Winter …

winter

It’s been a while. My first few weeks of 2017 have been eaten up by 2nd-year genetics and a 4th-year course on genome evolution. This is my third time teaching the BIG genetics course (Biology 2581B) at Western, and I still get super nervous before each lecture. Be sure to check out our various essays and research articles, including a study of the largest chloroplast genome ever found in a non-photosynthetic alga! Also, I wrote a long piece on scientific blogging, titled “confessions of science blogaholic” and a shorter essay, calling upon scientists of all stripes to communicate more effectively with the public. My undergraduate writers are still going strong – read the most recent pieces at Hipademic. Enjoy the winter and stay warm. ~david

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A walk in the park

walk-in-the-park

Fall is blowing by like a dried leaf in the wind. I’ve been checking out the bright autumn colours in my local park. I’m so fond of this park that I’ve managed to incorporate it into a commentary for the journal EMBO Reports. The article, aptly titled “A Walk in the Park“, talks about the recent popularity of Pokémon Go and its potential impact on biodiversity research.

My writers in res are hard at it: Udara Jay has a new piece about his startup company Tidl, which is re-envisioning and invigorating the online resume. And Karan Kumar writes about the techniques and ethics of building a designer baby.

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designer_babies_bnrMSc student Matheus Sanitá Lima and I have a short highlight article about a new software for analyzing organelle transcriptomes called ChloroSeq, which was published in Briefings in Bioinformatics. Matheus also organized this years Western Biology Graduate Research Forum, which took place on Oct 14 and 15. The event was a huge success, but Matheus is quite tired.

That’s all for now. ~david

 

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Introducing Hipademic

hipademic

Starting September 2016, Smith Lab Writers in Residence will be posting essays to Hipademic – a new publication on the blogging platform Medium. An essay will be published every Monday throughout the academic school year (Sep–April). Some of the essays will be new articles, others will be previously published pieces, but all of them will be intriguing, engaging, and totally ‘hipademic’.

We also have a hipademic Facebook page and a Twitter account (@hipademic). Western Science undergrad and design guru Udara Jay will be helping edit and publicize the magazine.

Our first article, titled Putting the “Pop back into popular science”, appeared this past Monday (12 Sep) and was written by Dennis He – one of the original Smith Lab Writers in Residence.

Stay tuned.

~david

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Goodbye summer, hello academic year

watermelon

Well, the summer zoomed by and now the students have swarmed the campus and are roaring to go for the new academic year. At the start of the Rio Olympics, writer in residence and varsity swimmer Charis Huddle published an inspiring article about her dreams of Olympic gold. On the research front, Smith Lab MSc student Matheus Sanitá Lima published an article on the “incomplete organelle genome” in Molecular Ecology Resources, and I wrote an opinion piece in their sister journal Molecular Ecology about the mutational hazard hypothesis. And if you get a chance, check out my essay “One scientist’s struggle to be a better writer” – it might just bring a tear to your eye :cry: Best of luck this term. ~david

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Summer updates

summer

Long time not talk. I’ve been out and about. Ate some lobsters in Nova Scotia and experienced winter in summer in Newfoundland. A few quick updates: Patrick Keeling and I have a new review out on crazy cool and totally weird gene expression in protists. It’s online now at the Annual Review of Microbiology, but if you don’t have access you can download the paper here. Also, check out writers in residence Neeraja Murali Dharan’s new article on leadership and Dennis He’s essay on science internships, both of which made the Western Science Homepage (pics shown below).

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Go go Gonium

GoniumTurn the music up and uncork the champagne – I’ve published a Nature paper! Well, technically it’s a Nature Communications paper and admittedly I’m buried deep in the author list. Nevertheless, the paper is awesome. The lead researcher is Erik Hanschen, a PhD student in Rick Michod’s lab at the University of Arizona, and the senior author is Brad Olson, an assistant prof at Kansas State University. The paper describes the Gonium genome. Gonium is a 16-celled green alga closely related to the unicellular species Chlamydomonas, which is the Brad Pitt of green algae. In short, the DNA sequence of Gonium when compared to that of Chlamydomonas provides some interesting insights into the origins of multicellularity. You can read the paper here and see various press coverage in EurekaAlert!, the Washington Post, and the the NewHistorian.

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Third time’s a charm

Boston_Marathon

Those who know me well, know that I’m addicted to coffee, red wine, dark chocolate, Raymond Chandler novels, cats, and running long distances at slow speeds. This past week I ran my ninth marathon and third Boston Marathon. Yes, when I’m not at the computer or in the classroom I like toeing the line with skinny dudes in short shorts, fluorescent sneakers, and silly headbands. The Boston Marathon is an academic’s dream course. The start is way – like 42.2 km – out of town and the course winds its way back to Boston passing multiple university campuses, including Wellesley College and Boston College, and coming very close to Harvard. At the halfway mark, just as my legs were starting to burn, I passed Wellesley, bringing back memories of the 2010 Chlamydomonas meeting, which was held there. Nothing gives a tired marathoner inspiration like fond recollections of a five-day conference on the finer points of a unicellular green alga. Later, I wiped the snot and Gatorade from my beard and grabbed a quick kiss from a student a Boston College (all runners are offered free kisses, seriously), which kept me going to the end. It was a beautiful, sunny day and I made it to finish in 2 hours and 53 minutes, giving me lots of time to check my email and respond to like a zillion emails from second-year-genetics students who have their midterm this Wednesday. I don’t know when I’ll tackle my next marathon, but hopefully I have a few more in me. ~david

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Hot and sunny Miami

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Just got back from Miami University. That would be Miami University in Oxford, Ohio. Hey, it wasn’t so bad – the leaves were on the trees, which is more than I can say for London, Ontario.

Miami U is an old old university and branded as “the original public ivy“, meaning that it is “a public university that provides an exceptional return on your education investment, has a rich history and tradition, and has a picture-perfect campus.” Well, I don’t know about the return on the education investment, but the campus is picture perfect.

But I was doing more that just drooling at the ivy-covered buildings and manicured gardens. I gave a seminar to the microbiology department on the coolness of organelle genomes. I also had lunch with the Microbiology grad students, who were all very nice (almost as nice as the students from Western Biology).

My host at Miami was Rachael Morgan-Kiss. Unlike me, Rachael is a “real” biologist – she actually goes into nature and observes living things. Even cooler, she goes to the Antarctic to study algae in permanently ice-covered lakes (the picture above shows Antarctic algae growing in her lab).

Thanks for the fun visit, Miami U. And although I’ve never been to Miami, Florida, I bet it is not nearly as nice as Oxford, Ohio.

~david

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Quick, pass me the disinfectant!

Microbiome

If there’s one thing that’s guaranteed to make your skin crawl, it’s the thought of tiny creatures living all over your body. We inherently think of bugs and ‘germs’ as evil intruders that need to be exterminated as quickly as possible. But while some bacteria do cause dangerous illnesses, such as pneumonia and meningitis, the vast majority of the 30 trillion microbes that coat our bodies are ’good guys’. From head to toe, we are quite literally plastered in bacteria and many of them contribute to our health and wellbeing. Small changes to this invisible world’s population of bugs – broadly called our microbiome – can have serious consequences. A disturbed microbiome has been linked to long-term health conditions, such as Type 2 diabetes, inflammatory bowel disease, depression, anxiety, and even obesity. Life is lived best with a healthy coat of bacteria, so it’s the time to stop squirming and stat learning to love your microscopic friends.

Read the full article by writer in residence Jessica Bertschmann in the most recent issue of Guru.

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Life aquatic: the amazing self-purifying properties of the Ganges River

life aquatic

The Ganges River – an ancient, beautiful, and life-sustaining river of dark-green waters that runs for hundreds of kilometres through some of the most diverse landscapes on Earth. Now picture that same river saturated with a slew of chemical pollutants, raw sewage, and dead bodies. How do you think these contaminants would impact the river’s purity and sustainability? Presumably, they’d be the river’s demise, leading to an undrinkable and unusable aquatic trash heap. And yet you might be surprised to discover that the Ganges River has a remarkable – even mysterious – ability to regenerate and self-purify. It is even believed by some to be incorruptible.

Read the full article by writer in residence Yesh Rai in the most recent issue of Guru. 

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Let’s do away with the auto-reply email

out_of_office

I recently had a life-altering experience – one I am lucky to have survived to tell the tale.

It happened a few months ago while I was in the final preparations for a science conference in Singapore. My bags were packed and waiting patiently by the front door for the next morning’s early cab ride to the airport. My talk was prepared, practiced and polished; the slides were saved on multiple devices and were accessible online in case I lost my luggage. I had a bundle of half-written manuscripts ready to work on during the 15-hour overseas flight. My running shoes and toiletries were neatly tucked away in my carry-on.

There was only one thing left to do before I switched off the lights and turned in for one final night’s rest in my own bed: set my university email to auto-reply.

I launched MacMail on my laptop, accessed the preferences and proceeded to script a short ‘out-of-the-office’ letter. Admittedly, I had only done this once before – prior to a summer kayak trip a few years earlier.

I hesitated about what to write in the auto-reply message box. Should I include details about the conference or just say I will be away from the university? Should I start with ‘Hello’ or get right to the point? Should I be light-hearted or serious? Should I include emergency contact details? Ultimately, I settled on the following:

“Hi. I am at a conference and will be away from my office until Feb 9. Please send me a reminder email if you don’t hear back from me by Feb 12. Cheers, David.” 

Done.

I clicked OK. Closed my laptop and went to brush my teeth.

Being an email junky, I checked my inbox one last time before bed. To my surprise, I had received dozens of emails in the 15 minutes since turning on the auto-reply. More surprising, many of the emails were from friends and colleagues wishing me safe travels and an enjoyable meeting. As I was reading and deleting these messages, more well wishes trickled in.

How, in such a short amount of time, could so many people have received my auto-reply informing them of my travels? Then it hit me, my automatic response, instead of only replying to new email messages, replied to every existing email in my account.

I began to sweat I as I did the math – I must have hundreds, if not thousands, of saved emails. This meant that countless colleagues, friends, collaborators, administrators, journal editors, students and family members received an email from me announcing my departure from the office.

Pouring a strong drink, I thought to myself: it’s a good thing I’m leaving town.

Ironically, one of the consequences of my email blunder was that I was inundated with other people’s out-of-the-office email. In other words, I received numerous auto-replies to my own auto-reply. The number of people who were currently away astonished me, as did the fact I was apparently the only one among them who did not know how to operate email settings.

Scanning through the automated messages, I saw a range of styles and formats.

Some were succinct: “Traveling. Back soon.” Others provided exhaustive, point-by-point itineraries: “First stop Brussels … then on to Helsinki …” Many were funny: “For the next five days you can find me at the pub across the street from the 8th International Conference on …” A handful were earnest: “In the case of a serious disaster please call …” Some were from coworkers I had seen earlier in the day and who I knew were in their offices. And a few were from colleagues I follow on Twitter. A quick scan of their accounts showed that although unable to answer email, they were still actively tweeting.

My email-induced embarrassment began to fade the following day, and I eventually realized I never really needed the auto-reply feature in the first place. After leaving my home, I checked my email in the taxi, at the airport before boarding, during my layover in Toronto, and again over the Pacific Ocean (using the in-flight Wi-Fi, which cost me $25). I checked my email immediately upon arriving in Singapore and after checking in at the conference hotel. Jetlagged, I checked my email repeatedly throughout the night. At the meeting, I was rarely off of my email. In fact, I was on it more being away from work than I was when at work. And therein lies the problem.

Many of us are addicted to email, and our increasingly large armoury of digital devices is worsening the dependence. The mail icons on our laptops, smart phones and tablets are always just a finger-twitch away, and they look so innocent and inviting until they bombard us with to-do lists, requests and distractions.

And often, as quick as we are to check email, we are equally as slow in replying to it.

All of this causes anxiety and, perhaps, this is one of the reasons why more and more people are setting their email to auto-reply. When we write, “I’m away from the office,” maybe we really mean “I’m fed up with emailing.” Maybe we are looking for a way to escape our enslavement to email, even if only for a few days.

Let us not fool ourselves. Our inboxes might be out of hand, but auto-reply is not the solution.

And for those of you who do have it switched on, we are on to you. We know you are checking your email right now, and again and again and again …

[this piece originally appeared in Western News, Mar 31]

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Spring

Spring

Oh, mamma. Winter is finally over. I’ve been bogged down the last three months with teaching second-year genetics. This was my second go at the 1100-person course and things weren’t nearly as stressful as the first try, which you can read about here. Other updates: I’ve come to the conclusion that I suck really bad at scientific social media and lamented my struggles in a Science & Society piece for the journal EMBO Reports. But I didn’t stop there. I ranted about Publon, a social media service that allows scientists to get credit for peer review, in an essay for BioScience.

I know what you’re thinking: does this guy ever do research or does he just write essays about social media? Well, my former honours student Yan the Man got his thesis published in Molecular Phylogenetics and Evolution. Great stuff. And Yan’s good friend Marc Possmayer, a PhD student at Western who I collaborate with, published an article in The Journal of Phycology about a super-cool green alga that lives in the Antarctic. Yes, algae are tough little buggers.

A shout out to Western Rez Life who invited me to take part in REAL Talks – a TED-talk-style event about “how to win at life.” I don’t know much about winning at life, but I do know a lot about losing, so I talked about that and how to avoid it. Listening to the other speakers, including professors Joel Faflak and Hubert Pun, was inspirational, particularly because Prof. Pun did 50 pushups on stage. (I could do more, but I didn’t want to be a showoff.)

Finally, undergraduate writer is residence Neeraja Dharan wrote a lovely piece about how there ain’t no hacks at hackathons, which was published in Western News and made the Western Science homepage.

Next up is a trip to Miami to give a talk. That would be Miami, Ohio, in case you were wondering.

Take it easy,

David

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Genomic jet lag

jet lag

Just got back from a meeting in Singapore and Bintan, Indonesia. It was a two-part meeting on the evolution of cells, genomes and proteins. The first part was at Nanyang Technological Institute (where my sister did her PhD) and was open to the general scientific community and the public with special invitations to Singapore Junior College students interested in biological sciences. The second part was a closed “circle” meeting in Bintan (a small Indonesian island off the coast of Singapore). Here’s a list of speakers and talk titles in Singapore and Bintan. Speakers included Nobel laureates Sydney Brenner and Michael Levitt as well as a slew of other top-notch genome and protein scientists. Lots of fun. But I’m pretty darn tired. ~david

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teaching away…

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Yo. I’m crawling through the winter semester … Susanne Kohalmi and I are back at it: teaching 1100 second-year genetics students in Bio2581b. It’s a blast, but also exhausting. On other fronts, I’ve been ranting about my ineptitude with social media (see my commentary “Are you failing at scientific social media?” in EMBO Reports). Writer in residence Neeraja Dharan has a new piece titled “There ain’t no ‘hacks’ at hackathons” published in Western News. I’m soon off to Singapore for a meeting on the origin and evolution of cells and genomes. It’s going to be a long flight but a cool meeting. I’ll keep you posted. ~david

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Adapting to the Arctic

iceburg

If you want to start the new year with a scientific splash, then check out the new pop-sci article by writer in residence Jenny Ge and me, titled Genome sequencing suggests Inuit are adapted to the Arctic (published in the January issue of Above & Beyond). In addition to writing about Inuit genetics, Jenny Ge is actually studying it! As part of a 4th-year-thesis project in Prof. Rob Hegele’s lab, Jenny is looking into the genetics of various Canadian Inuit populations.

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Merry Christmas

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Happy holidays from David, Marmite, and the entire Smith Lab. We hope that the new year brings you many high-impact papers, bountiful grants, productive grad students, and kind-hearted undergraduates.

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Undergrad writers

Just giving a quick shout out to my undergraduate writers in residence. Neeraja wrote a wonderful essay about her research internship in Germany this past summer, which made the home page of Western Science and was used to promote Western’s International Student Week. In addition to some great pics, the article includes a recorded interview with Neeraja. On other fronts, long-time Smith Lab member Dennis He adapted an earlier article on the human brain project for an essay in the most recent issue of Guru Magazine. Stay tuned for more student articles, including one about Greenlander genetics, set to be published in Above and Beyond, a piece about designer babies for Guru, and much much more – maybe even something by me (the scribbler in residence). Take it easy. ~david

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