Life as No One Knows it

Mike's Notes

Astrobiologist Sara Imari Walker takes up complex and abiding questions in Life as No One Knows It: The Physics of Life’s Emergence.


Below is another wonderful article by Maria Popova republished from The Marginalian.

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Last Updated

17/05/2025

The Great Blind Spot of Science and the Art of Asking the Complex Question the Only Answer to Which Is Life

By: Maria Popova
The Marginalian: 4 November 2024

“Real isn’t how you are made… It’s a thing that happens to you,” says the Skin Horse — a stuffed toy brought to life by a child’s love — in The Velveteen Rabbit. Great children’s books are works of philosophy in disguise; this is a fundamental question: In a reality of matter, what makes life alive? A generation later, the Ukrainian Jewish writer Vasily Grossman answered with a deeply original proposition: that life is best defined as freedom, that freedom is the boundary between inanimate matter and animacy.

To me, freedom is the boundary condition where matter reaches for meaning — life, after all, is the only component of the universe free to comprehend the rest. And yet all of our technologies of thought have so far failed to discern what life actually is, how it emerged from non-life, and what to look for when we are looking for it in our laboratories and in the great unfolding experiment that is the universe itself. We have sequenced the human genome and discovered the “God particle,” yet genetics and particle physics have found no common language for communicating and harmonizing their respective discoveries to address the complex question the single answer to which is life.

A century ago, the philosopher Simone Weil admonished against this fragmentation of the problem of reality into parochial questions addressed by disjointed scientific disciplines — “villages” of thought, she called them — each too blinded by its own axioms to make headway on illuminating the whole. “The villagers seldom leave the village,” she wrote. Watching her mathematician brother — the number theory pioneer André Weil — try to reduce the problem of reality to his own science, watching the founding fathers of quantum mechanics do the same, she lamented: “The state of science at a given moment is nothing else but… the average opinion of the village of scientists [who] affirm what they believe they ought to affirm.”

An epoch later, the villages have drifted so far apart as to grow foreign to each other. Gravitational waves, radioactivity, and DNA belong to the same reality — the reality that made life possible — and yet cosmology, chemistry, and biology are too mute to each other to make sense of the deeper meaning behind their respective discoveries. We are still left wondering how reality happens unto life and how life becomes reality.

Astrobiologist Sara Imari Walker takes up these complex and abiding questions in Life as No One Knows It: The Physics of Life’s Emergence (public library).

Trained as a theoretical physicist and disenchanted with her discipline’s insistence that life is a conceptually banal scientific problem subservient to the fundamentals of space, time, energy, and matter, she holds modern physics accountable for providing “a fundamental description of a universe devoid of life” — that is, a description of the universe that negates the very existence of its describers, we who are very much alive. She writes:

We cannot see ourselves clearly because we have not built a theory of physics yet that treats observers as inside the universe they are describing.

In this quest to understand ourselves and the universe that made us, she argues, the vitalists of the eighteenth century — who believed that a concrete non-physical element, a “vital spark,” grants life its aliveness — were no more misguided than the modern materialists who believe that life — that poetry, that whale song, that love — is just a property of physical matter. Reckoning with a colleague’s startling remark that “life does not exist,” she considers the deeper logic beneath this koan-like formulation of the great scientific blind spot of our time:

What modern science has taught us is that life is not a property of matter… There is no magic transition point where a molecule or collection of molecules is suddenly “living.” Life is the vaporware of chemistry: a property so obvious in our day-to-day experience — that we are living — is nonexistent when you look at our parts. If life is not a property of matter, and material things are what exist, then life does not exist.

(And of course, none of it had to exist at all. Life seems to be the imperative of the unnecessary. Long before modern physics, Darwin marveled at how, on this planet shaped by unfeeling forces and moved by fixed laws, “from so simple a beginning endless forms most beautiful and most wonderful have been and are being evolved.” Here was a biologist trained as a geologist shining a sidewise gleam on a cosmological question — a rare vagabond between the villages of science, from a time before they had become separate continents of thought.)

At the heart of the book is the rigorous, passionate insistence that we need a softer and more elastic explanatory membrane between the three hard problems of reality: the hard problem of consciousness (rooted in the mystery of qualia, that inarticulable essence of what it feels like to be oneself, the felt interiority of being alive in a particular embodiment and enmindment), the hard problem of matter (the fact that everything observable arises from the interaction of particles and forces), and the hard problem of life (sculpted of information and an observer of information). Sara writes:

Cast in this way, all three hard problems become one more fundamental problem we cannot seem to avoid any more than we can seem to answer it: Why do some things exist (or experience existence) and not others? It is perhaps the most perplexing question of our existence that anything should exist at all. And if something exists, then why not everything?

By contracting the pinhole of our scrutiny to the question of life, she intimates, we might be able to begin extrapolating an answer to this largest of questions — something that calls not only for new principles but for a new theory of physics and a dismantling of disciplinary boundaries. A century after Weil, Sara points to the same paradox standing between the life of science and the science of life in our own time:

We don’t yet have a general understanding of the category of things that we should group together and call “life.” Therefore either our categorization is wrong or life is not something to be categorized.

[…]

We cannot always see this clearly because of the arbitrary boundaries we set between the current classification of disciplines we think are needed to solve the problem, which are based on paradigms not suited for solving what life is.

Observing that “the boundary between the phenomena we want to think of as life and not life is fuzzy at best and may not exist at all,” she considers the present state of our disciplinary parochialism:

Biologists approach the problem by defining life in terms of observed features of life on Earth, which is not especially useful when you’re looking for life’s origins or for life elsewhere in the universe. Astrobiologists need guiding principles to inform how they conduct their search, but they, too, end up being overly anthropocentric in their reasoning: their search is most often directed at signs of life that would indicate biology exactly as we observe it here on Earth. Chemists either think life does not exist or that it is all chemistry (probably these are equivalent views). Computer scientists tend to focus too much on the software — the information processing and replicative abilities of life — and not enough on the hardware, i.e., the fact that life is a physical system that emerges from chemistry, and that the properties of chemistry literally matter. Physicists tend to focus too much on the physical — life is about thermodynamics and flows of energy and matter — and miss the informational and evolutionary aspects that seem to be the most distinctive features of the things we want to call life. Philosophers focus too much on the need for a definition or the flaws of providing one, and not enough on how we can move as a community beyond the definitional phase into a new paradigm.

Nature does not share these boundaries between disciplines. They are artifacts of our human conception of nature, our need to classify things, and historical contingencies in how our understanding of the reality around us has evolved over the last few centuries. That is, they are the product of paradigms established in the past. We are in part pre-paradigmatic in understanding life as a general phenomenon in the universe because there is no defined discipline that can fully accommodate the intellectual discussion that needs to be had about what life is.

The solution to the unsolved problem of life, she argues, may not be one of new evidence but one of new explanation, just as we watched the planets move for eons before we discerned the laws of their motion to concede a heliocentric universe. Without a clear explanatory model for life here on Earth, she argues, we might never be able to detect life on other worlds — the central task of her own science. With an eye to how the new science of plant intelligence deepens the mystery of what a mind is, Sara considers what kindred blind spots may be afflicting astrobiology:

Plants are just one example that makes clear how the boundary of our imagination does not even intersect with what it is to be among the other multicellular life that surrounds us on this planet.

If we cannot even shift our reference frame enough to understand what it is like to be other inhabitants of our own planet, how could we possibly imagine the truly alien? “Truly alien” here should be understood as other life that does not share any ancestry with our own: that is, that has an entirely unique history with an independent origin. There are no aliens on Earth because as far as we know, all the life we have encountered shares a common history. Even artificial intelligences — sometimes described as alien, are not alien; they are trained on human data, which is itself the product of nearly four billion years of evolution on Earth. AI is as much a part of life on Earth as any of the biological organisms that have evolved here.

A century and a half after the Victorian visionary Samuel Butler presaged the emergence of a new “mechanical kingdom” extending the kingdoms of biological life into our machines, Sara argues that our mechanical and algorithmic creations may not only alter the definition of life but help illuminate its origins:

The emergence of a technosphere may be precisely what is required for a biosphere to solve its own origins and therefore to discover others like it. To make this transition and make first contact, it may be critical to where we sit now in time that we recognize how thinking technologies are the next major transition in the planetary evolution of life on Earth. It is what we might expect as societies scale up and become more complex, just as life simpler than us has done in the past. The functional capabilities of a society have their deepest roots in ancient life, a lineage of information that propagates through physical materials. Just as a cell might evolve along a specific lineage into a multicellular structure (something that’s not inevitable but has happened independently on Earth at least twenty-five times), the emergence of artificial intelligences and planetary-scale data and computation can be seen as an evolutionary progression — a biosphere becoming a technosphere.

“Wherever life can grow, it will. It will sprout out, and do the best it can,” Gwendolyn Brooks wrote in one of her finest, least known poems. A proper understanding of life, Sara argues, must account for that fact — for the tenacity with which life not only continues to exist despite the infinitely greater odds of nonexistence (which anchored Richard Dawkins’s wonderful counterintuitive insistence on the luckiness of death) but continues to exist in its particularity despite the infinitely many other possible configurations. She writes:

If we are ever to understand what life really is, we need to recognize that among the unimaginably large number of things that could exist, or even the smaller subset of ones that we can imagine, only an infinitesimal fraction ever will. Things come into existence when and where it is possible to — and what we call life is the mechanism for making specific things possible when the possibility space is too large for the universe to ever explore all of it.

Out of this arises a crucial distinction between life and being alive (highlighted in the biological fact that most of you is dead). Nearly a century after cybernetics pioneer Norbert Wiener made the then-radical assertion that “we are not stuff that abides, but patterns that perpetuate themselves,” Sara adds:

DNA cannot exist unless there is a physical system (e.g., a cell) with memory of the steps to assemble it. All objects that require information to specify their existence constitute “life.” Life is the high-dimensional combinatorial space of what is possible for our universe to build that can be selected to exist as finite, distinguishable physical objects. Being “alive,” by contrast, is the trajectories traced through that possibility space. The objects that life is made of and that it constructs exist along causal chains extended in time; these lineages of information propagating through matter are what it is to be “alive.” Lineages can assemble individual objects, like a computer, a cup, a cellular membrane, or you in this very instant, but it is the temporally extended structure that is alive. Even over your lifetime you are alive because you are constantly reconstructing yourself — what persists is the informational pattern over time, not the matter.

[…]

The fundamental unit of life is not the cell, nor the individual, but the lineage of information propagating across space and time. The branching pattern at the tips of this structure is what is alive now, and it is what is constructing the future on this planet.

In the remainder of Life as No One Knows It, Sara goes on to explore assembly theory — a new framework for understanding the complexity of living organisms by discerning the minimal number of steps required to assemble them from the most fundamental building blocks — as a possible solution to the abiding problem of what we are. Complement it with pioneering biologist Ernest Everett Just — one of the first scientists to consider this question holistically — on what makes life alive, then revisit Meghan O’Gieblyn on our search for meaning in the age of AI and Alan Turing’s favorite boyhood book about the strange science of how alive you really are.

Ontohub

Mike's Notes

I read the article, partially republished below from Applied Ontology, which had a link to Ontohub, a repository of Ontologies. It could be helpful.

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17/05/2025

The role of ontologies in Linked Data, Big Data and Semantic Web applications

By: Mike Bennett and Kenneth Baclawski
Applied Ontology: 20/09/2017

Abstract

Since the beginnings of the Semantic Web, ontologies have played key roles in the design and deployment of new semantic technologies. Yet over the years, the level of collaboration between the Semantic Web and Applied Ontology communities has been much less than expected. Within Big Data applications, ontologies appear to have had little impact. These communities, along with the Linked Data community, all share the need for a common semantic understanding and a formal representation of the domains being studied, but they have taken very different approaches to deal with the challenges of large scale applications and linking of vast heterogeneous data. Because of this situation, the Ontology Summit 2014 focused on building bridges between these four communities. It was felt that identifying and overcoming ontology engineering bottlenecks is critical for all of these communities. This special issue is an effort to continue the process that began in 2014. The papers in this issue are concerned with the various aspects of the barriers identified at the Ontology Summit, and propose approaches for addressing them.

The Semantic Web and Linked Data communities acknowledge the role that ontologies play in designing and employing their respective technologies. Yet, collaboration between these communities and the Applied Ontology community has been much less than expected. A more striking situation is that ontologies appear to have had little impact in Big Data applications, in spite of the clear need for better understanding of the meaning of the data and the results of data mining. In an attempt to address these concerns, the Ontology Summit 2014 focused on building bridges between the Semantic Web, Linked Data, Big Data, and Applied Ontology communities. While these communities all share the need for a common semantic understanding and a formal representation of the domains being studied, they have taken very different approaches to deal with the challenges of large scale applications and linking of vast heterogeneous data. The Ontology Summit 2014 brought together representatives from all of these communities to better understand the barriers and challenges that hinder the use and reuse of ontologies by the Semantic Web, Linked Data and Big Data communities. Figure 1 is a graphic depiction of the main barriers and challenges that were identified at the summit, expressed as gaps between and among the approaches used in these communities. The summit sponsored a wide variety of events, including a four-month online discussion forum, four conference tracks, six hackathons, an online community library and an ontology repository. The summit culminated in a two-day symposium, and issued a communiqué that summarized the results of the summit (Obrst et al., 2014). ..."

Complete list of repository clone-urls

git://ontohub.org/additive-manufacturing.git
git://ontohub.org/adhoc.git
git://ontohub.org/algebrablending.git
git://ontohub.org/ali_85595.git
git://ontohub.org/amalgams-music.git
git://ontohub.org/amalgams-owl-examples.git
git://ontohub.org/appliedontologyontohubpaper.git
git://ontohub.org/automation-i4-0-ontology.git
git://ontohub.org/baall.git
git://ontohub.org/baco.git
git://ontohub.org/bfo.git
git://ontohub.org/bioportal.git
git://ontohub.org/bioportal_mappings.git
git://ontohub.org/boc2016.git
git://ontohub.org/boc2017.git
git://ontohub.org/boc-2017.git
git://ontohub.org/boc2018.git
git://ontohub.org/boc2019.git
git://ontohub.org/boc2020.git
git://ontohub.org/boc2022.git
git://ontohub.org/botanic-data-set.git
git://ontohub.org/built-heritage-ontology.git
git://ontohub.org/cadence.git
git://ontohub.org/cadencextrm.git
git://ontohub.org/canis-care.git
git://ontohub.org/casl.git
git://ontohub.org/casl-basic-libraries.git
git://ontohub.org/character-computing.git
git://ontohub.org/character-computing-ontology.git
git://ontohub.org/cl-structural-ontology.git
git://ontohub.org/cluj-parking.git
git://ontohub.org/coinvent_meeting.git
git://ontohub.org/coinventtechrepo.git
git://ontohub.org/colore.git
git://ontohub.org/colore4.git
git://ontohub.org/colore-oor-net.git
git://ontohub.org/colore-sample.git
git://ontohub.org/complex-blend.git
git://ontohub.org/computational-creativity.git
git://ontohub.org/conceptportal.git
git://ontohub.org/cost_function.git
git://ontohub.org/dan-examples.git
git://ontohub.org/daniel-worthing-examples.git
git://ontohub.org/danny-maths-examples.git
git://ontohub.org/dataminingproject.git
git://ontohub.org/defence-ontology.git
git://ontohub.org/demf.git
git://ontohub.org/dni.git
git://ontohub.org/documentary-work-for-music.git
git://ontohub.org/dol-examples.git
git://ontohub.org/dol-testing.git
git://ontohub.org/dota-2-ontology.git
git://ontohub.org/dronetology.git
git://ontohub.org/eispatternsontology.git
git://ontohub.org/emmo.git
git://ontohub.org/enterprise-architecture-ontology.git
git://ontohub.org/esslli_2016.git
git://ontohub.org/esslli-2016.git
git://ontohub.org/event-ontology.git
git://ontohub.org/example_rep.git
git://ontohub.org/external.git
git://ontohub.org/festival-ontology-kbs.git
git://ontohub.org/film_2017.git
git://ontohub.org/fixture-design-ontologies.git
git://ontohub.org/fois2016.git
git://ontohub.org/fois2016_ontology_comp.git
git://ontohub.org/fois-ontology-competition.git
git://ontohub.org/food-sustainability-ontology.git
git://ontohub.org/forver.git
git://ontohub.org/foustexperiments.git
git://ontohub.org/front-end-frameworks-comparative.git
git://ontohub.org/gfo-bio.git
git://ontohub.org/gfo-bio-owl.git
git://ontohub.org/godp.git
git://ontohub.org/goodrelations-axioms-v1.git
git://ontohub.org/harry-potter-game-ontology.git
git://ontohub.org/hets-lib.git
git://ontohub.org/hmfaheem.git
git://ontohub.org/horont.git
git://ontohub.org/houseboat.git
git://ontohub.org/hugo-rt.git
git://ontohub.org/iaonto.git
git://ontohub.org/imageschemafamily.git
git://ontohub.org/iswc2014.git
git://ontohub.org/jurisjfes.git
git://ontohub.org/katona-aron-repository.git
git://ontohub.org/kbs.git
git://ontohub.org/kbs_lab.git
git://ontohub.org/lacl.git
git://ontohub.org/lemma-examples.git
git://ontohub.org/linkedun.git
git://ontohub.org/literature_ontologies.git
git://ontohub.org/lok-project.git
git://ontohub.org/loubna.git
git://ontohub.org/maria-testing.git
git://ontohub.org/math.git
git://ontohub.org/mereotopology.git
git://ontohub.org/meta.git
git://ontohub.org/mie1510_liutuocheng.git
git://ontohub.org/mnolte2.git
git://ontohub.org/mobivoc.git
git://ontohub.org/monster-blend.git
git://ontohub.org/neem-godps.git
git://ontohub.org/ocd-ontology.git
git://ontohub.org/ontnetgroup.git
git://ontohub.org/ontocloud.git
git://ontohub.org/ontohubaopaperexamples.git
git://ontohub.org/ontologie-aufgabe.git
git://ontohub.org/ontologies-geobia.git
git://ontohub.org/ontologybuildingcompetition.git
git://ontohub.org/ontology-for-the-humanities.git
git://ontohub.org/ontologylaw.git
git://ontohub.org/ontology-of-data-anonymization.git
git://ontohub.org/ontology-of-units-of-measure.git
git://ontohub.org/ontology-summit-2014.git
git://ontohub.org/ontorepo_cc_transportation.git
git://ontohub.org/owo-open-world-ontology.git
git://ontohub.org/pblontology.git
git://ontohub.org/pegaso.git
git://ontohub.org/perfectcadence7.git
git://ontohub.org/pizza.git
git://ontohub.org/productontologies.git
git://ontohub.org/product-ontology.git
git://ontohub.org/pronto-redefinition-ema.git
git://ontohub.org/rgr.git
git://ontohub.org/robot2019.git
git://ontohub.org/romulus.git
git://ontohub.org/romuluspublic.git
git://ontohub.org/sandbox.git
git://ontohub.org/sandbox2.git
git://ontohub.org/saref.git
git://ontohub.org/saref_li.git
git://ontohub.org/sbc-repo.git
git://ontohub.org/scheduling-ontology-network.git
git://ontohub.org/secure-development-ontology.git
git://ontohub.org/secure-development-ontology-sdo.git
git://ontohub.org/semtech2017.git
git://ontohub.org/socop.git
git://ontohub.org/socudo-scaclo.git
git://ontohub.org/spaceportal.git
git://ontohub.org/sparqlpresentationfiles.git
git://ontohub.org/spatiotemporal_ontology.git
git://ontohub.org/sports.git
git://ontohub.org/ssh_test.git
git://ontohub.org/ssn-axioms.git
git://ontohub.org/ssw24.git
git://ontohub.org/ssw601.git
git://ontohub.org/sweet.git
git://ontohub.org/syrian-cinema-ontology.git
git://ontohub.org/testabc.git
git://ontohub.org/test_blending.git
git://ontohub.org/test_dol_bunny.git
git://ontohub.org/testejaqueline.git
git://ontohub.org/test-ifc.git
git://ontohub.org/tones.git
git://ontohub.org/tptprepository.git
git://ontohub.org/tqc-competency-questions.git
git://ontohub.org/travel-ontology.git
git://ontohub.org/turism.git
git://ontohub.org/uniprov.git
git://ontohub.org/uniprov-provenance-management.git
git://ontohub.org/veronto.git
git://ontohub.org/vpp-artss.git
git://ontohub.org/yoneda-path.git

IAOA Series

Mike's Notes

The International Association for Ontology and its Applications (IAOA) has useful resources.

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Last Updated

18/04/2025

CEUR Workshop Proceedings: IAOA Series

By: 
IAOA: 

The CEUR Workshop Proceedings: IAOA Series includes proceedings of events organized by the IAOA, or organised and edited by some of its members and endorsed by the IAOA. The IAOA series provides an overview of the research activities carried out by members of the association, and covers especially new and emergent topics.

The CEUR IAOA Series was established in 2018, with the proceedings of that year’s edition of the Joint Ontology Workshops (JOWO) as its first volume. Additionally, certain CEUR volumes, meeting the inclusion criteria and published before series establishment, have been retrospectively associated with the Series. These can also be found on the series home page."

Volumes of the IAOA Series at CEUR-WS.org

  • Vol-3833 Data meets Ontologies in Explainable AI 2024.
  • Vol-3824 Linked Data in Architecture and Construction 2024.
  • Vol-3821 Value Modelling and Business Ontologies 2024.
  • Vol-3805 International Conference on Biomedical Ontologies 2022.
  • Vol-3637 The Joint Ontology Workshops 2023.
  • Vol-3633 Linked Data in Architecture and Construction 2023.
  • Vol-3603 International Conference on Biomedical Ontologies 2023.
  • Vol-3595 Ontologies for Autonomous Robotics 2023.
  • Vol-3564 Ontology Research in Brazil 2023.
  • Vol-3511 The Seventh Image Schema Day 2023.
  • Vol-3493 PLanning And onTology wOrkshop 2023.
  • Vol-3346 Ontology Research in Brazil 2022.
  • Vol-3256 Companion Proceedings of the 23rd International Conference on Knowledge Engineering and Knowledge Management 2022.
  • Vol-3249 The Joint Ontology Workshops 2022.
  • Vol-3240 Formal Ontologies meet Industry 2022.
  • Vol-3213 Linked Data in Architecture and Construction 2022.
  • Vol-3140 The Sixth Image Schema Day 2022.
  • Vol-3073 International Conference on Biomedical Ontologies 2021.
  • Vol-3081 Linked Data in Architecture and Construction 2021.
  • Vol-3050 Ontology Research in Brazil 2021.
  • Vol-2998 International Workshop on Data meets Applied Ontologies in Explainable AI 2021.
  • Vol-2969 The Joint Ontology Workshops 2021.
  • Vol-2728 Ontology Research in Brazil 2020.
  • Vol-2708 The Joint Ontology Workshops 2020.
  • Vol-2636 Linked Data in Architecture and Construction 2020.
  • Vol-2519 Ontology Research in Brazil 2019.
  • Vol-2518 The Joint Ontology Workshops 2019.
  • Vol-2389 Linked Data in Architecture and Construction 2019.
  • Vol-2347 TriCoLore 2018: Creativity - Cognition - Computation.
  • Vol-2205 The Joint Ontology Workshops 2018.

Volumes published at CEUR-WS.org by members of the IAOA prior to the installation of the IAOA Series include

  • Vol-2228 Ontology Research in Brazil 2018.
  • Vol-2160 Computational Creativity, Concept Invention, and General Intelligence 2017.
  • Vol-2159 Linked Data in Architecture and Construction 2018.
  • Vol-2071 Comprehensibility and Explanation in AI and ML 2017.
  • Vol-2050 The Joint Ontology Workshops 2017.
  • Vol-1908 Ontology Research in Brazil 2017.
  • Vol-1862 Ontology Research in Brazil 2016.
  • Vol-1767 Computational Creativity, Concept Invention, and General Intelligence 2017.
  • Vol-1692 Ontologies and Data in Life Sciences 2016.
  • Vol-1660 The Joint Ontology Workshops 2016.
  • Vol-1616 The Shape of Things 2015.
  • Vol-1517 The Joint Ontology Workshops 2015.
  • Vol-1442 Brazilian Ontology Research Seminar 2015.
  • Vol-1333 Formal Ontologies meet Industry 2014.
  • Vol-1301 Ontologies in Conceptual Modeling and Information Systems Engineering 2014.
  • Vol-1248 Workshop on Modular Ontologies 2014.
  • Vol-1081 Workshop on Modular Ontologies 2013.
  • Vol-1041 Ontology Research in Brazil 2013.
  • Vol-1007 The Shape of Things 2013.
  • Vol-938 Ontology Research in Brazil & Metamodels, Ontologies and Semantic Technologies 2012.
  • Vol-812 The Shape of Things 2011.
  • Vol-776 Ontology Research in Brazil & Metamodels, Ontologies and Semantic Technologies 2011.

Reimagining Life. Emergent Complexity from Non-Living to Living

Mike's Notes

This paper was listed in the weekly Complexity Digest of 09/12/2024. It's an excellent summary and overview of many scientists who have advocated for emergence. Pipi is based on these conclusions.

The summary tables presented here would be a good place to begin Ajabbi Research.

The author, Gordana Dodig-Crnkovic, is based in Sweden.


"Gordana Dodig-Crnković is Professor of Interaction Design at Chalmers University of Technology and Computer Science at Mälardalen University, Sweden. She holds Ph.D. degrees in Physics and Computer Science. Her research focuses on the relationships between computation, information, and cognition, including ethical and value aspects. She is a member of the editorial board of the Springer SAPERE series, World Scientific Series in Information Studies, and various journals. She is a member of the Karel Čapek Centre for Values in Science and Technology and a Board member of the International Society for Information Studies, IS4SI." - https://informatics.tuwien.ac.at/news/2608

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17/05/2025

Reimagining Life. Emergent Complexity from Non-Living to Living

By: Gordana Dodig-Crnkovic [1] [2]
Preprints.org: 25 November 2024

1 Department of Computer Science and Engineering, Chalmers University of Technology, Gothenburg;

gordana.dodig-crnkovic@chalmers.se

2 Division of Computer Science and Software Engineering, Mälardalen University, Västerås, Sweden

Abstract

The development of naturalistic approaches to complexity of life continues a lineage of thought from Prigogine’s thermodynamics to contemporary complexity science. The paper highlights the central themes of self-organization, emergence, and the interplay between physical, informational, and biological processes. Prigogine’s concept of dissipative structures and irreversibility provided a foundation for understanding complexity in physical systems, which later expanded into biology through Kauffman’s models of creativity and evolution. Margulis's endosymbiosis theory illuminate the cooperative dynamics underpinning life’s complexity, while Walker's work integrates thermodynamics and information theory to bridge the gap between chemistry and biology through multiscale interactions and adaptive dynamics. By synthesizing these perspectives, this article situates life as an emergent phenomenon shaped by interactions across scales, proposing a unified framework for understanding complexity in the natural world.

Keywords:

Origins of Life; Life and Complexity; Self-Organization; Dissipative Structures; Multiscale Interactions; Origins of Life; Biological Complexity

Subject:

Biology and Life Sciences - Ecology, Evolution, Behavior and Systematics

1. The Contributions of Ilya Prigogine

Ilya Prigogine demonstrated that open thermodynamic systems, particularly those far from equilibrium, exhibit remarkable properties such as pattern formation and the emergence of order from apparent disorder. His work delves into the concepts of time, complexity, and the transition from being to becoming, highlighting the critical role of uncertainty in scientific inquiry.

Order Out of Chaos: Man’s New Dialogue with Nature

In this seminal work, Prigogine and Isabelle Stengers challenge the deterministic view of classical science by illustrating how non-linear processes and instabilities can lead to new forms of order. The concept of dissipative structures—systems that self-organize far from equilibrium—underscores how interactions with the environment foster complexity and unpredictability (Prigogine & Stengers, 1984).

From Being to Becoming: Time and Complexity in the Physical Sciences

Prigogine redefines the nature of time by proposing irreversibility as a fundamental aspect of physical reality. This book critiques classical mechanics for its emphasis on reversibility and deterministic laws, introducing the arrow of time as an essential component linked to entropy (Prigogine, 1980).

The End of Certainty

Here, Prigogine challenges the classical deterministic framework by presenting a probabilistic view of reality. He explores the interplay of quantum mechanics, thermodynamics, and uncertainty, proposing that unpredictability is inherent to natural processes (Prigogine, 1997).

2. Ideas of Kauffman and Roli’s “A Third Transition in Science?”

Kauffman and Roli’s paper critiques classical physics’ limitations in describing the creative, evolving dynamics of living systems. They argue that classical paradigms, like Newtonian and quantum physics, rely on fixed phase spaces, which fail to account for the continuous emergence of novel biological possibilities. In contrast, living systems generate new constraints and phenomena that elude deterministic or mathematical models.

Prigogine and Kauffman/Roli share a vision of transcending deterministic frameworks. Prigogine’s focus is on the role of entropy, instability, and far-from-equilibrium dynamics in physical systems. Kauffman and Roli extend these principles to biological systems, emphasizing biospheres’ creativity and unpredictability.

Biological Dissipative Structures and Creativity

Prigogine introduced dissipative structures, systems operating far from equilibrium that maintain order by exchanging energy and information with their environment. Biological systems, from cells to ecosystems, embody these principles. They metabolize nutrients, regulate internal states, and adapt dynamically, driving evolution and diversification.

Kauffman and Roli expand this notion by highlighting biospheres’ capacity to construct new constraints and possibilities. They argue that the creative evolution of life continuously expands phase spaces, introducing forms and adaptations beyond deterministic frameworks.

3. Extending Complexity Science: Contributions from Other Key Researchers

Numerous researchers, including Brian Goodwin, Humberto Maturana, Jeremy England, Lynn Margulis, Terrence Deacon, Denis Noble and others, have contributed significant insights that complement the ideas of Prigogine and Kauffman/Roli. Their work affirms the role of complexity, emergence, and adaptability in understanding life, offering diverse perspectives that enrich the naturalistic approach to complexity.

Brian Goodwin

Brian Goodwin emphasized how patterns and structures in biology arise through self-organization rather than solely from genetic determinism. In his book How the Leopard Changed Its Spots (1994), Goodwin explores the role of intrinsic dynamical properties in creating biological forms, focusing on morphogenesis—the process by which organisms develop their shapes. He demonstrated how nonlinear interactions at the cellular and molecular levels could give rise to emergent patterns, such as the spots on a leopard or the spirals in flowers. Goodwin’s work challenges reductionist views by showing how developmental processes are shaped by internal dynamics, not just external selection pressures. His vision advocates a shift from gene-centric biology to a holistic understanding of emergent order in living systems.

Stuart Kauffman

Stuart Kauffman’s earlier works, including The Origins of Order (1993) and At Home in the Universe (1995), independently expanded on themes of emergence and creativity in biology. He introduced the concept of the “adjacent possible,” describing how biological systems continually expand their "space of possibilities" through creative evolution. Kauffman’s models of simple networks demonstrated how self-organized criticality—the tendency of systems to naturally evolve toward a critical state—underpins biological complexity. His work illustrates how ecosystems, genetic networks, and biochemical systems explore the adjacent possible, creating novel forms and behaviors that drive evolution. By emphasizing the interplay of order and chaos, Kauffman provided a framework for understanding how life’s complexity emerges through self-organization. He presents those ideas in the books “The Origins of Order: Self-Organization and Selection in Evolution” and “At Home in the Universe: The Search for Laws of Self-Organization and Complexity”, see Kauffman (1993, 1995, 2000, 2008).

Humberto Maturana and Francisco Varela

Humberto Maturana and Francisco Varela introduced the concept of autopoiesis, defining living systems as self-maintaining, self-producing entities. In their seminal work Autopoiesis and Cognition (1992), they explore how living organisms maintain their integrity through continuous self-regulation and interaction with their environment. Autopoiesis places circularity and autonomy at the heart of life’s definition, arguing that living systems are both products and producers of their environments. Their insights challenge reductionist approaches by focusing on the dynamic interplay between internal processes and external influences. This perspective aligns with complexity science’s emphasis on feedback loops and self-organization as key drivers of biological systems.

Jeremy England

Jeremy England proposed a thermodynamic explanation for life’s emergence, suggesting that systems exposed to energy flows naturally evolve toward greater complexity. His theory, detailed in Every Life Is on Fire (2018), argues that energy dissipation plays a central role in driving the self-organization of matter into living systems. England demonstrated that molecular systems subjected to sustained energy gradients, such as sunlight, tend to organize themselves in ways that optimize energy dissipation. This thermodynamic perspective bridges physics and biology, offering a unifying explanation for the transition from non-living to living systems. England’s work complements Prigogine’s ideas by emphasizing how physical principles govern the emergence of life’s complexity.

John Holland

John Holland developed the concept of complex adaptive systems (CAS), emphasizing how interactions between individual agents give rise to emergent, global behaviors. In Emergence: From Chaos to Order (1998), Holland explores how systems as diverse as ecosystems, economies, and neural networks exhibit adaptability and resilience through self-organization. His work provided a computational framework for studying emergence, particularly through genetic algorithms and agent-based models. Holland demonstrated that adaptability is a defining feature of complex systems, enabling them to evolve and coalesce into higher-order structures. His ideas have profoundly influenced fields ranging from biology to artificial intelligence, highlighting the universality of complexity science principles.

Simon Levin

Simon Levin’s research on the self-organization of ecosystems shows how individual behaviors aggregate to produce emergent ecological properties. In Fragile Dominion (1999), Levin examines how interactions between species, resources, and environmental conditions create complex, adaptive ecosystems. He highlights the delicate balance between stability and change, showing how ecosystems maintain resilience in the face of disturbances. Levin’s work underscores the importance of diversity and decentralized decision-making in ecological systems, aligning with complexity science’s focus on emergent order and collective behavior. His insights into the adaptive dynamics of ecosystems contribute to understanding life’s broader organizational principles.

Lynn Margulis

Margulis made groundbreaking contributions to the understanding of complexity and the origins of life through her endosymbiosis theory, which demonstrated that symbiotic relationships drive the evolution of complex life forms. According to her theory, eukaryotic cells, which contain nuclei, originated from a symbiotic merger between primitive prokaryotic organisms. This process emphasized how collaboration and integration, rather than competition alone, foster evolutionary innovation. Margulis’s work highlighted the significance of networks and interdependence in the emergence of biological complexity, positioning cooperation as a fundamental driver of life.

In her book with Dorian Sagan What is Life? (1995), Margulis explores the interconnectedness of life, arguing that living systems cannot be understood in isolation from their environments. The book bridges biology, philosophy, and complexity science, offering a holistic view of life as a cooperative and adaptive phenomenon. The authors emphasize how symbiosis, at all levels of biological organization, has been central to the emergence of life’s complexity.

Her contributions extended beyond the cellular level. She collaborated with James Lovelock on the Gaia hypothesis, which proposed that the Earth functions as a self-regulating system, with living organisms and their environments interacting to maintain conditions conducive to life. Margulis’s perspective challenged traditional Darwinian views by focusing on the cooperative dynamics that underpin evolution. This approach aligns closely with the principles of complexity science, particularly the role of interdependence and emergent order in shaping systems.

Her contributions extended beyond the cellular level. She collaborated with James Lovelock on the Gaia hypothesis, which proposed that the Earth functions as a self-regulating system, with living organisms and their environments interacting to maintain conditions conducive to life. Margulis’s perspective challenged traditional Darwinian views by focusing on the cooperative dynamics that underpin evolution. This approach aligns closely with the principles of complexity science, particularly the role of interdependence and emergent order in shaping systems.

Terrence Deacon

Terrence Deacon explored the emergence of life and consciousness, focusing on how self-organization and thermodynamic constraints lead to higher-order structures. In Incomplete Nature (2012), Deacon introduced the concept of teleodynamics, describing how goal-directed behavior emerges from interactions among physical and chemical systems. His work bridges the gap between non-living and living systems, proposing that life and mind arise through the interplay of self-organization and emergent constraints. Deacon argues that the dynamics of living systems are shaped by both intrinsic tendencies and external influences, creating a framework for understanding how complexity and purpose co-evolve. His contributions extend complexity science into the domains of cognition.

Denis Noble

Denis Noble challenged reductionist views of biology by advocating for a systems-level understanding of life. His books The Music of Life (2006) and Dance to the Tune of Life (2018) present a vision of biology where functions emerge from networks of interactions rather than being dictated by individual genes. Noble emphasizes the role of feedback loops and multilevel interactions in shaping biological processes, arguing that life’s complexity cannot be fully explained by linear causation. His perspective highlights the interconnectedness of physiological systems, positioning life as an emergent phenomenon shaped by both bottom-up and top-down dynamics. Noble’s ideas resonate with complexity science by emphasizing holism and adaptability in biological systems.

4. Sara Imari Walker: Integrating Information and Complexity

In this context the recent work of physicist Sara Imari Walker, active in complexity science, is of interest, particularly understanding biological systems and the origins of life. Walker’s work connects thermodynamics, information theory, and evolution to explain life’s emergence. She argues that life is characterized by the causal closure between informational and physical processes, which enables self-organization and adaptability.

The following are her contributions related to complexity science, and biological systems.

Information as a Key Driver of Biological Systems

Walker focuses on the role of information and computation in biological systems, suggesting that the emergence of life is fundamentally tied to the flow and organization of information. She proposes that biological systems are unique because they exhibit causal closure across informational and physical domains. Biological systems not only process information but use it to control and influence their physical environment. This feedback loop between information and physical processes is central to life’s complexity.

Origins of Life and Complexity

One of Walker’s key research areas is understanding how life originated from non-living matter. Her work integrates complexity science with thermodynamics and information theory to argue that the transition from chemistry to biology involves emergent properties that arise from the interaction of chemical and physical systems far from equilibrium with critical thresholds where the system begins to process and act on information in a life-like manner. Walker explores how prebiotic chemistry might self-organize into systems capable of storing and propagating information—a concept closely tied to Prigogine’s dissipative structures.

Life as a Computational Process

Walker suggests that life represents a new kind of complexity, where information processing plays a central role. She emphasizes the algorithmic nature of life, proposing that living systems can be understood as information-processing networks that adapt and evolve over time. This builds on complexity science by integrating computational principles with biological evolution, extending traditional thermodynamic models.

Emergent Causal Structures

Walker’s research highlights the importance of causal emergence in biological systems. In living systems, higher-level processes (e.g., cellular function) can shape lower-level dynamics (e.g., molecular interactions). This contrasts with reductionist views, where causation flows only from lower to higher levels. Her work aligns with complexity science by emphasizing the multilevel organization of living systems and the feedback between levels.

Walker’s Approach and Complexity Science

Walker’s research represents a clear application of complexity science principles to biological systems. Walker emphasizes emergence as central to understanding life. She explores how life’s properties—such as self-replication, metabolism, and evolution—emerge from the interaction of non-living chemical systems. This mirrors the broader goals of complexity science: understanding how higher-level behaviors arise from lower-level interactions. Nonlinearity is a core feature of the systems Walker studies, from the self-organization of prebiotic chemistry to the evolution of biological networks. These dynamics explain how small changes in molecular interactions can lead to major evolutionary innovations.

Information Theory

Walker integrates information theory with complexity science to argue that life’s complexity cannot be understood solely in terms of energy and matter; it also depends on the flow and organization of information. Her use of information theory complements the thermodynamic focus of figures like Prigogine, extending complexity science into new domains.

Multiscale Interactions

Complexity science often focuses on systems with interactions across multiple scales (e.g., atoms to cells to ecosystems). Walker’s work highlights how these interactions drive the emergence of life and its ability to process information.

Summary

As a way of summary, I provide three tables that outline the contributions of several key researchers to the development of naturalistic approaches to complexity and life. These tables encapsulate their perspectives on emergence, self-organization, and the interplay of physical, informational, and biological systems, showcasing the evolution of thought in this interdisciplinary domain.

Table 1. Comparing Prigogine, Kauffman, and Walker.

Aspect Ilya Prigogine Stuart Kauffman & Andrea Roli Sara Imari Walker
Core Philosophy Irreversibility and self-organization in physical systems. Emergence and creativity in biospheres. Informational and computational basis of life.
Scope Physical and chemical systems. Biological and ecological systems Transition from chemistry to biology via information.
Role of Time Central, emphasizing irreversibility. Indirectly addressed through evolutionary novelty. Focused on causal organization, less on time per se.
Emergence Driven by bifurcations in thermodynamic systems. Rooted in self-organization and the adjacent possible. Tied to information processing and causal structures.
Reductionism Opposed; emphasizes new laws at higher complexity. Critiques deterministic frameworks in biology Rejects reductionism; multilevel causality is critical
Uniqueness of Life Extension of physical principles to living systems. Creative exploration of novel evolutionary possibilities. Unique due to information processing and causal dynamics

Table 2. Contributions of Other Key Researchers.

Researcher Core Contribution Focus Philosophical Implications
Brian Goodwin Self-organization in biological patterns. Morphogenesis and nonlinear dynamics in biology. Shifted focus from genes to holistic, emergent processes.
Humberto Maturana & Francisco Varela Autopoiesis: Selfmaintenance in living systems. Circularity and autonomy of biological networks. Life is defined by its self-organizing and adaptive nature.
Jeremy England Energy dissipation drives complexity. Thermodynamics of prebiotic chemistry. Linked life’s emergence to physical principles.
John Holland Development of complex adaptive systems (CAS). Interactions of agents leading to emergent global behavior. Highlighted adaptability, emergent order, and co-evolution across domains.
Simon Levin Self-organization of ecosystems. Interactions between individuals and ecological dynamics. Emphasized emergent properties in ecological systems.
Lynn Margulis Endosymbiosis and symbiotic evolution. Symbiotic relationships as a driver of biological complexity. Shifted focus from individual competition to cooperation and networks as central to evolution
Terrence Deacon Emergence of life and mind from matter. Role of self-organization and thermodynamic constraints. Proposed teleodynamics—goaldirected dynamics as emergent from physical and chemical systems
Denis Noble Systems biology critique of reductionism. Feedback networks in biological systems. Advocated for multilevel interactions over gene-centrism.

Table 3. A more detailed comparison of the philosophical implications of Ilya Prigogine, Stuart Kauffman & Andrea Roli, and Sara Imari Walker.

Aspect Ilya Prigogine Stuart Kauffman & Andrea Roli Sara Imari Walker
Core Philosophy Challenges deterministic, time-reversible classical physics. Introduces a framework based on irreversibility, nonequilibrium thermodynamics, and self-organization. Critiques reductionism in biology, emphasizing self-organization, adjacent possible, and the creativity of biospheres. Focuses on the informational and computational dynamics of biological systems, proposing life emerges from information processing.
Scope Broad application to physical and chemical systems, including thermodynamics, chemistry, and dissipative structures. Primarily focuses on biological and ecological systems, exploring evolution and the emergence of novelty. Targets the transition from chemistry to biology, emphasizing the informational basis of life’s complexity.
Role of Time Time is central: introduces the arrow of time and irreversibility as fundamental to physical processes. Time is indirectly addressed through the evolutionary creation of novelty and new possibilities. Time is less emphasized; focuses on the causal organization and flow of information in living systems.
Emergence Emergence arises through bifurcations and fluctuations in far-fromequilibrium systems. Emergence arises from self-organization and the exploration of the adjacent possible in biospheres Emergence is tied to information processing and the causal closure of biological systems.
Philosophical Implications Redefines the relationship between science and nature by showing that unpredictability and creativity are intrinsic to physical systems. Calls for a shift in scientific paradigms to recognize the adaptive creativity and dynamic potential of life. Proposes a new philosophy of biology grounded in information theory and causality, connecting physical and computational realms
Reductionism Strongly opposes reductionism, arguing for the emergence of new laws at different levels of organization. Opposes reductionism in biology, emphasizing the holistic dynamics of ecosystems and evolution. Critiques reductionism, proposing multilevel causality where informational and physical processes interact.
Uniqueness of Life Sees life as a natural extension of physical laws, governed by the same nonequilibrium principles Views life as distinct due to its creative exploration of evolutionary possibilities. Argues life is unique because of its ability to process and act on information, creating new causal dynamics.
Determinism vs Creativity Highlights how deterministic systems give rise to unpredictable novelty through bifurcations and fluctuations Focuses on the emergent creativity of biospheres as they evolve new, unpredictable possibilities. Emphasizes how informational processes introduce a new level of causal creativity in biological systems.

5. Conclusion. Toward a Unified Paradigm of Complexity

From Prigogine’s thermodynamics to Walker’s information theory, these thinkers collectively advance our understanding of life and complexity. Their contributions converge on the rejection of reductionism, emphasizing the active properties of matter—such as self-assembly and self-organization—along with emergence, creativity, and the dynamic interplay between physical and informational processes that shape life in the natural world.

References

  1. Corning, P. A., Kauffman, S. A., Noble, D., Shapiro, J. A., Vane-Wright, R. I., & Pross, A. (2023). Evolution "on purpose": Teleonomy in living systems. MIT Press.
  2. Deacon, T. W. (2012). Incomplete nature: How mind emerged from matter. W.W. Norton & Company.
  3. England, J. L. (2018). Every life is on fire: How thermodynamics explains the origins of living things. Riverhead Books.
  4. Goodwin, B. (1994). How the leopard changed its spots: The evolution of complexity. Princeton University Press.
  5. Holland, J. H. (1998). Emergence: From chaos to order. Addison-Wesley.
  6. Kauffman, S. A. (1993). The origins of order: Self-organization and selection in evolution. Oxford University Press.
  7. Kauffman, S. A. (1995). At home in the universe: The search for the laws of complexity. Oxford University Press.
  8. Kauffman, S. A. (2000). Investigations. Oxford University Press.
  9. Kauffman, S. A. (2008). Reinventing the sacred: A new view of science, reason, and religion. W.W. Norton & Company.
  10. Kauffman, S. A., & Roli, A. (2024). A third transition in science? Journal of the Royal Society Interface.
  11. Levin, S. (1999). Fragile dominion: Complexity and the commons. Perseus Books.
  12. Margulis, L., & Sagan, D. (1995). What is life?. University of California Press.
  13. Maturana, H. R., & Varela, F. J. (1987). The tree of knowledge: The biological roots of human understanding. Shambhala.
  14. Maturana, H. R., & Varela, F. J. (1992). Autopoiesis and cognition: The realization of the living. Kluwer Academic Publishers.
  15. Noble, D. (2006). The music of life: Biology beyond the genome. Oxford University Press.
  16. Noble, D. (2018). Dance to the tune of life: Biological rhythms, evolutionary origins, and the mysteries of mind. Oxford University Press.
  17. Prigogine, I., & Stengers, I. (1984). Order out of chaos: Man’s new dialogue with nature. Bantam Books.
  18. Prigogine, I. (1980). From being to becoming: Time and complexity in the physical sciences. W.H. Freeman.
  19. Prigogine, I. (1997). The end of certainty: Time, chaos, and the new laws of nature. Free Press.
  20. Walker, S. I., & Davies, P. C. W. (2013). The algorithmic origins of life. Journal of the Royal Society Interface, 10(81), 20130593. [CrossRef]
  21. Walker, S. I., & Davies, P. C. W. (2016). The ‘hard problem’ of life. Philosophical Transactions of the Royal Society A: Mathematical, Physical, and Engineering Sciences, 374(2089), 20150079. [CrossRef]
  22. Walker, S. I., & Packard, N. H. (2021). Transitions beyond the paradigm of mechanism. Entropy, 23(12), 1633. [CrossRef]
  23. Walker, S. I., Packard, N. H., & Cody, G. D. (2017). Re-conceptualizing the origins of life. Philosophical Transactions of the Royal Society A: Mathematical, Physical, and Engineering Sciences, vol. 375, no. 2109, Dec. 2017.

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