DoctorAl Digest 20

A great new website with blog posts targeted at research supervisors is The Supervision Whisperers. An excellent piece on stress and self-care for graduate students was posted several days ago.

Terry over at Small Pond Science is an insightful blogger. His latest on The deficit model of STEM recruitment is bang on.

If you’ve ever had the feeling that you are alone in having your manuscripts rejected from multiple journals, this post over at Scientist Sees Squirrel will be reassuring! The snazzy title is Persistence in publishing: the Tubthumping strategy. Now I have a 90’s ear worm

 

DoctorAl Digest 19

An exciting article in University Affairs about Laurentian’s new MSCom (Master’s in Science Communication) program launching this fall.

Samantha Oester’s (@samoester) Twitter feed from yesterday drives home the fact that it isn’t just harassers that drive women out of science; the clueless and unsupportive other members in the community also contribute.

I’m really enjoying the Period Podcast by Dr. Kate Clancy.  You’d think as a middle aged woman I’d know all that there is to know about menstruation…but you’d be wrong.

When I became a principal investigator of a lab I began managing people for the first time. I’ve found the Ask a Manager website an amazing resource. Some of the stories are so wild that you’d think that they can’t be true! A great source of examples of how not to manage, and excellent advice from Alison on how to solve problems and effectively manage your staff.

 

Review: Ctrl-V Virtual Reality Arcade

Last Thursday my family and I went to Ctrl-V in Waterloo. It’s essentially a virtual reality arcade. We’d heard about it from Twitter and the local media and thought that it would be cool to check out. I will admit to being a bit skeptical; virtual reality was supposed to take off in the 90’s and never really reached critical mass. When I think of virtual reality, I think of bad movies like The Lawnmower Man. I was prepared to be underwhelmed. My other concern was that I can’t handle IMAX movies or planetarium shows; they give me motion sickness. My worst experience was in the Canadian pavilion at Epcot and the 360° hell that was O, Canada!

The booking process is simple and can be completed online. We had two coupons that gave us 50% off the experience, so for 4 people to each play 1 hour cost us ~$50. Prior to arrival they ask that you read and sign a liability waver and watch a short (and highly amusing) orientation video. Upon arrival we were greeted warmly by Will who is a credit to the organization as he was enthusiastic, professional, and very helpful during our session.

Each person is assigned their own pod, and the gear consists of two controllers that you hold in your hands in order to interact with the simulation, a headset that contains the screen, and a set of earphones for sound. The gear isn’t too clunky, but it felt a bit weird to be tethered to the pod via the headset and by the end of the hour the headset was very heavy and was compressing my neck. It didn’t take long to get set-up.

My first game selection was an escape room called Escape the Bunker. I’ve never done an escape room in person, but the virtual version was pretty cool. I was able to open a combination locker (this took multiple attempts) and a lock using a key. It was neat to open lockers and a fridge and explore the room. I got stuck when my propane tank went missing from the environment (I was going to make it explode using some beer and a lighter) and decided to switch games. Next up was a first person shooter called Space Pirate Trainer which was lots of fun! Multiple guns could be selected, or you could use a shield and a really cool lasso to pull in the targets. Three of us then did 9-holes of mini-golf in Cloudlands using a local multi-player option. It wasn’t our cup of tea, but would be great for people who aren’t into fast paced action games. I then went a few rounds on Light Blade which is for those of you who have ever wanted to be a Jedi or Sith. It’s basically Luke doing lightsabre training on the Millenium Falcon in Star Wars. Tonnes of fun! My last activity was essentially like being in the ocean. There was a simulation featuring a whale encounter, a coral reef, and the deep sea; all of which were quite relaxing and well done.

All 4 of us had a great time and really enjoyed the experience. While happy that we were able to use coupons to reduce the cost, I believe that this activity is well worth the $25/person cost, especially if this would be your first visit. If you are looking for something cool and fun to do in Waterloo with friends or family be sure to check out this neat option!

 

4th Year Undergraduate Research Thesis Opportunity #2

Investigation into the Structure of the Oyster Alternative Oxidase Protein

An undergraduate student position is available to conduct a BI499 or HE490 thesis research project in the McDonald lab in the Department of Biology at Laurier. The McDonald lab prides itself on being a diverse and friendly working environment.

Description of the Project:

Research in our lab focuses on the mitochondrial protein alternative oxidase (AOX) which is involved in the electron transport system in mitochondria. This project will focus on developing a protocol for isolating mitochondria from the yeast Saccharomyces cerevisiae that are expressing the oyster AOX protein. These yeast mitochondria will then be exposed to various chemical cross-linkers in order to determine whether oyster AOX is monomeric, dimeric, or oligomeric by using protein gel electrophoresis and Western blots.

Skills Required:

Ability to effectively conduct literature searches and to analyze and synthesize information from primary research papers.

Knowledge of the theory of protein gel electrophoresis and Western blotting techniques.

Attention to detail and ability to work safely in a biological laboratory.

Strong written and oral communication skills.

Effective time-management and project management skills.

Highly self-motivated and resilient in the face of project challenges.

Interested students should email Dr. Allison McDonald at amcdonald@wlu.ca by Jan. 31, 2017 with a resume/CV and to set up a time for an interview in early February.

4th Year Undergraduate Research Thesis Opportunity #1

Searching for Animal Alternative Oxidases

An undergraduate student position is available to conduct a BI499 or HE490 thesis research project in the McDonald lab in the Department of Biology at Laurier. The McDonald lab prides itself on being a diverse and friendly working environment.

Description of the Project:

Research in our lab focuses on the mitochondrial protein alternative oxidase (AOX) which is involved in the electron transport system in mitochondria. This project will focus on conducting a literature review and searches of molecular databases using bioinformatics to look for AOX sequences in animals. The final goal of the project will be to identify taxonomic distribution trends and to reveal phyla/orders of animals that are lacking data about the presence or absence of AOX.

Skills Required:

Ability to effectively conduct literature searches and to analyze and synthesize information from primary research papers.

Knowledge of bioinformatics tools and how to conduct sequences similarity searches (the ability to code is a strong asset) and maintain a database of sequences and their associated information.

Strong written and oral communication skills.

Effective time-management and project management skills.

Highly self-motivated and resilient in the face of project challenges.

Interested students should email Dr. Allison McDonald at amcdonald@wlu.ca by Jan. 31, 2017 with a resume/CV and to set up a time for an interview in early February.

 

Movie Review: Rogue One

This review contains spoilers! Continue reading at your own peril!

 

 

My family and I went to see Rogue One two days after it opened in December. We are all huge Star Wars fans and had high hopes for this film. We all really enjoyed the movie, but for different reasons.

The typical crawl of narrative up the screen is missing from the beginning of the film; not sure how I feel about that overall. The first 20 minutes of the film jumps around a lot, complete with planet names appearing at the bottom of the screen, which feels a bit weird for a Star Wars film.

This is a dark and gritty Star Wars film which I appreciated. You find that out in the first few minutes when Jyn Erso’s mother is shot by Stormtroopers and in a scene a few minutes later when Cassian Andor (who is a Rebel) murders an informant. It’s refreshing to see that the Rebellion is not as squeaky clean as once thought or conveyed in Episodes IV to VI.

Jyn’s father Galen is the galaxy’s leading expert on kyber crystals (which also power lightsabers incidentally) and is needed by the Empire to help them design and power the Death Star. He’s not keen, but they essentially kidnap him. During the 15 years he’s been working on the Death Star he’s secretly introduced a design flaw into it that will allow it to be destroyed. I called this particular plot point months before the film was released.

Jyn escapes and hides in a bolt hole and is saved and raised by Saw Gerrera, a local anti-Imperial extremist. Fast forward 15 years and Jyn is in Imperial custody for various petty crimes. The Rebellion has gotten wind of a new Imperial weapon and needs more information. They know that Saw Gerrera is holding an Imperial pilot defector (Bodhi) who has information on the weapon. They bust out Jyn and force her to get them access to Saw and the former Imperial pilot so that they can find out what he knows.

Jyn, Cassian, and a dryly humourous re-programmed Imperial droid named K-2SO, head off to hunt down Saw on the planet Jedha. The Imperials are pillaging the main city as it once housed a Jedi temple and is a huge goldmine of kyber crystals. The main characters get surrounded by Stormtroopers and are helped out by the blind Chirrut and his faithful sidekick Baze. K-2SO gets them out of a tricky situation and they are captured by Saw’s crew.

The next part of the film was my least favourite segment. The Saw character lacks depth and his portrayal by Forest Whitaker is pretty uneven. He seems to be both depressed and insane, half mechanical, and keeps taking puffs from a tank of gas that he carries around with him. I figured he was a drug addict, but others seem to think it was oxygen. Jyn watches a hologram of her father who explains that the Death Star has a flaw, but that they’ll have to get the plans to find out what it is. This is a stupid plot point; he could have simply said that shooting a charge down a particular exhaust port will blow it up, but I suppose that would be too easy. If you have enough memory to store a hologram, you can probably include some specs or a map right?

The first test of the Death Star occurs on Jedha and the special effects are pretty awesome. Our heroes head to an Imperial mining facility on Edu to find Galen and determine the Death Star’s flaw. Galen is killed, but manages to tell Jyn that she’ll have to get the Death Star plans that are stored on Scarif. The gate allowing access through the planetary force field is pretty cool; the archaic means of retrieving data within the facility is pretty laughable. There is an awesome piece by Sarah Jeong that speaks to the ridiculousness of data storage in the Star Wars universe. They obtain the plans, destroy the gate and realign a dish to transmit the data, and a huge space and land battle ensues. The second test of the Death Star destroys the entire planet and all of our heroes die. It says a lot about the lack of character development that both of my children were sadder about the death of the droid K-2SO than any of the human characters.

There are a few cheesy scenes in this film. The first is the appearance of Ponda Baba and Colonel Evazan on Jedha; these are the two thugs that give Luke a hard time in the cantina in Mos Eisley in Star Wars. The second scene is a meeting between Krennic (the new bad guy in this film) and Darth Vader. There is an incredibly bad pun used here that is groan worthy and completely out of character for Vader. The third is a quick cameo by R2-D2 and C3PO.

There are two human characters that are partially CGI. Grand Moff Tarkin is done fairly well, but looks like he belongs in a video game rather than on the big screen, and Princess Leia has had some work done in the final scene of the film.

The coolest and most disturbing part of the film comes at the end when Vader mows down dozens of Rebels in an attempt to recover the plans, but is thwarted as Leia’s ship gets away. This scene almost makes up for Anakin/Vader’s dreaded “Noooooo” scream at the end of Episode III. The scene in Rogue One makes you remember that Vader is a scary and dangerous guy. This provides a solid transition into Episode IV.

Overall, I enjoyed the film; probably because it had aspects that reminded me of The Empire Strikes Back which is my favourite Star Wars movie.

 

 

Service Review: AirBnB

I will admit to being very late to the game in using AirBnB as an option for looking for housing for either personal or conference trips. The number one issue that I had was safety and security which included my personal safety during interactions with the provider and financial security when it came to payments. The second concern that I still have (in some markets) is the lack of regulatory oversight and some of the horror stories that I’ve seen in the media from both sides of the service interaction; things like bed bugs, trashed houses, inconveniencing neighbours, fraud, etc.

I used AirBnB for the first time this past summer during a sabbatical trip and a family vacation in Europe. Our first order of business was to find housing in Palma de Mallorca, Spain for 3 weeks for the research portion of our trip. We wanted housing that would house 2 adults and 2 children fairly comfortably. We ended up finding a two bedroom, one bathroom apartment in Old Town via AirBnB, but then contacted the rental office directly to make arrangements. The apartment was perfect for our needs. The only issues that we had were that the company wanted payment in full up front (the other option was to pay in cash upon arrival) and that the representative was 45 minutes late meeting me at the apartment to give me the keys. A few bumps, but once we got into the apartment it was clean, tidy, and great! Overall, a pretty positive experience and value for our money. A “family” room at an apartment hotel 15 minutes outside of town cost the same for 1 week as what we paid for the 3 weeks at our rental apartment in town.

Our next bookings were all for personal travel in various cities. First up was Paris. We found an initial booking that was great, but it was cancelled a few weeks later by the host and the reason given was that their last guest had been awful and antagonized the neighbours all around the unit and the host was being threatened with eviction if any other AirBnB rentals took place. This example speaks well to the numerous legal/financial/regulatory issues that can arise with this business model. AirBnB notified us that the funds that we had paid could be used on any other booking and we had no problem securing another apartment. The location of that booking was in a neighbourhood that had seen better days, but the unit was secure, clean, and worked for us. The only issues here were that the hosts had changed the locks that afternoon and had difficulty getting into the unit later that day (our kids found the swearing in French highly entertaining) and the bathroom was tiny and a strange configuration. The price was great, but this unit would have been a no go for anyone with mobility issues. Getting our heavy luggage up 4 flights of curving stairs was a challenge.

Next up was London. We booked a great place in a Southbank neighbourhood that was handy to transit and many of the sights around Westminster. This one was quite spacious and had a great layout. The renter’s partner had to meet us to give us the keys and this involved us trying to find each other for about 30 minutes. This apartment was noisy at night due to sirens etc. as we were located right behind a police station. It was very clean, tidy, convenient, and one of our better rentals.

Our next rental was in Edinburgh. We were able to pick up the keys on time and the location was pretty good; both for walking and for parking our rental car. This turned out to be the worst rental of the lot unfortunately as cleanliness was an issue, there was a bug problem, and they were addressing a sewer problem in the unit. They were quick to respond to our concerns, but it put us off during the rest of our stay.

Our final booking was in Dublin and it was great. A very spacious apartment that was tastefully decorated and professionally maintained. We had notified them of a late arrival due to flight delays and they were still able to have someone wait at the unit with the keys. The location was great and we enjoyed our time there. The only weirdness was some feather art on the wall that was housing a large number of tiny moths. When told about that issue (which we thought was fascinating and didn’t find distressing during our stay) they indicated that it was pretty common given the dampness of Dublin and thanked us for bringing it to their attention.

Overall, the bulk of our experiences were positive and we avoided any complete disasters or horror stories during our trip. I do have a few tips to offer based on our experiences.

1) Do your homework and due diligence before making a booking. This includes investigating the neighbourhood where the apartment is located, transportation options to get to/from the apartment (e.g. transit, taxis, airport shuttles, etc.). Be sure of the number of bedrooms, beds, bathrooms, layout, and appliances available before you commit and ensure that the booking will suit your needs.

2) Read each and every review on the AirBnB site for the booking. We did not book any places with no reviews and tried to only book places with >10 positive reviews. You will sometimes need to read between the lines of the reviews. For example, 2 reviews on the Edinburgh apartment said that issues were addressed quickly. This is the polite way of saying that there were issues and we should have picked up on that prior to our booking. We also did not book anything where the host had cancelled a prior reservation on someone else.

3) AirBnB properties come in three varieties: people’s homes that they are renting out sometimes to earn extra income (they may be on vacation or staying somewhere else in town while you rent it), timeshares or vacation homes that would otherwise sit dormant, or entrepreneurs who own several properties and rent them out all of the time. Our best experiences were with the latter group as we found the properties to be professionally cleaned and maintained. You can often tell what type of rental you are dealing with by looking at the photos; if it’s fairly spartan and staged it’s likely more professionally managed, if you can see toys, knick-knacks, and personal effects it’s likely someone’s home.

4) Key pick up is often a weird experience and if there are any problems it’s a bit of a crap-shoot as to whether they will get addressed to your satisfaction. This was the aspect of the experience that annoyed me the most. This in my opinion is the major disadvantage vs. a hotel where someone is always working the front desk, although that being said I’ve had some nightmare situations happen during hotel stays also.

Hope that these tips are helpful! Feel free to share your experiences using AirBnB in the comments!

 

Book Review: Good Strategy Bad Strategy: The Difference and Why It Matters by Richard Rumelt

I ended up reading this book based on the recommendation of the author of this blog. I often find that she has excellent book recommendations that are somewhat unusual, but quite useful when applied to my work.

Often we think of strategy as something employed by warmongers and generals, but an easy way to think of strategy is predetermining what you want to accomplish and developing an effective plan and the actions/steps needed to successfully complete it. That sounds pretty much like every science project/experiment, course, and service obligation that I’ve ever taken on. I figured that this could be a useful book.

The most memorable part of this book are the awesome case studies that the author uses to illustrate his points. I learned a huge amount about the rise of Silicon Valley in California and many old-school U.S. companies. When successful, these companies started out as flexible, innovative, and agile, and later got weighed down by bureaucracy and rigidity. There are some really neat stories included in this book that I found wonderfully entertaining; they were so engrossing that I shared many of them with my husband who probably got really sick of them after a time. In today’s climate of commercializing higher education, it was interesting to read the author’s scathing view of mission and vision statements; he considers them a waste of time as they don’t contain concrete steps for how to achieve their bullet points and therefore can’t be considered a strategy.

I haven’t taken any business courses, but the case studies used in this book and the walk-throughs are very interesting. I think that most scientists would find a few useful gems here that can be applied to how they approach their work.

 

Good-bye to 2016

All in all, 2016 was a good year for me. During the first semester of the year I taught a course, mentored several students, and found out that my NSERC Discovery Grant was renewed. I also hit 100 followers on Twitter which I thought was pretty cool. In February I started Bullet Journaling as a system of time management and I really like it. The part that I think that I like most is that it’s a written record of everything that I was able to accomplish this past year and that the system can be modified to suit your individual needs.

The second semester during the summer saw me switch gears significantly as I was preparing for my first sabbatical in July. I attended two conferences in cities where I did my post-doc and Master’s degrees respectively, so it was a bit of a homecoming for me which was neat. At the end of June I left for Italy to attend a conference and then my family and I spent 3 weeks in Palma de Mallorca, Spain. That trip was a conscious effort to push myself out of my comfort zone, but I need not have worried as my hosts were wonderful! While I was working with a collaborator, my family explored the city and the island’s beaches. We then took a family vacation in August to Paris, England, Scotland, and Ireland which was fantastic!

The fall term found me getting a new groove and I was able to be much more proactive rather than reactive due to being on sabbatical. The biggest success that term was finally publishing a manuscript that was the result of 6 years of laboratory work. That was a huge win for me. I was happy to watch the Blue Jays in post-season baseball for the second year running; unfortunately they were eliminated by the team from Cleveland. The year rounded out with time spent with family and friends over the holidays.

I hope that your 2016 was productive and that you are looking forward to 2017!

 

Perseverance

I started a project about 2 years into my post-doc in the early months of 2010. It involved an idea that was a bit out there and I wasn’t sure that it was going to work. After discussing it with my post-doc supervisor I went for it. It was a molecular biology project and I successfully created some expression constructs and some yeast transformants. About 5 months into the project I received my faculty job offer and the strains sat in the freezer until the summer of 2011. Such is the advantage of molecular biology projects; you can put them into a deep freeze and reawaken them later. From 2011-2013 two wonderful fourth year thesis students and a talented graduate student generated the bulk of the data and protocols for the project and wrote up their results as theses. The manuscript based on these results was rejected by three different journals over the next 1.5 years. The reviews that I received certainly improved the quality of the final article, but it is hard to feel optimistic in the face of continued rejection. It is also really hard to not feel like you might be in the wrong line of work. Based on the suggestion of several reviewers, I went into the lab and collected new data using a different technique. I submitted the manuscript to a more specialized journal and was asked to do major revisions to the paper this summer. I am pleased to say that the article was accepted for publication last week.

This is the most technically challenging project that I have done as a scientist and the most professionally and personally draining publication process that I have faced to date. There were several times during the past 6 years when I almost gave up on the project and tried to evaluate if the sunk cost of time and effort already invested should be written off. It is great in this case that perseverance paid off in a publication for my lab group. I wish that there was a formula that we could use as scientists that would help us to determine when to give up on zombie projects and move on with other things. This one in particular is a great example of the project that refused to die, mostly because I was stubborn and refused to give up on it. I’m taking this one as a win.

How do you decide if and when to let a project die? Is it a conscious choice, or did the project go silently into the night never to be heard from or seen again? Do you have skeleton projects hiding in your lab’s closet?