Openness and Science
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Rigour and Openness in 21st Century Science at the University of Oxford
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Openness and Science
- 1. Rigour and Openness in 21st Century Science Sir Mark Walport, Chief Scientific Advisor to HM Government
- 2. 2 Rigour and Openness in 21st Century Science, 11-12th April 2013 Knowledge translated to economic advantage: Promoting the contribution of science, engineering, technology and the social sciences to economic growth by linking industry, academia and government • Infrastructure resilience: Developing the capabilities that are vital to the infrastructure that underpins our security, well-being and resilience • The right science for emergencies: Providing the best scientific advice in the case of emergencies • Underpinning policy with evidence: Ensuring the best use of quantitative and qualitative analysis across government • Advocacy and leadership for science: Providing advocacy and strong leadership for science inside and outside government Government Chief Scientific Adviser
- 3. 3 Rigour and Openness in 21st Century Science, 11-12th April 2013 A taxonomy of openness Inputs OutputsResearch Open access Administrative data (held by public authorities e.g. prescription data) Public Sector Research data (e.g. Met Office weather data) Research Data (e.g. CERN, generated in universities) Research publications (i.e. papers in journals) Open data Open science Collecting the data Doing science openly
- 4. 4 Rigour and Openness in 21st Century Science, 11-12th April 2013 Examples: • Genome project • Citizen science: – AshTag – Galaxy Zoo Benefits: • Collaboration • Scale • Statistical power Collecting the Data: professional community working in a different way
- 5. Unraveling the genome… • Human Genome Project • SNP consortium • Hapmap • Cancer Genome Project • Copy Number Variation • WT Trust Case Control Consortium • 1000 Genomes • Encode • UK 10,000 Genomes • Deciphering Developmental Disease • H3 Africa 5 Rigour and Openness in 21st Century Science, 11-12th April 2013
- 6. Common denominators… •collaboration •funding partnership •public/private •openness 6 Rigour and Openness in 21st Century Science, 11-12th April 2013
- 7. 7 • Infrastructure to accelerate advanced materials discovery • Time frame for incorporating new classes of materials into applications is typically about 10 to 20 years from initial research to first use. • $100M initiative proposes: open innovation; advances in modelling algorithms; a data exchange system. • Aims to shorten cycle by 50%. Rigour and Openness in 21st Century Science, 11-12th April 2013 Materials Genome Initiative
- 8. • Openly collected science is already helping policy makers. • AshTag app allows users to submit photos and locations of sightings to a team who will refer them on to the Forestry Commission, which is leading efforts to stop the disease's spread with the Department for Environment, Food and Rural Affairs (Defra). 8 Rigour and Openness in 21st Century Science, 11-12th April 2013 Chalara spread: 1992-2012 Citizen Science
- 9. • Novel communication technologies are changing the social dynamics of science • Massively Collaborative Mathematics: Tim Gowers and the Polymath Project. • A blog serving as an open forum for contributors to work on a complex unsolved mathematical problem: “A new combinatorial proof to the density version of the Hales-Jewett theorem” •27 people made more than 800 comments • In just over a month, the problem was solved 9 Rigour and Openness in 21st Century Science, 11-12th April 2013 Massively Collaborative Mathematics
- 10. 10 • Intelligible • Accessible • Assessable • Useable Rigour and Openness in 21st Century Science, 11-12th April 2013 Data per se often of little value
- 11. • Data • Information • Knowledge • Application Societal benefit 11 Rigour and Openness in 21st Century Science, 11-12th April 2013 From data to knowledge to society
- 12. Presentation title - edit in Header and Footer Vemurafenib – oral targeted therapy for treatment of metastatic malignant melanoma in patients whose tumors carry the BRAFV600E mutation. Approximately 60% of melanoma patients have tumors that carry this mutation 12 Rigour and Openness in 21st Century Science, 11-12th April 2013 From data to knowledge to society
- 13. Openness not an unalloyed good A challenge to: • Commerce • Privacy • Security …Need intelligent openness …Some dilemmas 13 Rigour and Openness in 21st Century Science, 11-12th April 2013
- 14. 14 Structural Genomics Consortium • Not-for-profit public-private partnership to conduct basic science. • Determine 3D protein structures which may be targets for drug discovery. • Once such targets are discovered, they are placed in the public domain. Rigour and Openness in 21st Century Science, 11-12th April 2013 Privately collected data often can be open… …but not always - and what about issues of public safety: - Clinical trials, - Aircraft safety
- 15. 15 Rigour and Openness in 21st Century Science, 11-12th April 2013 Dual use science Developed for one context, used for others • Civilian Military use • Science subverted to do harm • Civilian: developed in one domain – used in others
- 16. 16 Rigour and Openness in 21st Century Science, 11-12th April 2013 • Flu: Spanish flu sequencing 2005, H5N1 • Avian flu controversy, Netherlands and US teams introducing genetic changes to understand H5N1 transmissibility between species • Publication in Nature and Science put on hold 2012 • International actors explored the issues: • Research is not risk free • Need to get framework right (legislative, ethical, physical) • Tools to address risks: risk assessment, ethical standards, checks and balances, eg peer review • Self governance and the role of scientists – research funders, science press: putting in place standards and guidance to balance benefits of publication vs potential harm Dual use science Image: Science Photo Library
- 17. The default should be openness • Where it has worked • Where lack of openness has caused problems • Where there are genuine difficulties 17 Rigour and Openness in 21st Century Science, 11-12th April 2013
- 18. • E-coli outbreak spread through several countries affecting 4000 people • Strain analysed and genome released under an open data license. • Two dozen reports in a week with interest from 4 continents • Crucial information about strain’s virulence and resistance 18 Rigour and Openness in 21st Century Science, 11-12th April 2013 Gastro-intestinal infection in Hamburg
- 19. 19 Rigour and Openness in 21st Century Science, 11-12th April 2013 Climate change transparency
- 20. 20 Rigour and Openness in 21st Century Science, 11-12th April 2013 Developing world - Indonesian flu • There are difficulties in ensuring access to data from developing countries. • Some uneasy at the prospect that those with greater scientific resources will benefit overseas interests, to the detriment of home researchers. • Indonesia ceased providing access to their flu samples in 2007 • This policy was reversed only after the World Health Organisation put in place protocols for equitable access to vaccines and medicines in future pandemics.
- 21. Open Access • Research isn’t finished until it is published • Maximise impact of research by maximising distribution • Publication is a cost of research • IT revolution enables revolution in methods in disseminating the findings of research 21 Rigour and Openness in 21st Century Science, 11-12th April 2013
- 22. Open access offers much more than just the ‘paper’ 22 Rigour and Openness in 21st Century Science, 11-12th April 2013 • Massive data sets and metadata • Data display • Text mining • Community annotation and feedback • Other linkages
- 23. Rigour • How we can improve process: – Scale, collaboration – Scrutiny – Enabling reproducibility • Honest error vs fraud • The best way forward is through openness 23 Rigour and Openness in 21st Century Science, 11-12th April 2013
- 24. 24 • Muon neutrinos fired 730 km from CERN to the Gran Sasso National Laboratory, central Italy • Neutrinos seemed to travel faster than the speed of light • CERN opened the result to broader scrutiny • More than 200 papers appeared on arXiv.org attempting to debunk or explain the effect • Team later reported two flaws in equipment set-up: a fiber optic cable attached improperly & a clock oscillator ticking too fast Rigour and Openness in 21st Century Science, 11-12th April 2013 ‘Faster than light’ neutrinos Image: Science Photo Library
- 25. Societal benefit The right open data enables: • Measurement • Accountability • Better execution • Innovation 25 Rigour and Openness in 21st Century Science, 11-12th April 2013
- 26. Harnessing ICT: A national diabetes system for Scotland Total Scottish Population 5.2M People with diabetes : 251,132 (4.9%) People with Type 1 DM : ~27,000 (0.5%) All patients nationally are registered onto a single register; the SCI-DC register SCI-DC used in all 38 hospitals Nightly capture of data from all 1043 primary care practices across Scotland Courtesy of Andrew Morris 26 Rigour and Openness in 21st Century Science, 11-12th April 2013
- 27. 27 Rigour and Openness in 21st Century Science, 11-12th April 2013 PercentageofPatients Data recorded within the previous 15 months http://www.diabetesinscotland.org.uk/Publications/SDS%202010.pdf Courtesy of Andrew Morris Scottish Diabetes Survey – over 90% capture of key variables since 2007 Recording of Key Biomedical Markers
- 28. Diabetes Care 2008Diabetic Medicine 2009 Courtesy of Andrew Morris Improved clinical outcomes 28 Rigour and Openness in 21st Century Science, 11-12th April 2013
- 29. 29 • Personal information is individual & precious to each one of us – it’s vital that we treat it properly • A balancing act…between the right to privacy and the necessity to hold and share data • A framework is needed: - to protect individuals - build & maintain confidence - facilitate research Rigour and Openness in 21st Century Science, 11-12th April 2013 Privacy and confidentiality
- 30. 30 • Formed in December 2011, reported in December 2012. • Examined the best procedures and mechanisms to make administrative data available for research safely • Aim allow research that is already technically feasible to be undertaken with integrity in a much more consistent, reliable and efficient manner • Value to academic research, but also research and policy evaluation within government departments Rigour and Openness in 21st Century Science, 11-12th April 2013 Administrative Data Taskforce Challenge to bring together data sets: • across government • and from the private sector Good policy depends on the best data
- 31. 31 5 key recommendations: • An Administrative Data Research Centre (ADRC) should be established in each of the four countries in the UK • Legislation should be enacted to facilitate research access to administrative data and to allow data linkage between departments to take place more efficiently • A single UK-wide researcher accreditation process, built on best national and international practice, should be established • The centres should put in place plans for engaging with the public • Funding should be provided Rigour and Openness in 21st Century Science, 11-12th April 2013 Administrative Data Taskforce Government to respond by Summer 2013
- 32. 32 Rigour and Openness in 21st Century Science, 11-12th April 2013 Summary Open science requires: • Collecting the data in the best way • Sharing the data openly • Making the products of research available openly But open data per se not an unalloyed good. Needs to be: • Intelligible • Accessible • Assessable • Useable When we get that right we are able to ensure: Data → Information → Knowledge→ Application→ Societal benefit
Hinweis der Redaktion
- Lots of interchangeable and fluid terms but many shared principles.
- Lots of interchangeable and fluid terms but many shared principles.
- Lots of interchangeable and fluid terms but many shared principles.
- Lots of interchangeable and fluid terms but many shared principles.
- Advanced materials are essential to economic security and human well-being, with applications in multiple industries, including those aimed at addressing challenges in clean energy, national security, and human welfare. Accelerating the pace of discovery and deployment of advanced material systems will therefore be crucial to achieving global competitiveness in the 21st century. The Materials Genome Initiative will create a new era of materials innovation that will serve as a foundation for strengthening domestic industries in these fields. This initiative offers a unique opportunity for the United States to discover, develop, manufacture, and deploy advanced materials at least twice as fast as possible today, at a fraction of the cost. At present, the time frame for incorporating new classes of materials into applications is remarkably long, typically about 10 to 20 years from initial research to first use. As today’s scientists and engineers explore a new generation of advanced materials to solve the grand challenges of the 21st century, reducing the time required to bring these discoveries to market will be a key driving force behind a more competitive domestic manufacturing sector and economic growth. To achieve faster materials development, the materials community must embrace open innovation. Rapid advances in computational modeling and data exchange and more advanced algorithms for modeling materials behavior must be developed to supplement physical experiments; and a data exchange system that will allow researchers to index, search, and compare data must be implemented to allow greater integration and collaboration. Currently, no infrastructure exists to allow different engineering teams to share data or models. Data transparency may have the largest impact after the material has been deployed, due to the fact that every industry relies on materials as components of product design. A product designer who needs a material of certain specifications may not be aware that the material has already been designed because there is no standard method to search for it. Data transparency encourages cross-industry and multidisciplinary applications.
- Ash dieback, caused by the fungus Chalara fraxinea, was found in the UK in October outside of plantations and nurseries in East Anglia, raising fears of a repeat of Dutch elm disease which killed 25 million mature elms in the 1970s and 80s. In an attempt to map and help prevent the spread of the disease across the country, a team of developers and academics worked through the weekend to create an app that smartphone owners can use to report suspected cases of infection. Infected ash trees are recognisable by lesions on their bark, dieback of leaves at the tree's crown, and leaves turning brown – though experts say the arrival of autumn makes the latter harder to accurately spot. zThe AshTag app for IOS and Android devices allows users to submit photos and locations of sightings to a team who will refer them on to the Forestry Commission, which is leading efforts to stop the disease's spread with the Department for Environment, Food and Rural Affairs (Defra).
- Novel communication technologies permit modes of interaction that change the social dynamics of science and exploit the collective intelligence of the scientific community. Free online resources and search engines have become integral to science in ways that have replaced the library as a source of information, searches and cataloguing. New tools, for example, myExperiment, offer much more enhanced abilities to share and execute scientific workflows. Live and open debate played out via wikis and blogs have changed the dynamic of academic discussion – sometimes in extreme ways. In January 2009 Tim Gowers, an eminent mathematician and recipient of the Fields Medal, launched the Polymath Project , a blog serving as an open forum for contributors to work on a complex unsolved mathematical problem. He posed the question: “Is massively collaborative mathematics possible?” He then set out the problem, his ideas about it and an invitation for others to contribute to its solution. 27 people made more than 800 comments, rapidly developing or discarding emerging ideas. In just over a month, the problem was solved. Together they not only solved the core problem, but a harder generalisation of it. In describing this, Gowers said, “It felt like the difference between driving a car and pushing it”. Fold.it: The fold.it website offers participants a game in which players solve the intricate puzzles figuring out the ways in which amino acids fold to create different protein molecules. Galaxy Zoo: Galaxy Zoo enables users to participate in the analysis of the imagery of hundreds of thousands of galaxies drawn from NASA’s Hubble Space Telescope archive and the Sloane Digital Sky Survey. BOINC: Numerous Citizen Science projects employ so-called volunteer computing, where individuals provide the resources of their home computers to contribute to big science research. Today there are over 50 active projects based on the BOINC platform developed at the University of California Berkeley.
- The changes that are needed go to the heart of the scientific enterprise and are much more than a requirement to publish or disclose more data. Realising the benefits of open data requires effective communication through a more intelligent openness: data must be accessible and readily located; they must be intelligible to those who wish to scrutinise them; data must be assessable so that judgments can be made about their reliability and the competence of those who created them; and they must be usable by others. For data to meet these requirements it must be supported by explanatory metadata (data about data). As a first step towards this intelligent openness, data that underpin a journal article should be made concurrently available in an accessible database. We are now on the brink of an achievable aim: for all science literature to be online, for all of the data to be online and for the two to be interoperable.
- The Structural Genomics Consortium (SGC) is a not-for-profit public-private partnership to conduct basic science. Its main goal is to determine 3D protein structures which may be targets for drug discovery. Once such targets are discovered, they are placed in the public domain. By collaborating with the SGC, pharmaceutical companies save money by designing medicines that they know will ‘fit’ the target. The SGC was initiated through funding from the Wellcome Trust, the Canadian Institute of Health Research, Ontario Ministry of Research and Innovation and GlaxoSmithKline. More recently other companies (Novartis, Pfizer and Eli Lilly) have joined this public-private partnership. The group of funders recently committed over US$50 million to fund the SGC for another four years. OTHER EGs InnoCentive is a service for problem solving through crowdsourcing. Companies post challenges or scientific research problems on InnoCentive’s website, along with a prize for their solution. More than 140,000 people from 175 countries have registered to take part in the challenges, and prizes for more than 100 Challenges have been awarded. Institutions that have posed challenges include Eli Lilly, NASA, nature.com, Procter & Gamble, Roche and the Rockefeller Foundation. Rolls-Royce University Technology Centres Imanova is an innovative alliance between the UK’s Medical Research Council and three London Universities: Imperial College, King’s College and University College. It trains scientists and physicians, and hopes to become an international partner for pharmaceutical and biotechnology companies. Syngenta The Technology Strategy Board and Syngenta are building a system that helps scientists visualise the similarities between the molecules in ChEMBL, an openly accessible drug discovery database of over one million drug-like small compounds, and those in their own research.
- The Structural Genomics Consortium (SGC) is a not-for-profit public-private partnership to conduct basic science. Its main goal is to determine 3D protein structures which may be targets for drug discovery. Once such targets are discovered, they are placed in the public domain. By collaborating with the SGC, pharmaceutical companies save money by designing medicines that they know will ‘fit’ the target. The SGC was initiated through funding from the Wellcome Trust, the Canadian Institute of Health Research, Ontario Ministry of Research and Innovation and GlaxoSmithKline. More recently other companies (Novartis, Pfizer and Eli Lilly) have joined this public-private partnership. The group of funders recently committed over US$50 million to fund the SGC for another four years. OTHER EGs InnoCentive is a service for problem solving through crowdsourcing. Companies post challenges or scientific research problems on InnoCentive’s website, along with a prize for their solution. More than 140,000 people from 175 countries have registered to take part in the challenges, and prizes for more than 100 Challenges have been awarded. Institutions that have posed challenges include Eli Lilly, NASA, nature.com, Procter & Gamble, Roche and the Rockefeller Foundation. Rolls-Royce University Technology Centres Imanova is an innovative alliance between the UK’s Medical Research Council and three London Universities: Imperial College, King’s College and University College. It trains scientists and physicians, and hopes to become an international partner for pharmaceutical and biotechnology companies. Syngenta The Technology Strategy Board and Syngenta are building a system that helps scientists visualise the similarities between the molecules in ChEMBL, an openly accessible drug discovery database of over one million drug-like small compounds, and those in their own research.
- e The benefits of intelligently open data were powerfully illustrated by events following an outbreak of a severe gastro-intestinal infection in Hamburg in Germany in May 2011. This spread through several European countries and the US, affecting about 4000 people and resulting in over 50 deaths. All tested positive for an unusual and little-known Shiga-toxin–producing E. coli bacterium. The strain was initially analysed by scientists at BGI-Shenzhen in China, working together with those in Hamburg, and three days later a draft genome was released under an open data licence. This generated interest from bioinformaticians on four continents. 24 hours after the release of the genome it had been assembled. Within a week two dozen reports had been filed on an open-source site dedicated to the analysis of the strain. These analyses provided crucial information about the strain’s virulence and resistance genes – how it spreads and which antibiotics are effective against it. They produced results in time to help contain the outbreak. By July 2011, scientists published papers based on this work. By opening up their early sequencing results to international collaboration, researchers in Hamburg produced results that were quickly tested by a wide range of experts, used to produce new knowledge and ultimately to control a public health emergency. Wikipedia A novel strain of Escherichia coli O104:H4 bacteria caused a serious outbreak of foodborne illness focused in northern Germany in May through June 2011. The illness was characterized by bloody diarrhea, with a high frequency of serious complications, including hemolytic -uremic syndrome (HUS), a condition that requires urgent treatment. The outbreak was originally thought to have been caused by an enterohemorrhagic ( EHEC ) strain of E. coli , but it was later shown to have been caused by an enteroaggregative E. coli ( EAEC ) strain that had acquired the genes to produce Shiga toxins . Epidemiological fieldwork suggested fresh vegetables were the source of infection. The agriculture minister of Lower Saxony identified an organic farm [2] in Bienenbüttel , Lower Saxony, Germany, which produces a variety of sprouted foods , as the likely source of the E. coli outbreak. [3] The farm has since been shut down. [3] Although laboratories in Lower Saxony did not detect the bacterium in produce, a laboratory in North Rhine-Westphalia later found the outbreak strain in a discarded package of sprouts from the suspect farm. [4] A control investigation confirmed the farm as the source of the outbreak. [5] On 30 June 2011 the German Bundesinstitut für Risikobewertung (BfR) ( Federal Institute for Risk Assessment ), an institute of the German Federal Ministry of Food, Agriculture and Consumer Protection ), announced that seeds of fenugreek imported from Egypt were likely the source of the outbreak. [6] In all, 3,950 people were affected and 53 died, including 51 in Germany. [7] A handful of cases were reported in several other countries including Switzerland , [8] Poland , [8] the Netherlands , [8] Sweden , [8] Denmark , [8] the UK, [8] [9] Canada [10] and the USA. [10] [11] Essentially all affected people had been in Germany or France shortly before becoming ill. Initially German officials made incorrect statements on the likely origin and strain of Escherichia coli . [12] [13] [14] [15] The German health authorities, without results of ongoing tests, incorrectly linked the O104 serotype to cucumbers imported from Spain. [16] Later, they recognised that Spanish greenhouses were not the source of the E. coli and cucumber samples did not contain the specific E. coli variant causing the outbreak. [17] [18] Spain consequently expressed anger about having its produce linked with the deadly E. coli outbreak, which cost Spanish exporters 200M US$ per week. [19] Russia banned the import of all fresh vegetables from the European Union until 22 June. [20] A novel strain of Escherichia coli O104:H4 bacteria caused a serious outbreak of foodborne illness focused in northern Germany in May through June 2011. The illness was characterized by bloody diarrhea, with a high frequency of serious complications, including hemolytic -uremic syndrome (HUS), a condition that requires urgent treatment. The outbreak was originally thought to have been caused by an enterohemorrhagic ( EHEC ) strain of E. coli , but it was later shown to have been caused by an enteroaggregative E. coli ( EAEC ) strain that had acquired the genes to produce Shiga toxins . Epidemiological fieldwork suggested fresh vegetables were the source of infection. The agriculture minister of Lower Saxony identified an organic farm [2] in Bienenbüttel , Lower Saxony, Germany, which produces a variety of sprouted foods , as the likely source of the E. coli outbreak. [3] The farm has since been shut down. [3] Although laboratories in Lower Saxony did not detect the bacterium in produce, a laboratory in North Rhine-Westphalia later found the outbreak strain in a discarded package of sprouts from the suspect farm. [4] A control investigation confirmed the farm as the source of the outbreak. [5] On 30 June 2011 the German Bundesinstitut für Risikobewertung (BfR) ( Federal Institute for Risk Assessment ), an institute of the German Federal Ministry of Food, Agriculture and Consumer Protection ), announced that seeds of fenugreek imported from Egypt were likely the source of the outbreak. [6] In all, 3,950 people were affected and 53 died, including 51 in Germany. [7] A handful of cases were reported in several other countries including Switzerland , [8] Poland , [8] the Netherlands , [8] Sweden , [8] Denmark , [8] the UK, [8] [9] Canada [10] and the USA. [10] [11] Essentially all affected people had been in Germany or France shortly before becoming ill. Initially German officials made incorrect statements on the likely origin and strain of Escherichia coli .[12][13][14][15] The German health authorities, without results of ongoing tests, incorrectly linked the O104 serotype to cucumbers imported from Spain.[16] Later, they recognised that Spanish greenhouses were not the source of the E. coli and cucumber samples did not contain the specific E. coli variant causing the outbreak.[17][18] Spain consequently expressed anger about having its produce linked with the deadly E. coli outbreak, which cost Spanish exporters 200M US$ per week.[19] Russia banned the import of all fresh vegetables from the European Union until 22 June.[20]
- e The benefits of intelligently open data were powerfully illustrated by events following an outbreak of a severe gastro-intestinal infection in Hamburg in Germany in May 2011. This spread through several European countries and the US, affecting about 4000 people and resulting in over 50 deaths. All tested positive for an unusual and little-known Shiga-toxin–producing E. coli bacterium. The strain was initially analysed by scientists at BGI-Shenzhen in China, working together with those in Hamburg, and three days later a draft genome was released under an open data licence. This generated interest from bioinformaticians on four continents. 24 hours after the release of the genome it had been assembled. Within a week two dozen reports had been filed on an open-source site dedicated to the analysis of the strain. These analyses provided crucial information about the strain’s virulence and resistance genes – how it spreads and which antibiotics are effective against it. They produced results in time to help contain the outbreak. By July 2011, scientists published papers based on this work. By opening up their early sequencing results to international collaboration, researchers in Hamburg produced results that were quickly tested by a wide range of experts, used to produce new knowledge and ultimately to control a public health emergency. Wikipedia A novel strain of Escherichia coli O104:H4 bacteria caused a serious outbreak of foodborne illness focused in northern Germany in May through June 2011. The illness was characterized by bloody diarrhea, with a high frequency of serious complications, including hemolytic -uremic syndrome (HUS), a condition that requires urgent treatment. The outbreak was originally thought to have been caused by an enterohemorrhagic ( EHEC ) strain of E. coli , but it was later shown to have been caused by an enteroaggregative E. coli ( EAEC ) strain that had acquired the genes to produce Shiga toxins . Epidemiological fieldwork suggested fresh vegetables were the source of infection. The agriculture minister of Lower Saxony identified an organic farm [2] in Bienenbüttel , Lower Saxony, Germany, which produces a variety of sprouted foods , as the likely source of the E. coli outbreak. [3] The farm has since been shut down. [3] Although laboratories in Lower Saxony did not detect the bacterium in produce, a laboratory in North Rhine-Westphalia later found the outbreak strain in a discarded package of sprouts from the suspect farm. [4] A control investigation confirmed the farm as the source of the outbreak. [5] On 30 June 2011 the German Bundesinstitut für Risikobewertung (BfR) ( Federal Institute for Risk Assessment ), an institute of the German Federal Ministry of Food, Agriculture and Consumer Protection ), announced that seeds of fenugreek imported from Egypt were likely the source of the outbreak. [6] In all, 3,950 people were affected and 53 died, including 51 in Germany. [7] A handful of cases were reported in several other countries including Switzerland , [8] Poland , [8] the Netherlands , [8] Sweden , [8] Denmark , [8] the UK, [8] [9] Canada [10] and the USA. [10] [11] Essentially all affected people had been in Germany or France shortly before becoming ill. Initially German officials made incorrect statements on the likely origin and strain of Escherichia coli . [12] [13] [14] [15] The German health authorities, without results of ongoing tests, incorrectly linked the O104 serotype to cucumbers imported from Spain. [16] Later, they recognised that Spanish greenhouses were not the source of the E. coli and cucumber samples did not contain the specific E. coli variant causing the outbreak. [17] [18] Spain consequently expressed anger about having its produce linked with the deadly E. coli outbreak, which cost Spanish exporters 200M US$ per week. [19] Russia banned the import of all fresh vegetables from the European Union until 22 June. [20] A novel strain of Escherichia coli O104:H4 bacteria caused a serious outbreak of foodborne illness focused in northern Germany in May through June 2011. The illness was characterized by bloody diarrhea, with a high frequency of serious complications, including hemolytic -uremic syndrome (HUS), a condition that requires urgent treatment. The outbreak was originally thought to have been caused by an enterohemorrhagic ( EHEC ) strain of E. coli , but it was later shown to have been caused by an enteroaggregative E. coli ( EAEC ) strain that had acquired the genes to produce Shiga toxins . Epidemiological fieldwork suggested fresh vegetables were the source of infection. The agriculture minister of Lower Saxony identified an organic farm [2] in Bienenbüttel , Lower Saxony, Germany, which produces a variety of sprouted foods , as the likely source of the E. coli outbreak. [3] The farm has since been shut down. [3] Although laboratories in Lower Saxony did not detect the bacterium in produce, a laboratory in North Rhine-Westphalia later found the outbreak strain in a discarded package of sprouts from the suspect farm. [4] A control investigation confirmed the farm as the source of the outbreak. [5] On 30 June 2011 the German Bundesinstitut für Risikobewertung (BfR) ( Federal Institute for Risk Assessment ), an institute of the German Federal Ministry of Food, Agriculture and Consumer Protection ), announced that seeds of fenugreek imported from Egypt were likely the source of the outbreak. [6] In all, 3,950 people were affected and 53 died, including 51 in Germany. [7] A handful of cases were reported in several other countries including Switzerland , [8] Poland , [8] the Netherlands , [8] Sweden , [8] Denmark , [8] the UK, [8] [9] Canada [10] and the USA. [10] [11] Essentially all affected people had been in Germany or France shortly before becoming ill. Initially German officials made incorrect statements on the likely origin and strain of Escherichia coli . [12] [13] [14] [15] The German health authorities, without results of ongoing tests, incorrectly linked the O104 serotype to cucumbers imported from Spain. [16] Later, they recognised that Spanish greenhouses were not the source of the E. coli and cucumber samples did not contain the specific E. coli variant causing the outbreak. [17] [18] Spain consequently expressed anger about having its produce linked with the deadly E. coli outbreak, which cost Spanish exporters 200M US$ per week. [19] Russia banned the import of all fresh vegetables from the European Union until 22 June. [20]
- There are difficulties in ensuring access to data from developing countries. Whereas some are developing open access journals (for example the journal African Health Sciences32), others are uneasy at the prospect that those with greater scientific resources will benefit overseas interests, to the detriment of home researchers. Indonesia ceased providing access to their flu samples in 2007 because of worries that more scientifically developed countries would create flu vaccines based on their data, with no benefit to Indonesia. This policy was reversed only after the World Health Organisation put in place protocols for equitable access to vaccines and medicines in future pandemics.
- Recent developments at the OPERA collaboration at CERN illustrate how data openness can help in the scrutiny of scientific results. The OPERA team fired a beam of muon neutrinos from CERN to the Gran Sasso National Laboratory, 730 km away in central Italy. In September 2011, and to the surprise of the experiment’s scientists, the neutrinos seemed to travel faster than the speed of light – understood to be a universal speed limit. Hoping for ideas to explain this apparent violation of physical law CERN opened the result to broader scrutiny, uploading the results in unprecedented detail to the physics pre-print archive, arXiv.org. More than 200 papers appeared on arXiv.org attempting to debunk or explain the effect. A large group of papers focused on the technique used to time the neutrinos’ flight path. On 23 February 2012, the OPERA collaborators announced two potential sources of timing error. There was a delay in the stop and start signals sent via GPS to the clock at Gran Sasso due to a faulty fibre optic cable, and there was a fault inside the master clock at Gran Sasso. It was announced in June 2012 that attempts to replicate the original result with four separate instruments at Gran Sasso found that neutrinos respected the universal speed limit, confirming the suspected experimental error.
- Privacy The use of datasets containing personal information is vital for a lot of research in the medical and social sciences, but poses considerable challenges for information governance because of the potential to compromise individual privacy. Citizens have a legitimate interest in safeguarding their privacy by avoiding personal data being used to exploit, stigmatise or discriminate against them or to infringe on their personal autonomy (see box 3.4).159 The legal framework for the “right to respect for private and family life” is based on article 8 of the European Convention on Human Rights (ECHR)160 for member states of the Council of Europe. Some aspects of privacy rights are codified by the EU Data Protection Directive (95/46/EC) and implemented in the UK by the Data Protection Act 1998 (DPA). There is a live issue with the EU Data Protection Regulation, specifically that the research community are very concerned that amendments proposed by the rapporteur of the LIBE committee will prevent or severely impair scientific research studies using personal data. BIS and DH are working with MoJ (who are in the lead on negotiations) to address. Series of public perception flashpoints e.g. 2 CDS 25m items of child benefit data (2007), Google Maps, Street View.
- Improving access for research and policy The Administrative Data Taskforce (ADT) was formed in December 2011 by the Economic and Social Research Council (ESRC), the Medical Research Council (MRC) and Wellcome Trust, and chaired by Sir Alan Langlands. The ADT has been working with a range of government departments, academic experts, the funding agencies and representatives from all four nations in the UK to examine the best procedures and mechanisms to make administrative data available for research safely. The report from the ADT (available below) was published in December 2012. The ADT recommendations propose a UK Administrative Data Research Network that would be responsible for linking data between government departments. The proposed network will provide a single governance structure that will allow for consistent and robust decision-making. "Our recommendations would allow research that is already technically feasible to be undertaken with integrity in a much more consistent, reliable and efficient manner. This would be of huge value to academic research, but would also benefit research and policy evaluation within government departments, whose researchers are also constrained by the existing arrangements." - Professor Paul Boyle, Chief Executive of the ESRC
- Improving access for research and policy The Administrative Data Taskforce (ADT) was formed in December 2011 by the Economic and Social Research Council (ESRC), the Medical Research Council (MRC) and Wellcome Trust, and chaired by Sir Alan Langlands. The ADT has been working with a range of government departments, academic experts, the funding agencies and representatives from all four nations in the UK to examine the best procedures and mechanisms to make administrative data available for research safely. The report from the ADT (available below) was published in December 2012. The ADT recommendations propose a UK Administrative Data Research Network that would be responsible for linking data between government departments. The proposed network will provide a single governance structure that will allow for consistent and robust decision-making. "Our recommendations would allow research that is already technically feasible to be undertaken with integrity in a much more consistent, reliable and efficient manner. This would be of huge value to academic research, but would also benefit research and policy evaluation within government departments, whose researchers are also constrained by the existing arrangements." - Professor Paul Boyle, Chief Executive of the ESRC