February 2017

Summary of Proposal (Compile in English within 3 pages.)
Host institution: National University Corporation Tokyo Institute of Technology
Head of host institution: Yoshinao Mishima, President
Research center: Earth-Life Science Institute (ELSI)
Center director: Kei Hirose
Chief center-project officer (in December 2012): Kei Hirose
Administrative director: Takashi Sakurai

1) Project summary
ELSI aims to answer the fundamental question "when and where did life originate and how did it
evolve?" This question, which originated with the Greek philosophers, has been one of the mostimportant topics of natural science. We will focus our research on understanding the wide range ofplanetary processes and environments on the early Earth that may have been essential to the birth oflife, and on their subsequent changes, with the main aim to study the origin and early evolution of lifeand persistent ecological systems in their geological context. We will use the enormous diversity of
microbial biochemistries, physiologies, and ecologies as windows to identify how the biosphere has
depended in detail on its planetary home from the past to the present, and to suggest the domains
within chemistry and the planetary environments that are most likely to have been pivotal. We willapproach the primordial environment of the Earth through explorations of diverse proxy environmentson the present Earth, ranging from deep-sea and sub-surface microbial ecosystems to extraterrestrial
primitive asteroids. In addition, we will critically examine the universality of these processes, todetermine the uniqueness of our planet, with implications for the search for extraterrestrial life, both in
the solar system and beyond.
2) Mission statement and/or center’s identity
So far, discussions about the origin of life on Earth have been mostly limited to the biochemistry of
proto-life forms. While the Earth environment has been described as a “cradle of life”, the image of a“cradle” points to a supporting background role, rather than a dynamic interplay. In ELSI, we want toradically broaden these discussions by focusing equally strongly on both sides of Earth and Life. For one
thing, life is preserved through a continuous exchange of matter and energy with the surrounding
environment. For another, it is a two-way interaction: as soon as life forms are present, they start toinfluence the environment, just as the environment is influencing life. Our basic outlook is reflected in
the name of our proposed center: ELSI stands for Earth-Life Science Institute, in which Earth sciencesand Life sciences will be equally represented.
In contrast to NASA’s Astrobiology Institute (NAI) whose research topics are broadly similar to ours,
we emphasize the role of the Earth as a whole in the origin and evolution of life. Most importantly, ELSI
will not be a virtual institute like NAI and has been firmly established as a physical entity with vigorous
internal communications through a series of daily, weekly, and monthly events, following the Programfor Interdisciplinary Studies at the Institute for Advanced Studies (IAS) in Princeton as a model. This IAS
program has been a satellite center for ELSI.
We have strongly encouraged interdisciplinary research within ELSI, which attracts a wide variety of
top scientists to visit ELSI to interact with members there and also with each other. We do not want todefine job specifications too strongly beforehand. Rather, we prefer to attract top scientists first, andthen to finetune the research program around their skills and interests.
We combine our research with outreach and education. The on-going Hayabusa-2 mission as well as
Earth-Life Science Institute (ELSI)Tokyo Institute of Technology - 1

the future plan called MMX mission to the Mars moons, questions about the formation of Earth and theorigin of life, and extraterrestrial life are of strong interest to the general public, and thus perfect foroutreach. As for education, we will create a Summer Internship Program for high school students, basedon nation-wide competitions in high schools in Japan. These activities will also help not only ELSI but
also its host, Tokyo Tech, to further increase both its international and its domestic visibility.
3) Research fields
Target research field:
Interdisciplinary Research on Solid-Earth Science, Planetary Science, Geology, Environmental
Microbiology, Microbial Genome Science, Systems Chemistry, Complex Systems Science, andComparative Emergence
Recent progress:
Major progresses have been made recently in the three areas of early Earth environments, primordial
ecological systems, and extraterrestrial life: 1) laboratory experiments that reproduce the conditions at
the beginning of the Earth’s history, 2) investigations of ecological systems under extreme
environments, 3) empirical study of prebiotic chemistry as well as computational chemistry, and 4)
theoretical modeling of planet formation and the observation of Earth-like exoplanets. Our PIs havemade major contributions to the progress in all of these areas.
Our superiority:
Our superiority is clear in the areas of the proposed research. We study the unique environments on
the early Earth by combining the research utilizing high-pressure/high-temperature experiments, theoryof planet formation, and decoding the Earth’s history, all of which are areas in which research at Tokyo
Tech is ahead of that at other places, nationally and internationally. In addition, we have been playing
leading roles in molecular and evolutionary microbiology, in the study of wide-ranging microbial
ecosystems including many in extreme environments, and in connecting the comprative analysis of
microbial energetics to detailed geological contexts.
4) Research objectives
Our research will answer the following scientific questions:- How were the environments at the beginning of the Earth’s history?
- When and where did the primordial ecological system originate?
- How did the Earth and the Universe affect the evolution of life?
- How unique is our planet?
We will also contribute to the planning of explorations of the solar system and observations of exosolar
systems based on the outcome of our research.

Earth-Life Science Institute (ELSI)Tokyo Institute of Technology - 2

5) Outline of management
The center has been established as an independent organization inside Tokyo Tech. The center
director has the authority to make all decisions related to ELSI including the appointment of all staff
members, budget implementation, etc, with advice from the steering committee, Directors’ office andthe international advisory Board. The center has a research-oriented English-based administrative
system led by the administrative director. In addition to university research administrators (assistantdirectors) who provide a wide range of support to researchers, a life advisor is assigned to each nonJapanese family. A PR chief is in charge of overall outreach activities. A coordinator of international
initiatives seeks research funds and offers assistance with recruitment of non-Japanese scientists.
6) Researchers and other center staffs, satellites, partner institutions[Principal Investigators] 15 (incl. 8 non-Japanese) – as of April, 2017
[Total number of researchers] 63 (incl. 25 non-Japanese) – at the end of FY2016[Total number of staffs] 117 (incl. research assistant, excluding short visitors) – at the end of FY2016[Main principal investigators] (affiliation)
Piet Hut (Inst. Adv. Study, Princeton/ELSI), Joseph L. Kirschvink (Caltech/ELSI), Jack Szostak (Harvard
Univ.), Tetsuo Irifune (Ehime Univ.), Kei Hirose (ELSI/University of Tokyo), Shigeru Ida, John W.
Hernlund, Shigenori Maruyama, Naohiro Yoshida, George Helffrich, Erich Smith, Irena Mamajanov,Yuichiro Ueno, Shawn McGlynn, Ryuhei Nakamura (Tokyo Tech)[Satellite organizations] Ehime University, University of Tokyo, Institute for Advanced Study in Princeton,
Harvard University7) Outline of research environment- The center will ensure that all researchers can concentrate on their research. Both of the university
research administrators and life advisor will provide a full range of support to non-Japanese scientists
and their families. Tenured professors were reassigned to ELSI, and exempt at least from the duty ofteaching undergraduate students.
- The center will provide each PI from abroad with seed funding of JPY10 to 20M. Additional support
may be given upon discussion with the center director.
- English-based research-orientated administrative systems has been created through adopting someunique new practices. The administrators are informed of the latest research results.
- Evaluation of the research activities by each scientist will be made on the basis of academic
Earth-Life Science Institute (ELSI)Tokyo Institute of Technology - 3

achievements. Contributions to other activities of the Center such as public outreach will be also
considered. These will reflect in the annual salary renewal.
- The university has reserved sufficient research space (about 4,973 m2 f) for the center at its Ookayama
Campus, which accommodates middle-sized symposia within the center.
8) Outline of indicators for evaluating a center’s global standing
We conduct a comprehensive assessment with consideration of various criteria such as levels of
research activities and recognition of the institute and its researchers. It is equally important to carefully
assess the progress of efforts to promote interdisciplinary research and to create a new researchdomain. Current assessment demonstrates that ELSI has well established as a WPI center and suggests
good prospects for further development.
9) Securing research funding
By FY2016, ELSI has been continuously acquiring other competitive research funds which exceedsthat of the WPI research funds. The university research administrators support researchers with winningmore funds such as Grants-in-Aid for Research.
Also Tokyo Tech is applying for non-profit incorporation overseas to actively seek and stabilize further
funding and donations from abroad.
10) Appropriations plan
FY

Total

2017

2018

2019

2020

2021

6.1

6.1

6.1

6.1

6.1

30.5

0.9

0.9

0.9

0.9

0.9

4.5

7.0

7.0

7.0

7.0

7.0

35.0

($ millions）

WPI grant

Funding forpreviouslyinitiatedcenterbuilding
efforts (if any)
Total

(Exchange Rate: JPY/USD=100)
11) Summary of host institution’s commitment-Tokyo Institute of Technology laid out its goal of becoming one of the world’s top 10 research
universities by 2030, and has been strengthened the research management system and reformulated
our research systems and environments. Our mid-term plans clearly state that ELSI will remain as anindependent research organization directly under the jurisdiction of Tokyo Tech president, andtherefore the university will provide long-term full support to ELSI.
- The university will provide ELSI with JPY90M every year from the President's Discretionary Fund.
-6 tenure-professors were transferred to ELSI and Tokyo Tech will provide necessary support of staff
members.
- Tokyo Tech assured approximately 2,670 m2 of research space in an existing building for ELSI-2 andadditionally a new research building (ELSI-1: 5,000m2) was completed in FY2014 to become an
appropriate research environment. We are prepared to provide more space depending on request of
ELSI.
- Already before the end of the WPI program, Tokyo Tech as a whole will internally adopt widely thoseparts of ELSI's innovative systems that will have proven to be effective.

Earth-Life Science Institute (ELSI)Tokyo Institute of Technology - 4

February 2017

Research Center Project (in English)
Host institution:

National University Corporation Tokyo Institute of Technology

Head of host institution:

Yoshinao Mishima, President(Name, position title)

Research center:

Earth-Life Science Institute (ELSI)

Center director:

Kei Hirose, Tokyo Institute of Technology, Professor

Chief center-project officer(in December2012): (Name, affiliation, position title (in December2012))Kei Hirose, Graduate School of Science and Engineering,Tokyo Institute of Technology, Professor

Project summary

 Briefly describe the general plan of the project.

1. Research Objectives

The Earth-Life Science Institute (ELSI) aims to answer the fundamental question "when andwhere did life originate and how did it evolve?" This question, which originated with the Greek
philosophers, has been one of the most important topics of natural science. We will focus our research onunderstanding the wide range of planetary processes and environments on the early Earth that may havebeen essential to the birth of life, and on their subsequent changes, with the main aim to study the origin
and early evolution of life and persistent ecological systems in their geological context. We will use theenormous diversity of microbial biochemistries, physiologies, and ecologies as windows to identify how
the biosphere has depended in detail on its planetary home from the past to the present, and to suggest
the domains within chemistry and the planetary environments that are most likely to have been pivotal.
We will approach the primordial environment of the Earth both through planetary measurement, theory,and modeling, and by using the many proxy environments available on the present Earth, ranging fromdeep-sea and sub-surface microbial ecosystems to extraterrestrial primitive asteroids. In addition, we will
critically examine the universality of these processes, to determine the uniqueness of our planet, with
implications for the search for extraterrestrial life, both in the solar system and beyond.
ELSI has been thoroughly interdisciplinary since its inception, integrating five areas in science that are
essential for understanding the early stages of Earth and life. Addressing the challenges within thesetogether will culminate in the ability to compare and more deeply understand emergent phenomena, which
we call comparative emergence.
1. Geological sciences, including geology, geochemistry and geophysics of the early Earth, as the sciencesthat describe the environment in which life first originated, and which shaped, and in turn was shapedby, its further evolution.
2. Chemical sciences, including synthetic, computational, and systems chemistry, as the sciences of theunique physical medium that hosts living structure and dynamics.
3. Biological sciences, ranging from biochemistry and systems biology to environmental microbiology, andmicrobial ecology, as the sciences that both seek to understand the function and evolution of life, andthat also contain our most important information about its deep connection to the detailed planetary
context on Earth or possibly elsewhere.
4. Astronomical sciences covering scales from planets to galaxies, as the sciences that describe how the
Earth was formed and what the surface environment of early Earth was like when life was born, andwhich explore how unique or common the Earth is in the galaxy and the possibility of life in othercelestial bodies in our Solar systems and exoplanetary systems.
5. Broadly interdisciplinary input from a range of other scientific fields, from mathematics and physics all
the way to computer science and cognitive science, to shed completely new light on the age-old
question of what the nature of life is, and how that first appeared and then evolved.
Why these five areas? The most fundamental shift that we propose to make in studying the origin ofEarth-Life Science InstituteTokyo Institute of Technology - 1

life is understanding that life is inherently a planetary process. It is the particular architecture and dynamics
of a forming planet that not only hosts life, but also defines the framework within which living order forms
and persists. The biological sciences, understood in this context, not only provide details about possible
early life forms, and the history through which they became more complex and robust, but also principles
to help understand in what ways life is a novel addition to a planet, and in what ways it is a continuationof planetary organization already present. Third, the life we know is inherently a chemical process. We
need chemistry to understand how life's building blocks formed and how they first supported evolution,
but for life to be chemical means much more. Chemistry is not only a science of techniques to produce
and manipulate molecules, but a set of concepts explaining how simple rules give rise to complex
organizations, because of the discrete and diverse character of atoms, bonds, and phases. Each of thesethree bodies of domain knowledge therefore carries some of the concepts essential to understanding life's
origin and nature.
If there was any good agreement about roughly where and how life formed, those three areas taken
together might be enough to produce more and more refined models of the co-evolution of life andenvironment, right from the appearance of the first living cells. However, currently we are still rather far
from such a situation. The debate about how life may have formed continues to range over a huge
spectrum of possible environments, together with a wide set of theories of which molecules combined
how to produce self-sustaining reactions that were both robust enough to be preserved and flexible
enough to admit increasing growth in complexity through early forms of evolution. As long as we don't
really have a strong clue as to which ideas are correct, it is a good idea to step back from the immediate
details, and to solicit ways of thinking from other areas in science and mathematics.
Recent astronomical observations suggest that more than 20% of solar type stars harbor Earth-size or
super-Earth size planets in their habitable zones. These observations combined with theoretical modelingof planet formation will give important clues on how unique or common the Earth is within the galaxy.
Discussions on habitable planets, which may have diverse surface environments, have led us to consider
the possibility of life in the subsurface oceans of icy satellites in our Solar systems, in addition to that oflife on exoplanets in habitable zones of other stars. These arguments will enable us to see our Earth andlife on the Earth from a more general point of view. This is where the fourth area comes in.
The fifth area comes in, combining a range of broadly interdisciplinary sciences.
For example, in the last century some well-known physicists have moved into biology and thereby havetriggered novel theoretical ways of thinking. In a similar fashion, it may well be that abstract modeling ofself-sustaining processes, grounded in an understanding of chemical principles but capable of generalizing
where appropriate, may teach us how to think on higher levels of abstraction about the origin of life.
Computer science may have a unique importance for the problem of origin of life. More appliedcomputation can support the analysis of systems such as chemical reaction networks at levels of complexity
not previously possible, while the abstract understanding of algorithms may capture aspects of chemicaland evolutionary function not normally recognized. The key to ELSI's interdisciplinary approach will be totightly integrate both roles of computation. And finally, cognitive scientists with experience in patternrecognition and pattern generation and other cognitive processes may help in other ways: they may
approach the interactive needs of the most primitive proto-cells in ways that biologists who are trained towork with current life forms may not easily stumble upon.
More specifically, here are the main research topics at ELSI, focused on the following questions:(A) Origin of the Earth
A1. How was the Earth formed?
A2. How did the magma ocean phase connect early formation/differentiation to conditions when life
emerged, including the essential element of water?
A3. How has the Earth's structure, composition, and dynamics evolved through time?
(B) Birth of Earth-Life system
B4. What was the state of the ocean and the atmosphere when life emerged?
B5. How did the geological conditions of the early Earth influence the origin of life?
B6. What was the nature of the first genetic systems employed in the "progenote"?
(C) Evolution of Earth-Life system
C7. What were the major transitions in bioenergetic systems, what drove them, and how did they affectthe spread of life?
C8. How were ancient enzymes and genomes different from modern ones, and can we reconstruct models
Earth-Life Science InstituteTokyo Institute of Technology - 2

of ancestral phenotypes?
C9. How did the thermal evolution of the solid Earth change the ecosystem?
(D) Bioplanet in the Universe
D10. How unique is our planet?
D11. How should we search for extraterrestrial life?
D11. What principles lead to life in a planetary context?
Our superiority in these studies is clear. We will study the unique environments on the early Earth bycombining the research utilizing high-pressure/high-temperature experiments, theory of planet formation,and decoding the Earth’s history, all of which are areas in which research at the Tokyo Institute ofTechnology (Tokyo Tech) is ahead of that at other places, nationally and internationally. In addition,
Japanese scientists are also playing leading roles in molecular and evolutionary microbiology, in the studyof wide-ranging microbial ecosystems including many in extreme environments such as hydrothermal
vents, and crucially, in connecting the comparative analysis of microbial energetics to detailed geologicalcontexts.
Moreover, we already have a rich tradition at Tokyo Tech in addressing many of these issues, basedon unprecedented interdisciplinary research on Solid-Earth Science, Planetary Science, Geology, Materials
Science, Environmental Biology, Molecular Biology, and Microbial Genome Science. Such collaborative
research has been carried out by teams similar to ours since 2004 through the 21st century COE (Centerof Excellence) Program and the Global COE Program. Based on our achievements in these programs, theresearch at ELSI will emphasize the roles of Earth’s interior and the Universe in the origin and evolutionof the Earth-life system. The main novel addition will be the even broader interdisciplinary connections in
the fifth area listed above, for which we will make strong international connections with interdisciplinarygroups elsewhere, such as the Program in Interdisciplinary Studies at the Institute for Advanced Study in
Princeton.
2. Organization
The center is led by the director, Prof. Kei Hirose, who has the overall responsibility to create a worldleading research center. He will continue to recruit leading scientists from around the world and give themboth clear roles and freedom in research. The center director makes the final decisions regarding themanagement of the institute, and appoints all the research and administrative staff members. The steeringcommittee and the Director’s office, in collaboration with the international advisory board will support andadvise the director in the overall operation of the center, appointment and evaluation of each staff member.
ELSI has fifteen principal investigators, as of April 2017, including eight non-Japanese, one women,
and three from the Satellite institutes (Ehime University, Institute for Advanced Study in Princeton &Harvard University). ELSI also has Associate Principle Investigators who have longer appointment morethan five years. Young researchers at ELSI, called Research Scientists, have much freedom in researchwith loose connection to a specific group. Young researchers receive structured feedback and monitored
throughout the year by mutually-agreed mentors. The research activity by research scientist will be
evaluated annually. Based on such evaluation, the high achievers are given the incentive awards. Top
scientists from various disciplines serve as ELSI fellows. Based on their expertise, they provide researchguidance and advice to research groups and individual researchers.
Interdisciplinary research is promoted through extensive communications between the different groups.
Piet Hut, Professor of Interdisciplinary Studies at the Institute for Advanced Study (Princeton), has built
regular events such as daily coffee time, twice-a-week lunch talks, monthly ALL-ELSI meeting, and ELSI
assembly presentations that stimulate broadly interdisciplinary interactions.
The operations and administration is led by the administrative director, Dr. Takashi Sakurai, who hasrich experience in the institutional management and development at the National Astronomical
Observatory of Japan, with the aid of Executive Administrative Director. Proper administrative officers ofTokyo Tech have been assigned to ELSI, providing the primary interface with existing administration officesof the university. Other administrators also have highly professional skills in research administration andEnglish.
ELSI will have four Satellite Centers at Ehime University, University of Tokyo, the Institute for Advanced
Study in Princeton, and Harvard University (Figure 10). We have also made strong connections with theInstitute of Space and Astronomical Science (ISAS) of the Japan Aerospace Extrapolation Agency (JAXA),
and the Japan Agency for Marine Science and Technology (JAMSTEC). These two agencies perform largeEarth-Life Science InstituteTokyo Institute of Technology - 3

scale investigations of extraterrestrial bodies and deep-sea hydrothermal systems, and their researchtargets are closely related to our scientific goals. In addition to these institutes, we have been collaboratingwith ten centers abroad on the basis of the ELSI Origins Network (EON) project funded by the John
Templeton Foundation, with which we hire joint postdocs who spend half time at ELSI and the other halfin the overseas centers. Such collaboration through joint postdocs is an important part of ELSI’s mission
to become an international hub of research interactions.

<Major changes from initial project plan:>• ELSI has strategically enhanced its research organization. ELSI appointed new PIs with strong
expertise in Biology and Chemistry. By setting up the fourth Satellite Center at the University ofTokyo, ELSI will further reinforce Earth and Planetary Sciences. We set up dialogue-based forums
to discuss strategic development goals and accelerate interdisciplinary collaboration.
• By acquiring the large research fund from the John Templeton Foundation, ELSI launched the ELSI
Origins Network (EON) project, which has expanded ELSI's international network and attracted adiverse collection of young talents in the Origin of Life studies.
• Following discussions over the institutional development described above, ELSI has conceptualized
the idea of a new research domain. ELSI aims to crystallize this idea of "Comparative Emergence"in the coming five years.
• ELSI has introduced a mentoring system to ensure structured feedback to early-career researchers.
• ELSI has started accepting PhD students and is eager to recruit more prospective PhD students.
<Mission statement and/or center’s identity>

 Briefly and clearly describe the mission statement and/or the project’s identity as WPI center.

So far, discussions about the origin of life on Earth have been mostly limited to the biochemistry of
proto-life forms. While the Earth environment has been described as a “cradle of life”, the image of a“cradle” points to a supporting background role, rather than a dynamic interplay. In ELSI, we want toradically broaden these discussions by focusing equally strongly on both sides of Earth and Life. For one
thing, life is preserved through a continuous exchange of matter and energy with the surrounding
environment. For another, it is a two-way interaction: as soon as life forms are present, they start toinfluence the environment, just as the environment is influencing life. Our basic outlook is reflected in thename of our proposed center: ELSI stands for Earth-Life Science Institute, in which Earth sciences andLife sciences will be equally represented.
In addition, we will replace the biology question of the “origin of life” with the more relevantinterdisciplinary question regarding the “birth of a persistent ecological system.” An important goal in our
research will be to clarify the initial ecological system that allowed a stable and persistent existence of life
even under the various harsh and violent changes of the environment at the beginning of the Earth’s
history.
And while we will study life in the context of the early Earth environment, similarly we will also study
how the Earth itself was formed and how its conditions changed, inside the Earth as well as on the surface.
In the course of these studies, we will critically examine the universality and uniqueness of our planet thatgave birth to life as we know it, with implications for the search for extraterrestrial life in both solar andextra-solar systems.
We will perform our research through cutting-edge lab experiments, computer simulations, and fieldobservations. We may also need to develop wider pictures of metabolism and self-reproduction on more
abstract meta levels through a broadly interdisciplinary approach. How such abstract models are thenimplemented on molecular levels may differ between life on Earth and elsewhere.
In contrast to NASA’s Astrobiology Institute (NAI) whose research topics are broadly similar to ours,
we emphasize the role of the Earth as a whole in the origin and evolution of life. Most importantly, ELSI
will not be a virtual institute like NAI. People from different fields will gather together at ELSI to make it aforemost interdisciplinary research institute. We will promote internal communications through a series ofdaily, weekly, and monthly events, following the Program for Interdisciplinary Studies at the Institute for
Earth-Life Science InstituteTokyo Institute of Technology - 4

Advanced Study (IAS) in Princeton as a model. This IAS program has been a satellite center for ELSI.
The success of ELSI will depend strongly on its research environment, and the recruitment of goodscientists. We have strongly encouraged interdisciplinary research within ELSI, which attracts a wide
variety of top scientists to visit ELSI to interact with members there and also with each other. We do notwant to define job specifications too strongly beforehand. Rather, we prefer to attract top scientists first,
and then to finetune the research program around their skills and interests. In addition to promotinginternal communications, the center director is responsible for providing the best research environment.
A very efficient research-oriented secretary system has been created through evaluation and education ofadministrators.
ELSI is now playing a strong role as a communication center. We have promoted interdisciplinaryconnections between researchers internationally and nationally. In addition, we combine our research withoutreach and education. The on-going Hayabusa-2 mission as well as the future plan called MMX mission
to Mars moons, questions about the formation of Earth and the origin of life, and extraterrestrial life areof strong interest to the general public, and thus perfect for outreach. As for education, we will start aninternational graduate program with top-level students including many from abroad. These activities help
not only ELSI but also its host, Tokyo Tech, to further increase both its international and domestic visibility.

1.

Research fields

 Specifying the inter-disciplinary field(s) to which the project may be closely related.
 Describe the importance of the proposed research, including domestic and international R&D trends in the field and Japan’s
advantages.
 If centers in similar fields already exist in Japan or overseas, please list them.

Interdisciplinary Research on Solid-Earth Science, Planetary Science,
Geology, Environmental Microbiology, Microbial Genome Science, Systems Chemistry,
Complex Systems Science, and Comparative Emergence
We will promote integrated research in fields related to the formation of the Earth in the early solar
system, the environment and the creation of life on the early Earth, and the co-evolution of the Earth-Lifesystem, using the keyword “early Earth”. Through the study of Earth, we will clarify both universal andunique aspects of the Earth, from which life emerged and evolved, and we will predict the presence orabsence of life on other planets. In order to immediately apply our research results to search forextraterrestrial life, we will work in close cooperation with space exploration missions and astronomical
observation teams. To overcome the frequently-claimed problem of an “n = 1” sample for both Earth andLife, we will apply the range of comparative methods across physical and biological sciences to understandcommon aspects of the emergence of novelty among the many subsystems that make up each domain.
We refer to this application of modern comparative methods to a systematic study of emergence as anatural phenomenon in its own right using the keyword “comparative emergence”.
Importance and trend of the research field
The life science and Earth science should be linked, simply because life is a phenomenon that can exist
only through the exchange of energies and matter with the surrounding environment. We will therefore
integrate research on the Earth and life, and explore “how our life can originate and continue on thisplanet” through a detailed study focused on the early Earth. This is one of the most important questions
that natural science, beginning with Greek philosophy, has asked until this modern age. It is amazing andfascinating that so much progress has been made during the last 20 years, in related fields, on a questionthat has been at the heart of science for 2700 years. Four trends will be described in the following sections.
1. Understanding the Earth
Recently, rapid progress has been made in analyzing the deepest parts of the Earth, and we now havea detailed image of the Earth’s interior, including the core of the Earth. One of the major factors in thisprogress has been a drastic advancement in ultrahigh pressure experiment techniques by Hirose, Center
Director, and Irifune, a PI based at the Ehime Satellite Center. Fifteen years ago, most experiments
covered a depth of only 2000 km, but currently experiments studying the center of the Earth, 6371 km
deep, are being routinely conducted. Large volume high pressure experiments can now be performed up
Earth-Life Science InstituteTokyo Institute of Technology - 5

to conditions of the deep mantle in Irifune’s lab, using a technique that strongly complements and supports
the technology in Hirose’s lab. As a result of these developments, Hirose et al. discovered that thelowermost mantle is composed of a previously unknown mineral phase, post-perovskite. Furthermore,
Hirose et al. have analyzed crystal structures of the inner core at the center of the Earth. As a result, theactual state of the Earth’s core, which so far had been a topic of speculation, is now a regular subject ofexperimentation in ELSI laboratories. These are great accomplishments achieved in Japan. The highpressure experimental achievements of Hirose and Irifune have raised the global visibility and importanceof frontier geoscience in Japan, which has led to growth in international collaborations and advances in
our understanding of Earth’s evolution.
Most of the past ultrahigh pressure experiments were conducted to understand the “present Earth,”
however, the direction of research enabled by recent developments now allows us to directly target “theevolution of the Earth” and “the early Earth.” For example, PI Hernlund and his team used the discoveryof post-perovskite, combined with seismic imaging, to constrain the rate of cooling of Earth’s core, a criticalparameter controlling Earth’s long term evolution and dynamics. The high cooling rate of the core impliedby this result led Hernlund to propose the “Basal Magma Ocean” hypothesis, which was experimentallyconfirmed by experiments performed in Hirose’s lab. PI Helffrich recently used seismic imaging to show
layering in the outermost core of the Earth which is connected to chemical exchanges between the coreand mantle that are simulated at high pressure by Hirose and Irifune. And a major discovery has recently
been made in Hirose’s lab showing that the core crystallizes SiO 2 , providing an explanation for how Earthcould have maintained a geomagnetic field more than 3.5 billion years, as suggested by paleomagnetic
evidence. At the same time, PI Kirschvink and his group have developed micro-magnetometer techniquesthat permit us to measure Earth’s remnant magnetic field recorded in zircon crystals older than 4 billion
years, before the rock record. Thus we are able to extend our evolution constraints back to Earth’s
formation period 4.5 billion years ago, where we can connect with unique constraints from planet
formation models like those pioneered by PI Ida. From this work, it is apparent that the extensive
differentiation of the Earth due to magma oceans is a major factor controlling the subsequent evolutionof the Earth, which in turn determines the conditions of the surface environment.
Complementing these discoveries, the progress of research on geology and geochemistry of the early
Earth environment is remarkable. As a result, on a macro and long-term time scale, it is becoming clearthat Life and Earth evolved together. In the 1980’s, the Precambrian Paleontology Research Group led byBill Schopf found many bacterial fossils in Precambrian rocks older than 1 billion years ago. This revealed
that life was active on the early Earth. Unfortunately, it was impossible to classify the fossil bacteria basedon their simple forms, and it was unknown “what functions and metabolisms were active on the early
Earth.” After that, the geochemical bio-indicators such as stable isotope ratios of bio-essential elements
were established, and certain physiological natures and metabolisms could be continuously read off thegeological records. Currently, the biogeochemical cycle of C, N, S, and Fe, etc. can be traced back to 3.8
billion years ago. Furthermore, this research on geochemistry is reaching a level that produces quantitative
estimates of the chemical environment on the early Earth, including the atmospheric composition andredox status of the oceans. The “decoding whole-Earth history” project led by Kumazawa and Maruyama,
Institute PI, pioneered this research in Japan since 1995. Then, internationally, the Agouron Institutestarted their scientific drilling project in the Kalahari Desert in South Africa (PI, Kirschvink), followed by
the NASA Astrobiology Institute and continental drilling programs of France and Australia, etc. Research
programs by Tokyo Institute of Technology COE/G-COE programs also played a role in the research of theevolution of the Earth.
The results of this research uncovered unexpected aspects of atmospheric evolution, such as the Great
Oxidation Event, and climate changes, such as Snowball Earth, found by Kirschvink, an Institute PI,
implying an important relationship between environmental changes and the evolution of life. The ultimate
causes for these environmental changes have not yet been identified; however, changes of the solid Earth(rapid continental growth, increase in sedimentary rocks, intense volcanic activities and geomagnetic field
intensity changes), sudden biological evolution of oxygen-releasing photosynthesis, and the impact fromgalactic events (increase in cosmic rays on Earth), have been actively discussed. A number of new concepts
have originated from interdisciplinary research by Tokyo Institute of Technology’s G-COE program. To
determine the origin and evolution of life on Earth, it is time to pay close attention to the relationshipbetween the thermal evolution of the Earth including its deep mantle and core and long-term changes inthe Earth-Life system.
2. Earth-Life Geobiology and Comparative Microbial Genomics
Microorganisms seem especially good at adapting to extreme physical and chemical conditions, andEarth-Life Science InstituteTokyo Institute of Technology - 6

the diversity of these conditions is in turn connected to the development of the vast diversity of life on theplanet. Furthermore, the existence of microorganisms in apparently very extreme environments motivatesthe idea that extraterrestrial life may have a capacity to thrive in a wide array of chemical environments.
However, the relationships between physical-chemical conditions and microbial evolution have not been
established. Nor have the time scales and magnitudes of microbial driven global chemical change beenclearly delineated. Connecting biological evolution to planetary evolution is a key goal of ELSI, and in thescientific community the recognition of the importance of this connection led to the establishment of suchconcepts as “biogeochemistry”, “geomicrobiology”, and also broadly, “geobiology”.
To understand the collective relationships between biological-abiotic-geological interactions during longand very evolutionarily significant time scales requires diversity of intellectual breadth and at the sametime substantial focus. This intellectual breadth has now been achieved in the unique ELSI environment.
For example, ELSI researchers investigate microbial biogeochemical interactions and their evolution froma number of angles and also using distinct yet integrate-able study systems including: hyperthermophilicviruses, the bioenergetics of archaea and bacteria, protein catalyst evolution and its geological fingerprintin the rock record, the evolution of major bioenergetics transitions such as photosynthesis, microbial biomineralization processes, advanced next generation genomics analyses, and cutting edge single cell
analytical techniques to enumerate cellular activities as they exist in natural environments.
The establishment of a new field of cellular ecology based around the perspective of individuals has
also shifted research focus at ELSI and worldwide. Now, it is possible to construct an understanding of
microbial ecology directly from thousands of individual observations; in the future, these observations willturn into millions, extending the perspective of the individual throughout microbial ecosystems. Thesedevelopments assist in interpreting how and why genomically identical individuals within populations varysignificantly between each other, and how these differences might be closely linked to the geologicallydetermined physico-chemical environment. This perspective on cellular individuality connects and supplies
contrast directly to other ELSI research on the “progenote” – which references a time in biological evolution
when individuality did not exist in the current form.
In addition to the ability to perceive ecology from the individual cell perspective, microbial genome andmetagenome sciences are keys to understand the early and modern ecosystems and to extract generalprinciples from the great complexity of ecosystem formation and behavior. Still, the unknown diversity of
microbial genomes and their physiologies remain vast, however rapid development of next-generation
sequencers and data analysis methods enable us to obtain, extract and interpret enormous amount ofdata and information, expanding our knowledge at unprecedented rates. Using these approaches new
perspectives on the evolution of bioenergetics capacities such as photosynthesis and hydrogen oxidation
can be gained. These capabilities clearly establish genome sciences as a key strength within ELSI.
3. Messy Chemistry: from components to system-studies of the Origin of Life
While a precise definition of life is yet to be rendered, it is understood that a living organism is not amere collection of molecules, but an extensive complex dynamic network of interlinking processes. It istherefore reasonable in the search for the origin of life to give attention to prebiotically plausible chemicalsystems that could have sustained life-like processes. As it stands a number of experiments simulating
early earth conditions, such as Miller-Urey experiment (Miller, 1953), hydrogen cyanide polymerization(Matthews and Minard, 2006), formose reaction (Breslow, 1959), have been shown to be complex chemicalsystems invoking a large number of reaction mechanisms and yielding a vast array of products. We
describe such systems as “messy chemistry”. While these systems are usually reported as sources of
biological building blocks, within them processes leading to the synthesis of amino-acids, nucleobases andcarbohydrates are by far not the predominant ones. In fact, the major product is usually the mixture of
intractable structurally complex polymers referred to as “tar” or “asphalt”. How did such undesired
processes get suppressed in the prebiotic world without enzymes to favor relevant ones? Alternatively, did
the “tar” play an important role in the process of chemical evolution?
Conditions of the earth and specific geological phenomena are likely to have shaped the prebiotic
chemical systems. Of fundamental importance to all synthetic chemical systems are free-energy sources,
among which natural nuclear reactors combining ionizing radiation with wet-dry cycling are one possibility,
and organized electrochemical potentials at chimney structures in hydrothermal vents are another. These
relatively recently-investigated sources could have acted independently of or in parallel with other longinvestigated energy sources including oxidation/reduction potential from mixed non-equilibrium fluids, andfar-from equilibrium chemistry in space producing organized molecules that could be delivered to Earth.
Active areas of research at ELSI in natural-environment modeling will emphasize possibilities for nuclear
geysers in the Hadean (more ancient than those preserved in known geological formations), utilizing Tokyo
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Tech’s unique irradiation facilities, and hydrothermal vent experiments and laboratory models focused on
the reduction of CO 2 to form organics that could plausibly have existed on prebiotic Earth. Given thecentrality of redox reactions in contemporary metabolism, the study of geological triggers for this type ofchemistry is of particularly importance.
Complex systems chemistry is a relatively young field, basic tenets of which are still being formulated
without the added constraint of prebiotic plausibility. One group of approaches that guides ELSI’s research
program is artificial chemistry, a computational field wherein chemical reactions are computer simulated,yielding insight on emergent phenomena, self-organization and evolution in general. Our inquiries will
focus in-depth on intermolecular force driven self-organization and selection, both in silico and in thelaboratory. The experimental studies within the framework will concentrate on chemical systems that are
not necessarily prebiotic but discernable by the established analytical techniques.
An important parallel contribution to ELSI’s research in systems chemistry comes from advances incomputational methods for handling the combinatorics of both molecular state spaces and reaction
systems. Partly these advances come from increases in computing power in the last decade, and partly
they draw from advances in the abstractions with which reactions can be represented and analyzed. The
widespread use of abstract molecule representations such as SMILES and INCHI (Weininger and Weininger,
1989; IUPAC 2016) have enabled database approaches and context-sensitive representations of reactions,but these systems have also revealed weaknesses in the molecular representation that render theminsufficient for unlimited extension. Recent improvements in the representations of molecules and reaction
abstractions in terms of graphs and graph-rewrite rules, combined with computational advances in costly
algorithms such as graph-isomorphism search and integer linear programming, now enable the automatedgeneration and characterization of networks that would have been prohibitive even ten years ago. New
tools, introduced by ELSI collaborators, network affiliates, and even postdoctoral fellows, include themolecular structure calculator MOLGEN (www.molgen.de/), and the graph-grammar reaction-modelingframework MedØlDatschgerl. (cheminf.imada.sdu.dk/mod/).
In parallel with discrete methods to represent molecules and reaction systems, advances in molecular
dynamics, density functional theory, and ab initio methods (propelled significantly by their use in thepharmaceutical industry) have made possible the quantitative modeling of enzyme-substrate fit andreaction transition states, to a degree that can be calibrated against experiment and used to predict isotope
effects or consequences of mutation or atomic substitutions. With these we can pursue the reconstructionof ancient enzymes and deduce the aspects of molecular phenotype that were essential to their evolution.
Complex systems methods relevant to understanding the emergence of order in driven systems also
include general theory of pattern-formation and robustness from non-equilibrium stochastic processes.
At ELSI we will apply these, not only to traditional problems in reaction-diffusion theory where they remain
relevant and challenging, but also to new domains such as the topologically and computationally complex
systems known as chemical reaction networks, following the pioneering work of Feinberg, Horn, andJackson (Horn and Jackson, 1972; Feinberg, 1987). Other important influences on ELSI complex systems
studies include a fully modern understanding of evolutionary dynamics, across levels ranging frommolecules to ecosystems, and even theories that seek to abstract the essence of cognitive capabilities,
where we collaborate with innovative centers such as Araya Brain Imaging.
Messy chemistry is an interdisciplinary approach combining the expertise of earth science, complex
system physics, organic and biochemistry. Consequently, ELSI is uniquely positioned to apply messy
chemistry to the origins of life studies.
4. Discovery of “Earth-like” exo-planets
Since 1995 when extra-solar planets were first found, the number of planets newly discovered has
increased drastically; as of 2016, 3500 extra-solar planets have been confirmed. Many terrestrial planets("super-Earths" and "Earths") have been discovered beyond the solar system in the last decade, and theminimum detectable planetary sizes have reached down to the Earth's size. The most recent observations
and theoretical models suggest that more than 20% of solar-type stars have super-Earths or Earths intheir habitable zones, stimulating discussions about extraterrestrial life within the field of astronomy. Fromthese diverse and ubiquitous super-Earths/Earths, we can understand our Earth more deeply.
At ELSI, planet formation theory has been developed to discuss formation of both our Solar systemand exoplanetary systems. ELSI is now one of world-leading centers on planet formation theory. An
Institute PI, Shigeru Ida, developed a planet population model that enables us to directly compare between
the theory and exoplanet observations, which have been significantly referred to by many exoplanet survey
projects in the world. N-body simulation of planet accretion is also a strong point of ELSI. Now,
cosmochemical data are also combined to the theoretical simulations, in addition to astronomical
Earth-Life Science InstituteTokyo Institute of Technology - 8

observation data of protoplanetary disks and exoplanets.
In a parallel development, the discovery of past water traces on Mars and the observations that strongly
suggest the existence of internal oceans in Europa (a satellite of Jupiter) and Enceladus (a satellite of
Saturn), have given us great expectations that there might be other celestial bodies in the solar systemthat harbor life. Formation model of icy satellites has been also intensively investigated by ELSI researchers.
Thus, it might be becoming possible to find (signatures of) life on extraterrestrial celestial bodies. Using
current or future astronomical observation, we can begin to look for biosignatures of extraterrestrial life.
The major idea is to detect atmospheric components of possible biological origins, such as ozone or
methane, by direct spectroscopic observation of extra-solar planets. Such an observation is one of thehighlights of next-generation large ground-based telescopes such as TMT (Thirty Meter Telescope) and EELT (European Extremely Large Telescope) planed by international consortiums. On the other hand, ALMA
(Atacama Large Millimeter/submillimeter Array) radio telescope developed by international collaboration
has already started observations and is discovering complex organic matter in interstellar molecular clouds
and revealing the detailed structure of protoplanetary disks around young stars, where planets are forming.
The search for extraterrestrial life includes in situ analysis or sample return by space missions inaddition to the remote sensing by telescope observations. While many space missions have been targeted
to in situ surveys of surface of Mars, sample return missions such as “Hayabusa-2” by JAXA are also
promising. In samples from a primitive C-type asteroid (Ryugu) that will be obtained by Hayabusa-2, waterand organic matter should be found. JAXA is also planning a sample return mission to a Martian satellite(Phobos or Deimos) called MMX (Martian Moons eXplorer), which may be launched in 2024. MMX will give
an important clue not only to the origin of Martian satellites but also primitive Martian surface environments,
because it is expected that the samples also include debris generated by early impacts to Mars. ELSI
researchers have been committing to science goal discussions of MMX, and ELSI is expected to play animportant role in MMX mission plan.
As just described, science missions searching for extraterrestrial life have already started, andatmospheres of extra-solar Earth-like planets will be investigated through spectroscopic observation within
next 10 years. Thus, the understanding of the universality and uniqueness of our Earth, and the presenceor absence of biological activity on extraterrestrial celestial bodies will dramatically advance. In this way,
Earth and planetary sciences will be revolutionized, upon finding habitable celestial bodies beyond ourcurrent imagination. For such observations, we need to establish a new field of “Bio-planetology” that will
predict the conditions of planets (or other celestial bodies) allowing existence of life and what observation
methods should be used for finding them. This should be an urgent issue for earth and planetary sciences
and astronomy. In 2015, Japan AstroBiology Center (ABC) was founded. Its main objectives are to develop
instruments for TMT and promote on-going extra-solar planet search programs. ELSI researchers havebeen involved as board members of ABC. Close corporation between ELSI and ABC is expected.
List of centers in similar research fields
International:- NASA Astrobiology Institute (NAI)- SETI (Search for Extraterrestrial Intelligence) Institute- Harvard Origins of Life Initiative- Heidelberg Initiative for the Origins of Life (HIFOL)- Centre for Earth Evolution and Dynamics (CEED)- Institut de Physique du Globe de Paris (IPGP)- Centro de Astrobiología (CAB), CSIC-INTA- Simons Collaboration on the Origins of Life (SCOL)- Center for Chemical Evolution (CCE)- Continental drilling programs (France, South Africa, Europe), Deep-sea drilling programs (ODP, etc.)
Domestic:- Japan Agency for Marine-Earth Science and Technology (JAMSTEC)- Institute of Space and Astronautical Science/Japan Aerospace Exploration Agency (ISAS/JAXA)- AstroBiology Center (ABC), National Institutes of Natural Sciences (NINS)Japanese expertise
In this institute, we “recreate the Earth” through ultrahigh pressure experiments and simulations basedon planet formation theory. We increase our understanding of the origin and early evolution of the EarthLife system through geological and microbiological research, and study the universality of life-hosting
planets through generalizing from the case of the Earth. Among these, ultrahigh pressure experiments
Earth-Life Science InstituteTokyo Institute of Technology - 9and planet formation theory are, without a doubt, world-renowned specialties of the Japanese in the fields
of earth and planetary sciences. In the ultrahigh pressure experiments, the multi-anvil apparatus anddiamond-anvil cell apparatus are the two major high-pressure instruments that are most widely used. The
former apparatus was mainly developed by Naoto Kawai in Osaka University in the 1960’s. The apparatus
itself and experiment techniques have been exported worldwide from Japan. The person at the leadingedge of developing these techniques is Irifune, an Institute PI. The latter apparatus has the disadvantagethat microscopic samples are used; however, it has become a major apparatus for high-pressure earthscience with the advent of radiation light facilities. Only the group led by Hirose, the Institute director, canrealize the ultrahigh pressure and high temperature environment at the center of the Earth. Both groups,
led by Irifune and Hirose, have achieved great results based on their world-class ultrahigh pressure
experiment techniques, and the superiority of those results will certainly continue for the next 5 years. In
addition, particle beams are required to analyze microscopic samples under high pressure. Having theworld’s most advanced high pressure sample analysis facilities, such as the world’s largest facility forsynchrotron radiation, SPring-8, and the Japan Proton Accelerator Research Complex, J-PARC, forms partof Japan’s superiority.
Equally leading internationally, the classical standard model of planet formation was established from
“Kyoto model” and Safronov model in the 1980’s. Currently Ida’s group in the Tokyo Institute ofTechnology (an Institute PI) has taken over, and a new “Tokyo Tech model” is being established. This
process is closely connected with the development of large scale computer systems and comprehensively
synthesizing multi-layered processes of planet formation. Makino, an ELSI Fellow, has contributed greatly
to the development of the world’s fastest super computer by a unique approach of integrating thedevelopment of hardware, algorithms, and software and scientific research, and his expertise will be
invaluable.
In the 1990’s, a project on “decoding the whole Earth history” was promoted mainly by Maruyama, an
Institute PI. In this project, ahead of the inception of the encoding the evolution of life on the early Earthby the NASA Astrobiology Institute, much progress was made in collecting, encoding, and analyzing rocks
from the early Earth worldwide. Rock samples collected from all over the world reached a total of over
165000 samples. These samples are stored at the Tokyo Institute of Technology and made available forcollaborative research all around the world. Collecting rocks in consideration of the changes in the solid
Earth is an exclusive part of this project.
For deep-sea hydrothermal exploration, Japan has the best capability in the world, led by the Japan
Agency for Marine-Earth Science and Technology. Takai, an ELSI Fellow, et al. have initiatedgeomicrobiology of the deep-sea hydrothermal systems and have provided basic principles of interaction
between the geo- and life-systems through more than 10 years of exploration by his group, utilizing worldclass, large-scale research facilities.
While Europe and the U.S. lead the way regarding the observation of extra-solar planets in the universe,
Japan has also achieved many essential results, such as sample return missions from asteroids via
Hayabusa and Hayabusa-2 by JAXA and direct imaging of extra-solar planets using the Subaru Telescope.
Another sample return mission to a Martian satellite (Phobos or Deimos) is also planned by JAXA.
In addition to the expertise of each individual researcher, the collective research done in the “project
on decoding the Earth evolution”, “Tokyo Institute of Technology COE project: the Earth” and “Tokyo
Institute of Technology Global COE Project: From the Earth to Earths”, provided interdisciplinary integrated
research by geoscientists, planetary scientists, and life scientists. These research projects, starting 25
years ago, have firmly established Japan’s leading role in these fields, internationally.
International appeal of ELSIELSI has quickly become a key place for scientists to get together and develop new ideas. International
appeal of ELSI can be distilled to two major points: 1) ELSI addresses fundamental questions to understandthe origin and evolution of the Earth and life with equal focus on the Earth/Astronomical Sciences andLife/Chemical Sciences and 2) ELSI transformed vision into reality by establishing such interdisciplinary
research institute as a physical entity. The unique features and the global status of international
collaborative research centers are described in more detail below.
Recent decades witnessed increased international activities in fields such as Astrobiology, exoplanet
observation, and investigations into microbial ecosystems in diverse and extreme environments. There is,however, little concerted effort by any other single institute except ELSI to make such a detailed
collaborative effort to address the most ambitious questions of Earth and life sciences: the origin of Earth(planets) and the origin(s) of life. ELSI’s interdisciplinary approach to these questions has been extremely
successful in raising a very high international profile in just several years.
Earth-Life Science InstituteTokyo Institute of Technology - 10

ELSI’s international appeal is evident in the involvement of other institutions in international projects
instigated by ELSI. ELSI was launched with its international network that consisted of three Satellite
Centers, two of which located in overseas, and many overseas institute in cooperation. This global network
was substantially enhanced through the ELSI Origins Network (EON). EON has founded a network of“affiliated centers” around the world, each of which shares a postdoc with ELSI who works on a joint
project. These centers include groups in the US (at Emory university, Rutgers university, Caltech, UC San
Diego, NASA Goddard and NASA Ames), Europe (at University of Southern Denmark and Institut desSystèmes Intelligents et de Robotique in Paris) and the UK (at Cambridge university).
It is obvious that interest in the origin and evolution of Earth and life is common among humankind in
all ages and places. The possible existence of life on Mars and the icy moons Europa and Enceladus withpotential internal oceans has been extensively discussed as a near future target for space exploration.
Recently, a large number of extra-solar planets have been found, and some of them may have oceans like
Earth. In this age when the existence of life in the universe is beginning to be scientifically discussed, weface an increasing importance of understanding the origin of the Earth, from which life has grown. The“early Earth” that we focus on, is an almost untouched field so far, waiting for the experimental andnumerical techniques that we plan to use and are using today. As there is little direct physical evidence,research on the early Earth is a great challenge for geology and life science. It is clear that the early Earthand early Life followed a path of joined evolution. ELSI, as an international institute that researches onsuch unresolved important fields has attracted the eyes of the world.
What has established ELSI as an international hub among these in a short time is the fact that ELSI isan institute built in the university campus whereas others are mostly virtual organizations where
researchers in different fields do their research separately in their own institutes. Researchers in different
fields gather and interact at ELSI, and this face-to-face collaboration has destroyed the barriers that exist
between research fields and cultures and is succeeding in integrating disciplines. As a result, the roles ofthe solid Earth and the universe in influencing the origin and evolution of life have been receiving growing
attention as key concepts. This unique and increasingly globally recognized “ELSI brand” of Earth-Life
science will continue to spur a wide range of interests and to advance research on the origin and evolutionof the Earth and life, highlighting ELSI as a pioneer institute. In the next phase of the institute, we expect
continued and even more dramatic international visibility and appeal.

2.

Research objectives

 Describe in a clear and easy-to-understand manner the research objectives that the project seeks to achieve by the end of the grant
period. In describing the objectives, the following should be articulated in an easily understandable manner: What kind of research do
you plan to implement by fusing various fields within the environmental domain? In the process, what world-level scientific issues aresought to be resolved? What is the expected impact of the scientific advances to be achieved on society in the future?
 Describe concretely the research plan to achieve these objectives.

We focus on the early Earth when life emerged, and will answer the following scientific questions:(A) How was the Earth formed within the solar system? (B) How was the earth's first ecosystem established,and (C) How can the earth and life evolve after the first state. Through the study of the Earth, we clarify
universality and uniqueness of the planet Earth harboring life. Further, we utilize the outcomes of theresearch (D) to provide guidance for the search for life on other planets and moons. Each of those themesis performed under an interdisciplinary fusion of different fields. Each question to be solved is discussed
in detail below.

Earth-Life Science InstituteTokyo Institute of Technology - 11

Figure 1. Summary of research objectives.
A) Origin of the Earth
The main goal of our study is to understand how the planet Earth was formed and harbored life. Itis critical to determine the original state of the Earth from the core, through mantle and crust, to theocean and the atmosphere. First, we aim to understand (1) how the earth was formed in the solar
system, examining the theoretical model from the viewpoint of the chemical composition of the Earth.
(2) Breaking through the conventional idea of habitable zone (i.e. just presence of liquid water), we willfind out factors which determined the appropriate level of ocean water on the Earth. And finally, (3) we
experimentally reproduce material differentiation of the early Earth before and after the birth of life.
A1. How was the Earth formed?
The classical standard planet formation model was built from Safronov and Kyoto models in the 197080's to explain planetary configuration in the solar system. However, recent findings of diverse extrasolar planetary systems show that the classical model cannot be applied to the extra-solar planetarysystems. We need to take into account many processes that were missing in the classical model torebuild the planet formation theory, in order to explain both our solar system and diverse extra-solar
planetary systems consistently. On the basis of the renewed planet formation model, we discuss deliveryof volatile elements such as water and organic molecules that are essential for life. Presence of liquidwater conventionally has been considered as one of the conditions for habitable planets, and the rangeof orbital radii in which liquid water can exist is called a habitable zone. Coexistence of ocean and land
could also be a condition for a planet for life to emerge. However, the factors that determine the amountof water on a planet have not been clarified yet. Furthermore, we verify our theoretical models by
clarifying the chemical composition of the bulk Earth and by determining the composition of the present
core and lower mantle of the Earth on the basis of super-high-pressure experiments.
A2. How did the “magma ocean” phase connect early formation/differentiation to conditions
when life emerged, including the essential element of water?
Terrestrial planets and moons are thought to form in an environment characterized by energetic
accretion and extensive melting events called “magma oceans” that processed material delivered to the
Earth-Life Science InstituteTokyo Institute of Technology - 12growing planet and facilitated its differentiation into core, mantle, crust, ocean, and atmosphere. Magma
ocean studies are therefore of critical importance to understand the birth of terrestrial planets and moons,and is a key bridge between research fields concerned with planetary accretion (A1) and subsequentevolution (A3).
A3. How has the Earth's structure, composition, and dynamics evolved through time?
As the magma ocean was formed and solidified, the earth materials were differentiated into the core,
the mantle, the crust, the ocean, and the atmosphere. Such material differentiation at the beginning of
the Earth determined the subsequent mantle dynamics and thermal evolution of the Earth. Throughvolcanic activity, continental growth, and magnetic field formation, it should have had a significant
influence on changes of the surface environment and the evolution of life. Surface conditions includingthat of the atmosphere couple influences ranging from the geomagnetic field generated in the deep
earth out potentially to the scales of galactic structure. We investigate such a material differentiation by
high-pressure experiment and computer simulation.
B) Birth of Earth-Life system
In 1977, Woese and Fox proposed the concept of the progenote to refer to a period of biologicalevolution in which vertical inheritance was not yet the dominant form of information transfer. Thus,
before phylogenetically distinct lineages emerged, a genetically co-interacting community existed out of
which emerged what we now perceive as the three domains of life. This recognition leads to the notionthat the so-called “origins of life” should be discussed as entirely different phenomena from theemergence of the most ancient living ecosystem of our ultimate ancestors. We focus on the first EarthLife system including the atmosphere, the ocean, the rocks, and the biological community that coevolved finally into the progenote and subsequently life as we know it. Our goal is to understand when,
where, and how, the Earth-Life system was established. In ELSI, we will try to solve the following
questions.
B4. What was the state of the ocean and the atmosphere when life emerged?
What was the composition of the initial atmosphere, the ocean and the crust at the time of the birthof life? It is still largely an unsolved scientific question. We will build a verifiable model for the first ocean
and atmosphere by 1) a forward approach based on the high-temperature experiments and theoreticalsimulations of A1 to A3, and 2) a reverse approach from the geological record. With the technicaldevelopment of geochemical tracers, we will decode the chemistry of the early ocean and theatmosphere from rock records dating back to 4 billion years ago, and we will test the theoretical model
thoroughly.
B5. How did the geological conditions of the early Earth influence the origin of life?
The elucidation of the origin of life is a complex multi-layered undertaking. The solution requires thediscovery of chemical reaction network in the context of geophysical constraints capable of supporting
the emergence of life-like processes. On the one hand we explore the chemistry triggered by naturally
occurring energy sources, such as nuclear geysers and geologically sustained electrochemical potentials
provided by the hydrothermal vents. On the other, we make use of abstract computational methodology,
artificial chemistry, to understand the dynamics and the emergent properties of complex system.
Concentrating on function rather than structure, we investigate the enzyme-like function of prebioticallyplausible heterogeneous polymers. Finally, through a top down approach we study the evolution of themodern cellular structure.
B6. What was the nature of the first genetic systems employed in the "progenote"?
We seek to go beyond the goal of understanding the last common ancestor of archaea, bacteria, andeukarya (LAABE; commonly presented as the LUCA). Starting from simple pre-biotic compounds which
formed complex and functioning large molecules, life was born as a community. What was the gene setof the first community like? How did these genes “flow” between community members? What are thefactors that enabled sustainable and evolvable ecosystems to be built? In addition, where was the initialenvironment located that was able to utilize 20 kinds of amino acid and genetic codes? How did it
become a life system? We approach those fundamental problems experimentally.
We lead the field of OOL (Origins of Life) by re-framing the question of what life's emergence means:
it is not one stage but many stages, which could have involved many planetary locations andprocesses. We introduce the premise that the creation of biochemistry did not only take place in theevolutionary era of cells, but began in geochemical processes that produced and partially selectedcomplex organics, and continued in later cellular eras. Similarly, cellularization included stages of
producing components and then combining them into functioning systems.
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C) Evolution of the Earth-Life system
After the emergence of life on Earth, the biosphere and the crust/atmosphere/ocean system coevolved in composition and complexity. We aim to understand and ultimately to reconstruct stages inthis coevolution, through a joint study of the geological record and the comparative analysis of moleculardiversity in the biosphere today. Our investigations here are directed at three aspects of long-term
evolutionary change: (1) major transitions in the bioenergetic systems that organisms achieve to enablebiochemistry and physiology on a changing planet, (2) what molecular comparative analysis andsynthetic biology can tell us about long-term changes in gene architecture and enzyme function acrosstime, and how to reconstruct experimental models of ancestral states, and (3) how long-term secularchanges from thermal evolution of the Earth combined with Earth-life co-evolution to change the surface
environment for life.
C7. What were the major transitions in bioenergetic systems, what drove them, and how did
they affect the spread of life?
The evolution of life from the Hadean eon to the present has in many ways been an evolution inmethods that couple energy-releasing physical processes to energy-requiring biochemical
processes. The two primary forms of life’s energy metabolisms have been chemotrophy — utilization of
the disequilibrium between the bulk Earth and the atmosphere/ocean system — and phototrophy —coupling of chemical transformations to the absorption of light and emission of heat. Life during theArchean evolved several qualitative innovations in chemotrophy that allowed it to colonize ever morediverse and extreme environments, and that led to increasing ecological complexity. Sometime in theArchean, life also evolved the capacity to harness sunlight to drive biosynthetic chemistry andphysiology. After many innovations in phototrophy, the latest — oxygenic photosynthesis — ended theArchean EON and began the Proterozoic, so completely did it change the surface geologicalenvironment. Changes in bioenergetic systems may have been partly driven by changes due to thermal
evolution of the solid Earth (considered in C9). They unquestionably fed back to change most aspectsof the surface environment, from mineralogy to Carbon chemistry, and altered the nature of subsequentevolution. ELSI will seek to understand both the historical sequence and the geological and evolutionary
constraints and causes of innovation in bioenergetic systems throughout the Archean, and how theseenabled the specialization and spread of life on Earth.
C8. How were ancient enzymes and genomes different from modern ones, and can wereconstruct models of ancestral phenotypes?
As biochemistry and bioenergetics have co-evolved with changes in geochemistry (C7), the functionsof the two key informational molecule classes — polypeptides and polynucleotides — have also changed
in form and complexity. Additionally, their organization in both genomes and ecosystems has done thesame. Information about these changes is recorded in the diversity of molecular sequences among livingorganisms today. It can be extracted by established comparative methods of molecular biology, and areaugmented by new techniques in single-cell genomics and laboratory experimentation aimed atunderstanding fundamental mechanisms of molecular interaction that have governed evolution at all
historical periods. At ELSI we combine comparative and functional analysis with synthetic biology tools,
not only to infer ancestral states but also to construct functioning models of ancestral phenotypes in thelaboratory. Our efforts will focus on i) the evolution of pathways for autotrophic carbon fixation, which
is a fundamental function that has governed evolution at all stages in life’s history and ii) sulfur
metabolisms and the enzymes which facilitate them. These catalyst classes provide links between theorigin of the first cells, contemporary energy metabolism, and also Earth evolution.
C9. How did the thermal evolution of the solid Earth change the ecosystem?
We will explore how the long-term cooling of the solid Earth influenced the co-evolution of life,
atmosphere and ocean. We will elucidate the changes in the chemically-stratified structure of the Earth’s
interior over time based on convection simulations with parameters defined by our high pressure
experiments (A3), and we will evaluate the intensity of the volcanic activities and growth rate ofcontinents. Using the physical properties of the core determined by A3, we will perform numericalsimulations of the convection in the core and its change through time. We will estimate the timing of
the birth of the inner core, which probably changed the geomagnetic intensity. In addition, using thegeological samples, we will analyze paleogeomagnetic intensity through time, large-scale volcanic
activity, continental growth, and we will thoroughly verify the simulation results. Taking the surface
environmental changes brought by the solid earth evolution into account, we will re-evaluate the causesof the two evolutionary events: the emergence of eukaryotes and the emergence of metazoans.

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D) Bioplanet in the universe
A common emphasis in all of sections A—C is to understand the particular history of life on Earth asa realization of general principles of life that determine how and where it arises among the possible
planetary conditions and histories. The goal of a universal planetology and a universal biology is to makegeneralizations and apply these to the characterization of planets throughout the universe in theircapacity to generate or host life, to guide searches for life outside the Earth, and to understand what
the search for the Origin of Life teaches us more generally about the nature of life as a planetary property.
D10. How unique is our planet?
Through the study of Earth, obtained from A1 to C9, and by comparing Earth with the other terrestrial
planets (in our solar system and possibly beyond), we will clarify both universal and unique aspects ofour home planet. The next step is to attempt to generalize these aspects of Earth and construct a set of
conditions that leads to “Bio-Planetology”. We base ‘Bio-Planetology’ on “Comparative Planetology”,
which is the study of the complete set of extrasolar planets and understanding the underlying processes
that generate the distribution of outcomes. With Bio-Planetology we aim to predict the presence orabsence of life on other planets and what planets could be inhabited.
D11. How should we search for extraterrestrial life?
We will work closely with those in the fields of space missions and astronomical observations, in order
to apply the research results of the above points A to C for the detection of life on other planets, satellites
and similar objects. Within the next 10 years, spectroscopic observations will start to yield information
about the atmospheres of extra-solar Earth-like planets in the habitable zones, which may have oceanson their surface. Before that, we will establish criteria for life-harboring planets using the results of our
explorations on the early Earth and its subsequent evolution. We will also actively participate in science
discussions of an on-going space mission (Hayabusa-2) and lead science plan of future mission (MMX).
D12. What principles lead to life in a planetary context?
To understand the scientific meaning of the origin of life, and the role of the biosphere as part of aplanetary system, requires much more than a scenario for the origin of biomolecules or cells. This would
be true even if we knew which scenario is the historically correct one: a history of empirical events does
not distinguish which aspects of life are accidental and which are essential; it does not explain whether
our biosphere is robust and if so, why; and it does not identify the key abstract properties that makeliving systems different in essential ways from nonliving ones. In practice, the search for scenarios forthe emergence of life is so difficult that without a strong theoretical framework there is reduced likelihoodthat our proposed hypotheses will be valid. Therefore, guided by a deep understanding of the empiricaland model-based analyses from A1 to C9, and drawing on theories of organization across physics,
computer science, and the life sciences, we will work to define the abstract properties essential to theorigin of life, and seek to quantitatively demonstrate conditions for their emergence in a planetary system.
[Social Impact]
The ultimate goal of this study is to go back to the origin of science, and ask ourselves "why are we
here?" There is no question that the results of our research activities will revolutionize our views of Earthand life, as state-of-the-art scientific achievements and the most advanced attainments of intellectual andcultural activity of human beings. Our research will stimulate young people who will carry the future of
the scientific nation of Japan by reminding them of the intellectual desire and curiosity that is the original
instinct of human beings, through which they distinguished themselves from other creatures.
Each research plan is conducted with clear scientific objectives while developing new advanced
techniques. As a result, there are countless effects on the society in the short term. For example,
development of techniques for ultra-high-pressure and ultra-high-temperature experiments; developmentof high speed large-scale computer systems; design and development of organic molecules on the basisof chemical evolution experiments; finding previously unrecognized factors controlling global
environmental change; innovation of advanced techniques of environmental measurements, analysis anddecoding; discovery and a wide spectrum of application of novel and unique extremophilic microorganisms;
large-scale acquisition of microbial genetic information and resources; developing, analyzing and mining
enormous quantities of genomic data; making progress in space exploration technology driven by theintellectual desire of human beings, and so on. However, these short-term impacts are only by-productsof this program.
[Research plan]
We will try to answer the above 12 questions from A1 to D12 through interdisciplinary investigations.
Each research plan is described in detail below.
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A1. How was the Earth formed?
We aim at theoretical understanding of Earth formation from formation and evolution of protoplanetarydisks through late impacts to the Earth by leftover planetesimals. We utilize first principle simulations andcombine their results to build a general planet formation model by calibration with astronomical
observantional data of extra-solar planets and geo/cosmochemical data of our solar system.
The important physical processes that were not considered in the classical model are protoplanetary
disk evolution, accretion of disk gas, dust grain growth to pebbles in turbulent disk, pebble
formation/migration, pebble accretion by planets, planetary orbital migration due to planet-disk
interactions, tidal orbital evolution, and orbital instability. Observations of protoplanetary disks developedsince the 1990’s after establishment of the classical model and recent observations by ALMA radio
telescope provide amazing information of the disks. Grain growth in turbulent disks is recently understoodby high-performance computer simulations, and pebble accretion has been proposed that would be equallyimportant to the classical idea of planetesimal accretion. The importance of orbital evolution due to planetdisk interactions, star-planet tidal interactions, and instability has been highlighted by discovery of diverse
extra-solar planets. We build a general planet formation model by incorporating these new processes todiscuss the Earth formation process on the basis of the general model.
Recent development of computer simulations enables us to simulate impact history to the Earth after
its formation. The giant impact that formed the Moon is essentially important for mixing of Earth’s interior
and evolution of initial atmosphere and ocean. The late impacts by leftover planetesimals are essentially
important to infer surface environments of early Earth where life may have emerged. The theoreticalresults have become detailed enough to be compared with geo-chemical data. The computer simulations
are now revealing formation history of Mars and asteroid belt as well, which can be compared with cosmochemical data of meteorites from there. We combine high-performance computer simulations with thegeo/comso-chemical data to reveal the first 500 M year history of the Earth from dynamical point of view.
The temperature of the disk regions where building blocks of the Earth were formed, was not low
enough for volatile elements such as H 2 O ice and organic molecules to condense there. In a protoplanetarydisk, H 2 O ice dust can be condensed from the disk gas only in regions beyond 3AU with temperature
below 160-170K. Even if planets are located in habitable zones, they may not be able to harbor life without
H 2 O and organic molecules. We explore how H 2 O and organic molecules are delivered to planets inhabitable zones including our Earth, using the new planet formation model and high-performancecomputer simulations. One idea to deliver water to the Earth is accidental impacts of asteroids or comets
formed beyond 3AU. As scattering phenomena are chaotic, simulations show that delivered water isdistributed broadly from zero to tens of wt% of Earth’s mass. The coexistence of ocean and land could
also be a condition for a planet for life to emerge (the Earth's ocean mass is 1/10000 wt% of the Earth'smass). If this mechanism is responsible for the water delivery, creation of life is determined by pure
coincidence. We will re-examine this model, on the basis of the rebuilt planet formation model. We will
also investigate other possibilities such as formation of H 2 O by interaction between a primitive hydrogen
atmosphere and a magma ocean (Genda and Ikoma, 2008) and a new pebble accretion model for planet
formation (Sato, Okuzumi, Ida, 2016).
Internal ocean of an icy satellite (Europa or Enceladus) is one of possible sites where life exists. Icy
satellites of gas giant planets are believed to form in circum-planetary disks in a similar way to planet
formation in circumstellar protoplanetary disks. The standard model of icy satellite formation has not been
established at all. We also build the satellite formation model by applying the new planet formation model.
Experimental studies are also important. It is important to identify the chemical composition of thelower mantle, which accounts for 60% of the volume of the earth and the light element content in themetallic core, in order to elucidate the original composition of the Earth. Our ultra-high-pressure
experiments with geochemical/geophysical information can constrain the original concentration of volatileelements such as O, S, and Si in the metallic core, resulting in great progress in the elucidation of the
Earth’s building blocks. How much water can be included in the mantle and the core is also important toconstrain the water delivery process. The total amount of ocean is only 0.02 wt.%. It is likely that the
mantle and the core can include water much larger than the ocean mass. These establish importantboundary conditions for the simulation of the formation process of the early solar system and elucidate
how the Earth was formed, and its uniqueness and universality in the planet formation process.

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Figure 2. The formation of the Earth in the solar system will be examined by a combination of computer
simulations of planet formation, with the aid of laboratory experiments and information about
extraterrestrial bodies (related to question A1).
A2. How did the “magma ocean” phase connect early formation/differentiation to conditions
when life emerged, including the essential element of water?
At ELSI we have assembled a diverse team of leaders in magma ocean studies, ranging in backgroundfrom planetary formation theorists, atmosphere modelers, geodynamicists, mineral physicists, andgeochemists. As a collaborative fusion effort we are now organizing activities around particular aspects ofthe problem that require very diverse expertise and assembling teams to solve some of the greatest
questions in Earth science. ELSI PIs Hirose, Ida, Hernlund, and Helffrich are anchoring ELSI efforts tocreate this bridge between planet formation modeling and early planetary evolution.
I nform ing evolution m odels w ith high-pressure ex perim ents : Our ELSI team has bothmodelers and high-pressure experimentalists who already have experience working together to bridge
results from their disciplines. The important connection between them is that models can only makeconcrete predictions if they are constrained by reliable experimental data regarding physical and chemical
properties. Sometimes models can use existing experimental data, but often in the course of investigation
it is necessary to find new constraints and so a productive and synergistic feedback loop can be establishedbetween the modeling and experimental teams. Magma oceans are also an excellent opportunity to forma bridge between planet formation modeling and geodynamical modeling, and understand the physics ofthe planet assembly and subsequent evolution in an integrated manner.
The prim ordial ocean and atm osphere : Magma oceans simultaneously equilibrate with metals thatform the core and with the proto-atmosphere that will partly condense to form the first water ocean (B4).
Magma can readily absorb high amounts of water, and therefore acts as a conduit for early volatile
distribution between the deep Earth and surface environment. Furthermore, the presence of volatiles
exerts an important feedback upon the dynamical evolution of magma oceans. The outcome is sensitive
to the timing and amount of volatiles delivered to Earth. We will combine our models of volatile delivery
to the proto-Earth with magma ocean evolution scenarios in order to map out the range of potential
behavior. The results of these models will inform targets for high-pressure experiments that can be used
to test hypotheses and narrow the range of uncertainty.
The first crust : The solidification of the magma ocean following the late stages of accretion produced
the very first solid surface of the planet. The “first crust” is an important target because the chemical
environment it establishes will govern the kinds of organic chemical reactions that can take place, byregulating the supply of bio-elements and also providing energy sources for early metabolism (B4, B5).
We may also find strong evidence that the first crust was not conducive to life, and therefore had to be
replaced or modified by later geological processes in order to allow for the origin of life on Earth. We will
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combine fluid dynamical models of magma freezing processes with petrological data that govern thefractionation of elements during crystallization and allow us to predict the composition of the first crust.
Understanding the Diversity of P lanets : Magma oceans are planetary forges, and as such they
are responsible for producing planetary diversity in the solar system and elsewhere in the universe. A
better understanding of the earliest stages is fundamentally important for making predictions regarding
the state and habitability of exoplanets (D10, D11) based on primary astronomical data such as the
distribution of planet sizes and epicentral distance. Using forward models constrained by high-pressure
experiments, we aim to discover how planets of different kinds can be formed as an outcome of distinct
evolutionary histories during the magma ocean phase, and make predictions regarding their evolved states.
This positions fundamental research conducted at ELSI firmly in the center of upcoming exoplanetaryobservation missions, because it will address the connection between planet formation, evolution, andcurrent state (only the latter can be directly observed). This timely contribution is an investment that will
ensure ELSI’s relevance and maintain its high profile into coming decades.
A3. How has the Earth's structure, composition, and dynamics evolved through time?
Low er m antle : First, we need to clarify the structure and chemical composition of the lower mantle,
which composes 60% of Earth in mass. ELSI members have already proposed the existence of silicaenriched viscous domains (bridgmanite-enriched ancient mantle structures, BEAMS) in the lower mantle,
which is different in composition from the upper mantle material. In the next five years, we will need tofind firm evidence for its presence. Moreover, we will explore how such compositionally-distinct domains
were formed based on high-pressure experiments and computational simulations. These will tell us 1) how
a magma ocean solidified, and 2) the chemical compositions of Earth building blocks.
Core com position : The chemical composition of the core is one of the most important problems inthe solid Earth science. Our high-pressure experiments and computational simulations will clarify the soundvelocity and density of liquid Fe-alloys, differentiation of light elements at the inner core boundary, andthe dissolution of light elements from the molten mantle into the core at the giant impact events on theearly Earth, all of which provide important constraints on the identification of core light elements.
The determination of chemical compositions of the lower mantle and core will elucidate the bulk Earthcomposition. Then, comparing the result with cosmic abundances of refractory elements, we can examineconsistency with the theoretically-derived Earth-formation scenarios obtained in A1 above.
M agma ocean and proto-crust : We also examine the primordial layered structure inside the Earth,from the core to the proto-crust. We will reproduce experimentally the solidification of the magma ocean,which most likely extended to the whole mantle at the time of the Moon-forming giant impact event. Whileit has been believed that its solidification occurred from the bottom, recent experimental and theoreticalstudies suggest that magma is denser than surrounding solid and thus solidification started at the middleof the mantle, eventually spreading upward and downward, which changes the whole view of thesolidification process.
The chemical composition of the Earth’s proto-crust forming from the final residual melt after extensive
crystallization of the magma ocean may have been significantly enriched in incompatible elements
including phosphorus, the essential element for life. Indeed, the unusual type of rock called KREEP (K,REE, P-enriched) is found on the Moon’s crust, but it can be different from the Earth’s.
Core evolution and geom agnetic field : Working from an improved understanding of its
composition, we study the thermal and dynamical evolution of the Earth’s core. Based on interdisciplinary
collaboration between ELSI members, we have recently revealed that the Earth’s core has changed its
composition to a large extent by crystallizing SiO 2 oxide. Despite our discovery of high thermal conductivityof the core, convection has been driven by chemical buoyancy associated with SiO 2 crystallization, which
may have formed Earth’s geomagnetic field since its early history.
At the same time, by using vast amounts of Precambrian rock samples collected by our geology team,changes in paleomagnetic intensity will be examined. We will apply new techniques developed mainly by
the PI, Kirschvink to improve the database of paleogeomagnetic intensity for Precambrian times, andthereby test the predicted changes. Numerous intrusive complexes from large igneous provinces are being
discovered and dated accurately with U/Pb techniques, and simple shallow drilling operations could provide
pristine samples amenable to the modified Thellier/Thellier techniques needed for robust paleointensity
determinations. Magnetic microscopy using Superconducting Quantum Interference Device (SQuID)
technology may even allow these techniques to be used on detrital grains of Hadean age. These studies
are link with the theme C8.
Surface conditions and influence of the galactic environment : Conditions on the surface of thesolid Earth are governed by the interface with the atmosphere, a system locally protected by the
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geomagnetic field, but at the same time influenced by dynamics on scales as large as the galactic
environment. It is known that cosmic forcing can change the surface environment of the Earth at small
scales such as local meteorological changes (due to cosmic ray influence on cloud formation), but has also
been proposed that such changes could be large enough to account for global freezing events (Kataoka,
2013, 2014; Nimura 2016), with important consequences for long-term evolution (Ebisuzaki, 2015). The
influence of galaxy structure on atmospheric forcing is expected to come through the three major channelsof (1) Large changes in star-formation rates, (2) Collisions between molecular clouds and the solar system,and (3) Supernova explosions in the vicinity of the solar system. Recent advances in simulation
technologies led by the ELSI Fellow Makino and his team have enabled us to theoretically analyze theorigin and evolution of our Milky Way Galaxy, leading to a view significantly different from common belief(Fujii, 2011; Baba, 2012, 2015, 2016). Whereas it was formerly assumed that the solar system followed acircle in the galaxy through roughly static spiral arms, the new work suggests both non-circular motion of
the solar system and non-stationary maintenance of arms, with implications for star-forming rates andlocations, and solar system interactions with resulting molecular clouds. These calculations may suggest
links between a 150-million-years cycle of changes in Earth’s climate and in the position of the solar systemin our galaxy.
ELSI is fully equipped to investigate the solidification of the magma ocean and chemically-stratified
structure of the mantle, as well as to determine the primordial crust composition. Studies on core andlower mantle described above are primarily based on property measurements and calculations of ironalloys and silicate minerals, employing high pressure and temperature (P-T) experiments andcomputational simulations. At this point, the Hirose team is the only group in the world which cansimultaneously create extreme high P-T conditions that exceed that of the center of the Earth (364 GPa,
~6000 K) by static experiments using the diamond-anvil cell (Tateno, Hirose et al., 2010, Science).
Combining such leading-edge technology and synchrotron radiation X-rays, the group has achieved several
outstanding results. These include the discovery of post-perovskite, a major mineral in the lowest mantle(Murakami, Hirose et al., 2004, Science), determination of the crystal structure of iron in the inner core,
the discovery of a phase transition of FeO under outer-core pressure (Ozawa, Hirose et al., 2011, Science),
and the discovery of the cubic structural phase of SiO 2 (Kuwayama, Hirose et al., 2005, Science).
Furthermore, we have developed a new methodology for measuring properties such as the electrical andthermal conductivity (Ohta et al., 2008, Science; 2016, Nature), seismic velocity (Murakami et al., 2012,
Nature), and element partitioning (Nomura et al., 2011, Nature; Hirose et al., Nature, in press) under highpressure, which resulted in making major breakthroughs. Also, pioneering research has been conductedon mantle materials by Irifune’s team based on precise measurements in a multi-anvil apparatus (Irifune,
1994, Nature; Irifune et al., 1998; 2010, Science; Irifune et al., 2008, Nature; Irifune and Isshiki, 1998,
Nature). More recently, they succeeded in making the first measurements of elastic wave velocity underlower mantle P-T conditions. Meanwhile, as reported in Irifune et al. (2003, Nature), the team started
applying the world’s hardest nano-polycrystalline diamond for the multi-anvil apparatus. This technology
is expected to enable precise experiments under the entire range of mantle conditions.

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Figure 3. Chemical differentiation within the Earth from core to atmosphere will be reproduced by highpressure/high-temperature experiments. Subsequent chemical and thermal evolutions inside the Earthwill be also examined (related to question A3).
B4. What was the state of the ocean and the atmosphere when life emerged?
By extending the high-temperature experiments and theoretical computations of A1-3, we will makeforward estimations of the composition of the atmosphere and oceans. To verify our theoretical predictions
on the basis of geological evidence, we will analyze the early geological record dating back to 4 billion
years ago.

Theoretical and Ex perim ental Approach : Our objective is to specify the physico-chemical
environment of the primordial Earth on which life emerged. According to the conventional theoreticalmodel, the Earth's primordial atmosphere formed from volatiles (secondary atmosphere) produced by thedegassing of planetesimals, the building blocks of the Earth. It is generally believed that the degassed
volatiles consisted primarily of H 2 O vapor, CO 2 and N 2 . As the Earth’s surface cooled, H 2 O turned to liquid(i.e. ocean), while a CO 2 -rich primordial atmosphere remained. Under such a CO 2 -rich (i.e. oxidizing)
atmosphere, however, it is extremely difficult to follow pre-biotic synthesis of organic matters that arenecessary for the emergence of life. On the other hand, recent research results rather suggest a more
reducing primary atmosphere, possibly rich in H 2 , CH4, and CO based on theoretical calculation andgeoological evidence. It is also important to study resetting the atmospheric composision by reactions withmeteorites that fell after the Magma Ocean. Our research at G-COE has suggested the possibility that themoon-forming impact ejected fragments that returned to Earth during 100 million years after the impact.
These re-entering fragments may be large enough (10 to 100 times larger than impact from the Late
Heavy Bombardment event) to have converted a substantial amount of primordial ocean into H 2 (Sasaki
et al., 2012, in our team). Because these early atmospheric conditions also define the origins of H 2 O on
Earth, they are extremely important for understanding the origins of seawater and its total volume as
discussed in A1. For re-evaluating these new scenarios, we will first perform numerical simulations byextending the planet formation theories developed in A1. In particular, the H 2 O content of planetesimals
and their accumulation process after solidification of the magma ocean are important aspects on which
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we will focus in our simulations. Furthermore, the mass of the early atmosphere and oceans is controlled
by the cooling process of the magma ocean that we can constrain by using the high-pressure experimentsof A2 and A3.
In addition, the composition of the atmosphere was modified by gases released from the mantle
through volcanic activity. This process has been studied on the basis of research using today's subaerial
volcanoes. The early Earth, however, was covered with oceans and had almost no land. Hence, input tothe atmosphere and ocean system would come not from high-temperature volcanic gases, but fromsubmarine hydrothermal gases resulting from reactions between rock and seawater. Hence, we will
perform hydrothermal experiments on rock types from the Earth's earliest oceanic crust determined by A3
to systematically understand the volatile and elemental flux into the early atmosphere and oceans. The
experimental setup has already been developed and utilized to study this issue by the group of the ELSI
Fellow, Takai and PI Maruyama (e.g., Yoshizaki et al., 2010).

Geological and Geochem ical approach : Our theoretical predictions must be thoroughly verified on
the basis of geological evidence. Unfortunately, the means for such verification for the Earth's environment
during the Hadean (before 4.0 billion years ago) are extremely limited because there is no geologicalrecord except for tiny mineral grains in clastic rocks. In the past ten years, however, dramatic advancesin research on the early ocean and atmosphere during the Archean (4.0 to 2.5 billion years ago) havebeen made by rapidly developing chemical and isotopic indicators recorded in sedimentary rocks that now
provide useful boundary conditions to verify the Hadean environment. In particular, 1) over 10 years ofgeologic mapping of the PI, Maruyama’s group has identified many fragments of the past oceanic crust inArchean cratons and their comprehensive metamorphic petrology, making it now possible to quantify the
CO 2 concentrations in the Archean ocean (e.g., Nakamura et al., 2004; Shibuya et al., 2007; 2012, in ourteam). Moreover, 2) after the discovery of a sulfur isotope anomaly in Archean sedimentary rocks thatproved extremely low oxygen levels of the Archean atmosphere (Farquhar et al., 2000), recent advancesin research on the isotope fractionation of photochemistry makes it possible to quantify not only oxygen
levels but also the concentration of green-house gases and volcanic flux into the atmosphere (Lyons,
2007; Danielache et al., 2008; Ueno et al., 2009, in our team).
In this context, we will reproduce the composition of the Archean oceans by using systematic chemical
and isotopic analysis with thermodynamic computations on the rock samples. Tokyo Tech's Earth history
archives already house numerous Archean oceanic crust samples. While we have already obtained fixedpoint data based primarily on detailed field mapping in designated regions and metamorphic petrology,
we will now significantly broaden our scope in order to describe temporal changes across the entire
Archean. For decoding the Archean atmosphere, while much data has been collected on isotopic anomalies
regarding their role as atmospheric proxies, the inherent potential of this research has not been fully
realized because the basic mechanisms for producing the isotope anomaly are still inadequately
understood. Hence we will conduct spectroscopic studies and reaction experiments with numericalsimulations of photochemical reactions to understand the dependencies of UV wavelength, atmosphericcomposition, temperature and pressure on the isotopic effects in order to constrain the Archean
atmosphere quantitatively. The PI, Yoshida and his group has determined photochemical isotope effects
by a number of key reaction steps (e.g., Danielache et al., 2008; Ueno et al., 2009; Hattori et al., 2011;
Enghoff et al., 2012) and will extend this research to produce testable models of the Archean atmosphereby using geologically preserved isotope anomalies.

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Figure 4. Chemistry of the early atmosphere and oceans will be determined by planet formation theory
and tested by geological evidence (related to question B4).
B5. How did the geological conditions of the early Earth influence the origin of life?

How did the geological phenom ena influence the prebiotic chemistry?

Triggered by interdisciplinary studies that have promoted as JSPS KAKENHI Grant-in-Aid for Scientific
Research on Innovative Areas “Hadean Bioscience,” which launched in 2013, the Institute PI Shinegori
Maruyama et al. proposed the “natural nuclear geyser scenario” (Maruyama and Ebisuzaki, 2016), which
presumes that the radioactive placer deposits could have formed the geyser system as water andradioactive minerals reacted in a fashion similar to that in modern nuclear reactors. Utilizing the γ-radiation
facility at Tokyo Tech, the research team led by ELSI Fellow Masashi Aono and H. James Cleaves has
initiated the radiolysis experiment designed to mimic the radiation-induced syntheses of organic
compounds in the natural nuclear geyser and succeeded in converting water and acetonitrile to formamide(results to be submitted soon), which offers promising prospects for abiotic synthesis of building blocks oflife (e.g., amino acids, nucleobases, and lipids). Inspired by the geyser concept, Aono and collaborators
have developed a so-called “geyser reactor,” an intermittent experimental setup that repeats the wet-dry
cycle in a confined flask, and demonstrated amino acid oligomerization by high-temperature heating
without a catalyst (results to be submitted soon). Catalytic amino acid polymerization is investigated at
ELSI as well, specifically polymerization on mineral surfaces. Amino acids undergoing polymerization in
the presence of minerals, e.g. pyrite, are assumed to adsorb and condense only on specific surface sites.
Quantitative measurements of amino acid adsorption on the pyrite surface using atomic force microscopy(Narangerel et al., 2016) are expected to elucidate the mechanism of prebiotically reasonable peptide
formation. Further investigations into radioactivity-induced chemistry inspired by the natural nuclear
geyser scenario and mineral surface driven polymerizations will become core areas of inquiry connecting
early Earth and Life.

Can “m essy” prebiotic chem istry sustain life-like processes?

Nuclear geyser reactor could have initiated and sustained prebiotic chemical networks capable ofsynthesizing biological building blocks and possibly sustaining life-like processes. Other notable examplesof similar systems include Miller-Urey experiment (Miller, 1953), HCN (Moser et. al., 1968) andformaldehyde polymerization (Cody et. al., 2011). There is a commonality to most of these systems —Earth-Life Science InstituteTokyo Institute of Technology - 22

they are qualitatively messy. The systems produce large assortments of compounds through a wide variety
of mechanisms. Biological systems are strikingly different; they are well-orchestrated enzyme-controlled
networks. How did the transition from prebiotic messy chemistry to the organized biology resembling
reaction network occur? In our goal to shed light on the issue we employ a number of approaches. An
effort fronted by Nathaniel Virgo concentrates on artificial chemistry, the study of abstract artificial
chemical reaction networks and their emergent dynamical properties. Virgo’s prior work in collaboration
with Takashi Ikegami of the University of Tokyo suggests that simple chemistries in the thermodynamicallyreversible regime can self-organize to form complex autocatalytic cycles, with the catalytic effects
emerging from the network structure (Virgo et. al., 2016). Further inquiries will include in depth study ofintermolecular interaction driven self-organization of complex reaction networks, both experimentally andin silico. Polymers formed by the messy chemistry might have played an important role in chemical
evolution, e.g., as prebiotic enzyme mimics. In modern biology the control over complex metabolic
networks is achieved through the use of enzymes. Enzymes are intricate biopolymeric complexes thatcatalyze biochemical reactions and shape metabolic pathways. Enzymes usually work with small molecule
cofactors that actively participate in reaction mechanisms and complex, usually globular, polymeric
structures capable of specific substrate binding, encapsulation and orientation. Moreover, the globular
structures of enzymes possess cavities with modulated microenvironments, facilitating the progression ofreaction(s). The globular structure is assured by long folded protein or RNA strands. Synthesis of suchelaborate complexes has proven difficult under prebiotically plausible conditions. In our endeavors weconsider the concept of protoenzyme, an enzyme-like structure that uses alternative simpler polymericscaffolds derived from the “tarry” prebiotically plausible materials. Research efforts fronted by Mamajanov,
ELSI PI, are based on hyperbranched polymers, macromolecules with a high degree of branching assuring
their globular structure. The recent study (Mamajanov and Cody, submitted) has successfully shown theability of unresolved mixtures of tertiary amine-bearing hyperbranched polyesters to form hydrophobic
pockets as a reaction promoting medium for the Kemp elimination reaction. Further studies will involve
hyperbranched polymer based metalloenzyme mimics.

Did electrochemical processes triggered by the hydrothermal vents constrain the “m essy
chem istry”?

Hydrothermal vents on the early Earth were likely to have been more active than they are now (Shibuya,
Takai, et al., 2016). The geo-electrochemical potentials they provided could have served as a driving force
for the CO 2 reduction followed by the formation of organic compounds essential for the origin and early
evolution of life (Kitadai, et al., 2016). We have designed an array of experimental setups that can simulate
electrochemically driven CO 2 reduction and help evaluate the reaction energetics and estimate the catalytic
potential of the geothermal environment. While ELSI Fellow Takai and collaborators excel at discovering
the diversity and properties of deep-sea hydrothermal vents, the research effort lead by Shawn McGlynn(ELSI PI), Norio Kitadai (ELSI Research Scientist) and Riyuhei Nakamura (newly appointed ELSI PI) areapplying the newly discerned parameters to the prebiotic chemistry studies. The outcome of their studies
will not only elucidate the chemistry relevant to transition between geochemistry to biochemistry at theearly stages of chemical evolution (Aono et al., 2015), but will also provide relevant constraints for future
JAXA and/or NASA space missions targeting the search of extraterrestrial life. Hydrothermal activities are
believed to be present on the surfaces of certain planets and satellites found in the Solar System (Kurokawa
et al., 2014).

W hat is the role of compartm entalization in the em ergence of life?

Compartmentalization is yet another means to restrict the diversity of prebiotic chemistry as it would
limit the diffusion of chemical towards and away from a given chemical system. Besides,
compartmentalization in a form of cell is a necessary attribute of life as we know it. A program led by
Yutetsu Kuruma sets an ambitious goal of elucidation of the formation and subsequent evolution of thecellular membrane, from the theories of the protocell to the cell of nascent biology to the contemporary
cell. Lipid membrane vesicle is crucial as an outer envelope of cell. All necessary metabolisms, glycolysis,gene replication, gene expression, lipid synthesis, and energy production, must be set up within the vesicle.
Especially, lipid synthesis is important process because it directly leads the self-reproduction of cell.
According to Mercier and Kawai et al. (2013, Cell), only a continuous over-biosynthesis of lipid molecules
is enough for cell division even without the cell wall and cell division machineries such as FtsZ ringformation. This style of division is called as L-form, and it is thought to have occurred in early stages inthe emergence of cell. In order to verify this phenomenon by constructive approach, we try to reconstruct
the metabolic system of lipid synthesis by combining responsible enzymes, substrates, and co-factors.
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Fatty acid is a basic structure constructing phospholipids and synthesized by 8 kinds of Fab (fatty acidbinding) enzyme, ACP (acyl carrier protein) and TesA. These enzymes elongate hydrocarbon chain fromthe resource of acetyl-CoA and malonyl-CoA. We have so far finished the purification of the enzymes andwill try to drive fatty acid synthesis reaction inside a lipid vesicle of artificial cell. Detecting themorphological change of artificial cell where lipids are synthesized and supplied onto the membrane, we
try to clarify the condition of cell division in very early stages of cellular life and how first cells evolved tothe modern cell form.
The transition between geo- and biochemistry is a multifaceted question. A satisfactory answer requiresa multidisciplinary research program merging the expertise of a number of branches of physical sciences,which is certainly descriptive of ELSI.

Figure 5. Schematic representation of the scope of the ELSI research into geologically driven chemical
evolution. Formation of simple biological building blocks, polymers and larger functional supramolecularassemblies will be investigated (related to question B5).
B6. What was the nature of the first genetic systems employd in the "progenote"?
To achieve a sustainable and stable existence without extinction, a robust life system was necessary,
yet certainly many – perhaps even most – ancient lineages became extinct. Those that survived did so by
chance and selection, resulting in cellular and ecological systems which could cope with environmental
disruptions. While research on the robustness of cellular systems has progressed in the life sciences andecological systems, very little has been done to consider community robustness in an era prior to theemergence of phylogenetically distinct lineages. This area of research will therefore aim to elucidate
dynamics that produce ecosystems that are both sustainable and capable of evolving in the absence of astrict dependence on vertical inheritance; it is undertaken with the objective of tracing genomic
diversification and ecosystem formation which led to the formation of life as we know it today.

How did peptide: nucleic acid interactions proceed to the point of translation?

An important aspect of early systems concerns i) the type of amino acids initially used for protein
construction and ii) how did these amino acids become recognizable to oligonucleotides. In previous
sections B4 and B5, we have dealt with the chemical environment of the early Earth, as well as therelationship of this environment to the formation and interactions between small molecules which may
have been substrates for the first living systems. Here, we ask deeper questions as to how these molecules
could have interacted in self referencing ways. Since polymers hold considerable potential to act in self
Earth-Life Science InstituteTokyo Institute of Technology - 24

referencing ways, and since the LAABE used a two component polymeric system based on peptides andoligonucleotides, we will investigate polymer-polymer interactions through a high throughput andcombinatorial approach. Already, we have purchased a robot to conduct a high number of experiments
towards these ends, and researchers Fujishima, Virgo, and Aubert-Kato are currently perusing thesegoals.

How w ere Lipid M embranes originally functionalized by the progenote?

For cellular life, the existence of the membrane is essential, and many origin of life researchers havesought to interpret the emergence of cells as connected to an ability to form a membrane structure. Whatis often forgotten though is that for a contemporary cell, up to ~50% of the total protein content can beassociated with the membrane. This is a reflection of the membrane itself; while being a barrier, it is alsoa pathway of transport, and the totality of ion, molecular, and electron transport processes mediatedselectively within and across the cell membrane together make up a critical functional aspect of what itmeans to be a living cell. Given this knowledge, our experiments led by Kuruma probe the ability of lipid
membranes to become functionalized by proteins in artificial membrane models (Kuruma et al., 2015).
Because all cells contain membrane-bound proteins, this work paves an important experimental thread for
all theories of life’s origin based on the emergence of cells.

W hat form of energy utilization w as used by progenote comm unity m embers?

All life forms utilize energy to organize and propagate their cellular material, and contemporary
microbiology has revealed myriad ways that energy in the environment can be harnessed to power cellularconstruction and replication. Furthermore, the type of energy used by progenote community members, inaddition to the mechanism of use by these members, remains almost completely unconstrained byexperiment. Indeed, too often, experiments meant to investigate early cellular physiology have been run
as they approach equilibrium, disregarding the observation that life itself operates as an open system andfeeds off of energy from the environment for equally as valid of reasons as life feeds off of material fromthe environment – life operates away from equilibrium.
So, what was the first energy source which powered the organization of living systems? First we cannote that all known life survives by employing electron transfer reactions (redox chemistry) of a form
where electron flow from a negative to positive redox potential and this is associated with doing someform of work. We will address the nature of the first utilized electron sources and sinks using knowledge
from contemporary biochemistry and microbial physiology, where we will consider molecules such as H 2 ,S, CO 2 , as possible early energy sources in the form of favorable redox couples. We will also research thepossibility that early (and contemporary) life may be powered by geo-electric currents. Of course, thisexperimental line is greatly informed by ELSI investigations into the nature of the first atmospheres andoceans (B4), as well as the molecular assemblages made possible through two polymer type molecularinteractions and feedbacks.
We will establish whether or not the first organisms were chemiosmotic, or relied on other mechanismsof energy conservation such as substrate level phosphorylation and even alternatives such as
thioesterification. We seek to establish the expected energy budget and cellular yields associated withprogenote communities on this or other planets, and compare these data to our ELSI generated
expectations of the state of the early Earth.

W hat is a pathogen before vertical descent?

In a world where vertical passage of information is not critical to community function, the idea that
one member can become a parasite of another becomes significantly blurred, since freedom from thebindings of information passage by vertical transmission corresponds to a state where the health of any
daughter cell is not required for the retention of genetic information. This curious situation may have only
been possible at the time of the progenote, but it may have been a defining feature of the progenotecommunity. Therefore, we seek to test the nature of “selfish” genes, cells, and their interactions in cases
where information transfer can happen easily and frequently by what is known today as horizontal genetransfer. We seek to define “extinction” based on the propensity of sequence retention in an ecosystem,
and also to shed light on the nature of evolution without vertical descent.

W hat is the ecological positioning of viruses at the tim e of the progenote?

It has been suggested by Forterre that viruses may have been ancient components of oligonucleotide
based cellular processes. From this point of view, the evolution of RNA is most appropriately interpreted
in the context of competing and complimenting cells and viruses. A major limitation on all evolutionary
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interpretations involving viruses though, is that despite the fact that their abundance in the modern
ecosystem outnumbers the cellular organisms in the order of magnitude, they remain vastly under sampled
in comparison to cellular life. Simply, there are too few examples of known viruses from the naturalenvironment, and from the ones which are known, we can be sure that very big surprises await incontinued exploration of viral diversity. Because of this lack of knowledge, ELSI is pursuing a dedicatedline of research aimed at advancing our knowledge of viruses and their interactions with host organisms.
Preliminary data by our research group led by researcher Mochizuki suggests the possibility of alternative
nucleobase utilization, and also novel viruses in various geothermal environments are being explored,
including the Hakuba Happo onsen environment. The weak point of the RNA world theory is the chemical
instability of RNA polymers, especially in thermal conditions. All modern organisms use more stable DNA
as their genetic material, except for RNA viruses. As no RNA virus has been found from any thermophilic
environment, the possibility of thermophilic RNA virus is currently being investigated.

M icrobial Ecology from the P erspective of the I ndividual :In considering the progenote, where vertical inheritance takes place to a lesser extent than tocontemporary biology where vertical inheritance dominates, the evolutionary concept of the individual
becomes blurred. If the progenote was comprised of cells, and if these cells horizontally exchanged DNA
rather than vertically replicated it, what would be the metabolic relationships that could be expected to be
in existence between community members? To begin addressing this question, we have begun to use
analytical techniques which allow the visualization and discrimination of cellular activities within wholecommunities at the level of the individual. Already, PI McGlynn has conducted analyses over 5,000
individual and phylogentically identified cells within a complex sedimentary matrix (McGlynn et al., Nature,2015), and these techniques have subsequently revealed unprecedented variability within what werepreviously thought to be homogeneous populations (Kopf, McGlynn et al., 2015) and a novel mechanismof cellular interactions by direct interspecies electron transfer (Scheller, McGlynn, et al., Science, 2016).
Now, we are using these same cutting edge techniques to better inform our understandings of cellularcommunity interactions as they exist today. This data is the first of its kind and supplies a foundation fromwhich to consider and hypothesize about the types of cellular interactions which were occurring at thestage of the progenote.

Figure 6. In-between a period of geochemically mediated (pre)biological transformations and the lastcommon ancestor of archaea, bacteria, and eukarya, was a period known as the progenote (Woese,
1977); ELSI has become a forefront research center for investigating the progenote experimentally(related to question B6).
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C7. What were the major transitions in bioenergetic systems, what drove them, and how did
they affect the spread of life?
Our research methods will be to combine wide-ranging molecular systematics and microbiology of the
major carbon and energy metabolic pathways with high-resolution decoding of geological records tounravel the major evolutionary transitions in chemotrophy, and the innovations that led from chemotrophy
to phototrophy, in the context of concurrent changes in the atmosphere/ocean system. We will address
the following questions: What were the biological and environmental drivers of diversification andoptimization of autotrophic carbon fixation pathways over time? Did early innovations in bioenergetics for
Carbon-fixation pathways depend directly on geological processes such as the generation ofelectrochemical potentials? How complex are the changes in bioenergetic systems required to enablemajor reversals in biochemical pathways, which have occurred independently several times, and how isthis complexity attained by organisms? These questions are major goals in the work of PI McGlynn and PI
Nakamura. In what background of geology and biochemistry did the innovations of oxygenic
photosynthesis arise? When and how did the atmosphere first become oxidized? Was the birth ofeukaryotes caused by the rise of oxygen, and were Snowball Earth events crucial drivers of this transition?
Placing geological and geochemical constraints on this transition is a major goal of PI Kirschvink and his
group.

Bioenergetic system s for autotrophic carbon fix ation, and possible connections to geologicalelectrochem istry

One of the oldest Carbon fixation pathways is the pathway for direct reduction of one-Carbon units on
cofactors, known as the Wood-Ljungdahl pathway. It is present in methanogens which branch deeply intree of domain Archaea, and in acetogens deeply within the domain Bacteria, and has been suggested tobe the first Carbon-fixation pathway. However, the bioenergetic systems used in these two branches arestarkly different in their architecture, and each is highly optimized for the low-energy environments inwhich these organisms live. ELSI will seek to understand why these pathways diverged, and what moreprimitive bioenergetic systems could have supported them, as a path to understanding the origins ofCarbon fixation. In particular, could such pathways have operated with less energetic optimization thanthey have in modern organisms, or augmented by different geochemical energy sources?
A connection of particular interest is the recent discovery by newly-joined (from April 2017) ELSI PI
Ryuhei Nakamura, ELSI Fellow Ken Takai, and Masahiro Yamamoto at JAMSTEC, that hydrothermal
environments which are known to host acetogens and methanogens also support direct electrochemical
potentials (ordinary Voltages) across the walls of hydrothermal chimneys that stand between deep
alteration fluids and unaltered seawater. Many experiments in the Nakamura lab, and also those by ELSI
Research Scientist Norio Kitadai, have shown that one-Carbon reduction resembling that in the WoodLjungdahl pathway can be driven directly by electrochemical potentials mimicking vent potentials. We willseek to understand whether such geochemical supports led to either independent evolution, or gradualchange, of the bioenergetic systems used by acetogens and methanogens, as well as whether any modern
organisms use direct electrochemical potentials as their obligate bioenergetic system for carbon fixation.

The “great reversals” in biochemistry, and how they w ere achieved bioenergetically

The Wood-Ljungdahl pathway of methanogenesis and acetogenesis is not only used for Carbon fixationfrom CO 2 : when it is reversed it serves as a foundation for many varieties of carbon intake from reducedCarbon sources, such as Anaerobic Methane Oxidation (ANME). This relation is probably one of the oldestof the “great reversals” that have occurred in biochemistry and is a major interest of PI McGlynn, who
intends to collaborate with ELSI Fellow Kamagata on this topic. Another is the reversal from reductive
Citric Acid cycling as a Carbon fixation pathway to the modern oxidative Citric Acid cycle (or Krebs cycle).
The coupling of bioenergetic systems to biochemistry is different in important ways between oxidative andreductive directions in both pathways, but the differences do not require many new molecules andmechanisms, leading to the observation that modest molecular innovation and genome restructuring canlead to extensive metabolic change.
On the other hand, there have been during evolution the introduction of truly new types of molecularchemistry and energy too, for example that dealing with O 2 and light, which seems to have resulted in
massive genomic modification and evolution. In addition to studying “reversible” energy metabolisms suchas those discussed above, we will also seek to understand the determinants and evolutionary history ofhigh potential (oxidizing) metabolisms such as that which works with O 2 . Here, we seek to deriveknowledge on how the variables of metabolism, evolution, and Earth interact to establish novel chemistries
during the prolonged evolutionary time scales experienced on the planet, and also during the shorter
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scales which were relevant at life’s emergence.”

Causes and consequences of the rise of oxygen on Earth

The rise of oxygenic photosynthesis occurred in a context that was already highly complex withmechanisms derived from chemotrophy. At least two photosystem reaction centers existed (preserved
independently in anoxygenic green-sulfur and purple bacteria); the major steps in chlorophyll biosynthesis
were in place; the key carbon fixing enzyme (RuBisCO) appears to have existed in the group-IV outgroup,
and auxiliary proteins such as the Carbonic Anhydrase were serving other functions in ancient groups suchas methanogens. From the biological perspective, we will investigate the question of the rise of oxygen
through the lens of ancestral enzyme state reconstruction linked to isotope fractionation factor
determination. This effort, led by A-PI Kacar (Harvard satellite) represents a highly novel linkage of protein
bioinformatics and genome analysis to the tools and data of geochemistry; namely isotope fractionation.
The wedding of these two disciplines can be expected to result in insights into the evolution of enzymes(in biological catalyst evolution what comes first, specificity or velocity?) and also for the interpretation of
isotope enrichments or depletions in ancient sediments.
The transition from chemosynthesis to photosynthesis must be recorded in Archean geological records.
Recent development of stable isotope geochemistry has enabled us to identify the activity of someanaerobic metabolisms (e.g., methanogenesis and sulfate reduction) from isotopic information ofPrecambrian rocks. PI Yoshida’s group, Ohkouchi and Ueno in our team have developed novel isotopic
techniques to trace specific metabolic activities from geological rock samples (e.g., Ueno et al., 2006;
2008; Ohkouchi et al., 2007). Additionally, we have obtained information about anaerobic photosynthesis
and other key metabolisms of anaerobic organisms are predicated by specific biochemical reactions to
produce reaction centers – work which is led by ELSI researcher Tsukatani. In the nitrogen cycle, forexample, nitrogen fixation, has been traced from within geological records by Fellow Takai’s group(Nishizawa, Takai, and others, 2014).
We have explored proxies of biological metabolism in an analogous environment to anoxic early Earthand also with incubation experiments during the first half of the project. And we will also apply newtechniques currently under development to geologic samples of isotope systematics (e.g., H, C, N, O, S,
Fe) at the same time or during the second half of the project year, and we have also expanded our study
environments of interest to include anaerobic hot springs which contain high concentrations of reduced
iron, which is relevant to considering pre-oxygenic iron metabolisms. Conventional obstacles to this typeof research have been metasomatic overprints and contamination of exotic compounds into sedimentaryrocks long after deposition. There have also been technical obstacles that have prevented us fromobtaining information from carbonaceous macromolecules (kerogen) in sediments, which should not beaffected by post-depositional petroleum migration. Developing a method to overcome these technicaldifficulties is key. We will establish a new reliable geochemical method of extraction that focuses on organic
nitrogen, hydrogen, and sulfur, and we will strive to develop techniques that can test for their syngenetic
origin within their host rock. Consequently, we will unravel the evolution from chemosynthesis tophotosynthesis in the realm of microorganisms based on geological evidence (e.g. Johnson, Kirschvink etal., 2013). The goal in our work will be to understand which factors in the origin of photosynthesis wereof geophysical origin, which were evolutionary bottlenecks, and to determine what subset of thesequestions can be answered from evidence preserved in the geological record. We will also consider isotopic
and fossil evidence connecting the rise of oxygen to the detailed timing of eukaryogenesis and the origin
of multicellular animals, in C9.

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Figure 7. What drives major transitions in bioenergetic systems, and how do we accurately interpret thesechanges in the planetary perspective? We integrate biochemistry, isotopes, and geochemistry to uncover
the relationships throughout time (related to question C7).
C8. How were ancient enzymes and genomes different from modern ones, and can wereconstruct models of ancestral phenotypes?
ELSI research on molecular complexity and the reconstruction of ancestral phenotypes will concentratein two areas. We will use comparative molecular systematics, microbial cultures, and empirical andcomputational protein biochemistry, to reconstruct protein sequences of a more primitive kind than any
that exist on Earth today — a field known as “paleoenzymology” (Benner et al., 2007; Perez-Jimenez etal., 2011) — focusing on the enzymes in Carbon Fixation pathways. Then, we will join these comparativeand functional studies with genomics and synthetic biology methods to assemble reconstructed ancientmolecules into functioning systems or cells with truly primitive phenotypes, helping to create the next
generation of evolutionary analysis, which we call “molecular systems evolutionary biology”. A particulararea of emphasis will be to show how biochemical systems coevolved with bioenergetic systems and withchanges in the geochemical environment, as developed in C7, as well as connecting evolution to the
biological isotope record, which was ultimately derived from at the level of particular catalysts. In this way,
we will link enzyme evolution, reaction mechanism, microbial physiology, and isotope geochemistry.

P aleoenzym ology of proteins in autotrophic carbon fixation pathw ays: M olecular systems
evolutionary biology

Molecular phylogenetics is an established method leading to hypotheses about the functions of ancientorganisms and ecosystems. However, if quantitative methods are applied only to single sequences at atime (the current practice for most evolutionary reconstruction), the consistency of these hypotheses canbe poor. The next step in evolutionary reasoning is to jointly reconstruct multiple interacting molecular
histories, to deduce the evolutionary history of functioning systems by integrating knowledge from these
histories. ELSI has three projects in process of this kind.
The first will reconstruct three ancestral-state proteins, which together are the ancestors of six of theeleven proteins in the reductive Citric Acid (rTCA) cycle of carbon fixation. This cycle, which is known to
be one of the most ancient carbon-fixing pathways in the biosphere, was shown to possess three cases of
enzyme homology suggesting that the catalysis performed by six specialized enzymes in modern organisms
was once performed by three enzymes in the ancestor, each having two functions. This molecularfingerprint suggests an answer to a key puzzle of how organisms could have evolved complex functions
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such as carbon fixation when they originally possessed only limited genomes and crude enzymes: the early
enzymes were multi-functional precisely because they were crude. The work is a specialization of ELSI
Research Scientist Masafumi Kameya, a former member of the laboratory that discovered these preserved
homologies in the rTCA proteins. A second project, by Betul Kacar (ELSI A-PI in the Harvard satellite) aims
to reconstruct sequences across the historic tree of the proteins RuBisCO and Carbonic Anhydrase whichfunction in the Calvin-Benson cycle of carbon fixation uniquely associated with oxygenic photosynthesis.
Our laboratories have all required capabilities to synthesize all reconstructed proteins, to test them for the
hypothesized ancestral functions, and to determine using computational models which features
determined their evolution from multi-functionality to selectivity. Both rTCA and Calvin-Benson cycle
reconstructions are being performed in collaboration with ELSI PI Eric Smith and EON fellows Christopher
Butch and Donato Giovannelli.
In a separate but related project, PI McGlynn/A-PI Kacar are pursuing reconstruction of the ancestralform of the CODH/ACS. In enzyme phylogenies, this enzyme cleanly splits the archaeal and bacterial
domains and can therefore be interpreted as ancient. However, since all contemporary sequences are justthat – relevant only today, the study of these proteins poses serious problems for the interpretation ofancient physiologies which may have used the CODH/ACS system. Paleoenzymological recovery of
predicted ancient homologs will allow an unprecedented look at the kinetic-isotope evolution of thisenzyme family through time, and will be of great usefulness for the interpretation of ancient C, as well as
S isotope signals.
P aleoenzym ology of sulfur m etabolism s : Also in the vein of linking enzyme evolution to isotope
fractionation, PI McGlynn leads a project in collaboration with Caltech and University of Seoul Faculty
which aims to determine the sulfur isotope fractionation evolutionary biochemistry of the enzymes involved
in microbial sulfate reduction. This process is currently the dominant microbial lever on the sulfur cycle inanoxic environments, and relating electron transfer processes, enzyme evolution, and the Earth’s sulfur
isotope record will allow a much more complete picture of enzyme evolution and the mark it leaves on aplanet.
The m icrobial phenotype in the presence of ancient enzym es : These ELSI projects on ancestral
enzyme reconstruction are also accompanied by genomics efforts to re-introduce the ancestral-form
enzymes into living organisms, in order to study the phenotype produced with enzymes of different
functions or entirely different levels of complexity from modern enzymes. The questions ELSI will pursue
for rTCA carbon fixation are how an organism can survive and evolve with cruder enzymes in its deepest
core pathways. The questions ELSI will pursue for Calvin-Benson cycle carbon fixation concern thefunctions of ancient RuBisCO and Carbonic Anhydrase ancestors, which created the evolutionary context
for the emergence of a Carbon-fixing function. Carbon fixation using RuBisCO, in particular, has distinctive
isotope-fractionation signatures, which depend not only on the central enzymes, but also on Carbon
concentration mechanisms that RuBisCO requires to function in different marine or terrestrial contexts ineras with different CO 2 and O 2 levels. In the case of sulfur respiration enzymes, we might be able to trace
phenotype evolution of sulfur, sulfate, and even nitrate metabolisms through phenotypic analysis of cells
which contain inferred catalytic ancestors.
Connection to the isotope record and isotope geochemistry : With our expertise in protein
biochemistry, enzyme evolution, microbial physiology, and frontier level isotope geochemical analyses,
ELSI has become poised to be the leader in a field we call isotope-paleoenzymology. Through thesecollaborations, we seek to directly link cellular physiology and individual catalysts (enzymes) to thehistorical isotope record. The isotope geochemistry group, under the direction of ELSI PIs Yoshida andUeno, has developed new super-sensitive isotope ratio mass spectrometry techniques which allow direct
isotope fractionation factor determination of the enzymes discussed above, as well as their assay throughevolutionary time by ancestral state reconstruction analysis. For example, we will be able to assess theevolutionary history of RuBisCO and its associated biochemical proteins by comparing the genomic historyof the photosynthetic reaction centers I and II to isotope records in an effort to understand theevolutionary interdependence of innovations that took place in both biochemistry andbioenergetics. Additionally, looking at enzymes involved in sulfur metabolism mentioned above may allow
for the ability to link isotope fractionation to the evolution of sulfur respiration.
Evolution of photosynthesis : An additional ELSI project on ancient enzymes and genomes concerns
the possible duplication, and the genetic ancestry, of the two photosystems (Photosystems I and II) thatwork together to provide high-energy charge separations for oxygenic photosynthesis. This work, a
specialization of ELSI researcher Yusuke Tsukatani, seeks to determine whether these now-separate
photosystems arose through duplication and divergence of ancestral proteins in a single reaction center,
and whether they entered the ancestors of cyanobacteria through conserved vertical descent from thisEarth-Life Science InstituteTokyo Institute of Technology - 30

ancestor, or through horizontal transfer from either green-sulfur or purple bacteria, which host themseparately today, supporting questions about the rise of oxygen (C7).

Com parative m icrobial genom ics and reconstruction of
bioenergetics pathw ays in ancient Earth analog environm ents

coupledbiochemical

and

ELSI researchers are exploring the microbial activity and diversity of early Earth analogs to gain insight
into what the first microbial communities were like, and how their collective activities may have forced orcontributed to the evolution of the Earth’s global elemental cycling. These valuable early Earth analogs
provide an environmental context of life as it may have existed in much more reduced environments thanare usually accessible on today’s Earth.
EON fellow Nancy Merino uses single-cell genomics to understand the interactions of member species
in serpentinite-hosted hydrothermal systems as models of the earliest biosphere, doing comparative
analysis at the Hakuba-Happo Onsen in Nagano Prefecture and the Cedars in California. This work is incollaboration with the Hadean Bioscience collaboration led by ELSI Fellow Ken Kurokawa. Furthermore,working with ELSI PI McGlynn, Merino has acquired samples suitable for single cell-stable isotope studies
using nanoSIMS. Measurements will be conducted in collaboration with Prof. Sano of the University ofTokyo, and these measurements will represent the first direct physiological characterization of HakubaHappo onsen.
Other projects concern the microbial activity and ecology of early archaean ocean analogs. Projects led
by PI McGlynn at Oku-oku hachikuro Onsen in Akita and in collaboration with Prof. Takashi Kakegawa(Tohoku University), and also at Jinata Onsen are allowing for a picture of possible archaean microbiology
to be formed. Geochemically, these hot springs span the likely ocean chemistry from the Archean to theProterozoic within the spatial confines of meters. At these locations, we are assembling and comparing
microbial genomes, especially with relevance to possible early iron, light, and/or hydrogen, iron, and sulfur
based metabolisms.
C9. How did the thermal evolution of the solid Earth change the ecosystem?
The long-range evolution of the biosphere as well as the atmosphere and ocean is deeply connectedwith the thermal evolution of the solid Earth. The links between these categories of evolution have been
dramatically reconsidered in recent years. Subject matters that have been revisited include the following:(1) Changes in and evolution of atmospheric composition through volcanic activity and differentiation of
the Earth's crust and mantle. (2) Changes in the supracrustal material cycle through plate tectonics, andthe link with the emergence of multicellur animals. (3) Effects of the inner core formation and resulting
changes in geomagnetic field intensity on the biosphere. (4) True Polar Wander and the Snowball Earthhypothesis (Kirschvink). The driving force in these is related to the differentiation of the solid Earth throughthe cooling of the Earth. The record of the Earth's history reveals that there were drastic changes in the
Sr isotopic composition at 2.1 billion and 600 million years ago. These changes in composition imply theonset of extensive weathering of continents, increase in sedimentary rocks owing to the expanded land
areas, and the supply of nutrients to the ocean. The times of the changes appear to coincide with the
emergence of eukaryotes and of metazoan animals when the levels of oxygen increased. These
coincidences imply possible causal links between these climatic and evolutionary events that may
ultimately reflect the thermal evolution of solid Earth. Particularly, the increase in oxygen levels 600 million
years ago may have been an inevitable physical trajectory of a cooling planet.
We will clarify how the Earth's core, mantle, and crust differentiated over 4.6 billion years, andespecially when radiogenic heat sources were first distributed, and subsequently spread by mantle
convection. To do so, we will first determine the physical properties of key substances and their elemental
partitioning in the Earth's interior based on the results of experiments under high temperature andpressure in A3 above. Using these parameters, we will simulate the convection of the mantle through time
to identify when the convection transformed, and we will identify when the inner core was formed. In
addition, we will conduct a dynamo simulation of the metallic core to understand how the geomagnetic
field intensity changed by the formation of the inner core.
These simulations should be compared with actual observational evidence. We will measure
paleomagnetic intensity of rock specimens from various times in the history of the Earth to study the link
between the core evolution and magnetic fields. PI Kirschvink established a method of analyzing measured
paleomagnetism as described in A3. PI Maruyama and his team discovered that continental growth was
episodic throughout the history of the Earth (Rino et al., 2008). Igneous activity is closely linked to thethermal evolution of the solid Earth. Comparing the implied solid Earth evolution with the surface
environmental changes shown in the study of drill core samples will establish links between the Earth's
Earth-Life Science InstituteTokyo Institute of Technology - 31

interior and surface environment. In regard to direct influence of environmental changes on the biosphere,
we will examine changes in composition of the atmosphere and ocean by extending the method describedin B4. To study links between plate tectonics and the biosphere, we will conduct a geochemical analysis
and model biogeochemical cycling of key elements not only within biosphere but also include crust andmantle in a longer timescale. PI Maruyama and his team studied changes in temperature and pressure of
subducted plates in regional metamorphic belts, and arrived at the conclusion that, as the Earth cooled,subducted oceanic plates carried water to the mantle, and the total quantity of seawater decreased
thereafter (Maruyama et al., 1996; 1997; Maruyama and Liou, 2005). The decrease in seawater exposed
vast areas of continent above sea surface. The denudation of the continents increased the supply ofnutrients to the ocean and substantial organic carbon burial into sediments, possibly triggering theelevation of oxygen levels that may have triggered emergence of animals at 600 million years ago.
Focusing on the times 600 million years ago, our G-COE project has carried out continental drilling over
10 sites and performed thorough geochemical and paleontological analyses (e.g., Sawaki et al., 2010). In
this project, we will focus on even earlier times to obtain pristine drill core samples of critical events.

Figure 8. The evolution of the Earth’s interior should have affected surface environments throughenhancement of geomagnetic field, landmass, and sedimentary rocks. (related to question C9).
D10. How unique is our planet?
Fundamental questions about the formation and evolution of habitable terrestrial planets such as "Whatis the diversity of terrestrial planets, and how does Earth fit in?" and “What is special about life on Earth?”
can now be addressed in quantitative ways based on actual observations, experiments and simulations.
We assemble the ever-growing data of extrasolar planets (more than 4000 exoplanets, and observed
detailed characteristics of some planets) and our solar system bodies (8 planets and the other small bodies),
and we clarify both universal and unique aspects of our Earth (Comparative Planetology). Then, we findconditions for life to emerge and its subsequent long-term evolution, and identify how these conditions
Earth-Life Science InstituteTokyo Institute of Technology - 32

can be reproduced in the “Comparative Planetology” framework. We will review and synthesize results
concerning the composition and the amount of the atmosphere, the amount of ocean (ocean to land ratio),the effect of the large moon(s), the possible onset of plate tectonics, generation of a magnetic field,
evolution of planetary interior, and positional relationships between planets and the Galaxy evolution. We
promote the study of the Earth based on comparison with its closest neighbors and more distant cousins,using both Earth specificity and planetary diversity to advance towards a better understanding of planetsas a whole. This integrated knowledge will be able to be used for narrowing down the targets that
potentially host extraterrestrial life, which is related to D11. In future JAXA’s planetary exploration missions
after Hayabusa-2 and MMX missions, and in future large telescopes such as TMT and E-ELT, we will
actively and scientifically collaborate with JAXA and NAOJ.

Figure 9. We will participate in future space exploration projects (such as the mission to a Martian satellite
by JAXA) as well as in science plans to look for biomarkers by remote sensing of terrestrial planets
outside the solar system using a next-generation large telescope, TMT, which Japan participates in(related to questions D10 & D11).
D11. How should we search for extraterrestrial life?
The research outcomes from the above A to C will be utilized for remote sensing observation by groundtelescopes and space exploration missions, particularly for search for biosignatures of extra-solar Earthlike planets in the habitable zones and on-going Hayabusa-2 and scheduled MMX missions.
Spectroscopic observation of the atmosphere of extra-solar terrestrial planets in habitable zones will
be available by next-generation large telescopes, TMT and E-ELT. Since National Astronomical Observatory
Japan is a formal partner for TMT, Japan ABC (AstroBiology Center) is focusing on instrument development
for TMT. We will try to establish more generalized biology that can be applied for remote sensing ofbiosignatures on these planets and make clear what can be biosignatures and how to observe them, incollaboration with Japan ABC.
As for a discussion of life diversity in the universe, we will link data on life in extreme environmental
conditions on the Earth and those from searches for extraterrestrial life with date from geology, discussionsof planetary condition based on the state-of-art planet formation theory, the history of the Earth, andEarth's interior physics. To be more specific, as case studies, we will consider the possibility of existenceof life on celestial bodies with subsurface oceans of icy satellites in the solar system and planets in habitablezones around M-type stars. Compared to our sun, M-type stars are so faint that the habitable zones arevery close to the central stars. Owing to tidal actions, the planet's rotation and revolution should be
Earth-Life Science InstituteTokyo Institute of Technology - 33

synchronized, with one particular side facing the central star. The planets receive intense X-rays andultraviolet fluxes owing to its proximity to the central star. These planets, although they are in habitablezones, have environments that differ significantly from that of the Earth. These discussions are also applied
to discussions on possible life in deep subsurface ocean of icy satellites of Jupiter and Saturn (Europa andEnceladus).
Commitments to sample return missions are also important roles of ELSI.
JAXA’s Hayabusa-2 will return samples from a primitive C-type asteroid (Ryugu) in 2020. Water andorganic matters are expected to be found in the samples. We focus on developing scientific scenarios,
rather than mission details. We use the renovated planet formation model to interpret the sample analysis
results and consider their implications for prebiotic chemistry.
The sample return mission from a Martian satellite (Phobos or Deimos), called MMX (Martian Moons
eXplorer), by JAXA will be launched in 2024. MMX will give important clues not only on the origin of Martiansatellites but also on primitive Martian surface environments. Because Phobos and Deimos closely orbit
Mars, debris generated by early impacts to Mars may be injected to the surface of these satellites and thedebris from early Mars may also be found in the samples. Using our findings of more general biology on
early Earth, we will also discuss early Mars as another suitable site of origin of (primitive) life.
D12. What principles lead to life in a planetary context?
ELSI research will focus on the aspects of life for which theoretical problems couple most directly to
the geological, chemical, and microbial data and models that are the Institute’s unique strength. We will
advance methods to reason about complex chemical systems (B5), to understand how biochemistry is
related in detail to geochemical conditions (B6, C7), and to understand why motifs such as cellular andgenomic individuality are so fundamental to biological organization, and how living systems embody
models of their world and use these to become partly independent of its constraints. Specific areas of
specialization include: 1) advanced computational methods to map the large combinatorial spaces of both
molecules and possible reaction systems; 2) efforts to understand which aspects of life are robust due tofamiliar principles of irreversibility in reaction-diffusion systems, and which require new physics that
includes mesoscale fluctuation and irreversibility; 3) the nature of concepts such as memory, individuality,
agency, and cognition, which underlie both the existence and autonomy of cells and higher organisms,
and thereby enable the Darwinian dynamics of heredity and selection by which they evolve. The EON
program at ELSI has been a particularly valuable network through which to identify and recruit talented
scientists working in these areas.

Advanced Com putational Chem istry

Many core problems in pre-biotic chemistry require the ability to assemble constraints on molecularform, or the generating mechanisms of reactions, into complex networks, and then to search and reason
systematically about the properties of these networks. To address these needs, we are developing newcomputational chemistry tools in multiple parallel tracks. Our first program, directed by James Cleaves,concerns the combinatorial spaces of molecules. Our second program, supervised by PI Eric Smith, centersaround new techniques of graph-rewrite-grammars for representing large reaction networks.
In one example of the way combinatorial computational chemistry can help show whether biologicalproperties are necessary or frozen accidents, Cleaves et al. generated an exhaustive set of amino acids
comparable to the biological inventory, and used this to compare chemical properties provided by the 20
genetically encoded amino acids with those provided by randomly chosen alternative sets. They foundthat the biological set may represent a largely global optimum, reflecting strong natural selection (Ilardo
et al., 2015), and suggesting that independent instances of life would employ similar sets. Other projects
enumerate lists of alternatives to RNA in order to understand what makes RNA unique (Cleaves et al.,2015; Wang et al., 2016), and to deduce what types of other molecules could have carried memory insequence information before RNA and DNA appeared (Guttenberg et al., 2015).
ELSI’s second program in computational chemistry centers on the use of graph re-write rules to abstract
reaction mechanisms so that they can be applied in an unlimited range of molecular contexts. Fromgraphical representation of reaction patterns, molecular reaction networks of arbitrary size may begenerated recursively from a few starting molecules. All atom positions and bond configurations may be
tracked through the entire network, enabling detailed comparison with position-specific isotope signatures
measured in the group of ELSI PI Yoshida. EON fellow Jakob Andersen is a world leader in chemical graphgrammar methods (Andersen et al., 2012; 2014a, b), who has modeled multiple large systems of prebiotic interest, including the formose network that produces sugars including ribose (Andersen et al.,2013a), and the Hydrogen Cyanide polymerization and hydrolysis network (Andersen et al., 2013b; 2015),
Earth-Life Science InstituteTokyo Institute of Technology - 34

which produces nucleobases. Extensions of these methods at ELSI will introduce stereochemistry andcatalysis by metal centers, enabling us to explore a class of reactions widely believed to be fundamental
to the emergence of metabolism from geochemistry (Braakman and Smith, 2014; Smith and Morowitz,2015).
A third, independent approach to overcome the combinatorial complexity of the constraints imposedby chemical consistency, using biological models of parallel signaling systems, is pursued by ELSI Fellow
Masashi Aono. Aono and others developed a heuristic search model to solve various constraint satisfaction
problems and demonstrated the capacity of the model to simulate unknown chemical reaction kinetics ina semi-quantitative and resource-saving manner (Aono et al., 2015; Aono and Wakabayashi, 2015).
Other research at ELSI seeks to understand the dynamics of complex chemical systems at a more
abstract level, through the construction of computational “toy models” that exhibit some features oforganic chemistry without reproducing every detail. The aim of this research is not to model one specificchemical system, but to understand what kinds of chemical properties and driving forces are needed forthe “messiness” of prebiotic chemistry to transition into ordered states, and for phenomena such as
information transmission and natural selection to arise. Current ELSI researchers include PI Eric Smith andresearchers Nathaniel Virgo and Olaf Witkowski.

N onequilibrium physical foundations

The hypothesis that life on Earth was inevitable, driven into existence by thermodynamic stresses, hasexisted in its modern form for about 40 years, and has been elaborated by many authors (for summaryand bibliography, see Smith and Morowitz, 2015). Yet it is not known whether this hypothesis is correct,
or even whether it requires only classical thermodynamics or also additional microscale and mesoscale
physics. A multi-part theoretical program under the direction of PI Smith is addressing these questions.
As an example of current research on this problem, Stuart Bartlett (joint with NASA JPL and one of thefounders of the hydrothermal Origin of Life scenario, Michael Russell (Russell et al., 1998; Russell et al.,2014)), is exploring the limitations of classical theories such as Maximum Entropy Production (Kondepudi
and Prigogine, 1998), and the relations between thermal and chemical pattern-formation in ventenvironments, in relation to the emergence of a proto-metabolism.

M em ory, individuality, agency, cognition

A widely known NASA definition of life — “a self-sustaining chemical system capable of Darwinianevolution” — contains no reference to almost any of the specific architectures that are fundamental tobiochemistry, molecular biology, cells, or organisms on Earth. ELSI PI Piet Hut has advanced acomplementary definition of Origins that abstracts the key features of life omitted in the NASA formulation:“The Origin of Life was the spontaneous emergence of autonomous agents in a complex system.” Projects
supervised by Hut seek to understand how ordinary matter, driven by the stress of thermodynamic
disequilibrium, is forced into architectures that take on the abstract properties of memory, individuality,
agency, and cognition. Nathaniel Virgo and Nicholas Guttenberg developed a dynamical “reservoir” model
to show how hereditary memory enabling evolution could have arisen from bulk chemical systems before
genomic heredity was possible (Virgo and Guttenberg, 2015). Other work by Virgo, relating the topology
of a reaction network system to its dynamics, shows how autocatalysis can arise in simple chemistries
where it provides focusing and amplification (Virgo et al., 2016). Hut and Olaf Witkowski, jointly with Araya
Brain Imaging, are studying the origin of autonomy and how it can lead to the most basic capacities forcognition, the fundamental property of life to categorize its environments and respond in ways that reflect
its adaptedness.

Com parative em ergence as a new fusion domain

A common theme in many of the above projects linking Earth and Life is the emergence of new
hierarchical levels with properties different from any of those of their components. A second motif sharedby these projects is the many advanced methods of comparative analysis, in domains from planetology tobiology. Although there is only one Earth harboring Life that we know, there is enough internal diversity
in both systems that comparative analysis can be very informative about law and causation; our science
is not limited by a statistic of “n = 1” in the way that is sometimes claimed. We propose to create a new
fusion domain by applying comparative analysis to the origin of novel structures and functions across the
Earth and Life sciences, to understand common aspects of the emergence of novelty across cases. We
refer to this study with the term “comparative emergence”.

Earth-Life Science InstituteTokyo Institute of Technology - 35

3.

Managementi)Center director

 Provide the name of the center director, his/her age (as of 1 April 2017), specialties, and brief career profile(within 5 lines).
 If there is a plan to change the center director, how does the new center director intend to construct the center and what is his/hervision of objectives to be achieved? Provide a synopsis written by the new center director (free format).

Name of Center Director:
Name:
Kei Hirose
Age:
49
Director of the Earth-Life Science Institute and Professor at Tokyo Institute of Technology. A highpressure geoscientist who has won many awards: 2006 Inoue Prize, 2007 Japan IBM Science Prize, 2007
Thomson Scientific Research Front Award, 2011 Japan Academy Prize, 2011 Science Innovation Award –Ringwood medal from the European Association of Geochemistry, and most recently, 2016 Fujihara Award
from the Fujihara Foundation of Science.
ii)

Administrative director

 Provide the name of the administrative director, his/her age (as of 1 April 2017), and his/her brief career profile(within 5 lines).

Name of Administrative Director:
Name:
Takashi Sakurai
Age:
66
B.S. in physics, 1973, Tokyo Institute of Technology; D.Sc. in astronomy, 1978, University of Tokyo.
He was at the University of Tokyo in 1978-1992, then moved to the National Astronomical Observatory ofJapan (1992-2016). His research field is solar physics, and was awarded the JpGU fellow in 2014. He wasappointed as administrative director of ELSI in 2016 April.

iii) Composition of administrative staff

 Concretely describe how the administrative staff is organized.

Under the leadership of the center director, ELSI has built a comfortable research and living
environment particularly for foreign researchers so that they can concentrate on their research. An
administrative director with rich experience in research, internationalization and management oversees
ELSI’s operational and administrative division which is as follows.
・Administrative director, administrative vice director
・General affairs: 1 chief and 1 staff
・Financial affairs: 1 chief and 1 staff
・Life advisor: 1 staff
・Secretaries’ office: 7 staff
・Public relations office: 1 chief and 1 staff
・Computer network system: 1 staff
・Coordinator of international initiatives: 1 staff
・University research administrators (assistant directors): 2 staff
Key areas of responsibilities:
・General affairs and financial affairs handle our institutional rules, labor management, financial
accounting and budgeting, procurement, travel expenses, management of items, facilities, health andsafety, and liaisons with the rest of Tokyo Tech etc.
・The life advisor provides foreign researchers and their families with assistance and language support
to help them adapt to life in Japan. For example. immigration, housing, child daycare services,Japanese classes and more.
・The secretaries’ office is in charge of administrative tasks for the directors and researchers. Their role
includes hosting international symposia and workshops.
Earth-Life Science InstituteTokyo Institute of Technology - 36

・The public relations office is responsible for promotional and outreach activity, such as sending out
information via our website, social media and printed materials, building media relations, holding
public lectures and outreach events, and welcoming visitors from high-schools and overseas research
institutions, in order to introduce mission and activities of ELSI and the entire WPI program.
・The computer network system supports information and communication technology, the ELSI
network, and provides common computing resources and information security.
・The coordinator of international initiatives plays an active role in seeking research funds and donations
from external foundations and enterprises. She offers assistance with recruitment of non-Japanesescientists.
・The university research administrators or assistant directors serve to coordinate between administratorsand researchers, assist in handling grant proposals and procurement.
Administrative staff members are fluent in English and possess rich administrative and technicalexperiences, which helps the director to make decisions.
The secretaries’ office was centralized in one office so that secretaries can accumulate and share useful
information and know-how among themselves. Upon researchers’ request, a one-stop research support
system has been developed and a contact person was assigned to each researcher.
The administrators and secretaries keep each other up to date and exchange information regularly.
In addition, Tokyo Tech research strategy office, international office and research administration center,and other divisions of the University provide enough support to ELSI.
iv) Decision-making system Concretely describe the center’s decision-making system.

The center director will have the authority to make all decisions except for those concerning the final
selection/removal of the center director himself. The responsibilities of the center director include theoperation and management of the institute, fully assisted by the administrative director. This will enable
a flexible and fast decision-making system.
Based on advice from the directors’ office meetings, steering committee meetings and related
committee meetings, the director makes administrative decisions on general issues concerning the institute.
One of the vice directors is responsible for the secretaries’ office and research promotion, and anothervice director (foreigner) leads internationalization such as the recruitment of young researchers, visitorsand students from abroad.
The directors’ office consists of the director, two vice directors, the administrative director, two
assistant directors and the coordinator of international initiatives. They hold a regular weekly meeting todeliberate over the latest and most important issues. This enables them to give unified instructions to thecommittees as well as to ensure the institute runs smoothly.
ELSI has a monthly steering committee consisting of the center director as a chair person, two vicedirectors, the administrative director, and two other principal investigators, to assist the center director in
making decisions on a wide range of matters, such as negotiation with the host university, internal
adjustment of policies, and discussions of research environments and personal affairs. In order to promptly
share tasks and information, assistant directors, administrative staff above chief-level and secretaries
attends the steering committee meeting.
ELSI organized several specialized committees to take action in regards to its smooth running andfusion of interdisciplinary studies. For example, Scientific Committee supports the director to set thestrategic direction of science and promote research interactions.
The international advisory board consists of top scientists including non-Japanese, and the board
members offer advice from an international perspective. ELSI director receives advice from them, but
makes the final decisions by himself.
v)

Allocation of authority between the center director and the host institution’s side Concretely describe how authority is allocated between the center director and the host institution’s side.

While the president of Tokyo Tech has the authority concerning the final selection/removal of thecenter director, the center director will be empowered to regulate the rest of the management andoperations concerning the center. Opinions are exchanged once a month with the university executives(president, executive vice president for research, executive vice director for general affairs and finance)
Earth-Life Science InstituteTokyo Institute of Technology - 37

and center director in order to maintain close coordination between Tokyo Tech and ELSI.

4.
i)

Researchers and other center staffs, satellites, partner institutions

The “core” to be established within the host institutiona) Principal Investigators (full professors, associate professors or other researchers of comparable
standing)
numbers

Researchers from within
the host institution
Foreign researchers invitedfrom abroad
Researchers invited from otherJapanese institutions
Total principal investigators

Final goal

At beginning

As of April, 2017

(Date: October,
2019)

6

12

12

3

2

3

4

1

1

13

15

16

 Describe the concrete plan to achieve final staffing goal, including steps and timetables.
 Attach a list of principal investigators using the Appendix. Place an asterisk (*) by names of the investigators considered to be ranked
among the world’s top researchers. Describe the policy and strategy for inviting the PIs who are to be included after 1 April 2017.

Since its inception, ELSI has strategically recruited new PIs from abroad and other Japanese institutions
and built up a superb lineup of 15 PIs including one female non-Japanese PI and eight non-Japanese PIs.
3 PIs work in three Satellite Centers at IAS, Harvard University, and Ehime University. Although the current
set of PIs cover top-rate scientists from a range of diverse disciplines to achieve our scientific missions,
ELSI is always looking for more talents, especially in younger generations, to think ahead toward thefuture of ELSI.

b) Total members

Numbers

Researchers
Principal investigators
Other researchers
Research support staffs

Final goal

At beginning

At end of FY 2016

23
<3,13%>[0,0%]
13<3,23%>[0,0%]
10<0,0%>[0,0%]

63<29,46%>[11,17%]19<8,42%> [1,5%]
44<21,48%>[10,23%]

70<35,50%>[16,23%]
16<9,56%>[1,6%]
54<27,50%>[15,28%]

0

29

29

(Date: October,
2019)

Earth-Life Science InstituteTokyo Institute of Technology - 38

Administrative staffs

5

25

25

Total number of people who form
the “core” of the research center

28

117

124

 Enter the total number of people in the columns above. In the “Researchers” column, put the number and percentage of overseas
researchers in the < > brackets and the number and percentage of female researchers in the [ ] brackets.
 Enter matters warranting special mention, such as concrete plans for achieving the Center’s goals, established schedules for employing
the main researchers, particularly principal investigators.

ii)

Collaboration with other institutions

 If the “core” forms linkages with other institutions, domestic and/or foreign, by establishing satellite functions, Provide the name of thepartner institution(s), and describe the role of the satellite functions, personnel composition and structure, and collaborative framework
between the host institution and the said partner institutions (e.g., contracts to be concluded, scheme for resource transfer).
 If some of the principal investigators will be stationed at satellites, attach a list of these principal investigators and the name of theirsatellite organizations using the Appendix.
 If the “core” forms organic linkages with other institutions, domestic and/or foreign, without establishing satellite functions, provide thenames of the partner institutions and describe their roles and linkages within the center project.

1) Satellite Center
ELSI will have four Satellite Centers, i) at the Geodynamics Research Center, Ehime University, (ii) atthe Department of Earth and Planetary Science at the University of Tokyo, (iii) at the Interdisciplinary
Program, Institute for Advanced Study in Princeton, and (iv) at the Origin of Life Initiative, Harvard
University. Each satellite function is as follows.
Geodynamics Research Center (GRC), Ehime University
GRC has shown globally leading research results in the fields of deep Earth science. Prof. Tetsuo Irifune
will join ELSI as a Principal Investigator and Satellite Director. Some more GRC members (including one
female scientist) will also join this Satellite Center.
The main role of this Satellite Center at Ehime University is to conduct research on the origin andevolution of the solid Earth, primarily based on the high-pressure/high-temperature experiments using
multi-anvil apparatus (large-volume press). Such multi-anvil experiments have a great advantage incontrolling sample temperature over experiments by other techniques such as a laser-heated diamondanvil cell, although the experimental pressure-temperature range is limited. The combination of bothdiamond-anvil experiments (K. Hirose at Tokyo Tech) and multi-anvil experiments (T. Irifune at Ehime
Univ.) would provide the best answers to questions on the deep Earth structure and dynamics.
Department of Earth and Planetary Science, University of Tokyo (EPS/U.Tokyo)
In April 2017, ELSI will launch a new satellite in the Department of Earth and Planetary Science (EPS)at the University of Tokyo. The Institute Director Hirose will promote his own research on the formationand early evolution of our planet in collaboration with experts in geochemistry and thermal evolution
modeling at the EPS/U.Tokyo and lead collaborative research between ELSI and EPS/U.Tokyo. In order tofacilitate the launch of this new satellite, the Institute Director Hirose will be cross-appointed by the
University of Tokyo as of April 2017 and will work 20% of time at the EPS/U.Tokyo. The EPS/U.Tokyo hasstrong research groups in astrobiology, planetary science, solar system exploration, early Earthgeochemistry, and the evolution of life. Importantly, their research is complementary to that of current
ELSI members. Director Hirose will lead joint research between ELSI and the EPS/U.Tokyo satellite centerin the study of the formation, evolution, and habitability of planets in solar and extrasolar systems and thestudy of geology, geochemistry, and life on the early Earth. Such collaboration will be built through hiring
Research Scientists who work at both campuses, co-hosting visitors, and co-organizing international
workshops.
Interdisciplinary Program, Institute for Advanced Study (IAS) in Princeton
Prof. Piet Hut is based at the IAS in Princeton. He will divide his time between Tokyo Tech and Princeton,
half and half. During his stay at Princeton, the Institute for Advanced Study will host scientists from ELSI
and EON. The IAS is, of course, a world-leading research institute, always hosting more than a hundred
Earth-Life Science InstituteTokyo Institute of Technology - 39

visitors from around the world. This is an ideal place for ELSI and EON scientists to exchange ideas withother top-class scientists and to establish their own personal connections.
Origin of Life Initiative, Harvard University
Prof. Jack Szostak will participate as a Principal Investigator and a Satellite Director on behalf ofHarvard University Origin of Life Initiative. He is a world-leading scientist in synthetic biology. ELSI andHarvard satellite center will exchange young scientists to explore questions about the origin of life, basedon new findings about the early Earth environments, which are under investigation at ELSI.

Figure 10. Collaboration with domestic and overseas research institutes, including the Satellite Centers ・If the “core” forms organic linkages with other institutions, domestic and/or foreign, without establishing satellite functions, provide
the name of the partner institutions and describe their roles and linkages within the center project.

2) Affiliated centers
ELSI will have strong connections with domestic and overseas research institutions, such as (i) Japan
Agency for Marine Science and Technology (JAMSTEC), (ii) Harvard University, (iii) California Institute ofTechnology and (iv) Columbia University. ELSI concluded a coordination agreement with JAXA (Japan
Aerospace Exploration Agency)/ISAS (Institute of Space and Astronautical Science). Additionally, ELSI
has been collaborating with affiliated centers abroad on the basis of the ELSI Origins Network (EON)
project funded by the John Templeton Foundation, with which we hire joint postdocs who spend half timeat ELSI and the other half there (Figure 13). ELSI promotes collaborative research with these institutions
by exchanging people and ideas.

5.

Research Environment

 Concretely describe measures to be taken to satisfy each of the requirements outlined below, including steps and timetables.

i)

Provide an environment in which researchers can devote themselves exclusively to theirresearch, by exempting them from other duties and providing them with adequate staff
support to handle paperwork and other administrative functions.
Earth-Life Science InstituteTokyo Institute of Technology - 40

The Earth-Life Science Institute (ELSI) will provide the best environment for researchers to concentrate
on research. PIs (principle investigators), specially appointed associate / assistant professors and postdocs will work together and pursue their research interests freely with loose connection to a specific group.
A few university research administrators with academic backgrounds provide additional support in orderfor researchers to avoid miscellaneous tasks which are non-essential to their research. They also help nonJapanese researchers in general ways, including offering assistance with writing a proposal,
communicating with external Japanese scientists, etc. PIs joining from Tokyo Tech have been reassigned
as Professors of ELSI, which grants them a reduction in non-research responsibilities. They must at least
be exempted from the duty of teaching undergraduate students.
The center director is responsible for minimizing the administrative work of all researchers at thecenter. For this purpose, a very efficient research-oriented administrative division has been createdthrough several unique systems. Each administrator will be evaluated and given incentives, similarly toscientists. The center holds a regular event to inform administrators of the center’s latest research results,
which leads to smooth communications between researchers and administrators and more importantly
motivates the administrators to work for the research.
ii)

Provide startup research funding as necessary to ensure that top-caliber researchers
invited to the center do not upon arrival lose momentum in vigorously pursuing theirwork out of concern over the need to apply immediately for competitive grants.

Each PI invited from overseas will be granted JPY5 to 10 million, depending on whether they conduct
theoretical or experimental work, as start-up funding for his/her research project. Further support will
possibly be given at the discretion of the center director, until he/she obtains external funds based on thediscussion with the center director. The center will provide non-Japanese researchers with a full range of
support to acquire competitive funds in Japan.
The director’s fund will be utilized to encourage interdisciplinary concepts borne out of young
researchers’ free and flexible ideas or from discussions between researchers with different backgrounds.
The fund is meant to support feasibility studies and then to acquire competitive funds. The center director
receives and reviews joint proposals about twice a year, in the spring and fall. The center keeps track of
their progress and will determine how the internal funding system should be managed in later stages.
iii) As a rule, fill postdoctoral positions through open international solicitations.

Through open international solicitations, the center hires three ranks of researchers besides PIs: 1)
post docs, 2) specially appointed assistant professors, and 3) specially appointed associate professors.
Their expertise and strengths should fit within ELSI’s scientific interests and goals, and they should be
open-minded to collaborate with other researchers from diverse backgrounds both in and outside of ELSI.
Young researchers have more freedom in their research with only loose connections to specific groups.
Their academic independence was guaranteed in ELSI’s open and flat research structure that departed
from the conventional one in which young researchers assisted PIs under the PI’s leadership. Instead,young researchers at ELSI form their own networks and seek advice and cooperation from various PIs andresearchers with whom young researchers’ interests align. Such dynamic collaboration and fusion among
researchers will be encouraged, and the research structure will be reviewed and improved.
Now that ELSI has recruited top scientists and their research environments are settled, the strategic
addition of new members will speed up collaborative research projects, leading to more results.
iv) Establish English as the primary language for work-related communication, and appoint

administrative personnel who can facilitate the use of English in the work process.

The official language must be English for non-Japanese and Japanese alike. Every document will be
written in English. A few officers of Tokyo Tech who can use English will be assigned to the center as apriority. We will also have excellent English-speaking staff members from the outside, and we will actively
encourage the employment of staff, Japanese and non-Japanese, with international experience.

Earth-Life Science InstituteTokyo Institute of Technology - 41

v)

Adopt a rigorous system for evaluating research and a system of merit-based
compensation. (For example, institute a merit-based annual salary system primarily for
researchers from outside the host institution. As a basic rule, the salaries of researchers
who were already employed at the host institution prior to the centers’ establishment
are to be paid by the host institution.)

The research activity by each scientist will be evaluated annually. The evaluation process has been
restructured into several layers. Firstly researchers review their activities and submit a report on
publications in academic journals, the scientific merit of his/her research, their contribution to ELSI’s overall
activities and the acquisition of external competitive funds. Then newly assigned mentors add statements
and forward the assessment results to senior PIs and Director’s office. For outstanding research outcomesor contributions, the center will provide better research environments (space, financial support etc) andtreatment (salary raise and extension of contract) as incentives. While every researcher is to get feedbackon the results, it will be important for researchers who need assistance can receive suggestions for
improvement, to be discussed with their mentors and collaboratively monitored throughout the year. In
addition, the directors regularly communicate with researchers, in order to exchange opinions on and to
discuss future directions for his or her research.
Administrator will be evaluated and given incentives for notable achievements.
vi) Provide equipment and facilities, including laboratory space, appropriate to a top world-level research center.

Tokyo Tech has secured sufficient research space (about 1500 m2 from the start and an additional
area of approximately 5000 m2 by 2015) for the center at the Ookayama campus, close to the buildingof the department of Earth and planetary sciences. In addition to research space (offices, laboratories),
we will keep a common room to promote internal communications, which is key for interdisciplinary studies.
Both researchers and administrators gather in this room for their short break and for daily and weekly
events.
The access to research equipments, in particular to large scale parallel computers for simulations, isabundant. The computer center of Tokyo Tech (GSIC) has the most advanced supercomputer TSUBAME
among research institutes in Japan. In addition, GRAPE series of custom-built supercomputers, developed
by J. Makino's group, will be accessible to researchers of the center. Also, 10-Petaflops K computer andits successor, the post-K supercomputer, as well as other supercomputers in national research institutes,
including the National Astronomical Observatory, JAXA and JAMSTEC are accessible.
vii) Hold international research conferences or symposiums regularly (at least once a year)

to bring the world’s leading researchers together at the center.

An international symposium will be held annually. They will cover a wide range of topics, with different
clear-cut key concepts in each year, based on original research at the center. World-leading scientists andyoung active researchers will be invited from abroad with and without travel support. Other relatively small
workshops on specific hot topics and interdisciplinary topics will be held several times each year.
viii) Other measures to ensure that top-caliber researchers from around the world can

comfortably devote themselves to their research in a competitive international
environment, if any.

Living conditions will probably be the biggest concern for most non-Japanese scientists. To best serve
them and their families, the center will assign a “life adviser” to each family before they even move toJapan. This adviser will guide them through all the difficult processes and will always be available to advise
on subjects such as visas, schools, bank accounts, special diets, garbage, transportation, taxes, pensions,etc. The adviser essentially acts as a personal assistant for non-Japanese scientists when needed. Tokyo
Tech has an accommodation facility called the 100th Anniversary International House with 100 single
rooms and 20 family rooms at Ookayama campus. It can be used temporally by non-Japanese scientists
Earth-Life Science InstituteTokyo Institute of Technology - 42

and their families until they find a place to live elsewhere.
Another challenge for non-Japanese scientists will be the acquisition of external funds for their research.
ELSI’s university research administrators will be heavily involved in their preparation of proposals.
Additionally, the university’s research administration center, research promotion department andinternational affairs department will support non-Japanese scientists in acquiring competitive funds.

6.

Indicators for evaluating a center’s global standing Describe concretely the following points.

i)

Criteria and methods to be used for evaluating the center’s global standing in thesubject field

Evaluation of a "globally visible" research center requires a comprehensive assessment withconsideration of various criteria such as levels of research activities and recognition of the institute and its
researchers. Specific evaluation indicators include 1) the number and quality of publications, number ofconference presentations, number of scientific events hosted, and acquisition of research funding for
research activities and 2) degree of international research cooperation, number of visitors, and academic
awards for recognition of the institute and its researchers.
It is equally important to carefully assess the progress of efforts to promote interdisciplinary researchand to create a new research domain.
ii)

Results of current assessment made using said criteria and methods

Current assessment of research activities
8 out of 15 PIs in ELSI have “h-index” higher than 35. It is clear that ELSI exhibits a strong prospective
to stand out globally as top-level research center in the world. Six PIs are under fifty years old and are
expected to play leading roles in making major advances in academic activities.
Recent publications (since 2014) of note include the followings:- Experimental determination of the electrical resistivity of iron at Earth's core conditions (2016)
Nature 534: 95-98.
- Lunar true polar wander inferred from polar hydrogen (2016) Nature 531: 480–484.
- Evidence for global electron transportation into the jovian inner magnetosphere (2014) Science
345: 1581-1584.
- Low Core-Mantle Boundary Temperature Inferred from the Solidus of Pyrolite (2014) Science 343:
522-525.
- The Charon-forming giant impact as a source of Pluto’s dark equatorial regions (2017) Nature
Astronomy 1: 0031.
- Oligoarginine peptides slow strand annealing and assist non-enzymatic RNA replication (2016)
Nature Chemistry 8: 915-921.
- Synthesis and stability of xenon oxides Xe 2 O 5 and Xe 3 O 2 under pressure (2016) Nature Chemistry
8: 784-790.
- Pressure-induced nano-crystallization of silicate garnets from glass (2016) Nature Communications
7: 13753.
- A key genetic factor for fucosyllactose utilization affects infant gut microbiota development (2016)
Nature Communications 7: 11939.
- Carbon-depleted outer core revealed by sound velocity measurements of liquid iron-carbon alloy(2015) Nature Communications 6: 8942.
- Klebsormidium flaccidum genome reveals primary factors for plant terrestrial adaptation (2014)
Nature Communications 5: 3978
- Accretion of Phobos and Deimos in an extended debris disc stirred by transient moons (2016)
Nature Geoscience 9: 581–583.
- Computational support for a pyrolitic lower mantle containing ferric iron (2015) Nature Geoscience
8: 556-559.
- Water contents of Earth-mass planets around M dwarfs (2015) Nature Geoscience 8: 177-180.
- Stability of hydrous silicate at high pressures and water transport to the deep lower mantle (2014)
Nature Geoscience 7: 224-227.
- Origin of microbial biomineralization and magnetotaxis during the Archean (2017) PNAS DOI:
Earth-Life Science InstituteTokyo Institute of Technology - 43

10.1073/pnas.1614654114- A virus of hyperthermophilic archaea with a unique architecture among DNA viruses (2016) PNAS
113: 2478-2483.
- On the universal structure of human lexical semantics (2016) PNAS 113: 1766-1771.
- Hadal biosphere: Insight into the microbial ecosystem in the deepest ocean on Earth (2015) PNAS
112: E1230-E1236.
- Oxygenic photosynthesis without galactolipids (2014) PNAS 111: 13571-13575.
ELSI acquired a sum of $5.5 million USD (approx. 670 million yen) from the John Templeton Foundation(US) for the period from July 2015 to March 2018 and launched a project titled “ELSI Origins Network(EON)”. ELSI researchers have been successful in securing research funding. Notably, large KAKENHI
funds, such as Grant-in-Aid for Specially Promoted Research, Grant-in-Aid for Scientific Research on
Innovative Areas, and Grand-in-Aid for Scientific Research (S), were acquired. These assure continued
development of research projects.
Recognition of the institute and its researchers
ELSI’s researchers from different generations are held in high esteem at their respective levels. Seniorresearchers such as PIs have received awards including the Medal of Honor with the Purple Ribbon, theJSPS prizes, and the Fujihara Award. They have also become fellows of notable societies such as the RoyalInstitute of Navigation. Meanwhile young researchers have also received awards that target young
professionals, such as the IUPAC-SOLVAY International Award for Young Chemists.
Promotion of interdisciplinary research and creation of a new research domain
ELSI's efforts to promote interdisciplinary research have been resulting in publications (e.g., Earth
Planet. Sci. Lett. 2014 386: 112-125; Astrobiology 2015 15: 430-441; PLoS ONE 2015 10: e0140663;
Geochim. Cosmochim. Acta 2016 177: 205-216; Orig. Life Evol. Biosph. 2016 DOI: 10.1007/s11084-0169516-z). In addition to the institutional activities for scientific discussion, informal discussion groups havebeen organized voluntarily on various topics, promising more avenues for future interdisciplinary
collaborations.
ELSI researchers have conceptualized an idea of a new research domain, which is called "Comparative
Emergence," and aim to crystallize this idea of "Comparative Emergence" in the coming five years.
iii) Goals to be achieved through the project (at time of final evaluation）a) Establish position as world leader among research institutes in related fields.
b) Establish a sound financial base by steady acquisition of donations and competitive research funding.
c) Expand the research community driven by ELSI further and thereby contribute to its diversification andinternationalization.
d) Contribute to the fostering of next-generation researchers and their career development. This will bedone by strategically planning the exchange, acquisition, and training of research-related humanresources as a hub for idea exchange between researchers, collaborators, and guests.
e) Create a new fusion domain, Comparative Emergence, by applying modern comparative methods to asystematic study of the emergence of novel structures and functions across Earth and Life sciences.
f)7.

Securing research funding

ELSI has already secured adequate research funds including the Grant-in-Aid for Science Research(KAKENHI), sponsored research funds, collaborative research funds, and university grants/operating
subsidies.
ELSI’s main source of funding as of FY2016 are funds from the John Templeton foundation based in
the U.S., along with large-scale KAKENHI such as Grants-in-Aids for specially promoted research and forscientific research in innovative areas. The research fund from the John Templeton foundation isapproximately 5.5 million US dollars in total and has strengthened ELSI’s infrastructure to accelerate
research related to origins of the Earth and life. In addition, we secured new research funding in FY2016
from NEDO and JSPS’s Grant-in-Aids for specially promoted research.
Future prospects
Earth-Life Science InstituteTokyo Institute of Technology - 44

 Describe the concrete prospects for securing resources that match or exceed the project grant.
 Calculate the total amount of research funding (e.g., competitive funding) based on the percentage of time the researchers devote toresearch activities at the center vis-à-vis the total time they spend conducting research activities. Be sure the prospects are realistically
based on the past record.

The following table shows the expected amount of research funds to be obtained annually at ELSI
from FY2017 and onwards. This shows that ELSI’s capabilities of securing research funding aresubstantially matched to the requirement by the WPI program

Grants-in-Aid for Scientific Research(KAKENHI)
Corporate Collaborative Researchand Donation for Research, etc.
Sponsored Research
University Grants / Operating
Subsidies
Total per fiscal year

Research funds to be obtained annually at ELSI from
FY2017-2021(Unit million yen)
363
146
18
102
629

In order to ensure that the expected funding appears as above, we provide the following structured
and strategic efforts to all researchers at ELSI.
- By creating an environment in which all researchers at ELSI can concentrate on research, we willallow them to apply for more competitive funding programs.
- University research administrators will fully assist researchers in acquiring funds. For example, they
will arrange grant applications in cooperation with Tokyo Tech’s research administration center,
research promotion department and international affairs department.
- We will provide comprehensive support to individual investigators in preparing competitive grant
proposals to funding agencies in Japan and elsewhere; English and Japanese language editorial
support; opportunity identification; training and mentoring of early-career researchers in proposal
development; mediating of internal and external collaborations; and rigorous internal review prior to
proposal submission.
The center and administrative directors should regularly develop some trend analysis of national policy
objectives, related subsidies, and competitive funding programs with the help of the policy making bodyof Tokyo Institute of Technology. This will ensure a cost-effective approach to support basic funding
applications and a more complicated and demanding approach necessary for foundations and other large
sources of funds. We will propose new future-oriented large-scale projects to the government on the basisof the trend analysis.
Others Describe activities and initiatives to be taken after project funding ends.
 Describe expected ripple effects （e.g., how the research center project will have trailblazing components that can be referred to byother departments in the host institution and/or other research institutions when attempting to build their own top world-level research
centers）.
 Describe other important measures to be taken in creating a world premier international research center, if any.

1) Activities after the end of the program period
The director will do his utmost to seek donations to ELSI from international nonprofit corporations andfrom companies with close relations to Tokyo Tech. Major scientific mission of ELSI, questions about theformation of Earth and the origin of life, extraterrestrial life and the space craft “Hayabusa2”, and sample
return mission to Mars moons are of general interest to the public, which could help us to collect donations.
It is notable that ELSI has received 5.5 million USD (approximately 670 million JPY) from the John
Templeton Foundation in the U.S. Using these global funds as a resource, ELSI has further strengthened
Earth-Life Science InstituteTokyo Institute of Technology - 45

its research infrastructure and accelerated scientific investigation to elucidate the origin and evolution of
the Earth and life. We have launched the EON (ELSI Origins Network) project where ELSI—as a worldclass research hub—develops an international network of researchers across various research fields.
Building upon the John Templeton Foundation grant acquisition and the success of EON project, ELSI
vigorously seeks for more overseas funding.
Even after the end of the support under the WPI program, the activity of ELSI will continue based on1) external funds acquired by principal investigators and other members, 2) continued support from theuniversity, and 3) donations.
2) Effects on other institutions
ELSI has already realized the following three goals, which have large ripple effects on institutions
nationwide. Our main achievements are as follows:i)

English-based administration
Internationalization is one of the important goals of WPI program, and ELSI has introduced following
practice- English-based administration- Merit-based annual salary & incentive award- Non-Japanese family support systems will be secured at the center.
These serve as role models for other institutions to host researchers from abroad.

ii)

Research-oriented environment
ELSI has established a highly research-oriented environment. For this purpose,- Annual evaluation will be conducted to review the research results of each scientist, the outcomeof which will be reflected in the revision of annual salaries and incentive award given by the center
director.
- University research administrators with academic backgrounds will provide a wide range of support
to all scientists.
- PIs from Tokyo Tech will be reassigned to the center and exempt from the duty of teachingundergraduate students.
- A research-oriented administrative structure has been created and the latest research results are
disseminated widely to the administrators (See 3. Management iii) and iv) sections). These uniquesystems should be helpful for other organizations to become more highly research-oriented.

iii) ELSI will have stronger connections to the general public.

- PR chief with academic backgrounds will be in charge of overall promotional and outreach activities.
- The PR office will organize domestic and overseas press releases, outreach events for the generalpublic including high-schools students, and manage interactive digital communication with various
stakeholders, to introduce mission and activities of ELSI and the entire WPI program.
- Active promotional and outreach activities will make the ELSI and the host institute more visible
from the outside, which will be a big advantage for both.

3) Other plans important for the establishment of a leading global research centeri) World-wide interaction of researchers
ELSI will continue its efforts to enhance its international status as research hub in related research
fields. We will invite top-level professors on sabbatical leave to stay for half a year or a year as wellas support short stays by both established and young active scientists. At the same time the center
will encourage all scientists including postdocs to stay at overseas partner institutions for a while toexchange ideas and conduct collaborative research. Notably postdocs of the EON project, who spend
approximately half of their contract terms at an overseas institution.
ii)

Publication of research findings
Researchers are strongly encouraged to present research findings and to organize scientific sessions
at relevant international conferences. This contributes to the high visibility of ELSI and to attract
Earth-Life Science InstituteTokyo Institute of Technology - 46

researchers and students to ELSI.
iii) Fostering mutual understanding to build synergistic relationships

As a newly-established interdisciplinary research institute, we launched efforts to promote internal
communications within ELSI. We have done this by setting up a common room as well as holding
daily, weekly, and monthly events following the model of IAS, Princeton, where PI Prof. Piet Hut, oneof ELSI PIs, is based. ELSI will continue to offer opportunities to share research targets and toassemble adequately research talents and foster greater mutual understanding among researchers.
Such opportunities were developed into several types, ELSI seminars, assemblies and youchien(kindergarten). ELSI seminar is a place for lectures and discussion to which external researchers areinvited to speak. ELSI assembly is a science meeting conducted by ELSI researchers, and important
issues such as strategic, long-term research objectives are presented and discussed at the initiativeof the Science Steering Committee. ELSI also schedules a series of assemblies for ELSI researchers
to present their research activities conducted in the last year and latest work-in progress. This helps
to share academic interests and to exchange regular feedback with each other. ELSI youchien(youchien is a Japanese word for kindergarten) aims to remove the barrier that exists between
different disciplines and sections. Young researchers present their research and specialties to other
ELSI members including the administrative staff in simple language.

iv) Reorganization of the research environment

We already have years of experience of interdisciplinary research between geoscience and life sciencethrough 21stCentury COE, G-COE, and WPI programs. Additionally, ELSI has several plans to unite
the team in exploring the early Earth environments and the origin of life. First, we have reviewed theresearch organization and clarified the roles of PIs in response to the midterm evaluation results, and
the PIs in a revised organization are expected to play leading roles to achieve these ELSI's scientificmission. Second, the areas of research focus and institutional strategy to achieve these research
objectives have been under discussion by the directors, PIs, and young researchers. These efforts
generated a shared sense of goals among ELSI researchers, which contributes to further promotionof research interaction and interdisciplinary collaboration.

v)

Nurturing the next generation of scientists
ELSI has been making steady progress in contributing to graduate education. Some non-Japanese
PIs and Associate Professors are now becoming affiliated with Tokyo Tech Schools and Departments
across campus, as main or sub supervisors. ELSI is eager to recruit more prospective PhD students
and has succeeded in mentoring students on site. ELSI is expecting more PhD students to join (underapplication). ELSI researchers will also be assigned to teach classes and be encouraged to set up aninternational educational program. By doing so, such PhD students and supervisors will
simultaneously develop interdisciplinary research both at ELSI and other departments.

Earth-Life Science InstituteTokyo Institute of Technology - 47

The Goal of Research at the Earth-Life Science InstituteCenter Director of the Earth-Life Science Institute (ELSI):

Kei Hirose
1. The Main Purpose of Research at ELSIThe main purpose of our research will be to solve one of the most fundamental questions of humankind:when and where and how were the first life forms born, and how did they evolve? This question, which
originated with the Greek nature philosophers, has been one of the most important topics of natural science.
However, it has remained largely dormant because of the great difficulty of making inroads into a problem
with such enormous complexity together with an almost complete lack of direct observational evidence.
Only the last few decades have seen various areas of science maturing enough to begin to tackle thesefundamental questions head on.
The name of our proposed institute reflects this recent maturity, in which geophysics, geology,
biochemistry, molecular biology as well as computer science and other fields in science are teaming up
together. ELSI, or Earth-Life Science Institute, aims at bringing together scientists from all fields related tothe study of the early Earth in relationship to the study of early forms of life.

What distinguishes ELSI from other institutes studying life sciences is the emphasis on the "origin of(Host institution：National University Corporation Tokyo Institute of Technology Center name：Earth-Life Science Institute (ELSI)）

1

life in context", namely on Earth, in a specific ecological system. So far, discussions about the origin of life
have primarily taken off from the viewpoint of biochemistry, against the backdrop of a particular choice of
natural environment, a type of rock or pool or ocean floor, but with most of the attention directed to thebiochemistry of proto-life forms. We want to change that, by focusing equally strongly on both sides ofEarth and Life, because life is a phenomenon that is preserved through exchange of energies and materials
with the surrounding environment.
It is highly probable that the environment of the Earth around the time of the birth of life wassignificantly different from that of the present. For example, the Earth may have been surrounded by a seaof sulfuric acid. We will approach this problem from two directions: forwards, using theoretical models of
the formation of the Earth and backwards, tracing back the geological record.
The forwards approach starts with the origin of the Earth. Through the theory of planet formation andmaking use of the world's cutting-edge computer simulation technology, the formation process of the Earth
in

the

solar

systemwill

bemodeled

from

first

principles.

In

addition,byutilizinghigh-pressure/high-temperature experiments, which is Japan’s specialty, we will investigate the material’s
differentiation of the Earth and replicate its core, mantle, crust, atmosphere, and oceans.
The backwards approach needs a rich data base mapping out the geological record. Fortunately, we canutilize the 165000 samples spanning the history of the Earth, stored in the Museum of Evolving Earth atTokyo Tech. We will thus investigate changes in the environment back to 3.5 billion years ago, and estimate
as best as we can the environment in the Hadean Eon. We will study “places” on the early Earth, which
could have provided both energy and nutrients indispensable to life. This will help us to specify theenvironment that gave birth to life.
In the field of genomic science, relations between specific environmental factors and the gene pools of
microorganisms are now being documented, and stored in data bases. We will utilize these to estimate the“initial genome” of life born in a special environment on the early Earth. Furthermore, we will attempt toactually reconstruct one of the initial cells by using a synthetic biological approach. In other words, we will
replace the biology question for the “origin of life” with the more relevant interdisciplinary question
regarding the “birth of a persistent ecological system.” An important goal in our research will be to developthese data base systems further, in order to clarify the initial ecological system that allowed a stable andpersistent existence of life even under the various harsh and violent changes of the environment that
happened on the early Earth.
We will complement these more theoretical approaches with research directly based on experiments andobservations. One PI in our institute is in charge of a search for micro organisms in hydrothermal systems
at the deep-sea floor, using the “Shinkai 6500” submersible. Another PI is in charge of an investigation ofprimitive asteroid using the spacecraft “Hayabusa-2”. The deep-sea floor hydrothermal system andprimitive asteroid may have provided energy and material necessary for the birth of life on Earth,respectively.
As a result of the Earth-Life focus in our research, we will be able to understand what was special about
the Earth, as the planet where life originated, that ultimately gave rise to our existence. As a corollary of(Host institution：National University Corporation Tokyo Institute of Technology Center name：Earth-Life Science Institute (ELSI)）

2

our research, we will contribute to a wider understanding of the universality of life and its possible modesof origin on other planets, in our solar system and beyond. We will also proactively participate in space
exploration projects (such as missions to Europa and Enceladus, which have an internal ocean) as well as inprojects using next-generation telescopes now under construction, in order to look for biomarkers by
remote sensing of terrestrial planets outside the solar system.

2. Setting Up a Research Environment of Great Excellence
The research environment of Tokyo Tech is already quite good, and the individual results by each of the
Principal Investigator are at the world’s top level. However, most results so far have been obtained withinwell circumscribed and established research disciplines. What we need to progress further is a strong
enhancement of hybrid forms of research, spanning different fields. This requires substantial effort, coupledwith a willingness to lower the barriers that currently mark the boundaries of different disciplines. Our
greatest challenge is how to set up a research environment that exhibits great diversity in disciplines while
retaining the great excellence that Tokyo Tech has established in individual disciplines.
Interdisciplinary research has been recommended in various research programs, including the WPI
program. However, translating these good intentions into actual thriving collaborations is far from trivial.
For one thing, researchers trying to cross boundaries between different fields typically continue to havetheir offices in different buildings, making communication already much less natural and frequent. Even
when well funded, in practice these barriers greatly reduce the efficiency of multi-disciplinary
collaborations.
In ELSI our foremost concern is to create a physical environment which naturally encourages and infact enforces daily communication between all its researchers. ELSI will be housed in a single building,with a Common Room in which daily activities will be organized to promote many kinds of exchanges
between all researchers and staff members. However, that in itself will not be sufficient, and we know manycases in most universities where even people in adjacent offices rarely talk to each other. Something moreis needed.
The well-known Institute for Advanced Study (IAS) in Princeton has four roughly equal groups ofresearchers in the very different areas of mathematics, natural sciences, social sciences, and historicalstudies. After a long period of trial and error, during the first seventy years of its existence, there was still
little direct communication between these four main groups. In order to remedy this situation, ten years ago
a new Program in Interdisciplinary Studies was started at IAS, which has been greatly successful informing rich bridges between the four groups, as documented in a recent report by an external visiting
committee.
Encouraged by the success of that Program of Interdisciplinary Studies, we have approached the Headof the program, Professor Piet Hut, inviting him as a PI for our new center, in a two-fold function.
First, we would like him to repeat the success of the development of his program in the environment ofTokyo Tech. Second, we would like to establish his original program at IAS as a Satellite Center for our(Host institution：National University Corporation Tokyo Institute of Technology Center name：Earth-Life Science Institute (ELSI)）

3

WPI center, encouraging two-way exchanges between both scientists and administrators between ELSI and
IAS. After we explained our vision, Professor Hut enthusiastically agreed to play this double role within
ELSI.

Japan is still lagging far behind Western nations in international exchanges. There exist significant
obstacles that foreign researchers must overcome in order to do their research in Japan. The biggest
obstacle might be a sense of alienation brought about by the language barrier. Therefore, we willthoroughly enforce the use of English as the official language at ELSI. Also, we will dispatch some of theleading administrators at ELSI to our overseas satellite center at IAS, for stays of up to several months inorder to learn how the IAS functions in practice on a day-to-day basis, encouraging an atmosphereconducive to open and free ranging research. We will hire more than 30 researchers from abroad and invite
famous foreign researchers on sabbatical to stay at ELSI. We will also ask Japanese researchers to visit theoverseas satellite center or other collaborating organizations in order to expand their contacts throughinternational networks.

3. Strengthening of the Public Relations Division
The success of ELSI is directly connected with its visibility. In order to attract researchers from abroad,active young and upcoming researchers as well as famous older scientists, it is essential to establish a broad
awareness of ELSI, of its mission as well as its accomplishments. And in the long run, after the initial WPI
funding runs out, high visibility of ELSI will increase our ability to attract competitive funds by principal
researchers as well as continued support from the university and contribution from external foundations and(Host institution：National University Corporation Tokyo Institute of Technology Center name：Earth-Life Science Institute (ELSI)）

4enterprises.
We are therefore highly motivated to make every effort to promote public relations activities within
ELSI. The Center Director will reach out to the general public at every opportunity, both in Japan andabroad. Several principal researchers are serving as chairs for their relevant academic societies. Theirinternational networks will also be helpful.
Actual public relations activities will be carried out by a group of dedicated science communicators.
First of all, they will proactively share the results of research projects at ELSI. In addition to events
surrounding specific publications of broader interest, they will periodically organize press conferences withgeneral writers, journalists, and science writers. They will also hold regular seminars for the general public
and summer intern programs for high school students. Fortunately, outreach activities are poised to be
successful already by the very nature of ELSI, since questions like the origin of life, and life on otherplanets, are sure to grab the attention of the public. For example, the return of “Hayabusa” received great
attention in Japan, while books and movies related to astrobiology, planets beyond the solar system, thecenter of the Earth, and snowball Earth have been released. Thanks to those, some of the main key words
related to research at ELSI are already widely recognized.
In addition, we will make connections between the public relations activities of ELSI and those at
Tokyo Tech. This will also increase awareness of Tokyo Tech itself as a top-level university within Japan.
Currently, the general public in the U.S. has a much greater awareness of the existence and excellence of
MIT or CalTech, compared with the awareness in Japan towards Tokyo Tech. It is high time to change thatlack of awareness within Japan, as well as from outside Japan. This will be one important way in which
ELSI can perform an essential service for its hosting university, Tokyo Tech. For this reason, theuniversity’s Public Relations Division needs to be strengthened.

(Host institution：National University Corporation Tokyo Institute of Technology Center name：Earth-Life Science Institute (ELSI)）

5

Host Institution’s Commitment (in English)
Date 21 February, 2017

To MEXTName of host institution: Tokyo Institute of Technology,
Name and title of head of host institution: Yoshinao Mishima, President
Signature
I confirm that the measures listed below will be taken faithfully regarding “Earth-Life Science
Institute (ELSI)” adopted under the World Premier International Research Center Initiative.

<Provision in host institution’s mid-to-long-term plan>・Describe clearly the host institution’s mid-to-long-term strategy plan and how the center is positioned within that strategy.

Tokyo Institute of Technology (hereinafter Tokyo Tech) laid out its new goal of becoming one of theworld’s top 10 research universities by 2030 – a year shy of the university’s 150th anniversary – andreformulation of its educational and research systems has since progressed. Our primary research
objectives are:(1) Strengthen the research management system to press on with internationally competitive research(2) Establish flexible research organizations which constantly develop and conform to the expectations ofsociety, while generating research findings with the aim of examining scientific principles andsystemizing knowledge, contributing to industry and creating next-generation industry sectors, andsolving problems in terms of sustainable development(3) Allocate and operate the university’s resources efficiently, and improve the environment to enhancecomprehensive research strengths
Our 2nd mid-term objectives and plans clearly state:<Mid-term objectives>(1) Objectives regarding research standards and findings
I-2-2. develop values created at Tokyo Tech, aim to apply them to society and actively open up new andinterdisciplinary fields.
<Mid-term plans>(1) Measures to achieve objectives regarding research standards and findings[25-2] At the Earth-Life Science Institute, a globally competitive research center focused on the study ofearly Earth, promote research which aims to elucidate the origin and evolution of the Earth and life andto focus on reforming its organization.
Similarly, our 3rd mid-term objectives and plans starting from fiscal year 2016 clearly state:<Mid-term objectives>(1) Objectives regarding research standards and findings
I-2-2. In order to attract both internal and external researchers to lead in innovative science andtechnology, develop knowledge created at Tokyo Tech and actively open up new and interdisciplinary
fields.
<Mid-term plans>(1) Measures to achieve objectives regarding research standards and findings[15] At the Earth-Life Science Institute, a globally competitive research center focused on the study ofearly Earth, utilize the university president’s discretionary resources and other funding to promoteresearch which aims to elucidate the origin and evolution of Earth and life.

The mid-term objectives and plans cite that Tokyo Tech positions the Earth-Life Science Institute as “ahighly strategic and ambitious objective and plan”.

<Concrete Measures>・Describe the concrete measures that the host institution will take to satisfy the following requirements.

(1) How it will support the center’s need to secure resources that match or exceed the
project grant through such means as competitive grants obtained by researchers
participating in the project, in-kind contributions and other forms of assistance by thehost institution (including partial payment of salaries, provision of research space),
and/or external donations.
Tokyo Tech will support ELSI’s need to secure resources as follows:- About 90 million yen per year from president’s discretionary budget will be provided to ELSI as theoperating cost of WPI program. Space charge for the president’s discretionary research space will be
partly exempt.
- 6 tenure-professors were transferred to ELSI. Tenured professors were exempt from educational duties
for undergraduates, and Tokyo Tech provided 3 substitute researchers. Two administrative staff
members were also assigned at no cost to ELSI. Tokyo Tech will continuously provide such necessary
support.
- Tokyo Tech assured approximately 2,670 m2 of research space in an existing building for ELSI-2 andadditionally a new research building (ELSI-1: 5,000m2) was completed in FY2015 to become an
appropriate research environment.
- Tokyo Tech research administration center, research promotion department and international affairs
department provide extensive guidance to foreign members of ELSI to be competitive in attracting
external grants. Tokyo Tech offers financial support for submission and publication charges ininternational academic magazines and journals, Kakenhi coaching seminars in English, and advice andpractice for interviews. In order to attract more grants from an overseas foundation, Tokyo Tech isapplying for non-profit incorporation overseas.
(2) How it will institute a system under which the center’s director is able to makesubstantive personnel and budget allocation decisions necessary to implementing thecenter project—a system, which in practice, allows the center director autonomy inmaking decisions regarding the center’s operation.
- ELSI will be established as an independent research organization directly under the jurisdiction ofTokyo Tech president and encouraged to establish a more flexible research system than conventional
operational systems. Tokyo Tech regards ELSI as a pioneer to reform research organization and to
improve its recognition internationally, which leads to attracting more researchers from abroad. The
director of ELSI has the authority to make all decisions related to the center, including personnel affairs(excluding hiring and firing of the center director him/herself) and execution of the budget. The director
therefore manages ELSI’s organizational reform, international recruitment of scientists, and ELSI’sbudget and director’s discretionary funds. The center director will evaluate both researchers andadministrative staff members, and can provide them with extra incentives based on their performance.
(3) The support it will provide to the center director in coordinating with other departments
within the host institution when recruiting researchers for the center, while giving
reasonable regard to the educational and research activities of those departments.
- Tokyo Tech will make arrangements directly with those departments that provide researchers
belonging to ELSI, to ensure that those researchers will have unusual amounts of time and freedom toconcentrate on their research, for example by appointing substitute professors for educational activities.
- Tenured professors were exempt from bachelors-level education, so Tokyo Tech assigned 3 substituteresearchers to the department to meet the educational needs. This enables more researchers from otherdepartments to get involved in research activities at ELSI.
(4) Its flexibility in applying, revising, or supplementing the host institution’s internal
systems as needed for the center to effectively implement new management methods(e.g., English-language environment, merit-based pay, top-down decision making)（Host institution：Tokyo Institute of Technology

2

Title of Center Project：Earth-Life Science Institute）

unfettered by conventional modes of operation.
- Tokyo Tech has enacted an agreement on the merit-based salary of fixed-term employees at ELSI sothat they are paid according to their performance and abilities. We also reformed the system thatprovides extra financial incentives for researchers and administrative staff members in recognition of
their proven abilities and performance.
- We have introduced a cross-appointment system to recruit top level researchers and to promoteresearch.
- We have organized a support system in English for foreign researchers. To facilitate their prompt
settlement and research activities in Japan, we have secured 20 guest rooms at the international houseon campus and provide foreign researchers with support to help them adapt to life in Japan. For
example, immigration, registration and opening bank accounts for international researchers. We alsooffer Japanese language classes so that they can acquire conversational skills for living.
- Tokyo Tech president, vice presidents for research, general and financial affairs and the ELSI director
have a monthly meeting so that Tokyo Tech can take necessary measures in flexible ways, leaving room
for revisions and additions of campus rules relating to ELSI’s smooth organization.
(5) Its accommodation of the center’s infrastructural requirements (for facilities, e.g.,laboratory space; equipment; land, etc.).
- In order to create an environment where researchers from different fields communicate andcollaborate on a daily basis, Tokyo Tech assured approximately 2,670 m2 of research space in anexisting building for ELSI-2 and additionally provided another research building (ELSI-1: 5,000m2), which
was completed in FY2015.
- 20 rooms of our on-campus accommodation, the international house, will be reserved for preferential
occupancy by ELSI’s foreign researchers.
- The Ookayama Campus of Tokyo Tech, housing ELSI, is located near a train station about 30-minutes
away from the center of Tokyo. It has a number of large and small conference halls that can hold aninternational symposium, a main hall, a library, and a restaurant. Therefore, the campus is suited formeetings of world-leading researchers. We will provide support for preferential usage of such common
spaces.
- We are prepared to organize space on its campus and to provide more space depending on additional
growth of ELSI.
(6) How it will support to sustain the center as a world premier international research
center after the WPI-grant period ends.
- Tokyo Tech will position ELSI as a special research district even after the WPI-grant period ends, andwill continuously provide support, so that ELSI remains the world premier international research center
permanently. We promise 10 full-time equivalent PIs (of which 6 are tenured) and necessary support
staff, in addition to president’s discretionary expenses (JPY 90 million per year) and research space.
- We will provide an adequate environment for research, graduate educational opportunities to nurture
young scientists, interdisciplinary collaboration with top-level scientists and enough support for overseas
researchers.
- Based on the success in acquiring a large grant from John Templeton foundation in the U.S., we areapplying for non-profit incorporation overseas in order to attract more global funds. Tokyo Tech willcontinuously aid ELSI in obtaining continuous support from outside of Tokyo Tech, in terms ofcompetitive funds and contribution from foundations and enterprises.
-We will provide enough support to sustain ELSI as a world premier international research center, as
stated in our 3rd mid-term plans: “At the Earth-Life Science Institute, a globally competitive research
center focused on the study of early Earth, utilize the university president’s discretionary resources andother funding to promote research which aims to elucidate the origin and evolution of Earth and life.”(7) Other types of assistance it will provide to give maximum support to the center inachieving its concepts and objectives and becoming a world premier international
research center in both name and deed.
- It is beneficial for ELSI’s world-class researchers to supervise graduate students and to nurture next
generation researchers, so Tokyo Tech will support to establish ELSI’s unique international educational（Host institution：Tokyo Institute of Technology

3

Title of Center Project：Earth-Life Science Institute）

system.
- In order to develop ELSI into a truly global research institute, it is very important to publicize theactivities of ELSI both inside and outside of Japan, in order to highlight its presence. From such a
viewpoint, ELSI’s PR activities will be integrated with the PR activities of Tokyo Tech to effectively
advertise the research activities and results together.
- Utilizing ELSI’s successful know-hows, Tokyo Tech led World Research Hub Initiative (WRHI) andlaunched Institutes of Innovative Research (IIR) aiming to create new research fields and nextgeneration industry. This enables to invite world-class researchers in order to broaden international
networks and to activate international collaboration conducted by the students and researchers. Tokyo
Tech aims to become a global S&E research hub to attract academic knowledge and human resources,
and ultimately achieve “true internationalization”.

（Host institution：Tokyo Institute of Technology

4

Title of Center Project：Earth-Life Science Institute）

（Appendix）(in English)

List of Principal Investigators
・If the number of principal investigators exceeds 10, add columns as appropriate.
・Place an asterisk(*) by the name of the investigators who are considered to be ranked among the world’s top researchers.
・Give age as of 1 April 2017.
・For investigators who cannot participate in the center project from 1 April 2017, indicate the time that their participation will start in the“Notes” column.

Name

1

Kei
HIROSE*

2

Shigenori
MARUYAMA*

3

Shigeru
IDA*

4

Piet
HUT*

5

NaohiroYOSHIDA*

6

TetsuoIRIFUNE*

7

Joseph Lynn
KIRSCHVINK*

Age

49

67

56

Current affiliation(organization, department
and specialties)

Tokyo Institute ofTechnology,
Earth-Life Science
InstituteTokyo Institute ofTechnology,
Earth-Life Science
InstituteTokyo Institute ofTechnology,
Earth-Life Science
Institute

Academic
degreePh.D.
High-pressure
Geoscience
Ph.D.
Geology, Tectonics,
History of Life andthe Earth

Ph.D.
Planetary
Sciences,
Planetary Physics.

64

Institute for Advanced Study,
Princeton, Program ofInterdisciplinary Studies.
Tokyo Institute of Technology,
Earth-Life Science Institute

Ph.D.
Theoretical
Astrophysics,
Interdisciplinary
Studies

62

Tokyo Institute ofTechnology,
Department of Chemical
Science and Engineering

Doctor of Science
Environmental
Chemistry, Global
Change Analysis

62

Ehime University
Geodynamics ResearchCenter63

Ph.D.
California Institute of Technology,
Division of Geological and Planetary Geobiology,
Sciences.
Paleomagnetism,
Tokyo Insitute of Technology,
Biophysics,
Earth-Life Science Institute
Neurobiology

Ph.D.
High-pressure
geosciences,
Materials sciences

8

John HERNLUND

44

Tokyo Institute ofTechnology,
Earth-Life Science
Institute

9

Jack W. Szostak*64

Harvard Medical School Molecular biology

10

George HELFFRICH

64

11

Eric SMITH

51

12

Irena MAMAJANOV

41

13

14

15

Yuichiro UENO

Shawn McGLYNN

Ryuhei NAKAMURA

42

33

40

Tokyo Institute ofTechnology,
Earth-Life Science
InstituteTokyo Institute ofTechnology,
Earth-Life Science
InstituteTokyo Institute ofTechnology,
Earth-Life Science
InstituteTokyo Institute ofTechnology,
School of Science,
Department of Earthand Planetary Sciences
Tokyo Institute ofTechnology,
Earth-Life Science
InstituteTokyo Institute ofTechnology,
Earth-Life Science
Institute

Notes

Ph.D.
Geophysical Modeling,
Fluid and Solid
Dynamics

Ph.D.

Synthetic biology

Ph.D.,
Geological
Sciences
Ph.D.
Aerospace
Engineering
Electric Propulsion

Ph.D.,
PhysicalChemistry
Doctor of
Science.,
Biogeochemistry
Ph.D.,
Evolutionary
biology,
Microbiology

Doctor of
Science,
Biofunctional
Catalyst Research（Tokyo Institute of Technology：

1

Earth-Life Science Institute：）