Tag Archives: open access

How space dust teaches us about scientific progresses

30 Sep

Sometimes I feel that it sucks to be a physicist.

(Just to clarify – I am not one, and this is my personal opinion, having worked years in a department full of physicists, and with a background in non-physics fields. This is not after any discussion with other physicists in my dept – they might agree, they might not)

There was a major announcement back in March that results from BICEP2, a telescope sitting in the South Pole, showed evidence of cosmic inflation. This was, at the time, considered a Nobel Prize worthy discovery – I rounded up a few links on this back then.

The sun sets behind BICEP2 (in the foreground) and the South Pole Telescope (in the background). (Photo: Steffen Richter, Harvard University via BICEP2 image release gallery)

The sun sets behind BICEP2 (in the foreground) and the South Pole Telescope (in the background). (Steffen Richter, Harvard University)

However, recently new results from Planck, a space telescope run by the European Space Agency, showed that the patterns in cosmic wave background detected by BICEP2 are likely just space dust.

The Planck telescope up close (Photo: ESA for public use)

The Planck telescope up close (Photo: ESA for public use)

Suddenly the internet space is filled with criticism – like Big Bang blunder bursts the multiverse bubble, or When Science Gets Ahead Of Itself .

Enough, people.

The reason you are seeing all these in the public is because physicists are known to be open about their research results. There is no (or very little) “I am hiding this so that I can get rich off it” or “I think someone else is going to scoop my research.” Data are often shared as soon as they are available via the open access arXiv. People make results open so that others can criticize it. So that the public can better understand science. So the field as a whole can progress as much and as fast as possible. In fact, there was already some talk about data sharing between the BICEP2 and the Planck team. Physicists are years, if not decades, ahead of other fields in the openness and rapidness in sharing information.

In my mind, this is what science is about.

I completely agree with Philip Ball, as he said in his article in the Guardian:

The team involved has been criticised for publishing results before they were peer reviewed. But this is what science is: debate, discussion, deliberation.

This is also what makes science interesting. It is constantly changing, not static; it is the collective knowledge, not lines of facts. As mentioned by Astrophysicist Mario Livio,

As disappointing as these new results may sound, they provide for a powerful demonstration of how science truly progresses. Advances in science are far from being a direct march to the truth. Rather, they consist of a zigzag path that often results in false starts or blind alleys. The important point, however, is that through continuous checks, testable predictions, and new observations, science is able to self-correct and find the right way.

After Higgs Boson was found, Stephen Hawking (who lost $100 in a bet about it) said,

Physics would be ‘more interesting’ if Higgs boson hadn’t been found.

Let’s not go back to the age of waiting for years before the results are published. I say that realizing BICEP2 might come from dusts keeps the discussion of cosmic inflation interesting. And, this definitely means that the bet between Stephen Hawking and Neil Turok is not over yet.


Links to the original publications:

Ade P.A.R., M. Amiri, D. Barkats, S. J. Benton, C. A. Bischoff, J. J. Bock, J. A. Brevik, I. Buder, E. Bullock & G. Davis & (2014). BICEP2. II. EXPERIMENT AND THREE-YEAR DATA SET, The Astrophysical Journal, 792 (1) 62. DOI: http://dx.doi.org/10.1088/0004-637x/792/1/62

Ade P.A.R., D. Barkats, S. J. Benton, C. A. Bischoff, J. J. Bock, J. A. Brevik, I. Buder, E. Bullock, C. D. Dowell & L. Duband & (2014). Detection of B-Mode Polarization at Degree Angular Scales by BICEP2, Physical Review Letters, 112 (24) DOI: http://dx.doi.org/10.1103/physrevlett.112.241101

Planck Collaboration, R. Adam, P. A. R. Ade, N. Aghanim, M. Arnaud, J. Aumont, C. Baccigalupi, A. J. Banday, R. B. Barreiro, J. G. Bartlett & N. Bartolo (2014). Planck intermediate results. XXX. The angular power spectrum of
polarized dust emission at intermediate and high Galactic latitudes, arXiv: http://arxiv.org/abs/1409.5738v1

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: http://phylogame.org/game-play/

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

Resources Page

31 Mar

I came across some wonderful resources, articles, and references in the past few years working on science outreach and communication. Sometimes I even lost track of them myself. I figure that I should set up a Resources page to keep a record of them.

Hope that you find the page useful. I will update the page regularly. Feel free to let me know if you have any questions or suggestions.

Check out the Resources page

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 ArXiv.org (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 🙂

Open science and the understanding of science [quote]

6 Feb

The route for real-time communication presented by open science offers the opportunity for public groups to engage not just with the published outcomes of science but also with its processes, including methodologies, codes, models, and raw data. This changes the context: Rather than science being a series of definitive experiments from which emerge polished results, open science supports the understanding of science as a dynamic, tentative, uncertain, and constantly revised activity.

from Open Science: A New “Trust Technology”? by Ann Grand, Clare, Wilkinson, Karen Bultitude and Alan F. T. Winfield. Science Communication 2012 34:679 originally published online 23 September 2012. DOI: 10.1144/1075547012443021 (Unfortunately full text is available only through subscription…*sigh*)

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