MAKING_LIFE 2014–2015

W 2 Day 1
posted by admin on 8 June 2014

Insistent though as Andy was that  it was nothing more than an introduction, it was clear, given the topics mentioned during his introduction - vitalism, astrobiology, organic chemistry, abiogenesis, xenobiology, extromophilia and protocells - that we would be grappling with profound subject matter over the coming 5 days.

Andy's presentation set out how the progression of the next 5 days' activities would proceed from the general to the particular; from pondering issues such as whether clay theory crystals were constitutive of life, towards working with protocells.

In the spirit of providing a passing review of the slew of topics touched by Andy. The presentation started with, not least, the question of life. Indeed, grand beginnings. And matching the profound realms, a tragic story - Andy started his presentation by showing a painting by Paul Gauguin entitled  D'où Venons Nous / Que Sommes Nous / Où Allons Nous -  which roughly translates to English (if such feat is possible) Where Do We Come From? What Are We? Where Are We Going? The painting provided much inspiration to his childhood teacher Bishop Dupanloup. A sombre story hovers over the painting. Gaugin felt compelled to try and provide an answer to the questions alluded to in the title, which in turn led him to attempt suicide short after finishing the painting. Without succeeding, he went on to die later of natural causes.

More profound and difficult answers were to follow. Andy went on: Are there other biologies? What are possible future biologies? This touches on notions of Astrobiology and extremes. A working definition of astrobiology is that it seeks to understand the origin of the building blocks of life, how these biogenic compounds combine to create life-like affects - and is affected by the environment from which it arouses. Finally, it is aimed at understanding where and how life expands beyond its planet of origin.

In short, astrobiology is an exploration of the origins of life, "The more we understand life on earth the more we can see the possibilities beyond". However, to be able to consider the extremes and possibilities, we need first to study the what, why and the how of life. Thus, Andy ceremoniously declared, this edition of Making_Life workshop 2 is to be structured in two parts:

Session 1: Origin and Extremes
Session 2: Encapsulation and Protocells

At this point, a number of theories and topics were introduced, which will prove to be the backbone (a not-so-gratuitous biological metaphor) of the days to follow. A curation in no particular order. There was mention of Clay Theory by Graham Cairns-Smith, which creates a bridge between inorganic compounds and life itself through clay crystals and their self-replication in solution. Conceptually linked, Organic Chemistry falsified the hypothesis of vitalism, which involved an invisible life force which was thought to imbue life into matter. Fast forward in history, the Miller-Urey experment set out to simulate prebiotic conditions of earth to explore the possibility of organic matter arising from inorganic compounds. Artist Adam W. Brown and scientist Robert Root-Bernstein have replicated the experiments with variations of setups and have been able to attain organic compounds.

To give a sense of what is to come, more concepts were mentioned. In fast succession: abiogenesis, RNA worlds, xenobiology, non-natural biologies, novel biochemistries, origin of life theories, genetic firewalls, novel lifeforms, extremophiles.

Moving on from a highly philosophical exploration of life, the principal theory dump we received was courtesy of Markus Schmidt, who has joined our working group as a participant (Markus, you might remember, delivered a comprehensive overview of the disciplines which comprise Synthetic Biology at the last Making_Life workshop).

Markus started by presenting three closely related topics which are, more often than not, interchangeable in the scientific context: xenobiology, exobiology and astrobiology. The subtleties, however, come from their etymology. Xenos is used in Greek tradition, from Homer onwards, to denote stranger, enemy or stranger. Exo is used as a prefix that alludes to something which comes from the outside. Finally, astro makes reference to celestial objects and outer space.

With these nuances in mind, Astrobiology deals with the study of the potential, origin, evolution, distribution, and future of life in the universe, which also includes extraterrestrial and terrestrial life. Exobiology is similar to astrobiology, yet it narrows its range of action to specifically cover search of life beyond Earth and the effects of extraterrestrial environments on living things. Xenobiology, conceptually related, is defined as biology based on foreign chemistry.

Markus then served us with an assortment of concepts central to the mission of Xenobiology, namely creating new forms of life with different biochemistry and genetic code to that found on earth. First there is the need for a radically new genetic material made of XNA, which stands for an alternative genetic polymer not found in nature, and which makes use of a new set of (xeno) nucleic acids. In a near homograph seemingly designed to cause confusion, there is also xDNA, which uses the traditional DNA with an enlarged base pair structure.

A number of concepts derive from these two possibilities. For instance, there is the work on novel polymerases and ribosomes, which allow for the replication, transcription and translation of the new set of nucleic acids (XNA). Also, non-canonical amino acids provide an extended repertoire for the construction of proteins.

These emerging areas hint at the artificial evolution of genetic code, with extended possibilities for the creation of novel synthetic organisms. One such possibility is, for instance, the creation of a stepped evolution process, in which components are slowly evolved and transformed onto another. This is reminiscent, Markus suggested, of the OULIPO poetic techniques. The Ouvroir de Littérature Potentielle, roughly translated as Workshop of Potential Literature, explores literary creation under pre-established structural constrains. For instance, narratives are written such that none of the words use letter E.

Ramping up physical activity quite dramatically and in a departure from scheduled proceedings, the afternoon was spent constructing Winogradsky Columns, curious devices created to construct cultures of multiple microorganisms. The contraption mixes sand and mud with sources of carbon and sulfur. After several months of incubation in sunlight, it provides a gradient of aerobic-anaerobic activity. Finnish winter might widen the incubation time though.

To assemble the columns, it was necessary to source the base components from the grounds nearby. One group fetched mud from the shoreline, and another from a nearby pond on the Aalto University campus. The columns will hopefully be the first of many hermetically sealed ecosystems constructed during this workshop.

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As both Andy and Erich noted, these works will be the more ambitious experiments we have attempted so far in this time frame.

The last session of the day was our attempt at creating a chemical garden, which is an experiment involving solid metal salts in an aqueous solution of sodium silicate (waterglass). This results in the generation of crystals which, as the name promptly suggests, grow in a plant-like structure. Very interesting results in the pictures.

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A couple of projects elaborating on this. First, Roots installation by Roman Kirschner,  and Phantom Lucid Messenger by Herwig Weiser.