Reading club of the Self-generating Structure（RCSGS）

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【Some claim that peeling an onion will cause you to cry because as you remove each layer, you will realize that the onion has no heart. - Yang Zongwei, 《Onion》

Life has a heart (consciousness), but when you peel away the layers of life's tissues, there is simply a heart and no "mind"; when you expose the cerebral cortex, you can see individual neurons, but there is no "consciousness." Life is spontaneously formed from non-life, whereas consciousness is spontaneously generated from life. Life and consciousness appear to have strikingly comparable self-generating systems. What alternate structure would be the most probable if this assumption holds? 】

To obtain a deeper knowledge of the self-generating structure of complex living systems, Swarma Club's scientist Xiaomuqiu (Qiu Weiyi) teamed forces with Zhou Liqian, Wang Dong, Dong Da, Liu Yu, Yuan Mingli, Fu Wocheng, Zhang Yanbo, etc. in philosophy of science and computer science. Co-sponsored by front-line researchers in areas including physics,biology,philosophy of science and computer science.They organized this three-season "Self-Generating Structure Series Reading Club" together with the Swarma Club.

Among these, the first season of "Consensus - Research Background of Self-Generating Structure and Self-Reproducing Automata" will explore with you numerous possible structures of self-referentiality, their relationship with the self-generating structure of living awareness, and this Reading club's framework overview.

Background for the Self-Generating Structure Series Reading Club

Self-Reproducing Automata, autocatalysis, and autopoietic theory, which are closely related to the "Self-reference" structure but dissociated from each other, are buried in computer science, biochemistry, and cognitive science and are nearly isolated from each other, indicating "old" theories that solve different problems. What is their underlying relationship, do they have the possibility for structural "isomorphism," and may their collision and "intersection" provide substantial inspiration for overcoming the fundamental challenges of life and consciousness? If we discover such a structure, we will no longer find the heart by peeling away the living tissue layer by layer, but rather we will discover the heart's self-regeneration from the self-regeneration of the live tissue. Does this imply that we may further define life and awareness, or perhaps create them from scratch?

Background

Since the 1970s, the study of complex systems has been conducted from two distinct perspectives.

One line,using statistical physics as the thinking paradigm, distributed emergence as the typical phenomenon, nonlinear dynamics as the mathematical foundation, and the Ising model and multi-agent simulation as the computer model, it is possible to attempt to discover the simple principles of unity underlying the macroscopic nature of complex systems. This sparked an emergent trend in complexity study, which continues to flourish due to the advent of data and network science and distributed neural network-based artificial intelligence.

Another line, after constructing an electronic computer that simulates the human brain based on the Turing machine model and Von Neumann theory,with Godel's theorem and self-reference structure as its core and structural analysis as its thinking paradigm, has sparked an unprecedented information revolution. This stream of thought and research with self-reference and self-generating structures at its core has propelled human society into a new historical epoch; nevertheless, it has not flourished since then and has instead evolved into a comprehensive grasp of complex research. A marginal issue or "dark thread of silence."

Despite being a black thread, this study paradigm has advanced and expanded in various domains. In computer science, it is artificial life research with self-reproducing automata as the core theory; in systems biology and biochemistry, it is the theory of the origin of life with autocatalysis and hypercycle as the core; in the fields of philosophy of science and sociology, it is generative research centered on autopoietic theory; in the fields of mathematics and logic, it is also formal structures and semantic logic centered on self-reference as the core are advanced.

Regarding the self-reference structure and its function in the genesis of life and intelligent creation, we observed that various disciplines have different cognitive levels and language obstacles. In the philosophy of science, for instance, self-reference-centered hierarchical generation is nearly a consensus; in computers and physics, positive feedback and its generative dynamics in networks are still the mainstream research directions; in biology, the reductionist mind, based on the central law, is still dominant, even though it has life, the most abundant source of material and thought, however, the research on the origin of life with self-generating structure as its core is still in limbo. When we combine various disciplines, conflicts and sparks erupt.......

Brief introduction to the Self-Generating Structure Series Reading Club

This series of Reading Club aims to pursue the theoretical frontier related to Self-reference in different subjects through communication and joint learning. It established an interdisciplinary consensus with the "Self-Generating Structure" as the core and distinguishes the roles of subject emergence and Distributed Emergence in the formation of complex living systems to investigate the qualitative comprehension and quantitative characterization methods of Self-reference and Self-generating structures, as well as a new comprehension of the complexity of life and life-like living systems.

The objectives of the reading club are as follows:

1. Commonality and definition;

2. Description and characterization;

3. Measurement of complexity.

For these objectives, the "Self-Generating Structure" reading club will have three seasons. Focusing on researching the "Self-Generating Structure" of complex life systems/life-like systems, the reading club will be launched in the following structure. The three seasons of the book club are all conducted online and are anticipated to last approximately one year.

-Season 1: consensus: research background of Self-Generating Structure and Self-Reproducing Automata

-Background and consensus of Self-Generating Structure?

-Self-Reproducing Automata Theory

Season 2: Structure: A Qualitative Theory of Self-Reference and Self-Generating Structures

-Self-reference and Autocatalysis

-Self reference and Autopoiesis

-Self-reference and Self-awareness

Season 3: Computation - Quantitative Characterization of Emergent and Self-Generating Structures

- Complexity Measurement - Measurement of Emergence and Hierarchy

- Complexity Measurements - Measurement of Agent-Based Complexity

Sponsor

Qiu Weiyi :

Qiu Weiyi is a resident scientist of the Swarma club. She obtained her Ph.D. in the field of Molecular Genetics. She has been engaged in the research and development of anti-tumor antibody drugs and currently focuses on the origin of life and systems biology.

Cosponsor

Wang Dong is a lecturer in the School of Marxism, Beijing Technology and Business University. He obtained his Ph.D. In the field of philosophy. His research is focused on the general philosophy of science, philosophy of artificial intelligence, and cognitive science.

Zhou Liqian ：

Zhou Liqian is an associate professor in the Department of Philosophy, School of Humanities, Shanghai Jiao Tong University. He obtained his Ph.D. In the field of philosophy. His main study topics are philosophy of information, philosophy of biology, philosophy of mind and cognition, and general philosophy of science. He has published hundreds of related academic works in domestic and foreign academic journals such as Synthese, Information and Culture, Cybernetics & Human Knowing, Dialectics of Nature Communications, and Research on Dialectics of Nature.

Dong Da：

Dong Da is currently working at the Research Center of Brain, Mind and Education, Shaoxing University of Arts and Sciences. He obtained his Ph.D. In the field of philosophy. His research is focused on the philosophy of cognitive science, history of psychology, and history of neuroscience. He currently focuses on the history of ideas related to the concept of "mind" (such as "consciousness", "emotion", "reflex", etc.)

Liu Yu：

Liu Yu is a Distinguished Associate Research Fellow at the International Science Center for Complex Systems, Beijing Normal University (Zhuhai). He holds a Ph.D. in Applied Mathematics and Statistics from Uppsala University, Sweden, and has held research positions at the Department of Chemistry, Glasgow University, United Kingdom, the Department of Chemical Biology, University of Groningen, the Netherlands, and the Mittag-Leffler Mathematical Institute in Sweden. His research is focused on complex systems and the intersection of biology, chemistry, and mathematics. He currently focuses on two themes: 1. How to characterize and measure the complexity of life (including chemical molecules and gene sequences), and how does this complexity emerge and evolve from simplicity? 2. How to apply this theory of describing complexity to the modularization of gene sequences, the evolution of neural networks, the design of new drugs, etc.

Fu Wocheng：

Fu Wocheng is a resident scientist of the Swarma club and a scholar at Swarma-Kaifeng Study Camp. He obtained his Ph.D. In the field of Physics from Nanjing University, and currently working at the Institute of Physics and Chemistry as a postdoctoral fellow.

Zhang Yanbo：

Zhang Yanbo is a scholar at Swarma-Kaifeng Study Camp. He is graduated from the Physics Department of the University of science and technology of China and once visited Karolinska Medical College in Sweden. Currently, he is studying for a doctorate in complex systems at Arizona State University. His research interests include statistical physics, complex systems, etc.

Yuan Mingli：

Yuan Mingli is currently working in Caiyun technology. His interests focus on engineering, language, knowledge, intelligence, mathematics, etc., and he is full of curiosity and confusion about the world.

Main contents and references of the three seasons

Season 1: Consensus - Research Background on Self-Generating Structures and Self-Replicating Automata

The main goal of the first season is to establish a basic consensus on Self-reference and Self-Generating Structure. We will introduce each discipline's understanding of Self-Generating Structure (emergence of subjectivity) from disciplines such as philosophy of science, biology, the overview of complex science (including artificial life), and basic concepts. Then, we will study "Theory of Self-Reproducing Automata" (Von Neumann's five lectures) as a paradigm for subsequent discussions on life and self-consciousness/intelligence essence structure, etc., introduce progress in the direction of artificial life and introduce following more in-depth conversations regarding the origin of life, the nature of life, and the organization of self-consciousness.

The background and consensus of Self-Generating Structure and Self-Reproducing Automata

The theoretical origin of the essence of life in contemporary biological philosophy

  • Bedau, M. (2008). What is Life?

https://www.cambridge.org/core/books/abs/the-nature-of-life/what-is-life-selections/295D60C5FE17B13DA3293FDB02A5370D

  • A Companion to the Philosophy of Biology[M]. John Wiley & Sons, 2010.

https://www.google.com/books?hl=zh-CN&lr=&id=eg2283WZSkAC&oi=fnd&pg=PR11&dq=A+Companion+to+the+Philosophy+of+Biology&ots=f2z87Ap0Hx&sig=wYiUJ4Lfzr_7nwehqQ0iFCmpBqY

  • Weber B H. On the emergence of living systems[J]. Biosemiotics, 2009, 2(3): 343-359.

https://link.springer.com/content/pdf/10.1007/s12304-009-9060-6.pdf

  • Bitch, L. & Green, S. (2018). Is Defining Life Pointless. Synthese, 2018, 195: 3919-3946. https://doi.org/10.1007/s11229-017-1397-9生物学哲学中关于生命本质问题的概览。An overview of questions about the nature of life in the philosophy of biology.

The topic of this part is the CAS system and J.England's theory, which belongs to the field of complex science.

  • England J L. Statistical physics of self-replication[J]. The Journal of chemical physics, 2013, 139(12): 09B623_1.https://arxiv.org/abs/1209.1179 (自复制过程中的最小熵产生的定量分析)(Quantitative analysis of minimum entropy generation during self-replication)
  • England J L. Dissipative adaptation in driven self-assembly[J]. Nature nanotechnology, 2015, 10(11): 919-923.

https://www.englandlab.com/uploads/7/8/0/3/7803054/nnano.2015.250__1_.pdf

  • Holland J H. Signals and boundaries: Building blocks for complex adaptive systems[M]. Mit Press, 2012.

https://books.google.com/books?hl=zh-CN&lr=&id=jUy9AAAAQBAJ&oi=fnd&pg=PR5&dq=Signals+and+boundaries:+Building+blocks+for+complex+adaptive+systems.+&ots=yasc03fBh2&sig=4nkwnzA1QoX2uwf7xF6w2J4KesA

  • Holland J H. Hidden order: How adaptation builds complexity[M]. Addison Wesley Longman Publishing Co., Inc., 1996.

https://dl.acm.org/doi/abs/10.5555/225764

The topic of this part is the the difference between life emergence and subject emergence, which belongs to the field of Philosophy of Science

  • Boogerd F C, Bruggeman F J, Richardson R C, et al. Emergence and its place in nature: A case study of biochemical networks[J]. Synthese, 2005, 145(1): 131-164.

https://link.springer.com/article/10.1007/s11229-004-4421-9（突现/涌现概念面临根本困难，这篇论文利用systems biology的研究成果，展示了突现的可能性）(The concept of emergence faces fundamental difficulties, this paper uses the research results of systems biology to show the possibility of emergence)

  • Brian P. Mclaughlin.“The Rise and Fall of British Emergentism”, In Ansgar Beckermann, H. Flohr & Jaegwon Kim (eds.),Emergence or Reduction?: Essays on the Prospects of Nonreductive Physicalism. W. De Gruyter. pp. 49-93 (1992) DOI: 10.1515/9783110870084.49（对早期突现理论的综述）(A review of early emergent theory)

https://philpapers.org/rec/MCLTRA-4

  • Bedau M A. Is weak emergence just in the mind?[J]. Minds and Machines, 2008, 18(4): 443-459. DOI: 10.1007/s11023-008-9122-6（使用不可压缩的计算性来定义突现）(Using incompressible computability to define emergent)

https://link.springer.com/article/10.1007/s11023-008-9122-6

The topic of this part is the frontiers in the origin of life research, which belongs to the field of Biology.

  • Preiner M, Asche S, Becker S, et al. The future of origin of life research: bridging decades-old divisions[J]. Life, 2020, 10(3): 20.

https://www.mdpi.com/2075-1729/10/3/20 详细综述了生命起源领域的各个方面，包括实验、理论、模拟等A detailed overview of all aspects of the origin of life, including experiments, theory, simulations, etc.

Self-Reproducing Automata theory

  • 冯诺依曼《自复制自动机》翻译：东方和尚，点评：张江
  • Von Neumann's "Self-Reproducing Automata" translation: Oriental monk, review: Zhang Jiang

Hypotheses and models of artificial life, with a preference for computer science

  • Chan B W C. Lenia-biology of artificial life[J]. arXiv preprint arXiv:1812.05433, 2018.

https://arxiv.org/abs/1812.05433

  • Gershenson C, Trianni V, Werfel J, et al. Self-organization and artificial life[J]. Artificial Life, 2020, 26(3): 391-408.

https://ieeexplore.ieee.org/abstract/document/9204917/

  • Lehman J, Clune J, Misevic D, et al. The surprising creativity of digital evolution: A collection of anecdotes from the evolutionary computation and artificial life research communities[J]. Artificial life, 2020, 26(2): 274-306.

https://doi.org/10.1162/artl_a_00319

Season 2: Structure - A Qualitative Theory of Self-reference and Self-Generating Structures

Season two is the highlight of the Series Reading Club. From the cycle theory based on autocatalytic set theory, we will examine the genesis of life and the essential structure of life, and introduce the relevant ideas and the most recent advances in biochemistry and synthetic biology. Through theoretical models such as Autopoiesis, hypercycles, and chemical ions, we will revisit the link between self-reference and hierarchical emergence. Since the autopoietic theory, like the Self-Reproducing Automata, is also a theoretical model that analyzes life and consciousness simultaneously, we will also utilize it as a foundation to challenge some of the existing mainstream research methodologies on self-awareness and intelligence.

It should be underlined that the "relational biology" established in the 1950s by Robert Rosen, a contemporary of von Neumann, from the standpoint of category theory was an essential source of inspiration for autopoiesis theory. Highlights of this season's discourse include rediscovering and mining Rosen's ideas, understanding the structure of the (M,R)-system, and monitoring its present boundaries. Specifically, can we leverage significant advancements in areas such as category theory and causal emergence as tools to better comprehend and characterize the link between self-reference and hierarchical development?

Self-referential and autocatalysis

The topic of this part is Kauffman, Ganti, and Formose Reaction, which belongs to the field of systems biology.

  • Kauffman S A. The origins of order: Self-organization and selection in evolution[M]. Oxford University Press, USA, 1993.

https://scholar.google.com/citations?view_op=view_citation&hl=zh-CN&user=yoPM0F8AAAAJ&citation_for_view=yoPM0F8AAAAJ:AXPGKjj_ei8C

  • Kauffman S, Kauffman S A. At home in the universe: The search for laws of self-organization and complexity[M]. Oxford University Press, USA, 1995.

https://scholar.google.com/citations?view_op=view_citation&hl=zh-CN&user=yoPM0F8AAAAJ&citation_for_view=yoPM0F8AAAAJ:9vf0nzSNQJEC

The topic of this part is RAF and COT theory, which belongs to the field of biomathematics.

  • RAF Theory (Self-Replicating Networks), a relatively new summary article

Hordijk W, Steel M. Chasing the tail: The emergence of autocatalytic networks[J]. Biosystems, 2017, 152: 1-10.

https://www.sciencedirect.com/science/article/abs/pii/S030326471630274X

  • Full theoretical article on COT

Dittrich P, Di Fenizio P S. Chemical organisation theory[J]. Bulletin of mathematical biology, 2007, 69(4): 1199-1231.

https://link.springer.com/article/10.1007/s11538-006-9130-8

The topic of this part is The Nature of Life: Philosophy and Science (Deacon Theory), which belongs to the field of philosophy of science

  • 1）From Kant to the naturalization of teleology
    • Classic Collections of Contemporary Biology and Philosophy of Biology
    • Bedau M A, Cleland C E. The Nature of Life[M]. Cambridge University Press, 2018.
    • Ernst Mayr,Classic essay on biological teleology

Ernst Mayr. Teleological and teleonomic, a new analysis[M]//Methodological and historical essays in the natural and social sciences. Springer, Dordrecht, 1974: 91-117.

https://doi.org/10.1007/978-94-010-2128-9_6.

  • A naturalistic understanding of Kant's intrinsic teleology

Weber A, Varela F J. Life after Kant: Natural purposes and the autopoietic foundations of biological individuality[J]. Phenomenology and the cognitive sciences, 2002, 1(2): 97-125.

https://link.springer.com/article/10.1023/A:1020368120174

  • 2）Goal Dynamics and Self-Generation
    • Self-generating model and its comparison with Chemoton, protocell, AL

Deacon T W. Reciprocal linkage between self-organizing processes is sufficient for self-reproduction and evolvability[J]. Biological Theory, 2006, 1(2): 136-149.

https://link.springer.com/article/10.1162/biot.2006.1.2.136

  • Systematic discussion of objective dynamics and autogen

Peterson G R. Terrence Deacon, Incomplete Nature: How Mind Emerged from Matter .New York: WW Norton, 264-325. 2012 (提供中译文)

https://www.tandfonline.com/doi/full/10.1080/14746700.2013.836898

  • Provides criteria for distinguishing purposive kinetics from thermodynamics and self-organization, and discusses the hierarchical dependencies of the three kinetic forms.

Terrence Deacon. Teleodynamics: Specifying the dynamical principles of intrinsically end-directed processes. Proceedings of IAISAE, International Conference on Thermodynamics 2.0, June 22-24, 2020. Worcester, MA, USA. ICT2.0: 2020-W1xx.

The topic of this part is the chemical origin of life and advances in autocatalysis theory, which belongs to the field of biochemistry

  • Preiner M, Asche S, Becker S, et al. The future of origin of life research: bridging decades-old divisions[J]. Life, 2020, 10(3): 20.

https://www.mdpi.com/2075-1729/10/3/20

Self-reference and Autopoiesis

The topic of this part is a comparative study of (M, R)-system and autopoiesis, which belongs to the field of mathematics and philosophy

  • 1）autopoiesis
    • Varela F, Maturana H. Autopoiesis and Cognition: The realization of the Living[J]. 1980. (Read the chapter: a quick scan of the full text to get an overall impression)

https://philpapers.org/rec/MATAAC-3

  • Thompson E. Life and mind: From autopoiesis to neurophenomenology. A tribute to Francisco Varela[J]. Phenomenology and the cognitive Sciences, 2004, 3(4): 381-398.

https://doi.org/10.1023/B:PHEN.0000048936.73339.dd

  • Chinese translation: "Mind in Life: Biology, Phenomenology, and the Science of Mind". (2013). Translated by Li Hengwei, Li Hengxi, Xu Yan. Hangzhou: Zhejiang University Press) (read chapter: Chapter 5 "Autogenesis" : The Organization of Life"; 6.2. "Autopoiesis and Teleology"; 8.5. "Biological Naturalism")

https://book.douban.com/subject/25660918/

  • Varela F. Principles of biological autonomy[J]. 1979.

(Read the chapter: a quick scan of the full text to get an overall impression)

https://philpapers.org/rec/VARPOB

  • (M,R) system
    • Rosen R. A relational theory of biological systems[J]. The bulletin of mathematical biophysics, 1958, 20(3): 245-260.
    • Doi: 10.1007/BF02478302https://link.springer.com/article/10.1007%2FBF02478302
    • Rosen R. Life itself: a comprehensive inquiry into the nature, origin, and fabrication of life[M]. Columbia University Press, 1991. (Read the chapter: a quick scan of the full text to get an overall impression)

https://books.google.com/books?hl=zh-CN&lr=&id=DR8L4snDnkIC&oi=fnd&pg=PR11&dq=+Life+itself:+A+comprehensive+inquiry+into+the+nature,+origin,+and+fabrication+of+life.+New+York,+NY:+Columbia+University+Press.&ots=jMDdPg_i22&sig=ieQA47VrRHigaj7PHVDG_dg1stE

  • 3）Comparative study of autopoiesis and (M, R) systems:
    • Cornish-Bowden A, Cárdenas M L. Contrasting theories of life: historical context, current theories. In search of an ideal theory[J]. Biosystems, 2020, 188: 104063.

https://www.sciencedirect.com/science/article/pii/S0303264719302151

  • Letelier J C, Cárdenas M L, Cornish-Bowden A. From L'Homme Machine to metabolic closure: steps towards understanding life[J]. Journal of Theoretical Biology, 2011, 286: 100-113.

https://www.sciencedirect.com/science/article/pii/S0022519311003389

  • Letelier J C, Marın G, Mpodozis J. Autopoietic and (M, R) systems[J]. Journal of theoretical biology, 2003, 222(2): 261-272.

https://www.sciencedirect.com/science/article/pii/S0022519303000341

  • Cárdenas M L, Letelier J C, Gutierrez C, et al. Closure to efficient causation, computability and artificial life[J]. Journal of Theoretical Biology, 2010, 263(1): 79-92.

https://www.sciencedirect.com/science/article/pii/S0022519309005360(Note: For technical discussions, please refer to Chapter 4)

Hypercycle kinetics, biased towards biophysics

  • Eigen M, Schuster P. The hypercycle[J]. Naturwissenschaften, 1978, 65(1): 7-41.

https://link.springer.com/article/10.1007/BF00420631

The third generation of system theory, biased towards science and philosophy

  • Hideo Kawamoto, "The Third Generation of Systems Theory: Theory of Self-Generating Systems"https://book.douban.com/subject/27102835/

H.Louie and Nomura's development of Rosen's theory, biased towards science and philosophy

  • Nomura T. Formal description of autopoiesis for analytic models of life and social systems[C]//Proc. 8th Int. Conf. Artificial Life (ALIFE VIII). 2002: 15-18.

https://dl.acm.org/doi/10.5555/860295.860299

Semiotics, symbolic dynamics and self-awareness, with a mathematical bias

  • Hofstadter: GEB, My Mind, I'm a Strange Circle

https://book.douban.com/subject/30335756/

  • Pierce: On Symbols

https://book.douban.com/subject/26220450/

  • Willie: Symbolic Self

https://book.douban.com/subject/6790636/

  • Applied Symbolic Dynamics and Chaos

https://book.douban.com/subject/26678718/

  • Cariani P. The semiotics of cybernetic percept-action systems[J]. International Journal of Signs and Semiotic Systems (IJSSS), 2011, 1(1): 1-17.

https://www.igi-global.com/article/semiotics-cybernetic-percept-action-systems/52600

  • Cariani P. Symbols and dynamics in the brain[J]. Biosystems, 2001, 60(1-3): 59-83.

https://www.sciencedirect.com/science/article/abs/pii/S0303264701001083

  • Tani J. Exploring robotic minds: actions, symbols, and consciousness as self-organizing dynamic phenomena[M]. Oxford University Press, 2016.

https://books.google.com/books?hl=zh-CN&lr=&id=NtooDQAAQBAJ&oi=fnd&pg=PP1&dq=Exploring+Robotic+Minds:+Actions,+Symbols,+and+Consciousness+as+Self-Organizing+Dynamic+Phenomena&ots=Xj2DuNU1ZB&sig=pyyBCqAca_1-sYmBgeOTXeJS5qE

The Consciousness Hypothesis and Its Application from the Perspective of Predictive Coding

  • Safron A. An Integrated World Modeling Theory (IWMT) of consciousness: combining integrated information and global neuronal workspace theories with the free energy principle and active inference framework; Toward solving the hard problem and characterizing agentic causation[J]. Frontiers in artificial intelligence, 2020, 3: 30.

https://www.frontiersin.org/articles/10.3389/frai.2020.00030/full

  • Safron A. Integrated world modeling theory (IWMT) revisited[J]. 2019.

https://psyarxiv.com/kjngh/download?format=pdf

  • Friston K. The free-energy principle: a unified brain theory?[J]. Nature reviews neuroscience, 2010, 11(2): 127-138.

https://www.nature.com/articles/nrn2787/boxes/bx1

  • Dehaene S, Changeux J P, Naccache L. The global neuronal workspace model of conscious access: from neuronal architectures to clinical applications[J]. Characterizing consciousness: From cognition to the clinic?, 2011: 55-84.

https://link.springer.com/chapter/10.1007/978-3-642-18015-6_4

  • Friston K. Am I self-conscious?(Or does self-organization entail self-consciousness?)[J]. Frontiers in psychology, 2018, 9: 579.

https://www.frontiersin.org/articles/10.3389/fpsyg.2018.00579/full?utm_source=F-AAE&utm_medium=EMLF&utm_campaign=MRK_624802_69_Psycho_20180503_arts_A

  • Kanai R, Chang A, Yu Y, et al. Information generation as a functional basis of consciousness[J]. Neuroscience of consciousness, 2019, 2019(1): niz016.

https://academic.oup.com/nc/article-pdf/doi/10.1093/nc/niz016/31162573/niz016.pdf

  • Manjaly Z M, Iglesias S. A computational theory of mindfulness based cognitive therapy from the “bayesian brain” perspective[J]. Frontiers in Psychiatry, 2020, 11: 404.

https://www.frontiersin.org/articles/10.3389/fpsyt.2020.00404/full

  • Demekas D, Parr T, Friston K J. An investigation of the free energy principle for emotion recognition[J]. Frontiers in computational neuroscience, 2020, 14: 30.

https://www.frontiersin.org/articles/10.3389/fncom.2020.00030/full

Category theory proof of Gödel machine and Gödel's theorem, biased towards mathematical logic

  • Schmidhuber J. Gödel machines: Towards a technical justification of consciousness[M]//Adaptive Agents and Multi-Agent Systems II. Springer, Berlin, Heidelberg, 2004: 1-23.

https://doi.org/10.1007/978-3-540-32274-0_1

  • Steunebrink B R, Schmidhuber J Ã. Towards an actual gödel machine implementation: A lesson in self-reflective systems[M]//Theoretical Foundations of Artificial General Intelligence. Atlantis Press, Paris, 2012: 173-195.

https://people.idsia.ch//~juergen/selfreflection.pdf

  • F William Lawvere: Diagonal arguments and cartesian closed categories. In: Category theory, homology theory and their applications II, 1969. Reprints in Theory and Applications of Categories, No. 15, 2006, pp. 1–13.

http://emis.matem.unam.mx/journals/TAC/reprints/articles/15/tr15.pdf

  • Yanofsky N S. A universal approach to self-referential paradoxes, incompleteness and fixed points[J]. Bulletin of Symbolic Logic, 2003, 9(3): 362-386.

https://www.cambridge.org/core/journals/bulletin-of-symbolic-logic/article/universal-approach-to-selfreferential-paradoxes-incompleteness-and-fixed-points/9C490EC9520C0C96AEEF06E59BFD428B

  • Frumin, Massas: Diagonal arguments and Lawvere's theorem

https://groupoid.moe/pdf/diagonal_argument.pdf

The structure and related thinking of self-consciousness machine, biased towards computer-biology

  • Marcolli M. Topological Model of Neural Information Networks[C]//International Conference on Geometric Science of Information. Springer, Cham, 2021: 623-633.

http://www.its.caltech.edu/~matilde/TopModelsNeuralInfoNets.pdf

  • Selfx: a self explorer

https://doi.org/10.5281/zenodo.5196181

Season 3: Computation - Quantitative Characterization of Emergent and Self-Generating Structures

The third season will be the most difficult in the Series Reading Club, and we expect it will yield crucial actionable research spots.

The very logic of contemporary science implies the transformation from qualitative to quantitative. It can be said that the development process of complex science, particularly the data- and network-based development perspective, is also the process of understanding the system from qualitative observation to quantitative characterization. Therefore, the structural description, characterization and complexity measurement of multi-level complex living systems are this season's most pressing concerns.

The first issue in the quantitative characterization of complex systems is the nonlinear growth of basic measures caused by the formation of structures and new levels, also known as the so-called "complexity explosion," which renders the original measurement instruments and measurement units invalid. This pushes the subject to adopt a new "observation perspective," resulting in "emergent" observations. From this perspective, the problem of complex system cognition is primarily the difficulty of comprehending and describing the structure of complex systems. The newly established "hypergraph" method in network science, for instance, is an attempt to integrate system metrics from the standpoint of hierarchical structure. The measuring perspective of complex systems has moved from thermodynamic-based entropy to information entropy, and from quantity-based measurement to probability-based measurement, as a result of the development logic of scientific discovery. In this season, we will examine and evaluate the mainstream perspectives and research tools for measuring complexity, as well as explore the idea of characterizing complexity based on "self-generating structure."

Complexity Measurement - Measurement of Emergence and Hierarchy

The topic of this part is the dimension reduction phenomenon in biological evolution, which belongs to the field of Biophysics.

  • Furusawa C, Kaneko K. Formation of dominant mode by evolution in biological systems[J]. Physical Review E, 2018, 97(4): 042410.

https://journals.aps.org/pre/abstract/10.1103/PhysRevE.97.042410

  • Sakata A, Kaneko K. Dimensional reduction in evolving spin-glass model: correlation of phenotypic responses to environmental and mutational changes[J]. Physical Review Letters, 2020, 124(21): 218101.

https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.124.218101

  • Sato T U, Kaneko K. Evolutionary dimension reduction in phenotypic space[J]. Physical Review Research, 2020, 2(1): 013197.

https://journals.aps.org/prresearch/abstract/10.1103/PhysRevResearch.2.013197

  • Tang Q Y, Hatakeyama T S, Kaneko K. Functional sensitivity and mutational robustness of proteins[J]. Physical Review Research, 2020, 2(3): 033452.

https://journals.aps.org/prresearch/abstract/10.1103/PhysRevResearch.2.033452

  • Tang Q Y, Kaneko K. Dynamics-Evolution Correspondence in Protein Structures[J]. Physical Review Letters, 2021, 127(9): 098103.

https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.127.098103

Cai Ting's "Proving Darwin", which belongs to the field of mathematics

  • Chai Ting "Proving Darwin"

https://book.douban.com/subject/26282599/

Rosen, Efficient Processes and Natural Laws, which belongs to the field of mathematical

  • Rosen 1988 - Effective process and natural law

https://www.researchgate.net/publication/234782458_Effective_Processes_and_Natural_Law

Kaneko's Self-Referring Model - with Emergence, which belongs to the field of Biophysics.

  • Naoto Kataoka and Kunihiko Kaneko. Functional Dynamics. I: Articulation Process[J]. Physica D: Nonlinear Phenomena, 2000,138(3-4): 225–50.

https://doi.org/10.1016/S0167-2789(99)00230-4.

  • Naoto Kataoka and Kunihiko Kaneko. Functional Dynamics: II: Syntactic Structure[J]. Physica D: Nonlinear Phenomena, 2001,149(3): 174–196.

https://doi.org/10.1016/S0167-2789(00)00203-7.

Self-reference dynamics model of the SaraWalker cellular automaton, which belongs to the field of biophysics.

  • Sara Imari Walker. Evolutionary Transitions and Top-Down Causation[A]. Proceedings of the ALIFE 2012: The Thirteenth International Conference on the Synthesis and Simulation of Living Systems[C]. East Lansing, Michigan: ASME, 2012, 283-290.

https://direct.mit.edu/isal/proceedings/alife2012/24/283/98663

New theory of complexity measurement, which belongs to the field of biomathematics

  • A new theory for measuring complexity (applied to chemical molecules, etc.)

Liu Y, Mathis C, Bajczyk M D, et al. Exploring and mapping chemical space with molecular assembly trees[J]. Science advances, 2021, 7(39): eabj2465.

https://chemrxiv.org/engage/chemrxiv/article-details/60c75885ee301ce974c7b74e

Self-similarity, renormalization and self-referential dynamics, which belong to the field of complex science.

West's "Scale"

  • E. P. Hoel, L. Albantakis, and G. Tononi. Quantifying Causal Emergence Shows That Macro Can Beat Microh[A]. Proceedings of the National Academy of Sciences[C], 2013, 110(49): 19790–19795.

https://doi.org/10.1073/pnas.1314922110

  • Li S H, Wang L. Neural network renormalization group[J]. Physical review letters, 2018, 121(26): 260601.

https://doi.org/10.1103/PhysRevLett.121.260601.

  • Tononi G, Boly M, Massimini M, et al. Integrated information theory: from consciousness to its physical substrate[J]. Nature Reviews Neuroscience, 2016, 17(7): 450-461.

https://doi.org/10.1038/nrn.2016.44.

  • Sara Imari Walker. Evolutionary Transitions and Top-Down Causation[A]. Proceedings of the ALIFE 2012: The Thirteenth International Conference on the Synthesis and Simulation of Living Systems[C]. East Lansing, Michigan: ASME, 2012, 283-290.

https://doi.org/10.1162/978-0-262-31050-5-ch038

  • Hou Shida: Gödel, Escher, Bach - The Great Compilation of Different Bis[M]. Translation Group of "Godel, Escher, Bach - The Great Compilation of Different Bis", translation. Commercial Press, 1996.

https://book.douban.com/subject/1291204/

  • Moloney N R. Complexity and criticality[M]. Imperial College Press, 2005.

https://doi.org/10.1142/p365

About the organizer and the Reading club of Swarma Club

Organizer: Swarma Club

Co-organizer: Swarma Academy

Swarma Club, which was founded in 2003, is a group of explorers who conduct academic research and enjoy scientific recreation. In addition, this is the first scientific community in China to investigate artificial intelligence and complex systems. It promotes multidisciplinary research and exchanges with an equitable and open attitude and the spirit of scientific evidence, and aims to establish a "wallless research center" in China.

Swarma Academy,which was founded in 2016, and the Swarma Club has fostered its entrepreneurial spirit ever since. Swarma Academy is dedicated to sharing cutting-edge knowledge and emerging technologies, such as complexity science and artificial intelligence, and fostering knowledge inquiry and ecological creation in the field of complex science.

For the vast majority of scientific researchers, the Swarma Club Reading Club is a set of dissertation study activities. The objective is to collaboratively study and discuss a scientific topic in depth, to comprehend the progress of the frontier, to inspire scientific research, to encourage scientific research cooperation, and to reduce the barrier to scientific research.

Since its inception in 2008, the reading club has covered over forty themes, including complex systems, artificial intelligence, brain and consciousness, life sciences, causal science, computational social sciences, etc. It has brought together a large number of eminent scientists, fostered scientific research collaboration in order to publish articles, and nurtured a large number of scientific research products. For instance, the "Deep Learning" reading club in 2013 gave rise to the Caiyun Weather APP, while the "Collective Attention Flow" reading club in 2015 created the crowdsourced book "Approaching 2050."

取自“https://wiki.swarma.org/index.php?title=Reading_club_of_the_Self-generating_Structure（RCSGS）&oldid=32284”