The time has come for me to move on to the next adventure. I’ll be leaving the I-DEEL group to start up my own group at the Australian National University! My time at UNSW was nothing short of amazing, and I must admit, I am very sad to be leaving all the wonderful people that are part of the I-DEEL group, and UNSW more generally.
 
I recall back to when I first started; it was just Shinichi, Losia, Rose and I. How much it has changed since 2015. Us four kicked off all the fishy work together, in collaboration with Dan Hesselson at Garvan. Much of the initial work really formed the foundation for Rose’s amazing set of empirical projects…I think Rose is one of the most efficient people I know and probably has collected more data than just about any PhD student on the planet (although, I think Fonti is a pretty close second). I’ve always been so impressed with how she can juggle huge experiments and then two weeks later come with a wonderfully written manuscript (I need to learn how to do that). In any case, I’m excited to see what Rose gets up to in the future, no doubt it will be very cool stuff.

In addition to all of us, the group has now expanded to include Susi, Dom, Hamza, Maddy, Nathan, Yong and Donny. It’s actually getting so large now that I think we need to start holding lab meetings in a bigger room, and probably cater in sweets every week so Rose and Fonti don’t kill themselves baking so much. Nonetheless, it has been very exciting having them all as part of the group and I’d like to thank them for being such great people and teaching me a bunch.

Of course, I can’t thank Shinichi and Losia enough for all that they have taught me. It has been one of the most pleasant, productive and enriching periods of my academic career and I really could not have landed the job at ANU without their support and encouragement. I’m really looking forward to continuing working with them up until they retire. Although Shinichi says this will happen, I may actually retire before him ;)

While I am leaving, I’m not that far away, and I am really excited that I can continue working with all the wonderful people in the I-DEEL group for some time to come; probably forever given how many papers we need to write! Shinichi and I should probably tally this number up at some point; thankfully his “sticky note” wall will remind us of all the fun times we still have ahead!

by Yong Zhi Foo 

Travelling is an essential part of academia. Academics travel for many reasons, ranging from short-term conferences and research visits to long-term resettlements for new jobs. But managing the logistics of moving to a new place can be daunting. Having recently moved to Sydney to join the I-DEEL lab for a research fellowship, I thought I might share some useful tips on moving to Sydney.

Housing rental 

Finding a place to stay is probably one of the biggest issues for someone moving to Sydney, where rental demand is always high (although apparently the housing and rental market is cooling down at the moment). So, this is one of the main things that I will be talking about in this post. There are several things to take note when finding a place to stay:
 
Sources of rental: There are two main options when renting: finding your own place or sharing with others. Some of the popular websites for finding your own rental place include domain.com.au and realestate.com.au. Most housing agents advertise on these two websites. One important thing to note about the ads on these websites is that the photos are not always representative of the actual property. If the ad does not explicitly say that the property is furnished, you should assume that it is not, even if the photos show a fully-furnished place.
 
If you are keen to share with someone else, flatmates.com.au is a good option. I found my current place from there. For shorter-term visits, there is Airbnb.
 
Costs: Just as a ballpark, at the time of this blog, a decent (i.e. not breaking apart, does not have mouldy walls/carpets etc.) 1-bedroom apartment in suburbs surrounding UNSW costs at least AUD450 per week (yes PER WEEK). At this price, the place would most probably be unfurnished. For sharing, depending on the number of people that you are sharing with, the price would be north of AUD200 per week.
 
Besides the weekly rent, there are other potential start-up and ongoing costs, such as rental bond (usually 4 weeks’ rent), purchasing furniture and white goods, home internet, and utilities.
 
Where to stay: Many people working/studying at UNSW stay in the nearby suburbs, such as Randwick or Kensington, for the convenience. If you enjoy going to the beach, Clovelly and Coogee are pretty nice and still relatively close. If you are keen to stay closer to the City, places like Surry Hills or Paddington might suit you. I chose my place based on proximity to the food places that I like (see the photos below for evidence :D).

When to start looking: Rental in Sydney moves really quickly. Plus potential tenants are required to inspect a place before they can submit a rental application. Therefore, I would not advise people start looking too early. Instead, plan your move so that you have some time to go around and inspect places personally at the start. You can probably begin looking on websites a few days ahead to create a potential shortlist of places.
 
Getting around
 
Sydney is pretty well connected in terms of public transport. If you are taking public transport, get an Opal Card and load funds into it for travelling on trains, buses, and ferries.
 
Tip: There are several options for traveling to and from Sydney Airport, including train, bus, taxis, etc. I find that Uber offers the best value for money. Once you make a request, your Uber ride will be directed to a special pick-up spot. Just go to where it is indicated on the app to wait for your ride.
 
Mobile/Internet
 
Some of the major mobile/internet network providers include Vodafone, Telstra, and Optus. Some of my friends have used companies such as TPG and reported good things about them. A typical mobile plan is around AUD50 and home internet is around AUD60 and above. Pre-paid is another option for mobile plans.
 
Banking
 
Any of the major banks, like Westpac, ANZ, or Commonwealth should fit your needs. Just go in and speak to the banking staff and they will sort you out. With any banking or mobile applications, international people will need to bring their passport for identification purposes.
 
Hopefully this post will be of use to people moving to Sydney! 

by Shinichi

It has been nearly 4 years after starting I-DEEL with only 4 initial members (Losia, Rose, Dan and me in 2015). We now have a bigger group with over 10 people. Great (yet sad) news is that Dan got a job at the Australian National University (ANU) and is leaving us soon. I often tell Losia that I want to clone myself because I chronically have too much to do. Dan is probably the closest it can be to my clone. Dan, however, is even better, as he is more patient and codes much better than I could. It will be hard without his capable hands. At the same time, I am curious about what a cool research group Dan will establish at ANU (farewell!).

It has actually been a little shy of a decade since I got my first job as a lecturer at the University of Otago. And I have just achieved my long-term goal of becoming a full professor. At this special occasion, I think of two things. First, I have been extremely lucky with people I have worked with. Among these people, I have my 3 wise men – Jarrod Hadfield, Wolfgang Forstmeier and Tim Parker. It is especially memorable that open science movement brought all of us together to work on the same publication. Second, working smart is really important although some tasks just take a lot of time. Around 2 years ago, I decided to get up early and work from 6 am. This gives me 2 hours of an uninterrupted working time before breakfast (especially great for writing).

For now, I seem to have lost an audacious goal to pursuit (I need to find one soon). But, for the time being, I like the sound of this: “Japanese working ethics and Scandinavian efficiency” (i.e. working hard and smart). Actually, Susi told me about this the other day because, she thought, I was unusual in asking both from my people not just one (i.e. asking for a Darwinian demon = no trade-off). I believe striving for this principle will bring something amazing over the next 10 years or so not only to me, but to all. I will make this as an ideal for I-DEEL.

by Losia Lagisz

Managing research projects is not easy. It gets even more complicated if there is more than one person involved. Not only many project participants need to know what needs to be done and by whom, but also what others just finished and what they are currently working on. This applies especially to meta-analyses.

Robust meta-analytic process requires at least 2 people involved in screening and extracting data. The other steps of the process (planning, searching, analysing and writing up) also greatly benefit from having more than one person involved. Large teams are not uncommon and the whole process can drag for months and even years. Both large and small teams need efficient communication and job management tools to get a good quality output in reasonable time.

There a few communication and job management software tools that worked for us, so far. For general, lab-level, across the projects and teams, task management we use a Todoist (basically an online “to-do list”), and for communication we use Slack. Last year, we started using Workstreams add-on for Slack, which appeared to be a good tool for managing systematic review and meta-analytic projects.

Workstreams have at least three big advantages:

1) Workstreams are integrated with Slack – so, no new sign-ups, setting and all the hassle of new system. Slack channels can be used to display alerts on what is happening with the tasks and you can also use shortcuts directly from Slack to crate tasks and change their status.

2) Workstreams are visual – the system it is based on a concept of a Kanban board (see the screenshot of one of our taskboards, below). Rather than just displaying the list of tasks that need to be done, it has three columns (you can add more and customise). The default columns are: planned, in progress and finished – you can drag the tasks between the columns, as needed. The tasks can also be assigned to people, labelled, priority reordered, commented on, have attached files, etc. So, Workstreams have quite a lot of functionality, but they are also easy and intuitive to use.

3) Workstreams are free - at least the basic version. The PRO version is quite pricey (user/month $9.99) and it comes with a few more functions, of which only one is really useful – setting deadlines and reminders (however, we can go around this problem by using /remind bot function from Slack).

You can learn more about Workstreams here. From my experience, if used consistently by the team members, Workstreams (with Slack) is a good tool for managing research projects such as systematic reviews and meta-analyses (and other projects), especially if you are not a big fan of traditional (even digital) to-do lists.

Last week (14-15 Nov), I went to Melbourne for a workshop (“From Replication Crisis to Credibility Revolution”). The workshop was hosted by my collaborator and “credibility revolutionary” Fiona Fidler.

I suspect many workshops and mini-conferences of this nature are popping out all over the world as many researchers are very much aware of “reproducibility crisis”. But what was unique about this one is its interdisciplinary nature; we had philosophers, psychologists, computer scientists, lawyers, pharmacologists, oncologists, statisticians, ecologists and evolutionary biologists (like myself).

I really like the idea of calling “reproducibility crisis” “credibility revolution” (hence the title). A speaker at the workshop, Glenn Begley, wants to call it “innovation opportunity” (he wrote this seminal comment for Nature). What a cool idea! And these re-namings make things a lot more positive than a bit of doom-and-gloom feel of “replicability crisis”. Indeed, there are a lot of positive movements toward Open Science and Transparency, happening to remedy the current ‘questionable’ practice.

Although I live in Sydney, I was also in Melbourne early last month (4-5 Oct) for a small conference. This is because Tom Stanly invited me over, as an evolutionary biologist, to give a talk on meta-analysis to a bunch of economists who love meta-analyses. To my surprise, I had a lot of fun chatting with meta-enthusiastic economists.

Tom is not only an economist but also a credibility revolutionary, like Fiona. He has asked me to invite ecologists and evolutionary biologists to comment on his blog about a credibility revolution. It is an excellent read. And if you can make comments to join the conversation, Tom will appreciate it a lot, and get conversations going. Disciplines need to unite together to make this revolution successful or make the most of this innovation opportunity. So, join the credibility revolution!

by Rose O'Dea

Measuring fish. In my short research career this is the activity I’ve done the most. ​Whether measuring mosquitofish or zebrafish, the method has been:

1. Photograph fish next to a scale
2. Rename photo with the ID of the fish and the date
3. Measure photo using ImageJ

Here I share my tricks to renaming photos using R.
​

Step 3: Generate a file with the name of each fishTo link the marking of the fish to their records, we save a file that contains three pieces of information: the tank ID, the fish ID, and the marking of each fish. The file is exported from our master records, and requires a bit of manipulation so that we only have the records of the marked fish in our particular tanks. In this example we are only renaming photos from the tank called “DTG03”.

# note that working directory is already set to our project folder (this is automatic if you use an R Project)
# importing excel document
library(readxl)
marking <- read_excel("Fish Records.xlsx", sheet = 1)
# renaming columns to remove "::" (which filemaker uses this to distinguish related table fields)
names(marking) # before

## [1] "fish_group_ID"
## [2] "individual_fish main 3::fish_indiv_ID"
## [3] "individual_fish main 3::marking"

names(marking) <- gsub(".*:", "", names(marking)) names(marking) # after
## [1] "fish_group_ID" "fish_indiv_ID" "marking"

# finding fish in the tank "DTG03", which we are renaming
# the problem is Filemaker doesn't export the repeating records for fish_group_ID, so we need to
# take the first instance of DTG03, and every subsequent NA until the next tank record
marking <- marking[which((marking$fish_group_ID == "DTG03") == T):nrow(marking),] # first record of DTG03
marking <- marking[1:(which(!is.na(marking$fish_group_ID)==T)[2]-1),] # removing everything not in DTG03

Step 4: Import the old file names, and create a corresponding vector of new file names.

old <- list.files("./original_DTG03_15_03_17") head(old, 5)

## character(0)

# Taking the markings of these fish so that they can be matched to their unique IDs
photomark <- gsub(".JPG", "", old) head(photomark, 5)

## character(0)

# Using indexing to check we're using `match` correctly
marking$marking[match(photomark, marking$marking)] == photomark # all match

## logical(0)

# saving JPEG names of new photos
new <- paste0("15_03_17_", marking$fish_indiv_ID[match(photomark, marking$marking)], ".JPG")
head(new, 5)

## [1] "15_03_17_.JPG"

Now we should have two vectors of equal length for the old and new names of photos:

length(old) == length(new)

## [1] FALSE

If this isn’t TRUE, then we need to go back and work out why. Usually one of the photos has been mislabeled, but this can also catch bigger mistakes such as missing or misplaced fish.


Step 5: Rename photos.First we will create an empty destination folder where we want the photos to go: in this case it’s called photos_to_measure. We then add the file path to the old and new file names.

oldfile <- paste0("./original_DTG03_15_03_17/", old) head(oldfile, 5)

## [1] "./original_DTG03_15_03_17/"

newfile <- paste0("./photos_to_measure/", new) head(newfile, 5)

## [1] "./photos_to_measure/15_03_17_.JPG"

file.rename(from = oldfile, to = newfile)

​## [1] TRUE

​Note that this function file.rename will transfer the photos from the old folder into the new folder, leaving nothing behind (i.e., something’s gone wrong if the old folder isn’t empty):

​Not just for fish photos!

Whenever you want to rename a bunch of files, file.rename could save you lots of time.


R is found in tRial and eRRoR

file.rename is a base function. Whenever I discover that something I’ve been doing in R for ages can be more easily done using a simple base function, I’m alternately amazed and infuriated. Before I found file.rename I renamed thousands - thousands! - of photos using a looping method that is more complicated and slower.

library(jpeg)
oldfile <- paste0("./original_DTG03_15_03_17 copy/", old)
newfile <- paste0("./photos_to_measure/", new)
for(i in 1:length(newfile)){
    writeJPEG(image = readJPEG(oldfile[i]), target = newfile[i], quality = 1)
}

I don’t regret the time it took me to discover file.rename, for a couple of reasons. The loop allows you to specify the file size of the renamed image by specifying quality on a scale form 0 to 1 (see ?writeJPEG). In our database we sometimes store photos of important fish, and to keep the file size lower it’s useful to export these photos with quality = 0.3. More importantly, R is about the journey as well as the destination. That small piece of code I wrote in 2016 - which took at least an hour of trial and error! - was the first loop I ever wrote and used regularly. My inelegant code taught me a lot, and watching it rename photos was immensely satisfying. Still, we need to pick our R battles, and I hope file.rename will leave you more time for your own.

by Susi Zajitschek
​​
​The fast pace of life that rules our modern world can have profound effects on our wellbeing. Burnout and depression have unfortunately become common in many professions, and mental health problems are also accumulating in academia. While it seems to be a topic that isn’t often talked about – sometimes it seems “we” (scientists) are not supposed to feel unhappy – after all we are following our chosen part, directing our own research questions – and are getting paid for it, too … (I won’t be getting into why science is important now, and ways to defend it to sceptics – that is a topic for a future blog post!)

​Stress can be avoided (at least to some degree). And here I mean – take measures to stay on track, not avoid working! Procrastination will not solve your problem, but merely add guilt and more stress later on.

• Being organised and able to prioritise (and re-prioritize!) can help seeing the big picture while dealing with the small steps that will take you in the right direction. On a weekly basis, setting daily tasks and anti-procrastination deadlines for the not-so preferred tasks (such as writing up that one experiment that just didn’t show clear-cut results) can help. Having a “what do I want to achieve within the next 5 years?” plan that also identifies not only your overall goals, but also the skills that you need to acquire, and will identify misalignments early. That way you may avoid having to wonder why you wasted a large chunk of your life on something you actually don’t really want to do.

 

• Should stress and anxiety become overwhelming after all, try mediation and relaxation techniques. Even a few minutes of just breathing can help calm down and de-clutter your mind, even if in the heat of that moment it may seem like you might be wasting your time. Nonetheless, stress clouds your thinking, and mediation helps to focus your mind. Not taking the time to re-set is like being the wood-cutter who says “I don’t have time to sharpen my axe, there’s too much wood to cut”!

 

• Work-life balance: Brooding over your projects all day and night may seem admirable, but sacrificing social contacts and hobbies for work can negatively impact your mental health. It is important to shut off sometimes, relax, do something you love! Solutions to problems often present themselves after a break. Having hobbies and friends will help with that!

 

• Physical exercise and sufficient sleep are well-known factors contributing to mental health, so make sure to work out from time to time, and don’t sacrifice sleep on a regular basis (sometimes deadlines will require an all-nighter, but don’t let this become a habit – consider ramping up your organisational and time management skills instead!).

 

• And last but not least – attitude… This of course is a life-long task to accomplish, much easier said than done, and deeply philosophical. But a positive outlook and seeing learning opportunities in the most adverse of events make you resilient, and not to let stress direct your life. Here some quotes from famous people on life attitude: 

We can complain because rose bushes have thorns, or rejoice because thorn bushes have roses.
​Abraham Lincoln

Whether you think you can or can’t – you are right. 
Henry Ford

​Life is a shipwreck, but we must not forget to sing in the lifeboats.   
Voltaire

by Rose and Losia
​
Originally published as an online "Behind the Paper" article at https://socialsciences.nature.com/users/177900-rose-o-dea/posts/39046-slow-and-steady-our-meta-analysis-on-greater-male-variability-in-academic-performance

The paper, authored by us (Rose and Losia) and our co-authors Michael and Shinichi, is freely available in Nature Communications: https://bit.ly/2N2ymie.

The seed for this paper was planted five years ago. Michael was sat at Losia and Shinichi’s kitchen table in Dunedin, New Zealand, listening to Shinichi describe a new meta-analysis technique he’d been developing. This technique could test for differences in variability between two groups, while controlling for differences in means. Michael suggested we use this technique to test the greater male variability hypothesis.
It would be easy. Losia found a recently published meta-analysis that tested for gender differences in average school grades; we’d do a re-analysis. It would be a simple project for Michael’s honours student, Rose, to learn some meta-analysis basics; she was joining Shinichi’s new lab in Sydney, Australia, at the beginning of 2015. The paper would be finished (we all thought) within a year, before Rose started a PhD. But it took that long just to get the data, never mind analysing and writing up our results.

The descriptive statistics of studies included in the original meta-analysis were not available. So, we downloaded the papers and re-extracted the necessary data, and contacted the authors of papers that hadn’t reported descriptive statistics. We also updated the original systematic search to find papers published since mid–2011. Losia and Rose each screened over 3,000 abstracts (thanks abstrackr), and by the start of 2016 we finally had our comprehensive dataset.

But by then, this was a side-project. Not part of anyone’s grant or thesis, it was often relegated to the bottom of our priority lists. Having each other as co-authors was essential: the project never fully stagnated because there was someone else to keep it moving. Had we been doing the project alone it would probably lay abandoned.
We were also challenged by our ignorance of the field – we are evolutionary biologists and behavioural ecologists, not social scientists or psychologists. It took time to find, and read, studies that informed our introduction and discussion. Often we were missing jargon that was the key to unlocking this information. Here we are thankful to popular science communicators for bridging these gaps (e.g. the term ‘occupational segregation’, which appears in our introduction, was learnt on an episode of Freakonomics Radio), and to psychologists who commented on earlier drafts.

by Dony Indiarto

Earlier this year, a team of researchers published a study on Indonesia’s Bajau people that made a highlight in evolutionary biology. Bajau people have been widely known as extraordinary divers. The study unveiled that these people have significantly bigger spleens compared to those live in the nearby farming communities. Bajau people spend most of their days freediving and hunting underwater for generations. The researchers also identified 25 distinctive genes that are plausibly associated with the sea gipsies’ unique lifestyle, as reported in Cell. No doubt, this research has revealed crucial evidence on human adaptation under extreme condition. Scientifically, there has been no flaw or concerns about the research and its findings. Nevertheless, the publication has been disconcerting for some Indonesian scientists, who revealed concerns over western scientists’ behaviours.

Helicopter science
The story above reflects a bigger social phenomenon, the so-called ‘helicopter science’, where foreign scientists come and collect data for a short period of time in a particular local area. They then go back home, analyse and write their research in their institution, often disconnected from the local contexts, from the local knowledge, and from those who have been focusing their research in longer term, often for their entire career. Two potential misses: (i) the research results might be biased due to small samples and also lack of local contexts; (ii) without true collaboration with local scientists, if any, long-term research for covering breadth and depth of exciting findings will not be feasible. The study may bring some progress to science, but by leaving behind the local researchers, the knowledge and capacity gaps among the scientific community will be widened, primarily due to lack of funding and resources to support scientific research in developing countries. The problem is magnified specifically for basic natural science that needs advanced technology and expensive lab works, such as in genetic studies.

This issue often happens in biodiversity-rich developing countries, where data are scarce and badly needed, but funding some particular research topics are not yet a priority. These countries are often alleged for enforcing complicated procedures and unclear regulation in facilitating and hosting foreign researchers and in permitting samples to be taken out of the country. While this is factual, it does not tell us the complete story. Cultural and language barrier can also create misunderstanding and unmet expectation between scientists. The front desk officers who implement the procedures are blind to the reason behind the regulation. Local counterparts are often employed as logistic support or leg workers and ended up having narrow space, if any, in participating in doing science. Not unlike Trump’s current policy for balanced trade, developing countries’ protection policy can retaliate back by imposing stricter regulations for research by foreign scientists. This is also similar to meta-analysis scientists who are called as “research parasites” by other scientists who collect primary data. As a result, this tit for tat will slow down new scientific discoveries in under-researched areas.
 
Call for inclusive science
“Helicopter science” is just one form of implicit biases and inequalities that do exist and persist in the scientific community. The wall between countries in doing science should be removed through collaboration driven by ethics.  The scientific partnership should be built on mutual respect and benefit. Of course, this is easier said than done. Scientists in developing countries are hindered by limited financial and institutional support, technical skills, as well as exposure to the advances in scientific discoveries. Practical or applied research is often more relevant for the locals than basic research, and therefore the collaboration in such areas will be truly fruitful.

On the other hand, local scientists should actively engage in reducing “helicopter science” practice by being pro-active. One good example is from African scientists who have taken a step forward by declaring the ethical handling of samples for genomic studies. Like everything else, the sociology of science will be rich and flourished when diversity is cherished.  In reaching so, collaborative research has to bring benefit to all parties.