MAKING_LIFE 2014–2015

W 1 Day 5
posted by admin on 15 May 2014

"What I cannot create, I do not understand"    -Richard Feyman

The morning started with a talk on "Synthetic Biology for a Suitable Bioeconomy" and tour at VTT by Merja Penttilä.

VTT is a non-profit research organisation that provides research for both Aalto University and commercial businesses. The talk informed us of VTT's hope to contribute to change for the future, focusing much of its research into replacement for oil, novel technologies, prevention of CO2 Climate Change, industry transition, diverse bioeconomy.

Merja made two clear distinctions for the terms Biotechnology; the use of living organisms or their parts in industrial production, and Synthetic Biology; design of new biological functionalities by man. She led us through a number of examples for potential biological systems that could be used to our advantage including:

- Algae + Sun and CO2 = Energy

- Bacteria that use internal magnets for orientation.

- Tree cellulose - sugar + yeast = Lactic Acid = Plastic

Many of the larger coporations are now turning to biotechnology including Dupont, DSM, BASF, Total, BP and Neste oil for solutions to the depletion of oil, but at the moment the production of waste from the industry is still a problem which needs to be addressed.

For more information on VTT see:

Thierry concludes the morning's discussion with this thought...

“We make patents not money”


One of the lab experiments is to harvest the Sporomusa ovata for turning electricity into acetate.

Markus Schmit

Introduction by Erich Berger:

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)


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


  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


  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:

    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.



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.

After the talk we went to the lab and got enlightened by green fluorescent E.coli - the bacteria we transformed on Day 2.

And we managed to test our DIY illuminator from Saturdays workshop... looking good!

Then onto Paul Vanouse's talk concerning - DNA imaging, microorganisms and restriction enzymes.

Paul Vanouse introduced us to the world of restriction enzymes.

Restriction enzymes cut double stranded DNA at specific recognition sites. These enzymes were discovered in bacteria. They use them to cut foreign DNA (viral) out of their genome, to prevent self cutting the restriction sites in their own genome which are methylated and cannot be detected by the enzymes (see
The recognition sites are normally 4-8 base pairs long and form an inverted repeat. The enzyme cuts DNA either at the same point leaving blunt ends or in a staggered fashion leaving DNA overhangs, the so called 'sticky hands'.
Restriction enzymes are extremely useful in genetic analysis (DNA fingerprint) and genetic engineering (cloning of genes into a vector). After the introduction Paul gave us the challenge to find the cutter of the lambda DNA, a bacteriophage.
The suspects were:

  • EcoRI gaattc

  • HindIII aagctt

  • PstI ctgcag


So we went to the lab bench and started pipetting.

Additionally we transformed some old E. coli with the bead based assembled plasmid from Day 2. And we were looking at the bacteria we collected the day before.

Oron - Protocell

Oron ends the day with introducing protocell and showing us his work exhibited in Science Gallery, Dublin earlier last year.

The Mechanism of Life - by Stéphane Leduc, published in 1911:


Using seductive imagery of mainly diffusion and osmosis, Leduc attempted to prove the mechanistic aspects of life and challenge vitalism, the theory that the origin and phenomena of life are dependent on a force or principle distinct from purely chemical or physical forces.

The Mechanism of Life - After..   by Oron Catts (FI), Ionat Zurr (UK) and Corrie Van Sice (US)

A photo gallery from the day: