SBPWG:Meetings/Nov 15 2011
Meeting Notes: November 15 2011
November 15th 6:30-8:30pm @ UCSF Mission Bay (room TBA)
- Chris Anderson, assistant professor of Bioengineering at UC Berkeley and SynBERC PI, joined the working group to pitch, discuss and get feedback on several prospective biosafety-related projects addressing challenges in biological design, education and management.
- Megan Palmer (Stanford)
- Ryan Ritterson (UCSF)
- Jay Vowles (Stanford)
- Connie Eaves (UCSF)
- Veronica Zepeda (UCSF)
- Andy Chang (Stanford)
- Josh Wolf (UCSF)
- Nathan Hillson (JBEI)
- Kevin Costa (SynBERC)
- Chris Anderson (Berkeley)
- Derek Greenfield (LS9)
- Mike Fero (Teselagen)
- Eduardo Abeliuk (Teselagen)
- Ellick Chan (Stanford)
See slides here
Download audio file here
Notes transcribed by Ellick Chan
Please see the timestamps below to jump to a particular section.
- Working Group Origins at Synberc Spring retreat. Issues covered in practices. Translation, safety, security.
- Recombinant DNA, film
- Discovery Days science festival
- Biotech bootcamp
- Megan intro to Safety issues
- Chris: topics covered
- 1) Containment
- 2) Training
- 3) Assessing risk
Don't want people making smallpox - not directly issue of synthetic bio. No one is working in that area.
Politics of biosafety - economics. Models for risk. Responding to risks. No financial collapse. Actively mitigate risk.
- Making an effective containment strategy - Auxotrophy
- Self-kill device in cell: problems
- containment of org
- codon swapping
- containment of DNA
- Dapd auxotropes
- unnatural amino acid dependence
- self destruct device
- synthetic auxotrophes
- What's the edit distance to something dangerous?
- What is dangerous?
- Lack of a theory to assess danger
- modifications cannot escape by complementation
- cannot revert through natural mutation
- sufficiently inexpensive to use in a bioreactor
- no adverse impact on viability of the cell
- be extensible to industrially relevant organisms
- pick a gene that can't be knocked out or complemented
- small molecule dependency
- allele exchange of new copy with mutant copy
- 300 essential genes in ecoli
- tour based selection system
- another paper based on a similar technique
- design to contain nature. if it breaks out, it may be our fault.
- what's the bar for regulation?
- assay to prove safety/effectiveness
- not our role to set our own bar - someone else should set it
- ques: academic research on rates? chris - industry will say so
- NSF needs curriculum for SynBERC
- Berkeley has classes, but most other institutions don't
- Ethics class?
- Online training module for biosafety
- heart of the problem - no theory on safety
- BUA - Biological Use Authorization -> NIH guidelines
- explosion of genes - no one knows all the risks of them off the top of their head
- risk assessment
- 6 categories
- environmental stability
- potential for nefarious use
- sign off by committee if necessary
- never seen them say no. may give you recommendations
- rarely/never re-review in the case of new identified risk
- quizzes are basically a checklist of thoughts that the student should consider
- megan - does such a flowchart exist?
- biosafety guys aren't that scared of synth bio compared to other risks
- subjective questions
- risk should be considered from factors other than the originating organism
- risk based on features
- if it can be programmed, there should be enough formalization to do so
- formalism simplifies things
- evaluation of risk depends on biologist's perspective
- first attempt
- minimize risk - example in radiation safety
- payload delivery
- risk group is max risk at any stage
- transposon not caught
- chassis can be dangerous
- device can be more dangerous than sum of its components
- substance could be dangerous in a different context
- unintentional promoter can express gene in unknown ways
- accidental recombination
- act ontology
- feature, family, device
- autorepression device
- verification and synthesis
- families - by hand
- features - partially automated
- main issue: how to populate list
- all knowledge in literature, but not enough manpower to pursue
- inference of devices resulting from modifications
- map dangerous functionality to devices
- scenarios of things that are dangerous, but not obviously dangerous
- engineered peanut allergy on salmonella
- curate high level families for danger
- what's the difference between a strain (cell+genome+plasmid mods) and a device(modification, composition of devices can create a strain)?
- strains as combination of devices. complex network.
- look at interactions between added features + original genome
- Peanut peptide combining with transporter
- Megan: is there a theory on what constitutes danger on a given agent. Weaponization of anthrax - what's the special knowledge needed to make it harmful
- 2001 list doesn't consider starting path and possible paths to dangerous agents
- megan: can we classify existing dangerous agents and process of creation?
- megan: how do we hedge our bets in making sure we're doing good work in this area? From DARPA's perspective? Safe chassis development vs automated monitoring vs surveillance vs forensics
- megan: partnerships/funding
- nsf cares about training
- megan: orthogonal genome vs selective growth environment
- orthogonal genomes very academic, but probably not industrializable - whole platform required to make this work
- what are axes of risk?
- danger from synergistic reaction adding to risk
- expert system, review committee
- megan: is there a politically-safe way to get a group to look at these issues? what would pr think?
- most of these are obvious
- is there an arms race for risk assessment schemes?
- ACT theory is open knowledge
- value will be in list of devices to query for risk
- this can be used to find dangerous devices…
- Naming devices and rubric is interesting
- Doing exercise around context of training module
- Siebel foundation event coming up
- New ways to fund biosafety
- OSTP request for info - december 6th
- Leaders in practice, 1 week bootcamp in summer - in DC