If Microbes begat Mind

From Microbes to Mind Book jacket:
S A McNamara
This workshop series on the creative process in science looks at how scientists and cross-disciplinary teams tackle ultra hard problems on the frontiers of science, showing the role that design thinking plays in their process. We zoom in on intertwined grand challenges, where finding clues in one domain can offer clues in others:
  • what artificial life simulations reveal,
  • synthesizing a living cell,
  • debating how the origin of life on Earth occurred,
  • hypotheses about the evolution of mind, and
  • exploring how design enables scientific discovery and technology innovation.
These workshops explore how scientists apply design methods to come up with hypotheses for hard problems. Extending debates and questions raised in Zann Gill’s book, If Microbes begat Mind, DV records of these brainstorming sessions allow us to see how design thinking enables cross-disciplinary problem-solving. Better understanding of the dynamics of discovery and innovation aims to improve support for cross-disciplinary teams.

  From Games to Apps:
Artificial Life Challenges

past event — University of Indiana
Bloomington, Indiana


ALife animation: Lightcycle

At the ALife X conference a lively international group with scientists from the UK to Italy, from Spain to New Zealand, debate what ALife can contribute to science and technology, brainstorming concepts for competitions. The driving questions:

  • What, in your opinion, are three key unanswered questions that ALife may someday answer?
  • What significant challenges/ competitions would you propose where ALife models could make a unique contribution toward answering these questions (or relevant sub-questions)?
  • For ultra hard questions, what benchmarks would you propose — significant achievements enroute to the “golden fleece”?
  • How do you think competitions/ challenges in each of these domains should be structured?
  • What do you see as the most important implications of your proposed challenge for science and technology?

Competition challenges proposed: Evolving a Robot Brain, controller for a robot to accomplish defined tasks, combating evolution of drug resistance by viral or bacterial agents (e.g. HIV), and “The Evolution Prize.”

The DV record captured in the June 4 session, and subsequent interviews with key players, is the first step toward developing a DVD to observe cross-disciplinary design brainstorming on this topic. We’ll select from among the ideas that surface the most promising to develop when we turn this raw material into a DV segment, working with Mark Bedau, Editor-in-Chief of Artificial Life (M.I.T. Press Journal) on an associated written publication.

  Design Challenges Harnessing C-IQ:collaborative intelligence, emergence & complexity

past event — International Conference on Complex Systems
Marriott Boston Quincy, Boston, MA, USA

Discussion of ways to harness C-IQ to conceive and support design challenges. Competitions are Petri dishes to culture and study C-IQ, harnessing “empty constructs” that enable implicit ideas to emerge and become explicit as convergent process tracking observes the collaborative dynamics. Collaborative intelligence embeds emergent principles into interactive frameworks for decision support, e.g. collaborative intelligence prompters, recommender systems, and semantic meta-tagging.



Animation: Jared Schiffman
  Searching for
Extremophiles, the Limits of Life

From abandoned mines to Yellowstone geysers, from dives deep sea vents to theorists using their computers to study complexity and information theory, the theory of limits is honed by scientists in search of the limits of life.

1. Yellowstone National Park: terrestrial analog studies, such as this search for extremophiles. 2. “Ox-eye”: the famous landmark for astronauts in the Mauritanian desert caused by sediment from primeval ocean being pushed up to the Earth’s surface. 3. Blanca: tropical storm. 4. A mission to a deep ocean vent.

The term “extremophiles” is the name given to the organisms (mostly bacteria and archaea) living in places that are physically and chemically extreme (from our human perspective). Their habitats include boiling mud of geothermal hot springs, super-heated waters of submarine hydrothermal vents, frozen soils of Siberia, sea-ice of the arctic, extremely high pressures at the bottom of the deepest parts of the oceans, and a variety of places where the local chemistry would be instantly toxic to human beings. Extremophiles are adapted to these habitats, and would die in habitats that we find hospitable.

1. Chris McKay at an ice hole, Antarctica. 2. Jonathan Trent on an Astrobiology expedition to Kamchatka, Siberia. Inside the Mutnovski caldera. 3. Nathalie Cabrol at the summit of the volcano Licanbur in the Bolivian Andes, where an astrobiology team did field work, finding extremophiles at Laguna Verde (the highest lake in the world). 4. Underwater diving training at Lassen (2500 m).

Extremophiles known as thermophiles live in hot springs (>50°C); they are metabolically “frozen” when they are cooled to what we consider a comfortable temperature. Extremophiles known as psychrophiles grow at temperatures below 20°C and are able to grow at 0°C; they are “cooked” at our body temperature (37°C). Extremophiles known as piezophiles or barophiles live at the bottom of the deepest parts of the ocean at >1,000 atmospheres pressure. They die rapidly when decompressed to one atmosphere. Extremophiles known as halophiles live in waters saturated with salts. They burst in fresh water. Acidophiles thrive in concentrated acid (pH 0.5) and are destroyed at neutral pH. Other extremophiles are specifically adapted to live in areas with high levels of radiation, concentrated toxic chemicals, a paucity of nutrients, or a scarcity of water. Taken together, extremophiles represent the ingenuity and versatility of evolution to exploit energy sources and adapt to harsh conditions.

Our knowledge of extremophiles on Earth continues to expand as we explore more remote and seemingly inhospitable environments using advanced technologies. Molecular probes have revealed that conventional microbiological methods provide us with information about <1% of the diversity of organisms in most habitats; i.e. over 99% of the organisms have yet to be described and characterized. Molecular techniques and advances in microscopy and sampling procedures provide tools to discover the more extreme extremophiles and to understand the molecular basis of their existence. In return, extremophiles provide macromolecules and inspiration to address fundamental questions in biology, biotechnology, and nanotechnology, such as

  • What are the physical and chemical limits of life on Earth?
  • What molecular adaptations allow living systems to inhabit extreme environments?
Extremophiles have inspired scientists from conceiving new drugs for the pharmaceutical industry to developing new ways to address environmental pollution. How can we apply what we learn from extremophiles to important problems in biotechnology, nanotechnology, and planetary protection?
  Unraveling clues to
The Origin of Life

The Origin of Life is a Rosetta Stone, requiring translation and integration of findings in a range scientific disciplines and demonstrating the role design methods play when scientists tackle hard, cross-disciplinary problems.

A range of theorists have examined the origin of life from different perspectives: from Jack Szostak, whose lab at Harvard studies the synthesis of precursors of a living cell, to Stuart Kauffman, theoretical biologist and complexity theorist, to Graham Cairns-Smith (clay theory of the origin of life) and Peter Ward and Donald Brownlee (“The Rare Earth Hypothesis”). Perplexing questions drive our search for clues to the origin of life:

  • Was life a chance event or a foregone conclusion? Is the fine-tuning that favors life on Earth a coincidence or a clue?
  • Did life’s rules govern its origin? Did life invent its rules? Or both?
  • Did life start, and evolve, solely by random mutation and environmental selection? Or were other principles at work?
  • Beyond the extremes of Darwinian Blind Chance and Intelligent Design, is there a “third option”?

1. Origins of life and limits of life studies overlap, since the extremes of life provide evidence of how life might have endured space travel or originated in the extreme conditions on early Earth. Extremophile bacteria Deinococcus radiodurans (D. rad) can survive extreme levels of radiation, dehydration, extreme temperatures, and exposure to genotoxic chemicals. 2. Tubeworms in the the boiling water of thermal vents are home to bacteria, which thrive at these temperatures and may provide clues to the origin of life. 3. Stromatolites survive as our earliest fossil record of life on early Earth some 3.8 billion years ago. 4. Simulations of cellular proteins M2 protein in a membrane. Through simulation experiments, Andrew Pohorille’s group studies membrane behavior. 5. The Fruiting Body is one of the most primitive examples of collaboration; one-celled organisms are attracted to form a community, which generates this fruiting body.

Astrobiology integrates many disciplines and so is an ideal testbed for cross-disciplinary scientific and engineering collaboration. Geologists study how the Earth evolved and when it might have had the constituents for life. Paleontologists examine the fossil record. Chemists form hypotheses about what kind of chemistry might have made the leap from non-life to life and how that process might have occurred. Astronomers seek other planetary systems where life might exist.

Biologists look at replication and metabolism in biological systems and imagine what their precursors might have been. Computer scientists construct simulations to see what emerges from artificial evolution in the ecosystems they build. Physicists wonder if the key to life's origin lies in the physics of far-from-equilibrium systems, or in that pervasive force that played a key role in forming our universe - gravity. Newer sciences, such as information theory and complexity theory, explore the origin of life from their theoretical perspectives, harnessing tools like cellular automata and artificial life. And this only samples the surface.

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