Transcript Designing the Microbial Research Commons Session 5 Overview of the Governance Considerations A Framework for Discussion Tom Dedeurwaerdere Centre for the Philosophy of Law Université catholique.

Designing the Microbial Research Commons
Session 5
Overview of the Governance Considerations
A Framework for Discussion
Tom Dedeurwaerdere
Centre for the Philosophy of Law
Université catholique de Louvain, Belgium
Washington DC, 9th October 2009
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 principles
V. Applications to some core components:
I.
I.
II.
III.
Ongoing Oversight and Administration
High Level Institutional Coordination
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 multidirectional
dispersal from
Iran
New variants
likely to follow
a similar route
Similar issues
with fusarium
graminearum
in US and
Canada (Cletus Source : Amri Ahmed, 2nd microbial commons expert
Kurzman)
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 Biodiversity of the Culture of
Matsoni Yoghurt in Georgia
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 Batumi
E-3276 Teleti

E-3263 Tabakhmela 
E-3265 Tabakhmela 
E-3266 Tabakhmela 
E-3270 Shindisi 
E-3273 Teleti
E-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 grouping of S. thermophilus strains
isolated in different geographycal regions in
Georgia based on F-Rep-PCR analysis
UPGMA dendrogram
Source : Nino Chanisvili, 2nd microbial commons expert workshop, Brussels, 25th of March 2009
UNU/IAS database on bioprospecting in Antarctica
www.bioprospector.org/bioprospector/Antarctica/home.action
Pharmaceuticals/medical
technologies
Food/beverage industries
5% 2%
24%
Cosmetics/personal care
15%
0%
Molecular
biology/biotech
Chemical processing
17%
Environmental
remediation
Industrial applications
17%
15%
5%
Aquaculture/agriculture
Nutraceuticals
Users of Antarctic genetic ressources
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
infrastructures
 A 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
countries
cc1
cc2 cc3 cc4
cc5 cc6 cc7 cc8
Total numbers of strains in the collection:
N/A
N/A N/A
Estimation of percentage of total strains deposited before 1993?
accessions
05
51
N/A
90 N/A
436
886
55 2812 104
%without restrictions
98
N/A
100
%with res, non-commercial
2
N/A
0
%other-restrictions
0
N/A
0
Depositors
*
N/A N/A approx.N/A
200020000
%
65
45
98
others
%
35
55
2
foreing countries
18
14
1
35 40
86 79
0
540
2500
50
40
50
90
50
32 272
150
736
0
108
100
0
100
98 100 N/A
0
2
0 N/A
0
0
0
14 21
0
0 N/A
0
0
0
*
national
cc10 cc11
cc9
*
*
86 70 100
99 N/A
57 nr
100
0
1 N/A
43 nr
0
8
0
1 N/A
23 nr
0
14 30
3
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
0
0 N/A
N/A nr
19
Collaboration patterns between culture collections
Total number of new accessions in
2005 in the 119 WFCC culture
collections : approximately 10.000
Academic and
hospital research
collections
Own collecting
effort
From other WFCC
culture collections
Total number of strains delivered in 2005
by the 119 WFCC culture collections :
approximately 120.000
30%
23%
45%
Survey amongst 119
WFCC culture
collections
20%
None of these categories
(for example dying
industry collections)
58%
To academia research
collections
To private sector
10%
To other WFCC
culture collections
5%
9%
None of these
categories (to
hospitals and for
teaching mainly)
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 cooperation
 Today 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 Administration
B. High Level Institutional Coordination
C. 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
The unique strain number stays the same, while the knowledge of
taxonomy is evolving and sub-species diversity is evolving
TAXONOMIC DEVELOPMENT IN THE “BACILLUS SUBTILIS GROUP”
before ‘73
Gordon et al. ‘73
Appr. Lists ‘80
up to 2003
‘87 ‘89
‘94 '95 '96
‘99 ‘01
B. subtilis subsp. subtilis 
B. subtilis subsp. spizizenii

B. vallismortis

(B. clausii)

B. mojavensis

B. atrophaeus

B. amyloliquefaciens

~ 30 named
species
B. subtilis
B. subtilis
~ 10 named
species
B. licheniformis
B. licheniformis
~ 20 named
species
B. pumilus
B. pumilus
~ 2 named
species
B. firmus
B. firmus
B. firmus 
B. lentus
B. lentus 
B. licheniformis 
B. sonorensis

B. pumilus 
B. sporothermodurans
Source : Dagmar Fritze, FAO Workshop, Brussels, 25.-26.03.09

Strain number disambiguation through Globally
Unique Identifiers
original isolate
end user
GUID:
Ford 13
W.W. Ford (13)
GUID:
Gibson 971
T. Gibson (971)
first BRC deposit
GUID:
NCIMB 9373
NCIMB 9373
GUID:
NCTC 2599
NCTC 2599
GUID:
NRRL B-3711
NRRL B-3711
Accession
form
GUID:
new isolate
GUID:
ATCC 14579
isolate entities
Accession
form
ATCC 14579
culture entities
Accession
form
Accession
form
end user
end user
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 holdings
 Minimal information set defined by the participating
collections
 Common 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
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
Reference : Lynne Sigler, Canadian Journal of Plant Pathology, 2004 ; and author’s calculations based on
information from WDCM database
• 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 AllRussian 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 payoffs 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.org
www.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