SBPWG:Meetings/May 10 2011

Meeting Notes: May 10th 2011
Tuesday May 10th 6-8pm

Byers Hall Room 211, UCSF Mission Bay Campus [map]

Agenda
0. Welcome & Practices@SynBERC Update

1. Discussion of Proposed Working Group Vision, Goals and Formats

2. Breaking Down Practices v1.0 - Informal Presentations and Discussion

3. Drafting of Topic and Invited Guest List for Future Meetings

4. Discussion of Additional Opportunities for Practices Engagement

5. Next Meeting - Content and Scheduling

Welcome, Update, Goals
Megan Palmer's [[Media:05_10_11_SBPWG_v2.ppt | intro slides]]

Welcome to meeting; update of last meeting

Practices@SynBERC Update: Currently Accepting SynBERC Practices Proposals

Review of working group goal statement: Currently highlights deficiencies and not strengths. Megan to update (done - see v3!)

Two potential formats for this working group:
 * 1. Practices in practices – invite community member to propose address problems, followed by a write-up
 * 2. Breaking down practices – in-depth topic/case discussion, possibly with expert

Decided should ideally do both (number 1 informs number 2, and vice versa), but definitely 2

Additional Goal: creating a list of “Top Ten Gaps (Open Challenges) to Syn Bio”

There may be lessons for us to learn from Synthetic Society, a now-defunct working group started at MIT among early synbio practitioners
 * what was the rationale and driving force behind Synthetic Society?
 * interesting questions and meeting notes on OpenWetWare [here]

Breaking Down Practices v1
5-min presentations from individuals on Practices areas of interest


 * Ownership, Sharing and Innovation- Ryan, Joseph
 * Safety - Robin (could not attend)
 * Security - Mike
 * Ethics - Marlee (could not attend)
 * Philosophy - Reid
 * Communication, Education, Outreach - Danielle
 * Applications - Megan

For this meeting, each leader was asked to plan a 5-minute informal presentation attempting at answering the following:


 * what are new, real challenges that SB poses in this domain? (try to list 2)
 * how might this relate to your current or future work?
 * what case studies might be relevant? (try to list 2)
 * who are people that might help us work through these problems? (try to list 2)
 * can you find articles we might draw upon for background? (try to list 2)

The aim of this exercise was to help us in brainstorming an initial list of potential 'gaps' in synthetic biology practices, and resources to begin exploring them.

(1) Ownership
Presented by Ryan Ritterson

Overview based largely on Arti Rai (2007)

If you create a new organism, how to patent, should you be able to patent?

Currently two methods for protecting intellectual property: copyright & patent Synthetic organisms may fall into both categories. They also replicate, raising questions such as how to we prevent use of “inventions” that drift across the oceans or blow across the fields
 * copyright is intended to protect artistic creation/instance (not functional)
 * patents are supportive of functional elements, not artistic

Many have pointed to flaws of current system, but few have stepped up to say what things SHOULD look like. If we could invent intellectual property protections for biological entities from scratch, what would we want things to look like?

Personal perspective:
 * reasonable protections, not overarching, but provide sufficient incentive
 * want to avoid patent thickets (layered patents), submarine patents (latent)
 * Biology Commons needed? pool of stuff free to share


 * Rettberg believes biological parts should be protected by copyrights


 * Do we need a new third type of protection, or specifically extend copyright/patent to biological entities? Precedent is getting stretched thin, and as laws are extended into areas they weren’t designed for, there may be unintented consequences
 * New laws would have to be created by legislative branch

Some models for protection/innovation:
 * GNU (copyleft) or GPL - free use where derivative works must be free
 * BSD license - source code open, derivatives may be sold (Mac OSX)
 * DMCA (digital music) - (bad example) you cannot decrypt/recreate digital materials (e.g., DVD)

How does this relate to our work?: what property rights do we want? not want? and not violate others’ rights?

Potential speakers on this topic:
 * in-house legal counsel for companies like LS9: if you could reform intellectual property law, how would you do it? how to balance restrictions vs. innovation?
 * Electronic Frontiers Foundation - created to define RIAA and MPAA, enforce GNU - protect both software
 * history of gene patents: violation of the original spirit of the patent law, now related to specific uses
 * industry/commons lawyers, who protect artists’ rights as well as defend music industry


 * A conversation about open commons at retreat could be productive
 * Laws should be revamped ways that protect existing patents
 * What is the cost to industry to do business this way?
 * Stanford open source model - allows researchers to put works directly into the public domain
 * Practices is starting an Innovation and Sharing research program


 * See also paper by Gaymon Bennett at BioFAB on [Open Technology Platforms]

(2) Security
Presented by Mike Fisher

How to walk the line between mitigating risk and not hampering research?

New challenges from synbio:
 * genomes can be easily assembled
 * How should DNA synthesis companies be regulating this
 * Gov’t released guidelines, less stringent than companies'
 * Companies have a vested interest in doing the right things
 * DIY: one-year ann of NY community biology lab (Gemspace)
 * Technology dissemination

Case studies:
 * Wemmer synthesizing polio viris (could he do it again today?)
 * Federation of American Scientists: Case studies in dual use (http://www.fas.org/biosecurity/education/dualuse/index.html) (altho more safety than security oriented)

One possibility: more thorough background checks on researchers in professional way (although this wouldn’t cover the DIY community)

Extra reviews in addition to IRB

Danielle: In dealing with EH&S, she has to re-write every scope. So the review part is tough, but the enforcement part is slack (e.g., announce their visits)

Danielle: Also, use of organisms like salmonella seemed unconcerning/out of scope to IRB

“If you see something, say something”

“The Demon in is the freezer” chapter about mobile Iraqi anthrax units tells story of security challenges

There is a bias toward human therapeutics - human infectious viral vectors

A challenge: Trying to teach biosafety in a way that is engaging, inspiring

If there were an accident/event, what would the synbio community have to do to convince authorities that it’s okay to proceed?

E.g., the chemical industry must prepare for an anthrax attack, but how does it track the DIY community?

Ryan - could be fun and instructive to hide our credentials and try to “red team” the synthesis industry

Reid: We’re constantly imagining short-scale issues, but what about long-term issues? (e.g., underbleaching over many years)

Kevin: Could we improve security (and not create additional work for ourselves) by engaging with IRBs to develop more effective guidelines for emerging threats?

(3) Contextualizing engineering practices with other fields
Presented by Reid Williams

we constantly use metaphors: where do these metaphors break down, and what does that tell us?

What’s unique about synbio, and how can we put that back into the engineering field?
 * one unique characteristic: specific desired behavior using directed evolution without understanding underlying mechanism

There are already a couple examples of biology put back into other fields
 * genetic algorithms
 * enzymatic computation

What can we learn from looking at other engineering disciplines?
 * history and failure - our bias is to look only at recent past, as if engineering builds upon itself in a strictly linear fashion
 * architecture of complexity - what common definition of complexity is useful

Potential speakers:
 * David Mandell (MIT) - looks broadly across disciplines and history
 * speaker from engineering and design, industrial design/engineering

Case Studies
 * Recent engineering milestone: Software code validated to be correct (microkernel unix)
 * Examples of software systems failures: x-ray burns, east coast blackout, flash crash

(4) Communication & outreach
Presented by Danielle Tullman-Ercek


 * There is much incentive for us to educate our stakeholders (e.g., funding, public support, science literacy)
 * Is there something new about synbio? Not sure, but it’s a reason to renew the conversation with the public

Case study #1: nanotechnology
 * Compared to synbio, has the opposite PR problem: People have a hard time figuring out how it can be used, and a hard time figuring out why it might be dangerous
 * Most people have no opinion (or not a negative opinion)
 * But in general, people who don’t understand something fear it

Case study #2: Nuclear technology
 * Education/outreach has been poorly executed in general, esp. in US
 * There’s an association with weaponization
 * From beginning, treated as something dangerous, secretive


 * Regarding case studies, we could spend a lot of time drawing risk parallels, but maybe we shouldn’t
 * We should spend time talking about positive aspects (beneficial applications)
 * Is there a case study of something that is hopeful yet appropriately wary?


 * As a community, we need to figure out best way to communicate this info so as not to set off nightmares or unrealistic promises

Potential speakers:
 * People in participatory technologies
 * E.g., in fields that require sophisticated understanding, consider a model of paying a lay panel learn about and then discuss topic
 * David Guston is a proponent of such models


 * How to put a face on synthetic biology?

(5) Applications
Presented by Megan Palmer. Slides can be found [[Media:05_10_11_SBPWG_Applications.ppt | here]]

New, real challenges that SB poses in this domain Justifying / distinguishing syn bio vs trad genetic eng approaches
 * Abstraction, standardization, composability enabling complex systems engineering
 * Difference in process vs kind (e.g. fast, cheap, safe vs altogether different)
 * Taking advantage of biology’s toolkit (reproduction, evolution, interaction)

Success often evaluated largely by applications, whereas greatest benefit may be cross-cutting technology platforms (i.e. tools)
 * Stated differently, a field is often identified by its artifacts (e.g., artemisinin), but it is sustained by the questions that it asks (e.g., how best can we assemble biological parts)
 * e.g. (SynB)ERC top-down model in which testbeds drive technology
 * Merits of high vs low risk / benefit technologies (Lim e.g. ‘toys’)?

Articulating present reality, future promises and intermediate successes

Relation to current/future work
 * Working to answer these questions is my job :)
 * (Re-)inventing the wheel (challenges in saying we’re different yet the same)
 * Fragmented regulatory landscape; largely application-dependent

Case studies that might be relevant SynBERC’s testbed portfolio - rationale (or lack thereof) as motivating for technology platform development
 * Retired Testbeds: TDB
 * Current Testbeds: MCF, ‘Industrial’
 * Future Testbeds: Cyanobacteria, Stem Cells

‘Syn bio’-labeled commercial applications
 * e.g. biofuels. artemisinin

People that might help us work through these problems
 * Jay Keasling - SynBERC’s model
 * Adam Arkin - Recent white paper on ‘the new bioeconomy’
 * Harvey Blanch (CSTO @ JBEI) - BioEconomics
 * Tom Kalil @ OSTP - Roadmap for Fed Investment in Biotech

Articles (or other resources) we might draw upon for background Innumerable Reviews Touching on ‘Application Landscapes’ and Roadmaps
 * Khalil and Collins. Nat Rev Genetics. 2010.
 * Purnick and Weiss. Nat Rev Mol Cell Biol. 2009.

Synthetic Society Meeting Notes Synthetic Society

Arkin White Paper on ‘The New Bioeconomy’ (MJP needs to ask permission to add)

Other Notes
 * Nita Farrahany (Presidential bioethics commissioner) is now at Stanford. Most of the questions commission felt the field asked were about distant future, so commission intentionally took an optimistic view in order not to unduly restrict ongoing research
 * Success often evaluated largely by applications, but its greatest impact may be in tools (cross-cutting technology applications)
 * example of Pipes-programs vs. discovery-design (Adam Arkin’s model for R&D)
 * Apollo program resulted in many new technologies. steam engine, too

Next Steps
Next meeting: - choose top three things (open challenges/gaps) we’re interested in working on - week right before SB5

Before the next meeting

Go to OpenWetWare Site and:
 * Request addition to listserv
 * Add yourself to members page
 * Upload notes, slides, materials to meetings page
 * Suggest future meeting topics/guests on meetings page
 * Add potential gaps or open challenges to gap page

Tell Others

Let megan know if you’re interested in bay area science festival. Please provide ideas (e.g., game show!)

Harvard group interested in writing white papers on biological design principles -- socially responsible design, taking advantage of biological properties - let megan know