Category:Science

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This section should cover both scientific concepts about P2P (network theory and such), but also the use of P2P practices within the field of science.

Ported so far are three first columns of the Encyclopedia and the Resources section.

The three most important aspects of an Open Science model are: 1) Open Access to scientific journals; 2) access to the raw material as Open Data; and 3) access to the transparent Open Process of the research methodologies itself.

Or [1]:

  • Transparency in experimental methodology, observation, and collection of data.
  • Public availability and reusability of scientific data.
  • Public accessibility and transparency of scientific communication.
  • Using web-based tools to facilitate scientific collaboration.

John Wilbanks insists that: Open Science differs from Open Source Software!!


Please join us at the Open Science Summit: in Berkely, July 29 to 31


See also concerning methodology:

  1. The Participatory Turn in Research‎, i.e. Participatory Inquiry
  2. Predrag Cicovacki, A Critical Reflection On The Three Pillars Of Transdisciplinarity: An important take on the integral 'transdisciplinary' method which is crucial to the full understanding of P2P phenomena. [2]





Introduction

1. Openess in science [3]:

  1. Open Access, where publications are made available on the web without charge
  2. Open Courseware is a movement that invites educators to make their course-material directly available on the web
  3. Open Source Hardware and Open Source Software, where plans for apparatus and tools for analysis are made freely and openly available
  4. Open Stimuli, where stimulus sets or corpi are made available for use in replications or new experiments
  5. Open Workflows, in which researchers can freely share chains of experimentation, analysis, and visualization
  6. Open Data, where individual researchers release their datasets, either as the data is collected, upon publication, or after a suitable embargo period
  7. [[Open Model Repositories, where computational models from published papers can be centralized
  8. Open Research, where open lab notebooks are used to describe ongoing details of a particular strain of research.


2. The seminal papers for the Open Science community:

  1. Bill Hooker’s three parter 1, 2, 3 at Three Quarks Daily
  2. Nature Precedings on Open Notebook Science
  3. Michael Nielsen’s essay The Future of Science
  4. Shirley Wu’s Envisioning the scientific community as One Big Lab


Read also:

  1. Can Open Source Licences be used in Science?
  2. Mitchell Waldrop: Science 2.0 -- Is Open Access Science the Future?. Scientific American, April 21, 2008.
  3. The Value of Openness in Scientific Problem Solving. By Karim R. Lakhani et al.
  4. A Primer on Open Access, Peer Review and the Scientific Publishing Business Steven Harnad.
  5. Why we need Open Source Clinical Trials Databases
  6. Should we replace Peer Review with a ex-post bottom-up peer comments system? By Grazia Ietto-Gillies.
  7. Thinh Nguyen: Freedom to Research: Keeping Scientific Data Open, Accessible, and Interoperable
  8. Peter Suber: Open access and the self-correction of knowledge
  9. Watch this webcast: François Grey on the Implications of Citizen Cyberscience


3. Key Open Science entries:

  1. http://p2pfoundation.net/Open_Bioinformatics_Foundation
  2. http://p2pfoundation.net/Open_Biology
  3. http://p2pfoundation.net/Open_Genomics
  4. http://p2pfoundation.net/Open_Health
  5. http://p2pfoundation.net/Open_Licenses
  6. http://p2pfoundation.net/Open_Notebook_Science
  7. http://p2pfoundation.net/Open_Science_Licenses
  8. http://p2pfoundation.net/Open_Scientific_Books
  9. http://p2pfoundation.net/Open_Scientific_Papers
  10. http://p2pfoundation.net/Open_Source_Biology
  11. http://p2pfoundation.net/Open_Source_Biomodels
  12. http://p2pfoundation.net/Open_Source_Biotechnology
  13. http://p2pfoundation.net/Open_Source_Drug_Discovery
  14. http://p2pfoundation.net/Open_Source_Pharma
  15. http://p2pfoundation.net/Open_Source_Science
  16. http://p2pfoundation.net/Openness_in_Science

Discussion

  1. Open Science Mailing List [4]
  2. DIY Bio list [5]


Short Citations

On the relativity of the role of experts

We will always have experts in various fields, but to limit contributions to knowledge as a whole to experts only is to deprive all of humanity of its enormous potential for distributed intelligence.

- M. Guedon [6]


On open scholarly publishing as a superior model

Studies by Ted Bergstrom show that in economics the scholarly societies are publishing the highest quality journals for a fifth of the cost (on a per-page basis) of the corporate publishers who currently hold a majority of the titles in this field.

- John Willinsky [7]

Biological tinkering

"the tinkering networks we see in the software industry will be mirrored in synbio. Further, the skill sets associated with synthetic biology will be as widely dispersed as software programming is today and the tools will be just as inexpensive/ubiquitous."

- John Robb [8]

Long Citations

On the need for distributed intelligence to tackle global problems

"(have) we now hit a point where scientific problems are so complex that one person alone can’t solve them? It would certainly seem that way. The problems science is pursuing today—issues like global warming and genomic mapping—demand a distributed approach across disciplines. But currently, journal articles, data, research, materials and so on are stopped by contracts and copyrights at such a rate that it’s become nearly impossible to pull them together."

- John Wilbanks [9]

"The power of the unaided, individual mind is highly overrated: the Renaissance scholar no longer exists. Although creative individuals are often thought of as working in isolation, the role of interaction and collaboration with other individuals is critical. Creative activity grows out of the relationship between an individual and the world of his or her work, and from the ties between an individual and other human beings. The predominant activity in designing complex systems is that participants teach and instruct each other. Because complex problems require more knowledge than any single person possesses, it is necessary that all involved stakeholders participate, communicate, and collaborate with each other."

- Transcending the individual human mind [10]

On the benefits of open sharing in science

"The most rapid advances in science come with open sharing of information, and collaboration. That is how the world's scientists accomplished the mapping of the human genome in a matter of years. If traditional publishing practices had been followed instead of open sharing, it seems likely that mapping the human genome would have taken decades, if not centuries."

- Heather Morrison [11]


"Just as the Enlightenment ushered in a new organizational model of knowledge creation, the same technological and demographic forces that are turning the Web into a massive collaborative work space are helping to transform the realm of science into an increasingly open and collaborative endeavor. Yes, the Web was, in fact, invented as a way for scientists to share information. But advances in storage, bandwidth, software, and computing power are pushing collaboration to the next level. Call it Science 2.0."

- Business Week [12]


Science needs a Commons

"One of the reasons I believe so deeply in the commons approach (by which i mean: contractually constructed regimes that tilt the field towards sharing and reuse, technological enablements that make public knowledge easy to find and use, and default policy rules that create incentives to share and reuse) is that I think it is one of the only non-miraculous ways to defeat complexity. If we can get more people working on individual issues – which are each alone not so complex – and the outputs of research snap together, and smart people can work on the compiled output as well – then it stands to reason that the odds of meaningful discoveries increase in spite of overall systemic complexity."

- John Willbanks [13] (see also [14])

Towards a science of relationships

1.

"It is impossible to deny that science has made great progress by taking things apart. However, what is left out of this approach is the problem of understanding relationships between the parts.

Indeed, the importance of this understanding should be self-apparent. If all systems around us were made of the same elementary particles, and their relationships were irrelevant, then all systems would be identical. Obviously, this is not the case. Our quest to understand the parts becomes so detailed that we forget what we were trying to understand at the start. Moreover the strategy of looking at parts may blind us to the way properties of a system arise from the relationships between the components. This reflects itself in what we think about in general. More specifically, it affects how we approach problem solving when we try to solve problems in society. Indeed one of the main difficulties in solving problems is that we think the problem resides in the parts themselves, when, in actuality, it is to be found in the interactions between the parts. As a result, many crucial questions can only be addressed by thinking carefully about connections in a system as a whole."

- Yaneer Bar-Yam [15]


2.

"While the classical sciences isolated physical systems from their surrounding, the new thinking connected to digital fluidity is founded on the realization that all systems in nature are connected and subject to flows of matter and energy that move constantly through them. Dynamic equilibriums result from chaotic energy and manifest themselves in creative processes that generate richly organized patterns – patterns that teeter on the complex stable and the complex unstable."

- Joseph Nechvatal [16]


How open source biology and horizontal gene transfer will replace Darwinian speciation and evolution

"[We can speculate about] a golden age... when horizontal gene transfer was universal and separate species did not yet exist. Life was then a community of cells of various kinds, sharing their genetic information... Evolution could be rapid... But then, one evil day, a cell resembling a primitive bacterium happened to find itself one jump ahead of its neighbors in efficiency. That cell, anticipating Bill Gates by three billion years, separated itself from the community and refused to share... [But] now, as Homo sapiens domesticates the new biotechnology, we are reviving the ancient... practice of horizontal gene transfer, moving genes easily from microbes to plants and animals, blurring the boundaries between species. We are moving rapidly into the post-Darwinian era, when... the rules of Open Source sharing will be extended from the exchange of software to the exchange of genes. Then the evolution of life will once again be communal, as it was in the good old days before separate species and intellectual property were invented." (http://science.slashdot.org/article.pl?sid=07/06/30/1927205)

Source: New York Review of Books, The Future of Biotech. Freeman Dyson. URL = http://www.nybooks.com/articles/20370


Two kinds of scientific revolutions

"There are two kinds of scientific revolutions, those driven by new concepts and those driven by new tools. These are analogous to biological revolutions driven by speciation and by symbiosis, or to astronomical revolutions driven by symmetry-breaking and by gravitational binding. When a field of science is overturned by a new concept, the revolution starts from the inside, from an internal inconsistency or contradiction within the science, and results in a rapid transition to a new way of thinking. When a field of science is overturned by new tools, the revolution starts from the outside, from tools imported from another discipline, and results in a symbiosis of the two disciplines. In both types of revolution, the final outcome is usually a new subdiscipline of science and a new species of scientist, specialized in the new ideas or in the new tools as the case may be."

- Freeman Dyson [17]

Key Resources

Open Access for the Developing World


Articles on General Science

On Science and Participatory Democracy:

  1. Sheila Jasanoff. Technologies of Humility: Citizen participation in governing Science. Minerva, 2003
  2. “Sheila Jasanoff. A manifesto for socially-relevant science and technology”. December 2008
  3. Sheila Jasanoff. The Essential Parallel Between Science and Democracy. Seed Magazine, February 17, 2009


On Open and Free Science:

  1. Overview: Open Science

Policy:

  1. Policy Implications for the Evolving Phenomenon of User-Led Scientific Innovation. Victoria Stodden [18]


Other articles:

  1. John Wilbanks: Applying Open Source Principles to Science: how does it match?, open source is the wrong metaphor fo science, because it ties us too closely to the artifact that is open source software. Science is not software, and we shouldn't treat it the way we treat software.
  2. Back to Basics: How Technology and the Open Source Movement Can Save Science. David Koepsell
  3. Michael Nielsen: Toward a more open scientific culture. How can the internet benefit science?
  4. A three part introduction to open science practices: 1) Open access for scholarly publishing; 2)Defining Open Science; 3) Current applications of Science 2.0.
  5. What is Free Science?. Christopher Kelty.
  6. Principles of Distributed Innovation. Karim Lakhani & Jill Panetta.
  7. Manuel De Landa: How Synthetic Reason is overturning established paradigms
  8. A Personal View of Open Science: Part one discusses Open Access to publications; the availability of Open Data and the transparency of Open Process. Part two discusses the tools for open science.
  9. Aaron Hirsh: Distributed citizen science as an alternative to centralized Big Science. (New York Times)
  10. The republic of science by Michael Polanyi: classical normative account of open science
  11. Open Source Patent Licensing. By Boetinger, S. and D. Burk, 2004 [19]

Report:

  1. Open Science at Web-scale JISC. Research 3.0


On the history of open science:


On Collaborative Science:

  1. Yochai Benkler on commons-based research: Chapter 9 of The Wealth of Networks
  2. Alessandro Delfanti: Collaborative Web between open and closed science, JCOM 7 (2), June 2008.
  3. Paul David et al.: Collaborative Research in e-Science and Open Access to Information/
  4. Rai, A., 2005, Open and Collaborative Research: A New Model for Biomedicine, in Hahn, R. (ed.) Intellectual Property Rights in Frontier Industries, AEI-Brookings Press 2005), Washington DC

Special issues:

  1. Special issue of the MIT journal Innovations on Collaborative Innovation and Collective Intelligence with case studies of Networked Innovation Initiatives
  2. Special issue on Web and collaborative science, Jcom 7 (2), June 2008 (editor).
  3. Peer to Peer and User-Led Science. Special issue of JCOM.



Science as a Commons:

  1. Ruth Chadwick and Sarah Wilson: Genomic Databases as Global Public Goods?: An analysis about the ambiguity of the concept of public goods applied to genomic databases.
  2. Health Commons: Therapy Development in a Networked World John Wilbanks and Marty Tenenbaum [20]
  3. Commons-Based Agricultural Innovation. By Yochai Benkler [21] Case discussion: CAMBIA-BIOS.
  4. Yochai Benkler: Commons-Based Strategies and the Problems of Patents, 305 Science 1110 (Aug. 20, 2004)[22]


Free software in science:

  1. Using Free Software in Science
  2. Role of Free Software in Scientific Computing


Science funding:

  1. Open Source Drug Discovery as a Business Model


Miscellaneous:

  1. Arguments for and against open science: journalistic approach to the topic, but interesting nevertheless
  2. New Institutions for Doing Science: from databases to Open Source Biology. By Stephen Maurer, 2003.
  3. Promoting Public Good Uses of Scientific Data (J. H. Reichman & Paul Uhlir)
  4. The Politics of Prediction Markets. Michael Abramowicz.
  5. Research potential of virtual worlds
  6. Three part blog discussion of the limits of current Peer Review, by Samir Chopra and Scott Dexter: Part One ; Part Two; Part Three
  7. Everyone's a historian now: fascinating reportage about the role of amateur history buffs and their role in historical research
  8. The Epistemology of Mass Collaboration (especially Wikipedia): a special issue (February 2009, Vol. 6, No. 1) of Episteme
  9. The end of theory by Chris Anderson: how new science tools and distributed computing change the way we see science

Articles on Specialized Sciences

Agriculture:

  1. Commons-Based Agricultural Innovation. By Yochai Benkler [23] Case discussion: CAMBIA-BIOS.

Biology/Biotechnology:

  1. Janet Hope’s Thesis Open Source Biotechnology The Australian National University, Canberra, 2004. [24]
  2. Our Biotech Future Freeman Dyson on Open Source Biology
  3. The Pace and Proliferation of Biological Technologies by Rob Carlson
  4. Rob Carlson on Synthetic Biology 1.0 [25]; Bioeconomy
  5. The Economics of Synthetic Biology Stephen Maurer and Joachim Henkler
  6. Bellagio Metting on Open Source Biology Sept 05 [26]
  7. Cukier, “Open Source Biotech: Can a Non-Proprietary Approach to Intellectual Property Work in the Life Sciences?” ACUMEN JOURNAL OF LIFE SCIENCES (2003). [27]
  8. Science as Social Enterprise: The CAMBIA BiOS Initiative Jefferson Open Source in Biotechnology: Open Questions Boettinger and Wright [28]
  9. Rai, A., 2005, Open and Collaborative Research: A New Model for Biomedicine, in Hahn, R. (ed.) Intellectual Property Rights in Frontier Industries, AEI-Brookings Press 2005), Washington DC


Medicine and Healthcare

  1. Open Source Drug Discovery: Finding a Niche (or Maybe Several) Stephen Maurer [29]
  2. Can Open Source R&D Reinvigorate Drug Research? Bernard Munos Nature Reviews Drug Research
  3. Health Commons: Therapy Development in a Networked World John Wilbanks and Marty Tenenbaum [30]
  4. Rai, A., 2005, Open and Collaborative Research: A New Model for Biomedicine, in Hahn, R. (ed.) Intellectual Property Rights in Frontier Industries, AEI-Brookings Press 2005), Washington DC
  5. Maurer, S., A. Rai, and A. Sali, 2004, Cures for Tropical Disease: Is Open Source an Answer? Public Library of Science: Medicine, 1, 56.

Blogs

Review of science blogging at http://www.corporeality.net/museion/2008/07/31/science-blogging-science-communication-and-the-multitude/

  1. The Synergy blog of Peter Corning.
  2. Science in the Open, blog by Cameron Neylon
  3. Michael Nielsen
  4. Citizen Science Projects‎
  5. Monday begins on Saturday: blog by Yaroslav Nikolaev open science and with some "biogeek open notebook" reflections.
  6. Open Science blog, by Bora Zivkovic
  7. Science Commons
  8. openwetware
  9. nature's nascent
  10. Next Generation Science: established to examine emerging technologies, including but not limited to Web 2.0, and their impact on the scientific method, researchers and the general public.


In Print:

Annual science blogging anthologies: Open Lab 2008; 2007; 2006

Books

  1. A Bibliography on the Enclosure of Science and Technology: recommendations by James Boyle.
  2. Scientific Collaboration on the Internet
  3. Biobazaar: The Open Source Revolution and Biotechnology. Janet Hope (derived from previous thesis)

See also:

  1. Digital Code of Life: How Bioinformatics is Revolutionizing Science, Medicine, and Business. Glyn Moody. John Wiley, 2004
  2. Robert Plotkin. The Genie in the Machine: How Computer-Automated Inventing Is Revolutionizing Law and Business: "Tools such as 3-D modeling and digital prototyping have already taken much of the grunt work out of invention. With the advent of genetic programming and other machine learning techniques, however, software stands poised to take over higher-level aspects of invention as well."

On the science of Human Cooperation:

  1. The Compassionate Instinct: The Science of Human Goodness, coedited by Dacher Keltner, Jason Marsh, and Jeremy Adam Smith (January, WW Norton), 2009
  2. Why We Cooperate, by Michael Tomasello (Boston Review Books), 2009
  3. The Age of Empathy: Nature's Lessons for a Kinder Society, by Frans de Waal (Harmony Books), 2009

Conferences

2010:

  1. Science Online 2010
  2. Open Science Summit


2009:

  1. Open Science Workshop: January 2009
  2. Third Annual Science Blogging conference: January 2009
  3. Sciences and Democracy World Forum: On January 26th and 27th, 2009, the Sciences and Democracy World Forum will be held in Belém (Brazil). Unions and researchers’ associations, social and civic movements, and NGOs are going to discuss the stakes of the democratization of sciences and technologies


Also:

  1. The Living Knowledge conferences focus on participatory science modes of research.
  2. Open Access in Scholarly Publishing
  3. Cyberinfrastructure for Collaboration and Innovation. Papers by First Monday.
  4. 4th International Digital Curation Conference: "Radical Sharing: Transforming Science?" 1-3 December 2008, Hilton Edinburgh Grosvenor Hotel, Edinburgh, Scotland

Experts

  1. With the P2P Foundation: Delfanti, Alessandro

Key Open Science Advocates:

Interviews

  1. Annette Holtkamp on Open Repositories for the Physics Community
  2. Antony Williams on Open Science, Open Chemistry and ChemSpider
  3. Basarab Nicolescu on Transdisciplinarity
  4. Harold Varmus on Open Access and the Public Library of Science
  5. John Wilbanks on Sharing the Physical Tools of Science
  6. Karim Lakhani on Open Source Science
  7. Peter Murray-Rust on Open Data in Science 2.0
  8. Richard Jefferson on Biological Open Source
  9. Rufus Pollock on the Use of Open Source Principles for Open Science
  10. Vitek Tracz on Open Access and BioMed Central

Reports

  1. FOSS in Scientific Applications
  2. Role of FOSS in Scientific Computing
  3. Who Owns Nature? Corporate Power and the Final Frontier in the Commodification of Life. ETC Group, 2008. [32]. Implications of commodifying Synthetic Biology
  4. Nancy L. Maron and K. Kirby Smith, Strategic Services Analysts, Ithaka: “Digital Scholarly Communication: A Snapshot of Current Trends.” The authors examined eight types of digital scholarly resources: E-Only Journals; Reviews; Preprints and Working Papers; Encyclopedias, Dictionaries, and Annotated Content; Data Resources; Blogs; Discussion Forums; Professional and Academic Hubs. [33]

Tools

  1. Social network sites for scientists: Nature Network; ResearchGATE; SciLink ; Epernicus; BiomedExperts ; Academia.edu ; Laboratree ; myExperiment
  2. Reference tools: CiteULike ; Connotea ; Mendeley ; 2collab ; Labmeeting

Open Scientific Data Sharing

  1. openPSI – making publicly collected data avalilable
  2. Swivel – platform for sharing data
  3. many eyes – platform for sharing data

Open Scientific Process Sharing

  1. OpenWetWare - the open notebook wikis
  2. myExperiment – exchanging workflows


Medicine and Healthcare

  1. 50 Open Source Projects that are changing Medicine

Webcasts

  1. François Grey on the Implications of Citizen Cyberscience

Pages in category "Science"

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