Alternative Chemistries of...

Alternative Chemistries

of Life

Empirical Approaches

CALL to ACtion

By defining the genome of Earth’s oceans and the chemical composition of exoplanets within habitable zones around other stars, we step ever closer to defining life and the chemistry that underlies its range. Could life on Earth represent the single solution, radiating from a point across space and time, or are there different forms, alternative chemistries that emerge in very different molecular environments? Any discovery of alternative chemistries that oper-ate orthogonal to and independent of our current central biochemical dogma will change the understanding of our place in the universe. this workshop was a first critical step, bringing together diverse constituencies to not only define alternative chemistries, but also to focus on where and how to look. the collective results are profound, both in terms of scientific necessity and our future survival. in this report, we share the implications and the actions that emerged both to inspire and expand collaborations across scientific and international research communities and to mobilize our collective wisdom in shaping and guiding our biochemical future.


of Life

Empirical Approaches

A Report from a Workshop on Alternative Chemistries of Life: Empirical Approaches

this material is based upon work supported by the national Science Foundation and the national Aeronautics and Space Administration

under Grant no nSF CHE1212371

the opinions, findings, interpretations, conclusions or recommendations expressed in this material are those of its authors and

do not represent the views of the funders.

Copyright 2014. All rights reserved.

iSBn:

Editors

Jay t. Goodwin

David G. Lynn

Co-authors

Cynthia Burrows

Sara Walker

Shady Amin

E. Virginia Armbrust

AcknowledgmentsWith funding from the national Science Foundation (nSF) and the national Aeronautics and Space Administration (nASA), we were able to bring together a remarkably diverse group of innovative and accomplished researchers for our 2012 workshop held in Washington, DC. We sincerely thank these scientists for their enthusiasm, their creativity, and their willingness to engage collaboratively in the discussions of what represents alter-native chemistries of life and where we go from here.

We gratefully acknowledge David Berkowitz and Katherine Covert of the Mathematics and Physical Sciences Directorate, Division of Chemistry at nSF, as well as Michael new and Mary Voytek of the Astrobiology Program at nASA, for their cross-agency coordination, guidance, and support in helping us organize, run, and report on the workshop.

And most specifically, we thank Marilyn Fenichel of Cassell & Fenichel Communications, LLC (publications management) and Gail Peck of Peck Studios, Inc. (graphic design) for their expertise, creativity, and masterful patience in bringing this report to fruition.


of LifeEmpirical Approaches

The report’s authors, from left to right: (back) David Lynn, Jay Goodwin, (front) Sara Walker, Ginger Armbrust, Shady Amin, and Cindy Burrows.

For more information visit http://chemistry.emory.edu/home/assets/alternativechem.pdf 5

alternative chemistries of life Empirical Approaches

i n April of 2012, researchers from Emory University, Arizona State University, the University of Utah, and the University of Washington jointly hosted a

workshop, sponsored by the national Science Foundation (nSF) and the national Aeronautics and Space Administration (nASA), focused on research into alternatives chemistries of life. Such research opportunities are driven by the emergence of numerous technologies, including metagenomic analyses and meta-data processing, as well as rapidly accelerating discoveries of exo-planets beyond our solar system. Accordingly, the purpose of the workshop was to bring together diverse scientific communities that have not histori-cally collaborated but could directly guide these opportunities and engage in them. Both nASA’s astrobiology and nSF’s chemistry programs support researchers working in the broad areas of alternate biopolymers, alternative metabolism and new metabolic functions, and the identification and charac-terization of organisms in extreme environments. these programs fund scien-tists whose theoretical and experimental expertise provide the tools needed to advance our understanding of newly revealed alternative chemistries.

Scientists working in different disciplines, including chemists, physicists, microbiologists, and virologists, came together in this workshop to discuss alternative chemistries research from their distinct perspectives. A number of fundamental topics were addressed, including alterative biopolymer back-bones, novel chemical reactivity within dynamic networks, and the emergent properties of macromolecular assemblies and complex systems that consti-tute living matter. Small breakout groups considered a series of questions, with each group reporting back to the collective workshop participants. Given the relative novelty of bringing these diverse disciplines together, distil-lation of the important concepts involved finding a common nomenclature, elaboration of the recent advances and primary questions of different disci-plines, and identifying the opportunities that truly connected the individual interests. We have done our very best to capture the richness of the discus-sion and to focus the findings around implications and next steps. However, it was possible to capture only a small portion of the marvelous ideas that sur-faced across those few days. therefore, our major conclusion is that this event

Preface

http://chemistry.emory.edu/home/assets/alternativechem.pdf

6

PREFACE

needs to be repeated often given the wealth of scientific opportunities that are now emerging.

We are immensely grateful to all workshop participants for their time, energy, and ideas. this report reflects many of the discussions that surfaced during the workshop. Like a pebble landing in a pond, we hope the radiating energy continues to spread throughout our community.

Various topics are organized in chapters on top-down causality, bottom-up emergence, and the diverse interface now forming between and connecting the two in a region we call the golden spike. in each chapter we develop a set of research implications and next steps that we distilled from the discus-sions. We certainly anticipate other opportunities will appear with time, and we hope the identified actions will catalyze the development of a road map for future discussions and research opportunities, as well as other workshops and symposia. in the spirit in which this report was developed, we urge you to circulate it widely among your colleagues in all relevant dis-ciplines and at professional societies and foun-dation meetings, and to participate in what we hope will be multiple follow-up workshops and symposia.



ContentsExecutive Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

Background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8top-down Causality . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8Bottom-up Emergence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9the Golden Spike : Where Top-down Causality and Bottom-up Emergence Converge . . . . . . . . . . . . 9Policy implications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9What the Future Holds: A Call to Action . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

1. Defining Alternative Chemistries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .13

Disequilibria . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14Modes and Flow of information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14Cooperative Dynamic networks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15the Ribosome as an Example of a Dynamic Chemical network . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .16

2. Causality and the Diversity of Life from the Top-down . . . . . . . . . . . . . . . . . . . . . . . . .17

Mission: Planet Earth . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18the Chemical networks of Life . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19Moving away from the Chemical networks of the Central Dogma . . . . . . . . . . . . . . . . . . . . . . . . . . . .22Findings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .22Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .25

3. Emergence in Macromolecular Order from the Bottom-up . . . . . . . . . . . . . . . . . . . .27

Looking at the Chemical Evolutionary Landscape . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28networking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28the Art of the Possible . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29Jump-starting Bottom-up Chemical Evolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .32 Findings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .33Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .36

4. Where Causality and Emergence Meet: The Golden Spike . . . . . . . . . . . . . . . . . . . . . .39

imagining the Possible . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40navigating Spiky Domains . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41orthogonal but not immaterial . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41the Shadow Biosphere . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42Findings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .42Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .45

5. Systems of Networks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .47

the next Frontier . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48Findings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .48Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .50

Appendix 1: Workshop Organizers and Participants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .52

Appendix 2: Workshop Agenda . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .54


8

Executive Summary

A wordle constructed from the workshop notes.

BACkgroundFor thousands of years, scientists have been both fas-cinated and perplexed about the origins of life. they wondered what life is, where it might exist, and what forms it might take. With scientific knowledge increas-ing at exponential rates, we are at the crossroads of our understanding. Recent developments in empirical and theoretical chemistry and biology have resulted in new ideas that are expanding our definitions of life and prompting a search for alternative chemistries on our planet and beyond.

intrigued by these new possibilities—and aware that it will take scientists from a range of disciplines to tackle these issues—nASA and nSF convened a work-shop, titled Alternative Chemistries of Life: Empirical Approaches, for biological and inorganic chemists, marine virologists, microbiologists, physicists, and other experts. the value of having so many scientific disci-plines represented was that it became possible to see how each perspective provides insights and contrib-utes to a more holistic examination of the origins of life. Beginning with the “central dogma” of biology, which defines the molecular basis of biological lineages and the Darwinian threshold of cellular life, the participants explored the general concept of alternative chemis-tries, particularly at the interface where top-down cau-sality and bottom-up emergence converge.

Figure E.1: The ribosome represents the invention that allows two biopolymer classes, nucleic and amino acids, to cooperatively set the central dogma of biology.

this report highlights three research realms, identified as top-down causality, bottom-up emergence, and the golden spike. Each is summarized in the following sections.

Top-down CAusAliTyAdvances in genome sequencing technology have allowed the molecular blueprint of all living things to be traced back to the emergence of the ribosome. From this molecular digital-to-analog converter radi-ated all cellular life. But we also learned that this blue-print is both far simpler and much more complex than we ever imagined. While the number of human genes is far fewer than we expected, our knowledge of the remarkable epigenetic coupling with the environ-ment and extensive lateral gene transfer throughout

evolution has radically changed our view of molec-ular heredity.

to truly understand this system, the range of diverse chemistry that makes it possible, and

the extent to which alternate chemistries may have been discovered and abandoned, we must now map the molecular underpinnings of life on Earth today.



the environment organisms live in—either here or on another planet—affects their growth, as does the diver-sity of organisms living together side by side. the nature of these relationships raises questions about how the environment affects and even alters genes, how the diversity of populations of organisms influences bio-chemical innovation, and how such interactions among organisms influence and shape environmental dynam-ics. the answers to these questions will significantly impact future survival.

BoTTom-up EmErgEnCEWhile the ribosome may be a pinnacle of molecu-lar innovation, unlocking the explosion of biological diversity on Earth that is still going on, this Darwinian threshold of cellular life was itself a result of eons of chemical evolution, directed not by a set of genotypic blueprints, but rather from the inherent, self-organizing properties of dynamic chemical networks.

Recognizing the importance of chemical networks, research in this realm is taking shape through the development of new models in the laboratory. these models allow scientists to explore how separate and chemically distinct genotypic and phenotypic molecu-lar representations emerge. this work not only extends the space of standard biochemistry, but also requires completely new formats in the realm of chemical evo-lution. the ultimate goal is to sort out the chemical and environmental determinants that both allow for devel-opment of autonomous chemical networks and shape their evolution into unique functional forms.

ThE goldEn spikE Where Top-doWn CausaliTy and BoTTom-up emergenCe Convergethe term “golden spike” refers to the last spike driven into the rails connecting the Central Pacific and Union Pacific Railroads, creating the country’s First transcontinental Railroad. Similarly, research at the intersection of top-down causality and the molecular diversity of bottom-up emergent dynamic chemical networks explores a unique space between chemical and biological evolution. Just as a pebble thrown into a pond creates ripples moving

outward from the center, so alternative forms of life may emerge from the golden spike. it is even possible that there are other forms of life alongside those pow-ered by the central dogma—what is often referred to as the shadow biosphere—at this juncture.

Although research at this juncture presents significant challenges, it also offers remarkable opportunities for alternative biochemical innovation. First, this opportu-nity encourages scientists to visit regions of the evo-lutionary landscape not previously explored through Earth’s history. Second, research findings could change what we currently think of as the pre-Darwinian threshold—before the appearance of the ribosome —through the discovery of new signatures that emerge from dynamic chemical network research.

in fact, the best way to understand dynamic chem-ical networks is by looking at these three research realms holistically. Genetic information (genotype), physical characteristics (phenotype), and environment are engaged in a highly complex, integrated dance, informing how we search for alternative chemistries and where. As discussed in a 2004 workshop spon-sored by the national Research Council of the national Academies, the same thinking may apply to the search for nonstandard biochemistry (i.e., different from what we find as the extant biochemistry of Earth) in known solar system environments and conceivable extra-solar environments. the workshop report, Limits of Organic Life in Planetary Systems, also identified scientific oppor-tunities that might guide research directions. this report preceded the initial findings from the Kepler Mission about the abundance of planets around nearby stars, some in habitable zones. taken together, these two dis-coveries further raise the possibility of varied life forms

outside our solar system and highlight the emerg-ing technology capable of detecting life

where we least expect it.

poliCy impliCATionsthe following policy implications are meant to serve as guidelines for the scientific community, government agencies, and policymakers as they

consider how to support continued research.


10

ExECUtiVE SUMMARy

guidelines for Top-down researchn the search for signatures of alternative forms of bio-

chemistry is currently taking place in diverse and extreme environments. these efforts must continue and be expanded so that the research has a more comprehensive, global reach. For example, research such as the proposed Earth Microbiome Project, designed as a collaborative initiative to map micro-bial communities across the globe, will be broadly impactful.

n the extraordinary wealth and volume of data resulting from these searches will require building meta-databases that can map multiple, autonomous systems. to complement these databases, informa-tion technologies will be needed to facilitate data analysis and interpretation throughout the broader scientific community.

guidelines for Bottom-up research n Domestic support for systems chemistry and

dynamic chemical networks research must continue and be expanded, with an eye toward greater inter-national collaboration.

n the need to experimentally develop autonomous chemical networks that manifest the entirety of evo-lutionary characteristics and operate at the interface of two or more of the defining properties of living matter will be critical to successfully anticipating alternative biochemistries.

n the need to extract defining “signatures” from these dynamic chemical networks amenable to identifying these and related systems in the field will also be criti-cal to success. this endeavor will drive the repurposing and modification of existing analytical methods and the potential for developing new technologies and experimental methods for detection, signal amplifica-tion, and characterization of alternative biochemistries.

guidelines for research at the golden spikeMuch work needs to be done before we can realize the potential of research at the golden spike. Below are some steps that need to be taken:

n Define where the living/non-living interfaces join.

n Define and explore orthogonal, or parallel, chemistries that operate differently from extant biochemistry.

n Determine the limitations in terms of where we inter-cede in extant biochemistry.

n Explore how extant biochemistry might pro-vide a platform for the evolution of alternative biochemistries.

n Develop tools for exploring a shadow biosphere.

n Determine how environmental characteristics might circumscribe the possible diversity of alternative chemistries derived from extant biochemistry.

n identify the fundamental signatures of alternative biochemistries and which signals can be detected from within the background noise of extant biochemistry.

n Determine what bioethics and biosafety issues must be addressed.

whAT ThE FuTurE holds: a Call To aCTionit must be emphatically stated that no one research realm will have an exclusive purchase on finding alter-native chemistries of life here on Earth and elsewhere in the universe. Rather, the way these research direc-tions complement each other and the collaboration that takes place among those involved in each type of research will be critical in determining success. these ongoing efforts, combined with other new ini-tiatives, will demand visionary “Big Science” and “Big Data” programs in order to most effectively capture, catalogue, and interpret results. in fact, these demands will continue to drive innovations in new experimental methods and technologies, along with sparking the imagination of the scientific community and the gen-eral public.

to continue the dialogue among different scientists from different disciplines and sustain interest in the search for alternative biochemistries, the following guidelines could inform future efforts in this area.

guidelines for Continued dialoguen the inaugural workshop proved to be a remarkably

productive event for reviewing current state-of-the-art science, establishing cross-disciplinary dialogue, and generating new ways of thinking about the outstanding questions for alternative biochemis-tries. it is strongly recommended that similar efforts be made to bring together scientists with diverse interests spanning the fields required to address



these global scientific questions, further elaborate innovative approaches, and strengthen collaborative efforts. Guiding examples for these future workshops include the nSF ideas Labs initiative.

n national and international scientific conferences can be used to engage the broader community to consider other empirical approaches to these ques-tions. Print and social media are also ways to raise awareness.

n the broader significance of the public’s under-standing of scientific theories can be highlighted and re-cast in the study of chemical evolution. new StEM (Science, technology, Engineering and Mathematics) to StEAM (StEM + Art) initiatives should be directly engaged.

n the broader impact of the search for alternative chemistries of life can be anticipated along a variety of pathways, including motivating more students to take courses in StEM disciplines and learn about ongoing research. A broader engagement of the public on issues related to StEM research and edu-cation will increase support for governmental, aca-demic, foundational, and industrial efforts to address domestic and global grand challenges, such as eco-nomic development, environmental sustainability, and climate change.


“there is grandeur in this view of life . . . from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.”

Charles Darwin, The Origin of Species



the workshop clearly established that we find ourselves on the threshold of a broad multi-dimensional understanding of

the chemistry that underlies biology. Furthermore, many of the necessary research innovations are currently in place to explore the alternative limits of what we now call life. these innovations include a top-down, systems-biological survey of extreme envi-ronments; a bottom-up, systems-chemical approach to assessing emergent behavior of inanimate yet dynamic chemical networks; and a third path, working at the interface of inanimate and living matter and moving concentrically outwards to explore the poten-tial landscape of alternative biochemistries.

Any consideration of what is “alternative” must be placed within the context of the known range and diversities of extant chemistries of life. initial considerations of current biochemistry might suggest that life has already searched every corner of the periodic table to create a set of marvelously complete dynamic chemical networks. that said, however, there is the possi-bility of alternative biochemistries within the known networks of life, as well as novel chemical reaction networks. As we explore ever more remote niches on Earth, subtle changes in resident biochemistries allow for different strategies to exploit the available physical, geochemical, and biotic richness. But as these niches become more extreme, from deep in the oceans to the limits of our atmosphere, from the planets of our solar system to the exoplanets of other suns, how might these chemistries change?

the workshop participants were charged with considering the chemical foundations of living systems, how these foundations might constrain life as we understand it in these diverse environments, and what experimental approaches are now available to better define these limitations. therefore, we begin with three essential criteria that define the chemical foundations of living systems: disequilibria, modes and flow of information, and cooperative dynamic networks. these criteria emerged during the workshop as ways to identify the role of chemical evolution in revealing the potential diversity of alternative chemistries and constraints on their development.

Chapter 1

Defining Alternative Chemistries

NUCLEICACIDS

LIPIDS

PROTEINS PEPTIDES& AMINO ACIDS

Figure 1.1: The most com-monly accepted theory about the origins of life on Earth is that it emerged from an evo-lutionary threshold combining nucleic acids, amino acids, and lipids into a functional core biochemistry.


14

Chapter 1: Defining AlternAtive Chemistries

1. disEquiliBriALiving systems display a progressive growth in molecu-lar order driven by an environment maintained far from equilibrium. the forces that maintain these disequilibria may come from planetary composition and the result-ing internal dynamics or from constant irradiation from a nearby star, but these energy sources are essential to shape chemical adaptation and selection. Earth has many local and global energy sources, and the diver-sity of niches that life fills as a result of these varied inputs is one of the great wonders of our planet. this diversity emerges through the evolutionary discovery of new biochemistries, yet much of this chemistry may remain hidden due to the small fraction of living organ-isms that have been cultured and studied in molecular detail. Metagenomics, the study of genetic materials recovered broadly from environmental niches, has made it possible to sequence the genomes of entire communities of organisms, including species that cannot yet be cultured and analyzed. Metagenomic surveys are giving us an unprecedented look into the structure of metabolic communities, including how metabolomes are shaped by the geochemistry of the organism’s host environment. these data sets are pro-viding new insights into how biochemical reaction net-works have evolved to harness diverse energy sources through the incorporation of novel chemical pathways tailored to specific environmental contexts.

2. modEs And Flow oF inFormATionDevelopments in next-generation sequencing tech-nologies have led to a veritable explosion in genetic sequence data; in 2012 alone, more than 10,000 new genome sequences were published. Advances in syn-thetic biology have allowed organisms to be re-engi-neered with new genes; even whole genomes crafted from chemically synthesized DnA have been trans-planted into existing cells (Gibson, 2008; Gibson, 2010). these technologies—sequencing and synthetic biol-ogy—are creating both a huge reservoir of informa-tion for reprograming biology and new fundamental insights into the chemical foundations of living systems. nowhere are these changes more obvious than in the realization of the prevalence of horizontal gene transfer as a pathway to biological diversity. What was once con-sidered a “tree of life” has morphed into a “coral of life” (Gaucher, Kratzel, and Randall, 2010), where information

flow is not limited to descendent lineage, but is also impacted by non-classical Darwinian gene transfers. Perhaps not surprisingly, the most prevalent genes found in the metagenome of our planet today code for transposases and retrotransposases, enzymes that mobilize genetic material from one organism to another across unrelated genomes (Aziz, Breitbart, and Edward, 2010). Also, it is now clear that the number of genes in an organism do not define its complexity. Rather, nature and nurture are critical parts of a web of information that not only informs the daily behavior of an individual, but also transmits that information to its progeny.

the discovery of novel groups of microbes, such as ammonia-oxidizing archae (Fuhrman, 1992), mimivi-ruses (Moreira, 2008, ogata and Calverie, 2008), and large megaviruses that carry more than 900 genes have challenged our notions of what constitutes new life. Do these viruses actually represent steps toward new life, or do they suggest clever twists on known chemistries that enable the exploitation of new environments? these genetic signatures, accessible through recent technological innovations, have reframed the questions of when, where, and how to look for alternative chem-istries and have opened a new window on alternate energy sources for living matter. Such approaches are, however, limited to the existing chemistries of genetic information flow in biology; any new, non-standard genetic systems driven by environmental perturbations may not be readily observable.

in addition, it is evident that nucleic acids are no longer the sole source of stored information; proteins define another form of heredity, one that lies outside genetics (epigenetics), where protein infectious particles follow a distinct, chemically guided evolutionary pathway of conformational propagation, selection, and diversifica-tion. Hereditable molecular information is therefore far more complex and multifaceted than that traditionally represented by the central dogma, even within extant biochemistries. Such epigenetic-like mechanisms operate synergistically and even in competition with traditional genetics, undercutting the simplistic central dogma model, where information flows only from gene to protein. As a result, our search widens to look for even more diverse forms of hereditable molecular infor-mation across dynamic chemical networks.



3. CoopErATivE dynAmiC nETworksDisequilibria and the forces that drive them on Earth are rarely constant over time and space such that any organism-defining information system must remain dynamic and responsive to acute as well as more long-term perturbations. Primary metabolism offers a well-explored example of an interweaving, interdepen-dent, and self-regulating network that appears univer-sally across the domains of life. Metabolism manages the cellular conversion of physical to chemical energy, the redistribution of raw materials according to organ-ismal needs, and the acute and chronic responses to environmental inputs. the far less regulated envi-ronment outside the cellular boundary is the source of possibly far more complex and dynamic informa-tion-defining viability. For example, humans harbor and co-evolve with bacterial cells that outnumber host cells by 3:1, and the genetic potential of this micro-brial community is estimated at 300 bacterial genes for every human gene (Reid and Greene, 2013.) We can therefore consider the human organism as a walking ecosystem, where the intimate symbiotic coordination with this microbiological community creates the work-ing whole (Mitreva and the Human Microbiome Project Consortium, 2012). it seems highly likely that the inter-cellular chemical signaling landscape between host and guest organisms must be at least as dynamic and information-rich as that of primary cellular metabolism, suggesting another driving force to diversifying bio-chemistries of living matter on Earth.

ThE riBosomE As An ExAmplE oF A dynAmiC ChEmiCAl nETworkthe rather stunning degree of chemical cooperation among widely divergent organisms may have its roots in, or at least be foreshadowed by, the collaborative molecular evolution that led to the information-pro-cessing machinery of contemporary cellular life. the ribosome, a supramolecular ribonucleoprotein assembly composed of up to four RnA subunits and more than 70 ribosomal proteins, is central to this processing and is considered a Darwinian threshold for the evolution of cellular life (Woese, 2002). this critical evolutionary tran-sition functions as a molecular digital-to-analog con-verter (DAC) for two distinct biopolymers, nucleic acids and proteins (Goodwin, Mehta, and Lynn, 2012). nucleic acids represent the digital part of the system, capable

of storing large amounts of information with exacting accuracy, while proteins are more analog in their physi-cochemical engagement within and among themselves as well as other molecular species, facilitating com-munication with a tremendous diversity of chemical networks, both intra- and extracellular. the ribosome combines these functions to form a single, dynamic molecular system. As a result, the ribosome can leverage chemical and physical environmental inputs to drive the selection and propagation of new biochemical func-tions while enabling the storage of genetic information, unifying biological genotype with phenotype. the evo-lutionary innovation of the ribosome is key to the bio-logical diversification that has led to the three domains of life characterizing our world today.

Figure 1.2: A model of how chemical and biological evolution came together, resulting in the central dogma, the Darwinian threshold for life.

taken together, Figures 1.1 and 1.2 broadly illustrate the concepts uniting chemical and biological evolu-tion. the ribosome represents the Darwinian threshold transitioning from abiotic chemical processes to cellular life. the chemical and physical properties and functions of living matter that emerge from the collaboration of dynamic chemical networks serve to frame the follow-ing discussions of the workshop outcomes.

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Chapter 1: Defining AlternAtive Chemistries

Summary the workshop discussions centered on disequilibria, molecular information, and progressive dynamic networks as necessary functional criteria for transitions from inanimate to living matter. We have addressed how each of these criteria impacts the three distinct research perspectives into alternative chemistries of life. Subsequent chapters focus on top-down, bottom-up, and the golden spike, the conceptual and experimental interface between extant biochemistry and novel dynamic chemical networks and research realms, as well as the likely policy implications in support of these research directions.

We live in a time when our understanding of complex systems is growing rapidly, when the discovery of new planetary bodies around nearby stars is accelerating, and when fundamentally new molecular-scale insights are changing our view of the potential cosmic uniqueness of humanity and life on Earth. the timing of this report is therefore critical to the sustained and long-term sup-port and guidance of the current exploration and future research directions into alternative chemistries of life.

Citations

Aziz, R.K., Breitbart, M., and Edwards, R.A. (2010). transposases are the most abundant, most ubiquitous genes in nature. Nuc Acids Res 38 (13): 4207-4217.

Furhman, J., (1992). novel major archaebacterial group from marine plankton novel major archaebacterial group from marine plankton. Nature 356(148-149).

Gaucher, E.A., Kratzer, J.t., and Randall, R.n. (2010). Deep phylogeny—How a tree can help characterize early life on Earth. Cold Spring Harb Perspect Biol (2): 1.

Gibson, D.G., (2008). Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science 319(1215).

Gibson, D.G., (2010). Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329(52-58).

Goodwin, J.t., Mehta, A.K. and Lynn, D. (2012). Digital and analog chem-ical evolution. Acc Chem Res 45(12): 2189–2199.

Mitreva, M., and the Human Microbiome Project Consortium. (2012). Structure, function and diversity of the healthy human microbiome. Nature (486): 207-214.

Moreira, D., and Brochier-Armanet, C. (2008) Giant viruses, giant chimeras: the multiple evolutionary histories of mimivirus genes. BMC Evol Biol 8(12).

ogata, H., and Claverie, J.M. (2008). How to infect a mimivirus. Science 321(1305-1306).

Reid, A., and Greene, S. Human Microbiome FAQ. (2013). Washington, DC: American Academy of Microbiology.

Woese, C.R. (2002). on the evolution of cells. Proc Natl Acad Sci 99(13): 8742-8747.



Chapter 2

Causality and the Diversity of Life from the top-down

Figure 2.1: The phylogenetic paths flowing down to the base of this tree culminate in the cell, the irre-ducible unit of known living matter. The central dogma serves as the Darwinian threshold that enabled the development of cellular life (Woese, 2002; Anolles, 2013), representing the quintes-sential collaboration between nucleic and amino acid polymers as the core of the central dogma and the base of the three domains of life: bacteria, archaea, and eukarya.

the true range and diversity of living matter on Earth remains unknown, and a complete understanding of

causality will require this knowledge. the tree of life provides a solid and ever-improving understanding of how diversity has emerged and documents the top-down historical tracings of the major branches of life in morphological, functional, and chemical terms. increasingly, however, the processes that inform our understanding of the origins of biological diversity reflect a coalescence of genetic information and environment, which together determine the structure of organisms and the chemical agency of biological evolution (Fig. 2.1).

Within this top-down view of biochemical causation (Walker and Davies, 2013), genome sequencing and improved com-putational algorithms have uncovered a remarkable variety of novel molecular mechanisms propelling biological and bio-chemical diversity. Pervasive horizontal gene transfer events (Dagan and Martin, 2006) blur the landscape into a massive system of chemical functional exchange, and epigenetic events incorporate immediate environmental fluctuations. the evolu-tionary forces can now be better viewed as a remarkable entan-glement of the flow of information that expands the traditional central dogma view of information transfer solely from DnA to RnA to protein to include interplay with the environment through the multi-directional flow of information. instead of a linear path, the flow of genotypic information appears as a series of overlapping chemical networks acutely responsive to their fluctuating environment. A deeper understanding of this larger web of life, driven by interactions with the environment and constrained by the fundamental physical-chemical proper-ties of matter, reveals new research opportunities.

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Chapter 2: Causality and the diversity of life from the top-down

mission: plAnET EArThDefining the true range and diversity of these chemical networks requires a more comprehensive accounting of what now exists on Earth, what is physically possible, and where these overlapping spheres may not con-verge. our view of living matter as an intertwining of environment with the translation of digitally encoded genotypic information into its analog, phenotypic man-ifestations is far from complete. Any attempt to catalog living matter and its associated biochemistries must be placed in the context of its interacting, intertwined envi-ronmental systems. in this chapter, we consider specific geological realms, the opportunities and restrictions they place on living systems, and how this confluence impacts and may drive existing dynamic chemical net-works (ignackiuk, 2012; Kasting, 2013).

the most basic divisions of environments on the sur-face of Earth are water, land, and atmosphere. Each has its own unique physical and geochemical character-istics, which in turn make possible the chemical net-works and life forms that emerge. An overview of this ongoing dynamic in each environment is considered in the following sections.

Aquatic realms oceanic realms are complex constructs of surface zones where the sun’s radiation impinges and pene-trates through a range of dynamic environments, all the way down to depths that sunlight can’t reach. We now know that these zones have distinct physical and geo-chemical characteristics, where other energy sources are required to sustain living matter. Marine environments are stratified by depth and temperature, which are circumscribed geographically by global currents such as the Gulf Stream and rotating currents (gyres). the regions closer to shore encompass the terrestrial and oceanic interfaces dominated by tidal dynamics. the vast size of the oceans and their material dynamics on a planetary scale, in terms of both vertical zones and horizontal long-distance conveyance such as through the

gyres, provide conduits for transport of genetic infor-mation, chemical nutrients, and thermal energy. these processes provide biogeochemical and global-scale connectivity to local ecologies and biomes in both freshwater and oceanic domains (Aufdenkampe, 2011). it is therefore critically important that highly accurate and precise spatial and temporal resolution accompany the mapping of genotypic information and metabolic inventories of aquatic environments (nSF Earth Cube; Aquarium of the Pacific and noAA, 2013).

Terrestrial Environmentsobservations of the diversity of plant and animal life around us, experiences that certainly inspired Charles Darwin, continue to motivate efforts to map the char-acteristics of soil, deserts, rainforests, and arctic climes, all of which influence local biome diversity. there is also a surprising degree of terrestrial biochemical diversity that remains hidden or uncharacterized in the sub-ter-restrial realm, not because we lack the tools to do so, but because these realms have not been more thoroughly searched (Rinke, 2013). At microscopic spatial scales and at individual and community levels, manifold factors determine the nature of biochemical and organismal dynamics. these factors include physical, mechanical forces of soil movement, such as particulate sieving and convective fluid flows, both of which allow for extraor-dinary biodiversity within very small environmental vol-umes. While terrestrial environments are generally more accessible to scientific search and survey than deep oceanic or atmospheric domains, they remain signifi-

cantly shaped by the dynamics of their connection with the other domains (Vos, 2013). nowhere is this more obvious than in the ever-increasing impact of human agricultural development, indus-trialization, and urbanization in shaping Earth’s aquatic and atmo-sphere realms.

Atmospheric domainsEarth’s atmospheric domain is perhaps the most dynamic and least well-understood part of our planet, in part because it touches both the terrestrial and marine



realms, and is sandwiched between them and the cos-mic space beyond Earth. As a result, this domain plays a vital role in filtering and shepherding the flux of cosmic energy and matter into and throughout Earth’s bio-sphere. Such cosmic “mobile elements” have historically contributed to the global molecular inventory, and they will continue to do so. in addition to continued depo-sition of organic matter onto Earth’s surface (Anders, 1989), this cosmic bombardment affects the atmo-sphere in several ways. Most obviously, the composition of the atmosphere is altered by the particulate matter, which can play a critical role in the reaction network of small molecules. this interaction then leads to alter-ations in spectral absorption and the reflection of the sun’s radiant energy, changing the amounts and very nature of solar energy and extraterrestrial matter that reach land and sea. Along with constant fluxes of bio-logical aerosols, or airborne particles that contain living organisms coming largely from marine surfaces into the atmosphere (Després, V. R., 2012), these processes provide templating surfaces that localize and concen-trate chemical reactions (Griffith, 2012) and adsorptive substrates to capture and transport microbial and viral species beyond their native geographic biomes (Whon, 2012). As might be anticipated from such complex sys-tems, these aerosolized chemical and biological partic-ulates likely feed back into global climate dynamics and geochemical processes themselves (DeLeon-Rodriguez and Lathem, 2013). the atmospheric dynamics, strat-ification, and diversity of associated geophysical and chemical processes, and the far-reaching connections to aquatic and terrestrial domains, suggest a much richer biogeographic realm, which has perhaps not been pre-viously considered in sufficient detail (Womack, 2010).

ThE ChEmiCAl nETworks oF liFEGiven the breadth and depth of Earth’s myriad environ-ments, how do we look for and characterize the range of associated biochemical forms? We are now posi-tioned to map the genetic sequences, metabolites, and non-equilibrium fluxes of electrons and chemical com-pounds within the context of the principal geological realms: marine, terrestrial, and atmospheric (Figure 2.2), but this task remains immense. Each environment dic-tates a differential availability of biochemically-relevant geochemical materials, including the elemental and molecular sources of the canonical “CHnoPS” inventory

and attendant metal ions. Moreover, the nature of sur-faces provided for chemical reactions and the conduits for energy flow maintaining disequilibria, such as redox reactions, chemiosmosis membrane potentials, radi-olysis via nuclear radiation, photolysis via sunlight, and the accompanying geothermal, spatial, and temporal dynamics (Sousa, 2013), suggest that no biological spe-cies and its attendant biochemistry operate in isolation from other organisms. And finally, the majority of genetic matter and biomass on Earth is found in the microbial realm, including bacteria, archaea, and single-celled eukaria. Viruses may outnumber microbes 10:1, rep-resenting enormous uncharted reservoirs of genetic dark matter that results in unseen consequences on the networks of life and serves as critical currency for genetic and biochemical innovations (DeLong, 2009; youle, 2012). Defining these chemical networks and their genetic currency offers an unprecedented opportunity to better understand and predict the range of alternative chemistries of life.

life Emerging from disequilibriathe extraordinary range and depths of Earth’s oceans and freshwater systems have yet to be fully explored, as clearly revealed by the steady flow of new discoveries, including the deep-sea alkaline hydrothermal vents of the Lost City Hydrothermal Field (Figure 2.3) (Kelly, 2001), where remarkable troves of unique life forms have been found. tiny, nearly transparent shrimp and crab living off methane and hydrogen may represent

Figure 2.2: Earth’s marine, terrestrial, and atmospheric realms.


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life driven by new redox chemistries, including the reduction of carbon by hydrogen to give off methane (Lane, 2012). these processes may be examples of early biochemistry, which exploited Fe(ii) and iron complexes and continued to evolve in new and unique directions as catalytic potential grew when other metals were captured. on a planetary level, radioactive decay, pho-tochemistry, and geochemical mixing also drive redox reactions, potentially over very long distances. For example, nielsen (2010) suggests that physical connec-tions between sulfidic and oxic zones of oceanic sedi-ments can drive electron flow through redox processes between different cell types.

Figure 2.3: Mineralized structures formed by hydrothermal vents at the Lost City.

Sequestered far from the light of day, operating at the boundaries of deep aphotic subsurface realms and ter-restrial and aquatic surfaces exposed to sunlight, there remains a wide range of uncharted uncharted areas uti-lizing an incredible diversity of biogeochemical disequi-libria. Adaptations to extremes of environment, such as to nonaqueous hydrocarbon milieu (Schulze-Makuch, 2011), suggest that different states of disequilibria drive the emergence of alternative biochemistries. Even within terrestrial realms, there is significant diversity of condi-tions, ranging from a high degree of connectivity among organisms to physical isolation, nutrient availability, and radiative and chemical energy input (ortiz, 2014).

The Flow of genetic informationGenotypic information flow is central to organism development, function, and evolution, but that infor-mation can be shared with other organisms and other species, often through viral pathways and horizontal gene transfer (Rohwer and thurber, 2009; Suttle, 2007). in fact, up to 10 billion microbes and as many as 100 billion viruses can be found in as little as 1 milliliter of seawater (Suttle, 2005). these particles play a critical role in the life cycles of other marine organisms, from microbial to mammalian, and the attendant flux of car-bon mass and elemental cycles throughout the oceans (Vardi, 2012). Environmental viruses can influence local biochemistries, which in turn feed into regional geo-chemical systems, atmospheric chemical and phys-ical processes, and hence global climate dynamics (Sinsabaught and Shah, 2012). Viral infections also facili-tate genomic diversification and the resulting biochem-ical innovations (Rohwer and thurber, 2009), serving both as genetic currencies, metabolic reservoirs, and transport systems to convey metabolic and functional chemistries into new microbial populations. these genetic transactions occur between all three domains of life, and given the globally connected nature of the land, sea and air, can spread genetic innovations beyond local ecosystems.

Exchange through a global Chemical internetCoordination of cooperative and symbiotic functions among members of a species or even between differ-ent species is mediated through chemical signaling and chemical/physical connections that appear as part of a global chemical “internet” within and between communities, as opposed to exchange of genetic material. Microbial populations use chemical signaling to coordinate behavior, such as quorum sensing, or communication among bacteria, (Waters and Bassler, 2005); the recognition of symbionts such as in legume symbiosis, in which bacteria induce nitrogen-fixing nodules on the roots of legumes to reduce the need for nitrogen in the soil; and as a defense against parasites and pathogens (Lin, 2008). Even in eukaryotes, spatial proximity and density can be tied to the ever-evolving chemistry that underpins the sophistication of cellular communication (Keyes, 2007).

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Exchange through mutualistic relationshipsClearly, “Life did not take over the globe by combat, but by networking” (Margulis and Sagan, 2001). the preva-lence of mutualistic and parasitic relationships within organisms offers a rich source for and evolutionary driver of new chemical inventions and alternative bio-chemistries. Large-scale, single-cell genomic analyses of uncultivated organisms (yoon, 2011) and surface ocean biomass (Swan, 2013) reveal the potential biochemical and genetic dynamics of complex microbial assemblies. Genome size has been correlated with such mutualistic networking, at least in bacteria; free-living species are larger than facultative intracellular organisms—those capable of reproducing either inside or outside of cells, which in turn are generally larger than those for obligate intracellular species—those that cannot survive outside the host cell—with the smallest average genome sizes found in obligate intracellular mutualistic organisms (toft and Andersson, 2010). novel metabolic interac-tion networks (Konwar, 2013) and previously unknown, metabolically capable giant viruses (Fischer, 2010), such as the one shown in Figure 2.4, have been revealed by the application of environmental genome sequencing. through more comprehensive and thorough genetic and biochemical analyses (Vardi, 2012), it is anticipated that novel, potentially alternative biochemistries will become more apparent.

Symbiotic relationships within and between microbial and marine animals evolve in the face of nutrient- and energy source-limited environments, such as within the ocean depths (Kleiner, 2012). Although the man-ner in which these remarkable symbiotic relationships develop remains shrouded, some of these pathways are coming into focus. they include the use of host waste streams of organic molecules, such as acetate; through

microbial symbioses; and through other small mole-cule species (carbon monoxide) generally considered toxic. other symbiotic pathways have been shown to leverage molecular hydrogen from the surrounding deep ocean vents, thereby bridging lithotrophic (those organisms that can subsist on inorganic substances) and oligotrophic (those that can subsist at low nutri-ents levels) food webs.

The role of Autotrophic organismsAutotrophic organisms, or the producers in a food chain, have been shown to use inorganic nutrients, such as dissolved nitrate and phosphate, in proportion to the ratio found in seawater, and upon death and decom-position, return those elements in the same proportion to the environment. this dynamic is referred to as the Redfield ratio (Falkowski, 2000 ). in this way, phytoplank-ton communities reflect and coordinate the chemical composition of whole oceans. Given this particular role of phytoplankton, it is possible that the concentrations of other inorganics, such as nitrogen compounds deter-mined by fixation and denitrification, are also biologically determined and linked together through microbial col-laboration (Dekas and Poretsky, 2009). By comparison, the availability of soluble inorganic phosphate appears to be determined principally by geological weathering and burial processes (Paytan and McLaughlin, 2007), and when in short supply, marine organisms find biochemi-cal workarounds (Van Mooy, 2009) to conserve limiting resources, likely for only the most vital and presumably intransigent biochemical processes. therefore, searching for chemical replacements for vital elemental nutrients in unusual niches (Wolfe-Simon, F., 2010) has tremendous potential for uncovering an ever-increasing array of alter-native biochemistries. Fluorinated natural products are a remarkable example of metabolites from alternative

dynamic networks, where non-canon-ical elements are utilized, even those that yield organic bonds traditionally considered highly reticent to biochemi-cal manipulations (Deng, 2004).

Figure 2.4: CRoV, currently the largest known marine virus, shown in comparison to other microbiological species.

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findingsthe scientific community is positioned to add significantly to our understanding of the relationship between environmental dynamics and development, evolution, and innovation in biological chemistry. Continued advances in theory, modeling, and sim-ulation of macrosystems ecology, geophysics, and systems-level research, combined with new analytical and sequencing methods, have made these advances possible. the implications for these advances in biochemistry, as well as their reach, will help build the foundation for our understanding of life on Earth, its origins, and its future sustainability. this workshop, however, was specifically concerned with how these new ideas will spur the discovery of alternative biochemistries, and it is these possibil-ities that are discussed in the following sections.

Moving away from the Chemical Networks of the Central Dogmait is possible that a true “shadow” biosphere exists as postulated by Cleland. this shadow biosphere would consist of living matter with a completely different biochemistry than that derived from extant central dogma. these alternative biochemical systems will have been invisible to us because, unlike current metagenomic approaches, we don’t yet have the proper “bait” to fish them from their hiding places—and they could in theory be hiding in plain sight. Clearly, this was the principal moti-vation for characterizing the bacteria in Mono Lake, California, because of the potential that arsenate instead of phosphate was biochemically incorporated into their genetic material. While the evidence has not sup-ported the existence of this alternative elemental substitution, the search for alternative biochemistries in extreme environments is certainly one of several valid approaches to consider. if we are going to move beyond “looking for our keys under the lamppost,” we will need alternative genetic polymers of distinctly different structural and chemical composition. We will also need to characterize the energetics of such systems in select-ing for self against non-self, excluding DnA and RnA from its alternative genomic materials. the possibility of protein machinery that provides for transcriptional and translational pathways to protein or even alternative phenotypic polymers that may supersede alpha-amino acid-based struc-tural and catalytic species will have to be pursued. these ideas and con-temporary research approaches will be considered in Chapter 4.



IMPLICATION 1: Elaboration and Expansion of Empirical Approaches for identifying Alternative BiochemistriesAlternative biochemistries can be found in many different ways. Within extant bio-chemistry, there are surely examples of diversity that we’ve yet to identify. therefore, we need to expand the search into unexplored and environmentally extreme domains around the globe. But we also need also to look into domains that might not be con-sidered extreme because a great wealth of genetic dark material is pervasive through-out terrestrial and aquatic environments. As a result, where and how we search, and how we address the complexity of what we find, requires addressing complex systems dynamics of biogeochemical and geographical hierarchies at multiple spatial and tem-poral levels. Genomic information, metabolomic species, and energy fluxes as principal signatures of developmental and evolutionary forces, placed in the context of imme-diate geochemical, geophysical, and biotic environments, can signify the presence of alternative, diverse biochemistries. through a comprehensive, collaborative effort to characterize the underlying chemistries of organisms represented by metagenomic and metabolomics signatures (overbeek, 2005), we have the capability to catalog the diversity of life’s chemistries on Earth. this effort will require continued in-the-field searching and surveying, correlating biochemical signals with their associated geo-chemical and geophysical temporal and spatial dynamics. Further, these broad-in-geographic-scope searches will require collaboration and coordination across national borders (Barbier, 2014), likely involving diplomatic and governmental science fund-ing-level engagements (nStC, 2013). Further, the manner by which we search for the signs of alternative biochemistries will continue to change with the advent of innova-tive, new technologies, driven by the need for providing robust data with a throughput necessary to encompass the scope and scale of Earth’s vast diversity of life. Examples of some of those challenges and empirical approaches are listed below.

NExT STEPS: improving signal to noise

Expanding the analysis of single cells

increasingly, chemical analyses can be carried out on smaller samples, and the ability of flow cytometers to rapidly segregate and analyze particles from samples

in situ (Muller and nebe-von-Caron, 2010; Martinez-Garcia, 2013) enables the analysis of single cells. Cells from various habitats, such as between coastal and open ocean water boundaries (Ribalet, 2010), can be used in conjunction with probes that target specific struc-tural features, such as biopolymers to confirm their association with uniquely identified individual microbial or viral species. Single-molecule analysis of genomes might reveal diverse chemical modifications in biopolymers whose presence would be lost in, for example, standard PCR amplification procedures.

Tracking the flow of matter through dynamic chemical networks

Stable isotope probing (SiP) can be used to quantify nutrient fluxes to organisms in their natural habitats. SiP relies on the transfer of nutrients containing a labeled element from one organism to another or from the

environment to an organism (Dekas and Poretsky, 2009; Close, 2013). these methods are culture-independent and can easily be applied to mixed biological communities.


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Characterizing the flow of genetic information

A major obstacle to comprehensively cataloging and characterizing microbiomes is that a majority of captured microbes simply cannot be cultured. Random (shot-gun) sequencing of uncultured microbes (the unknown majority) has resulted in huge breakthroughs by providing sequence information from whole communities of microbes through metagenomics (Simon and David, 2011). this approach relies on computer algorithms to stitch together short overlapping sequence fragments and generate contiguous longer fragments that may include multiple genes. the result is the production of gene inventories from different environments describing millions of potential microbial genes, which in turn enable the construction of entire genome sequences. these methods provide invaluable insight into the metabolism of organ-isms that cannot be cultured in their natural settings and their influence on their envi-ronment, including characterization of the unique interactions between organisms, which are not available when cultured in isolation. in combination with these analyt-ical methods, expansion of metagenomic and metatranscriptomic sequencing and analysis to single cells (Swan, 2013), along with continued improvements in sequenc-ing technologies (Shokralla, 2012), will provide a more comprehensive identification and in-depth characterization of alternative biochemical ecologies, as well as access to new and unique niches of diversity in all environments (Colwell and D’Hondt, 2013).

IMPLICATION 2: Embracing Complexityincreasing complexity is inherent to the flow from chemical to biological evolution (Lehn, 2002; Chaisson, 2011). While the search for and study of alternative biochem-istries is based on simplifying conditions by controlling for numerous variables and determinants, to truly understand the emergence and evolution of living matter and its possible alternative chemistries, we must address the complexities of the underly-ing networks (Woese, 2002) and their hierarchical relationships, from the molecular to the macro and planetary scales.

NExT STEPS: planning and Collaboration

Data management planning

the scope and scale of the accelerating search and survey of Earth’s biochem-ical diversity is driving exponential increases in the volumes and types of data. these metadata, including location and date/time of collection, inves-

tigators, and ambient environmental conditions, will require immediate, extensive, and highly-coordinated federation, quality control, curation, storage, and robust retrieval tools. these needs can leverage current “big data’” initiatives within government, indus-try, and academia, which are focused on these issues, as well as the development and application of innovations in cyberinfracture (hardware and software). Earth Cube, an nSF-sponsored program (www.earthcube.org) and the Fourth Paradigm (noAA, 2013) are among several contemporary efforts that can be emulated or built upon. With the wealth and diversity of data to be obtained through these search and survey efforts, systems-level modeling and simulations will be critical to constructing highly inte-grated, descriptive models defining and clarifying the causality of biochemical diversity (turuncoglu, 2011). Such modeling and simulation will in turn be vital to the prediction of alternative biochemistries in earthly realms yet to be searched and on planetary hosts elsewhere across the galaxy.

www.earthcube.org



Cooperation and collaboration across traditional disciplines

Locating and characterizing the signatures of alternative biochemistries will continue to employ a broad spectrum of scientific approaches and expertise. A powerful element of the workshop was the obvious need for perspectives

from physical geography, including aquatic, terrestrial, and atmospheric geochemistry and geophysics, to marine microbiology and virology, to analytical, organic, and physi-cal biochemistry. Data sharing, systems modeling, and meta-data information technol-ogies will be essential to coordinate these efforts.

Centrally organized workshops

Given the complexity of the search for and characterization of alternative biochemistries, as well as the need for cross-disciplinary collaborations, lon-ger-range planning for such fieldwork, data management, and modeling

efforts will be facilitated by setting up initial workshops in the mode of nSF “sandpits” and ideas Labs, along with other more regularly scheduled venues, such as the European CoSt Systems Chemistry meetings, Gordon Research Conferences, and multi-agency sponsored follow-up workshops.

Summary the inherent and hierarchical complex web of interactions of living matter within its biotic communities and across its geological environments has profound implications for how we understand sustainable living systems. the information will illustrate causality up, down, and across the web of life and reveal how the geological environment influences the development and evolution of biochemical diversity, processes that have significant agency impact-ing environmental and climate dynamics (the Royal Society, 2013). As developed in Chapter 3, the implications of the findings will richly inform “bottom-up” approaches both by adding greater granularity of environmental characteristics and dynamics (Leach, 2006) and informing “at the bench” chemical evolution/dynamic chemical network experiments.

Citations

Anders, E. (1989). Prebiotic organic matter from comets and asteroids. Nature 342:255.

Aquarium of the Pacific and noAA. (2013). The Report of Ocean Exploration 2020: A National Forum. Long Beach, CA: Aquarium of the Pacific.

Aufdenkampe, A.K., Mayorga, E., Raymond, P.A., (2011). Riverine coupling of biogeochemical cycles between land, oceans, and atmosphere. Front Ecol Environ 9: 53–60.

Barbier, E.B., Moreno-Maleos, D. Rogers, A.D.. (2014). Protect the deep sea. Nature 505: 475-477.

Chaisson, E. J. (2011). Energy rate density as a complexity metric and evolutionary driver. Ecol Complex 16(3), 27-40.

Close, H. G., Shah, S. R., ingalls, A. E., et al. (2013). Export of submicron particulate organic matter to mesopelagic depth in an oligotrophic gyre. Proc Natl Acad Sci 110(31), 12565-12570.

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Chapter 3

Emergence in Macromolecular order from the Bottom-up

As introduced in Chapter 2, a top-down view of biochemistry reveals a causal engagement of

form and function with the environment. Genome sequencing now displays in even greater relief the intricate molecular mechanisms that underpin life’s diversity. Each molecular blueprint highlights a com-plex, dynamic, progressive chemical system in constant flux, founded on deeply rooted and exquisite molecular networks. At the base of this molecular tree lie the seeds of the interface of abiotic chemical matter responding to envi-ronmental energy gradients. Christian de Duve described life as “a cosmic imperative” (de Duve, 1995), suggesting that the criti-cal elements of chemical evolution are an inherent property of matter (Davies, 2011).

our difficulties finding a definition for living systems suggest that our understanding of the evolutionary struggle toward sustainable chem-ical self-agency remains naïve. the enabling features and constraints that lead to a chemical evolutionary process, from inanimate matter to self-organizing, dynamic, and emergent properties of living systems, are not yet clear. Genome sequencing and improved computer algo-rithms have deepened our understanding of the evolution of biochem-ical systems, motivating the search for simpler, potentially abiological chemical networks and systems that self-organize with progressive, hierarchically structured molecular order. However, this bottom-up growth of chemistry is perhaps more difficult to investigate than an existing top-down system because complexity appears in a piecemeal manner, as an emergent property not necessarily predictable a priori.

CENTRAL DOGMA

DNA

RNA

PROTEIN

Figure 3.1: Bottom-up chemical evolution, where distinct chemical networks are represented by individual “cups,” each of which increases in diversity and complexity of composition as they progress in time (vertically). As these networks evolve, they can encounter other networks, resulting in the emergence of new and more complex chemical systems. The ribosome and central dogma of extant biochemistry represent the intersection and collaboration of ribonucleic and amino acid networks. This is shown here as the optimal evolutionary biochemical system on a hypersurface of many such possible systems, evolving from many distinct chemical networks.


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Chapter 3: EmErgEncE in macromolEcular ordEr From thE Bottom-up

looking AT ThE ChEmiCAl EvoluTionAry lAndsCApEAt early stages of “pre-biochemistry,” genotype and phenotype were probably not represented by separate molecular frameworks. With this simplifying assumption, the diverse organic and inorganic molecular inven-tories known today may interact with any number of planetary environments to yield chemical networks with the potential for emergent chemical function, as represented by Figure 3.1. As their functions build pro-gressively, cooperative molecular systems could emerge from multiple dynamic networks to magnify synergies via infection and parasitism. For example, cooperation could lead to the division of genotype from phenotype, a synergy that builds on the unique properties of each molecular scaffold, as is done today in information pro-cessing in extant biochemistry. Molecular cooperation in living systems exists at every level of information processing, with the threshold for cellular diversification attributed to the ribosome (Woese, 2002). this ribonuc-leoprotein, serving as the digital-to-analog converter for two biopolymer classes (Goodwin, 2012), may represent a pinnacle of chemical innovation. Such remarkable synergies are necessary for molecular networks to evolve toward the ever-increas-ingly sophisticated structures and functions of living systems (Fig. 3.2).

A good place to start in our search for emerging molecular net-works is to take a hard look at the chemical evolutionary landscape of Earth and determine how effi-ciently and thoroughly it has been explored over its history. our goal is to understand the physical limits constraining emergent functions; to assign “local minima” (the mini-mum features necessary for life to emerge) to evolutionary networks that are optimal only for their par-ticular environmental conditions; and to ascertain why and how they may have been selected over other environments. to realize this goal, we need methods to identify

alternative networks and/or their vestigial remnants in both unexplored geographical locales and directly under our feet. these chemical networks, potentially less robust in direct competition with those that have thrived in nature, could point toward the possibility of alternative biochemistries—shadow biospheres—not yet discovered here on Earth and elsewhere across the galaxy. the most logical place to begin this journey is with innovative and more in-depth exploration of chemical networks, how they can integrate into more complex systems, and how such systems might mirror the emergence of Earth’s web of life.

nETworkingLike metabolic pathways, cellular systems, and ecolog-ical communities, dynamic chemical networks (DCns) exist as fluctuating states of covalent and non-cova-lent assemblies, with their properties determined both by the inherent structures of network members and their potential for extracting sufficient energy from the environment to remain dynamic. As more complex structures assemble from simpler components within

a network, functional character-istics should emerge that lead to greater complexity through engagement with other chem-ical networks. the hereditabil-ity of DCns— their selection, propagation, and diversification of function over time—defines their evolutionary fitness.

the physical and functional manifestations of chemically evolving dynamic networks can be thought of as following a hier-archical “rule of three” (Fig. 3.3). the first dimension constitutes the covalent, macromolecular synthesis in sequence and chain length, with the complexity of the polymer reflecting the diversity in the monomer pool. the second dimension encom-passes the non-covalent folding and supramolecular associa-tions among the macromolec-ular species, where complexity

RNA PROTEIN

CHEMICALINVENTORY

CENTRAL DOGMA

CENTRAL CENTRAL

BA

CTER

IA

A

RCHAEA EUKA

RYA

Figure 3.2: The central dogma, emerging from a dynamic chemical network established the coop-eration between biopolymers and served as the Darwinian threshold for the three domains of liv-ing systems on Earth.



is reflected in the heterogeneity of the polymers and their folding diversity. the third dimension includes the chemical and physical functions emerging from the diverse structural networks of the first two dimensions. Dynamic feedback processes, both chemical and physi-cal, and across all dimensions of the network will under-pin the DCn’s evolutionary potential.

Simple chemical reactions are driven energetically downhill, but evolving systems operate in a state dis-placed from thermodynamic equilibrium. to main-tain the dynamics necessary for evolution, reversible non-covalent and covalent bonds have been used in model networks (Meguellati, 2012; Goodwin, 2012; otto, 2012; Giuseppone, 2012; Cougnon, 2012). Such networks can be subject to dynamic cycling or fluxes of materials and energy in both spatial and tempo-ral dimensions (Childers, 2012) as drivers of network evolution. Cycles of selection may well depend on the precise environment of the network (Epstein, 2012). Using biological networks as a guide, it may be possible for robust and agile DCns to respond to and capture changes in the environment and flourish through a progressive increase in functional capability.

ThE ArT oF ThE possiBlECollections of synthetic molecules competing through reversible chemical reactions have been shown to access macromolecular and supramolecular assemblies. Such dynamic networks can assemble into globular, linear, circular, helical, and columnar supramolecular arrays that have functions ranging from receptors to

sensors and catalysts (Schlizerman, 2010; Giuseppone, 2012; otto, 2012). the compositions of such systems have also been diverse, ranging from biologically derived materials (Li, 2011) to synthetic organic and inorganic systems (Ulrich, 2009; Long, 2009). our chal-lenge is to link the emergent potential of dynamic chemical networks back to the causality of top-down evolution. identifying the emergent functions present in simple networks will lead to functional connections and expression in other network dimensions for pro-gressive information exchange and evolution.

From our bottom-up perspective, the symphony of coordinated biochemical networks that define our current understanding of living systems serves as our guide. Many properties of the cell, the minimal unit of these systems, have been discussed from the per-spective of alternate solutions for chemical evolution in the December 2012 issue of Accounts of Chemical Research. For example, cellular confinement may range from encapsulation within sea-spray aerosol droplets, molecular adhesion to a two-dimensional surface, concentration within a eutectic salt/ice solution, or sequestration within bilayer assemblies. Extending this kind of analysis for understanding what might be pos-sible has been parsed into three basic categories: (i) Confinement, restricting chemical networks to defined two-dimensional surfaces or specific volumes; (ii) Metabolism, managing the network molecular inven-tory and transducing energy from the environment; and (iii) information, the chemical communication of the network with its surroundings and the molecular repository of hereditability. in further considering what might be possible in alternative biochemical frame-works of the cell, we have used these same categories to center our discussion.

Confinement Containment and confinement of chemical networks as provided by cellular membranes are necessary to separate and identify them as belonging to the organ-ismal “self,” distinct from the surrounding environmental “non-self.” At the same time, cellular membranes pro-vide for selective and specific chemical and energetic communication of the encapsulated chemical networks with the outside environment. Such feedback is critical to driving further development and evolution of the dynamic chemical systems. the features of abiogenic

TRANSLATION/GENOTYPIC INFORMATION

ENERGY TRANSDUCTION

TEMPLATING & CATALYSIS

SEQUENCE LENGTH

SEQUENCE COMPOSITION

1st DIMENSION:COVALENT

MACROMOLECULARINTERACTIONS

3rd DIMENSION: EMERGENT FUNCTIONALITY

AUTONOMOUS DYNAMIC CHEMICAL NETWORKS

INTRAMOLECULAR FOLDING

INTERMOLECULAR ASSEMBLY

HETEROGENEITY INCOMPOSITION

2nd DIMENSION:NONCOVALENT SUPRAMOLECULARINTERACTIONS

Figure 3.3: The three dimensions through which functional proper-ties emerge from dynamic chemical networks.


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containment can arise through a variety of physico-chemical processes. Geochemical environments can present interfaces such as air and water, aqueous and organic phases, and insoluble mineral surfaces in contact with water. Such environments are marvelously het-erogeneous in morphological structure and elemental composition, and can be very effective in concentrating certain materials. For instance, the water-air interface of aerosols provides advantages for chemical synthe-sis compared to bulk water, due in part to high surface areas and evaporation rates that concentrate interfacial materials. Aerosols can be long-lived, as well as dynamic, with high exposure to light and atmospheric reagents. As a result, the organic film at the surface of an aerosol concentrates and integrates organic chemistry into a two-dimensional reactor while also providing contain-ment for the polymer products (Griffith, 2012).

in the 1930s, Alexander oparin the-orized that complex coacervation, the phase separation that occurs when oppositely charged polymers assemble in solution, was a vehi-cle for abiogenesis. More recently, aqueous two-phase systems have been developed that separate into sub-compartments with their own unique compositions of lipid mem-branes, suggesting a mechanism for concentrating organic compounds into localized spaces (Keating, 2012). these physical phenomena likely

yield microreactors, similar to protocells, where nascent biomolecules can interact within physically confined volumes. At a far larger scale, the global geochemical process of dissipative redox chemistry can be distributed very differently across the planet, as was evident in our discussion of top-down causality. From microenviron-ments, to lakes and islands, to oceans and different plan-ets, any barriers to transport and dynamic fluctuations, even on these scales, can serve to compartmentalize and enable the emergence of alternative chemistries.

metabolism and Energy Transduction processes the possibilities for energy capture and transduc-tion are no less diverse. Living cells operate in a realm displaced from equilibrium, and maintain chemical potentials produced and consumed by a network of molecular reactions known as metabolism. Figure 3.5 shows chemiosmotic fluxes at hydrothermal vents, an example of chemical processes similar to metab-olism. the evolution of a chemical reaction network that catalyzes the synthesis of its constituent parts, an autotrophic network, may be achieved without a cell. Self-assembly and organization may well coexist with functional reaction networks that provide energy trans-duction in a way that can be utilized for replication and growth of the molecular network (Russell and Martin, 2010). Acquiring these functions may require complex systems, and finding simple models that mimic even the initial steps of such a network represent a primary research goal for future investigation.

in considering alternative biochemistries, an abundance of elements does not always correlate with an element’s use in biomolecules. For example, fluorine is highly

abundant in Earth’s crust, but bio-synthetically utilized in only a few natural compounds, likely limited by its particular electronic prop-erties (o’Hagan, 2008). the recent arsenate-containing DnA debate (Benner, 2013) has further sparked considerable interest in alternative compositions of nucleic acids and highlighted the need for microbiol-ogists and chemists to collaborate in developing innovative approaches for identifying and characterizing such alternative chemistries.

Figure 3.4: Aerosols can provide surfaces and volumes to confine and contain dynamic chemical processes.

Figure 3.5: Chemiosmotic fluxes at hydro-thermal vents mirror metabolic processes in living matter.



While extant biochemistry uses a limited set of mono-mers in the construction of biopolymers, their synthesis is in principle limited only by the constraints of the peri-odic table. Geochemical and planetary explorations have already revealed a broad range of chemical transforma-tions and energy transduction mechanisms for shuttling electrons and protons, and the opportunities for coor-dinating these redox networks into larger cooperative systems are exciting. the potential to exploit these func-tions through some cooperative engagement with other chemically distinct networks will require the storage and progressive transfer of molecular information.

informationMolecular information is the very essence of biology and the most critical category for our consideration of bottom-up growth of DCns, and potentially the most diverse. in DCns, genotypic information may not be separate from phenotypic structure and function, but rather embodied in a single, chemically-homogeneous molecular network. the evolutionary potential within digital and analog molecular representations of net-work information must be considered in the context of supramolecular engagement and the direct repli-cation of both covalently structured macromolecules and non-covalent assembly of conformationally uni-form species (Fig. 3.3). in all these situations, the digital genome is only one part of the information story.

the digital characteristics embodied in nucleic acids have been widely studied, and such knowledge is crit-ical to efforts attempting to comprehensively docu-ment the inventory of genes on Earth. As discussed in Chapter 2, the characterization of metagenomes, all the genetic material present in an environmental sample, and pangenomes, the full complement of genes in a species, have only just begun to illuminate the details of how living systems organize and manage informa-tion. the complementary analysis of biogeochemical and metagenomic data sets is revealing how environ-mental conditions constrain the chemical composition of living systems (Dick, 2011; Swingley, 2012), providing remarkable insights into how the chemical and physical conditions of organisms’ host environments shape bio-chemical selection. While such approaches are actually top-down, genetically mapping how continuous envi-ronmental signals (e.g., pH, temperature, and oxidation state) sculpt analog biological information, such as

metabolomic networks, the insights gained are broadly applicable. By directly mapping environment onto the selection of dynamic chemical networks, the physical constraints that shape the evolution of dynamic chemi-cal network can be revealed.

A bottom-up example of such direct environmental selection is nicely revealed by prions, small infectious particles composed of abnormally folded proteins. Prions and other misfolded proteins are responsible for many different diseases, yet they also represent confor-mational information, a direct form of analog chemical evolution (Goodwin, 2012). Heritable selection does not act on the digitally encoded nucleic acid sequence encoding the prion, but instead acts directly through its phenotypically-manifested protein conformation and inherent chemical function. Sequence-identical mol-ecules then propagate distinct heritable phenotypes based on template-directed replication of conforma-tional information.

yet another example of an alternative inheritance mech-anism that also relies on the propagation of analog infor-mation is “compositional inheritance,” where the heritable information consists of the relative ratios of molecules within organized assemblies (Segre, 2000). Different classes of replicating chemical systems may support different mechanisms of informational inheritance, be it digital or analog. therefore, it is critical to consider the alternative ways that DCns can manage their geno-typic, hereditable information. in mathematical parlance, digital sequence replication—characteristic of genetic informational inheritance in extant life—propagates the sequence permutation, whereas compositional inheri-tance relies on propagating information only of the com-bination of species and not macromolecular sequence


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Jump-starting Bottom-up Chemical EvolutionEngineering bottom-up chemical evolutionary approaches that manifest the full diversity and complexity of extant biochemistry will be extraor-dinarily challenging. After all, nature has had eons of trial-and-error over which to develop such sophisticated and robust dynamic chemical net-works, which work in concert to manifest the properties and functions of cellular life. However, we don’t need to limit our research efforts to only these pathways.

We can consider the possibility of using the established central dogma as a scaffold from which to shape and explore chemically and functionally distinct genetic platforms with the potential to operate orthogonal to and independent of extant biochemistry. this approach may jump-start the search for truly alternative biochemistries, which may represent a shadow biosphere here on Earth. Furthermore, these alternative biochemistries may be the basis of life elsewhere in the universe. these approaches are the focus of Chapter 4.

composition. in contrast to both these cases, conforma-tional inheritance is dependent neither on sequence permutation nor composition of the molecular popula-tion, but instead on physical three-dimensional structure (Fig. 3.3). A key challenge for chemical evolution research is to identify other possible modes of information inheri-tance that may rely on the propagation of analog and/or digital information.

the digital/analog dichotomy manifest in extant life is not solely limited to the distinction between genotype and phenotype. Digital information processing is also an important facet of the logical structure of dynamic biochemical networks. Biological regulation succeeds with threshold-controlled switches that operate as dig-ital logic operations. thus, the active use of information in biology is often not exclusively either digital or ana-log but rather a combination of both (Goodwin, 2012). therefore, a key challenge in the bottom-up design of chemical networks is likely to be running many com-peting chemical reactions in parallel, non-interacting and thus non-interfering (or orthogonal) pathways (Meyer, 2012; Pinheiro, 2012).

Unfortunately, maintaining orthogonal reactions in strictly analog reaction networks is cumbersome. As a figurative comparison, analog computers fell out of favor in the mid-twentieth century because of related issues of versatility; analog devices, regardless of their structure, are much more difficult to engineer or use in solving broad categories of problems than their digital counterparts. As a result, the early emergence of digital logic was likely a critical step in the origin of life because it enabled nascent life to control what reactions happened when, thus enhancing evolution-ary potential (Walker, 2013). Progress in the design of “life-like” dynamic chemical reaction networks therefore requires the development of more effective mecha-nisms to translate biological descriptions into the func-tioning of the logic circuits that underpin living systems at the chemical level (nurse, 2008). Greater understand-ing of how digital control might develop logic oper-ations may well emerge from the analysis of simpler dynamic chemical networks.



findingsGiven the range of molecular recognition strategies and the increasing diversity of dynamic chemical networks being characterized, restricting self-replication to nucleic acids seems remarkably limiting. A broad spectrum of non-nucleosidic molecular components have been demonstrated to self-assemble, to store molecular informa-tion, and to elicit a variety of functional consequences. From the crystallization of a pure substance to the non-covalent interactions of supramolecular assemblies, these phase changes can lead to organization, growth, and replication of molecular order based on distinct digital, analog, or hybrid molecular information.

the emergence of function in dynamic chemical networks, including catalysis, repli-cation, energy capture and exchange, signal transduction, structure formation, and confinement, can now be characterized in ways that were previously unimaginable. Variations in elemental composition and availability, solvent composition, proton gradients, ionic strength, temperature, pressure, molecular crowding, and other envi-ronmental influences will impact speciation of chemical networks, growing toward the emergence of autonomy. But it is the emergence of molecular collaborations (Goodwin, 2012), how analog and digital molecular networks cooperate, compete, engage constructively and/or parasitically to create a system of more complex net-works that becomes important to our understanding of alternative biochemistries. Given the historical focus of systems chemistry and chemical evolution of the prebi-otic origins of life, we have an initial framework for exploring how dynamic chemical systems might emerge, how they work, how they might arrogate survivability and evolve, and what their particular “signatures” in the diversity of terrestrial and non-ter-restrial environments might be. the following sections explicitly state the implications of these findings and suggest next steps that might logically follow.

IMPLICATION 1: developing synthetic dynamic Chemical networksDynamic chemical networks are not a priori constrained to the canonical elements and their relative ratios of extant biochemistry, and can even be designed to employ predominantly metallic and inorganic species limited in or devoid of organic, car-bon-based components. the opportunities for such synthetic dynamic chemical net-works, incorporating a wider variety of compositions limited only by physicochemical constraints on their functions, open rich new chemical frontiers. the available meth-ods critical to characterizing dynamics in macro- and supramolecular dimensions also remain nascent, and extending their reach in laboratory, field studies, and astrochem-ical realms will be increasingly important.

NExT STEPS: using high-End ToolsAdvances in LC-MS and multidimensional mass spectrometry, including ion-mobility methods; solution and solid-state nMR; spectroscopic interro-gation from far-UV to terrahertz methods; and imaging methods including

cryo-EM, will be critical to any broad exploration of chemical evolution (Jepsen, 2011; Bleiholder, 2011; 2008; Seager, 2013; Egelman, 2010). Spectroscopic measurements that provide averaged data from a bulk solution should be extended to new methods that sort and report on individual components of a dynamic mixture. From single-molecule methods that extend the mechanistic analysis of complex mixtures and interactions to


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high-throughput screening of environmental network perturbations, building on the methods developed for drug discovery (neuzi, 2011; Mehringer, 2013), can not only rad-ically accelerate our understanding of dynamic chemical networks, but should lead to the discovery of new catalysts and novel emergent biological activity.

IMPLICATION 2: searching Across a wider range of dCnsWe are positioned to consider a wide variety of coordinated and cooperative DCns, even those approaching the minimal functions of living systems. our top-down rubric suggests that for any series of nested networks to become autonomous they must create synergies, achieve progressive growth of molecular order and functions, and also be susceptible to parasitic invasions that drive innovation. information can be digital, analog, or possibly even system-wide compositional. this diversity is likely to expand even further.

NExT STEPS: Access to molecular informationAs analytical methods improve, we can determine in greater detail how dynamic chemical networks collaborate and compete with other networks, how environment influences their performance, and how many ways there

might be to generate hereditable information. We should explore how much chemical information can be practically digitized from a minimal inventory of building blocks to support evolutionary dynamics. For example, we should determine whether digital information storage is necessary to attain system complexities that approach those of living systems. if so, using digital information storage has the potential to give us a better handle on the dichotomy of genotype/phenotype. We should define the lim-its of conformational evolution, as represented by protein prions, for example, where sequence and conformational information are intimately linked. We should test the-oretical predictions of the robustness of such networks to mutations or corruption of fidelity. We should determine how much collaboration is required, and possible, among diverse chemical networks that approach the functional complexity of living matter.

IMPLICATION 3: Finding networks Capable of maintaining disequilibria of all the functions that must be elicited by these dynamic chemical networks, lever-aging energy from surrounding environments to maintain disequilibria and self-or-ganizing behaviors represents vast new research opportunities (Russell and Martin, 2010) for novel alternative chemistries.

NExT STEPS: Establishing novel ways to harness Energy sourcesthe role of gradients and chemical disequilibria as driving forces can take several forms and may be coupled with a wide variety of thermal, photochemical, or radiation energy sources.

Efficient ways of harnessing these sources may take the simple form of oscillating between two or more resource states (AtP), autocatalysis in simple subsystems, and interacting networks that add new nodes, which extend networks. All these options should be explored. non-organic (Ritchie,2009) or hybrid inorganic/organic networks point to new strate-gies (Dzieciol, 2012) for self-organizing networks (Mann, 2013), and offer very different opportunities for new chemistries.



IMPLICATION 4: describing network Behaviors through modeling and simulation Given the inspiration to explore the evolutionary potential of dynamic chemical net-works of a wide, abiological elemental composition, as well as the need to map out network behaviors across multiple and highly variable environmental determinants, there will be explicit requirements for modeling and predictive algorithms.

NExT STEPS: using mathematical and Computational modelsMathematical and computational models that describe the observed behaviors of these complex chemical networks can be extended to sim-ulate and predict changes in populations and properties with modifica-

tions in environmental determinants and initial network composition, facilitating iterative construct/test/design cycles. Design of experiment and genetic algorithm approaches can help with improved efficiencies in exploration of multidimensional network-space (Casciato, 2013; Richmond, 2012). the role of modeling and simulation in describing network dynamics and predicting behavior for distinct compositions and environments is equally important. Modeling and simulation are intimately inter-twined with experimental design and execution for iteratively advancing our under-standing applied to the search on Earth and elsewhere in the universe, locating signs of alternative and emerging biochemistries, and realizing the potential for technologi-cal advances in novel materials applications.

IMPLICATION 5: Facilitating the search for Chemically Evolving systemsthe focus of current research into dynamic chemical networks is on how they mani-fest the fundamental properties of living matter. the cell—the irreducible unit of liv-ing matter—provides the operational guidelines for such research.

the current bottom-up research focus is also on how extensive these chemical net-works are on the complete spectrum of evolutionary properties, and what physico-chemical features and environmental determinants constrain them from becoming more extensive. Even within the realm of bottom-up chemical evolution research, there is a wide range of conceptual constructs and definitions. At this point, there is a need for continued and expanded dialogue across the community, both within the U.S. and at the global level.

NExT STEPS: promoting and Expanding scientific discoursethere is a need for continued dialogue between practitioners of this research and those more focused on “top-down” in order to align defini-tions, experimental observables, and interpretation of network behaviors in

the context of what is understood about living matter and its interactions with its sur-roundings. Workshops and/or conferences should be organized to continue to bring together researchers from both “top-down” and “bottom-up” research realms to facili-tate these discussions and to drive future innovations in such research.

it is strongly recommended that conferences focused on research approaches under the rubric of chemical evolution or systems chemistry continue to be held, and that they bring together the international communities involved. Representative examples include the EU CoSt-supported Systems Chemistry conferences, which have histor-ically been located in Europe, and origins of Life Gordon Research Conferences held


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Citations

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Childers, W. S., (2012). Phase networks of cross-β peptide assemblies. Langmuir 28(15): 6386-6395.

Cougnon, F. B.L. and Sanders, J.K.M. (2011) Evolution of dynamic com-binatorial chemistry. Acc Chem Res 45(12): 2211-2221.

Davies, P. C. W. (2012). the epigenome and top-down causation. Interface Focus 2.1: 42-48.

De Duve, C.. (1995). Vital dust. new york: Basic Books 9: pp. 428-437.

Dick, J. M., and Shock, L. (2011).Calculation of the relative chemical sta-bilities of proteins as a function of temperature and redox chemistry in a hot spring. PLoS One 6(8): e22782.

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Egelman, E. H. (2010). Chapter Six - Reconstruction of Helical Filaments and tubes. in Methods Enzymol. Grant, J. J. (ed) Academic Press: Vol. 482, pp 167-183.

in the U.S. Coordination of these or related meetings with other sponsors, such as the American Chemical Society (ACS), nSF, and nASA, at different international locations will better serve the nascent research community and improve opportunities for global collaboration.

SummaryWe anticipate that listing these observations and opportunities will further encour-age the scientific community to engage in more detailed discussions and cross-dis-ciplinary collaborations, challenging these assumptions and stated opportunities. Ultimately, the hope is to develop a more peer-tested and far-reaching/impactful plan of attack for revealing the potential of alternative biochemical processes that may be occurring all around us and elsewhere in the universe. the significance of these efforts is enormous. Bottom-up, emergent dynamic networks can lead to new breakthroughs in intelligent materials, sustainability of chemical processes and pro-duction, the discovery and development of new therapeutics and disease diagnos-tics, and a holistic understanding of the chemical ecology of Earth and newly discovered exoplanets. DCns are alternative bio-chemistries, and they can provide for greater diversity of signals for potential alternative forms of life, as well as help in the search, both here on Earth and elsewhere in our solar system, for new life forms.



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Goodwin, J. t., Mehta, A. K. , and Lynn, D. G. (2012). Digital and analog chemical evolution. Acc Chem Res 45(12): 2189-2199.

Griffith, E. C., tuck, A. F., and Vaida, V. (2012). ocean–atmosphere inter-actions in the emergence of complexity in simple chemical systems. Acc Chem Res 45(12): 2106-2113.

Jepsen, P. Uhd, D. Cooke, G,. and Koch, M. (2011) terahertz spectros-copy and imaging–Modern techniques and applications. Laser & Photonics Rev 5(1): 124-166.

Keating, C. D. (2012). Aqueous phase separation as a possible route to compartmentalization of biological molecules. Acc Chem Res 45(12): 2114-2124.

Long, J. R., and yaghi, o. M. (2009) the pervasive chemistry of metal–organic frameworks. Chem Soc Rev 38(5): 1213-1214.

Mann, S. (2012) Systems of creation: the emergence of life from non-living matter. Acc Chem Res 45(12): 2131-2141.

Meguellati, K., and Ladame, S.(2012). Reversible covalent chemistries compatible with the principles of constitutional dynamic chemis-try: new reactions to create more diversity. Constitutional Dynamic Chemistry. Springer Berlin Heidelberg: 291-314.

Mehta, A. K., (2008). Facial symmetry in protein self-assembly. J Am Chem Soc 130(30): 9829-9835.

Meringer, M., Cleaves, H. J., and Freeland, S. J.. (2013). Beyond terrestrial biology: charting the chemical universe of α-amino acid structures. J Chem Inf Model 53(11): 2851-2862.

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“We are one of many appearances of the thing called Life; we are not its perfect image, for it has no perfect

image, except Life, and life is multitudinous and emergent in the stream of time.”

Loren Eiseley, The Immense Journey: An Imaginative Naturalist Explores the Mysteries of Man and Nature



Chapter 4 Where Causality and Emergence Meet: The Golden Spike

Figure 4.1: The hypersurface of potential genetic systems that may emerge from evolution of dynamic chemical networks. Central dogma of extant biochemistry represents our current understanding of the optimal result of such evolution.

CENTRAL DOGMA

DNA

RNA

PROTEIN

ten years after the publication of Charles Darwin’s The Origin of

Species, travel across the United States by rail was achieved with the ceremonial placement of a “golden spike” uniting dis-tinct railroad networks. the image of railroad crews meandering across new frontiers of a young nation searching to connect the two coasts, and finally succeeding at Promontory Summit by staking a commercial bridge across the United States, res-onates with the intellectual merger of our top-down and bottom-up evolutionary approaches. Just as the United States was unified, the study of the golden spike bridges chemical and biological evolutionary networks. From the top down, we trace causal hereditary lines, reinforced and extended through evolution, back to a last universal common ancestor, or LUCA. our understanding from the bottom up suggests many potential golden spikes, some lost to history and some fortified, bridging the transitioning of dynamic chemical networks into biology. Finding these connections, or phase transitions in chemical space, and understanding why connections are sustained in chemical evolution define this research realm.

Figure 4.1 is a conceptual representation of the genotype/phenotype special-ization that emerged from a functional ribosome, often defined as the central dogma (noble, 2013). the surface represents regions of distinct chemical net-works with the potential for alternative genetic functional capability, distinct from that known for extant cellular life (Woese, 2002). it is already clear that these networks are driven by a wide variety of environments, from extremes of pressure and temperature such as hydrothermal vents at the Lost City to the presumably mundane environments of our own backyards. However, the signa-tures of alternative functions that might have evolved and then have been lost remain masked by the predominant signals of the extant biosphere.

Conversely, bottom-up systems leading to the surface, as shown in Figure 4.1, can be built from emergent, self-organizing behaviors of simpler abiotic/pre-biotic chemical networks. Design of such systems benefits from our extensive


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Chapter 4: Where Causality and emergenCe meet: the golden spike

the genotype/phenotype emergence represented in Figure 4.1 is one of a series of thresholds or phase tran-sitions evolving from the dynamic chemical networks discussed in Chapter 3. the self-organizing assembly from constituents of primordial chemical inventories must lead to the formation of inorganic and organic spe-cies capable of transducing environmental energy into chemical potential, to the construction of supramolecu-lar species, and to the selection of spontaneous assem-blies that contain, concentrate, and protect dynamic reaction networks. As with the analogy to functional transcontinental railroads, all the pieces must coalesce as self-replicating or cross-replicating abilities among the distinct molecular systems (Caetano-Anolles, 2013), opening into the realm of the progenote (ibba, 1999). As the dynamic chemical networks become progressively more complex, more intertwined, and interconnected, evolutionary developments can occur vertically in the domain of biological evolution and traceable by top-down systems biological approaches.

Much as air travel has now largely replaced rail, success does not preclude continued contemporary chemical evolution. Ecological analyses show that local envi-ronments provide “centers of innovation” in spite of dominant chemical networks, where increasing com-plexity of hereditable structure and function emerge. Considering the likely limited exploration of possible geochemical and molecular diversity on Earth, together with the possible range of environments and their fluctuations over time, it is entirely possible that extant biochemistry is not a “global minimum” but rather a “kinetically-trapped” version on the much broader sur-face of all possible combinations of molecular diversi-ties and environmental fates (Caetano-Anolles, 2010).

Figure 4.2 presents an overview of this fertile chemical continuum that circumscribes a specific critical threshold for biological evolution. Within this continuum, like rip-ples in a pond, orthogonal biochemistry radiates outward within the broader context of chemical evolution. it is now increasingly possible to experimentally explore this chemical space and define the environmental contexts where different systems could evolve, exist, and thrive. it remains an open question whether such orthogonal chemical evolution is possible in this much broader realm encompassing biological evolution. Equally unclear is whether orthogonal chemical evolution could participate in the drive toward functional innovation.

Figure 4.2: Biological evolution is an outcome of chemical evolution-ary processes and continues to be influenced by it. Just as ripples in a pond expand outward from the center, distinct, orthogonal, and alternative genetic networks can be explored from established genetic systems in extant central dogma and moving outwards.

DARWINIAN THRESHOLDS

PHASE TRANSITIONS

CHEMICAL INVENTORY

POLYMERS

PROGENOTES

ENERGY TRANSDUCTIONCONTAINMENT INFORMATION

BIOLOGICAL EVOLUTION

ORTHOGONAL BIOCHEMISTRY

CHEMICAL EVOLUTION

PREBIOTIC CHEMICAL NETWORKS

CENTRAL DOGMA

knowledge of fundamental physical-chemical properties and how matter reacts in different environments, which has been acquired over decades of research. the compositional diversity of chemically-evolving dynamic molecular networks can be categorized to approximate one or more characteristics of living matter and extant biochemistry. Such possibilities, or golden spikes, represented across the periodic table for these networks, are remarkable, and they are only limited by our scientific imaginations. the opportunities for characterizing such top-down/bot-tom-up connections are fundamental to defining the alternative chemistries of life.

imAgining ThE possiBlE



nAvigATing spiky domAinsCarl Woese suggested that with the “cooling of the genetic temperature,” the dynamic networks of proge-notes began to crystallize into a more uniquely defined last universal common ancestor (LUCA), leading to the phase transition represented by the ribosome, fol-lowed by cellular life with its antecedent branching and speciation along the bacterial, archaeal, and eukarial paths (Woese, 1999). the most basic processes of this threshold are understood in terms of the expression of information, the execution of programs, or the inter-pretation of codes (Godfrey-Smith & Sterelny, 2008). While standard information-theoretic measures, such as Shannon information indices (Sherman, 2006), have proven to be useful in some biological contexts—for example, in the field of bioinformatics—more founda-tional questions regarding the origin and nature of bio-logical information have been notoriously recalcitrant to consensus. A crucial property of genetic information is that it provides a set of instructions, cast in a discrete or digitized mathematical code (the genetic code), which the translation machinery converts into protein. As such, DnA in biology is both a physical structure and a digital information repository. that the informa-tion stored in DnA is instructional or coded represents a major conceptual divide, separating the biological from the non-biological realm. the usage of informa-tional concepts in biology is not relegated exclusively to genetics, but is also important in other areas, such as developmental biology and evolutionary theory.

Alternative biochemical networks may have arisen from horizontal innovation in the plane of the ribosomal threshold, but environmental and/or chemical determi-nants as yet unknown interrupted their development and survival. insights into such processes are likely to be discovered from bottom-up analyses exploiting physicochemical diversity. A key challenge is that while informational concepts such as signaling, coding, tran-scription, and translation are routinely applied in the biological realm, they do not readily carry over to the underlying chemistry. Without a concrete understand-ing of how biological information is propagated and processed at the chemical level, including assessment of the variety of alternative chemical systems capable of achieving biological functionality, it remains difficult to determine what alternative chemical networks of liv-ing systems are possible. An important open question

is to identify strategies for determining how biological information acts through chemistry.

orThogonAl BuT noT immATEriAlAll known life relies on DnA and RnA for the storage, propagation, and processing of genetic information. this central role of nucleic acids in modern life has prompted a search for alternative genetic polymers capable of heredity and evolution that may contain polymeric backbones with linking functionalities and molecular recognition elements that could differ structurally and chemically from those known thus far, and therefore qualify as “alternative.” one approach to the search for alternative genetic polymers has involved a systematic assessment of the chemical etiology of nucleic acid structure (Eschenmoser, 1999). Engineering information transfer between different nucleic acid genetic systems opens the possibility of systematically stepping outward from extant life’s selection of nucleic acid architectures to identify increasingly exotic genetic polymers that are biologically viable (Hirao, 2012; Krueger 2011; takezawa, 2012). identifying pathways for stepping backward in time or outward across the plane in Figure 4.2 requires precise mapping of a landscape that allows nucleic acid architectures to exchange information with others. Such engineering must ultimately account for the two essen-tial requirements for viable, alternative genetic molecular platforms: functionality and the ability to evolve.

the surface shown in Figure 4.1 represents the postu-lated progenotes and Darwinian thresholds necessary for the ribosome, where chemical evolution/pre-life oper-ates as populations of many diverse chemical networks. these networks are capable of extensive exchange of molecular/functional innovation prior to phase-transi-tioning to biological evolution. in this domain, alternative chemistries might be assimilated into extant biochemis-try, suggesting the possible existence of “neogenetic” or “orthogonal” pathways. Growth might then occur out-ward from extant biology, both expanding backward in time toward prebiotically relevant genetic polymers, the so-called “proto-RnA” that may have played a role in early evolution, or expanding outward from extant biology. Such outward expansion might incorporate the design of novel nucleic acid architectures not found in nature, xnAs (“xeno,” or foreign, nucleic acids), which may be useful in drug design, along with informing our under-standing of exobiology (Pinheiro, 2012, 2014).


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ThE shAdow BiosphErE the molecular signatures of biochemical function are now increasingly revealed as components of the pangenome, or the core set of genes, through the poly-merase chain reaction (PCR). As a result, the search can address virtually any ecological niche, from the human microbiome to the depths of the oceans, which can be defined with remarkable gene sequence-level resolu-tion (Rusch, 2007). However, this genetic description is also limited to only those levels of information that can be replicated by the polymerase enzyme being used. Epigenetic events, analog function as seen in prions, and even subtle changes in monomer structures incor-porated in nucleic acid templates would be invisible to PCR interrogation. indeed, Davies has suggested that we can verify de Duve’s assertion of a cosmic impera-tive of life if we identify a “shadow biosphere” that pro-cesses information in a way that is orthogonal to the central dogma (Davies, 2011). the concept of working outward and orthogonally from extant biochemistry has proven to be quite successful.

For example, feeding alternative inventory feedstocks to an evolving microbial population over sequential growth and selection cycles has created populations that selectively incorporate the thymine isostere chloro-uracil into their genomes (Marliere, 2011). other directed modifications of translation have succeeded in incorpo-rating non-natural amino acids (Chin, 2003) that retain compatibility with the ribosome. Synthetic expansion of the extant genetic code with alternative and exclusive

base-pairing nucleosides (Benner, 2004; Leconte, 2008; Winnacker, 2013) is moving increasingly beyond the central dogma to orthogonal genetic information sys-tems (Pinheiro, 2012, 2014). these examples have the common thread of exploring the boundaries of extant biochemistry at the genotypic information-processing level, but at this point, the chemical systems do not fully manifest the characteristics of a truly orthogonal biochemistry.

in this context, we define orthogonal as alternative bio-chemistries that use genotypic platforms that do not directly engage with extant biochemistry. other alterna-tive forms of biochemistries might derive from metabolic function or biomolecular structure and composition. the perspective provided by the alternative and orthogonal chemistries build valuable foundations for searching for life that extends dramatically beyond what is possible by extant biochemistry. Working from extant biochem-istry as it is composed will necessarily circumscribe the considerations for viable, alternative forms of biochem-istry. in this broader context, should such alternative biochemistries be tied to some form of containment and selective chemical fluxes akin to the roles played by cellular lipid membranes? Further, will alternative bio-chemistries use functional polymers for fundamental operations such as energy transduction and metabo-lism? Finally, must genotypic information be embodied in linear polymers of some defined subset of monomeric species, particularly as research efforts move concentri-cally outward from extant biochemistry?

findingsAlternative biochemistries now take on a multitude of meanings in the golden spike realm. Certainly inventions that incorporate different elements in skeletons outside of extant biology, and functions that were discovered and discarded or never discovered, are alternative. A subset of these possibilities include chemistry that is orthogonal to existing biochemistry, driven by completely different envi-ronmental constraints or simply never accessed due to resource limitations. With these expanding opportunities for searching different environments on Earth and beyond, there are a significant number of implications and questions regarding both the manner in which such research proceeds and what we can learn along the way. these implications and next steps are by no means exhaustive, but rather should be considered as ideas to seed further questions and research directions that engage the interest and creativity of the broader scientific community.



IMPLICATION 1: going beyond Extant Biochemistry the ability to work experimentally from extant biochemistry as a platform toward alter-natives is expected to be moderated by the reticence of the biochemical networks of the central dogma to perturbation and modification, the inherent difficulty of altering genotypic format, or the introduction of alternative energy transduction platforms or processes into pre-existing, highly integrated molecular and chemical networks (illus-trative references). truly alternative genetic systems will be challenging, if not impossi-ble, to identify if we continue to use only extant genetic material for the search.

NExT STEPS: developing Alternative genetic platformsWe need to continue current research to develop alternative genetic plat-forms that operate within their own orthogonal-to-extant central dogma. Working outward from extant biochemistry to engineer or seed and evolve

alternatives will require the availability and selection of whole organisms as model platforms for exploration of these orthogonal alternative biochemistries. this research also will involve choosing functional subsets of extant biochemistry that is robust yet malleable enough to nurture hybridization with alternative chemistries from the bot-tom up. the difficulties and chemical challenges in introducing modified alternative biochemical inventories and pathways have been demonstrated in empirical work done to date. Part of the difficulty is due to the intricacies of molecular networks and specialization in genotypic information management and processing. these obsta-cles emphasize the need to work in incremental steps forward and outward from extant biochemistry, where the size of such steps remain to be defined and will likely be dependent upon the particulars of the experimental platform and approaches (Pinheiro, 2012; Krueger, 2011; Marliere, 2011; Leconte, 2008; Chin, 2003). Looking beyond the known, what are the fundamental signatures of alternative biochemis-tries, which are distinguishable from extant biochemistry, and which of their signals can be distinguished from the background noise of extant biochemistry?

IMPLICATION 2: how Context shapes dynamic Chemical CompositionWorking from extant biochemistry is akin to beginning the search for answers “under the lamppost” in that the top-down approach is focused in part on expanding and comprehensively detailing the illuminated area. on the other hand, the integration of bottom-up, chemically-evolving dynamic networks into extant biochemistry, as rep-resented by the golden spike, have the potential to complement these approaches. this can be accomplished by establishing the potential for non-standard biochemis-try tied to qualitative and quantitative measures obtained by empirical approaches.

NExT STEPS: looking beyond known EnvironmentsEfforts should be focused on how environmental characteristics circum-scribe the possible diversity of alternative chemistries. For example, living matter as currently known functions in aqueous milieu, using hydrophobic

forces to, among other outcomes, organize cellular containment, stabilize protein folds and supramolecular interactions, and strengthen selectivity and specificity of enzyme-substrate interactions, as well as contribute to the structure and fidelity of complementarity in nucleic acid polymer interactions. How much flexibility exists in moving to mixed aqueous/organic environments, or even non-polar solvents that


44


have been proposed with respect to other celestial bodies within our solar system, such as titan, Saturn’s largest moon?

We should consider if such alternative chemical systems could out-compete extant biochemistry for resources. is the central dogma the key linchpin for competitive-ness? Might these systems be competitive/winner-takes-all with respect to extant biochemistry, and would this necessitate isolated locales? How do we imagine such locales, how would we identify them, and given the potential for alternative chemical networks, what might be the defining signatures? is it possible for alternative pre-bio-chemistries to evolve as truly orthogonal chemical networks while co-localized in environments with and yet independent of extant biochemistry (e.g., non-carbon-based biochemistry)?

IMPLICATION 3: Ethical and safety Concerns for Alternative genetic systemsthis research realm overlaps significantly with synthetic biology. Given modifica-tions to extant biochemistry inherent in this research direction, what are the ethi-cal and safety considerations for these research directions, and how should they be addressed (Herdewijn, 2009; Schmidt, 2010)?

NExT STEPS: Enable dialoguethe scientific community must come together, through workshops, sympo-sia, and public lectures, to enumerate safety and bioethical concerns, edu-cate broadly about research findings, and develop solutions/approaches on

an ongoing basis with the entire community.

IMPLICATION 4: research innovations for Characterizing signatures of Alternative Biochemistries As is clear from the preceding sections, there will be a need for new analytical and spectroscopic techniques and instrumentation in order to characterize alternative biochemical signatures, including next-gen-eration sequencing of alternative biopolymers. in addition, it will be important to develop laboratory platforms that mimic a wide variety of environments under which these orthogonal biochemistries may be selected for and even thrive. there will also be a need to identify organ-isms, most likely microbial, which provide the appropriate “blank slate” similar to the dynamic progenote network, for the purpose of interfac-ing with the dynamic chemical networks that will emerge from bot-tom-up systems chemical and golden spike neogenetic research.

NExT STEPS: support for sustained researchSuch research may be considered high-risk and will need broad-level fund-ing support for sustained efforts. it will be important to consider several pathways, including chemically-specific modifications, gas phase fragmen-

tation chemistry and mass spectral sequencing, and analogous PCR (polymerase chain reaction) methods that leverage the unique genotypic/phenotypic relation-ships of the alternative orthogonal genetic platforms.



IMPLICATION 5: Engaging the Broader scientific CommunityGiven that research into alternative biochemistries through the coupling of top-down biological systems and bottom-up chemical evolutionary research approaches is in its relative infancy, the scientific research community is not as informed about these topics as we would like. the challenge will be in determining how these concepts and questions should be disseminated and how diversity in research directions and expertise should be brought together (beyond the discussions held at the first work-shop) to continue to fine-tune our understanding of the key questions and the man-ner in which they are addressed.

NExT STEPS: Expanding and Enabling scientific discoursePerhaps the most obvious next step is bringing together the multiple scientific disciplines relevant to orthogonal, and more broadly, to alterna-tive biochemistries, with concomitant development of multidisciplinary

approaches and new scientific training opportunities. it is also clear that innovations in new chemical and analytical methods and technologies/instrumentation will be required in order to support this emergent research realm. it is anticipated that empirical research efforts will also support and extend the knowledge and under-standing captured in the 2007 Weird Life report (Baross, 2007). in this way, new exper-iments and theories will improve our understanding of alternative forms of extant biochemistry, how they are selected, and how they may evolve and prosper. Along with a greater understanding of the role that environment plays in chemical (pro-to-life) and biological evolution, and how living matter shapes and transforms its environment, it is envisioned that golden spike research will generate modifications to extant biochemistry that may positively impact drug discovery and development, and lead to sustainable and innovative nanostructured materials. in addition, this work has the potential to lead to novel approaches to investigation and characteriza-tion of the interfaces between inanimate chemical networks and the dynamic biolog-ical networks of living matter.

Summarythe metaphorical golden spike, connecting the top-down and bottom up realms, is not a point or a place analogous to Darwin’s warm pond, but rather a dynamic region in space and time just preceding the emergence of biology. the physical and chemical processes and functional causality characteristic of both top-down biologi-cal causation and bottom-up chemical emergence converge at the critical threshold that exists within this third realm. As structural and functional order grows from the bottom up, the probability of golden spike thresholds should increase. Likewise, as biological diversity grows, the probability of alternative chemistries increases, even in the face of increasingly sophisticated mechanisms for extracting energy from the environment. ideally, our growing capability in the design and analysis of complex dynamic chemical networks and the extensive pangenome data sets for diverse eco-logical niches should intersect with this realm. the result will certainly inform the physical limits on chemical and biological evolution.


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tropical Pacific. PLoS biology 5(3), e77.

Schmidt, M. (2010). Xenobiology: a new form of life as the ultimate bio-safety tool. Bioessays 32(4): 322-331.

Sherwin, W. B., Franck, J., Rush, R., and Rossetto, M. (2006). Measurement of biological information with applications from genes to landscapes. Mol Ecol 15(10): 2857-2869.

takezawa, y., and Shionoya, M. (2012). Metal-mediated DnA base pair-ing: alternatives to hydrogen-bonded Watson–Crick base pairs. Acc Chem Res 45(12): 2066-2076.

Winnacker, M., and Kool, E. t. (2013). Artificial genetic sets composed of size-expanded base pairs. Angew Chem Int Ed 52(48): 12498-12508.

Woese, C. R. (2000). interpreting the universal phylogenetic tree. Proc Natl Acad Sci 97(15): 8392-8396.

Woese, C. R. (2002). on the evolution of cells. Proc Natl Acad Sci 99(13): 8742-8747.

http://plato.stanford.edu/archives/fall2008/entries/information

http://plato.stanford.edu/archives/fall2008/entries/information



Chapter 5 Systems of networks

At the beginning of the last century, our newtonian world- view began to change as physical scientists began

to explore materials at the atomic and subatomic scale. increasingly, matter was seen as built on dynamic interactions rather than on inert building blocks. Biologists, too, were uncov-ering intrinsically interconnected and mutually interdependent natural communities, revealing an organismic, and ecological understanding of living matter at a far larger scale. At the same time, psychologists were converging on the role of integrated perceptual patterns in cellular learning and memory.

the confluence of these seemingly divergent areas of study with common emerging foundational principles was formalized in the field of cybernetics, or the study of systems. Mathematical models addressing dynamic causality and feedback in complex networks suggested that new functions, greater than the individual network elements, could emerge. these distinct, yet conceptually connected perspectives, were pointing toward a dynamic “web of life” (Capra, 1996), one that is hierarchically disposed toward increasing evolutionary com-plexity and diversity as central to life’s robustness.

Against this background, the notions of a central dogma, RnA world scenarios, and a molecular blueprint for the cell have captivated the scientific commu-nity over the last several decades. these concepts have contributed critically to our understanding of the diverse elements of biology, and have provided the structural background and technology necessary for our understanding of the complex emergent properties of living matter. the information encoded in our genomes plays a central role in the network of a living cell. that information is clearly dynamic and ever responsive to epigenetic environmental inputs and horizontal exchange of genetic elements. Like the parts of an atom and the ideas emerging in our cellular brains, living matter is best viewed as not a sin-gle entity but as dynamic chemical networks that operate far from equilibrium, in a state of disequilibrium. Metabolism is the evolutionary manifestation of sophisticated and efficient ways to leverage environmental energy sources to maintain the disequilibrium status. this function serves to recycle vital, critical materials, minimize irretrievable waste pathways that poison metabolism, and maintain an environment optimal for network maintenance.

Figure 5.1: A schematic illus-tration of the convergence of top-down causation and bot-tom-up emergence, resulting in a new domain to search for alternative biochemistries.

DNA

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Chapter 5: SyStemS of NetworkS

findingsthe expansive and diverse nature of research in alternative biochemistry stretches beyond the traditional scope of astrobiology and any of the contributing scientific fields. the shear scope of research directions that fall under this broader umbrella challenges our ability to coordinate efforts and manage resources, and to ensure appropriate data formats and quality necessary to support systems-level modeling. For those reasons, we have broken the implications into the overarching categories of explorations, connections, and inspirations

To Exploreindividually and in combination, these research efforts will yield a staggering volume of data of remarkable diversity and range. the utility and value of these data will be contingent upon robust and well-maintained informatics networks, databases, and underlying cyberinfrastructure. Such “big data” issues have been widely acknowl-edged at the Federal level (Mattmann, 2013; White House Blog 2013), tied to a wide variety of social and economic issues. Given the investments of funding and inno-vations in technology, we will be able to build on our initial efforts to continue and expand informatics support for alternative biochemistry research.

ThE nExT FronTiErWe imagine a golden spike as the region where the top-down and bottom-up approaches to the evolution of alternative biochemistries meet. the image, however, is not of a single spike or branch, but rather a place in time where the chemical inventory is sufficiently com-plex to allow for passage through critical evo-lutionary thresholds. these thresholds would have been reached early in the history of planet Earth for the biochemistry of living mat-ter as we now know it to emerge, yet a similar process may very well be occurring now in alternative forms. the challenge we face today is where, when, and how to look for these crit-ical events, and how to couple them with the chemistry we now see in biology as well as the alternate chemistry that has either not been discovered by nature or has been discovered over and over again, but discarded for physical and chemical reasons.

We now inhabit a point in time where the biological perspective and the chemical and physical tools are sufficient not only to iden-tify golden spikes, but to create them anew, moving to a synthetic biology that extends the

principles of chemical evolution into new realms. there could not be a better time for these pursuits, positioned as we are with our rapidly expanding view of exoplan-ets and the spectroscopic tools to define the variety of physical and chemical constraints circumscribing the chemical networks of our universe and beyond.

Figure 5.2: A view of exoplanets.



We will need a well-developed, organized series of workshops and colloquia to bring the three primary research realms (top-down, bottom-up and golden spike) together to explore the synergies and emergent innovations, along with identifying new research opportunities and directions. With a focus on this infrastructure, there is the potential for a shift away from individual grant funding toward larger collaborative and center-based structures. While these larger collaborative initiatives will be necessary for success in the search for and characterization of alternative biochemistries, we must strike a proper balance in maintaining support for individual research groups as well. Larger collaborative efforts and centers will also require knowledgeable and credible managerial and administrative leadership and support in order to deliver efficiently and effectively on the anticipated promise of these larger research endeavors.

To ConnectBiological diversity and biome dynamics continue to influence and be impacted by the environment, climate and climate change, sustainability in environmental use practices, and human health (Holdren, 2008; Reid, 2010; ignaciuk, 2012). Understanding the range and diver-sity of standard biochemistry and emerging alternative forms will directly impact environmental sustainability, climate change, human health, and economic devel-opment (nAS, 2010, 2012; PCASt, 2012). our evolving understanding of these interconnected dynamics will be nurtured by long-term support for StEM research and education (nSF/AAAS, 2009) and broader communica-tion of alternative biochemistry research.

To inspireAs the pace of scientific discovery accelerates, there remains an ongoing and significant struggle within con-temporary society in grasping complex scientific theo-ries. the discussions of alternative chemistries of life will serve as a valuable platform for public engagement (Guston, 2014), and they have the potential to expand citizen science (Silvertown, 2009; newman, 2012). it is essential that the scientific community continue to expand its efforts to reach the broader public through consistent scientific communication (Sandu, 2011) as well as expanded and improved StEM education at all levels (nRC, 2011; Whitmer, 2010). We must develop better forums for outreach to the larger public because this is an essential part of our role as scientists and scholars (Haywood, 2014).


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Chapter 5: SyStemS of NetworkS

“Human beings, viewed as behaving systems, are quite simple. the apparent complexity of our behavior over time is largely a reflection of the complexity of the environment

in which we find ourselves.”

Herbert A. Simon, The Sciences of the Artificial

Summarythe impetus and narrative threads that led to this workshop and report are numer-ous. in particular, the NASA Astrobiology Roadmap (Des Marais, 2008) elaborates many of the key considerations for the search for life elsewhere and its emergence here on Earth, as well as suggested ideas for the process of searching itself. the contemporary report, The Limits of Organic Life in Planetary Systems (Baross, 2006), painted a much more detailed picture of the alternative biochemical processes that might potentially exist elsewhere in our immediate solar system and beyond.

Coupled with the provocative conceit of a potential shadow biosphere here on Earth (Davies, 2009), these documents have resulted in a variety of research efforts. the possibility that extreme environments may drive alternative biochemical systems continues to provoke the broader research community to consider the absolute requirements for collaborative, multidisciplinary approaches needed to tackle empir-ically such challenging research questions. the insight required to look beyond and within Earth environments that might otherwise be considered hostile or entirely unaccommodating to extant life continues to push the boundaries of our current knowledge beyond the realm of our planet. Therefore, our intention is that this report will complement its antecedents, and will help manifest and propel new, innovative, cross-disciplinary, and collaborative research into these challenging and fundamental questions.



Citations

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Davies, P. C., Benner, S. A., Cleland, C. E., et al. (2009). Signatures of a shadow biosphere. Astrobiology 9(2): 241-249.

Des Marais, D. J., nuth iii, J. A., Allamandola, L. J., et al. (2008). the nASA astrobiology roadmap. Astrobiology 8(4): 715-730.

Guston, D. H. (2014). Building the capacity for public engagement with science in the United States. Public Underst of Sci 23(1): 53-59.

Haywood, B. K., and Besley, J. C. (2014). Education, outreach, and inclu-sive engagement: towards integrated indicators of successful program outcomes in participatory science. Public Underst of Sci 23(1): 92-106.

Holdren, J. P. (2008). Science and technology for sustainable well-be-ing. Science 319(5862): 424-434.

ignaciuk, A., Rice, M., Bogardi, J., et al. (2012). Responding to complex societal challenges: a decade of Earth System Science Partnership (ESSP) interdisciplinary research. Curr Opin Environ Sustainability 4(1): 147-158.

Mattmann, C. A. (2013). Computing: a vision for data science. Nature 493(7433): 473-475.

national Academies. (2010). Rising above the gathering storm, revisited: Rapidly approaching Category 5. Washington, DC: national Academies Press.

national Academies. (2012). Rising to the challenge: U.S. innovation poli-cy for the global economy. Washington, DC: national Academies Press.

national Research Council. (2011). Promising practices in undergraduate science, technology, engineering, and mathematics education: Summary of two workshops. Washington, DC: national Academies Press.

national Research Council. (2011). Successful K-12 STEM education: Identifying effective approaches in science, technology, engineering, and mathematics. Washington, DC: national Academies Press.

national Science Foundation/American Association for the Advancement of Science. (2009). Vision and change in undergradu-ate biological education: A call to action. Washington, DC: American Association for the Advancement of Science.

newman, G., Wiggins, A., Crall, A., et al. (2012). the future of citizen science: emerging technologies and shifting paradigms. Front Ecol Environ 10(6): 298-304.

PCASt: Report to the President. (2012). transformation and opportu-nity: The future of the U.S. research enterprise. http://www.whitehouse.gov/sites/default/files/microsites/ostp/pcast_future_research_enter-prise_20121130.pdf

Reid, W. V., Chen, D., Goldfarb, L., et al. (2010). Earth system science for global sustainability: grand challenges. Science 330(6006): 916-917.

Rockström, J., Steffen, W., noone, K., et al. (2009). A safe operating space for humanity. Nature 461(7263): 472-475.

Sandu, o., and Christensen, L. L. (2011). outrageous outreach—uncon-ventional ways of communicating science. Communicating Astronomy with the Public 11: 22-30.

Silvertown, J. (2009). A new dawn for citizen science. Trends in Ecol Evol 24(9): 467-471.

Whitmer, A., ogden, L., Lawton, J., et al. (2010). the engaged university: providing a platform for research that transforms society. Front Ecol Environ 8(6): 314-321.

Wolfe-Simon, F., Blum, J. S., Kulp, t. R., et al. (2011). A bacterium that can grow by using arsenic instead of phosphorus. Science 332(6034): 1163-1166.

Zalasiewicz, J., Williams, M., Steffen, W., and Crutzen, P. (2010). the new world of the anthropocene 1. Environ Sci Technol 44(7): 2228-2231.


http://www.whitehouse.gov/sites/default/files/microsites/ostp/pcast_future_research_enterprise_20121130.pdf



52

APPEnDiCES

Appendix 1

Workshop organizers and Participants

workshop organizers

Shady Amin Postdoctoral Fellow School of oceanography University of Washington Seattle, WA http://armbrustlab.ocean.washington.edu/people/amin

E. Virginia Armbrust Professor and Director School of oceanography University of Washington Seattle, WA http://armbrustlab.ocean.washington.edu/

Cynthia Burrows Distinguished Professor and Chair Department of Chemistry University of Utah Salt Lake City, Ut http://www.chem.utah.edu/directory/burrows/index.php

Jay T. Goodwin Senior Research Fellow Department of Chemistry Emory University Atlanta, GA www.linkedin.com/jaytgoodwin

David G. Lynn Asa Griggs Candler Professor and Chair Department of Chemistry Emory University Atlanta, GA http://www.chemistry.emory.edu/faculty/lynn/

Sara Imari Walker Assistant Professor BEyonD Center Arizona State University tempe, AZ http://beyond.asu.edu/bio/sara-imari-walker

workshop participants

Daniel Appella Senior investigator Laboratory of Bioorganic Chemistry niDDK, national institutes of Health Bethesda, MD http://www.niddk.nih.gov/about-niddk/staff-directory/intramural/daniel-appella/pages/research-summary.aspx

Annelise Barron the W.M. Keck Associate Professor of Bioengineering School of Medicine Stanford University Stanford, CA http://www.stanford.edu/group/barronlab/

Tadhg Begley D. H. R. Barton Professor of Chemistry Department of Chemistry texas A&M University College Station, tx https://www.chem.tamu.edu/rgroup/begley/

Lee Cronin Regius Chair in Chemistry WestCHEM University of Glasgow Glasgow, UK http://www.chem.gla.ac.uk/cronin/

Andrew Ellington Wilson and Kathryn Fraser Research Professorship in Biochemistry Center for Systems and Synthetic Biology University of texas at Austin Austin, tx http://ellingtonlab.org/

Kent Gates Herman G. Schlundt Distinguished Professor Department of Chemistry University of Missouri Columbia, Mo http://chemistry.missouri.edu/people/gates.html

Samuel H. Gellman Professor Department of Chemistry University of Wisconsin - Madison Madison, Wi http://gellman.chem.wisc.edu/

Nicolas Giuseppone Professor of Chemistry institut Charles Sadron University of Strasbourg Strasbourg, France http://www-ics.u-strasbg.fr/spip.php?article754&lang=fr

Martha Grover Associate Professor School of Chemical and Biomolecular Engineering Georgia institute of technology Atlanta, GA http://grover.chbe.gatech.edu/

Steven J. Hallam CiFAR Scholar Canada Research Chair in Environmental Genomics Department of Microbiology & immunology University of British Columbia Vancouver, British Columbia, Canada http://hallam.microbiology.ubc.ca/

Piet Herdewijn Professor of Medicinal Chemistry Rega institute Katholieke Universiteit Leuven Leuven, the netherlands http://medchem.rega.kuleuven.be/index.go?ph

Nicholas Hud Professor School of Chemistry and Biochemistry Georgia institute of technology Atlanta, GA http://ww2.chemistry.gatech.edu/hud/node/3

http://armbrustlab.ocean.washington.edu/people/amin

http://armbrustlab.ocean.washington.edu/people/amin

http://armbrustlab.ocean.washington.edu/

http://armbrustlab.ocean.washington.edu/

http://www.chem.utah.edu/directory/burrows/index.php

http://www.chem.utah.edu/directory/burrows/index.php

http://www.linkedin.com/jaytgoodwin

http://www.chemistry.emory.edu/faculty/lynn/

http://www.chemistry.emory.edu/faculty/lynn/

http://beyond.asu.edu/bio/sara-imari-walker

http://beyond.asu.edu/bio/sara-imari-walker

http://www.niddk.nih.gov/about-niddk/staff-directory/intramural/daniel-appella/pages/research-summary.aspx



http://www.stanford.edu/group/barronlab

http://www.stanford.edu/group/barronlab

https://www.chem.tamu.edu/rgroup/begley/

https://www.chem.tamu.edu/rgroup/begley/

http://www.chem.gla.ac.uk/cronin/

http://ellingtonlab.org/

http://chemistry.missouri.edu/people/gates.html

http://chemistry.missouri.edu/people/gates.html

http://gellman.chem.wisc.edu/

http://www-ics.u-strasbg.fr/spip.php?article754&lang=fr

http://www-ics.u-strasbg.fr/spip.php?article754&lang=fr

http://grover.chbe.gatech.edu/

http://hallam.microbiology.ubc.ca/

http://medchem.rega.kuleuven.be/index.go?ph

http://medchem.rega.kuleuven.be/index.go?ph

http://ww2.chemistry.gatech.edu/hud/node/3

http://ww2.chemistry.gatech.edu/hud/node/3



Anitra Ingalls Associate Professor School of oceanography University of Washington Seattle, WA http://www.ocean.washington.edu/home/Anitra+ingalls

Christine D. Keating Professor Department of Chemistry Penn State University University Park, PA http://research.chem.psu.edu/cdkgroup/

Ram Krishnamurthy Associate Professor Department of Chemistry the Scripps Research institute La Jolla, CA http://www.scripps.edu/krishnamurthy/index.html

Sheref Mansy Assistant Professor of Biochemistry Center for integrative Biology University of trento trento, italy http://smansy.org/doku.php

Anna K. Mapp Professor of Chemistry and Director of the Program in Chemical Biology Department of Chemistry University of Michigan Ann Arbor, Mi http://www.umich.edu/~mapplab/

William Martin Professor institute for Molecular Evolution Heinrich Heine Universitat Dusseldorf Dusseldorf, Germany http://www.molevol.de/lab/martin.html

Ichiro Matsumura Associate Professor of Biochemistry Department of Biochemistry Emory University School of Medicine Atlanta, GA http://www.biochem.emory.edu/labs/imatsum/

Janet R. Morrow Professor Department of Chemistry University of Buffalo Buffalo, ny http://www.chemistry.buffalo.edu/imag-es/morrowLab.jpg

David O’Hagan Professor School of Chemistry EaStCHEM University of St. Andrew St. Andrew, UK http://chemistry.st-and.ac.uk/staff/doh/group/Home.html

Victoria J. Orphan Professor of Geobiology Division of Geological and Planetary Sciences California institute of technology Pasadena, CA http://www.gps.caltech.edu/content/victoria-j-orphan

Sijbren Otto Professor of Systems Chemistry Stratingh institute for Chemistry University of Groningen Groningen, the netherlands http://www.otto-lab.com/index.htm

Eriks Rozners Associate Professor of organic and Bioorganic Chemistry Department of Chemistry SUny Binghamton Binghamton, ny http://chemiris.chem.binghamton.edu/RoZnERS/rozners.htm Veronica Vaida Professor and CiRES Fellow Department of Chemistry and Biochemistry University of Colorado at Boulder Boulder, Co http://chem.colorado.edu/vaidagroup/

Benjamin Van Mooy Associate Scientist Marine Chemistry and Geochemistry Woods Hole oceanographic institute Woods Hole, MA https://www.whoi.edu/bvanmooy/

Willie Wilson Director, national Center for Marine Algae and Microbiota Senior Research Scientist Bigelow Laboratory for ocean Sciences East Boothbay, Maine https://www.bigelow.org/research/srs/william_h_wilson/

Michael Yarus Professor Molecular, Cellular and Developmental Biology University of Colorado at Boulder Boulder, Co https://mcdb.colorado.edu/directory/yarus_m.html


http://www.ocean.washington.edu/home/Anitra+Ingalls

http://www.ocean.washington.edu/home/Anitra+Ingalls

http://research.chem.psu.edu/cdkgroup/

http://www.scripps.edu/krishnamurthy/index.html

http://www.scripps.edu/krishnamurthy/index.html

http://smansy.org/doku.php

http://www.umich.edu/%7Emapplab/

http://www.molevol.de/lab/martin.html

http://www.biochem.emory.edu/labs/imatsum/

http://www.biochem.emory.edu/labs/imatsum/

http://www.chemistry.buffalo.edu/images/morrowLab.jpg

http://www.chemistry.buffalo.edu/images/morrowLab.jpg

http://chemistry.st-and.ac.uk/staff/doh/group/Home.html

http://chemistry.st-and.ac.uk/staff/doh/group/Home.html

http://www.gps.caltech.edu/content/victoria-j-orphan

http://www.gps.caltech.edu/content/victoria-j-orphan

http://www.otto-lab.com/index.htm

http://chemiris.chem.binghamton.edu/ROZNERS/rozners.htm

http://chemiris.chem.binghamton.edu/ROZNERS/rozners.htm

http://chem.colorado.edu/vaidagroup/

https://www.whoi.edu/bvanmooy/

https://www.bigelow.org/research/srs/william_h_wilson/

https://www.bigelow.org/research/srs/william_h_wilson/

https://mcdb.colorado.edu/directory/yarus_m.html

https://mcdb.colorado.edu/directory/yarus_m.html

54

APPEnDiCES

Appendix 2

Workshop Agendasunday, April 1 6:30 Reception (buffet dinner)

7:15 Welcome and introductions

7:30 Charge to the committee

7:45-9:15 three 20-minute talks Ginger Armburst: Limits to Life Victoria Orphan: Microbial Partnerships Christine Keating: Alternative Cellular organization— Why compartmentalization is important and several possible routes for achieving it

monday, April 2 8:00 Buffet breakfast

8:30-10:00 three 20-minute talks David O’Hagan: Fluorine in Biochemistry Lee Cronin: Alternative Chemistries of Life Andy Ellington: the importance of Being RnA

10:15 Final discussion before breakout

10:30 Coffee break

11:00-1:30 Breakout i (Bonds, Building blocks, Biopolymers)

12:00 Lunch break (boxed or buffet lunch delivered)

12:30-1:30 Continued discussion

1:30-2:00 Prepare notes for group presentation

2:00-3:00 Reports and discussion from Breakout i

3:00 Coffee break

3:30-5:30 Breakout ii (Alternative Biochemistries, Metabolism, and Systems Biology)

7:00 Dinner, informal discussions

Tuesday, April 3 8:00 Buffet breakfast

8:30-9:30 Reassemble in Breakout ii: Prep for whole group discussion

9:30 Coffee break

10:00-11:15 Reports and discussion from Breakout ii

11:30-2:00 Breakout iii (Field and Laboratory Experiments)

12:30 Working lunch

2:00-2:30 Prepare reports for whole group discussion

2:30 Coffee break

3:00-5:00 Reports and discussion from Breakout iii

6:30 Dinner, informal discussions

wednesday, April 4 8:30 Buffet breakfast

9:00 Charge for the final day

9:30 Final discussion and summary Key recommendations? What has been overlooked?

12:00 Dismissal/lunch available

1:00-3:00 Meeting of organizing committee.

TopiCs For BrEAkouT sEssions

BrEAkOuT I: Bonds, Building Blocks, BiopolymersUnusual environments might lead to alternative structural chemistry due to the incorporation of alternative elements, unusual bonds, or alternative biopolymers.

1. Are there fundamental characteristics of bonds/building blocks that are required for life? if so, what are these characteristics?

2. What features need to be considered when evaluating alternative protein, nucleic acid, lipid, carbohydrate or other structures that might be considered to support life?

3. What are the limits of extreme life? Are certain elements, tempera-tures, solvents, or atmospheres too extreme to be considered?

4. What laboratory and field experiments and needed tools will advance the discovery process?

BrEAkOuT II: Alternative Biochemistries, metabolism, and systems Biology Assemblies of molecules define a living entity that interacts with its environment and other organisms to undergo adaptation and energy transduction.

1. For which fundamental biochemical reactions could one consider substitutes?

2. What other reaction networks might exist to produce alternative metabolism?

3. What alternative molecular systems might be capable of evolving?

4. What laboratory and field experiments and needed tools will advance the discovery process?

BrEAkOuT III: overarching questions and Empirical Approaches What are the knowledge gaps and how do we build bridges across disciplines?

1. What near-term challenges can be experimentally addressed?

2. Which alternative molecules/reactions should be investigated?

3. Where are the environments on earth that would favor alternative, self-organizing behaviors?

4. Who are the collaborating communities?

5. How do we catalyze these collaborations (methods, databases, equipment, funds) to realize these goals?

See this report on the website at http://chemistry.emory.edu/home/assets/alternativechem.pdf

This material is based upon work supported by the National Science Foundation under Grant No. NSF CHE1212371.


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