry and it quickly developed into a massive financial loss for the country. As with any other industry in the USSR, whaling was not primarily meant to provide communal profit but to show proof of the efficiency and superiority of the communist system. In the case of whaling, proof was provided by being able to kill more whales than any other nation in a relatively short time.
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Soviet whale scientists: Ridiculed and silenced
In theory, catching numbers were in accordance with the conservation status of the targeted whale populations. Almost every factory ship had scientists on board who conducted research on the whales. The scientists regularly submitted recommendations on sustainable yields to government authorities. Most of the time, their advice was ignored. A group of Soviet biologists while well aware that any opposition to the status quo would severely impact their careers, repeatedly criticised the country's whaling practices in the 1960s. One was were eventually summoned to the Minister of Fisheries in Moscow. The biologist stated that if whaling continued at the current rate there wouldn’t be any whales left for their his grandchildren. The Minister of Fisheries responded to these objections by stating that ‘Your grandchildren aren’t the ones who can remove me from my job!’
To avoid being sanctioned for breaking international law, the USSR submitted reports with falsified data to the International Whaling Commission for more than 3 decades. The true dataset was considered highly classified. Ultimately, in 1993 the Russian whale biologist, Alexey Yablokov, who had worked for the whaling industry was the first to break the silence and set off an avalanche of publications about the true nature of Soviet whaling.
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‘The greatest environmental crime of the 20th century’
The commercial whaling activities of countries like England, Denmark, Norway, USA, Japan, South Africa and Chile had already significantly depleted the majority of world-wide whale populations, before the Soviet Union started its massive whaling campaign in the late 1940s. However, the whaling activities of the USSR caused a downward spiral of many populations to the point where the Southern Ocean humpback whales and the North Pacific right whales were almost extinct. The humpback whales were lucky. They have recovered remarkably over the past decades. Their numbers are believed to have almost reached pre-whaling status. However, the North Pacific right whale is currently facing a different fate. Only a few dozens of individuals are left in the eastern North Pacific population, and they may well never recover. Dr Phillip Clapham, a world's leading expert on large whales, called the illegal whaling activities of the USSR ‘one of the greatest environmental crimes of the 20th century’.
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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.
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Lab snorkeling at Little Bay

20/12/2020

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by Erin Macartney

Now that summer has officially begun, members of the I-DEEL lab spent a sunny Sunday snorkeling at Little Bay. While it was a little choppy out the back with some grey nurse sharks loitering around, we found some great sea creatures in the sheltered part of the bay, including some cuttlefish, an octopus, a moray eel, lots of colourful little fish, and some cool shimmery blue algae.
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It was a great way to welcome summer and enjoy some of Sydney’s amazing beaches right at our doorstep!
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Lab BBQ – together again!

10/12/2020

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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!
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Keeping stress at bay during a PhD (and life)

20/11/2020

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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.  

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3-MT Hacks for Zoomers

1/11/2020

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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.
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Socially Distant Science: Virtual Conferences

16/8/2020

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by Sammy Burke
Picture
Virtual group photo taken at vISEC of conference attendees [https://www.isec2020.org/]
In June 2020, the International Statistical Ecology Conference (ISEC) moved to a virtual setting (vISEC) as a creative solution to the current travel restrictions presented by the coronavirus. Despite the challenges of a new format, the conference was a resounding success and a wonderful experience. Conference attendance soared over past conferences with more than 850 participants – a statistic attributed to the accessibility of the conference to those with limited means to travel.

Participants and organizers were connected via a Slack workspace which acted as a program guide, Q&A forum, news bulletin, presentation and discussion rooms, and even social centers for chatting over a coffee. This streamlined the user experience, allowing for easy switching between mingling and learning. While this space was available at all hours, activities such as plenary talks and pre-organized social events (including a fun trivia night) were centered around two time slots which allowed for participants in any time zone to have at least one live session they could attend. This international accommodation made the conference incredibly accessible to all.

One of the great perks of conferences is the opportunity to network and meet other researchers in a similar field from other institutions. At in-person conferences, you can naturally introduce fellow lab-members to renowned colleagues during casual interactions. At virtual conferences, you must introduce yourself to someone in a direct message or join a random call with strangers who may have already been chatting for some time. You may find yourself overthinking when the right time is to join in a conversation, or how to smoothly contrive a new connection. These mildly awkward barriers seem to decrease the amount of mingling in “public” spaces.

Time also plays a role in mingling opportunities at virtual conferences. Because participants are spread out across multiple time zones, the people with whom you can chat in real time becomes skewed to those who share your time zone. For example, if you consistently attend the conference at 6pm AEST, you are unlikely to encounter many American researchers who are awake at 4am EST. However, with direct message chat features like those in Slack, you may still be able to reach out to someone with whom you’d like to speak. This feature nearly guarantees the opportunity to ask a question of almost any speaker during the conference, where you may not have gotten the chance to see them across a crowded room at an in-person conference.

I’ve always struggled with planning a schedule at conferences because there are often multiple talks I’d like to attend which occur at the same time or in opposite areas of the conference space. Virtual conferences are the best solution for this – allowing participants to switch easily between talks by simply clicking into a different video. At vISEC, participants were able to watch every talk as they were archived for viewing after the live session ended. This accommodated an international audience, allowing those who would normally be asleep during the live session to still hear it, or to just catch some extra information, at a more convenient time.

Many successes of this conference stemmed from an effective utilization of online services. This includes the “Slack Workspace” service - a website that allows teams to organize communication platforms into channels for different topics or groups. The video communication and streaming services Zoom and YouTube were also utilized for the presentation components. The vISEC organizers generated a virtual conference hub as well as a virtual stage that mirrored a near-normal conference experience for its participants around the globe.

While the virtual conference design format arose from the unprecedented circumstances of 2020’s global pandemic, many successful aspects of this virtual conference may – and probably should – be applied to future conferences. The connectivity, accessibility, and organization were of a high caliber, as were evidenced by the conference’s large attendance and positive reception. We can only guess where this will lead the future of international conferences, and how features of this conference will shape future experiences in science research networking and collaboration.
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