Synthetic Biology:SB2.0/Biosecurity resolutions

From OpenWetWare

< Synthetic Biology:SB2.0(Difference between revisions)
Jump to: navigation, search
(Community Input)
Current revision (11:32, 15 June 2006) (view source)
(Items That Need Addressing Before Community-Wide Vote)
 
(31 intermediate revisions not shown.)
Line 2: Line 2:
<div style="padding: 10px; width: 730px; color: #000000; background-color: #ccccff">
<div style="padding: 10px; width: 730px; color: #000000; background-color: #ccccff">
==Overview==
==Overview==
-
''From Jay Keasling:''<br>
+
This page is for organizing discussions around the discussions to be held at [[SB2.0]] concerning [[Synthetic Biology:SB2.0/Biosecurity and Biosafety|biosecurity and biosafety]] issues.  In particular, the following white paper proposing specific recommendations of action that the community can possibly take:
-
Over the past few years, synthetic biologists have thought hard about how to improve biosafety and biosecurity. Most of these ideas would require new regulations, laws, or treaties. Some, however, can be implemented at the community level. Day 3 of [[SB2.0]] conference will give us a chance to debate, vote and launch community initiatives. If we can take meaningful action on biosafety and biosecurity, that will be time well spent.
+
-
==Possible Resolutions==
+
''From Understanding to Action: Community-Based Options for Improving Safety and Security in Synthetic Biology''<br>
-
 
+
-
==Community Input==
+
-
There are a variety of ways to contribute to discussion of these and other possible resolutions. 
+
-
 
+
-
*Berkeley Town Hall Meeting. (April 18th, please see the [http://webcast.berkeley.edu/events/stream.php?type=real&webcastid=15700 webcast])
+
-
*MIT Town Hall Meeting. (April 21st, webcast pending)
+
-
*EU-USA Synthetic Biology Workshop. The organizers have offered to discuss the proposals as part of their previously scheduled workshop in Warren, Virginia (US) on April 23.
+
-
*We have established a listserv for interested parties. You can join by sending an e-mail to starrt AT berkeley DOT edu.
+
-
*Input is welcome on the Synthetic Biology Community pages and below.
+
-
 
+
-
==Wiki Discussion==
+
-
 
+
-
This is a placeholder page for discussions around the recent white paper:
+
-
 
+
-
From Understanding to Action: Community-Based Options for Improving Safety and Security in Synthetic Biology<br>
+
Stephen M. Maurer, Keith V. Lucas & Starr Terrell<br>
Stephen M. Maurer, Keith V. Lucas & Starr Terrell<br>
Goldman School of Public Policy<br>
Goldman School of Public Policy<br>
Line 26: Line 10:
[http://gspp.berkeley.edu/iths/UC%20White%20Paper.pdf PDF link]<br>
[http://gspp.berkeley.edu/iths/UC%20White%20Paper.pdf PDF link]<br>
-
Below the text from the executive summary is included as discussed at the MIT town hall on April 21, 2006.  (Note that this is slightly different text than that used in the proposed resolutions in the white paper).
+
Below you will find text from the executive summary of this white paper as well as comments noted during the MIT town hall on April 21, 2006.  (Note that this is slightly different text than that used in the proposed resolutions in the white paper).
-
<font color="green">[Editorial note: Depending on the amount of discussion, individual resolutions should be spun out to their own pages.]</font>
+
__TOC__
 +
 
 +
<font color="green">[Editorial note: Depending on the amount of discussion, individual resolutions should be spun out to their own pages.]
 +
Please follow comments with the following text <font size=2 face="courier new" color=red><nowiki>-- '''~~~~''':</nowiki></font> in order to sign and date your comment</font>
==A.1 Insist That All Commercial Gene Synthesis Houses Adopt Current Best Practice Screening Procedures.==
==A.1 Insist That All Commercial Gene Synthesis Houses Adopt Current Best Practice Screening Procedures.==
-
While most gene synthesis companies screen orders for dangerous sequences, a few do not. This gives both community members and outsiders access to feedstocks for both wild-type and genetically engineered bioweapons. Community members should stop doing business with any gene synthesis company that fails to implement current best-practice screening methods by January 1, 2007.
+
It is obvious that as gene synthesis continue to improve; the "dual purpose" of this technology will increase the attention of the biosecurity community. While most gene synthesis companies screen orders for dangerous sequences, a few do not. This gives both community members and outsiders access to feedstocks for both wild-type and genetically engineered bioweapons. Community members should stop doing business with any gene synthesis company that fails to implement current best-practice screening methods by January 1, 2007.
-
===Discussion summary===
+
===Items That Need Addressing Before Community-Wide Vote===
<font color="green">[Editorial note: Likely to have errors and/or omissions.  Please revise!  Additional contributions welcome.]</font>
<font color="green">[Editorial note: Likely to have errors and/or omissions.  Please revise!  Additional contributions welcome.]</font>
#Should explicitly enumerate those areas which this resolution fails to address.  [Laurie Zoloth]
#Should explicitly enumerate those areas which this resolution fails to address.  [Laurie Zoloth]
 +
##Gene assembly via synthesized oligos is a viable work-around to gene synthesis. A functional method for screening oligo synthesis orders has not yet been developed (“current best practices” = no action). This should be acknowledged to avoid creating a false sense of security.
 +
##What fraction of synthesis orders is in the hands of this community?
#Best practices should involve safety & security screening at multiple stages including [Brian Baynes]
#Best practices should involve safety & security screening at multiple stages including [Brian Baynes]
-
##Customer screening (''disputed'')
+
##Customer screening (e.g., rDNA protocol, select agent approval) (''disputed'')
##Customer verification (''disputed'')
##Customer verification (''disputed'')
##Sequence screening
##Sequence screening
##Sequence archiving
##Sequence archiving
-
#No specific discussion of how to decide compliance or how to reconcile disagreements. [Sri Kosuri]
+
#There is no statement for possible procedures, consequences, clarification, or dispute resolution of failing a putative screen. -- '''[[User:Skosuri|Sri Kosuri]] 21:02, 23 April 2006 (EDT)'''
-
#Need process for defining "best practices" [Natalie Kuldell]
+
#Need community agreement, beyond default company models, for defining "best practices." For example, what will be method for developing and reaching agreement? Who speaks for the community? How are we to decide? What enforcement/dispute resolution methods is the community embracing?  [Natalie Kuldell]
-
#Need methods for verifying. [John Cumbers]
+
#Can we explicitly employ methods of testing compliance to the resolution? [John Cumbers]
 +
#*[[Synthetic Biology:SB2.0/Biosecurity resolutions/Perhaps a randomized malicious ordering of genes sent to companies to see if they respond appropriately|Perhaps a randomized malicious ordering of genes sent to companies to see if they respond appropriately]] [Cumbers]
#Historical examples/consequences of secondary boycotts should be considered [Ken Oye]  
#Historical examples/consequences of secondary boycotts should be considered [Ken Oye]  
-
#Missing more?
+
#Jan 1 2007 date is arbitrary; we need a specification of path forward up to SB3.0 at least [ [[Endy]] ]
 +
#It is important to remember that the idea is not to design new "best practices" starting from a blank sheet of paper.  (The industry has already given this problem much more thought than the average community member and, in any case, is not likely to heed calls to scrap existing systems and start over.) Rather, it is to close a looophole in which a few companies gain competitive advantage by failing to follow procedures that already exist and are followed by most of the industry.  If people want to describe "best practices" in more detail, the way to do that is to find out empirically what most companies do today. [Maurer]
 +
#Gene synthesis companies are most likely to be "checking" oligonucleotide orders against a pathogen genomic databases by probably BLASTing the oligonucleotide request. Since the score and the hit are dependent of the length of the sequence and the size of the database, a skilled biologist interested in developing a bioweapon could order sequences similar to the pathogen of interest but absent in the database. This issue must be recognized by the industry as one of the MAIN problems. [Willy Valdivia]
 +
#In order to directly address the above issue, it is necesary to develop a RATIONAL, INTEGRATED and INTEROPERABLE  genomic barcode databases covering key regions of lethal pathogens. This information could be accessible ONLY to certified gene synthesis companies and certified members of the scientific comunity (debate is necesary anout way to implement this). However, the generation of genomis signatures and barcodes still challenging considering that less than 3% of GeneBank contains pathogens of the A-C category sequence information [Willy Valdivia]
 +
#The department of homeland security is already funding several efforts for the development of "barcodes-signatures". However, these efforts, fail to recognize the development of reverse eng. and computational technologies that generate possible variations which do not exist in nature, but have the same "lethality equivalence" and overcome filtering and screening databases. [Willy Valdivia]
 +
#This proposal seems unlikely to work in practice given a) the global availability of commercial DNA synthesis; b) largely unregulated access to DNA synthesizers and reagents; and c) the relative ease of making homemade synthesizers [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=507883].  More gene synthesis companies are likely to appear, and perhaps even inexpensive desktop devices, further complicating regulation.  Would energies not be better directed towards low cost biodetection systems to sample genetic flow in the natural environment, which could help detect natural pathogens of all types, plus greatly expand the relatively small base of knowledge on microbial biosystems? [Andrew Hessel]
==A.2 Create and Endorse New Watch-Lists To Improve Industry Screening Programs.==
==A.2 Create and Endorse New Watch-Lists To Improve Industry Screening Programs.==
Improved watch-lists and software tools can make industry screening more accurate and efficient. Members should prepare the necessary lists and tools in time for Synthetic Biology 3.0.
Improved watch-lists and software tools can make industry screening more accurate and efficient. Members should prepare the necessary lists and tools in time for Synthetic Biology 3.0.
-
===Discussion summary===
+
#This is the place where members can exercise leadership by going beyond the "best practices" which already exist and asking what they should be.  [Maurer]
 +
 
 +
===Items That Need Addressing Before Community-Wide Vote===
<font color="green">[Editorial note: Likely to have errors and/or omissions.  Please revise!  Additional contributions welcome.]</font>
<font color="green">[Editorial note: Likely to have errors and/or omissions.  Please revise!  Additional contributions welcome.]</font>
#Should outline procedures by which watch-lists and/or algorithms are developed. [Reshma Shetty, George Church]
#Should outline procedures by which watch-lists and/or algorithms are developed. [Reshma Shetty, George Church]
 +
#What will the watch lists be watching for? [ [[Endy]] ]
 +
#How will the use of watch lists be enforced?  How will watch lists work as synthesis moves to the benchtop? [Andrew Hessel]
==B.1. Create a Confidential Hotline For Biosafety and Biosecurity Issues.==
==B.1. Create a Confidential Hotline For Biosafety and Biosecurity Issues.==
All experimenters contemplating “experiments of concern” should obtain independent expert advice before proceeding. The community should make such advice freely available to all experimenters, including non-members (e.g. hackers) who cannot otherwise obtain such advice from formal university, company, or NIH safety committees.
All experimenters contemplating “experiments of concern” should obtain independent expert advice before proceeding. The community should make such advice freely available to all experimenters, including non-members (e.g. hackers) who cannot otherwise obtain such advice from formal university, company, or NIH safety committees.
-
===Discussion summary===
+
===Items That Need Addressing Before Community-Wide Vote===
<font color="green">[Editorial note: Likely to have errors and/or omissions.  Please revise!  Additional contributions welcome.]</font>
<font color="green">[Editorial note: Likely to have errors and/or omissions.  Please revise!  Additional contributions welcome.]</font>
#Redundancy with Recombinant DNA Advisory Committee or RAC. [Kris Jones Prather]
#Redundancy with Recombinant DNA Advisory Committee or RAC. [Kris Jones Prather]
Line 73: Line 72:
==E. Additional resolutions==
==E. Additional resolutions==
 +
#Upon the uncontrolled physical release of a synthetic biological organism, community members should release all available sequence information and relevant system documentation. [Reshma Shetty]
 +
#Upon construction/publishing/patenting of a biological organism (or system embedded within another organism), consider publishing a statement (or reaffirmation) of recommended (expected) safety and security level.  Also, perhaps a central area to store information on novel organisms and those organisms whose safety or security level change. -- '''[[User:Skosuri|Sri Kosuri]] 02:10, 24 April 2006 (EDT)'''
 +
#An ethics class should be mandatory for all synthetic biology curricula. Besides the "Don't be evil" portion, it could also include more grey areas, such as clinical trials and the issue of competing interests. Case studies would be useful. There's the University of Pennsylvania's human gene therapy experiment gone wrong. [[User:Salis|Salis]] 23:42, 23 April 2006 (EDT)
-
Upon the uncontrolled physical release of a synthetic biological organism, community members should release all available sequence information and relevant system documentation. [Reshma Shetty]
 
</div>
</div>
{{Synthetic biology bottom}}
{{Synthetic biology bottom}}

Current revision

Home        About        Conferences        Labs        Courses        Resources        FAQ       

Overview

This page is for organizing discussions around the discussions to be held at SB2.0 concerning biosecurity and biosafety issues. In particular, the following white paper proposing specific recommendations of action that the community can possibly take:

From Understanding to Action: Community-Based Options for Improving Safety and Security in Synthetic Biology
Stephen M. Maurer, Keith V. Lucas & Starr Terrell
Goldman School of Public Policy
University of California at Berkeley
PDF link

Below you will find text from the executive summary of this white paper as well as comments noted during the MIT town hall on April 21, 2006. (Note that this is slightly different text than that used in the proposed resolutions in the white paper).

Contents


[Editorial note: Depending on the amount of discussion, individual resolutions should be spun out to their own pages.]

Please follow comments with the following text -- '''~~~~''': in order to sign and date your comment

A.1 Insist That All Commercial Gene Synthesis Houses Adopt Current Best Practice Screening Procedures.

It is obvious that as gene synthesis continue to improve; the "dual purpose" of this technology will increase the attention of the biosecurity community. While most gene synthesis companies screen orders for dangerous sequences, a few do not. This gives both community members and outsiders access to feedstocks for both wild-type and genetically engineered bioweapons. Community members should stop doing business with any gene synthesis company that fails to implement current best-practice screening methods by January 1, 2007.

Items That Need Addressing Before Community-Wide Vote

[Editorial note: Likely to have errors and/or omissions. Please revise! Additional contributions welcome.]

  1. Should explicitly enumerate those areas which this resolution fails to address. [Laurie Zoloth]
    1. Gene assembly via synthesized oligos is a viable work-around to gene synthesis. A functional method for screening oligo synthesis orders has not yet been developed (“current best practices” = no action). This should be acknowledged to avoid creating a false sense of security.
    2. What fraction of synthesis orders is in the hands of this community?
  2. Best practices should involve safety & security screening at multiple stages including [Brian Baynes]
    1. Customer screening (e.g., rDNA protocol, select agent approval) (disputed)
    2. Customer verification (disputed)
    3. Sequence screening
    4. Sequence archiving
  3. There is no statement for possible procedures, consequences, clarification, or dispute resolution of failing a putative screen. -- Sri Kosuri 21:02, 23 April 2006 (EDT)
  4. Need community agreement, beyond default company models, for defining "best practices." For example, what will be method for developing and reaching agreement? Who speaks for the community? How are we to decide? What enforcement/dispute resolution methods is the community embracing? [Natalie Kuldell]
  5. Can we explicitly employ methods of testing compliance to the resolution? [John Cumbers]
  6. Historical examples/consequences of secondary boycotts should be considered [Ken Oye]
  7. Jan 1 2007 date is arbitrary; we need a specification of path forward up to SB3.0 at least [ Endy ]
  8. It is important to remember that the idea is not to design new "best practices" starting from a blank sheet of paper. (The industry has already given this problem much more thought than the average community member and, in any case, is not likely to heed calls to scrap existing systems and start over.) Rather, it is to close a looophole in which a few companies gain competitive advantage by failing to follow procedures that already exist and are followed by most of the industry. If people want to describe "best practices" in more detail, the way to do that is to find out empirically what most companies do today. [Maurer]
  9. Gene synthesis companies are most likely to be "checking" oligonucleotide orders against a pathogen genomic databases by probably BLASTing the oligonucleotide request. Since the score and the hit are dependent of the length of the sequence and the size of the database, a skilled biologist interested in developing a bioweapon could order sequences similar to the pathogen of interest but absent in the database. This issue must be recognized by the industry as one of the MAIN problems. [Willy Valdivia]
  10. In order to directly address the above issue, it is necesary to develop a RATIONAL, INTEGRATED and INTEROPERABLE genomic barcode databases covering key regions of lethal pathogens. This information could be accessible ONLY to certified gene synthesis companies and certified members of the scientific comunity (debate is necesary anout way to implement this). However, the generation of genomis signatures and barcodes still challenging considering that less than 3% of GeneBank contains pathogens of the A-C category sequence information [Willy Valdivia]
  11. The department of homeland security is already funding several efforts for the development of "barcodes-signatures". However, these efforts, fail to recognize the development of reverse eng. and computational technologies that generate possible variations which do not exist in nature, but have the same "lethality equivalence" and overcome filtering and screening databases. [Willy Valdivia]
  12. This proposal seems unlikely to work in practice given a) the global availability of commercial DNA synthesis; b) largely unregulated access to DNA synthesizers and reagents; and c) the relative ease of making homemade synthesizers [1]. More gene synthesis companies are likely to appear, and perhaps even inexpensive desktop devices, further complicating regulation. Would energies not be better directed towards low cost biodetection systems to sample genetic flow in the natural environment, which could help detect natural pathogens of all types, plus greatly expand the relatively small base of knowledge on microbial biosystems? [Andrew Hessel]

A.2 Create and Endorse New Watch-Lists To Improve Industry Screening Programs.

Improved watch-lists and software tools can make industry screening more accurate and efficient. Members should prepare the necessary lists and tools in time for Synthetic Biology 3.0.

  1. This is the place where members can exercise leadership by going beyond the "best practices" which already exist and asking what they should be. [Maurer]

Items That Need Addressing Before Community-Wide Vote

[Editorial note: Likely to have errors and/or omissions. Please revise! Additional contributions welcome.]

  1. Should outline procedures by which watch-lists and/or algorithms are developed. [Reshma Shetty, George Church]
  2. What will the watch lists be watching for? [ Endy ]
  3. How will the use of watch lists be enforced? How will watch lists work as synthesis moves to the benchtop? [Andrew Hessel]

B.1. Create a Confidential Hotline For Biosafety and Biosecurity Issues.

All experimenters contemplating “experiments of concern” should obtain independent expert advice before proceeding. The community should make such advice freely available to all experimenters, including non-members (e.g. hackers) who cannot otherwise obtain such advice from formal university, company, or NIH safety committees.

Items That Need Addressing Before Community-Wide Vote

[Editorial note: Likely to have errors and/or omissions. Please revise! Additional contributions welcome.]

  1. Redundancy with Recombinant DNA Advisory Committee or RAC. [Kris Jones Prather]
  2. Should be revised to focus on offering a RAC-like mechanism to the independent synthetic biology community outside of institutions with RACs. [Drew Endy]

B.2. Affirm Members’ Ethical Obligation to Investigate and Report Dangerous Behavior.

Members have an obligation to investigate and, if necessary, report dangerous behavior. Members should affirm this obligation by formal resolution at Synthetic Biology 2.0.

C. Create a Community-Wide Clearinghouse for Identifying and Tracking Potential Biosafety/Biosecurity Issues.

Members who notice potential biosecurity issues have an obligation to share them with the broader community. A central clearinghouse will help the community to identify, track, and if necessary respond to the biosafety/biosecurity implications of a changing technology.

D. Endorse Biosecurity/Biosafety R&D Priorities.

New technologies can potentially reduce current biosafety/biosecurity risks even further. Members should identify, endorse, and urge funding agencies to invest in priority technologies such as safe chasses and bar codes.

E. Additional resolutions

  1. Upon the uncontrolled physical release of a synthetic biological organism, community members should release all available sequence information and relevant system documentation. [Reshma Shetty]
  2. Upon construction/publishing/patenting of a biological organism (or system embedded within another organism), consider publishing a statement (or reaffirmation) of recommended (expected) safety and security level. Also, perhaps a central area to store information on novel organisms and those organisms whose safety or security level change. -- Sri Kosuri 02:10, 24 April 2006 (EDT)
  3. An ethics class should be mandatory for all synthetic biology curricula. Besides the "Don't be evil" portion, it could also include more grey areas, such as clinical trials and the issue of competing interests. Case studies would be useful. There's the University of Pennsylvania's human gene therapy experiment gone wrong. Salis 23:42, 23 April 2006 (EDT)

This site is hosted on OpenWetWare and can be edited by all members of the Synthetic Biology community.
Making life better, one part at a time.


Personal tools