Archive for: April, 2013

Science and the New Media Ecosystem, a talk by Bora Zivkovic at York University, May 6, 2013

Apr 29 2013 Published by under academia, culture of science, faculty liaison, yorku

A note for my Toronto area friends, Blogfather Bora Zivkovic will be giving a talk at York University in Toronto on May 6, 2013 from 2:00 to 3:30 pm.

Here's the info:

Science and the New Media Ecosystem

Bora Zivkovic, Blog Editor at Scientific American

Monday, May 6, 2013, 2:00 – 3:30 pm
Paul Delaney Gallery, Room 320, Bethune College
York University, Toronto

The whole media landscape is shifting and changing – newspapers on the decline with blogs, Twitter and YouTube on the rise.

Science is no different. Come listen to one of the pioneers of online science communication talk about how this new media landscape is shaping how science is done, evaluated and communicated in an increasingly connected world.

If you can't make the talk, there will be also be a ScienceOnline Toronto Tweetup at The Duke of York that evening starting at 7pm. Sign up at the Facebook page or just show up!

The talk is open to the public. If you'd like to attend but aren't sure about the logistics of getting to York, campus maps and directions are here. Subway construction has made getting to campus a bit complicated, so be aware of the various transit options on the map/directions page.

You can also just email me at jdupuis at yorku dot ca.

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Reading Diary: Keystone XL: Down the Line by Steven Mufson

What kind of place has Canada become?

The kind of place that closes world-class research facilities in the arctic and in lake country. (Thanks, Ontario!)

The kind of place where the government actively muzzles it's own scientists and librarians, the scientists for wanting to share their research and librarians who want to talk about the importance of preserving our heritage, scientific and cultural.

The kind of place where Environment Canada would take their own name off their weather service website. Really? Yeah, really.

The kind of place where the Federal Government slashes its own role in environmental reviews and downloads it onto the provinces.

And perhaps most significantly, it's become a place where the Minister of Natural Resources attacks respected climate scientists over their scientific views on the Keystone XL project (Apologies!).

Even when they set up an open data portal for oil sands information, it's hard for anyone to believe they aren't just greenwashing.

And that's why this whole Keystone XL pipeline debate in the US is so interesting to us Canadians. Our government is for it, but their record on anything even vaguely concerned with the environment is so abysmal that it's hard not to automatically oppose anything they support. They fact that south of the border, it's the cause of so much controversy and political and social wrangling seems almost quaint and irrelevant. We almost want to shout out, "No, you fools, don't do this! Can't you see it's a bad idea!"

I realize that there's lots of people against the project in the States: the EPA says it's a bad idea, Canadians are telling you the same story in your media, so are regular folk, environmental think tanks and fellow ScienceBloggers in a bunch of different places.

But there's a lot of support too, from industry shills, of course, but also quite a bit of political support on the Republican side. President Obama seems cautiously positive but undecided.

And that's sort of why I approach this new TED book, Keystone XL: Down the Line by Steven Mufson (Amazon Kindle), with some trepidation.

But I needn't have worried. Like the last TED book I reviewed, this one is actually pretty good. The premise is fairly standard: the author and his merry band of journalists go on a road trip from one geographic end of the Keystone XL story to the other. In other words, from Alberta to the US Gulf Coast. Along the way, they meet both ordinary folk and a few oddballs whose lives are bound by the future of the XL project. They also meet a bunch of oil biz big wigs who have huge stakes in what happens. Sprinkled in among all the local and international colour are in depth discussions of the history of the Keystone XL project in particular and the oil sands in general. The social, economic and environmental implications and controversies are also dealt with in quite a bit of detail, in a fairly standard more-or-less objective journalistic manner. Mufson doesn't explicitly take a stand on whether or not the pipeline should be built and he very clearly understands that you can't look at this one very specific issue out of the context of the worldwide supply and demand for energy. North Americans use an awful lot of oil and it has to come from somewhere.

Of course, at the end of the day the climate science isn't much in doubt, and the controversies are more manufactured than genuine. And this comes through very clearly. This is no climate denialist or industry apologist tract.

Overall, this is a solid, detailed exploration of the nature of the Keystone XL projects and the various issues surrounding it; there's enough colour and narrative to keep the info dumps and wonkish policy explanations moving. If you don't know much about the issue, there are worse ways to get up to speed. It's well worth what TED is charging.

What do I wish were a bit different?

First of all, the Canadian part of the road trip could have been a bit more central to the narrative, perhaps it could have started in the south and headed north. The intermixing of details and narrative also made both a bit fractured, something that would have been fixed by having a detailed chronology somewhere as part of the document. And speaking of the document, certainly this sort of ebook lends itself very easily to detailed citations of all the various facts and figures sprinkled throughout such a book. I really missed a bibliography. In particular, a book on such a contentious topic needs to show sources even more than most books. And I guess that's the key -- the TED Books need to feel more like books than extended newspaper pieces.

My final complaint is that the roadtrip/interviews/profiles/infodump template for this sort of story seems a bit too timeworn. The ebook format seems to present some possibilities to explore new ways to tell these sorts of stories and TED should be the place to explore those new ways.

But to end on a high note, here's a quote from the author giving a good sense of what the book is about and why it is such a solid read. It is from a recent interview on the TED site:

You say the pipeline is a Rorschach test of how Americans view energy issues. Can you elaborate?

For four decades, we have thought about oil as a scarce resource. We imported more and more at higher and higher prices and went to distant frontiers, whether onshore or offshore, to find oil and gas. The sheer scale of the oil sands in Alberta has been Exhibit A of those extremes. The Saudi oil minister has often said that prices had to stay above $60 a barrel to keep the Canadian oil sands economically viable. All of a sudden, the trends reversed and a slew of oil prospectors – like the North Dakota fracking pioneer Harold Hamm who is profiled in the book – and energy experts are talking about U.S. energy abundance. Imports have dropped nearly in half. U.S. oil output has climbed over 7 million barrels a day and the International Energy Agency has forecast that U.S. output will surpass Saudi Arabia’s by the mid-2020s. Canadian oil sands would compete for U.S. refinery space with Venezuela, and North Dakota, Louisiana and Texas shale oil has enabled the big refiner Valero to stop importing light, sweet crude oil.

It’s partly a matter of interpretation and partly a matter of outlook. There are the folks who worry about climate and make calculations about booming demand across the developing world. And then there are the optimists and industry people who see more opportunity – which in the case of prospectors and drillers translates into profitable opportunities.

So which is it? Are we energy rich or energy poor? The truth lies somewhere in between. Yes, the United States has surprising new resources at home, and U.S. consumption may have hit a plateau as fuel efficiency rises. This is a big benefit for the U.S. balance of trade and the domestic oil and gas industry. And while U.S. oil independence remains elusive, the Keystone XL pipeline would help make North American oil independence conceivable.

(Kindle version supplied by publisher. This version is missing all the audio/visual extras of the version sold through the TED Books app. But given my experience with the previous TED Book I reviewed, that's probably not too significant a factor for reviewing purposes.)

Mufson, Steve. Keystone XL: Down the Line. New York: TED Conferences, 2013.

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Books I'd like to read: Food, physics and horror

hardly ever does The Globe and Mail books section every Saturday feature more than one, maybe two, books that I'm interested in. They're pretty heavy on the Canlit side, with a heavy helping of the kind of public affairs books that don't really do it for me. The mystery roundup feature is usually my best bet. Well this week there were three -- count'em three -- books that really piqued my interest. And a pretty diverse bunch too, one physics, one horror fiction and another environmental non-fiction featuring the kind of intersection between food, science and policy that I find so interesting.

Here goes!

Time Reborn: From the Crisis in Physics to the Future of the Universe by Lee Smolin (reviewed by Dan Falk) (Amazon)

Considering the esoteric nature of some of the material being presented, Time Reborn is relatively jargon- and equation-free. There are some challenging concepts, but nothing to deter the lay reader. (Smolin has said that he’s also working on a more technical book on the same subject, to be co-written with philosopher Roberto Mangabeira Unger.)

I hope this is the start of an exciting new chapter in theoretical physics. But I fear that Einstein was right, and that the ultimate explanation for time’s apparent flow might come from the realm of psychology or neuroscience rather than physics. Science, after all, has a track record of overturning our “common sense” beliefs about the world. Again and again, things that were “obvious” – that the sun revolves around the earth; that humans are fundamentally different from other animals – have been shown to be artifacts of an anthropocentric worldview. Maybe the “obvious” passage of time is another of these illusions.

NOS4A2: A Novel by Joe Hill (Reviewed by Ilana Teitelbaum) (Amazon)

Hill is the son of Stephen King and, with this new novel, he emerges as a literary inheritor of his father. (Hill’s brother, Owen King, also recently released a new novel, Double Feature.) NOS4A2 contains familiar elements for Stephen King fans, such as the twisting of something beloved (in this case, Christmas) into something pathologically scary, and a maliciously sentient car. But despite its roots in traditional horror, this is a book about the dangers of idealizing innocence and traditional values, a message with clear political implications.

One of the standout qualities of Hill’s work is his ear for the rhythms of language, the creative metaphors that surprise and satisfy. His sentences crackle with wit and understated craftsmanship – the kind so skillful it is only visible if you’re paying attention. It is through language that Hill weaves the subtly disturbing atmosphere that permeates NOS4A2 even in its least threatening moments, such as in a description of a diner: “[She] didn’t like looking at the flypaper, at the insects that had been caught in it, to struggle and die while people shoved hamburgers into their mouths directly below.” Not long before, Hill describes the laughter of a group of girls as being “like hearing glass shatter.”

Consumed: Food for an Finite Planet by Sarah Elton (Reviewed by John Varty) (Amazon)

But I don’t think Elton’s all about casting off the “other side” with tidy dualisms. Indeed, she anticipates, even concedes, some of her critics’ main arguments. She’s aware that “conventional” agriculture tends to out-yield organic; she’s heard about studies challenging the energy efficiency of local food.

Trouble is, so many studies supporting industrial agriculture simply don’t provide a full-cost accounting. Yield, for instance, is clearly important; but preponderant evidence suggests that the total energy inputs of modern agriculture are not returned to us in calories. Not even close.

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Around the Web: Cool linky stuff for science undergrads (4)

Apr 27 2013 Published by under around the web

I have a son who's currently a first year physics student. As you can imagine, I occasionally pass along a link or two to him pointing to stuff on the web I think he might find particularly interesting or useful. Thinking on that fact, I surmised that perhaps other science students might find those links interesting or useful as well. Hence, this series of posts here on the blog.

By necessity and circumstance, the items I've chosen will be influenced by my son's choice of major and my own interest in the usefulness of computational approaches to science and of social media for outreach and professional development.

The previous posts in this series are here, here and here.

Please feel free to add your own suggestions in the comments.

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Friday Fun: 30 things to tell a book snob

I'll admit, I'm a bit of a book snob, a strange thing to say for a lifetime comics/science fiction/fantasy/horror/mystery fan, but there you go. Perhaps more precisely, I'm a snob about books versus other media.

But in my defense I'll maintain that I'm getting better as I get older -- more tolerant and accepting and less snobby. Perhaps not coincidentally, I think my takes in reading material are getting more diverse too.

In any case, let's all enjoy 30 things to tell a book snob.

1. People should never be made to feel bad about what they are reading. People who feel bad about reading will stop reading.

2. Snobbery leads to worse books. Pretentious writing and pretentious reading. Books as exclusive members clubs. Narrow genres. No inter-breeding. All that fascist nonsense that leads commercial writers to think it is okay to be lazy with words and for literary writers to think it is okay to be lazy with story.

3. If something is popular it can still be good. Just ask Shakespeare. Or the Beatles. Or peanut butter.

4. Get over the genre thing. The art world accepted that an artist could take from anywhere he or she wanted a long time ago. Roy Lichtenstein could turn comic strips into masterpieces back in 1961. Intelligence is not a question of subject but approach.

5. It is harder to be funny than to be serious. For instance, this is a serious sentence: 'After dinner, Alistair roamed the formal garden behind this unfamiliar house, wishing he had never betrayed Lorelei's trust.' That took me eight seconds to write. And yet I've been trying to write a funny sentence for three hours now, and I'm getting hungry.

Go read all the rest of the suggestions. Then fire up your reading device and/or dig deep into your bookshelves and read any damn thing that gives you pleasure. (Me on Goodreads plus my 2012 reading.)

Now, at the end of the day, I tend to think music snobs are just as bad. It would be fun to see a
"30 things to tell a music snob" post somewhere. Of course, most of the points would be similar, but slightly different.

Maybe we can invent one in the comments?

I'll start:

1. It doesn't matter whether or not the musician is living or dead, young or old, it's all just music. If you like it and it gives you pleasure, that's all that matters.

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Around the Web: Librarians dealing with data, Unbundling the university and more

Apr 23 2013 Published by under around the web

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Friday Fun: Mobile phone technology set to revolutionise things we already do quite easily

Apr 19 2013 Published by under friday fun

After a week like this, I think we all need something a little on the lighter side.

Mobile phone technology set to revolutionise things we already do quite easily

One of the biggest launches at this year’s Mobile World Congress in Barcelona is the I-open; an app which allows you to open your front door by just twisting your phone as if it was a door handle. ‘This is breakthrough technology’, said marketing manager Chris Davies, ‘the phone’s action even works with a gloved hand which is a big advantage when compared to the friction deficit presented by traditional door handles if used with gloves, mittens and greasy hands from chip-eating. This feature alone should make it a must buy for anyone who opens doors, whether professionally or just as part of their life-skills set.’

Read the whole thing, it actually quite clever. We should all take heed of the advice in the last couple of paragraphs.

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Around the Web: Access Copyright sues York University

Apr 16 2013 Published by under academia, Canada, education, yorku

Since I work at York University, I'm going to refrain from commenting on this lawsuit. However, as is my practice I'll be creating and maintaining a list of relevant articles and resources here to help me stay current on the matter.

I am not attempting to create a comprehensive list.



Some Related Items on Canadian Copyright from 2012 & 2013


Chronology & Background for Access Copyright/York University Lawsuit (including 2012 & Earlier)


As usual, if I've made any errors of if I've missed anything significant, please let me know in the comments or at jdupuis at yorku dot ca.

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Interview with Mark Patterson, Executive Director of eLife

Welcome to the most recent installment in my very occasional series of interviews with people in the publishing/science blogging/computing communities. This latest installment is with Mark Patterson, Executive Director of new OA publisher eLife. I attended an ARL Directors briefing conference call on eLife with Mark a little while back, highlighting for me just how interesting this project is and just how little I knew about it before the call.

Hence, this interview.

A huge thanks to Mark for agreeing to participate!



Q0. Mark, tell us a bit about yourself and how you ended up as Executive Director of eLife?

I started my career as an academic scientist in the field of genetics. After post-docs at Oxford and Stanford and a few years as a lecturer in Cambridge, I moved into publishing in 1994 to be the editor of one of my favourite journals at the time, Trends in Genetics. I moved to Nature a few years later, and helped to launch the Nature Reviews Journals. In 2002 I got the chance to join PLOS, which I leapt at. Partly because of my background in genetics, where I’d witnessed the profound impacts of completely free and open access to genetic and genomic data, I found the vision of a fully open research literature utterly compelling (and still do!). I stayed at PLOS for the longest time I’ve spent in any job, but after nine years got the opportunity to join another wonderful project, eLife. Although it was a difficult decision to leave PLOS, I felt that working on a project supported by three outstanding funding organizations was another opportunity that was too good to miss.


Q1. What is eLife and how is it different from a traditional journal?

eLife is an open-access journal that aims to publish great research covering life science and biomedicine. More broadly, eLife is a collaboration between the funders and practitioners of science, whose collective aim is to make research communication work better. We want to assist in the transformation of science journals publishing from a system developed in print media to one that is fully adapted to digital tools and serves the interests of science.

So our starting point is to launch a great journal, and experiment with various aspects of the publishing process. First we are exploring ways to make the editorial process work more efficiently. The key innovation here is that authors receive a consolidated letter that summarises the views of the reviewers (who also consult with one another after their reports have been submitted), so that the author knows exactly what needs to be done to get the work published. The aim is to eliminate unnecessary rounds of revision and review, and get work published faster. We publish the decision letters and responses on the articles, so other researchers can see how this works. Second, we’re looking at various ways to extend the reach and utility of open content – from the design of our website, to the dissemination of content via many other platforms (Github, Mendeley, Fluidinfo, PubMed Central and so on) – and to use article metrics and indicators to expose the ways in which that content has been used.

We have a terrific opportunity to experiment and learn, and as far as we possibly can we will share the results with our community. But something I also learnt from PLOS is that it makes sense not to go too far too fast, so we’re also trying to take measured and carefully chosen steps.


Q2. I know that there will be no author processing fees to begin with, but what are the longer-term plans for financial sustainability?

You’re right, the project is completely supported by the three funders, while we work to establish eLife firmly in the research community, as a venue for great new work. Our goals for eLife are ambitious, and we’re competing for content that would otherwise be sent to journals that are not open access or supported by publication fees. The funders felt that the best way to build a reputation for innovation and excellence was to avoid any publication fees for the first few years. Once this is achieved, we will most likely introduce publication fees, and consider other revenue streams to take the project on a path towards long-term sustainability. The publishing landscape is undergoing much transition at the moment as well, so our plans for sustainability will develop over the next months and years. What’s clear though is that the stronger our scientific foundation, the better placed we will be to achieve longer-term success.


Q3. There’s lots happening in the scholarly publishing industry right now -- the Finch Report, the OSTP policy memorandum, FASTR, PeerJ, Episciences and so much more, with seemingly a startling new announcement every week or so. Where do you see the ecosystem in 5, 10 or even 20 years? Will it even be recognizable?

Having been involved in open access publishing for some time now, it does feel that the pace of change has accelerated over the past couple of years in particular. 2012 was a big year in particular because of the policy developments, especially in the UK, but 2013 has had a pretty spectacular beginning as well with lots happening in the US. My sense is that these policies will give added momentum to open-access publishing, but that the growth will be concentrated in the born open-access journals, rather than subscription journals offering a hybrid option. I could be wrong of course, but I see PLOS ONE and the new journals that it has inspired (notably BMJ Open, Scientific Reports, AIP Advances and, most recently, PeerJ) gaining ground. And then there are more experimental approaches like F1000 Research and Figshare to consider as well. Other disruptive influences will be the move towards new metrics and indicators of article impact. Pioneered by PLOS, article metrics are now being provided by quite a few journals, including Nature, and sophisticated services have been developed to deliver these metrics, such as ImpactStory and Altmetric.

So, I really can’t predict what research communication will look like in say 10 years or beyond. I would say that by then the default will definitely be ‘open’, but my feeling is that there are sufficient new approaches, services, and publication venues right now to predict that there will also be fundamental change beyond open access - both to articles as the primary vehicle for research outputs, and journals as a mechanism to organize those outputs. One possible, and radically different, future was very nicely described by Jason Priem recently in Nature.


Q4. Librarians and traditional publishers (commercial and society alike) view a lot of these developments with a mixture of excitement and unease. How do you see the roles of these types of intermediaries evolving in an ecosystem that includes eLife and all those other exciting new players?

Well, I’m definitely in the excitement camp! But I also try and appreciate the challenges faced by other constituencies involved in research communication. There are many important functions of the conventional publishing process that need to be retained in the new digital ecosystem, but how we deliver those functions might completely change. This brings all sorts of opportunities for those involved, so long as they are able to respond to a changing environment and adapt to it. Open-access publishing is now so well established, that you can see publishers large and small getting stuck in. That said, some publishers are doing this in a more committed way than others, and so I think we can expect to see new organisations emerge as powerful players (as PLOS, BMC and Hindawi have done) and others probably diminish.

I don’t have so much knowledge of the library side of things, but I’ve certainly met some creative and energetic people who are also immersing themselves in the opportunities offered by digital media. Repositories have tremendous potential to organize and present the scholarly output of a particular institution. And there will also be lots of work to be done to help users make sense of the increasingly diverse and complex array of information sources and services to support scholarship and how to use those resources in the most productive ways.

Perhaps the biggest opportunity will be in partnerships and collaborations. Having recently returned from the Beyond the PDF meeting in Amsterdam, you can’t help feeling energized and occasionally bewildered by the range of possibilities. Smart people are coming up with ideas all the time. Those of us concerned with the implementation of those ideas need to join forces with the bright minds generating them, and the other constituencies supporting the research value chain to turn those ideas into powerful, sustainable services.


Q5. There have been insinuations online (particularly in the Scholarly Kitchen) about conflicts of interest and preferential treatment in the relationship between eLife and PubMed Central. How do you respond to these accusations?

The launch of eLife is supported by three world-class funders who are motivated to make a positive difference in the world. These organisations are very familiar with the handling of competing interests, and also the need to respect the concept of editorial independence. eLife is published by a separate non-profit organisation that was incorporated in the United States, and the editors who run the journal operate entirely independently of the funders. All reputable journals operate according to this principle. We think it’s important for all journals to make the funding sources that support an article very clear, and we’re providing this information at a very granular level (source, grant number if available, and the individual funded). We’ve been very clear that all research submitted to eLife is treated equally, and we welcome outstanding work regardless of funding sources.

During the run-up to the launch of the eLife website in December last year, we were able to make some initial articles available via PubMed Central. We felt this would be a great thing to explore with PubMed Central because it would get some excellent new science out into the public domain more quickly than we could otherwise manage. It was an unusual step to take, but the world of publishing is in transition, and eLife has a mandate to push boundaries, experiment, learn from things that don’t work as well as those that do, and even have some fun along the way. When you do try out new things then you have to expect some criticism too – when I was at PLOS we were on the receiving end of some of that as well. I believe you should listen carefully to criticism, learn from it where you can, and move on.


Q6. Issues of incentives and prestige not to mention fear around hidebound tenure processes drive a lot of publishing decisions for researchers. How do you answer questions like, “Why should I publish in eLife when it’s more immediately useful to my career to publish in a famous, established journal?”

That’s the most important question for any new journal. It doesn’t matter how good your processes, infrastructure, websites are if you haven’t got any content to show. And given that eLife is aspiring to publish really great work, it’s all the more challenging for us. When faced with this question then we have to recognise what authors want out of publishing – reputational reward and an outstanding (which mostly means fast) service.

Even before we’d published any content, we had two powerful things going for us – the reputation and prestige of the funders behind eLife, and the stellar team of academic researchers who run the journal. This really helped to convince some people to submit to the journal. On top of that, the editors had devised an editorial process that we all felt could be much better than the conventional process. As mentioned above, the goals of the process are to eliminate as much as possible of the pain and wasted time that’s often experienced in publishing. Prospective authors were very interested in this aspect of eLife, and it definitely encouraged quite a few authors to give us a try.

Now that we have published over 50 articles, we are in a much stronger position. The standard of science is really good across the board, and there are some particular papers that really stand out. Plus, the response to the editorial process has been extremely positive. These first few months are absolutely critical in providing the foundation that eLife needs to really flourish, and thanks to a great initial response from the scientific community, we are off to a terrific start.

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Around the Web: Yet more librarian angst, The business of literature and more

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