MAKING_LIFE 2014 - 2015

Schmidt
Synbio and technology bio-security/risk assessment
posted by sarah on 16 March 2016

Markus Schmit


Markus Schmit works in the company named BioFaction which mainly is about risk assessment in biotechnology. He also runs the BioFiction film festival. He had an exhibition called Synth-ethic in Vienna in 2011.

BioFaction is generally involved with the risk assessment of emerging new technologies, especially biotechnology. At the same time, the company also does science communication and public engagement, as well as art-science collaboration.

In the history of science development, we go through the phases where we observe, analyse, and synthesise the field of study. For example, Physics and Chemistry both have reached the stage that we are capable of synthesising things in the way we want. On the other hand, we are just starting to go into the synthesis phase in Biology.

Take engineering for example, we first observe birds, then we try out wings, and eventually we are capable of building airplanes.

The following are the engineering principles:


  • Standardisation

  • Modularisation

  • Hierarchies of abstraction

  • Design and fabrication

  • (Design -> Test -> Debug)


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Markus then introduces a few directions which will be the next waves of major topic in Synthetic Biology:


  1. DNA Synthesis

    1. Design, synthesis and assembly of Mycoplasma mycoides’ 1.08 Mbp genome

    2. Biosecurity: Synthetic virus


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  2. DNA based biological circuits

    1. Creating standardised bioparts

    2. Engineering systems – in risk assessment of a Transgenetic Organism it is always based on the host and the donor. In a synthetic organism, it’s more complex, then what’s the risk assessment? It’s yet unsolved . So a safety standard is required.

    3. In Do It Yourself (DIY) Biology **** Question from Oron: Why would you think artists sitting in the lab will be closer to DIY Bio than engineers in the university? If we are a bunch of engineers with no biological backgrounds, will you treat us the same? Andy: How would you associate DIY Bio as hobbyists then? Markus: Yes, we will treat the engineers like the artists. – Markus references to his article on EU DIYBio.

    4. DIYBio in the EU is more aware of biosecurity

    5. DIYBio Code of Ethics Europe


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  3. Minimal Genome – to make a genome as small as possible to be used as a chassis, reduced complexity

  4. Protocells – the question of from non-living to living matters

  5. Xenobiology – use atypical chemical reactions

    1. Code engineering – e.g. creating a different genetic code system

    2. non-canonical Amino Acids (ncAA)

    3. Proteins with ncAA

    4. More letters to the genetic alphabet (e.g. four codons forms a set)

    5. New base pair in vivo – using e.g. XNA GNA TNA HNA into ATCG. Reference: http://www.ncbi.nlm.nih.gov/pubmed/22704981

    6. How to improve safety through SB biosafety engineering?

    7. Conventional genetic safeguard strategies – only been theoretical, because sometimes nature finds it’s own way

    8. Horizontal Gene Transfer (Risk)

    9. Desulforudis audaxviator – very successful bacteria that has horizontal gene transfer. Monoculture. In Africa. It lives completely on its own. Found in gold mine. Having horizontal transfer from other bacteria until it can completely survive by itself.

    10. Anastomosis – web of life. This is a new model of organism evolution, where evolution is not a ‘tree of life’ with one origin, and many parallel strands, but a web where different species transfer and evolve their traits between two different strands.


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Q: Why is there no question about bio-weapons?

A: There is biosafety and biosecurity. Biosecurity is intended for misuse (bio weapons). In the US there’s biodefence. The question is do we know everything related with biosafety, biosecurity?

Q: About the bio-firewall.

A: A metaphorical idea from information technology. E.g. horizontal gene transfers.