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IPA@IAS

Interdisciplinary Perspectives on Abiogenesis at the Institute for Advanced Study


How can we distinguish evolvability from gradient descent in the origin of life?

[by Nicholas Guttenberg]

Our 23rd IPA@IAS lunch took place on March 20, 2014, with Nicholas Guttenberg starting the discussion; Nicholas wrote these notes.

Here is the abstract that Nicholas sent out before the meeting:

When looking at modern organisms, we have a good deal of understanding about how to describe their evolution at a fairly sophisticated level. However, when looking at systems for which individual organisms may be ill-defined, and for which the information-carrying structures may not be as cleanly separated from the organism's functionality, the picture becomes much murkier. If the inherent landscape of replication of information is itself very rugged (e.g. as the process of carrying forward information is initially emerging), then to a great degree there is an ambiguity between something which is simply going towards some steady-state and something with the flexibility of an `evolvable' system - one that can respond to various pressures. I would like to discuss possibilities for pinning down this distinction, so that we can better understand how `evolvability' itself first emerged.

There were a number of initial discussions related to the MOL weekly meeting that had happened that morning and the Category Theory workshop. After those discussions, we segued to a particular analogy Piet brought up - the difference between a river flowing down a mountain and the behavior of living organisms. The idea being that somehow, intuitively, there's a difference in the sorts of rules one would write down to describe the river and the sorts of rules one uses to describe the organism (even if they obey the same physics microscopically).

We picked this apart in detail, as the differences become a lot less obvious when you consider that there are many analogues for biotic processes in abiotic systems. For example, the river has a form of memory - if you take a short segment of the river, the location of the flow acts as a memory of uphill branching choices, which naturally arises from conservation of mass. There is also a form of 'selection', in that the most downhill paths are amplified by the natural dynamics of the water, and variation in the form of fluctuations in the flow and so on. So on the face of it, the river has all of the components usually ascribed to Darwinian Evolution - replication, selection, variation.

We discussed ways to measure the difference, or whether there was a difference. This covered comparing population models to particles in equilibrium and looking at the question of ergodicity breaking. In a population model, if one moves the fitness optimum, the entire population distribution changes (because it is set by mutational flow away from the optimum). If on the other hand you move the optimum of an energy landscape in an equilibrium system, it only changes the occupancy of those states whose energy you changed (up to a normalization factor). Furthermore, the information stored by a biological system is combinatorically large compared to the number of organisms - a river can sample the entirety of the mountain surface when it emerges from rainfall, but an evolving species cannot sample all possible genetic sequences.

Present were:

      Jeff Ames, Rutgers University, New Brunswick
      Nicholas Guttenberg, University of Oregon, Eugene
      Piet Hut, IAS, Princeton, and ELSI, Tokyo
      Tim Hutton, Derby, UK
      Koichi Nakamura, Tokyo University, Tokyo
      Hayato Saigo, Nagahama Inst. of Bio-Science and Technology, Nagahama, Japan
      David Spivak, MIT, Cambridge


The Question of life’s Origins: conflict and opportunity in the Physical-Chemical Sciences -- how to find the way forward?

[by George Cody]

Our 22th IPA@IAS lunch took place on March 13, 2014, with George Cody starting the discussion; George wrote these notes.

Here is the abstract that George sent out before the meeting:

Interest in the origins of life as a physically viable endeavor arose principally because of Harold Urey’s strong support of his chemistry graduate student - Stanley Miller and the famous spark discharge experiments. These experiments yielded, "apparently spontaneously", products that appeared biochemical. It is essential to understand that these data arose at about that the same time that biochemistry began to arise as a scientific field in its own right (before understanding of DNA). Somewhat simultaneously, members of the physics community began to consider the problem of life’s origin as a question worthy of consideration (e.g. Schrödinger and later Dyson). [Note. I provide the immediate disclaimer that I am not a science-historian - so historians are requested to chime in]. As a scientist active in in this field seriously for some time, I would submit that the conflict between physics and chemistry has artificially created barriers to the solution of one of the most compelling scientific problems. So how to move forward?
As an experimental chemist, I believe that chemists focus too much (regarding OOL) on detailed mechanism and yield. This focus on high yield feeds back on to questions of chemical necessity, i.e., conditions that yield a chemical product, must therefore be important to the problem of the Origins of Life. This view is in my view a problem as it appears to me that any synthesis scheme that provides high product yield also restricts chemical-reaction space -too much constraint hinders solution- was the OOL sloppy? Or highly refined chemical space? This places scaling into the equation - The scaling laws of OOL is an open area.
In my view a purely chemical approach will not succeed: if yield dictates scenario then one ends up with multiple scenarios to accommodate various products -this problem is not my idea- this goes back to Gustaf Arrhenius (and perhaps before), either way it requires scaling constraints and connectivity constraints. Yet, at the end of the day, life emerged on this planet (or some where) and chemistry relevant to life’s origins had to occur spontaneously. Ultimately, as a chemist I believe that physics will solve the origins of life question, but physicists will require clear-cut boundary conditions that chemists and geologists will ultimately provide. As so many organizations clamor for "interdisciplinary science", the OOL question is the "poster child" for interdisciplinary science.

The first topic that we discussed was the question that George brought up: "if you didn't know anything about the Earth, and you would look at the solar system, the Earth would be the last place to look for life". The reasons are various: the Earth doesn't have much carbon; it is a highly differentiated body, and on the surface there are many minerals that don't exhibit catalytic activity towards any interesting chemistry; water is present, but in itself is detrimental to biochemistry. But water may save the day, in enabling plate tectonics, which in turn creates a dynamical disequilibrium situation that has been in existence for billions of years, which may well be a signature of a living planet.

We also got into the subject of chemistry of primitive solar system objects like comets and carbonaceous chondrites. After a broad introduction to the topic, including radiogenic heating as a way to produce life-conducive environments, warm and wet.

A third topic linked all this together: for life on Earth to emerge, one had to first have a dynamic organic reaction network. A key there is to have a network that regenerates active compounds. We see evidence of such a network that was operating within the interiors of primitive bodies. This provides us with some guidance as to specific environments that may have been similar on Earth.

Many other topics were touched upon, such as X-ray absorption near-edge structure spectroscopy as used for thermometry of primitive bodies, and the history of origins of life theories spanning from the Miller-Urey experiments up to Günter Wächtershäuser's work.

Present were:

      Jim Cleaves, ELSI, Tokyo, and IAS, Princeton
      George Cody, Carnegie Institution of Washington, Washington, DC
      Douglas Duckworth, Temple University, Philadelphia
      Vera Gluscevic, IAS, Princeton
      Nicholas Guttenberg, University of Oregon, Eugene
      Piet Hut, IAS, Princeton, and ELSI, Tokyo
      Tim Hutton, Derby, UK
      Laura Landweber, Princeton University, Princeton
      Cara Magnabosco, Princeton University, Princeton
      Omer Markovitch, Weizmann Institute, Rehovot, Israel
      Kinnari Matheson, Princeton University, Princeton
      Matteo Monti, University of Bologna, Bologna
      Tim Morton, Princeton University, Princeton
      Ximo Pechuan, Albert Einstein College of Medicine, New York
      Cameron Smith, Albert Einstein College of Medicine, New York
      Ed Turner, Princeton University, Princeton


A view along the journey from inanimate matter to life

[by Jay Goodwin]

Our 21th IPA@IAS lunch took place on March 6, 2014, with Jay Goodwin starting the discussion; Jay wrote these notes.

Here is the abstract that Jay sent out before the meeting:

Life is characterized in no small part by its self-organizing behaviors, determined at the molecular level via Central Dogma - the conversion of digitally-encoded genotypic information into analog-structured phenotypic manifestations - as influenced by its immediate environment. Somewhere along the historical journey from a simple prebiotic chemical inventory to life as we understand it evolutionary thresholds of functional and operational complexity were crossed. Working from molecular species related to these simpler prebiotic chemicals, we are studying the potential for self-organizing properties of dynamic chemical networks, to illuminate how these evolutionary thresholds came about, and what that might tell us about the possibility of life emerging elsewhere in the Universe.

Jay provided a brief introduction, following his abstract above, to both the conceptual underpinnings and experimental design to address the question of how inanimate matter might evolve towards life as we currently understand it.

Specific questions arose regarding the nature of molecular information inherent in the distinct chemical networks of nucleic (characterized as `digital' in this discussion) and amino (described as `analog' here) acids. A metaphor to set these in context to each other is to consider that nucleic acids base-pairing is precisely, digitally matched by discrete patterns of hydrogen bond donor and acceptor pairs -- much like the digital information encoded in DVDs and CDs, and why nucleic acids serve this purpose in storing and managing genotypic information. Conversely, there are no 1:1 correspondences of amino-acid residue pairwise recognition that apply across all of peptide and protein supramolecular interactions. In fact there is a wide range and variety of physicochemical behaviors elicited by the 20 distinct AA sidechains -- and that variability, much as the continuously variable analog information embossed into vinyl records, is central to the phenotypic role played by peptides and proteins in extant biochemistry and the central dogma. We can design model chemical networks representing both `digital' and `analog' molecular information to see how they might evolve separately, constrained primarily by the robustness of the chemical species to environmental conditions, and by the methods for identifying and interpreting the experimental observables from the network behaviors. Lessons learned from these experimental platforms are anticipated to help with the search for the signatures of life and its potential alternative forms elsewhere in the universe.

Given the potential multidisciplinary approaches to studying dynamic chemical networks, there is also the question of how to unambiguously name these entities, and where there might be different definitions or relationships for different disciplines. Specifically, can the terms `network' and `system' be used interchangeably, or do they connote distinct entities and purposes? With astrophysics, political and social sciences, literature, and chemistry represented in the lunchtime discussion, some interesting definitions emerged. There was some consensus that `systems' represent a functional and structural definition within which `networks' will be found; for example, much in the way that there are biochemical networks of neurotransmitters that are subsumed within the larger nervous system, or specific network interactions of organisms within a larger ecological system.

Present were:

      Nickolas Barris, IAS, Princeton
      Jim Cleaves, ELSI, Tokyo, and IAS, Princeton
      Jay Goodwin, NSF, DC; and Emory University, Atlanta
      Piet Hut, IAS, Princeton, and ELSI, Tokyo
      Matteo Monti, University of Bologna, Bologna
      John Padget, IAS, Princeton, and University of Chicago
      Steve McMillan, Drexel University, Philadelphia
      Ed Turner, Princeton University, Princeton


Terrestrial Life - Anomalous and Alone?

[by Ed Turner]

Our 20th IPA@IAS lunch took place on February 27, 2014, with Ed Turner starting the discussion; Ed wrote these notes.

Here is the abstract that Ed sent out before the meeting:

There is no evidence which strongly contradicts the hypothesis that life arose on Earth due to such extraordinarily improbable events that it is extremely unlikely it has arisen or will ever arise elsewhere within the observable universe. Moreover, a few bits of evidence and lines of reasoning support this hypothesis, though none in a conclusive or compelling way. The ways in which molecular biology suggests combanitoric improbability, the Fermi(-Hart) paradox, "rare Earth" lines of argument, the failure to date of SETI, the apparent absence of multiple origins of life on Earth and the highly anti-racemic chemistry of life are among them. Moreover, some of the most common counterarguments to these inferences are flawed in fundamental ways. However unappealing it may be (to most, but not all), we should take the hypothesis quite seriously at our current state of knowledge. Some references: Argyle E, 1977, Chance and the origin of life. Origins of Life, 8, 287–298 Hart MH, 1975, Explanation for the absence of extraterrestrials on Earth. QJRAS, 16, 128 Spiegel & Turner 2012, www.pnas.org/cgi/doi/10.1073/pnas.1111694108

The conversation began by noting that the hyper-improbable event(s) scenario is so unappealing to most, but not all, concerned with the topic that it is typically treated quite differently from other OoL hypotheses. Namely, the most common reaction is to point out alternative possibilities for explaining the various facts/observations supporting the hyper-improbable model (listed above in the abstract). In contrast, other ideas for the OoL are normally evaluated positively for any aspect of life which they can explain plausibly, whether or not there are alternative explanations. We therefore spent a major part of the discussion by considering the hyper-improbable event scenario in terms of what it can explain (or even predicts, in a sense), thus trying to treat it on an equal footing with other hypotheses.

Proceeding on this basis, all of the points in favor of the model (as listed in the abstract) were discussed, some briefly and some at length. There were no claims that any evidence excluded the model nor any that it is supported by any compelling evidence. In the opinion of at least some (including ET), it should be regarded as no less likely to be correct than any of our other OoL hypotheses despite being so disagreeable to contemplate.

It was pointed out that the plausibility of the hyper-improbable hyporthesis depends strongly on the reality of an infinite universe and/or an infinite number of "bubble universes" in the multiverse.

During the final portion of the lunch, Mary Anne Peters led a discussion of tidally heated exomoons (THEM) and the possibilities of detecting them in the near term future via direct imaging in the thermal IR, which she and ET have been investigating. The abstract of their first published paper on the topic (Peters & Turner 2013, ApJ, 769, 98) is as follows:

We demonstrate the ability of existing and planned telescopes, on the ground and in space, to directly image tidally heated exomoons orbiting gas-giant exoplanets. Tidally heated exomoons can plausibly be far more luminous than their host exoplanet and as much as 0.1% as bright as the system's stellar primary if it is a low mass star. Because emission from exomoons can be powered by tidal forces, they can shine brightly at arbitrarily large separations from the system's stellar primary with temperatures of several hundreds degrees Kelvin or even higher in extreme cases. Furthermore, these high temperatures can occur in systems that are billions of years old. Tidally heated exomoons may thus be far easier targets for direct imaging studies than giant exoplanets which must be both young and at a large projected separation (typically at least tens of AU) from their primary to be accessible to current generation direct imaging studies. For example, the (warm) Spitzer Space Telescope and the next generation of ground based instruments could detect an exomoon roughly the size of the Earth at a temperature ≈600 K and a distance ≈5pc in the K, L, and M bands at the 5σ confidence level with a one hour exposure; in more favorable but still plausible cases, detection at distances of tens of parsecs is feasible. Future mid-infrared space telescopes, such as James Webb Space Telescope and SPICA, will be capable of directly imaging tidally heated exomoons around the nearest two dozen stars with a brightness temperature >=300 K and R >= 1 R⊕ orbiting a t>=12 AU from the primary star at a 5σ confidence level in a 10^4 s integration. In addition it is possible that some of the exoplanets which have already been directly imaged are actually tidally heated exomoons or blends of such objects with hot young planets. If such exomoons exist and are sufficiently common (i.e., nearby), it may well be far easier to directly image an exomoon with surface conditions that allow the existence of liquid water than it will be to resolve an Earth-like planet in the classical habitable zone of its primary.

Present were:

      Jim Cleaves, ELSI, Tokyo, and IAS, Princeton
      Piet Hut, IAS, Princeton, and ELSI, Tokyo
      Matteo Monti, University of Bologna, Bologna
      Mary Anne Peters, Princeton University, Princeton
      Ed Turner, Princeton University, Princeton


Hydrogen in the core and implications for water in Earth's building blocks

[by Kei Hirose]

Our 19th IPA@IAS lunch took place on February 20, 2014, with Kei Hirose starting the discussion; Piet Hut wrote these notes.

Here is the abstract that Kei sent out before the meeting:

It has been well known since 1952 that the Earth's metallic core includes substantial amount of light impurity element(s) in addition to iron and nickel. The identification of such light element(s) still remains highly controversial. On the basis of high-pressure and -temperature experiments, we recently determined the solidus temperature of Earth's primitive mantle to be only about 3600 K at the boundary between the rocky mantle and the core (Ryuichi Nomura et al.) which is lower by ~500 K than previous estimates. Since the bottom of the mantle is not globally molten, such solidus temperature provides the upper bound for the temperature at the top of the core. The outer core must be molten even under such low temperature, which could happen only with considerable amount of hydrogen in the core. Considering that the source of hydrogen is most likely water in a "magma ocean" formed at the beginning of our planet, the water concentrations in Earth's building blocks may be as high as 1 wt.% H2O, which is much more than the mass of present-day ocean (0.02 wt.%).

Kei gave an overview of recent developments concerning the physical conditions of the deeper parts of the Earth, especially the core. The suggestion that this may lead to a water content of the deep Earth far larger than that in the Earth's oceans has important ramifications for the theory of planet formation in our solar system, as well as the subsequent evolution of planets after formation.

A lively discussion followed among the fourteen participants, a record so far, with all of us just fitting around the long table in our small meeting room. Given that most of us had little background knowledge about the deep Earth, we had a great opportunity to rapidly learn, at least in a relative sense.

Halfway the discussion, we asked Cara Magnabosco to give us some impressions of her work on organisms that she and her colleagues at Princeton University had found in gold mines in South Africa that are kilometers deep, not only single-cell organisms, but even worm like critters (see also our lunch with Tullis Onstott on October 25, 2013, below).

Present were:

      Jim Cleaves, ELSI, Tokyo, and IAS, Princeton
      Walter Fontana, Harvard, Cambridge, MA
      Piet Hut, IAS, Princeton, and ELSI, Tokyo
      Laura Landweber, Princeton University, Princeton
      Cara Magnabosco, Princeton University, Princeton
      Matteo Monti, University of Bologna, Bologna
      Tim Morton, Princeton University, Princeton
      Sean Murphy, Howard Hughes Medical Institute / Janelia Farm
      Hyun Ok Park, York University, Toronto, and IAS, Princeton
      Hanako Ricciardi, ELSI, Tokyo
      Eric Smith, George Mason University, Fairfax, Virginia
      Steven Tainer, Institute for World Religions, Berkeley, CA
      Kengo Tomida, Princeton University, Princeton
      Ed Turner, Princeton University, Princeton


Our lunch scheduled for February 13, 2014, was canceled because IAS was closed, due to a snowstorm.


Lithopanspermia

[by Ed Belbruno]

Our 18th IPA@IAS lunch took place on February 6, 2014, with Ed Belbruno starting the discussion; Piet Hut wrote these notes.

Here is the abstract that Ed sent out before the meeting:

My introduction and discussion addresses whether life on Earth could have originated from another planetary system within the Sun's birth cluster by the mechanism of lithopanspermia. This is a process where meteoroids containing microorganisms are exchanged between planets of the systems. The discussion topic is on a transfer mechanism for this to occur. Previous studies have shown that the probability of transfer of solid material from the neighborhood of one star in an open star cluster to be captured by another star was very unlikely. This was due to the high ejection velocities from the originating planetary system. In a recent paper by this speaker, together with Amaya Moro-Martin, Renu Malhotra, and Dmitry Savransky [Chaotic Exchange of Solid Material Between Planetary Systems: Implications for Lithopanspermia, Astrobiology, 12, 2012] we show that by using the much slower weak escape mechanism, which is chaotic in nature, the probability of solid material to be captured by another star in the cluster increases dramatically by a factor on the order of one billion, thereby making the lithopanspermia much more likely and providing a viable transfer mechanism.

Ed gave some very interesting background about what led him to study chaotic orbits in the solar system, and to apply what he learned to rescue the Japanese satellite Hiten, and bring it to the moon in 1991. He then summarized his work on lithopanspermia, and we quickly got into a lively discussion about the question whether a single source of life anywhere in the Galaxy may have seeded the rest of the Galaxy through panspermia. That in itself seems far less likely than the kind of seeding that may have happened in the first few hundred million years in a slowly dissolving birth cluster, but perhaps not impossible.

These discussions triggered the question of prospects of us observing interstellar bodies crossing through the solar system. So far, all comets that we know of have been traveling on either elliptic or close to parabolic orbits, whereas a comet from around another star would cross the solar system at a very clearly hyperbolic orbit, with a velocity at infinity of order a few tens of km/sec. However, with the rapid increase of all-sky surveys, the day will surely come that we will find bodies moving on hyperbolic orbits, either comets of asteroids.

After our lunch, Piet contacted Robert Jedicke, who is working in the Pan-STARRS project in Hawaii, as a specialist of asteroid orbit calculations. The way Robert and Piet met was by Piet overhearing a conversation in a cafe in Manhattan, twelve years ago, where Robert talked about near-earth asteroids and impact dangers, after which Piet joined in with the conversation (a few years before that, Ed Belbruno and Piet met in a train between Manhattan and Princeton; lots of contingent encounters :-). Given that Robert had just sent an email, Piet replied, with CC to Ed Turner, who in turn pointed to a paper that he had written with Amaya Moro-Martin and Avi Loeb: Will the Large Synoptic Survey Telescope Detect Extra-Solar Planetesimals Entering the Solar System? This discussion started an email thread about future opportunities for such observations

Many other topics were discussed, including the relationships between pure and applied mathematics, with chaos being one obvious theme, given the earlier conversations. In this context, Ed Belbruno also talked about the large differences he has experienced in the nature of creative inspiration, while working in math compared to working in art, specifically in painting.

Present were:

      Ed Belbruno, Princeton University, Princeton
      Jim Cleaves, ELSI, Tokyo, and IAS, Princeton
      Piet Hut, IAS, Princeton, and ELSI, Tokyo
      Jeffrey Schenker, IAS, Princeton
      Ed Turner, Princeton University, Princeton


Pushing and Pulling at the Origin of Life

[by Jon Lindsay]

Our 17th IPA@IAS lunch took place on November 21, 2013, with Jon Lindsay starting the discussion; he wrote these notes.

Here is the abstract that Jon sent out before the meeting:

Scientific accounts of life have long been of two minds. Many accounts emphasize the physical causes which push matter around. Others, especially but not only in the social sciences, emphasize the ideas and interests which motivate or pull living entities around. It turns out that the world in which we live is a fantastic hybrid between these two perspectives. The problem of intentionality continues to pull stubbornly against our scientific world of causes. Is it possible that intentionality might actually be part of the answer, not just the obstacle, to understanding the origin and evolution of life?

Many scientific perspectives emphasize the physical causes or regularities which “push” matter around. Others, especially, but not only, in the social sciences, emphasize the ideas and interests which motivate, encourage, or “pull” living entities around. The world in which we live is a hybrid between these two perspectives, one mechanistic (even if non-deterministic) and the other functional (even if contested). In this conversation we explored why the problem of intentionality cannot be satisfyingly reduced to a scientific world of causes.

First we discussed a stylized history of the intellectual development of three “big questions” science has addressed across the milenia: physical mechanism, biological life, and social complexity. For prescientific humans, all three were probably unified in an animistic worldview. Aristotle then observed that observed that living things are special because their development and behavior appears to be guided by goals, not just efficient causes. He also pointed out that humans, as political animals, are especially concerned with advancing their interests, social and moral, guided always by future-directed intentionality. Then, many centuries later, Newton described a mechanistic universe in which three mathematical laws of motion were enough to explain the bumping and shoving of the material world. Yet man remained a special, even devine, being for Newton, even as other enlightenment thinkers emphasized more secular, economic, intentionality. Charles Darwin's theory of evolution through natural selection was at once a natural outgrowth of these ideas as well as an important update to the Newtonian worldview. Iterated over enough generations, the algorithm of natural selection can produce life forms that are remarkably well-adapted to their environment, and seemingly intentional or functional.

This story remains incomplete, however. While Darwinian evolution explains how biological functionality can be improved over time through natural selection, it still doesn't tell us where intentionality comes from in the first place. A more unified concept of physics, biology, and society may be possible, and may even be emerging now or in the near future. This concept would be able to unite cause and intentionality, pushing and pulling. In some ways this is a return to Aristotle's ambition to think broadly across the entire scope of human experience.

Total interdisciplinarity is daunting and may even be impossible. But perhaps something more modest, like a general theory of complex systems, might be possible, which helps to make sense of both intentionality and causation. Getting there, however, will require a lot more conversation. As we found in our conversation, there are some serious and cross-disciplinary ambiguities surrounding basic terms like intentionality, emergence, structure, function, and even science!

Present were:

      Nickolas Barris, IAS, Princeton
      Jim Cleaves, ELSI, Tokyo, and IAS, Princeton
      Piet Hut, IAS, Princeton, and ELSI, Tokyo
      Jon Lindsay, UCSD, San Diego
      Hyun Ok Park, York University, Toronto, and IAS, Princeton
      Michael Perryman, Princeton University, Princeton
      Siobhan Roberts, IAS, Princeton
      Jeffrey Schenker, IAS, Princeton
      Ed Turner, Princeton University, Princeton


Scientific Imagination and the power of Hollywood Visualization:
Exploring Conceptualization Models in Examining the Origins of Life

[by Nickolas Barris]

Our 16th IPA@IAS lunch took place on November 14, 2013, with Nickolas Barris starting the discussion; he wrote these notes.

Here is the abstract that Nickolas sent out before the meeting:

Based on my experience of having written over 200 dramatic works in my Hollywood career and having analyzed more than 4,000 submissions of literary works while working for Hollywood studios, I have developed a conceptualization model that utilizes objective data and research mixed with professional intuition to generate stories which maximize dramatic power and truth. This framework can also be applied to scientific hypothesis generation, which also uses the scientific data and known scientific boundaries as a starting point to posit new research pathways to realize new knowledge frontiers. I have successfully applied this model to create two award winning science- based documentaries. One of these documentaries featured Dr. Oliver Sacks exploring a new human giftedness phenomenon, Williams Syndrome. I hope to explore how these models can spark additional insights in the specialized investigations being done in Origins of Life.

Nickolas Barris began his discussion by analyzing the important role scientific imagination and conceptualization models had played in the previous talks in the series on Origins of Life to date. With the value of these elements illuminated, he visualized three additional conceptualization models, which might be helpful in future hypothesis generation within the Origins of Life : 1) Albert Einstein's conceptualization model for scientific theory generation, 2) Nickolas Barris's personal conceptualization model created when he participated in a global summit on creativity in 2012, and 3) the Hollywood Three Act Movie Structure created to propel dramatic writing.

Einstein's model describes an infinite line of 'sensory impulses', a radiating arc of non-linear hypothesis generation which creates a new axiom point, and then this axion point is logically evaluated as it moves back to the original infinite line of sensory impulses. Nickolas Barris' personal conceptualization model for fostering productive creativity begins with a series of flashes of insight which remain at a staging point until one new hypothesis rises in intuitive quality over the others. This idea is then moved through a dynamic plane of interdisciplinary models collected from the sciences and the humanities to be refined to a point where a new scientific hypothesis or creative story can be realized. This model also reflects the non-linear nature of fostering new scientific and creative insights. Lastly, the Hollywood Three Act movie structure was reviewed with an emphasis on how excellent character interaction in Hollywood storytelling is similar to the myriad of possibilities seen in nature -- for example in range of possible biochemical reactions.

Nickolas Barris cited three previous talks as examples of how their specific scientific approaches in the conceptual framework sense could be brought into the interdisciplinary space described in Einstein's model and his personal model. These included: Marcelo Gleiser's talk on Homochirality, Jim Cleaves' talk on Prebiotic Chemistry, and Yuka Fujii's talk on Biosignatures for the Quest for Inhabited Exoplanets. He concluded his review by suggesting that there should be a concerted effort by all those in the Origins of Life community to bring their scientific scholarship and hypothesis into an ongoing interdisciplinary space such as those in conceptualization models 1 & 2 where the broader community could interact with both the specific scientific data, scholarship, and hypothesis as well as the conceptualization models used to develop them.

Points and questions from the broader group included:

1) A point was made describing how these three visualized conceptualization models were all different from the already varied standard models for thinking about physics, cosmology, and the origins of life that have been refined through the history of the world of ideas. This now larger group of models was discussed as they were all quite different in their logic and dynamics;

2) An analysis was made as to how these three visualized models might add insight and clarity to the three big questions of how was matter formed, how life was formed, and how consciousness was formed. There was a broader group feeling that the models would be a beneficial addition to the current framework from which these foundational questions are explored;

3) Ed Turner queried how these models might be used in astrophysics and cosmology, and a broader discussion ensued from this point, with an emphasis on the role of gravity and lower entropy areas for enhancing conditions for life on earth. The discussion grew to a fascinating discussion about Ed's views about the likelihood of life in other parts of the universe.

4) Questions arose about how the Hollywood Three Act structure worked in general and specifically how it could be applied as a guiding framework for new stories of progressively more meaningful drama. This led to a discussion on how the Three Act Structure and other forms of structure like those applied by Shakespeare seek to tap into a universal constant in the condition of being human and how humans process ideas and emotions. This led into a broader evolutionary discussion on how other animals such as birds and monkeys display aspects of these processing forms as well as what we might learn from this;

5) The meeting ended with another call to encourage the broader Origins of Life community to collect and curate an ongoing interdisciplinary space where the above can be accessible in a systematic form and be expanded progressively in the future.

Present were:

      Nickolas Barris, IAS, Princeton
      Jim Cleaves, ELSI, Tokyo, and IAS, Princeton
      Yuka Fujii, ELSI, Tokyo, and IAS, Princeton
      Piet Hut, IAS, Princeton, and ELSI, Tokyo
      Douglas Duckworth, Temple University, Philadelphia
      Ed Turner, Princeton University, Princeton


The Homochirality Question

[by Marcelo Gleiser]

Our 15th IPA@IAS lunch took place on November 7, 2013, with Marcelo Gleiser starting the discussion; he wrote these notes.

Here is the abstract that Marcelo sent out before the meeting:

Since Pasteur and even before (Biot) there is clear evidence that amino acids and sugars have very specific chiralities in living organisms. I'll present some of the issues related to how chirality may be part of the OoL puzzle and how environmental effects may have played a key role in determining what happened here and possibly elsewhere in the universe. There will be as many questions as answers, hopefully more.

Marcelo Gleiser presented a brief summary of the problem of biological homochirality, or why life seems to prefer certain spatial orientations in some of its key biomolecules. For example, amino acids are levorotatory ("left-handed" in a more colloquial sense, they rotate the plane of polarized light to the left) while sugars in nucleic acids are dextrorotatory ("right-handed"). The puzzle arises from the fact that when such biomolecules are synthesized artificially the mixture is always racemic, that is, 50-50.

Some of the questions Gleiser discussed were:

1. Why is there a chiral complementarity between amino acids and sugars? Does it serve some functional optimization linked somehow to genetic reproduction? Nick Hud made interesting remarks about how protein folding and functionality depend on chiral purity due to the sheet structure of proteins.

2. What is the relationship between chirality and origin of life? Does chirality come first, at the prebiotic level, or does it emerge afterwards? Nick Hud suggested that it could come afterwards, during the evolution of reproductive apparatus; however, Gleiser countered arguing that once a polymer is mixed, it may be hard to "purify it", that is, to make it chirally pure; it would be easier to start with chirally pure biomolecules at the prebiotic level. Jim Cleaves suggested that meteorites do show some excess of homochiral compounds and that these may have played a role in seeding homochirality here.

Gleiser then explained his model of punctuated chirality (published in Origins of Life and Evolution of Biospheres), whereby chirality is determined by the coupling between the auto-catalytic polymerization reactions and the external environment. His group's conclusion and prediction is that the specific chirality found on Earth is accidental: a large sample of stereochemistry from alien worlds should yield a 50-50 distribution. This contrasts with the two other mechanisms suggested for biochirality: weak interactions -- predicting the same chirality across the universe; and circularly polarized light -- predicting the same chirality in a stellar neighborhood but not, for example, a cross the whole galaxy.

Nigel Goldenfeld questioned why should life on Earth be homochiral if it had random chirality in early Earth; Nick Hud added that indeed different chiral domains may have emerged, and it may have been a competition for resources where the slightest advantage would lead to "victory" of one of the chiral choices. Gleiser mentioned that his models of spatiotemporal homochirality show exactly that, although it is not clear what the chiral advantage would be.

Gleiser also pointed out that life may not have emerged independently at different spots on Earth but may simply have radiated out from one spot. Behind this discussion lies the more complex problem of how "easy" life is. Did life have many origins here or just one? Gleiser defends the position that life is hard; Goldenfeld that life is easy.

Also discussed was the issue of pathways to life: are there many ways through which biomolecules could self-organize to become a living entity? Or are these pathways very restricted?

Present were:

      Nickolas Barris, IAS, Princeton
      Jim Cleaves, ELSI, Tokyo, and IAS, Princeton
      Yuka Fujii, ELSI, Tokyo, and IAS, Princeton
      Ayako Fukui, Templeton Foundation
      Marcelo Gleiser, Dartmouth College
      Nigel Goldenfeld, University of Illinois
      Nick Hud, Georgia Tech
      Piet Hut, IAS, Princeton, and ELSI, Tokyo
      Eiko Ikegami, New School for Social Research
      Hanako Ricciardi, ELSI, Tokyo
      David Spiegel, IAS, Princeton
      Antje Teegler
      Inna Zakharevich, IAS, Princeton


Is it necessary to understand the origin of life as a cascade of non-equilibrium phase transitions?

[by Eric Smith]

Our 14th IPA@IAS lunch took place on October 31, 2013, with Eric Smith starting the discussion; he wrote these notes.

Here is the abstract that Eric sent out before the meeting:

In Origins of Life studies, we are at a stage when we don't know much about even the relevant domains of chemistry or environment. Is it still possible to put general constraints on how questions about biogenesis must be framed in order to be consistent? This question draws on a much larger community of expertise than those traditionally involved in Origins of Life questions.

The discussion started out with a question that is traditional but not (in the traditional formulation) very usefully phrased: "Was the origin of life on earth an accidental/improbable event or was it a necessary stage in planetary dynamics?" One way the question can be re-phrased, to make it closer to concepts for which we have some quantitative theory, is to ask whether the origin of life is similar to detailed sequences of microscopic events that are essentially unpredictable as (fully-detailed) instances, like the path of a particle under Brownian motion, or whether it was a kind of system re-arrangement of the chemistry and energetics of the whole planet, similar in character to the way a phase transition (freezing, dielectric breakdown, etc.) re-arranges the distribution of a system over its microscopic states or histories (respectively, for freezing or breakdown). Inna noted that perhaps this should be expressed as a question in Ramsey theory, about what conditions make a given property inevitable in systems with many elements. Though the other participants in the discussion were not familiar with this topic at the time, subsequent reading suggests this may be a good connection to pursue.

Several variations on this discussion took place, to try to refine the characterization of life that one uses -- because not all aspects of life are likely to be equally contingent or unpredictable, even if as a class their fates are coupled -- and to link classes of accidental or likely transitions in understood systems to observed sub-systems or features in the biosphere.

The discussion then turned to how much we know, both empirically and mathematically, that may constrain answers to this question. An important uncertainty is how much we know about relevant chemistry and planetary conditions, and the perspectives appeared to range from relatively optimistic (we know a lot that is likely enough to be relevant that it may be a strong constraint on theorizing) to more cautious (we know some things well but the search space is large and we are likely to need to know many new things before we can say much of anything with a better-than-circumstantial use of evidence).

The question arose whether features of life that we observe as universal (for instance, some core metabolic pathways, use of RNA and cells) are unique solutions that any biosphere under conditions like those on earth would need to employ, or whether they are historically contingent choices among many comparable options. (Obviously, this question too benefits when disaggregated to refer to more fine-grained subsystems of reactions, or classes of components, rather than treating the observed version as an exact template.) A closely related question (also perennial) is whether we should view the most-likely hypothesis for origin as one in which low-level (bulk-chemical property) dynamics dictated many of the possible patterns for life, and controlling systems such as genes and enzymes entered a world where many of their functions were pre-specified, or whether the most-likely path of origin was only through gene/enzyme control layers, and whether accidents on that path of emergence were essential to determining parts of the biosphere we have today.

The two questions are not necessarily alternatives, in the sense that evolutionary convergence can reflect the law-like character of paths of least resistance, or of underlying more-stable forms of order, in which case prior constraint or posterior convergence could lead to the same outcome. In such cases, from the outcome alone, the two explanations are confounded. If we can recover any of the operative laws acting during emergence from historical reconstructions, perhaps the confound can be partly removed. (It is worth noting that historical reconstruction can sometimes do more than simply propose ancestral states within the scope of the reconstruction. Sometimes it can uncover laws of dynamics that continue to apply outside the reconstructed window, and in that way it may place constraints on earlier ages than those directly inferable from history.) To the extent that a continuum may exist, from strict externally imposed constraint, through very strong convergence, to weaker convergence only exposed in the evolutionary long-term, a more productive direction may be to try to place various patterns or processes along this axis from constraint to contingency.

Several discussants seemed to be comfortable agreeing that a theory that could properly engage the chemical mechanics, and then give justified ground for choosing among these possibilities, would be desirable, but also that not much that one would regard as satisfying by both criteria currently exists. There did not seem to be any opinion that it is in principle out of reach.

Present were:

      Nickolas Barris, IAS, Princeton
      Jim Cleaves, ELSI, Tokyo, and IAS, Princeton
      Yuka Fujii, ELSI, Tokyo, and IAS, Princeton
      Piet Hut, IAS, Princeton, and ELSI, Tokyo
      Eric Smith, George Mason University, Fairfax, VA
      David Spiegel, IAS, Princeton
      Inna Zakharevich, IAS, Princeton


Prebiotic Chemistry: Self-Assembly, Emergence and Autopoiesis

[by Jim Cleaves]

Our 13th IPA@IAS lunch took place on October 24, 2013, with Jim Cleaves starting the discussion; he wrote these notes.

We began the discussion with a brief chalk talk by Jim Cleaves, who discussed the concept of self-assembly, using the examples of ice crystallization and micelle formation from fatty acids. We then proceeded to discuss more complex varieties of self-assembly, and the notion of autopoiesis, using as an illustration the work of Luisi on catalytic micelles derived from the two-phase octanoic anhydride/water system. We discussed the idea of nested or sequential autocatalysis, where products of a reaction speed up reactions which are upstream for their synthesis. We then moved on to a discussion of what other aspects such systems might need to become more complex, for example the suspected need of being composed of more than one component.

This led to the question of open-ended evolution. For example, it was discussed whether there truly are an infinite number of chess games, or whether the fixed number of playing pieces and the fixed size of the game board render this number merely very, very large. This led to a discussion of the comparison between chess and the game of *go*, and why it took so much longer for the development of artificial intelligence which could beat human players easily in the case of *go (*incidentally, according to chess master Emanuel Lasker: "The rules of Go are so elegant, organic, and rigorously logical that if intelligent life forms exist elsewhere in the universe, they almost certainly play Go"). This turns out to be the result of a number of factors, including the larger board, greater number of moves and greater subtlety of strategy relative to chess. The point of this discussion was to ask whether given sufficient computing power one could design an artificial life program which would spontaneously develop nested autocatalysis and open-ended evolution.

There ensued a discussion of the possible necessity of modularity in living systems, it being noted that while eukaryotes have modular compartments, prokaryotes do not, and this type of modularity is likely the result of limitations imposed by diffusion at the scale of the cytosol. There could be other levels of modularity, such as the separation of coding and catalysis in different types of molecules, or even the modularity inherent in genes. We discussed whether there was a connection between modularity and robustness, and finished with a discussion of whether modularity was likely a universal feature of living sysems.

An intriguing question came up about the optimal form that a living cell could take. Has evolution reached the most efficient type of bacteria, say, or is it conceivable that a very complex non-modular composition of molecular structures and pathways could be even more efficient? If such a bacterium could not be produced through evolution, could it in principle be made in a laboratory? Could it be reasonably robust? In other words, there are three ways of asking the question whether modularity is more a matter of convenience, or whether it really is the absolutely most efficient way to organize matter and processes in a living cell: 1) if we only insist that such a cell would be alive, at least for a while; 2) if we insist that such a cell and its progeny would be robust, able to live on through at least modest fluctuations in its environment; 3) if we insist that such a cell could be produced through a continuous path of evolution from prebiotic material.

Present were:

      Nickolas Barris, IAS, Princeton
      Jim Cleaves, ELSI, Tokyo, and IAS, Princeton
      Yuka Fujii, ELSI, Tokyo, and IAS, Princeton
      Piet Hut, IAS, Princeton, and ELSI, Tokyo


Deep inside the Earth, Up in the Air, Off to the Moon, and Looking Back from Alpha Centauri

[by Piet Hut]

The day after our 13th IPA@IAS lunch, on October 25, 2013, we had an additional lunch gathering with Tullis Onstott, who earlier had been scheduled to lead the discussion on the 24th, but had been unable to attend then.

Tullis told us about his work in South African Gold mines, several kilometers deep underground, to look for microorganisms in that environment, and to test the possibility that life might have originated there. He told us colorful stories about descending that deep into the Earth and dealing with the high temperatures there. He also mentioned the dangers and ingenuity of mining engineering at the enormous pressures in the rocks and in the water veins that are present in the rocks. Tullis discussed his latest thought about the possibly very long doubling time of bacteria in those rocks, the presence of very ancient pockets of water judging from noble element abundances, and indications of current biological activities there.

Ed Belbruno spoke about his new work on lithopanspermia in star forming regions, where simple lifeforms may have hitched a ride on meteorites, moving from planets in one solar system to planets in another. He also mentioned his older work, in which he rescued a Japanese satellite, Hiten, that had wound up in a wrong orbit, by calculating new types of transfer orbits requiring almost no fuel.

Yuka Fujii talked about her work on biomarkers, and one-pixel tomography of exoplanets. She is currently working on a study of the solar system, as seen from nearby stars, such as Alpha Centauri, to see through simulations what we might be able to observe from such a large distance. Such knowledge can then be applied to Earth-bound studies of planets around other stars.

We also discussed briefly recent measurements of simple life forms, such as diatoms, high up in the stratosphere. A large volume of sea water is being splashed into the atmosphere every day, through regular wave motions as well as the effects of hurricanes and other storms. Some microorganism, once carried aloft that way, can make it all the way to the stratosphere, and survive there for a considerable amount of time.

Present were:

      Ed Belbruno, Princeton University and Courant Institute, NYU
      Jim Cleaves, ELSI, Tokyo, and IAS, Princeton
      Yuka Fujii, ELSI, Tokyo, and IAS, Princeton
      Piet Hut, IAS, Princeton, and ELSI, Tokyo
      Tullis Onstott, Princeton University


Biosignatures for the Quest for Inhabited Exoplanets

[by Yuka Fujii]

Our twelfth IPA@IAS lunch took place on October 17, 2013, with Yuka Fujii starting the discussion; she wrote these notes.

Here is the abstract that Yuka sent out before the meeting:

Recent astronomical observations have revealed the universality of planetary systems outside the Solar system. Presumably rocky planets in so-called habitable zones have been already detected. These facts motivate us to search for inhabited exoplanets with further observations. A test of our ability to detect signatures of life (biosignature) is, to begin with, to examine the biosignatures of our own Earth which would be observed remotely. In the case of the present Earth, spectral features of oxygen, ozone, and vegetation's red-edge are recognized as useful biosignatures. In addition, time series of precise multi-band observation may allow us to recover surface environment (e.g. continents) to some extent. To go beyond the present Earth, a wide variety of existing forms of life and spectral signatures they could potentially produce are taken into consideration. I will introduce these efforts to explore the possibilities to investigate life on exoplanets.
Discoveries of about 1000 exoplanets have greatly motivated us to search them for life. The only realistic way to investigate the existence of life on exoplanets at an astronomical distance is to obtain planetary spectra or colors as point sources and look for signatures of life (biosignature) in them. Based on such current status, we reviewed the possible biosignatures proposed so far, focusing on 1) biosignature gas in the atmosphere and 2) scattering properties attributed to life.

Firstly we made a table of biosignature gases to compare their characteristics. We summarized abiotic production (which can lead to false positive), possible sinks, and the spectral ranges they can be observed. Among others, oxygen has been put forward as a promising biomarker, for it has no known good abiotic production. On the Earth, the oxygen in the atmosphere is caused by oxygenic photosynthesis (or the burial of the organic matter, because digestion or organic matter consume oxygen). One question which arose was how many years atmospheric oxygen would be sustained in Earth's atmosphere if all of the living things disappear suddenly; this is our homework.

Then we discussed the biosignatures in the scattering properties, in particular the step-function-like feature in the reflectance spectra of photosynthesizing creatures and the effect of phytoplankton on the visible colors of oceans. These features can be identified when we focus on a localized area, but can be seen marginally in the disk-integrated spectra depending on the observational configuration. While the universality of these features is uncertain, it would be worth assessing them once the planetary spectra are available.

Finally we talked about future prospects. It is technically challenging to detect the signal from Earth-size exoplanets by suppressing the effect of the star light. Preliminary attempts are ongoing, but this direction is widely regarded as our ultimate destination to go in to search for biomarkers and some future projects are under active discussion. We expect to be able to use such equipment in 10-20 years. In the meanwhile, using spectroscopy of transiting planetary systems (i.e. comparing the in-transit and out-of-transit spectra), upcoming telescopes such as JWST may be able to access some of the major features of super-Earths.

Present were:

      Nickolas Barris, IAS, Princeton
      Jochen Bruening, Humboldt University, Berlin
      Yuka Fujii, ELSI, Tokyo, and IAS, Princeton
      Piet Hut, IAS, Princeton, and ELSI, Tokyo


Non-Equilibrium Processes and the Origin of Life

[by Albert Fahrenbach]

Our eleventh IPA@IAS lunch took place on October 10, 2013, with Albert Fahrenbach kicking off the discussion; he wrote these notes.

The RNA World hypothesis supposes that before the familiar central dogma – in which DNA stores the genetic information that encodes for proteins which carry out cellular functions – RNA served both of these roles. Faith in this hypothesis has served as a guideline towards constructing model protocells in the lab, which aim to make use of RNA polymers that can undergo replication within the confines of a vesicle, split up to form daughter vesicles, and repeat this process indefinitely with a robustness needed to eventually reach a population of protocells capable of undergoing Darwinian evolution.

One of the key steps in protocellular replication involves the copying of the RNA polymers which act as the templates for their own syntheses from sequential reactions with activated RNA monomers. One of the practical challenges to realizing such a template-directed synthesis in the lab is the fact that the activated RNA monomers being in a high energy state, very quickly react with water before they can undergo polymerization on the parent template. This dead-end hydrolysis product is a consequence of thermodynamics: molecules have very little choice other than to move towards their lowest energy states, and once there, the ability to harness their free energy is lost.

Although one of the presumptions of the RNA World hypothesis supposes a time which was free of modern complex molecular machinery that would normally power cellular replication in today's cells, might there have existed vastly simpler versions constituted of RNA – so-called prebiotic molecular machines – capable of doing useful work at the molecular level, i.e., pushing a reaction uphill away from its equilibrium state by harnessing free energy available from the environment, that could have promoted template-directed RNA replication?

In pursuit of answering this question, I discussed my proposal of installing onto a functional RNA polymer (also known as a ribozyme) a molecule capable of capturing the energy from light. One such molecule is azobenzene, a photoactive compound capable of undergoing cis/trans isomerization upon exposure to ~400 nm light; in other words, this small molecule can harness the energy of light from the environment and convert it into a molecular scale contracting motion, acting as a “molecular muscle”. The muscle power from azobenzene might provide the necessary “oomph” to an appropriately selected ribozyme of the right sequence, such that the ribozyme could be capable of more than just catalysis, but could actually push a reaction uphill, e.g., the activation of RNA monomers into a high energy state. Such activated RNA monomers would not be so different from the modern day energy currency used by the cell, ATP.

The group went on to discuss a variety of topics pertaining to this idea, one of which was the question of what came first, metabolism or genetics? Activated RNA monmers might have originally been supplied from the environment, but at some point the supply would have become exhausted, and any protocell capable of harnessing energy from the environment to power its own replication would have had a huge advantage over those that could not.

The discussion continued further, and the point was brought up whether the origin of life requires a completely unique and singular set of circumstances to occur, i.e., a single very specific pathway, such that the emergence of life is so rare that it only has happened once in the universe, or could there be multiple possible pathways each of which leads to life forms not necessarily based on DNA, RNA and proteins, but rather any molecular substrate at all capable of information storage and function. This kind of question strongly highlights the need for a theory of life, with a predictive power capable of guiding and informing specific and reproducible experiments which make use of chemical substrates that can be carried out in the lab on a human timescale.

Present were:

      Nickolas Barris, IAS, Princeton
      Audrey Bauerschmidt, IAS, Princeton
      Jochen Bruening, Humboldt University, Berlin
      Harmen Bussemaker, Columbia University, New York
      Jim Cleaves, ELSI, Tokyo, and IAS, Princeton
      Albert Fahrenbach, Harvard, Cambridge
      Yuka Fujii, ELSI, Tokyo, and IAS, Princeton
      Piet Hut, IAS, Princeton, and ELSI, Tokyo
      Sean Murphy, Howard Hughes Medical Institute / Janelia Farm
      Ed Turner, Princeton University, Princeton


From Life to LUCA

[by Greg Fournier]

The first IPA@IAS lunch this semester took place on October 3, 2013. It was the tenth IPA@IAS lunch since we started in January, 2013.

To remind you: IPA stands for Interdisciplinary Perspectives on Abiogenesis. All extant living organisms originated from other living organisms, through what is called biogenesis, life arising from previous forms of life. In contrast, abiogenesis indicates the formation of life from non-living matter, the transition from more and more complex chemical reactions to biology.

Here is the abstract that Greg Fournier sent out before the meeting:

Life on Earth can trace its ancestry back to a Last Universal Common Ancestor (LUCA). However, cells at the time of LUCA were almost certainly not the first cellular life, and were descended from other cellular organisms. How much time and change occurred between the first living cells and LUCA? Can an accurate understanding of LUCA inform our understanding of the Origin of Life and the first cells? Logical inference and principles of continuity suggest yes, while the nature of derived traits within evolutionary history, and the unknown amount of environmental change spanning these times suggests, maybe not.
Greg started the discussion with a chalk talk outlining the major epochs of the evolution of life in terms of the Tree of Life. These major epochs were described as being (1) Earth's origin to prebiotic chemistry; (2) prebiotic chemistry to the first cells; (3) the first cells to LUCA (Last Universal Common Ancestor); and (4) the root of the Tree of Life until the present, or the "time of cellular life".

The complex evolutionary processes at work across the tree of life were shown to have likely been present before and during the time of LUCA, and likely included horizontal gene transfer, lineage sorting and coalescence, and mass extinctions. The possibility of early extinctions related to the Late Heavy Bombardment (LHB) were discussed with relation to both pre-LUCA and post-LUCA life, and their possible role in providing an evolutionary “bottleneck”, or even total “impact frustration” requiring multiple OoL events before life could establish itself enough to endure subsequent perturbations.

Jim observed that this would depend on the rate of life's spread in relation to the frequency of OoL events. He further observed that if the earliest life was heterotrophic, frustrated attempts at planetary expansion would consume accumulated high-energy organic molecules, and make subsequent attempts more difficult.

One difficulty that Ed proposed for LHB events in selecting for thermophilic, hot spring ancestors of Bacteria and Archaea is the “fine tuning” required, as the amount of energy transferred needed to sterilize the entire planet except those microbes at the bottom of the ocean may be an unreasonably narrow range.

Greg proposed a refinement of the bottleneck hypothesis that may relax the fine tuning necessary, observing that the temperature of the ocean and planet surface would only need to be raised to a sterilizing range for all but the pre-adapted hot vent organisms. Ocean vaporization down to all but depths containing thermal vent ecosystems would seem to be gratuitous.

Present were:

      Nickolas Barris, IAS, Princeton
      Harmen Bussemaker, Columbia University, New York
      Jim Cleaves, ELSI, Tokyo, and IAS, Princeton
      Greg Fournier, MIT, Cambridge
      Yuka Fujii, ELSI, Tokyo, and IAS, Princeton
      Piet Hut, IAS, Princeton, and ELSI, Tokyo
      Ed Turner, Princeton University, Princeton


Cellular Automata Simulations and Self-Replication

[by Alex Lamb]

Our nineth IPA@IAS lunch took place on March 21, 2013.

The discussion started off with a brief introduction by Jon Lindsay on his work on the nature of conflict, and changing culture in the military. He shared his experience of studying the organization of the Navy Seals, and the ways in which the strong collective identity both helped and hindered its adaptation to a changing geopolitical landscape.

Following this, I gave the group an overview of a new type of automaton I've been exploring, which is intended to shed some light on how and when self-reproducing systems arise. In this model, a machine head or 'ant' traverses a grid filled with randomly generated copying instructions, moving in a sequence of randomized jumps. At each location, the ant carries out the local copying operation described in that cell, and thus effectively overwriting a cell somewhere in the grid. The automaton includes the stipulation that no instruction is permitted to copy itself, or copies of itself. The automaton was designed to see if this would be sufficient to cause the emergence of self-reproducing patterns of multiple instructions, which it does very rapidly.

The idea behind this model is that self-reproducing patterns are a natural outcome for systems that equate to self-overwriting programs. The hope is that the model can provide a framework for further simulations that would more closely mimic the appearance of life in the nature, by making careful approximations to the ways in which computation can arise in chemical systems. The group had several valuable suggestions as to how the work might be extended, including exploring the minimal cases of the algorithm, including features such as mutation, and also transferring the approach to a more naturalistic lattice, such as a system of Voronoi tiles.

We discussed the notion that the principle of cooperation, as analogous to that in the prisoner's dilemma, was embedded in the structure of the simulation, and that game theory might yield useful tools for determining what kinds of physical system would be likely to produce complex outcomes. We also talked about how this connected closely to the idea of hypercycles in chemistry.

Present were:

      Jim Cleaves, ELSI, Tokyo, and IAS, Princeton
      Piet Hut, IAS, Princeton, and ELSI, Tokyo
      Alex Lamb, Princeton University, Princeton
      Jon Lindsay, UCSD, San Diego
      Ed Turner, Princeton University, Princeton


Workshop on the Origins of Life at CERN, Geneva, Switzerland

[by Piet Hut]

Our eighth IPA@IAS lunch took place on March 14, 2013.
Here is a summary of the first half of our rather long lunch.

Piet reported on his visit to CERN, to attend a rather informal workshop, from February 26 through March 1, on the theme of Origins of Life. It gave him a great opportunity to meet some of the main players in Europe, after first having participated in the Origins of Life conference in Princeton, a month earlier, where most of the participants were from North America. In addition, he enjoyed visiting the control room of the Atlas detector, one of the two detectors at the LHC that has discovered the Higgs particle, last year. Unfortunately, the most spectacular multi-color T shirts were sold out, so he had to make do with T shirts with simpler hadron collisions in monochrome depictions.

From a multidisciplinary perspective, the most interesting aspect of the whole meeting was the huge difference in attitude, approach, communication, way of working, well, in just about everything, between the particle physicists at CERN and the Origins of Life researchers visiting there for a few days. Of any group of scientists I had ever met, the experimental particle physics collaborations at CERN were the most regimented, hierarchically structured group, working according to strict task divisions and with very specified mutual understanding. They clearly had to work that way, otherwise it would have been impossible to get thousands of people to work together toward the clearly defined common goal of producing and analyzing hadron collisions.

In contrast, the nomadic band of very loosely organized Origins of Life scientists were anything but organized. They knew each other, had developed long-standing friendships, but that was just about it. Any attempt from the particle physics managers to ask them "please, bring me to your leader" was never answered, since there was not (yet) an organization, and hence no leader(s). Much of the discussions, especially towards the end, were focused on ways to organize the nomads, to shape them into possible partners for potential future collaborations with CERN.

All in all, it offered Piet a triply valuable experience, learning about CERN, about Origins of Life, and about extremes in meetings between different disciplinary structures (a bit like "Bambi meets Godzilla" but hopefully and likely with a more cheerful outcome :-).

Present were:

      Jim Cleaves, ELSI, Tokyo, and IAS, Princeton
      Douglas Duckworth, Temple University, Philadelphia
      Aaron Goldman, Princeton University, Princeton
      Piet Hut, IAS, Princeton, and ELSI, Tokyo
      Jenny Jim, College University, London, and IAS, Princeton
      Boaz Katz, IAS, Princeton
      Alex Lamb, Princeton University, Princeton
      Kinnari Matheson, Princeton University, Princeton


The best peer review process is public confirmation or confrontation

[by Boaz Katz]

Our eighth IPA@IAS lunch took place on March 14, 2013.
Here is a summary of the second half of our rather long lunch.

I described an initiative that the astro-group is considering, to improve the transparency of data and citations in the electronic publication systems. We believe that the arXiv is a powerful tool for efficient Scientific communication and are suggesting a few simple but important improvements that will strengthen it. We suggest to introduce minor changes that will allow the following: a. An easy and quick way to directly access electronic data which is presented in figures and tables. b. A flagged citation system which will allow easy access to objections or confirmations of published results. Instead of a uniform list of citations, you will be able to see separate lists of objections and confirmations.

During the discussion a few ideas came up: 1. direct access to programing codes which are used to obtained results. 2. A way to encourage people to use the required standards by having a symbol attached to papers which confirm with the agreed standards. 3. A more far-reaching goal of making electronic publications interactive (e.g. allowing the reader to choose new parameters and see their effect on the results).

Present were:

      Jim Cleaves, ELSI, Tokyo, and IAS, Princeton
      Douglas Duckworth, Temple University, Philadelphia
      Aaron Goldman, Princeton University, Princeton
      Piet Hut, IAS, Princeton, and ELSI, Tokyo
      Jenny Jim, College University, London, and IAS, Princeton
      Boaz Katz, IAS, Princeton
      Alex Lamb, Princeton University, Princeton
      Kinnari Matheson, Princeton University, Princeton
      David Spiegel, IAS, Princeton


Investigating Ancient Amino Acid Biosynthesis

[by Jim Cleaves and Kinnari Matheson]

Our seventh IPA@IAS lunch took place on March 7, 2013.

Kinnari began by discussing her rotation project concerning the evolution of the amino acid biosynthesis pathways. She described how she had compared the biosynthetic pathways presumably present in LUCA and found that the amino acids which presumably entered the genetic code last (Tyr, Trp and Phe) had the most highly conserved enzymes. This led to a discussion of how novel enzyme functions and folds arise, and how the biosynthetic pathways in general arose, and whether the patchwork hypothesis or the retrograde hypothesis was more strongly supported by existing data. We then discussed whether a minimal genome was a good representation of a primordial genome and the nature of parasitism, the origin of viruses, and how organisms lose function when it is compensated for by a host's metabolism.

The reoccurring theme in early molecular evolution of observing phenomena that are "just good enough" to perform certain reactions (frozen accident theory), possibly in the presence of a better mechanism of carrying out certain functions was mentioned. One member proposed an analysis of taxonomic distribution of two proteins of comparable function to resolve this idea. Discussion about an exploration of organisms that have biosynthetic pathways with proteins predicted to have ancient features followed. The flaws in the reverse citric cycle as a possibility for early metabolism were mentioned, as the citric acid cycle is more representative of eukaryotic metabolism.

Present were:

      Jim Cleaves, ELSI, Tokyo, and IAS, Princeton
      Aaron Goldman, Princeton University, Princeton
      Kinnari Matheson, Princeton University, Princeton
      David Spiegel, IAS, Princeton
      Ed Turner, Princeton University, Princeton


How many and what types of parts are needed for a universal constructor, or an open-ended Darwinian system?

[by Jim Cleaves]

Our sixth IPA@IAS lunch took place on February 28, 2013.

We began by discussing the number and types of agents that need to be involved in an open-ended evolvable system. This led to discussion of the recent publication of simple bi-molecular sets which spontaneously crystallize to form fibrous H-bonded structures, possibly of relevance for the spontaneous generation of proto-nucleic acids. This led to a discussion of the "primitiveness" of the ribosome, and why, given its relatively poor catalytic rate enhancement relative to protein enzymes, it has not been supplanted by a better system, and why there remain no vestiges of the previous system.

This in turn led to discussion of whether there could be a shadow biosphere based on non-ribosomal translation, or indeed of any other type of carbon-based biochemistry. We then discussed LUCA and horizontal gene transfer, and how the transition from Woese's postulated "communal LUCA" model could be explicable by game theory. We finished by a brief discussion of game theory and Dyson and Press's work on the iterative prisoners' dilemma.

Present were:

      Jim Cleaves, ELSI, Tokyo, and IAS, Princeton
      Aaron Goldman, Princeton University, Princeton
      Laura Landweber, Princeton University, Princeton
      Kinnari Matheson, Princeton University, Princeton
      David Spiegel, IAS, Princeton
      Ed Turner, Princeton University, Princeton


Thoughts on the meaning of "2"

[by Monica Nicolau]

Our fifth IPA@IAS lunch took place on February 21, 2013.

I started by introducing the idea that one of the characteristics that are deeply human is the need to tell stories about everything we observe. What we observe makes sense only when we put together our distinct observations into a coherent story, whether this story is "War and Peace" or an explanation of what happens when two galaxies collide, a mathematical theorem, or any scientific theory. I then moved on to recall my experience changing fields from pure mathematics to computational biology and how the nature of stories in each field is profoundly different. Observations in the wet lab were baffling to me at first and making the distinction between "a few" and "many", was difficult. In mathematics different numbers come equipped with a wealth of characteristics: some numbers are prime, others are squares, etc.

As well, when I first made the change the stories in biology were baffling. In pure mathematics stories begin with axioms and definitions, and they then proceed to develop into increasingly complex theories. In biology stories begin from the outside, noticing associations and working from the concrete, gradually to an explanation and a theoretical model. The different directions of building stories for explaining our surroundings make it just as difficult for a computational theorist to grasp the biology stories as it is for the biologist to grasp the mathematical stories. More confusing still is that we use the same words or labels for very different concepts or stories. To a mathematician the number 2 has extensive number theoretic properties: it is prime, it is the only even prime, mathematics involving the number 2 is profoundly different from mathematics not involving 2. To a biologist there is little difference between 2, 2.1, 1.9, 2.4, 1.93 and so on.

We went on to discuss how enriching it is to learn to understand the story language of different fields of study, from dance, to psychology, religion, biology or theoretical astrophysics.

The discussion was lively and continued for two hours.

Present were:

      Derek Bermel, IAS, Princeton
      Jim Cleaves, ELSI, Tokyo, and IAS, Princeton
      Sara de Freitas, Serious Games Institute, Coventry, UK
      Greg Fournier, MIT, Cambridge
      Piet Hut, IAS, Princeton, and ELSI, Tokyo
      Jenny Jim, College University, London, and IAS, Princeton
      Alex Masulis, Routledge, New York
      Sean Murphy, Howard Hughes Medical Institute / Janelia Farm
      Monica Nicolau, Stanford University
      David Spiegel, IAS, Princeton
      Ed Turner, Princeton University, Princeton
      Sheron Wray, University of California, Irvine


Valentine's Day Cookies

[by Piet Hut]

Our fourth IPA@IAS lunch took place on February 14, 2013.

We started with a string of discussions on a large variety of topics. Halfway there was a knock on the door of our little room, and in came a kitchen staff member carrying pots of coffee and a large tray of heart shaped cookies, ostensibly for Valentine's Day. We told him that it must be a mistake, by he was adamant and insisted to leave it all with us. First we wondered whether our new group, young as it was, already had acquired secret admirers. However, half an hour later we would hear that the coffee and cookies had been ordered for January 14, rather than February 14, that it was a clerical mistake, but that we should feel free to eat the cookies. Given the heart shape, we were quickly convinced that the cookies themselves were not one month old, but only the order, so we happily celebrated together.

Our conversation started around planets in the solar system. Ed mentioned the interesting coincidence that the current average pressure and temperature on Mars are close to the triple point of water. He also noted that not much of the surface of Mars is at the mean pressure. About half of the surface is lower, in what could have been the basin of an ancient ocean, leading to a higher pressure, while the other half is higher, with a correspondingly lower pressure.

We noted other curious coincidences, such as the fact that roughly 70% of the Earth is covered by water: it could easily have been almost all water, or almost no water. From there we moved on to the definition of a habitable zone around a star. Often, the temperature ranges used to delimit hability are given as 0 and 100 degrees Celsius, the freezing and boiling points of water. However, a salty solution of water can stay liquid to much lower temperatures. Perhaps definitions of habitable zones should be extended to 0 degrees Fahrenheit instead.

We also got into a discussion of basic chemistry. The question was raised by David of what is so fundamental about pH, the value that expresses the acidity or alkalinity of a solution. David asked why pH seems to be more fundamental than, say, salinity, in determining what kinds of life forms may flourish in a given environment.

Jim answered that the importance of pH in organic, inorganic and geochemistry can't be overestimated. pH has significant chemical effects with respect to solubility, reaction rates, redox reactions, etc. pH also has significant effects on the weathering rates of minerals, and the solubility and dissolution of ionizable gas species such as NH3 and CO2. In organic chemistry, pH exerts an important control on the ionization state of various functional groups, as well as their nucleophilicity, and the ease with which various moieties can serve as leaving groups in substitution reactions. pH also influences the structure and the function of many enzymes in living systems, and governs the keto-enol tautomer ratios in nucleic acids, which have significant effects on mutation rates in biological systems.

Finally we had a brief discussion about the complexity of Langton's Ant, a topic that had come up last week as well. We wondered whether any meaningful parallels could be drawn with questions related to the origins of life.

Present were:

      Jim Cleaves, ELSI, Tokyo, and IAS, Princeton
      Piet Hut, IAS, Princeton, and ELSI, Tokyo
      Hyun Ok Park, York University, Toronto, and IAS, Princeton
      David Spiegel, IAS, Princeton
      Ed Turner, Princeton University, Princeton


Tritium and the Anthropic Principle

[by Ed Turner]

Our third IPA@IAS lunch took place on February 7, 2013.
Here is a summary of the first half of our rather long lunch.

With only Jim, Piet and Ed present we began with a discussion of Andy Gould's paper Tritium as an Anthropic Probe.

In the first phase of the discussion we laid out the basic ideas in the Anthropic Principle as it is typically considered in cosmology and fundamental physics these days, namely that the universe in which we live is only one of some vast ensemble of universes among which the constants of nature vary in some (unknown) stochastic way and that the selection effect that we must occupy a universe in which those constants permit the development of intelligent life forms (like our putatively intelligent selves) is the explanation for their values. Gould's paper makes two points about this issue.

First he claims that exoplanet research and aastrobiology can (and will, he says) give us a better understanding of the physical conditions which may favor the emergence of intelligent life and thus shed light on the ensemble of universes and Anthropic Principle hypotheses, despite the view of some particle theorists and cosmologists that these fields are irrelevant to fundamental science.

Second he points out some parameters in nuclear physics, specifically the deuterium-tritium mass difference and the proton-neutron mass difference which could have led to a universe devoid of hydrogen, and thus perhaps of intelligent life, if they had been slightly different. He also discussed possible effects of such changes in these nuclear parameters on stellar evolution and planet formation. The two parts of his paper appeared to Ed to be largely disconnected.

Present were:

      Jim Cleaves, ELSI, Tokyo, and IAS, Princeton
      Piet Hut, IAS, Princeton, and ELSI, Tokyo
      Ed Turner, Princeton University, Princeton


Alien Life: Common or Rare

[by Ed Turner]

Our third IPA@IAS lunch took place on February 7, 2013.
Here is a summary of the second half of our rather long lunch.

After an hour or so of the above suggestion, Dave and his guest Linda Elkins-Tanton joined us, and the conversation soon evolved into one of the likely nature and prevalence of extraterrestrial life. How like life on Earth will it be? How common is it? Could we recognize it? Will it be mostly "low profile" (i.e., hidden in sub-surface environmental niches)? Etc.

This in turn led to questions about the OoL (Origins of Life) and the likely nature of the processes involved. Possibilities included:

1 - Extremely rare statistical events in which monomers chemically assembled to produce large "working" polymers such as nucleic acids and proteins versus

2 - Chemistry producing relatively simple/short (and thus not so improbable) oligomers with enough catalytic and replicative behavior to allow natural selection to begin versus

3 - Chemistry exploring the "space" of possible long polymers extremely sparsely but still producing life with high probability because a substantial fraction of such large polymers are (or allow the selective development of) life vs

4 - a model in which there are one or more intermediate levels of structure/organization between the monomers and biologically active/living complex polymers of extant life (this was termed "crossing the desert by taking advantage of oases along the way").

Although all agreed that we could not rule out any of the above scenarios (and perhaps others), there was fairly vigorous discussion, even debate, about which of the four seemed most plausible given what we know now. In the context of #4, there was considerable debate about how surprised we should be that these intermediate levels of structure/organization no longer exist on Earth (as far as we know), which is essentially Oparin's original proposal.

At the very end there was some musing about the possibility of writing one or more papers about either the four scenarios listed above and/or the general topic of repeated levels of structure emerging in systems of many interacting units of some sort . . . from a very general perspective and perhaps the possibility of relevant cellular automata calculations.

Present were:

      Jim Cleaves, ELSI, Tokyo, and IAS, Princeton
      Piet Hut, IAS, Princeton, and ELSI, Tokyo
      David Spiegel, IAS, Princeton
      Ed Turner, Princeton University, Princeton
      Linda Elkins-Tanton, Carnegie Institution, Washington DC


Replication or Metabolism First: False Dichotomy?

[by Aaron Goldman]

Our second IPA@IAS lunch took place on February 1, 2013.

This week, Aaron Goldman started the discussion by talking briefly about a topic that is often on his mind: the framing of research in the origin of life as a debate between two mutually exclusive approaches or dialectics. This often takes the form of "Metabolism First" vs "Replication First", but tangentially related or unrelated dichotomies are also presented, e.g. "Autotrophic Origin" vs. "Heterotrophic Origin" or "RNA first" vs. "Protein first". He began the discussion by introducing the "Metabolism First" vs "Replication First" debate and the important lack of semantic clarity that, in his view, perpetuates it (as well as the other two examples).

What is meant by "Metabolism"? What is meant by "Replication"? What is meant by "First"!?!? Here's an example of semantic ambiguity that we discussed: We may call a natural, non-biological process like that described by Günter Wächtershäuser "metabolism" if it does similar reactions to those seen in modern metabolism. But Aaron proposed that if we saw the same reactions happening today in a clearly non-biological context, we would hesitate to call it "metabolism". Also, the day before our conversation, a colleague told him that "metabolism" may be used to simply indicate a historical linkage between prebiotic chemistry and true biological metabolism. But, in this case, we were unable to imagine a scenario in which this assumption would not be true, either for "metabolism first" models or "replication first" models.

The conversation ended when we identified the source of the ambiguity of these terms, the murky understanding of the concept of life, itself. We came up with a somewhat satisfying, albeit incomplete, answer that life is somehow able to maintain low entropy while also generating a high level of chemical complexity. In the end, we decided that the only way to do this is a combination of "metabolism" and "replication" in which the whole system is subject to processes of natural selection.

Present were:

      Jim Cleaves, ELSI, Tokyo, and IAS, Princeton
      Freeman Dyson, IAS, Princeton
      Aaron Goldman, Princeton University, Princeton
      Piet Hut, IAS, Princeton, and ELSI, Tokyo
      Jenny Jim, College University, London, and IAS, Princeton
      Laura Landweber, Princeton University, Princeton
      Kinnari Matheson, Princeton University, Princeton
      Hyun Ok Park, York University, Toronto, and IAS, Princeton
      David Spiegel, IAS, Princeton
      Ed Turner, Princeton University, Princeton


IPA: A New Brew at IAS

[by Piet Hut]

Our first IPA@IAS lunch took place on January 25, 2013.

IPA stands for Interdisciplinary Perspectives on Abiogenesis. All extant living organisms originated from other living organisms, through what is called biogenesis, life arising from previous forms of life. In contrast, abiogenesis indicates the formation of life from non-living matter, the transition from more and more complex chemical reactions to biology.

These lunches will be held weekly, for a few months each semester, at the Institute for Advanced Study, hence IPA@IAS. They are organized by the Program in Interdisciplinary Studies, which has an affiliation with ELSI, the Earth-Life Science Institute at ELSI, in Tokyo, Japan. Present were:

      Jim Cleaves, ELSI, Tokyo, and IAS, Princeton
      Aaron Goldman, Princeton University, Princeton
      Piet Hut, IAS, Princeton, and ELSI, Tokyo
      Jenny Jim, College University, London, and IAS, Princeton
      David Spiegel, IAS, Princeton
      Ed Turner, Princeton University, Princeton
      Sara Walker, Arizona State University, Tempe

We all introduced ourselves, describing our various backgrounds: computational biology for Aaron, astrophysics for David, Ed and Piet, astrobiology for Sara, analytic chemistry for Jim, and clinical psychology and neuroscience for Jenny.

A wide range of topics were discussed, from computer simulations of artificial life forms, the possible role of viruses in the early evolution of life, the use of Bayesian statistical methods to estimate the frequency of the occurrence of life in the Universe, and finally the structure of lop-sided phylogenetic trees, such as those occurring for bacteria and for vertebrates.



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