Ioannis Economidis /Christina Naneva (European Commission ... · Ioannis Economidis /Christina Naneva (European Commission) ... Segovia, ES (June 2010) 3. What is ... supporting genome-scale

Ioannis Economidis /Christina Naneva (European Commission)Ioannis Economidis /Christina Naneva (European Commission)Sohi Rastegar (National Science Foundation)Sohi Rastegar (National Science Foundation)

Report1.1. What is Synthetic Biology What is Synthetic Biology vv2.2. Towards standards in Synthetic BiologyTowards standards in Synthetic Biology. A . A

Task Force Workshop, Segovia, ES (June 2010)Task Force Workshop, Segovia, ES (June 2010)3.3. What is a Task Force Working Group on What is a Task Force Working Group on

Synthetic Biology (Terms of reference/strategy Synthetic Biology (Terms of reference/strategy plan)plan)

4.4. Future activitiesFuture activities5.5. Actions in the granting systems taking into Actions in the granting systems taking into

account the account the existence of the WG on Synthetic existence of the WG on Synthetic BiologyBiology

Synthetic Biology Synthetic Biology the design and fabrication of

biological components and systems that do not already exist in the natural world and/or the re-design and refactoring of

existing biological systems.

The basic notion behind SB Any biological system can be considered as a complex

combination of functional, stand-alone elements (not unlike those found in man-made devices) It can be-deconstructed in a limited number of components

and reconstructed in an entirely different configuration for the sake of modifying existing properties or creating altogether new ones. SB has an aspect of developing general-use technological and

conceptual tools (biological parts, minimal genomes, artificial cells, DNA synthesis),

AddressingAddressinghitherto intractable hitherto intractable

problemsproblems Biosynthesis of complex

molecules, breakdown or recycling of

toxic chemicals, biological detection of

explosives, biological production of

H2 and other fuels

raising utterly novel raising utterly novel challenges challenges DNA computing, design of biological

pattern development targeting bacteria to tumor

cells expanding the genetic

code to non-natural amino acids

The central aspect of synthetic biology, is The central aspect of synthetic biology, is bound to have an immense impact in bound to have an immense impact in

Biotechnology,Biotechnology, The possibility of re-programming or creating new live

organisms through the logical combination of

standardizedstandardized biological components that are otherwise decoupled from their natural context. Challenges: the reliable formatting of biological

functionalities and the detailed description of the most basic biological constituents and their interfaces, similar to modern electronic circuits.

Facing the challengesFacing the challenges The use of Systems Biology to understand the design and

operation rules. The exploitation of such rules for re-engineer biological

systems la carte.

The challenge is thus to set reliable Standard Operating Procedures, principles and actual units of measurement that are useful for biological engineering, even if we may still miss some fundamental facts.

The use of Systems Biology to understand the design and operation rules. The exploitation of such rules for re-engineer biological

systems la carte.

The challenge is thus to set reliable Standard Operating The challenge is thus to set reliable Standard Operating Procedures, principles and actual units of Procedures, principles and actual units of measurement that are useful for biological measurement that are useful for biological engineering, even if we may still miss some engineering, even if we may still miss some fundamental facts.fundamental facts.

Five hard truths for Synthetic biology

Many of the parts are undefined The circuitry is unpredictable The complexity is unwieldy Many parts are incompatible Variability crashes the system

Nature 463, 288-290 (2010)

Report1.1. What is Synthetic Biology What is Synthetic Biology vv2.2. Towards standards in Synthetic BiologyTowards standards in Synthetic Biology. A . A

Task Force Workshop, Segovia, ES (June 2010) Task Force Workshop, Segovia, ES (June 2010) vv3.3. What is a Task Force Working Group on What is a Task Force Working Group on




Towards Standards in Synthetic Towards Standards in Synthetic BiologyBiology

An Exploratory Workshop of An Exploratory Workshop of the USthe US--EC Task Force in EC Task Force in

BiotechnologyBiotechnologyParador de Segovia (Segovia, Spain). June 4-6, 2010

Standards and StandardisationStandards and Standardisation [a] the adoption of specific

geometric shapes and size formats for the physical assembly of the components of a man-made system (e.g. the sizes and shapes of screw turns), [b] the definition of units of

measurement of relevant properties and parameters as well as conditions and procedures to calculate them (e.g. Amperes for current, Ohms for resistance, etc), [c] implementation of unambiguous

protocols for the manufacture of the engineered objects.

Standards and Standardisation in SBStandards and Standardisation in SB the establishment of rules for

the physical composition of biologial (expression) devices. the adoption of RNA

polymerase per second (PoPs) units as a universal reference to express promoter strength The calculation of a

translation efficacy index deduced from measuring the input/output function of the devices under the various growth and metabolic conditions.

The specific goals of the Workshop The specific goals of the Workshop Review and discuss the latest technical standards having to do with vector architecture and physical assembly of genetic material, in vivo measures of biological functions and parametrization

methods/algorithms, descriptive languages, graphical representations and formalisms for

modelling genetic elements, and data exchange supporting registries of standard biological parts.

Present and discuss the emerging standardisation requirements needed to develop one or more cellular operating systemscellular operating systemssupporting genome-scale engineering. Identify and prioritise scientific research areas that would critically

accelerate standards-driven biological engineering at the genome scale. Identify new research programs or resources needed to support the

preceeding goals

Deliverables Deliverables -- PlatformsPlatforms a list of top standardisation needs not met or realised yet via

current practice; a set of fresh scientific research areas that might be

strategically coupled to support current engineering goals in Synthetic Biology; a working list of now unmet programmatic or facility needs

necessary to see such work carried out in a timely fashion. an US-EU Group on Biological Standards which will act as

both as an observatory of bottom-up initiatives and as a think tank on research topics with a prenormative value.

Report1.1. What is Synthetic BiologyWhat is Synthetic Biology2.2. Towards standards in Synthetic BiologyTowards standards in Synthetic Biology. A . A


Synthetic Biology (Terms of reference/strategy Synthetic Biology (Terms of reference/strategy plan) plan) vv



WORKING GROUPS & WORKING GROUPS & ACTIVITIESACTIVITIES

ENVIRONMENTALBIOTECHNOLOGY

BIO-BASED PRODUCTS AND BIO-BASED ENERGY

PLANT BIOLOGY

MARINE GENOMICS

ANIMALBIOTECHNOLOGY

SYNTHETICBIOLOGY

BIO-INFORMATICS

BIO-INFORMATICS

NANO-BIOTECHNOLOG

Y

NANO-BIOTECHNOLOG

YETHICS

SOCIETALETHICS

SOCIETAL

MissionThe exchange of views and collaboration across the The exchange of views and collaboration across the

Atlantic on Synthetic Biology. Atlantic on Synthetic Biology.

Focus on Scientific and Technical progress in implementing

Synthetic Biology principles (standardsstandards, orthogonality, minimal genomes, etc.) Outstanding issues of Ethics, Biosafety (including

environmental safety) and Biosecurity. Educational approaches.

StructureSecretarial EU/EC: Christina Naneva; Ioannis Economidis US/NSF: Sohi Rastegar

MembersEU USV. De Lorenzo (ES) Drew EndyX XY YZ Z




4.4. Future activities Future activities vv5.5. Actions in the granting systems taking into Actions in the granting systems taking into


Planned activitiesAll five yearsAll five years Telephone/video conferences/webinarsTelephone/video conferences/webinars Meetings in conjunction to international relevant scientific

event.WorkshopsWorkshops (Possible ideas) - "Orthogonality and orthogonal systems in

Biology", Cell operative systems and Deep metabolic engineering Workshop on Ethical, Legal, and Social issues in relationship

(or in juxtaposition) to the scientific and technical progress of Synthetic Biology. Workshop on relevant contribution of Synthetic Biology to

different domains of Biotechnology

Questions to be answered by these workshops and follow up discussions

Define accurately the nature and boundaries of biological functions

Formalization and non-ambiguous representation of biological information is a major bottleneck for the development of SB

Development of consensus criteria for Biological Standards

What is a biological part? Its it possible to convert a natural, context-dependent module into an autonomous component?

Planned activitiesTraining ActivitiesTraining Activities Short term courses with theoretical and practical

(laboratory) sessions focused on basic techniques and principles of synthetic biology. Exploration of funding possibilities for short term

exchanges of US young scholars to EU research institutions with reciprocity of short term exchanges of EU young scholars to US research establishments.

Ethics and beyond

Safety Biosecurity, prevention of

bioterrorism and dual use Governance Patenting and common

heritage Trade and global justice Science and society dialogue Research

Public beneficence Public Funding Review and DisclosurePublic Funding Review and Disclosure Support for Promising ResearchSupport for Promising Research Innovation Through SharingInnovation Through Sharing

Responsible stewardship Coordinated Approach to Synthetic BiologyCoordinated Approach to Synthetic Biology Risk Assessment Review and Field Release Gap AnalysisRisk Assessment Review and Field Release Gap Analysis Monitoring, Containment, and ControlMonitoring, Containment, and Control Risk Assessment Prior to Field ReleaseRisk Assessment Prior to Field Release International Coordination and DialogueInternational Coordination and Dialogue Ethics EducationEthics Education Ongoing Evaluation of ObjectionsOngoing Evaluation of Objections

Intellectual freedom and responsibility Fostering Responsibility and AccountabilityFostering Responsibility and Accountability Periodic Assessment of Security and Safety RisksPeriodic Assessment of Security and Safety Risks Oversight ControlsOversight Controls

Democratic deliberation Scientific, Religious, and Civic EngagementScientific, Religious, and Civic Engagement Information AccuracyInformation Accuracy Public EducationPublic Education

Justice and fairness. Risks in ResearchRisks in Research Risks and Benefits in Commercial Production and Risks and Benefits in Commercial Production and DistributionDistribution





account the account the existence of the WG on Synthetic existence of the WG on Synthetic Biology Biology vv

Synthetic Biology in KBBE 2011Synthetic Biology in KBBE 2011 Towards standardisation in Synthetic Biology Applying Synthetic Biology principles towards the cell

factory notion in biotechnology Ensuring the safety of Synthetic Biology applications Synthetic Biology ERA-NET

Towards standardisation in Synthetic Biology

Standardization and orthogonalization of the gene expression flow for robust engineering of NTN (new-to-nature) biological properties (ST-FLOW)

The ST-FLOW Project merges the efforts of 15 leading European and US research groups for developing material and computational standards that enable the forward-design of prokaryotic systems with a degree of robustness and predictability that is not possible with customary Genetic Engineering.

Documents

Ioannis Economidis /Christina Naneva (European Commission ... · Ioannis Economidis /Christina Naneva (European Commission) ... Segovia, ES (June 2010) 3. What is ... supporting genome-scale