Overview of the Governance Considerations

A Framework for DiscussionTom Dedeurwaerdere

Centre for the Philosophy of LawUniversité catholique de Louvain, Belgium

Designing the Microbial Research CommonsSession 5

Washington DC, 9th October 2009

I. Examples of the benefits of microbial commons for the public and private sector

II. Emerging microbial commons in sequence data, literature and materials

III. Survey on current patterns of collaboration in the microbial commons

IV. Implications for the general design principlesV. Applications to some core components:

I. Ongoing Oversight and AdministrationII. High Level Institutional CoordinationIII. Managing Community Resources at the International Level

VI. Concluding Comments

I.Examples of the benefits of the microbial commons for public and private sector

Ug99 Pathway Update 2008

Known movements are following winds

Yemen – most likely source for Iran

Highly likely that Ug99 went undetected in southern Iran or southern Iraq?

High potential for multi-directional dispersal from Iran

New variants likely to follow a similar route

Similar issues with fusarium graminearum in US and Canada (Cletus Kurzman)

Source : Amri Ahmed, 2nd microbial commons expert workshop, Brussels, 25th of March 2009

Wine grape contamination by certain aspergillus niger species

Species of the Aspergillus section Nigri have been extensively used for various biotechnological purposes (e.g. fermentation industry to produce hydrolytic enzymes and organic acids) and are among the fungi best studied causing biodeterioration of commodities and food spoilage.

Source: Nelson Lima, 1st microbial commons expert workshop, Brussels, 18th of February

New species identified through collaborative research: Aspergillus carbonarius

Frequency of new species in the Grapes

Source: Nelson Lima, 1st microbial commons expert workshop, Brussels, 18th of February

Genetic grouping of S. thermophilus strains isolated in different geographycal regions in

Georgia based on F-Rep-PCR analysis

UPGMA dendrogram

W-3202 Senaki S-3203 Mckalchoka W-3207 Kutaisi E-3210 Gori W-3206 Kutais W-3213 Kutaisi W-3217 Kvitiri W-3221Godogani W-3222Godogani W-3225 Opurchketi S-3232 Kobuleti S-3233 Kobuleti W-3235 Senaki S-3238 Gantiadi S-3240 Gantiadi W-3236 Senaki S-3242 Gantiadi S-3245Ortabatumi S-3252 BatumiE-3276 Teleti E-3263 Tabakhmela E-3265 Tabakhmela E-3266 Tabakhmela E-3270 Shindisi E-3273 TeletiE-3275 Teleti E-3271 Shigeligi E-3279 Teleti W-11A Zestaphoni W-12A Zestphoni W-1D Khashuri E-3B Tkneti C-4ABakuriani *E-5B Tsxvarichamia*E-10B Metekhi E-10C Metekhi C-4B Bakuriani * E-6A Gombori * E-13B Tbilisi E-1720 Mtsketa DSM20617T

W-1B Khashuri E-3248 Pirveli Maisi E-3261 Tkneti E-3278 Teleti C-3211 Surami C-3212 Surami W-3219 Kvitiri

A

B1

B2

C

Genetic Biodiversity of the Culture of Matsoni Yoghurt in Georgia

Source : Nino Chanisvili, 2nd microbial commons expert workshop, Brussels, 25th of March 2009

24%

17%

5%15%

17%

0%

15%

5% 2%

Pharmaceuticals/medicaltechnologies

Food/beverage industries

Cosmetics/personal care

Molecularbiology/biotech

Chemical processing

Environmentalremediation

I ndustrial applications

Aquaculture/agriculture

Nutraceuticals

UNU/IAS database on bioprospecting in Antarctica

Users of Antarctic genetic ressources

www.bioprospector.org/bioprospector/Antarctica/home.action

Source: United Nations University & Belgian Federal Public service Health, Food chain safety and Environment, as contribution to the discussions on bioprospecting within the Antarctic Treaty Consultative Meeting (presented by Annick Wilmotte, 2nd microbial commons expert workshop, Brussels, 25th of March 2009

2. Emerging microbial commons for biological research materials and digital

research infrastructuresA brief terminology question: microbial commons

“resource shared by a group of people. In a commons, the resource can be small and serve a tiny group, it can be community-level, or it can extend to international and global levels”

(ref. Understanding Knowledge as a Commons, Charlotte Hess and Elinor Ostrom (editors), MIT Press, 2007)

So includes both semi-commons (partially restricted) fully open commons (totally open)

Emerging commons in microbial genetic materials

• Commercializing pressures: some collections adopt private sector models and move towards restrictive licence conditions:

•Use in host laboratory only•No redistribution without permission•Limits on derivatives

• On the other hand emerging commons models :• Contractually reconstructed public domain

• Culture collections : legitimate exchange in the European Culture Collection Organization, BIOTEC Thailand, etc.

• Related ex situ collections : Biobricks, algOS, … (Minna Allarkhaia)

• Pool (semicommons, typically EU projects, NSF projects)• Clearing house model (Science Commons model for the

neurocommons) (Thin Nguyen)• Public domain (ocean, antartica)

•

Emerging open knowledge environments

Service nodes: Webservices: Straininfo Bioportal (Peter Dawyndt) Standardisation/ontologies : Genomic Standards Consortium

(Dawn Field)

Digitally integrated thematic knowledge environments Science Commons neurocommons project (for Huntington

disease) Interdisciplinary and multi-scale bio-imaging at UCSD National

Center for Microscopy and Imaging Research (NCMIR) (Mark Ellisman)

Genomic Encyclopedia of Bactria and Archaea (GIBA); with type stains from DSMZ (filling in philogenetic gaps) (Nikos Kyrpides)

Design principles for governance

Problem : need of moving from a disjointed set of bottum-up initiatives towards an integrated distributed infrastructure

Research question : how to create the best possible fit between the governance structures of scientific infrastructures and the normative practices and needs of microbial research commons ? Problems of « crowding out » of productive norms and

practices by inadequate institutionalisation (cf. for example studies on paying for blood donation)

3. Survey on current patterns of collaboration in the microbial

commons

Deposit patterns in 11 major culture collections in developing and

developed countriescc1 cc2 cc3 cc4 cc5 cc6 cc7 cc8 cc9 cc10 cc11

Total numbers of strains in the collection: N/A N/A N/A N/A N/A approx. 2000N/A 20000 540 2500Estimation of percentage of total strains deposited before 1993? 51 N/A 90 N/A 35 40 50 40 50 90 50accessions 05 436 886 55 2812 104 32 272 150 736 0 108

98 N/A 100 86 79 98 100 N/A 100 0 100

2 N/A 0 0 0 2 0 N/A 0 0 0

0 N/A 0 14 21 0 0 N/A 0 0 0

Depositors * * * *national % 65 45 98 86 70 100 99 N/A 57 nr 100

others % 35 55 2 14 30 0 1 N/A 43 nr 0

foreing countries 18 14 1 3 8 0 1 N/A 23 nr 0

Country of origin

national % 26 10 98 98 60 53 99 N/A N/A nr 41

other countries % 74 90 2 2 40 47 1 N/A N/A nr 59

foreing countries 43 42 1 3 16 8 1 N/A N/A nr 19

uknown 35 1 0 19 0 0 N/A N/A nr

%without restrictions

%with res, non-commercial

%other-restrictions

Collaboration patterns between culture collections

Survey amongst 119 WFCC culture collections

Academic and hospital researchcollections

Own collecting effort

From other WFCC culture collections

None of these categories (for example dying industry collections)

To academia research collections

To other WFCC culture collections

To private sector

None of these categories (to hospitals and for teaching mainly)

30%

45%

20%

5%

58%

23%

10%

9%

Total number of new accessions in 2005 in the 119 WFCC culture collections : approximately 10.000

Total number of strains delivered in 2005 by the 119 WFCC culture collections : approximately 120.000

Open Access to published literature

Principal findings from research on journals in microbiology and related life sciences (Reichman et al. )

About 30% full open access (OA), including hybrid (both purchased immediate OA and subscription); 20% read-only; 50% subscription.

80% of subscription journals allow author self-archiving on personal websites, but almost 90% do not allow archiving on the author’s institutional websites and most are silent on external repository deposits (e.g., on PubMedCentral).

98% of subscription journals require transfer of copyright. About 75% of all journals surveyed are published by for-profit

publishers.

Source : Paul Uhlir, Microbial Commons Workshop, NAS, 8th of October

4. Implications for the general design principles

General principles Science community driven governance framework

Most decisions on governance (quality management, prior informed consent, etc.) imply a deep knowledge of the technical specificities of the field

Especially in thematic knowledge environments, the conservation decisions for materials and digital knowledge management decisions depend on a scientific appraisal of the scientific relevancy of the materials/digital content

Principle of multilevel governance/subsidiarity Heterogeneity of materials and research fields

represented in the culture collections (fungi, yeast, bacteria, vectors for genetic engineering, etc.). The governance mechanisms have to be adapted to the specific needs.

Some ex-situ collections produce international public goods and some produce national public goods (national general purpose collections). However, the vast majority of collections produce regional/transregional public goods (research materials as inputs for specialized knowledge communities organized in regional/transregional networks)

Principle of specialization and cooperationToday 557 WFCC Collections hold over 1,5 million

strains (1,526,805 ; WDCM database, accessed 9 october, but data largely outdated) ; even the largest collections such as ATCC (72000) and NRRL (87000) hold only a small portion of the total strain holdings of the WFCC members

Moreover, each of these collections contains an important set of unique strain holdings (on average 40% of unique strains for the major collections)

Many more strains are even conserved outside the culture collections that are member of WFCC (cf. example of Canada infra)

Consequences for the governance framework The overarching principle will be one of subsidiarity:

The main governance issues (such as quality controls, enforcement, administration) should be dealt with at the level of the open knowledge environments and regional networks of culture collections

Supported by appropriate incentives: through a combination of private ordering (rules of conditional reciprocity in sharing arrangements) and mandatory public policy (NIH open access mandate, cf. Jerry Sheehan)

Some coordination problems might be better solved at a higher institutional level (eScience advisory board (Paul David), repository of governance strategies (Minna Allarkhaia), standards, etc.)

At the international level, representation of the microbial science community (discussion on access to knowledge in WIPO, discussion on access to materials in CBD)

V. Applications to some core components

A. Ongoing Oversight and AdministrationB. High Level Institutional CoordinationC. Managing Community Resources at the International

Level

A. Ongoing Oversight and Administration in a decentralized

framework

A.1. Quality Controls for the Material and Digital Research Infrastructure

Steps of quality control (authenticity, viability and purity) At the entry : authentication control /

certification (Edward Moore, presentation 2009-03-26 Brussels)Based on tests with various methods, mainly :

morphological (phenotyping), fatty acid profiling (chemotyping) and 16S rRNA sequence analysis (genotyping)

For example, at the Culture Collection University of Gothenburg, approximately 10 % of requests for deposits are not what they are said to be !!

Importance of persistant and unique identifiers for the digital infrastructure Key tool : unique strain number = Accession

number for the strain, the unique identifier for one isolate at the collection

+ its synonyms (accession numbers of copies (clones) of the isolate in other collections)

Role of unique identifiers

‘87 ‘89 ‘94 '95 '96 ‘99 ‘01~ 30 named B. subtilis B. subtilis B. subtilis subsp. subtilis

species B. subtilis subsp. spizizenii B. vallismortis

(B. clausii) B. mojavensis

B. atrophaeus B. amyloliquefaciens

TAXONOMIC DEVELOPMENT IN THE “BACILLUS SUBTILIS GROUP”

before ‘73 Gordon et al. ‘73 Appr. Lists ‘80 up to 2003

~ 10 named B. licheniformis B. licheniformis B. licheniformis species B. sonorensis

~ 20 named B. pumilus B. pumilus B. pumilus species

~ 2 named B. firmus B. firmus B. firmus species

B. lentus B. lentus

B. sporothermodurans

Source : Dagmar Fritze, FAO Workshop, Brussels, 25.-26.03.09

The unique strain number stays the same, while the knowledge of taxonomy is evolving and sub-species diversity is evolving

T. Gibson (971)

W.W. Ford (13)

original isolate

GUID:new isolate

GUID:NCTC 2599

GUID:ATCC 14579

GUID:Gibson 971

GUID:Ford 13

GUID:NCIMB 9373

first BRC deposit

NCIMB 9373

NCTC 2599

NRRL B-3711

ATCC 14579

isolate entities culture entities

Accession form

Accession form

Accession form

Accession form

end user

end user

end user

GUID:NRRL B-3711

Strain number disambiguation through Globally Unique Identifiers

Source : adapted from Peter Dawyndt, 15th September 2006 and MOSAICS report

Other quality requirements related to building and digital integration of the microbial commons

Availability of all documents in full text searchable format (Samuel Kaplan)

On line catalogue of the holdingsMinimal information set defined by the

participating collectionsCommon ontologies, common data formats

A.2. Funding

Source : authors’ calculations based on Scott Stern, Biological Resource Centres, 2004

Illustration based on the case of the culture collections in Canada

• General data– 140 collections, of which 23 recognized of strategic

importance (1986 survey), 19 of these are WFCC members in 2009 (17 in the survey Sigler 2004)

– In 2009 (WDCM data), total number of strains in the 19 WFCC collections : 69363

Reference : Lynne Sigler, Canadian Journal of Plant Pathology, 2004 ; and author’s calculations based on information from WDCM database

Data from the 17 major

collections (survey in Sigler

2004)

Number of collections

Total number

of strains

Vulnarable at

retirement of curator

Acquired other

threatened collections

Government 5 15525 2 1 (acquired 5)

Grant to university

9 29440 3 1 (acquired 3)

Private non-profit 1 2300

Industry 2 2675

• Government supported (5) – Mainly Public Health Agency of Canada, Canadian Forest

Service and Agriculture and Agri-food Canada– Permanent endowment, but with the provison that

some revenue could be obtained from fees for services

– On average 1 full-time equivalent curator/collection

• Grants to university (9)– University-based collections recognized as being

« essential for science and cultural research and for training future generations of researchers »

– 3 year grants to universities through the Research Council of Canada (NSERC) through a competitive evaluation

– On average 1 full-time equivalent curator/collection– However : existence of the collections partially threatened

at each renewal (especially for specialized staff)

• Private non-profit (1)– Funded by 3000 forest industry companies (members

of the research institute), canada forest service and canadean provinces

– Funding insufficient

• Industry (2)– Mainly industrial strains for baker’s yeast and

brewery’s, but also developping probiotics, environmental, etc.

Lessons for sustainable funding of culture collections The vast majority of materials are distributed to public

sector recipients (77% according to a survy of 119 collections), for research and training purposes. This is reflected in the fact that more than 80% of the culture colletions that are member of the WFCC belong to public sector entities

Funding is often on a competitive basis, especially in the cases of universities. However, because of the very specific expertise required to curate microbials in a particular field of research, this is not appropriate for the funding of the core staff, which should be on a more permanent basis

Lessons for sustainable funding of the digital infrastructure Funding for the digital infrastructure in the thematic

knowledge environment could be part of the grants structure to the individual culture collections, when succesful can attract new grants

The generic webservices provide a service to all culture collections and could be constructed as a national digital infrastructure resource / or through international collaboration

A.3. Enforcement of Contracts

Use of contracts to foster sharing for non-commercial research European Culture Collections Standard Material Transfer

Agreement Legitimate Exchange Clause in some collections : the All-

Russian Collection, the Biotec collection in Thailand The FAO Standard Material Transfer Agreement (of the

International Treaty)

Enforcement through private ordering (cf. Peter Lee) Through peer pressure Through conditional reciprocity

Enforcement challenges in the compensatory liability rule Common quality management Tracking of transfer of materials within the research

commons (transactions for non-commercial use) Use of formal transfer agreements at each transaction Keeping track of the transaction history in the catalogue

Tracking of transfer of materials to commercial clients Currently, under conditions of secrecy

Enforcement of the open access license conditions for the digital content in the Open Knowledge Environment No major enforcement problem Mainly a normative and reputational issue (motivating

scientists to publish their content in the open access environment, to use theses licenses from the beginning)

B. High Level Institutional Coordination

B.1. Standard Setting

Two examples for the need of higher level institutional coordination Standards for unique strain numbers

Currently system based on WDCM accronyms, but potential errors upon multiple handling (and renaming) of copies of the same material

The service nodes could play a role in managing the Universal GlobalID system

The Science Unions (IUMS) and the Federation (WFCC) could play a role in working out agreements with publishers on the use of the unique numbers in publications

Minimal information disclosure requirements Distributed database infrastructure with minimal

information disclosure requirements : publication, course country, etc. (cf. CABRI or other standards)

Common ontologies : role of GSC Common format (xml) : role of standard software

package Could build upon existing initiatives

Common Access to Biological Resources and Information (CABRI), minimal data set http://www.cabri.org/guidelines/catalogue/CPds.html

Minimal Information about a Genome Sequence Specification (MIGS), published in Nature

B.2. Guidelines and norm building

An early example for an attempt to lay down common principles are the WFCC voluntary Guidelines (WFCC, 1992). These have been updated in various initiatives (WFCC 1998 ; OECD 2001)

More recently, the Demonstration Project for a GBRCN (Global Biological Resource Centres Network), the most recent networking activity of microbial culture collections, has as its major goal the establishment of a legal operational framework for the exchange of materials and information

C. Managing Community Resources at the International

Level

C.1. Representation of the community in policy Formulation on Biodiversity Related Issues

(Convention on Biological Diversity)

Convention on Biological Diversity Contribution to ex situ conservation (article 9) Contribution to in situ conservation (article 8), through

financial support from down stream commercial applications Example of Yellowstone Park in US (special agreement with

ATCC to retain residual rights on the microbial resources), of Merck-In Bio in Costa Rica (preferential access to samples of the national park system in exchange for research funding)

However, danger of proliferation of ad hoc arrangements (science friendly arrangements), or of emergence of restrictive access conditions (out of fear of commercial applications, example of access to soil samples of Rothamsted, UK)

Third objective of the Convention: fair and equitable sharing of benefits arising out of utilization of genetic resources (concerns of international equity) Limits of a voluntary scheme such as the microbial research

commons for an international access and benefit sharing regime: Even if the microbial research commons might contribute to

access and benefit sharing, for example through a standard compensatory liability clause, there is not obligation for the parties to put material in the research commons

Moreover the research commons are designed for resources with unknown and unlikely commercial value (where the scientific pay-offs of putting it in the open outweighs the expectations of direct commercial pay-offs), while the major equity concerns are raised for strains with known commercial value

However, in the absence of an agreement, some countries might (and do) restrict access to all biological resources (including those intended for non-profit research purposes)

Therefore for addressing the ABS concerns, there is a need of an approach that deals with all ex-situ resources, beyond the sub-set of resources deposited in the scientific research commons

C.2. Representation in policy formulation on Food and Agriculture, and Climate Change

Issues

The FAO Commission on Genetic Resources for Food and Agriculture (CGRFA) was asked to contribute to further work on ABS, in a direction supportive of the special needs of the agriculture sector, in regard to all components of biological diversity (10th session, 2005)

major contributions for addressing these problems can be expected from measures which:  provide for a standardized solution to the benefit-

sharing with the original providers of the strains to culture collections

support further standardization of the license conditions used in the various MTAs both for deposit and distribution of strains

Concluding Comments

There is no evidence that formalization of the commons as such is leading to more restrictive license conditions or an overly high administrative burden

These, and other points, lead to think about the possibility of developing common normative approaches and a repository of practical solutions to depositing and use of microbial materials and sharing of digital data and information

which in turn can support the further development of a fully integrated distributed infrastructure based on the emerging initiatives in the microbial commons

Thanks for your attention

www.microbialcommons.orgwww.straininfo.org

Some References

Designing the Microbial Research Commons, Jerome Reichman, Tom Dedeurwaerdere, Paul Uhlir, manuscript on file with the authors

Tom Dedeurwaerdere, Maria Iglesias, Sabine Weiland, Michael Halewood, Use and Exchange of Microbial Genetic Resources Relevant for Food and Agriculture, Report (under review at the Commission on Genetic Ressources)

Per Stromberg, Tom Dedeurwaerdere, Unai Pascual, The Contribution of Public Networks to Knowledge Accumulation (under review at Research Policy)

www.microbialcommons.org ; june 2008 conference proceedings (special issue forthcoming in the International Journal of the commons, January 2010)

Robert Cook-Deegan and Tom Dedeurwaerdere, “The Science Commons in Life Science Research: Structure, Function and Value of Access to Genetic Diversity”, in International Social Science Journal, vol.188, 2006, pp.299-318.

Peter Dawyndt, Tom Dedeurwaerdere, and J. Swings, “Explorating and exploiting microbiological commons: contributions of bioinformatics and intellectual property rights in sharing biological information. Introduction to the special issue on the microbiological commons”, in International Social Science Journal, vol.188, 2006, pp.249-258.

Tom Dedeurwaerdere, “The institutional Economics of sharing Biological Information”, in International Social Science Journal, vol.188, automne 2006, pp.351-368.

Acknowledgements

Participants to the FAO expert workshops, Brussels, 18-19 Feb 2009 and Brussels, 25-26 March 2009

Researchers of IAUP V/23, IAUP VI-06, REFGOV : Per Stromberg, Maria-Jose Iglesias, Sabine Weiland

Co-authors of the FAO report : Maria-Jose Iglesias, Michael Halewood and Sabine Weiland

Co-authors on the microbial commons project : Jerry Reichman, Paul Uhlir