Special workshop: Earth, Life and ALIFE

Full day, Friday 27th

Organizers: Nathaniel Virgo, Alexandra Penn, Matthew Egbert, Stuart Bartlett, Takashi Ikegami

Through the support of ELSI ― the Earth-Life Science Institute here in Tokyo ― we have a special workshop on Friday to build new collaborative interactions between Artificial Life and researchers in the life sciences and origins of life, as well as discussing the future of ALIFE, beyond AI.

The central themes for the workshop are interactions between life and its environment; how emerged and evolved; building and learning from synthetic living systems, and future possibilities and challenges for Artificial Life as a field. The workshop will continue on Friday afternoon and will end with a short talk from Takashi Ikegami and a discussion on the themes of the workshop and of the ALIFE 2018 conference.

Schedule Outline

Session 1: ALIFE and the origins of life

Friday morning, 11:00 to 12:15

Irena Mamajanov, Shawn McGlynn, Rudrarup Bose, Tom Froese

Session 2: Synthetic and Artificial Ecologies

Friday afternoon, 14:15pm to 15:30

Erik Hom, Steen Rasmussen, Stuart Bartlett

Session 3: The Post-AI Future of ALIFE

Friday afternoon, 16:00 to 17:15

Takashi Ikegami, Nicholas Guttenberg, discussion

After this we will decamp to a drinking establishment!

Detailed Schedule

Session 1: ALIFE and the origins of life

Friday morning, 11:00 to 12:15

Life is a complex, history-dependent self-producing system. But how did it come to be constructed in the way it is, and how was it shaped by its environment? Are the molecules of life determined by chemistry or by history, or both, and how can we use phylogenetics and information theory to probe the deep past? How can ALIFE help to answer these questions?

1. 5-minute Introduction: The origin of life as an ongoing process

Nathaniel Virgo

2. Rocks to Life: Messy Chemistry Approach to Evolution

Irena Mamajanov

The ultimate goal of any origin of life researcher is to build a model that takes into account all plausible Early Earth geological conditions and the coupled chemistry and distills the information to arrive at a plausible theory of the life’s emergence. Currently, we do not have enough data to build a model. One approach to fill in the gaps is to study relevant chemical and geological processes separately. Since the range of possibilities is vast, this “clean” approach is unrealistic. Systems science would cover more ground and tackles more prebiotically realistic processes. The “messy chemistry” research framework covers theoretical and experimental modeling of systems-level chemical evolutionary reaction networks.

3. How much can we learn about ancient cells from sequence analysis?

Shawn McGlynn and Sarah Berkemer

A longstanding goal is to apply molecular phylogenetics to understanding ancient physiological and evolutionary states. With the current explosion of molecular sequencing data, it is a good time to consider how far back we can peer with the comparative molecular lens, and ask if we can understand life in its nascent years. A standard test for inferring ancient genes is to analyze phylogenetic branch positions and determine if a gene separates the archaea and the bacteria, but this is well-known to be cluttered and difficult because of phenomenon such as horizontal gene transfer and non-orthologous displacement, making inferences difficult. In this presentation, I will give an overview of recent work in this area, and also present new analyses which aim at relating inter-domain transfer to alignment sequence entropy. We find that sequence plasticity viewed through the lens of information entropy varies between functional groups of proteins and also within groups. Moreover, interdomain gene transfer can be related to sequence alignment entropy. These findings will be discussed in the context of inferring the characteristics of the most ancient cells.

4. Adaptive properties of amino acid alphabet and its subsets

Rudrarup Bose

The standard alphabet of the 20 genetically encoded amino acids is considered to have been selected during early evolution from a larger pool of α–amino acids based on its coverage of the chemical space. Chemical space is here defined by charge, size and hydrophobicity, leading to 6–tuples representing coverage, which is composed of range and evenness in these three physico–chemical properties. We summarize findings of previous studies on the adaptive properties of the 20 encoded amino acids and show how we extend these computational experiments to subsets of the standard alphabet.

5. An artificial life approach to the origins of the genetic code

Tom Froese

A growing number of artificial life researchers propose that making progress on the problem of the origins of life requires taking seriously life’s embodiment: even very simple life-like systems that are spatially individuated can interact with their environment in an adaptive manner. This behavior-based approach has also opened up new perspectives on a related unsolved problem, namely the origin of the genetic code, which can now be seen as emerging out of iterated interactions in a community of individuals. Thus, artificial life demonstrates that the dominant scientific strategy of searching for the conditions of Darwinian evolution should be broadened to consider other possibilities of optimization.

Session 2: Synthetic and Artificial Ecologies

Friday afternoon, 14:15pm to 15:30

Synthetic Ecology builds multi-organism assemblages from scratch, often treating organisms as modular components, while wet ALIFE builds life-like systems from chemistry. But how can we understand and take advantage of the emergent properties and interactive nature of living systems? Finally, we discuss how a common understanding of biological emergence can draw connections between astrobiology, ALIFE, the planetary sciences and AI.

1. Synthetic Ecology.
Erik Hom, University of Mississippi

Biology is undergoing a microbial revolution that is facilitating how we frame the search for fundamental rules of life. I will share some lessons learned from our work in the young field of synthetic ecology, and offer my perspective as we “grope our way” forward towards a more predictive framework for understanding and instantiating new microbial ecosystems that are ecologically and evolutionarily stable.

2. Wet ALIFE.
Steen Rasmussen, University of Southern Denmark, Santa Fe Institute

Steen Rasmussen was one of the founders of the Artificial Life field in the 1980s. His main research effort over the last 15 years has been to explore, understand and construct transitions from nonliving to living materials.

3. The Philosophical Overlap between ALife, Origins of Life, Astrobiology and Artificial Intelligence
Stuart Bartlett

In this talk I will discuss the complementary nature of the different forms of the emergence problem and how ideas from multiple disciplines could revolutionise our understanding of natural and artificial worlds. Neuroscience and AI have made great strides in understanding the nature of learning, stochastic thermodynamics and molecular biology have opened our eyes to microscopic means for manipulating and storing information, and the fields of geo-, bio- and artificial chemistry have helped elucidate the characteristics of complex reaction networks. With the growth of knowledge and theoretical and experimental tools, we are now primed to construct a rigorous understanding of the spontaneous emergence of open-ended learning systems, i.e. life and intelligence.

Session 3: The Post-AI Future of ALIFE

Friday afternoon, 16:00 to 17:15

We are entering an age of big data and deep learning. We can easily expect more to come! What insights can be gained from the exponential growth of new computational platforms about the central questions of Artificial Life? Can new results in AI, including big data science and VR, inform us about and developing theories on the origin and evolution of life, or the nature of mind? How can we update our understanding of evolutionary systems with new concepts?

This last session of the conference will feature talks by Takashi Ikegami and Nicholas Guttenberg, and a discussion session will bring together the central themes of ALIFE 2018 and discuss future possibilities for our field.