Your one-stop link shop for the SCOTUS ruling on human gene patents

This morning, the Supreme Court of the United States (SCOTUS) ruled that human genes cannot be patented. This decision has been heavily anticipated, so naturally, the Internet is going bonkers on both sides. This post is an ongoing collection of links I find interesting related to the lead up and to the final SCOTUS decision today, so it will be updated as we go. Disclaimer: I am a Canadian genetics/genomics graduate student, so I’m leaning mostly in favour of the SCOTUS decision right now but I do see some negative implications down the road, and am watching this from an international perspective. This decision sets a huge precedent, and it will be interesting to see the fallout of this decision.

Given that the SCOTUS decision was unanimous (are these things ever unanimous?), and most scientists I have spoken with see the ruling on patenting human genes as a positive, I’m curious to hear the other side, apart from the obvious loss of revenue for Myriad (shares fell 5.6% on Thursday alone). The cDNA ruling is not something I was aware was on the table in the first place. Do you think the cDNA ruling will eventually be overturned in court?

Here are the links, and I welcome your contributions in the comments section as well!

News Outlets

• Wall Street Journal reports “Supreme Court Says Human Genes Aren’t Patentable“. The best bit of this report is the baseball bat metaphor wars near the end.
• US Supreme Court rules patents on ‘natural’ human genes invalid – Nature Blogs

• Supreme Court nixes patenting human genes – The Scientist
• Ban on patenting DNA cheers researchers – The Baltimore Sun – this article has several quotes from researchers, institutional directors, and professors, which a lot of the early reports lack due to the breaking nature of the story at their publication time

Blogosphere

• US Supreme Court Rules That Isolated DNA Is Not Patent-Eligible, But cDNA Is Eligible  on PatLit: the patent litigation weblog
• Genetic Errors in Supreme Court Decision – In the summary at the beginning, cDNA terminology is misused (cDNA conventionally means complementary DNA, NOT composite DNA as the SCOTUS syllabus reads; HOWEVER the term “complementary DNA” is correctly used on page 4 of the document linked at the beginning of this post (page 1 of the Opinion of the Court)
• Gene patent decision: in plain English – SCOTUS Blog

• Your genes cannot be patented, but it is too early to celebrate – Science, I Choose You (@TheresaLiao)
• SCOTUS ruling means cheaper genetic testing – Double X Science
• Myriad in the mire as SCOTUS rules against gene patents – BioMed Central Blog (Genome Biology)
• The gene patenting decision from a plaintiff’s point of view – ScienceNews. Includes comments from a researcher who received a cease and desist letter from Myriad for offering BRCA1 and BRCA2 tests

Twitter/Other Social Media

Media's coverage of SCOTUS Myriad decision is broadly misleading; the Court recognized the viability of cDNA patents. That's the real story.—
Joseph Adams (@josephbadams) June 13, 2013

The fact that cDNA is patentable is its most apposite characteristic. Not the science. Should call it #©DNA @matthewherper @sethmnookin—
Ryan Seals (@RMSeals) June 14, 2013

To be updated

The Culture of Science: Peering into the world of the people who study our world

[Note about the photo: This is Bill Nye talking about Mars. SCIENCE RULES! I took this photo at a talk Bill Nye gave at The University of Western Ontario last fall. The event was sold out in record time, all because Bill Nye had introduced us to science culture when we were children, and we loved it.]

Science and culture are two words that are quite familiar with being in each other’s company: science of culture, science in culture, science and culture. We spend a lot of time thinking about how science functions in culture, how we can use science to study culture. Science and culture go together like two peas in a pod, so to speak. But what if we remove those little connecting words that join them together? Science culture. Science culture. This term may bring to mind images of Petri dishes crawling with bacteria, but that’s not the kind of culture I mean.

When we as scientists complain about things in our day-to-day lives to our non-science friends, the issues certainly seem foreign to them. In my own experience of trying to finish up my Masters, I get a lot of reactions like “can’t you just call it quits and write it?“, “just change your experimental design!” or “what if you just publish your research in your blog?” The answer to each of these questions could be summed up by saying “that’s just not how it is done in science” – but that’s not very informative. Whatever we respond with, we are explaining some aspect of science culture.

Science culture itself is a very real thing, a real culture with its own traditions, customs, codes, and history in which millions of people today participate. Although we talk a lot about these factors individually, it is rare that we take a step back and look at the culture of science as a whole.

One sense of the word culture is defined by the Oxford Dictionary as “the ideas, customs, and social behaviour of a particular people or society”. Traditionally, we think of culture as more ethnicity-based. The example given by the Oxford Dictionary itself is Afro-Caribbean culture. Cultural awareness generally implies learning about people that are different from ourselves somehow, or learning about traditions handed down from our blood ancestors. Certainly all legitimate and important manifestations of culture. The diversity of cultures formed by humans as a species is vast and, if you think about all of the cultural festivals we’re so lucky to celebrate – quite delicious! (I say that as a big fan of international cuisine).

There are some cultures we remain a member of from birth to death, sometimes even well before and well after our time on this planet (think baby showers and birthing practices, funerals and legacies). But we often forget that the cultures that we identify with are not limited to where we come from, but is also heavily influenced by who we are now: the people we associate with, the traditions we choose to incorporate into our day to day life, the kinds of behaviours we display and deem to be acceptable from others. This is how we can slip in and out of membership to countless other cultures over the courses of our lives. Even the most permanent-appearing cultures may be shrugged off at some point. But there are some cultures we consciously choose to join, a club we want to be a part of. One such culture, and one that I slipped into many years ago and remain a staunch member of, is science culture.

My interest in science culture stretches back many years, but the spur in my side that urged me to write this post was a conversation I had recently with my PI. Our discussion centered around how to teach scientific ethics, what a course for that might look like, and what year in undergrad would we introduce it. Sure, there is a short online module first year students are mandated to complete dealing with definitions of plagiarism, but in my opinion this model is ineffective and the lesson does not run nearly as deep enough as it should. I argued that something as fundamental as the ethics in how we conduct and publish scientific research are not something that can be taught in a short course on the Internet. These are fundamental values that are rooted in science culture, and the issues are highly connected to other aspects of this culture. The pressure to publish big and publish often is more than just a value in science, it is a rock solid expectation that governs your membership to the club. As such, retractions are rampant, data are falsified, statistics are abused, because the name of the game is the end result. And unfortunately, it is a culture where some cheaters with a severe lack of morals manage to get ahead (Andrew Wakefield is a name that rings a bell). Of course, publishing in the first place is something that follows many other processes in science: paying for publishing (especially an issue with open access), getting funding for the reagents, equipment, and personnel to get the data in the first place, getting the academic position in which you are capable of getting this funding, getting the education needed to achieve this academic position, having the support (financially and culturally) to acquire this education, and having the access to this education with minimal roadblocks. Once you’ve published, you must keep publishing. Present at conferences. Push for tenure. Get more grants. Maintain your career at the highest level you’ve set for yourself (at least).

Long story short, every single step along this path requires participation in the established culture of science. Teaching students in a 30 minute online course the basics about plagiarism is certainly a good start, but it’s a conversation that needs to had throughout education, from undergrad through doctorate and beyond. And plagiarism is but a small, small part of it all, and impossible to really grasp why it matters so much when taken in isolation of the rest of science culture. Learning about the culture we as scientists operate in and what is expected of us at all levels and forms of engaging in science is quite a grand goal, but it needn’t be the nebulous smattering of snippets we are expected to just absorb the hard way along the way. Being culturally aware before we head into certain situations helps everyone turn to the same page, and gives context to the experiences we will almost inevitably have as we move through a career trajectory in science. But how do we become culturally aware in science?

We can start by reading about it.

In what will soon be a multi-post series, I will do my best to capture some aspects of science culture that I have encountered in my seven years of university science education as I try to finish up my masters thesis and look ahead to the next step (to give you a bit of context of where my experiences have been).

Part I: History (coming soon)

Part II: Cultural Issues (coming soon)

Part III: Government (coming soon)

Part IV: Geography (coming soon)

Part V: Food (coming soon)

Part VI: Holidays (coming soon)

Homemade iced coffee: for the broke grad student bound to a computer in the hot summer months

Today’s edition of Appetite for Awesome is dedicated to those who have an appetite (for caffeine at least) while trying to do awesome (aka, science). I will share with you one of my little secrets to beating the heat without breaking the bank, while cutting back on food & packaging waste.

Here is my recipe for a delicious Pickleswarlz Iced Coffee!

Step 1: Make coffee

Yes, MAKE it. Not buy. Make. Any old coffeemaker will do, and this will be infinitely cheaper than coughing up bucks on campus for that watery dribble they are serving in the next building.

Sidenote: I created a spreadsheet to calculate out where to go on campus at the University of Western Ontario to get the best deal for the amount of coffee you feel like drinking at the moment, including calculations based on use of the “buy 10 get 1 free” coffee card at the Grad Club. I’ll post that sometime in the future. It is still cheaper to make coffee at home.

Step 2. Make coffee cubes

Pour whatever leftover coffee you might have at the bottom of the pot into an ice cube tray. Leave it out to cool, and once it’s down to room temperature, pop it into the freezer. Now you’re not pouring anything down the drain, and you can start being a bit more conscious of how much coffee you actually do waste every day when you start storing it in little cubes in your freezer.

Step 3. Wait til the next morning

Oh my god, you are actually just waiting? What do you think you are, tenured? Not yet, my doctorate-less friend. Get out of bed. You’ve got a thesis to write. Work on it all day and all night, so that in the morning, you’ll need another cup of coffee to function. You may already be somewhat familiar with this cycle. Get used to it – we’re going deeper. Inception-style.

Step 4. Make coffee, again

Good MORNING! It’s a brand new day and you have the next 12-15 hours ahead of you to pump out a dissertation! You’re going to need another pot of coffee. Make it so. Once the coffee is made, pour out a mug. Mix in your desired amount of milk and sugar. Don’t try to do this when it’s over ice – dammit, Jim, you’re a scientist, not a doctor, and the principles of solubility will not be on your side when your solvent is cold. And nothing sucks more than grains of sugar at the bottom of an otherwise delicious beverage. If you are really picky about the sugar/milk/coffee ratio, you’ll probably want to add a bit more milk and sugar than you normally would, because when your coffee cubes melt they’re going to throw off the balance. Anticipate the state change of your coffee cubes and plan accordingly.

Whatever you do, DON’T use CoffeeMate. That’s just gross.

Leave it on the counter to cool while you get ready (don’t forget, just because you’re a graduate student in a hole of darkness does not mean you shouldn’t pull yourself together at least once a day).

Step 5. Ice that java!

Fill your travel mug (we’re being as eco-friendly as possible here) with the coffee cubes from the freezer. You might have to get a knife to pry the cubes out of the tray, coffee tends to be stickier than pure water. I would recommend prying out all of the cubes in one go and storing them in a Ziploc freezer bag. I’ve spent more than my fair share trying to clean up melting coffee chips from all over my kitchen early in the morning. Do it once and save yourself the cleanup for the rest of the week!

Pour your now room-temp coffee over the coffee cubes, slap on the lid (tightly!), and invert it 2-3 times to mix. Don’t shake it – you are a scientist, not James Bond, and though I don’t doubt for a moment you are just as suave and sophisticated, you have better things to be doing with your time than hanging around bars with a gun (like, oh, I don’t know, discovering the secrets of the universe, or whatever). You, my friend, are going to need those arm muscles to lift your thesis off of the printer later, because you now have harnessed the power of caffeine and controlling your internal temperature to pump out the most amazing dissertation of all!

Don’t forget to refill the ice cube tray with the leftover coffee in the pot. This is one vicious cycle you won’t want to get out of, since it at least gives you the benefit of binding something to your adenosine receptors.

Step 6. Repeat!

Never again shall you fork over your precious stipend to Tim Hortons or Starbucks.

Ever wondered what a naturally mummified mouse looks like?

For most people, this thought probably hasn’t crossed their minds. For most people, even if it did, they probably wouldn’t be keen on finding out the answer. But scientists are a different breed, and wonder is our collective middle name.

Here’s the back story, which will hopefully seem slightly less grotesque than what you are imagining.

I have a farm. On that farm, there is a workshop (formerly the chicken coop). In that workshop, there is a garbage bin. In that garbage can, there is usually a garbage bag. In those garbage bags, there is usually garbage added. When the bag is full, the bag + garbage is removed, a new bag is put in, and the cycle starts over. Typical cycle of a garbage bin, usually moves along without much problem.

One day, my father went to do his part in the cycle, which was to remove the full bag. Upon doing this usually mundane task, he saw a little critter at the bottom of the usually empty bin. But this critter was far from alive. In fact, it was so far from alive, it looked like it had been left in a desert to go the way of the pharoahs, minus the treasure hoards:

What we think happened is that somehow, our little murine friend made it into the bin somehow, probably lured by the olfactory promise of a feast, as garbage tends to give off. Since it was between the bag and the bin, we think that the weight of the garbage is what flattened it, probably after it was dead because if it had made an audible noise, someone would have checked. I sincerely hope so.

Whatever the story, the result is certainly interesting.

And now you never have to wonder what a naturally mummified mouse looks like.

@PeopleofLdnOnt in the news

Vanity time!

I wrote a post recently on my side project, the @PeopleofLdnOnt rotation curation account. Today, I’m delighted to share that the local paper has given it some press!

Screen cap from lfpress.com. Article by Dale Carruthers, photo by Mike Hensen (both of the London Free Press)

That’s me outside of the Biology & Geology building on campus, checkin’ out Twitter on my Playbook (yes, a Blackberry product). Sitting on a rock with my ginger hair flowing in the wind, like the Little Mermaid but with less ocean and more WiFi (similar penchant for collecting knickknacks though).

Good Friday in the Sifton Bog

We lucked out on having some phenomenal weather in London, Ontario over the Easter weekend. Having a stack of grading to do, I naturally spent the afternoon doing the exact opposite of holing myself up with my laptop; I grabbed my Canon dSLR and headed straight for the bog.

The Sifton Bog is listed as an Environmentally Significant Area (ESA) under the protection of the Upper Thames River Conservation Authority. It’s gone through many name changes. It used to be called the Byron Bog when Byron’s boundaries encapsulated it; locally, we oscillate between the Byron Bog and the Sifton Bog, and often it’s just called “the bog”.

The reason we can call it “the bog” is because there’s almost nothing like it for miles around. The Sifton Bog is one of Canada’s most southern bogs of this nature, and when you’re walking through it, it definitely feels like you’ve been warped up north. The traffic of Oxford Street just melts away, and you stand on the dock in Redmond’s Pond at the end of the boardwalk immersed in a peaty wilderness spiked with black spruce trees. It’s a far cry from the rolling agricultural lands that surround the city in Southwestern Ontario.

But luckily, since you’re still in the middle of the city, there’s plenty of cell service! I tweeted my journey as I went on my mini-hike, and promised to back up the visual claims made by my crappy Blackberrry 9700 camera with shots from my SLR. So, here I present to you my photo-supplemented Good Friday live-tweeted journey through the bog.

Was going to grade papers, but decided it's such good weather in #LdnOnt today, I'm going for a bog walk!—
Andrea Wishart (@pickleswarlz) March 29, 2013

The Sifton Bog is an Environmentally Significant Area in Oakridge, just west of Hyde Park. Tour time! #LdnOnt http://t.co/cWf2adhkHB—
Andrea Wishart (@pickleswarlz) March 29, 2013

Sifton Bog is the result of a kettle lake forming after the last glacial period on glacial till. http://t.co/o40FThagnh—
Andrea Wishart (@pickleswarlz) March 29, 2013

Lots of birds! The cardinals clearly want to get it on…—
Andrea Wishart (@pickleswarlz) March 29, 2013

Lots of water-loving trees here in the bog too, they are all creaking in the breeze http://t.co/h6SL2l3g6s—
Andrea Wishart (@pickleswarlz) March 29, 2013

The fact that THIS still exists in the city is a testament to the efforts of lots of groups like @UTRCAmarketing http://t.co/uL4ZV480rz—
Andrea Wishart (@pickleswarlz) March 29, 2013

Lots of goldfish in the water from people letting pets go free end up competing with native species. Don't do this http://t.co/iLjvhsm1cW—
Andrea Wishart (@pickleswarlz) March 29, 2013

Cattails are marsh species, the bog *should* be too acidic. The bog is changing because of runoff http://t.co/yTiXhB3Xku—
Andrea Wishart (@pickleswarlz) March 29, 2013

Spoke too soon – there are tadpoles swimming around! #SiftonBog #LdnOnt—
Andrea Wishart (@pickleswarlz) March 29, 2013

I was mistaken – it was a pollywog! They’re very good at camouflaging, and my photoshop skills aren’t enough to make him stand out. Here you go:

And here are some beautiful fungus & moss shots (feel free to help me ID them in the comments!)

I’m hoping to return later in the season to get some photos of the carnivorous plants that inhabit the bog (pitcher plants and sundews). I’d love to thank everyone that has ever had a part in conserving this amazing habitat, and for maintaining boardwalks, paths, and interpretive educational boards. It’s a gem of an area to have in a city!

@PeopleofLdnOnt, a Rotation Curation project

I’m deviating away from the recent burst of science posts to tell you a little bit about one of my side projects.

In the dizzy dash of trying to finish up my Masters this year, I unfortunately haven’t been able to do as much volunteer work as I like, telling myself that I must throw 150% of myself behind this thesis. Which is true – so many unforeseen obstacles have thrown themselves in the way of finishing, I need all the focus I can muster. While getting around obstacles is a fantastic exercise in problem solving and skill sharpening, it’s a reminder to me that this can’t be absolutely everything. Holed away in my office in a separate building from my labmates, with nothing but a pile of data and a lot of coffee, I realized how cut off from everything I felt, leeching my life force from the shaky internet connection that at least put me in touch with other human beings, albeit with digital interfaces.

Dramatic, I know. But I realized that I could easily turn what felt like my useless coffee break diversions into something a little bit more.

Many of you who are Twitter savvy will have heard of a project called Rotation Curation. This initially started with the government of Sweden handing its official Twitter account (@Sweden) over to a different citizen every week. This has since blossomed into a worldwide loosely linked grassroots project of nearly 100 different “rotation curation” Twitter accounts, each one run by a different person every week, and each account unique in the community it stands to represent (be it geographical or ideological).

I got to know the project through @PeopleofCanada, an account for Canada which, unlike @Sweden, is not affiliated with the government. I found this account through a professor in Vancouver who I already followed (@enniscath), who became the curator of @PeopleofCanada for a week. Not wanting to be left out of a week’s worth of her tweets, I decided to follow @PeopleofCanada myself. Watching her interact with so many Canadians and other users from different countries was fascinating, and by the time her week was up, I knew I was a permanent follower!

In the weeks since, I’ve seen users from Newfoundland, Ottawa, Toronto, and many other places take over and tweet about their day-to-day activities and interact with other users. But the one thing that stood out to me was that no matter where they were from, they all identified as “Canadian” – which is funny to me, because questioning “what it means to be Canadian” is as much a part of being Canadian as almost anything else. It’s that identity we collectively can’t quite put our finger on, and we’ll argue about until the end of time since no two Canadians are alike. Our vast geography splits us, and many hold contempt for other places (it’s REALLY hard to make non-Ontarian friends if you yourself are from Ontario, trust me ) but at the end of the day, @PeopleofCanada is exactly what it calls itself – voices of different people that have, at least at one point, called Canada home.

Rotation curation isn’t just a nationality thing. City accounts are cropping up everywhere! Just in Ontario, there was already one for Toronto and one for Ottawa. Not to be outdone by the big cities, I decided that London, Ontario should have one too. After all, the Twitter community in London is hyperconnected and overwhelmingly active. It’s never that surprising anymore when something from this city is trending Canada-wide. There are a lot of voices within this city. And really, it only takes 52 people curating to make the project last a year! Obviously to make it worthwhile it takes a lot more than 52 people, since interactions and connectedness are what the project is all about, but it doesn’t have to be big to get started.

So, one night after a long day of thesis-ing til nearly midnight, I came home totally drained, wishing I could do something with my life beyond defining features of the mouse genome that I feel only a handful of people on the planet would ever understand, let alone appreciate. That’s when it hit me – I didn’t have to wait around for someone else to start a rotation curation account in London. If nobody had done it yet, then the idea was mine…and if there is anything I have learned from graduate school in the sciences, it is that when an idea is yours, you bloody take control of it before it’s scooped and you’re left with nothing!

The next day I began setting up the account. First, I nabbed a Twitter handle – @PeopleofLdnOnt. Second, I started a WordPress blog to host information about the project. Third, I got a Gmail account to handle applications and Twitter notifications. Within an hour it was up! Not pretty, but up! Over the next month I spend my spare minutes and thesis-breaks building up followers by following people in the community. The response was positive! Several people commented on how they were excited to see how it panned out. I didn’t get one negative remark at all – something I definitely could NOT say about my thesis. So that was nice! I felt really encouraged by the people who asked for more info, who tweeted back, who started sending in applications. And today, March 24 2013, marks the end of our Week 1 with our very first curator. A huge success! Our second curator now has control of the account, I have a third scheduled for next week, and I am currently reviewing applications for future curators. As of right now there are over 300 followers, and it’s growing. Not bad for a smaller Canadian city project started by one chick in the midst of thesis writing.

And you know what? My thesis has since grown to 62 pages, and the rate that I’m getting data analyzed is way higher than it was before. So although all I hear is that I should be working on my thesis all day, every day, no time to sleep or eat, don’t even THINK about television or volunteering – I see now what really sparks my motivation. Connecting the community, giving a project back to my hometown, and taking control of an idea and seeing it grow into something I can say I achieved with the support of those who want to be a part of it – THAT’S achievement.

Science is fickle. I love it dearly, it fascinates me, it is what I want to put my life in service to, but it’s hard to find inspiration along the dark and lonely road of finishing a thesis. If I can create and set @PeopleofLdnOnt free, then I can finish this thesis knowing it won’t be the only mark of my achievement. The qualification of holding a degree isn’t – and shouldn’t be – everything, it’s what you do along the way that makes it count.

Check out @PeopleofLdnOnt on Twitter, and see peopleofldnont.wordpress.com for more information.