Don’t feed the trolls

I think that I was first introduced to trolls in the story of the Three Billy Goats Gruff . In children’s stories the troll is always an ugly character who is up to no good. I particularly liked the treatment of trolls in the film Willow  and the way that they climbed up walls. The next time that I thought about trolls was when my kids were younger and we went through a phase when we all watched a lot of Dora the Explorer . This troll wasn’t particularly threatening, but you did have to solve his riddle if you wanted to cross the bridge. He had a theme song that easily became an ear worm in our house. Recently my husband and I started watching previous seasons of the TV show Once Upon a Time  and there was one episode containing trolls on a bridge.

Last weekend I had an experience with a real-life troll. I am talking about the internet variety. I’ve been blogging for a little over a year now and consider myself fortunate that I haven’t had to interact with any trolls. I feel that way given the frightening amount of trolling that is directed towards women on the internet. I usually don’t check my email over the weekend, but last Sunday afternoon I did. Sitting in my inbox was an email from a person who I didn’t recognize, but I get lots of emails from students looking to do graduate work with me so that wasn’t particularly unusual. Unfortunately the contents of the email were not harmless and were of a sexually harassing nature. This person had taken the trouble to learn some personal pieces of information about me which was very disturbing and signed off the email as a secret admirer. It was thoroughly creepy, distracting, and made me feel very unsafe. It is also unwanted and unwarranted.

I accept that as part of my job as a professor that I will receive my share of unpleasant emails such as those that convey bad news about grants, complaints from students that I teach about my evaluations of their work, or disagreements with colleagues about how to solve problems. In my naïveté I never thought that I would be subject to anonymous sexual harassment by email. I’m now wondering how many of my colleagues have had to deal with something similar, but haven’t said anything out of fear, shame, or bewilderment. Sometimes ignorance really is bliss. I expect that I am not the only person to have had this experience, but I think that it’s important to talk about it and not sweep it under the rug.

I’d appreciate hearing from others who have had this experience and how they dealt with it.

Research Budgeting for Scientists

Prior to starting my job as an Assistant Professor, I had never managed a professional budget before. I’d certainly managed my personal finances previously, but I’d never before had total oversight of a research budget and been responsible for figuring out how to spend it effectively and ensure that I wasn’t going over budget. This is one of those myriad of skills that you aren’t always exposed to as a graduate student or post-doc, although I do know some colleagues who managed research budgets before starting their faculty positions.

I’m pretty conservative with money and how I manage my funds is informed primarily by two things: I think that shopping around for the best price is a good idea and I like to know what the current balances of my accounts are so that I don’t ever run a deficit. These two approaches have served me well in the first five years of my position.

In my personal life I do not particularly enjoy shopping as an activity. The most frequent type of shopping that I do is grocery shopping and we have recently started to use the app Flipp in order to compare prices any given week and to price match items across different stores. I have transferred this idea to how I do the shopping of consumables and supplies for my lab. Usually several suppliers will offer the same or a comparable product; let’s use the example of 1.5 mL centrifuge tubes. In my lab I prefer the tubes to be clear, to seal well, and to withstand high centrifugation speeds. Taking these specifications into account, there are many suppliers and manufacturers who can provide me with a tube that will do the job. My next step is to figure out the price per unit and see who offers a good product at a reasonable price. For most items I’m willing to shop around and to try a new product, especially if the price point is cheaper than what I have previously been using. One thing to keep an eye on is whether there are shipping and handling charges in play. Often an item will seem less costly, but when you factor in the shipping costs that is no longer the case. I also have to make sure what customs charges apply if I’m importing an item from Europe or the U.S. since I’m in Canada as those charges can add a lot to the cost of an item.

In order to avoid running a deficit it’s important to plan ahead and estimate your future costs and also to have a really good idea of the current funds that you have available. Some costs are easier to project (e.g. student stipends, larger pieces of equipment) while some are more challenging to estimate (e.g. the price of agarose 3 months in the future). I’ve found that it’s been useful to go with higher than expected estimates in order to build a buffer into budgets.

I choose to run my research budget in this way because the vast majority if my research funding comes from Canadian taxpayers and they have a right to expect me to be responsible when it comes to spending those funds. I also refuse to put myself and my students in the position of running out of funds for their stipends as I feel that it is morally wrong and irresponsible. I won’t take on a student if I can’t pay for my portion of their financial support package.

I’d be interested to hear how other faculty do their financial budgeting for their research grants. Please leave your thoughts or advice in the comments!

Helping students to draft CVs and resumes

In preparation for this week’s lab meeting I asked all of my students to put together a draft CV or resume. They each emailed it to the other members of the lab and we all made constructive comments on these documents. At our lab meeting each person gave feedback to each student on their document that was useful and insightful. It was also a great way to generate questions and have a good discussion about CVs and resumes.

One thing that all of my students noted was how time consuming it was to put together this document for the first time. We talked a lot about content (e.g. what should go into the document) and organization (e.g. what sections or headings to use?). I also impressed upon them the importance of updating the document regularly (I do mine once a month) because if you leave it too long it becomes very difficult to remember what you’ve accomplished. My students also have a tendency to undersell their skill set or they often don’t recognize that they have particular talents or skills. In a previous lab meeting we addressed that issue by brainstorming about transferrable skills and how to capture and describe them to an employer.

I also encouraged by students to take their drafts to our campus Career Centre. It’s been a while since I’ve been on the non-academic job market, or the academic job market for that matter, and the staff at the Career Centre are much better informed about current job market trends and application expectations. I think that part of my job as a faculty member is to help my students prepare for their next phase of life, whether that is looking for a job, further education, or some other goal. I think that professional development is an important part of training students in my lab.

Tips for designing experiments

One guarantee of being a scientist is that you perform many experiments in your career that do not work. I always warn trainees just joining my lab that this will happen and that they should expect it. This is an issue that I discuss in particular with undergraduate students because often the only lab experience they have is through undergrad labs run as part of a course and those experiments are designed to work and have already undergone extensive troubleshooting. I make sure to tell my students that they will run many failed experiments and that this is a normal part of doing science and is a cornerstone of the scientific method. I tell them that so far in my career I’ve only had a few experiments that worked out perfectly the first time and that a failed experiment can happen for reasons other than their abilities or talent for doing science.

That being said, there are things that you can do to decrease the chances that an experiment will fail right out of the gate. I offer some tips below:

1) The first thing that I suggest to students is that they do extensive reading of the literature and established protocols related to their experiment before starting to design it. I’ve heard the phase “one hour in the library can save you one month in the lab” and I absolutely believe it! It’s really important to understand the rationale behind a particular protocol and the nuts and bolts of why you are doing each step. In the days of commercial kits I think that many people forget this crucial step and it often causes issues later.

2) Make sure that you are including all reasonably possible positive and negative controls as part of your experiment. From talking with several of my colleagues recently it has become clear that many undergraduate and graduate students have not had explicit training in how to determine what the appropriate controls should be for an experiment or are simply not including them. By including controls in your experiment you allow yourself the capability of narrowing down where problems cropped up in your experiments. When an experiment fails, this step can save you a massive amount of time when it comes to troubleshooting and determining what went wrong. The presence of control and experimental groups also ensures that you will be able to conduct statistical analyses of your data in an attempt to demonstrate whether your results are significant.

3) Write up an extremely detailed step by step protocol for your experiment. Try to think about what might go wrong and where key steps are in the protocol. Attempt to troubleshoot the experiment before you even do it. The plans for your experiment should be written in your lab notebook and not on paper towels, scrap pieces of paper, etc. This will ensure that your experiment will be reproducible and will help you to identify potential issues before you get rolling. If someone in the lab has done the experiment or protocol before, go and talk to them. They may have tips or tricks that are not explicitly written down that are valuable. Write out the protocol in your own words with as much detail as you can. I tell my students that if they needed to perform the experiment without thinking about the steps, the protocol should be detailed enough that they could do this.

4) Ensure that all of the materials and reagents that you need for your experiment are available and ready to go before you start the experiment. There is nothing worse than getting part way through a long protocol only to realize that you’ve run out of Tris buffer and have to order more in from the supplier. Complete any prior steps that are needed before starting the experiment. Do you need to culture cells, wrangle critters, grow plants, etc.?

5) Conduct a small trial run of your experiment. Starting things off with a pilot experiment allows you to save money, time, and can allow you to discover problems with the design of your experiment before you fully commit large amounts of resources to it.

Designing good experiments is an art form that requires years of practice in order to get better at it. I am still working on designing the perfect experiment, but I have certainly improved this skill by extensive practice over the years. Due to the challenge of designing an effective experiment it is truly amazing when an experiment works beautifully on the first attempt. This is one of the eureka moments that scientists live for!

80’s Geeks Rejoice: Book Review of “Ready Player One”

What kind of world does the future hold? In the book “Ready Player One” by Ernest Cline it is a dystopian one with a twist. While the real world crumbles around global society, most people lose themselves in a massive multiplayer on-line simulation called the OASIS. The software and hardware involved in OASIS makes World of Warcraft look like child’s play. The OASIS has become reality for most people and is therefore a place where fortunes can be made and lost.

The plot of the novel revolves around a contest implemented by one of the founders of the OASIS when he dies. He’s embedded an “egg” prize within the code of the game and whoever completes a series of quests and puzzles and retrieves the egg inherits his estate which is worth billions. The hunt is on and we follow the adventures of the protagonist Wade and his friends in a race to the finish line.

I enjoyed reading this book because it had good pacing and was entertaining. A great deal of its entertainment value is due to the fact that I grew up during the 80’s. The number of pop culture references in this book for this time period is huge and I caught myself laughing out loud several times while reading the story. The story starts out rather lighthearted, but it quickly becomes quite dark given the fortune that is at stake. I also liked the overarching theme of the book which really made me think quite a bit about what influences how different people feel about what is reality and what isn’t. The world of the OASIS is so immersive that reality becomes a bit blurred for many of the characters in the novel.

My only complaint about the book is that the ending wrapped up a bit quickly for my liking, but this allows the author the option of revisiting the world that he has created in future novels. The movie rights for the book have been acquired and I think that with today’s technology it could make a very engaging film. The novel is a quick and simple read, but I still find myself thinking about many of the concepts and ideas that it introduces which I think is the mark of a great book.

If you are a geek and came of age in the 1980’s you’ll get a real kick out of this novel, but I think that its message will resonate with a wide variety of readers.

A thank-you to Mr. Leonard Nimoy

I was sad to hear on Friday that Leonard Nimoy had died. I remember discovering Star Trek (the original series) in Grade 7 while channel surfing one day after school. I was amazed by the show in terms of its positive setting in a universe where humans explored the vastness of space in the Enterprise. I also thought it was amazing that the ship had a Science Officer and that he was an alien. The use and study of science was interwoven with the issues explored in each episode and Mr. Spock generally played an important role in the plots. It was, as he would say, fascinating.

From that point on I realized that you could make a career out of doing science and that it could lead to the exploration of new frontiers and places. Mr. Spock helped me to see the usefulness of logic and generating hypotheses to explain phenomena in the universe around us. Star Trek helped me to see science as something useful, cool, and exciting and it is truly one of the reasons that I’m a biologist today. Spock had a highly successful career and had many friends on the show despite the fact that he was an outsider and continuously struggled to find out where he belonged. The child of a human mother and a Vulcan father, he wrestled with honouring both civilizations while making his way in the world. I have a great deal of respect for that and it was one of the many things that I liked about Mr. Nimoy’s nuanced portrayal of the character.

Thank-you Mr. Nimoy for opening a young girl’s eyes to the possibility of a life of science and the hope that the future can be a bright one for humanity.

Making word processing easier

When I was in Grade 8 my parents bought our first computer. It was a Tandy 1000 and it was awesome. My brother and I logged countless hours playing computer games like King’s Quest, Space Quest, Police Quest, and Hero’s Quest published by Sierra . We stayed away from Leisure Suit Larry because it was wildly inappropriate for kids. We also had a dot matrix printer hooked up to the computer that could be used with a very basic word processor and I used it a few times to do school assignments.

One skill that has proved very useful to me in my job as a scientist is the ability to type. I learned how to type in Grade 10 by taking a class for an entire semester. It is probably the most boring class that I have ever taken in my life, but it’s a skill that I use every day and it saves me tonnes of time. I learned to type on an electric typewriter and was pretty accurate and speedy; I rarely used the correction paper that we had to buy for class. I’m pretty sure that they don’t teaching typing in grade or high school anymore, perhaps assuming that kids these days use their computers so much that they pick up typing on their own. However, my own children who are 12 and 8 type using two fingers and appear mystified by the QWERTY keyboard. A few weeks ago there was a discussion on several blogs about whether scientists still left two spaces after periods at the end of sentences when they typed. It took me a while to break that particular habit since that is how I first learned to type sentences.

Since entering my undergraduate degree I’ve used several iterations of Microsoft Word as my word processing program. I was thrown quite a bit by the 2010 update and have recently switched over to the 2013 version. I’ve often wondered how other scientists do their word processing, since I know that some of my colleagues prefer to use LaTeX . Over the years I’ve picked up several tips and tricks for using Word, but I consider my skills to be merely adequate and I know that I don’t use the program to its full capacity or usefulness. I figure that improving my MS Word skills would be a good investment as it could serve to save me lots of time and improve my efficiency at doing certain aspects of my job. With that in mind I took out the book “Office 2013 (the missing manual)” from my local public library. I’ve only read up to page 83, but it’s been illuminating to say the least!

Some highlights so far:

1) I’ve known for years that lots of other people regularly use keyboard shortcuts. I often use Ctrl + C to copy, Ctrl + P to paste, and Ctrl + A to select an entire document. This book explained shortcuts for bolding and italicizing text that should have been obvious to me before now; I’d been using my mouse and clicking on buttons to accomplish the same thing which is pretty clunky and often interrupted my flow of writing.

2) The start pane in Word 2013 was a bit disorienting at first. I’ve learned how to pin documents to the top of the list of recently used documents that will save me the time that I previously spent pulling them up from whatever folder I’d previously saved them in.

3) I recently switched to a dual monitor set-up in my office which was pretty amazing. Finally figuring out how to split the screen or show documents side by side has been mind-blowing and frankly is something that I should have figured out years ago.

4) I used to select text by highlighting it with my mouse and clicking and dragging the cursor. Evidently you can select words, paragraphs, or sections with a couple clicks of the mouse. Who knew? I certainly didn’t.

This book has been amazing so far and I look forward to the other gems of knowledge that I’ll pick up from it. It’s also been a very effective ego check and has served to highlight the fact that spending a bit of time figuring out how to really use a piece of software is time well spent.

What tricks have you picked up in the word processing programs that you use in your day to day work as a scientist? Feel free to share in the comments!

Dressing for Success in Science as a Woman

When I was a little girl I apparently wore dresses; there are pictures in the photo album to prove it. As I got older I ditched the dresses and it was mostly about comfort. I hate nylon pantyhose and tights passionately and in the late 70’s/early 80’s the fashion rules of the day dictated that bare legs with dresses or skirts were a fashion faux pas. Maybe it’s because I’ve only worn cheap versions of these monstrosities, but the itching and pulling is enough to drive me insane. Once in the lab I cut up a pair of pantyhose to serve as a makeshift filtration device; it was immensely satisfying! From that point on I was firmly in the pants camp. Pants are also considerably warmer and you don’t need to worry about accidently flashing people when you wear them (take note Britney Spears ). You can easily run wild throughout the neighbourhood catching crayfish, tadpoles, and avoiding snapping turtles while wearing pants. The only time that I wear a dress or a skirt these days are at weddings or fancy dinners. From this perspective wearing pants was a personal choice. Since starting my scientific career it’s also been a practical and necessary one.

When I first started working in a lab, it didn’t make sense to wear skirts or dresses (or shorts for that matter) from a health and safety perspective. All of the labs that I’ve worked in have required the use of personal protective gear including a lab coat. That lab coat is there to protect you, but it can only do so much. If you have bare legs exposed underneath your lab coat due to wearing a dress, skirt, or shorts you are placing yourself at risk. Don’t think that it can happen to you? I have a co-worker who used to think that way until she accidentally spilled phenol on herself in the lab. Many of the experiments that I do are messy and it doesn’t make financial sense to destroy “nice” clothes if it can be avoided. The same goes for shoes. We aren’t allowed to wear open toed shoes or sandals in the lab for the same reason. When running around doing experiments I’ll go with a pair of sneakers or loafers every time. This is also a keen survival strategy for when the zombie apocalypse occurs and making a speedy get-away will be important. That being said, I’m sure that Dr. Isis will hold her own regardless of what fabulous shoes she happens to be wearing that day!

In addition to the practical reasons that inform my clothing choices, there are larger societal and cultural factors that influence my professional wardrobe. I was reminded about this topic by today’s post on Tenure, She Wrote. And here we get to the sticky point; the double standard when it comes to how female and male scientists dress for work and how they are perceived based on what they are wearing. It’s a tricky tight rope to walk and for me personally takes up way too much of my mental energy most mornings as I decide what to wear to work. Judging by previous blog posts on the topic, I’m not alone. A quick Google search on the topic turned up a pretty amusing article from 1998 on the ScienceCareers website about a graduate student looking for a professional outfit. More recently the topic has been covered by a super post by My Laser Boyfriend  which outlines some great fashion options that are realistic and tasteful. Neurotic Physiology also had a good post about the double standards of dress for men and women and how to deal with long hair in the lab. The Singular Scientist discusses how female scientists are portrayed on TV and in film  and on difficult conversations that she’s had to have with trainees about inappropriate clothing choices. A more academic analysis of this double standard can be found in this Tenure, She Wrote post.

It would be great to live in a world where your fashion choices didn’t influence what people think about your competence or abilities as a scientist, but as some of the posts above can attest, we do not live in that world. At each stage of my career I have made a conscious effort to dress more professionally based on the adage to “dress for the job you want” and I feel that so far it has served me well. I’m at the point in my career where I’m feeling comfortable and secure enough in my position that I can start to make some bolder fashion choices. Up until now my professional clothing choices have been very conservative. This past year I made the revolutionary decision to add scarves into my outfit rotations! With that in mind, here are some links to websites that I’ve found useful for getting some ideas about what components are useful to have in a professional wardrobe:

1) Corporette

2) Capitol Hill Style

3) Franish

4) Does my bum look 40 in this?

Some people may think that having an interest in fashion, dressing stylishly, and being a successful female scientist are mutually exclusive. They are not. I count as role models several strong women who are excellent scientists as well as very snazzy dressers. There may be hope for me yet…

Jill of All Trades and Master of None?

I have a confession to make. I am a scientific wanderer. I haven’t wandered as much as Darwin, both in terms of his areas of interest and his physical journeys, but I am easily distracted by new and shiny ideas.

My undergraduate and M.Sc. thesis projects were spent looking at the phosphate-starvation response in the yeast Saccharomyces cerevisiae and the influence of the commercial fungicide phosphite on those responses. I learned sterile technique, how to grow yeast strains and supplement media, how to do enzyme assays and kinetics, and gained a general understanding of 31P NMR. I did all of this in a plant biochemistry and metabolism lab and was the odd person who worked on yeast.

For my Ph.D., I moved to a plant physiology lab where I learned molecular biology, how to transform tobacco plants using Agrobacterium, how to grow diatoms and cyanobacteria, mitochondrial isolation techniques, SDS-PAGE, Western blotting, and a smattering of bioinformatics. Mid-way through my degree I switched gears a bit and started working with oysters. I gained a huge appreciation for the theory of serial endosymbiosis and the diversity of life forms on the planet. I studied the alternative oxidase of mitochondria, but also did some work on the plastoquinol terminal oxidase of chloroplasts.

My post-doc took place in an animal comparative physiology and biochemistry lab where I continued to practice my skills in molecular biology, bioinformatics, mitochondrial isolations, and picked up a better understanding of respirometry. I mostly studied oysters, but also worked with tissues from wide variety of other animals including nematodes, sea urchins, lamprey, hagfish, scallops and also worked on non-flowering plants including pines, spruces, ginko, etc. I also developed a heterologous yeast expression system at the end of my post-doc. I continued to work on AOX and PTOX, but in a new set of organisms.

Since starting my faculty appointment, my students and I have worked with yeast, moss, bacteria, tobacco, and a copepod. I continue to use a variety of techniques in the lab and am contemplating using CRISPR in the near future. Most of the time I think that having such a varied background has been a huge advantage to my career and for the science that I do. I attend both animal and plant science conferences and am thinking about adding bacterial meetings to the mix. Every once and a while my imposter syndrome gets the better of me and I envy my colleagues who work on a single model organism, pursue a very focused set of research questions, or use tried and tested techniques. My diversity of interests makes it difficult to write focused grant applications, but it allows me to qualify for a wider range of funding opportunities. I sometimes feel that I’m lurching around in the dark, but this approach has allowed me to make some significant contributions to my research field.

Are you a Jill or Jack of all trades? Or a master or mistress of a particular type of science?

Weird Science

James O’Hanlon has a cool post up right now on his website about the strange things that scientists do for science. It made me think about some of the weird things that I’ve done in the course of doing some of my research projects.

The first funny experience comes from when I was doing my Ph.D. I had discovered the enzyme that I work on, alternative oxidase (AOX), in animals for the first time using bioinformatics. I wanted to do some wet lab experiments in order to confirm that AOX was actually present in the DNA of an animal and that it was transcribed. At that time, I had AOX sequences from three animals: the sea squirt Ciona intestinalis, the nematode Meliodogyne hapla, and the Pacific oyster Crassostrea gigas. The sea squirt is an invasive species on the east coast of Canada, so getting my hands on tissue would have been tricky. The nematode is very tiny and a plant parasite, so that would have been a difficult sample to obtain. Pacific oysters are commonly eaten by people and I figured that would be the way to go. I called a wholesale seafood supplier to confirm the availability of Pacific oysters and drove about 1 hour to go and pick some up. When I arrived there were no Pacific oysters in the store front, so the owner had to take me into the warehouse to get them. It was pretty intimidating as this involved walking through several large pieces of plastic sheeting that separated the store front from the warehouse. I felt like I was in an episode of the X-files or a murder mystery and that I was being led to my doom. We got to the bin that was housing the oysters and the owner asked me how many I wanted. I figured that 24 oysters would get the job done. He started putting the oysters into thick plastic bags and we started chatting. Was I running a restaurant? Nope. (I guess that it’s unusual for individuals to buy 24 oysters at a time). Was I having a large dinner party? Nope. Well, what was I going to do with these oysters then? I said that I was a scientific researcher and that’s when things got weird. The guy completely panicked and started going on and on about how the oysters were safe to eat and were o.k. for human consumption. It turns out that he thought that I was a government scientist who was doing an unannounced, random inspection for the Canadian Food Inspection Agency! In retrospect it’s a hilarious story, but at the time I paid for my oysters and ran! The project was awesome by the way.

The second funny story is from my time during my post-doc. The university where I was working had a great arboretum (collection of trees) and I’d obtained permission to take leaf samples for a project that I was working on regarding the taxonomic distribution of AOX in non-flowering plants. When I went out to sample I used an ice bucket, lots of little tubes, scissors, etc. It would certainly look weird to anyone walking by. A few times I had curious people come up and ask me what I was doing and I enjoyed talking to them about my science. It was a great and unexpected opportunity to do some public outreach.

Head on over to James’ blog or follow the #strangethingsforscience hashtag to hear about some great science adventures!

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