Tag Archives: Phylo

Math, YouTube, and opening science

There’s a charming post (May 17, 2011) by James Grime, mathematician, at the Guardian Science Blogs about his and other science communicators’ YouTube videos. From the posting,

I’m a mathematician – and have the chalk marks to prove it – but I do not come from a family of academics. Growing up, my only access to that world was through the television. I remember Johnny Ball jumping up and down talking excitedly about the parabolic path of projectiles; Horizon’s documentary on the Andrew Wiles’ proof of Fermat’s Last Theorem; and at Christmas the theme music of the Royal Institution’s Christmas Lectures filled me with even more excitement than the bike that came with six sound effects.

Today the profile of science communication on TV may be at an all time high. My mum may not know what the Large Hadron Collider does, but she knows who Brian Cox is. But television remains a very 20th century method of communication. A channel will gear their science programming towards their perceived audience, be that BBC1 , BBC4 or a Channel 4 audience.

However, with the rise of new media, like YouTube, you no longer need to chase the audience. They find you.

He goes on to share one of his videos and a selection from other science communicators. It’s a great read and has attracted comments that include links to even more science videos.

Clearly, Grime’s main focus in this post is educational/popularizing/awareness raising for the general public.

Some scientists are trying to use social media such as YouTube to better communicate with each other. There are science videos (not many) wherein scientific papers are given video abstracts. For example materials scientists are doing this on their Materials’s Views Channel on YouTube. This is all part of a movement to make science more open through social media.

Science has been been opened up before according to the Open Science Manifesto,

In 1665, the first two scientific journals were published, and science was dragged out of its dark age of cryptic anagrams, secret discoveries, and bitter turf wars. Today we are living in another dark age of science: pay-per-access journals, unreleased code and data, prestige-based metrics, and irreproducible experiments.

As I kept on digging (clicking on the link to the dark ages reference), I found Michael Nielsen, previously an academic working in quantum computation (he has a PhD in physics according to Wikipedia) and now the writer of a forthcoming book, Reinventing Discovery, from the Princeton University Press in November 2011. He advocates strongly for the use of social media amongst scientists as you can see in this approximately 16 mins. March 2011 TED talk at Waterloo (Ontario, Canada),

I notice that his focus is on scientists using social media as a means of communication amongst themselves (and anyone else who may choose to join in) but control remains firmly with the scientists. In other words, science is practiced by scientists and there’s no discussion of citizen scientists where people reach beyond their general science awareness for some form of science activity. I believe it’s an unconscious assumption that the experts (scientists) are the only ones expected to participate while the rest of us gaze on. This is true too of James Grime’s piece where the rest of us are more or less passive viewers of his science videos and not expected to practice science.

There’s nothing wrong with these approaches and, most of the time, I’m perfectly to have scientists do their work and I’m hugely happy when they choose to share it with me.

However, when scientists talk about opening up science they usually mean that the public should learn more about their work (i.e. we are the tabula rasa and not expected to be able to reciprocate; our role is to listen and to be educated by the expert) or that research should be more easily available (mostly amongst themselves). There are some crowdsourced science projects (e.g. Foldit, which boasted some 50,000 authors and there’s also the recently launched Phylo at McGill University [my most recent posting on these projects] amongst others) where members of the public are invited to participate in science activities directly related to answering research questions.

My point is that ‘open science’ means more than one thing.

Democracy, participation, and science culture

Should citizens have any input into how science research is funded? Dan Hind in his Dec. 14, 2010 article, Time to democratise science, for New Scientist argues yes persuasively (from the article),

THE natural and social sciences exert a huge influence on the ways our societies develop. At present most of the funding for scientific research is controlled by the state and the private economy. Perhaps it is time to look at their track record and consider an alternative.

Science is not, and can never be, disinterested insofar as its objectives are concerned. Decisions to fund this research instead of that research can never be purely technical. Assessments of what is likely to produce interesting or useful knowledge are inevitably alloyed with the desires of those who control the money to develop particular forms of knowledge and with them new resources of power.

Given the mixed track record of the patrons of science it is surely time to consider an alternative. If we are serious about science as a public good, we should give the public control over the ways in which some – and I stress “some” – of its money is spent.

At the end of the article there is this note about the author,

Dan Hind is author of The Return of the Public (Verso), which argues for a new kind of participatory politics

There does seem to be seem sort of trend towards more participatory science as per citizen science or crowdsourced science projects such as Foldit (my Aug. 6, 2010 posting) and Phylo (my Dec. 3, 2010 posting).I’m not sure how much traction participatory science research funding is going to find. That said, there was a UK project run by EPSRC (Engineering and Physical Sciences Research) where members of the public were allowed to ‘vote’ on particular projects. You can read more about the project in the May 25, 2009 news item on Nanowerk describing the grants that were chosen. From the news item,

Ten research grants to help solve some of the biggest health problems facing the UK have been awarded by the Engineering and Physical Sciences Research Council (EPSRC)

The projects focus on developing new techniques for screening and treating major public health issues such as cancer, stroke, AIDS, influenza, MRSA and dementia.

The grants, worth £16.5m, have been given by the EPSRC, acting as the lead Research Council in a cross Research Council Programme called “Nanoscience through Engineering to Application.”

Segue: As for participatory politics (as per Dan Hind), I’ve noticed a local (Vancouver, Canada) backlash response to the notion of public consultations (city government officials want to increase population densities). Oddly enough, when people take the time to participate in a ‘consultation’ they expect that at least some of their comments will have an impact on the decisions that are being made. I gather some experts find this irksome and a challenge to their professional authority.

Back to the main topic: My impression is that the UK enjoys a science culture that is not to be found in Canada—not yet, anyway. There is discussion about public dialogue and engagement in science not just in the UK but elsewhere too that simply doesn’t exist in Canada. Yes, there are a few fragile attempts at creating a science culture here. I’m thinking of the Café Scientifique groups, Canada’s National Science and Technology Week, and the open houses put on by the universities but there really isn’t much.

The Year of Science (a science culture project) was declared in the province of British Columbia (BC) in the fall of 2010. From my Oct. 14, 2010 posting,

To inspire young minds across the province and foster a culture of research and innovation Premier Gordon Campbell today proclaimed the 2010-2011 school year as the Year of Science in B.C.

It’s good to see these kinds of initiatives, unfortunately this particular one is undercut by news such as this (from the Dec. 2, 2010 article, Teacher blasts cuts to Vancouver school science budgets; School science budgets slashed by 56 per cent compared to last year, by Naiobh O’Connor for the Vancouver Courier),

School science budgets were slashed by 56 per cent compared to last year and the district now allots only $4.61 per student each year to cover expenses—far below what Mike Hengeveld, Templeton secondary’s science department head and teacher, argues is adequate.

Limited budgets mean it’s difficult to replace equipment like broken beakers or to buy new equipment. Hengeveld even worries about buying a dozen eggs for a relatively cheap egg drop experiment or what’s needed to grow crystals for chemistry class.

“If I went and bought iodized salt or de-iodized salt and [students] make a solution by heating stuff in a beaker—which I hope doesn’t break—if I spend 15 bucks on salt at the store, I’ve blown three or four students’ worth of budget for them to learn how to grow crystals. It’s neat, but I can’t do that in a science class every day. I would just completely and totally run out of money and that’s just on cheap stuff,” he said.

I’m not trying to fault the Year of Science initiative just pointing out that the initiative is problematic when the science education budget for schools cannot support even simple research projects.

This is a larger issue that I can adequately cover in this posting but I did want to draw attention to some of the fragilities of the Canadian situation (and our own situation in BC) vis à vis creating a science culture and/or democratizing science.

Meanwhile, I read with some envy a report titled, International Comparison of Public Dialogue on Science and Technology,  from a UK organization, Sciencewise-ERC – the UK’s national centre for public dialogue in policy making involving science and technology issues. Canada is not mentioned and I imagine that’s due to the fact that we don’t have any public dialogue to speak of.

ETA Mar.3.11: I made some minor changes for clarity (added Segue: and Back to the main topic: and removed an extra space.

Phylo and crowdsourcing science by Canadian researchers

Alex Kawrykow and Gary Roumanis from McGill University (Montréal, Québec) have launched Phylo, a genetics game that anyone can play but is actually genetic research. From the article by Neal Ungerleider at the Fast Company website,

The new project, Phylo, was launched by a team at Montreal’s McGill University on November 29. Players are allowed to recognize and sort human genetic code that’s displayed in a Tetris-like format. Phylo, which runs in Flash, allows users to parse random genetic codes or to tackle DNA patterns related to real diseases. In a random game, a user found himself assigned to DNA portions linked to exudative vitreoretinopathy 4 and vesicoureteral reflux 2.

Players choose from a variety of categories such as digestive system diseases, heart diseases, brain diseases and cancer. All the DNA portions in the game are linked to different diseases. Once completed, they are analyzed and stored in a database; McGill intends to use players’ results in the game to optimize future genetic research.

This reminds me of Foldit (mentioned in my Aug. 6, 2010 posting) another multiplayer online biology-type game; that time the focus was protein folding. As Ungerleider notes in his article, gaming is being used in education, advertising, and media. I’ll add this,  it’s also being used for military training.

I was interested to note that the McGill game was made possible by these agencies,

* Natural Sciences and Engineering Research Council of Canada
* McGill School of Computer Science
* McGill Centre for Bioinformatics
* McGill Computational Structural Biology Group

On a side note, there’s another biology-type game called Phylo, it’s a trading card game designed by David Ng, a professor at the University of British Columbia. From the Phylo, trade card game About page,

What is this phylo thing? (Some interesting but relatively specific FAQs here)

Well, it’s an online initiative aimed at creating a Pokemon card type resource but with real creatures on display in full “artistic” wonder. Not only that – but we plan to have the scientific community weigh in to determine the content on such cards, as well as folks who love gaming to try and design interesting ways to use the cards. Then to top it all off, members of the teacher community will participate to see whether these cards have educational merit. Best of all, the hope is that this will all occur in a non-commercial-open-access-open-source-because-basically-this-is-good-for-you-your-children-and-your-planet sort of way.

The Phylo, trading card game is in Beta (for those not familiar with the term beta, it means the game is still being tested, so there may be ‘bugs’).

It’s nice to be able to report on some innovative Canadian crowdsourcing science.