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Pokemon + Biodiversity = the Phylo Card Game

25 Jul

For someone whose blog name was inspired by a Pokemon catchphrase, I am attracted to all things science & Pokemon. It therefore feels like my duty to talk about the Phylo card game. Even more importantly, there is a little back story here.

When I was still a graduate student, I spent a lot of time doing science outreach. One time, I attended an outreach workshop organized by the UBC Let’s Talk Science Partnership Program. This particularly workshop was led by David Ng, Director and Senior Instructor of the UBC  Advanced Molecular Biology Laboratory. Unfortunately, I don’t remember much from that workshop (sorry Dave!). But, one thing he talked about did stick with me. He mentioned a letter by Andrew Balmford and colleagues (you can read the excerpt here), who found that kids in UK could identify Pokemons (which are really just artificial “species”) better than identifying common wild life organisms. So – can we learn from this and come up with something that would help them discover real species and learn their names?

Little did I know back then, that this would soon be a new initiative led by David, and became a real game: Phylo, the trading card game. The game is much like the typical Pokemon trading card game you see kids play. The main difference? All the organisms on the cards are real. This is also an interesting artistic collaboration – there are some amazing art works done for the cards by many artists. Each card comes with the organism’s common name and Latin name, evolutionary tree info, key words, and more. If you browse the cards online, you can also read a bit more about each species.


What a Phylo card looks like. For more info visit:

The Phylo game is an open access project – you can download the card deck online for free (!!) and print the cards on card stock. There are also special decks put together by the London’s Natural History Museum and the 2012 World Science Festival. If you are in Vancouver, the UBC Beaty Biodiversity Museum now produces  professionally printed starter deck with organisms featured at the museum, for sale at the Museum Gift Shop for $12.99. Proceeds from the sale will go to outreach and education activities at the museum. Online sale is currently not available, but you can sign up online to receive an email when online sale begins. Or, you can just download this starter deck here.

This touches on something else about science communication – how many other mainstream, unconventional ideas haven’t we tapped into for science communication and education? Something to think about…


Sockeye Salmon

Why Do Scientists and Aaron Swartz Care So Much About Open Access (III. Solutions?)

19 Feb

This is part III of my 3 part series about Open Access. Read Part I. Read Part II.

With increasing digitization of research publications and improved ability to share information online, we finally have an opportunity to address the problems. With great power comes great responsibility! (wait, I heard of that somewhere before 😛 ). Here I will try to outline the two main approaches, provide basic information for the latest debate, and discuss how the Open Access (OA) movement is more than just making papers public.

The two approaches you might have heard about in the news are the Green OA, and the Gold OA.

With the Green OA, a scientist would submit a paper to an online repository that is open to the public. The paper can still be submitted to a journal for peer review and publication: According to the SHERPA-RoMEO  database developed by the University of Nottingham, 68% of the 1196 journals in its database accept having preprints (pre-reviewed) and/or postprints (post-reviewed) submitted to online repositories. Even though some of the articles in repositories might not have been peer-reviewed, typically there is some process in place to ensure the authors are credible and the papers do not contain significant flaws. Authors do not need to pay for submissions to repositories, and articles are typically available online in a few days, compared to the months typically required for a paper to be reviewed and then published by a publisher.

An example of Green OA repositories is the (for Physics, Mathematics, Computer Science, Quantitative Biology, Quantitative Finance and Statistics). ArXiv works on a moderator system, in which submissions were moderated by selected scientists approved by a committee. While there is no peer review, ArXiv has become a critical source of information particularly because how quickly scientists can exchange information online – at the time this is published, ArXiv contains 822,196 publicly accessible papers. Lately, Figshare presents itself as an option (or alternative) for those in fields not covered by ArXiv. Financially, these repositories do not generate revenues through the publication process. ArXiv sustains its operation by asking for pledges from 200 institutions with the heaviest usage (at $1500-3000 per institution), and by receiving grants from non-profit organizations (such as the Simons Foundation). Figshare is currently backed by Digital Science, a branch of the Macmillan Publishers Limited (although according to the news release Figshare will maintain its autonomy). The key to successful Green OA is likely to have a handful of key central repositories that everyone submits to, because this will make searching for papers a lot easier, and that might by why ArXiv has been so successful.

With the Gold OA, a scientist would submit a paper to an open access journal, and once the paper is accepted the journal will ask the scientist for an article processing charge (APC, usually ranges from $1 to ~$3000 USD, depending on the journal. UC Berkeley has a selected list of OA journals and their APCs on their Library Collections website). The article processing charge will then be used to support the logistics of making the paper open access, as well as to maintain the peer review system. This money will come from the authors’ own research grants, specific funds set up by their institutions for supporting open access publications, or occasionally personal moneys for smaller article processing charges (but some journals will waive the charge under specific circumstances). Here are a few examples of Gold OA journals: Public Library of Science (PLoS) (online only), BioMed Central (online only), and Sage Open (part of Sage, which publishes journals traditionally as well).

Gold OA journal examples

Gold OA journal examples

The Gold OA model is the one recently adopted by the UK government based on the famous (or infamous?) Finch Report (executive summary). If you are interested, Bo-Christer Björk and David Solomon published many articles analyzing APCs.

Regardless of which open access model it is, SPARC put together an excellent page on different income models that can be adopted for Open Access.

When it comes to Green vs. Gold, there are discussions and debates about which model is better for the scientific community (more specifically, which model institutions or governments should mandate their researchers to follow). Steven Harnad is a major proponent for the green model, while Stuart Shieber supports the adoption of the gold model (although, as Steven clarified in his comment, both of them favour Green Open Access). You can read about the cases they made: Steven Harnad’s “The Argument Against (Premature) Gold OA Support“, Stuart Shieber’s “The argument for gold OA support“. Also check out a good coverage by Times Higher Education.

But is open access simply about making the papers public? For me personally, it is more than that. For the Open Access movement to be really successful, we all need to start changing how we think of scientific prestige. For the past few decades, much of a scientist’s worth has been evaluated through the number of papers published, and through the journals the papers are published in. Each journal, as it stands now, has a number called the impact factor associated with it. Publications in journals with lower impact factors (usually newer, smaller, less popular journals) usually weigh much less than publications in those with higher impact factors, no matter how rigorous the science is (Postscript 1). For a scientist, this can affect anything from jobs, research funding, to awards or fellowships. The reason that some commercial publishers were able to charge high subscription fees without anyone complaining until now is simply because the money was not just to support the publication process, but also to buy and sell the scientific prestige that these journals represent. Is this going to change with OA? According to an analysis on the APCs of Gold OA and Hybrid OA journals by Theo Andrew, Open Scholarship Development Officer at the University of Edinburgh, there is a positive correlation between the APC and a journal’s impact factor (the higher the impact factors, the higher the APCs). While there are indeed costs associated with the publication process, what’s concerning is that there is no transparency to how the APCs are set, resulting in a huge variety in the numbers.

This move toward Open Access will take a while, because it is not just about changing the access model, but also about changing how we see science. If we continue to think that scientists can be evaluated exclusively by numbers and not by the science they do or by the people they inspire, and do not ask for any transparency in the scientific publishing systems, then the financial unfairness to scientists, as I described in Part II of my posts, will  likely happen again (granted, at least we will have open access…), and the OA movement won’t really achieve as much as what it sets out to achieve (Postscript 2).

Postscript 1. If you are interested in reading more about the effects of impact factors, here are a few great articles:

Postscript 2. I originally plan to include a few actions we can take to support to Open Access movement, and my personal take in the Green vs. Gold debate, but this post was getting too long. I will leave my call to actions in another post, and I don’t mind elaborating my point of view  if anyone asks specific questions in the comments section below 🙂

Why Do Scientists and Aaron Swartz Care So Much About Open Access (II. Problems)

27 Jan

(This is part II of a three-part series on open access. Read Part I here.)

Last time I wrote about the difficulties many scientists and I face almost everyday when we try to access scientific research articles blocked behind paywalls by journal publishers. For me, there are two major problems with the current model of publishing scientific papers in a closed system, where the access of scientific knowledge is restricted by the publishers.

First of all, financially speaking, this system is extremely unfair to scientists. I am not great with financial analyses, but this was written about on the SV-POW post “The obscene profits of commercial scholarly publishers.” Yes, the company needs to profit. Except, while other companies invest in inventory, technology, and creative ideas paid for by the companies, journal publishers don’t pay any of the scientists who review the articles and contribute to the quality of the journals are paid by the publishers. The publishers (particularly commercial publishers) ripped all the benefits without giving any compensation to the scientists and the public that support them (1).

As more journals offer digital subscriptions, the cost of physically printing and mailing journals to subscribers should have dropped. While I understand there are now costs to maintain servers and websites, I don’t believe that justifies the significant increase in subscription fees. What made the situation worse is that some commercial publishers sell “bundled” subscription packages to universities (also called the “big deal”). This means that in order to gain access to a prestigious journal, a library can be forced to subscribe to other unnecessary journals, raising the overall expenses.

The end result of this is that research information becomes extremely inaccessible to scientists, and universities scramble to pay subscription fees in order to afford their students and researchers access to journals.

Second, this “lockdown” of scientific knowledge means that we miss out on many incredible opportunities for better knowledge exchange, innovation, communication, and outreach. Here are a few examples I can think of off the top of my head:

For further reading, here is a great summary about who can benefit from open access on the The Scholarly Publishing & Academic Resources Coalition (SPARC) website. And, Jorge Cham, the creator of PhD Comics, made this animation, which covers the problems with the current publication model quite well.

More and more scientists have started pushing for open access. What is the progress? What are the potential solutions? What can we all do to help? I will continue on with this topic in my next post.

Read Part III. Solutions?

Postscript: By the way, I was going to quote a reference suggesting that, while in a similar industry, medical journal publishers have profit margins much greater than those of book and periodical publishers. Except, well, that paper is blocked behind a paywall by Elsevier right now…isn’t that funny…But reference #25 was used by Dorsey in his paper analyzing the finances of top US Medical Journals – and this one is open access published by a professional association, not by a commercial publisher.

Postscript2: There are some discussions/debates regarding whether to allow commercial reuse of open access research. To be honest I am still working out the benefits and disadvantages in my head. For further reading of this see Cameron Neylon’s article Science publishing: Open access must enable open use. You can be the judge and let me know what you think of it.

Why Do Scientists and Aaron Swartz Care So Much About Open Access (I. The Issue)

14 Jan

jan14featuredimageA few days ago Aaron Swartz (co-founder of reddit, co-author of RSS standards, who also helped developed creative commons license) took his own life. Many associated his death to the alleged case against him – because he “stole” millions of academic research papers from JSTOR through a computer connected to the MIT network.

The news of his death saddens many, particularly those of us in the research community. Why, you might be wondering – didn’t he steal all those academic papers? Shouldn’t we be mad that they were stolen?

I have been wanting to write something about open access for a long time – but it is really, really hard to find an angle that would get people  interested in reading about it (particularly those not familiar with the process of academic research). Perhaps this is the time. And here is my attempt.

Scientists share the discoveries with the world first-hand by publishing accounts of their work in scientific journals. The papers written by scientists go through a process called peer review: Very generally, a scientist submits a research paper to a journal, and the journal publisher will pass on this paper to a few other scientists to read and provide feedback (the scientists read them without being paid). If these scientists agree that the findings seem valid and significant, the article will then go through a few rounds of editing and refinement. Eventually the article is published to be read by scientists around the world. Most of these research projects are funded through government agencies using tax dollars.

So when an interesting scientific discovery becomes public, I (or any interested scientist) would  follow the paper trail to find the original publication. We will then get to see whether the study is reliable (what kind of experiments were done, is it from a reputable researcher, with a sufficient number of participants enrolled/samples tested, etc), with a conclusion that can be logically drawn from the results, if the conclusion has any significant implications, and if there are other relevant readings we can continue with.

So, you can imagine my frustration when I hit a pay wall, basically telling me that in order to read a paper based on research funded by public money,  reviewed by scientists who offered their service to the publisher for free, I will need to pay $45 dollars.

It feels like there is a bully standing in my way to the public library, asking me for my lunch money.

According to the Association of Research Libraries, the expenditures associated with journal subscriptions of North American research libraries increased by an incredible 381% between 1986 and 2009 (The overall inflation rate in Canada during this period of time was 72.71% and 95.7% in US – nowhere near the 381% increase). This is mostly due to subscriptions to journals published by commercial publishers — whose journals are typically 5 times the cost of those published by professional societies or associations. Working for a university, I can access articles through my university library (I will need to use a computer on campus, or connect to the university network, and this only works for journals my university has subscriptions for). This is not free – a university can be spending $5-10 million dollars each year in subscribing to hundreds and thousands of scientific journals for its students and researchers. For some libraries, journal subscription fees eat up more than half of the their budgets.

And if my library doesn’t have a subscription for the journal that I need access to? It will cost me $10-50 to purchase one article. To avoid this,  when I was in graduate school, I spent hours filling out library request forms to have the articles sent to me from other libraries with subscriptions (the librarians would photocopy the articles on paper…I don’t even want to think about how many trees I helped kill), or begged friends at another university with the subscription to send the paper to me. And from time to time there would be one that nobody seems to have access to, and I simply gave up or looked for alternatives.

This situation is bothersome for many, many reasons. I hope you are curious now – Why is it so expensive to access academic journals? Perhaps the publishers are not earning enough money to support their operations? How does this situation affect scientific discoveries? Why do we care so much about open access? I will continue with this in my next post.

Read Part II. Problems & Part III. Solutions?

Postscript – By the way, just to give you an idea, I had 194 references in my MSc thesis, most of which are journal articles. Luckily I was able to access them through my university subscriptions or through interlibrary transfers. Otherwise it would have cost me about $1940 – $9700 in journal accessing fees to finish my thesis.

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