Transcript Slide 1

Open Science
Picking up momentum
Now on it is only looking forward
Subbiah Arunachalam
Distinguished Fellow
Centre for Internet and Society, Bangalore
<[email protected]>
ICFOSS, Thiruvananthapuram
19 December 2014
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This is not an original research paper. My own perception of
open content and open access, why they are needed and
what their advantages are have been shaped by
conversations with many individuals and collaborators around
the world. I have borrowed freely from the writings of many
others and my own.
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Philosophy of Open Science
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This is the well recognized martyr for India’s
freedom – Bhagat Singh (1907 – 1931)
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Aaron Swartz
8 Nov 1986 – 11 Mar 2013
This is the first martyr for the cause of open
knowledge. A boy prodigy and a whiz kid, he
lost his life in an unequal fight with an
unreasonable US prosecutor.
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Aaron did more than almost anyone to make the
Internet a thriving ecosystem for open
knowledge, and to keep it that way. His
contributions were numerous, and some of them were
indispensable. When asked in late 2010 for help in
stopping Combating Online Infringement and
Counterfeits Act (COICA), the predecessor to the Stop
Online Piracy Act (SOPA) and Protect IP Act (PIPA)
Internet blacklist bills, he founded an organization
called Demand Progress, which mobilized over a million
online activists and proved to be an invaluable ally in
winning that campaign.
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Some people think that
Aaron Swartz went against
the law by downloading
copyright material. I want
them to know that
Mahatma Gandhi often
resorted to civil
disobedience, which in the
eyes of the prevailing laws
was a violation of law.
But his cause, like the cause Swartz wanted to uphold,
trumped the prevailing laws. The world glorifies Gandhi
but our laws punish Swartz. Unfair.
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This is the school kid who at the age of 15 invented a
test for some cancers, whose breakthrough would
have never come about were it not for free access to
online journals – what Internet guru Aaron Swartz was
promoting before his death.
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Jack Andraka created a novel paper sensor that detects
pancreatic, ovarian, and lung cancer in 5 minutes for as
little as 3 cents. He conducted his research at Johns
Hopkins University and won many awards and honours.
Jack later on worked with a team of teens (Gen Z) on
the Qualcomm Foundation Tricorder X Prize and speaks
about open access, STEM education, and universal
Internet availability. He has won awards at multiple
national and international math competitions.
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“Poor and rich people pay
taxes for the research that
goes into these journals. Only
those wealthy enough to pay
for subscriptions or go to
universities can reap the fruits
of their funding... It reinforces
fundamental social
inequalities.” - Swartz's best
friend and colleague in many
of his battles for free and open
Internet access Ben Wikler.
“Aaron would want all the Jack Andrakas to carry this
torch forward now (…) He'd also say, don't accept the lie
that the world has to be the way it is now,” Wikler says.
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Robin Hood, the legendary
outlaw, was known for
"robbing from the rich and
giving to the poor.“
Today our institutions and librarians are taking away
taxpayers’ money and paying it to journal publishers.
The leading publishers report profit margins of 3540% even when the economy is reeling under
recession and most industries are struggling to
survive. We are giving away money that can be used
for research.
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Prof. Elinor (Lin) Ostrom, the first woman Nobel Prize
winner in Economics, worked on ‘natural resources
commons’ throughout her life. She said the commons
approach alone can sustain the world. There is another
kind of commons, the ‘knowledge commons.’ And it is
only through free and unhindered access and sharing we
can ensure democratization of knowledge and its rapid
growth. This is the basic idea of open science.
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What is ‘open’ in the context of science?
OPEN = Digital content or data that is free to
use, reuse and re-distribute without
technical or legal restrictions
What are Digital or Knowledge Commons?
“Information and knowledge resources that are
collectively created and owned or shared between or
among a community and that is (generally freely)
available to third parties. Thus, they are oriented to
favour use and reuse, rather than to exchange as a
commodity."
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"Open science is the idea that scientific knowledge
of all kinds should be openly shared as early as is
practical in the discovery process". – Michael Nielsen
It is science carried out and communicated in a
manner which allows others to contribute,
collaborate and add to the research effort, with all
kinds of data, results and protocols made freely
available at different stages of the research process.
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Open Science is underpinned by the
following broad principles:
·Transparency in experimental methodology,
observation, and collection of data [Open
methods]
· Public availability and reusability of scientific
data. [Open data]
· Public accessibility and transparency of scientific
communication. [Open access].
· Using web-based tools to facilitate scientific
collaboration.
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“The European Commission is now moving beyond open access
towards the more inclusive area of open science. Elements of
open science will gradually feed into the shaping of a policy for
Responsible Research and Innovation and will contribute to the
realisation of the European Research Area and the Innovation
Union, the two flagship initiatives for research and innovation.”
But there are challenges to be addressed
issues raised by intellectual property rights
data analytics (also known as Text and Data Mining),
alternative metrics,
research e-infrastructure, and
inter-institutional, inter-disciplinary and international
collaboration among all actors in research and innovation.
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The distribution of science in 2001
Unequal contribution and participation in science.
Territory size shows the proportion of all scientific papers
published in 2001 written by authors living there.
http://www.worldmapper.org/display.php?selected=205
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If this trend continues, soon the whole continent of
Africa will disappear from this map and India and Latin
America will become thinner and famished.
If science were to be a truly global enterprise,
knowledge should flow freely and unhindered. That is
why all of us should adopt open science.
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One member of the larger set of Open Science is
Citizen Science.
The idea here is: Why use one brain when you can
use 7 billion?
1. The public can find new hypotheses and ‘think
outside the box’
2. Using citizens’ computing power
3. Using citizens’ brain power
4. Citizens can collect data
5. Citizens can help evaluate data
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Citizen Science, some examples
Polymath
The SkyNet
Galaxy Zoo
Moon Mappers
Foldit
EyeWire
Genographic Project
eBird
OSDD
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Galaxy Zoo is perhaps the most famous example of citizen
science, with over 200,000 volunteers classifying galaxy
images taken from a robotic telescope. Citizens have always
played an important role in astronomy but now anyone can
contribute without buying expensive equipment. We humans
are needed to describe the images but the task is too large
for a researcher or group of researchers to take on. Thus far
over 150 million galaxies have been classified by volunteer
astronomers (zooites) and a few have gone on to make really
neat discoveries.
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Foldit is an online puzzle video game about protein folding.
Developed by the University of Washington's Center for
Game Science in collaboration with the UW Department of
Biochemistry, the objective of the game is to fold the
structure of selected proteins as well as possible, using tools
provided within the game. The highest scoring solutions are
analysed by researchers, who determine whether or not
there is a native structural configuration that can be applied
to the relevant proteins. Scientists can then use such
solutions to solve "real-world" problems, by targeting and
eradicating diseases, and creating biological innovations.
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Open Source Drug Discovery (OSDD) is an Indian
initiative with global partnership. It provides a global
platform where the best minds can collaborate to
discover novel therapies for neglected tropical diseases
like Tuberculosis, Malaria, Leishmaniasis etc.
It brings together informaticians, wet lab scientists,
contract research organizations, clinicians, hospitals and
others. Many undergraduate students have taken part.
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A major component of Open Science is data. A
great example of open data is GenBank, the set of
40 databases maintained by NCBI. It contains
publicly available nucleotide sequences for more
than 280,000 named organisms, obtained
primarily through submissions from individual
laboratories and batch submissions from largescale sequencing projects. As of mid-December
2014 traditional GenBank database had data on
184 billion bases and 179 million sequences, and
Whole-Genome Shotgun database (WGS) 848
billion bases and 200 million sequences.
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P&G, the first major corporation to think of open
innovation, launched the Connect+Develop program
more than 10 years ago and has developed more
than 2,000 global partnerships, delivered dozens of
new products, accelerated innovation development
and increased productivity, both for P&G and its
partners.
The C+D website receives about 20 submissions
every weekday – or more than 4,000 a year – from
all over the world.
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What does open innovation mean to pharma
companies?
Pharmaceutical R&D is under pressure to counter
rising operational costs, depleted pipelines and
impending patent expiries. These challenges can be
met in the long term only by increasing R&D
productivity. Advances have been made through
Computer Aided Drug Design, high-throughput
techniques, and the ‘Omics’ revolution. But, what is
the next step?
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Radical new ways of working and a culture of external
collaboration are key elements in turning around
pharmaceutical R&D productivity and bringing new
medicines to patients faster and with more control on
costs.
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AstraZeneca adopted open innovation in order to
develop treatments for Alzheimer’s, cancer, and
diabetes. They decided to collaborate and share
knowledge and resources with other scientists and
organisations rather than work in isolation.
The AstraZeneca Open Innovation platform provides
a robust but simple process for linking their
expertise, experience, resources, and technology
with those of external experts and to explore
prospective partnerships that accelerate the
advancement of medical science and breakthrough
therapies for patients
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Champions of Change
On June 20, 2013, thirteen Champions of Change were honored at
the White House for their extraordinary leadership in "open
science." From left to right: First row: Jack Andraka, David Altshuler,
Rebecca Moore, Kathy Giusti, Jeremiah P. Ostriker, Eric Kansa, Paul
Ginsparg and David J. Lipman. Second row: Drew Endy, Atul Butte,
John Quackenbush, William Noel, and Stephen Friend.
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David J. Lipman
In his 25 years as the founding director of the
National Center for Biotechnology Information
Lipman has had a tremendous impact on the
amount
of
biomedical
data
and
health
information that are publicly and easily available.
His contributions include setting up GenBank and
PubMed Central.
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John Quackenbush
is Professor of Biostatistics and Computational
Biology at the Dana-Farber Cancer Institute. He
designed tools to handle the vast quantities of data
on human health and disease.
He founded GenoSpace, a company that develops
advanced software tools for collecting, interpreting,
and sharing clinical and genomic data to further
biomedical research and facilitate personalized
medicine. GenoSpace has created software portals
that engage patients as partners in defeating
multiple myeloma.
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Paul Ginsparg
Theoretical physicist Paul Ginsparg created an open
access system in 1991 for physicists to share their
cutting-edge results. Called arXiv.org, it serves as
the primary daily information feed for global
communities of researchers in physics,
mathematics, computer science, and related fields.
Today, arXiv.org provides access to more than
997,000 documents and supports hundreds of
millions of full-text downloads per year. Modelled
after arXiv, many subject-oriented repositories
were set up: e.g. The NASA Astrophysics Data
System (ADS).
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To conclude
We need to introspect. We can no longer delay throwing
open science and scholarship, our research publications
and data, our educational course ware and our libraries.
If organizations and our leaders are unwilling and
indifferent, the scientists and citizens should lead the
way.
In the US, before John Holdren came up with his OSTP
memo, more than 60, 000 people had signed a “We the
people” petition on the White House website.
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We should persuade students and other citizens
(taxpayers whose money supports most research) to
join the movement. We should write to our
Parliamentarians to enact laws to mandate open access
to publicly-funded research. And, however indifferent
they may be, we should keep trying to impress upon
the vast majority of our scientists to place the full texts
of all their research publications and their data in open
access repositories.
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Prof. Timothy Gowers of Cambridge University, a Fields
medalist with interests spanning several areas of
mathematics, is a very busy man. And yet he devotes
considerable time to fight injustice in the scholarly
communication space . He mounted the ‘Boycott
Elsevier’ movement. More than 14,000 researchers
have lent support. Not many Indian scientists have
shown any inclination to see a just order in this space.
He also founded the famous citizen science project
Polymath which has attracted a whole range of people
– from university dons to office goers – to collectively
solve difficult mathematical problems.
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We would like many Indian scientists to follow the
example of Prof. Gowers and not only perform world
class science but also champion open science.
Thank you.
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