Biosafety Needs to be Adaptable

 

TL;DR

The risk of biological terrorism goes up as technology around synthetic bio gets better, cheaper, and more common. This does not mean nothing has been done. Organizations have changed policies and put resources into preventing and responding to biological threats. There is still much room for improvement. Policies around biosafety need to be able to change quickly to deal with emerging technology.

 

Decreased Costs

So, the cost of printing genomes is going down.

By the end of 2004 the best instrumentation could output about 104 kbp(kilo base pairs) per instrument run. By the end of 2005 the best instrumentation could output about 1014 kbp per instrument run(Mardis, E. R. 2011).

That means the costs are dropping at a rate much faster than Moore’s Law(Wetterstrand KA).

Check out this graph showing the increases in ability to print genomes as Next Generation Sequencing technology spread

mardis

(Mardis, E. R. 2011)

 

New Technologies

Genome compilers are becoming a thing.

Software like TinkerCell, Genome Compiler, and Cello help people design sequences of DNA which could then be ordered from a printing company. Somebody made this handy list of resources in this area.

This is pretty cool. This tech can certainly be used for good. It may have medical or technological use and it might help us better figure out what genes do what things by making the experimentation process easier.

This also presents some problems. With increases in synthesizing tech, we need to be concerned about both known pathogens and designed pathogens.

Traits desirable for making a bioweapon could be combined from several different organisms, potentially making combinations of traits that don’t exist in natural pathogens (Mukunda, et al 2009). Trade-offs that seem to exist in nature between virulence, incubation period, and transmissibility might be avoided in a designed pathogen.

 

It was kind of easy to get that

In an article from 2006 the Guardian outlined how they obtained an altered smallpox DNA sample from a company synthesizing DNA.

This should not have been the case.

A newspaper should not be able to order hazardous genetic material.

Practices have changed since this failure, but it is not clear to me that this could not happen again.

 

Current Printing Safety

Standardized safety protocols are becoming more common.

The policies used by most of the gene synthesis capacity was updated in 2009 by the IGSC (International Gene Synthesis Consortium). It’s great that the general protocols include both screening ordered sequences for known pathogens and screening for potentially dangerous customers, but not all companies synthesizing DNA are part of the consortium. The IGSC represents about 80% of gene synthesis capacity.

Taken from the IGSC screening protocol.

  • All gene sequences ordered from participating companies are screened against a list of known and regulated pathogens.
  • If a pathogen is found by the automatic screening it is reviewed by a human and can be denied, approved, or approved with requirements.
  • IGSC members have minimum screening requirements and additional screening for regulated pathogens.
  • IGSC members also keep records of genes printed and where they were sent for 8 years.

 

Biological Pen Testing

Pen testing is trying to find the failure points and exploiting them to test security. In the case of biorisk, it would mean doing things like trying to get dangerous biological material. Pen testing should be done by professional third parties

I found a couple of biosafety testing and certification services, but it isn’t clear how much bioprinting services do pen testing. They may reasonably want to keep this information confidential.

Pen testing is common practice for information security and should be for biosecurity.

If biological pen testing isn’t standard for bioprinting services, it should be. Companies that print genomes should undergo regular testing that guides safety policy updates.

 

Agriculture as a high risk area

Both the CDC and the FBI are concerned about agriculture as a target of bioweapons.

An agricultural attack seems a lot less scary because it would be killing plants not people, but ab attack on agriculture could still do a lot of harm and would be much easier to pull off.

An attack on agriculture could be done simply by taking infected crops from a country where a particular infection is endemic to one where it is not. For example, infecting a few wheat tillers with stem rust could be enough to cause a pandemic (Wheelis et al 2002). Centralized production and wide distribution of the US food supply means a bioweapon targeting crops could do a large amount of damage (Sobel, et al 2002).

The cost of an agricultural attack could do damage to the economy on the level of billions of dollars. Much of the economic cost could come from sanctions made to prevent crops from crossing borders (Wheelis et al 2002).

Agencies involved in some way in dealing with foodborne outbreaks:

  • US Food and Drugs Administration (FDA).
  • US Department of Agriculture (USDA).
  • Center for Disease Control (CDC).
  • Local and state health epidemiology departments.
  • Public-health laboratories at the local and state level.
  • The Council of State and Territorial Epidemiologists.
  • the Association of Public Health Laboratories.
  • Agencies that have regulatory authority over foods include state departments of agriculture or food-safety divisions.
  • The federal food-safety regulatory agencies.
  • Both state and federal agencies are involved in the investigation of food borne illnesses. If bioterrorism is suspected, the FBI heads the investigation.
  • Public health response to an attack on the food supply involves an epidemiological investigation and a medical response to casualties

(Sobel, et al 2002).

 

Process Improvements:

  • Early detection is extremely important to preventing the spread of plant pathogens, but most farmers, veterinarians, plant pathologists, and agricultural extension agents are not prepared to adequately identify exotic plant and animal diseases. So providing training for this set of people could help catch outbreaks early.
  • Better support for state and regional labs to quickly diagnose plant pathogens.
  • Developing consensus for major agricultural bioterrorist threats and designing specialized response plans.

(Wheelis et al 2002) (Sobel, et al 2002).

 

We should exhibit Proportional Response as new factors in risk emerge

I hope I’ve been able to provide a decent picture of the biosafety landscape. Biosafety has the advantage of many long lasting institutions building infrastructure and plans. This does not mean all work is done. Synthetic biology is advancing quickly and it seems that safety is lagging behind. With each new biological innovation there should be updates to how biosecurity is performed. This is not an easy problem to solve, but implementing process improvements recommended by leaders in biosafety is a good first step.

 

Citations

IGSC(2009)  Harmonized Screening Protocol.

Mardis, E. R. (2011). A decade’s perspective on DNA sequencing technology. Nature

Mukunda, G., Oye, K. A., & Mohr, S. C. (2009). What rough beast? Synthetic biology, uncertainty, and the future of biosecurity. Politics and the Life Sciences

Sobel, J., Khan, A. S., & Swerdlow, D. L. (2002). Threat of a biological terrorist attack on the US food supply: the CDC perspective. The Lancet

Wetterstrand KA. DNA Sequencing Costs: Data from the NHGRI Genome Sequencing Program (GSP) Available at: www.genome.gov/sequencingcostsdata. Accessed 5/2/17
Wheelis, M., Casagrande, R., & Madden, L. V. (2002). Biological Attack on Agriculture: Low-Tech, High-Impact Bioterrorism. BioScience

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Process Mindset

Many people in the rationalist community like to get better at doing things they are averse to, but don’t think should be aversive. CFAR (Center For Applied Rationality) made a technique for it. It’s called CoZE (Comfort Zone Expansion). CoZE seems super useful, and I’m always happy to join in when a group is pushing the edge of their comfort zone. I’ve noticed a couple different mindsets around comfort zone expansion. I will call them goal mindset and process mindset.

Goal Mindset: The person knows expanding their comfort zone is a good idea, they want to have the results of doing so, but comfort zone expansion is an aversive subject in itself. So both the thing they want to become less averse to and the process of expanding their comfort zone are aversive.

Process Mindset:  The person knows expanding their comfort zone is a good idea and they’ve attached the feeling of successful change to the process of comfort zone expansion. In this mindset, each individual thing people work on can still be aversive, but the process of comfort zone expansion is exciting.

I suspect the mindset a person has depends on the number of successful aversive experiences vs the number of unsuccessful aversive experiences they’ve had. Recent experiences or more extreme experiences are probably given greater significance.

I definitely think it’s possible to shift someone from the 1st mindset to the 2nd mindset. I think the best way to do this is to be intentionally put into aversive experiences that are framed correctly and are built to create success.

I made a shift from goal mindset to process mindset in my teens by going to and working for a wilderness school. The instructors took time to find the edges of my comfort zone, got me excited about going over the edge, and brought me back into my comfort zone in a way that made the experience a success in my own mind. This included pushing my physical limits with survival challenges, my people interaction limits through teaching and interacting with student’s parents, and my emotional limits through practice of expressing emotion. I think my own adoption of process mindset came from more intense experiences that ended successfully, making future small CoZE experiences much easier. Here I’ll outline the steps I think necessary for the kinds of experiences that produce a shift from goal mindset to process mindset. I will call these Expansion Projects.

 

Steps for Expansion Projects:

Step 1: Choose a category you want to work on.

Things you might want to work on include getting more comfortable with dancing, spiders, introspection, physical discomfort, silence in social situations, etc. You can choose this yourself, take ideas from others, ask someone you trust to choose a thing for you. It should be something you can commit to doing and will push the limits of your capabilities in whatever area(s) you are expanding.

In my example I agreed to go on a 24 hour survival solo.

Step 2:Choose someone you trust to help you.

Ideally this is someone who knows you well and has a good idea of where your boundaries are. They should be able to take the matter seriously and be willing to push your limits. You also need to be OK with them pushing your limits.

In my example, this was my mentors in wilderness survival and education.

Step 3: Discuss your Expansion Project with them and agree on the conditions.

I think it helps here to set strict conditions of the experience and to commit to ending the experience if you break those conditions. So if you commit to not relying on a particular thing in a situation, relying on that thing ends the experience.

In preparation for my survival solo, I discussed with my mentor what I would bring along. I also made goals for things I would work on within the solo and introspective goals. It was clear that if I left the experience and returned early for any reason the experience would be over.

 
Step 4: Beginning the Experience

Have the person helping you mark the beginning of the experience, remind you of your commitment to doing the thing, and recognize the difficulty in a positive and serious way. Maybe this is a small ritual or short exchange of words. Something that is meaningful to you.

Some words were said before setting out. The tone was serious, there was recognition difficulty and a reminder of the commitments made.

Step 5: Go through the experience

Spending 24 hours alone in the woods was a really good experience. I don’t think just spending 24 hours in the woods would amount to much. I could spend 24 hours in the woods uncomfortable with no supplies and return fine having learned very little, but having the experience framed as a tool to learn things about survival and things about myself (with an emphasis on challenge and commitment) made the experience feel much more powerful.

Step 6: Ending the Experience

The person helping you greets you after the experience, recognizes your achievement, gives you food/emotional support, and helps you reflect and process the experience. I would also recommend spending some time alone reflecting on the experience and what you got from it.

If you are comfortable doing so, I’d recommend talking about the experience in front of some people. This can help because they will recognize your achievement (socially reinforcing the positiveness) and make you better at talking about aversive things and becoming less averse to them.

Upon return, those of us who went on solos were greeted with water, food, and an audience to relay our experience to. There was also more time to introspect on the experience and talk one on one with mentors.

 
Keeping the mindset:

Being framed as it was, I was ready for more such experiences as soon as I was done. While the framing was serious, the successful growth experienced made me want more. The excitement generated by this kind of experience made me excited about challenging myself in the future. I think staying excited about the doing things that are hard and out of your comfort zone is the most important thing for process mindset. Go forth and challenge yourself!