brain-constructs-perceptions.txt

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title: "Brain Constructs Perceptions"
author: "unknown"
tags: ["library"]
type: "essay"
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Brain Constructs Perceptions

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Brain Constructs Perceptions

Summarize: Not only does thinking filter reality; it constructs it, inferring an outside world from ambiguous input. In Being You, Anil Seth, a neuroscientist at the University of Sussex, relates his explanation for how the ���inner universe of subjective experience relates to, and can be explained in terms of, biological and physical processes unfolding in brains and bodies.��� He contends that ���experiences of being you, or of being me, emerge from the way the brain predicts and controls the internal state of the body.���


Prediction has come into vogue in academic circles in recent years. Seth and the philosopher Andy Clark, a colleague at Sussex, refer to predictions made by the brain as ���controlled hallucinations.��� The idea is that the brain is always constructing models of the world to explain and predict incoming information; it updates these models when prediction and the experience we get from our sensory inputs diverge.


���Chairs aren���t red,��� Seth writes, ���just as they aren���t ugly or old-fashioned or avant-garde ��� When I look at a red chair, the redness I experience depends both on properties of the chair and on properties of my brain. It corresponds to the content of a set of perceptual predictions about the ways in which a specific kind of surface reflects light.���


Seth is not particularly interested in redness, or even in color more generally. Rather his larger claim is that this same process applies to all of perception: ���The entirety of perceptual experience is a neuronal fantasy that remains yoked to the world through a continuous making and remaking of perceptual best guesses, of controlled hallucinations. You could even say that we���re all hallucinating all the time. It���s just that when we agree about our hallucinations, that���s what we call reality.���


Cognitive scientists often rely on atypical examples to gain understanding of what���s really happening. Seth takes the reader through a fun litany of optical illusions and demonstrations, some quite familiar and others less so. Squares that are in fact the same shade appear to be different; spirals printed on paper appear to spontaneously rotate; an obscure image turns out to be a woman kissing a horse; a face shows up in a bathroom sink. Re-creating the mind���s psychedelic powers in silicon, an artificial-intelligence-powered virtual-reality setup that he and his colleagues created produces a Hunter Thompson���esque menagerie of animal parts emerging piecemeal from other objects in a square on the Sussex University campus. This series of examples, in Seth���s telling, ���chips away at the beguiling but unhelpful intuition that consciousness is one thing���one big scary mystery in search of one big scary solution.��� Seth���s perspective might be unsettling to those who prefer to believe that things are as they seem to be: ���Experiences of free will are perceptions. The flow of time is a perception.���


Seth is on comparatively solid ground when he describes how the brain shapes experience, what philosophers call the ���easy��� problems of consciousness. They���re easy only in comparison to the ���hard��� problem: why subjective experience exists at all as a feature of the universe. Here he treads awkwardly, introducing the ���real��� problem, which is to ���explain, predict, and control the phenomenological properties of conscious experience.��� It���s not clear how the real problem differs from the easy problems, but somehow, he says, tackling it will get us some way toward resolving the hard problem. Now that would be a neat trick.


Where Seth relates, for the most part, the experiences of people with typical brains wrestling with atypical stimuli, in Coming to Our Senses, Susan Barry, an emeritus professor of neurobiology at Mount Holyoke college, tells the stories of two people who acquired new senses later in life than is usual. Liam McCoy, who had been nearly blind since he was an infant, was able to see almost clearly after a series of operations when he was 15 years old. Zohra Damji was profoundly deaf until she was given a cochlear implant at the unusually late age of 12. As Barry explains, Damji���s surgeon ���told her aunt that, had he known the length and degree of Zohra���s deafness, he would not have performed the operation.��� Barry���s compassionate, nuanced, and observant exposition is informed by her own experience:


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At age forty-eight, I experienced a dramatic improvement in my vision, a change that repeatedly brought me moments of childlike glee. Cross-eyed from early infancy, I had seen the world primarily through one eye. Then, in mid-life, I learned, through a program of vision therapy, to use my eyes together. With each glance, everything I saw took on a new look. I could see the volume and 3D shape of the empty space between things. Tree branches reached out toward me; light fixtures floated. A visit to the produce section of the supermarket, with all its colors and 3D shapes, could send me into a sort of ecstasy.


Barry was overwhelmed with joy at her new capacities, which she describes as ���seeing in a new way.��� She takes pains to point out how different this is from ���seeing for the first time.��� A person who has grown up with eyesight can grasp a scene in a single glance. ���But where we perceive a three-dimensional landscape full of objects and people, a newly sighted adult sees a hodgepodge of lines and patches of colors appearing on one flat plane.��� As McCoy described his experience of walking up and down stairs to Barry:


The upstairs are large alternating bars of light and dark and the downstairs are a series of small lines. My main focus is to balance and step IN BETWEEN lines, never on one ��� Of course going downstairs you step in between every line but upstairs you skip every other bar. All the while, when I move, the stairs are skewing and changing.


Even a sidewalk was tricky, at first, to navigate. He had to judge whether a line ���indicated the junction between flat sidewalk blocks, a crack in the cement, the outline of a stick, a shadow cast by an upright pole, or the presence of a sidewalk step,��� Barry explains. ���Should he step up, down, or over the line, or should he ignore it entirely?��� As McCoy says, the complexity of his perceptual confusion probably cannot be fully explained in terms that sighted people are used to.


The same, of course, is true of hearing. Raw audio can be hard to untangle. Barry describes her own ability to listen to the radio while working, effortlessly distinguishing the background sounds in the room from her own typing and from the flute and violin music coming over the radio. ���Like object recognition, sound recognition depends upon communication between lower and higher sensory areas in the brain ��� This neural attention to frequency helps with sound source recognition. Drop a spoon on a tiled kitchen floor, and you know immediately whether the spoon is metal or wood by the high- or low-frequency sound waves it produces upon impact.��� Most people acquire such capacities in infancy. Damji didn���t. She would often ask others what she was hearing, but had an easier time learning to distinguish sounds that she made herself. She was surprised by how noisy eating potato chips was, telling Barry: ���To me, potato chips were always such a delicate thing, the way they were so lightweight, and so fragile that you could break them easily, and I expected them to be soft-sounding. But the amount of noise they make when you crunch them was something out of place. So loud.���


As Barry recounts, at first Damji was frightened by all sounds, ���because they were meaningless.��� But as she grew accustomed to her new capabilities, Damji found that ���a sound is not a noise anymore but more like a story or an event.��� The sound of laughter came to her as a complete surprise, and she told Barry it was her favorite. As Barry writes, ���Although we may be hardly conscious of background sounds, we are also dependent upon them for our emotional well-being.��� One strength of the book is in the depth of her connection with both McCoy and Damji. She spent years speaking with them and corresponding as they progressed through their careers: McCoy is now an ophthalmology researcher at Washington University in St. Louis, while Damji is a doctor. From the details of how they learned to see and hear, Barry concludes, convincingly, that ���since the world and everything in it is constantly changing, it���s surprising that we can recognize anything at all.���


In What Makes Us Smart, Samuel Gershman, a psychology professor at Harvard, says that there are ���two fundamental principles governing the organization of human intelligence.��� Gershman���s book is not particularly accessible; it lacks connective tissue and is peppered with equations that are incompletely explained. He writes that intelligence is governed by ���inductive bias,��� meaning we prefer certain hypotheses before making observations, and ���approximation bias,��� which means we take mental shortcuts when faced with limited resources. Gershman uses these ideas to explain everything from visual illusions to conspiracy theories to the development of language, asserting that what looks dumb is often ���smart.���


���The brain is evolution���s solution to the twin problems of limited data and limited computation,��� he writes.


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He portrays the mind as a raucous committee of modules that somehow helps us fumble our way through the day. ���Our mind consists of multiple systems for learning and decision making that only exchange limited amounts of information with one another,��� he writes. If he���s correct, it���s impossible for even the most introspective and insightful among us to fully grasp what���s going  on inside our own head. As Damji wrote in a letter to Barry:


When I had no choice but to learn Swahili in medical school in order to be able to talk to the patients���that is when I realized how much potential we have���especially when we are pushed out of our comfort zone. The brain learns it somehow.


Matthew Hutson is a contributing writer at The New Yorker and a freelance science and tech writer

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The article discusses insights from three different books that explore the nature of human perception, consciousness, and intelligence.

"Being You" by Anil Seth focuses on how our brain constructs our subjective experiences by making predictions about the world based on sensory input. These predictions, often referred to as "controlled hallucinations," shape our perceptions of reality. Seth argues that our entire perceptual experience is a product of our brain constantly making and updating these predictions.

"Coming to Our Senses" by Susan Barry tells the stories of individuals who gained new senses later in life, such as sight or hearing. The book illustrates how the brain adapts and constructs perceptions in response to new sensory information, emphasizing that our experiences are not simply "seeing for the first time" but rather a complex process of interpretation.

"What Makes Us Smart" by Samuel Gershman delves into the organization of human intelligence, proposing two fundamental principles: "inductive bias" and "approximation bias." Gershman suggests that the brain is a collection of modules that exchange limited information, leading to mental shortcuts and adaptive decision-making based on limited data and computational resources.

In summary, these books shed light on the intricate and dynamic nature of human perception, consciousness, and intelligence, challenging traditional notions of how we understand the world around us.

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HUMANS AND TECHNOLOGY

Our brains exist in a state of ���controlled hallucination���

Three new books lay bare the weirdness of how our brains process the world around us.


By Matthew Hutsonarchive page

August 25, 2021

seeing is believing concept

ANDREA DAQUINO

When you and I look at the same object we assume that we���ll both see the same color. Whatever our identities or ideologies, we believe our realities meet at the most basic level of perception. But in 2015, a viral internet phenomenon tore this assumption asunder. The incident was known simply as ���The Dress.���


For the uninitiated: a photograph of a dress appeared on the internet, and people disagreed about its color. Some saw it as white and gold; others saw it as blue and black. For a time, it was all anyone online could talk about.


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Eventually, vision scientists figured out what was happening. It wasn���t our computer screens or our eyes. It was the mental calculations that brains make when we see. Some people unconsciously inferred that the dress was in direct light and mentally subtracted yellow from the image, so they saw blue and black stripes. Others saw it as being in shadow, where bluish light dominates. Their brains mentally subtracted blue from the image, and came up with a white and gold dress.

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The article discusses the phenomenon of "The Dress" that went viral in 2015, where people saw different colors in the same photograph of a dress (white and gold or blue and black). Vision scientists later explained that the variation in perception was due to the mental calculations our brains make when processing visual information.

The author highlights three new books that explore the peculiarities of human perception and consciousness:

"Being You" by Anil Seth proposes that our brains exist in a state of "controlled hallucination," constructing our subjective experiences by making predictions about the world based on sensory input. Seth argues that our entire perceptual experience is a result of our brain constantly making and updating these predictions.

"Coming to Our Senses" by Susan Barry tells the stories of individuals who gained new senses later in life and how their brain adapted and constructed perceptions in response to this new sensory information.

"What Makes Us Smart" by Samuel Gershman delves into the organization of human intelligence, discussing how our brain's limited data and computational resources lead to mental shortcuts and adaptive decision-making.

Overall, these books offer insights into the intricate and sometimes peculiar ways our brains process the world around us, challenging our assumptions about perception and reality.

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Context Changes Everything


Alicia Juarrero

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Alicia Juarrero's work titled "Context Changes Everything" explores the profound impact of context on how we perceive and understand the world. It delves into the idea that our interpretations, actions, and decisions are deeply influenced by the specific context in which we find ourselves. The book challenges the notion of universal laws or fixed rules governing human behavior and cognition, emphasizing that context plays a crucial role in shaping our experiences and interactions.

Juarrero's perspective suggests that understanding the complexity of context is essential in fields such as philosophy, cognitive science, and ethics. By recognizing the dynamic interplay between individuals and their environment, the book advocates for a more nuanced and comprehensive understanding of human behavior and decision-making. Overall, "Context Changes Everything" offers a thought-provoking exploration of the significance of context in shaping our perception and understanding of the world.

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I 1 What Went Wrong? The Backstory 3

Types, Kinds, and Essences 5

Primary and Secondary (Accidental) Properties 6

Interactions and Relations 10

Eff i cient Causality 13

Mereology 15

Physical Causal Closure and Overdetermination 16

2 The Path Forward 21

II

3 Constraints: An Introduction 35

What Are Constraints? 40

Spatial and Temporal Constraints 41

4 Context- Independent Constraints 49

Containers of Gas and Landscape Design 50

Vague and Ambiguous Constraints 54

Limited Message Variety 56

5 Why Context Matters��� An Interlude 59

Science 2.0 and Medicine 2.0 Are All about Context

Dependence 59

The Indirect Effects of Context 62

Contents

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viii Contents

6 Context- Dependent Constraints 67

Enabling and Constitutive/Governing Constraints 71

Temporal Constraints 73

Cardinality and Indexicality, Ordinality and Placement 75

Top- Down (Governing) Context- Dependent Constraints 79

Coordination Dynamics Satisfy Second Law 84

7 Catalysts, Loops, and Closure 87

Catalysts and Feedback Loops 87

Closure of Processes (Catalytic Closure) 90

Autocatalytic Closure 90

Constraint Closure 93

Statistical and Semantic Closure 96

Semantic Attractors 99

8 An Abundance of Constraints 103

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The book, titled "What Went Wrong? The Backstory" by Alicia Juarrero, delves into the concept of context and its profound impact on human perception, understanding, and decision-making. It explores various types of constraints and their role in shaping our experiences and interactions. The book also discusses context-independent and context-dependent constraints, highlighting the importance of considering context in different fields, including science and medicine.

The chapters in the book include discussions on primary and secondary properties, efficient causality, mereology, physical causal closure, and overdetermination. It further introduces the concept of constraints and explains their spatial and temporal aspects.

The book distinguishes between context-independent and context-dependent constraints, emphasizing their significance in enabling and governing various processes. It also delves into catalysts, feedback loops, and closure in processes, including catalytic closure and autocatalytic closure.

Overall, "What Went Wrong? The Backstory" presents a comprehensive exploration of the interplay between context and constraints, providing valuable insights into understanding human behavior and the complexities of the world around us.

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Repetition 104

Replication 105

Reproduction 107

Unity of Type in Species, Demes, and Memes 109

Density, Isolation, and Buffers 111

Isolation 112

Buffers and Other Shields 115

Motility and Migration��� The Relaxation of Constraints 117

Templates, Frameworks, Scaffolds, and Affordances 120

Scaffolding 122

Types of Scaffolds 124

9 Persistence��� Delaying the Second Law 129

Persistence and Thermodynamics 130

The Principle of Persistence 135

Selection by Persistence 139

10 Sedimentation and Entrenchment 143

Sedimentation, Memory, Records, and Registers 143

Entrenchment 145

Varieties of Entrenchment 148

Generative Entrenchment 151

Generative Entrenchment of Validated Constraints 153

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Contents ix

11 Many- to- One Transitions, Effective and Analog Control 155

Tagging Emergent Properties 163

Analog Control 167

Analog Control and Energy Management 169

Multiply Realizable Domains Are Analog Spaces 174

12 Of Holons, Holarchy, Heterarchy, and Hierarchy 177

Koestler���s Holons and Holarchies 177

Levels of Organization 183

Mereology Revisited 186

Extensional and Intensional Def i nitions 192

Control Hierarchy 194

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The book "What Went Wrong? The Backstory" by Alicia Juarrero continues its exploration into the interplay between context and constraints. The chapters delve into various concepts and phenomena, including repetition, replication, and reproduction. It discusses the unity of type in species, demes, and memes, as well as density, isolation, and buffers in the context of constraints.

The book further examines motility and migration, which represent the relaxation of constraints. It explores the concepts of templates, frameworks, scaffolds, and affordances, with a focus on scaffolding and its types.

Another significant theme in the book is persistence and its relation to thermodynamics. The principle of persistence and selection by persistence are discussed, highlighting how delaying the second law of thermodynamics plays a role in various processes.

Sedimentation and entrenchment are also explored, considering the concepts of memory, records, registers, and generative entrenchment of validated constraints.

The book delves into many-to-one transitions, effective and analog control, tagging emergent properties, and analog control's role in energy management and multiply realizable domains.

Additionally, the concepts of holons, holarchy, heterarchy, and hierarchy are discussed, along with levels of organization and control hierarchy.

Overall, "What Went Wrong? The Backstory" offers a comprehensive exploration of complex phenomena, providing valuable insights into the principles and dynamics of various systems influenced by context and constraints.

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III

13 The Backstory, Today 197

Functionalism 200

Chinese Room Objection 201

Principle of Supervenience 202

Multiple Realizability 204

The 4E Approach Today 205

14 Multiple Realization and Supervenience: A Philosophical

Case Study about Constraints 211

Shapiro and Gillett on Multiple Realizability 211

Lange��� Because without Cause 216

Principles and Laws 216

15 Empirical Research on Delayed Response: Neuroscience Case

Studies about Constraints 223

Mark Churchland���s Team 224

Preparatory and Perimotor Neural Activity 225

A Further Study 227

16 Concluding Remarks 233

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In the third part of the book "What Went Wrong? The Backstory" by Alicia Juarrero, the focus shifts to contemporary discussions and research related to context and constraints. This section covers philosophical case studies and empirical research on how constraints influence various phenomena.

Chapter 13 introduces the concept of functionalism and its relation to the Chinese Room Objection, the Principle of Supervenience, and multiple realizability. It also discusses the current status of the 4E approach, which stands for embodied, embedded, enactive, and extended cognition.

Chapter 14 presents a philosophical case study on multiple realization and supervenience, particularly exploring the ideas put forward by Shapiro and Gillett. Additionally, the chapter references Lange's work on principles and laws.

Chapter 15 focuses on empirical research, particularly in neuroscience, related to delayed response and constraints. The research includes case studies led by Mark Churchland's team, investigating preparatory and perimotor neural activity, and other related studies.

Finally, in Chapter 16, the book concludes with the author's closing remarks, summarizing the key points explored throughout the book and potentially providing some reflections on the significance of the interplay between context and constraints in understanding complex phenomena.

Overall, the third part of the book offers a contemporary perspective on the themes of context and constraints, combining philosophical analysis and empirical research to further our understanding of the dynamic interactions in various systems and processes.

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The controversy surrounding the concept of identity illustrates how phil-

osophical and scientif i c presuppositions that go without saying entangle

us in never- ending mazes.

In the history of ideas, claims that identity consists of a def i ning essence

have a long backstory. In fact, one could arguably claim that it is among

the oldest backstories in philosophy, a backstory that involves the paradox

of the One and the Many. What makes different entities (e.g., dachs-

hunds, boxers, chihuahuas, Great Danes) the same, that is, dogs? What

makes anything continue being the same thing? How is it that something

can persist as itself��� despite changes wrought by either developmental

processes, the environment, or internal malfunction?

Issues with identity are not new; the problem was fi rst posed in the sixth

century BCE. The classical version went as follows: If all the planks of the

ship of Theseus are replaced over time, is it still ���the ship of Theseus,���

even when not one of the original planks remains? Does anything persist

as the same thing, the ship of Theseus, despite such signif i cant alterations?

How is change compatible with remaining the same? What does same

mean, in this context or any other?

In 2019, Chinese scientists inserted a human gene into the brains of

eleven monkeys; those monkeys then outperformed normal monkeys in

tests of short- term memory. Even more striking, the modif i ed monkeys���

brain developed into an organ more like a human���s than like that of

the unmodif i ed monkeys (Regalado 2019). Are these animals now partly

human? In 2021, an international team of scientists injected human

stem cells into primates (Subbaraman 2021). The interspecies chimeras

grew for two weeks before being destroyed. If a human being���s body

parts are gradually replaced with silicon components until no original

organic material remains, would they still be human, or a cyborg? If all

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What Went Wrong? The Backstory

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4 Chapter 1

my memories disappeared, or if my beliefs suddenly became entirely dif-

ferent, would I still be me? What is it to be me? Just as the Ship of Theseus

is one of the oldest backstories in philosophy, tales of aliens taking over

the bodies of earthlings are among the oldest themes in science fi ction.1

Today���s controversy about identity is not just an old story; it is also

an oft- told story (Toulmin 1990; Juarrero 1999). However, the central

theme of this book is not identity, nor will this book be solely a survey

of these debates. The problem of identity happens to be a noteworthy

philosophical topic that encapsulates in a single controversy three cat-

egories that have been egregiously responsible for framing our views of

reality in a misleading manner. Our understanding of many concepts, not

only those that arise with respect to identity, continues to be misdirected

by outdated and erroneous ideas about three central issues:


��� Are wholes different from aggregates?

��� Are context and history part of the fabric of reality?

��� How do cause and effect work?

The three questions are so deeply interwoven in the way we see things

that a discussion of one inevitably brings to bear the others. The problem

of wholes and aggregates is the problem of Types or Kinds and Essences,

the problem of context and history is the problem of Interactions and

Relations, and the problem of causes and effects is, well, the huge philo-

sophical problem of Causation.

The last one, Causation, is the most recalcitrant and pervasive of the

three. It wraps around the other two: Do interactions among individ-

ual entities create real novelty in the form of coherent wholes? Can the

context in which an event occurs have any inf l uence either on whether it

happens at all or on exactly what happens?

This chapter presents highlights from the history of these ideas. It

describes how relations and interactions, context and history, came to be

thought of as causally impotent; how seemingly coherent totalities were

reduced to nothing but aggregates; and how the idea of cause and effect

came to be restricted to energy- transferring processes. These controver-

sies are problematic, not only because of what they have to say about the

nature of identity; they mainly arise because of our deeply fl awed views

about causality and coherence��� about the causes of coherence. Once we

understand what went wrong with these two notions, we can begin to rei-

magine a different and more inclusive interpretive framework that can also

make room for identity as contextually embedded coherence and interde-

pendence. The book takes preliminary steps in that direction.

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The passage discusses the philosophical and scientific controversies surrounding the concept of identity. It begins by mentioning the classical Ship of Theseus paradox, questioning what makes different entities the same (e.g., different dog breeds) and how something can persist as itself despite changes. The passage then mentions recent scientific experiments involving the modification of animal brains and bodies, raising questions about identity and whether alterations make them different beings.

The author highlights that issues with identity have a long history in philosophy and are intertwined with three central questions:

Are wholes different from aggregates? (Problem of Types or Kinds and Essences)

Are context and history part of the fabric of reality? (Problem of Interactions and Relations)

How do cause and effect work? (The problem of Causation)

The chapter aims to provide an overview of the historical development of these ideas and how they have influenced our understanding of identity. It addresses the reduction of seemingly coherent totalities to mere aggregates and the restriction of cause and effect to energy-transferring processes.

The passage concludes by asserting that these controversies are rooted in flawed views about causality and coherence, leading to the need for a different interpretive framework that considers identity as contextually embedded coherence and interdependence. The book aims to explore and reimagine such a framework.

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Types, Kinds, and Essences

The fable of the Scorpion and the Frog shows how ���identity��� has tradi-

tionally been thought to capture the essence that uniquely distinguishes

something from everything else��� everything else that something is not.

The scorpion asks the frog to ferry it across the river safely. When the

frog hesitates, fearful the scorpion would kill it, the scorpion protests

that doing so would mean that both would drown. The frog accepts that

reasoning. Halfway across the river the scorpion stings the frog. As they

are both drowning, the dying frog asks the scorpion, ���Why did you do

that?��� To which the scorpion replies, ���I couldn���t help it. It���s my nature.���

Thinking of identity in this way suggests that if certain properties, inter-

nal to the creature, were missing, it would no longer be itself because

those properties def i ne what it is to be a scorpion. They capture, that is, a

thing���s fundamental essence and therefore its identity.

The idea of nature or essence as internal and standalone is notewor-

thy because of the unacknowledged assumptions it uncritically accepts.

Essence as internal represents a refusal to acknowledge that interactions

and relations play a role in a thing���s nature; it also refuses to recognize that

relational properties like coordination, integration, and context embed-

dedness are real. It ignores both the past and current circumstances. It

underpins, in short, a worldview that dismisses time and place��� context

in general��� from reality. These become passive containers instead. Such

failures make it impossible to understand coherence and identity.

That backstory goes as follows.

Beginning with Thales in the sixth century BCE, pre- Socratic philoso-

phers embarked on a search for the essence and nature of reality. What

made pre- Socratics different from their precursors was their faith in

reason and logic, as opposed to an unquestioning acceptance of mythic

tales (Juarrero 1993). Is Water the foundation of reality, asked Thales?

Is there more than one fundamental essence��� perhaps, air, wind, fi re, as

well as water? Maybe all four, as Empedocles proposed? Or is the essence

of reality change (Heraclitus)? Or an unchanging Plenum (Parmenides)?

Lucretius, the fi rst recorded atomist, noted that whatever turns out to be

fundamental must be in- divisible��� a- tom. Otherwise, it could be decom-

posed into more simple stuff and so would not be fundamental. The late

Carl Sagan, host of the popular public television series Cosmos, lamented

that the history of ideas went wrong when Socrates veered from this

pre- Socratic interest in cosmological and natural questions and turned

instead to ethical and normative ones.


Fast forward to the eighteenth century. Modern English atomist John

Dalton noticed that chemicals could be combined into more complex sub-

stances or broken down into more fundamental elements. In a nod toward

Lucretius, Dalton called the fundamental particles atoms and identif i ed

weight as their primary property. In that same century, French chemist

Antoine Lavoisier added mass as a second primary property of atoms.

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The passage discusses the traditional understanding of identity and essence through the fable of the Scorpion and the Frog. The idea of identity capturing the unique essence that distinguishes something from everything else is explored. The concept of nature or essence as internal and standalone is highlighted, which overlooks the role of interactions, relations, and context in defining a thing's nature.

The historical backdrop of the search for the essence and nature of reality is presented, starting with pre-Socratic philosophers like Thales, who sought to understand the fundamental essence of reality. The passage mentions different perspectives, such as the proposal of multiple fundamental essences by Empedocles and the idea of change as the essence by Heraclitus. It also notes that the modern English atomist John Dalton identified atoms as fundamental particles with weight and mass as their primary properties.

Overall, the passage explores how the traditional understanding of identity and essence has evolved from ancient philosophical inquiries to modern scientific perspectives, and it raises questions about the role of interactions, context, and relations in defining the nature of things.

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Primary and Secondary (Accidental) Properties

Modern science and philosophy consolidated the idea of primary proper-

ties as the ground of reality and therefore of identity; only primary prop-

erties constitute the essence of things. One of the features that allegedly

makes primary properties primary is their ability to exist on their own,

independent of others; they do not depend on anything else either to exist

or to be perceived. Properties like atomic weight and mass��� those that

underlie solidity, extension, and quantity��� are often listed as preeminent

examples of primary properties. From this perspective, essence and iden-

tity are what might be called internalist concepts: they pick out proper-

ties that are internal to the entity in question; they are also objectively

measurable and observer independent.

Once the internalist def i nition was adopted, concluding that interactions

contribute nothing fundamental to reality followed. Relations with other

entities in the environment and with the past bring context to bear, but

because context was viewed as a container external to the thing���s essence,

it too was set aside as irrelevant to identity. The philosophical conundrum

posed by the measurement problem in quantum physics originates in this

framing.

Contrast the seeming ontological independence and self- suff i ciency of

atomic mass and weight with the context dependence of color and sound.

It has been known since classical times (Democritus) that fl avors, odors,

color, sounds, and even temperature are inherently relational and con-

textual. Inserting a hand in a bucket of tepid water feels cold if it comes

after inserting the hand in hot water, but it feels warm if it comes after icy

water. Because they are not independent of perception, relational proper-

ties dependent on an observer were considered subjective.2 In the language

of academic philosophy, properties that arise from interactions, especially

with human observers, are secondary or accidental properties. For that

very reason, they are also ontologically secondary, their reality derivative.

In natural philosophy, Kind traditionally refers to natural kinds and

is often used synonymously with Type and Universals to mean classes of entities or processes def i ned by common primary properties.3 ���It���s my [scor-

pion] nature��� follows that reasoning. On this view, kinds and types pick out

real, universal features in the world. Scorpionality, if you will, is real, the set

of primary properties that makes scorpions scorpions. The elements of the

periodic table are prototypes of natural kinds not least because they repre-

sent measurable and observer- independent properties such as the number of

protons in the nucleus. All instances of element X have Y number of protons

in their nucleus. This primary property constitutes their essence.

It is important to note that, even in classical times, types, kinds, and uni-

versals were understood to be multiply realized: differently embodied tokens

can realize the same type. Some actual scorpions are ground dwelling; others

are tree dwellers, but as scorpions, they possess the same basic primary prop-

erties. Likewise, whether isosceles, equilateral, or scalene, actual triangles are

tokens of the type triangularity. They all realize its essential, primary prop-

erties: three- sided, enclosed, two- dimensional fi gures whose interior angles

sum to 180 degrees. They would not be triangles if they did not.

According to Plato, even if material tokens of types ceased to exist, if

this triangle I drew in the sand got washed away with the tide, the essence

of triangularity would continue to exist even if no longer instantiated. Pla-

tonic Forms such as Justice, Goodness, Truth, and Beauty as well as tri-

angularity and numbers were thought to exist in a transcendental realm,

fi xed and eternal. They were considered real even if no actual triangles, or

written numbers, or actual cases of justice, goodness, truth, or beauty had

ever existed.

So, Carl Sagan did not get it quite right: Socrates was not entirely deviat-

ing from the tradition of the pre- Socratics. Platonic dialogues such as the

Republic (about justice) and Meno (about knowledge acquisition) narrate

Socrates��� attempts to elucidate and def i ne the universal and eternal essences

of justice, knowledge, truth, and goodness. Socrates��� efforts to articulate

the inherent properties of universals are therefore not entirely unlike pre-

Socratic attempts to discover the essential traits of natural phenomena.

Because types and forms can be realized in multiple instances or

tokens, each different from the next, providing a full list of actual realiza-

tions does not capture a type���s essence; to do so, scholars must discover

the full set of its primary properties. That is what real (as opposed to

ostensive) def i nitions do. Even after Plato���s inf l uence gave way to Aristo-

tle���s, and well before formulating natural laws became the central aim of

science, classifying natural kinds such as types of rock (igneous, sedimen-

tary, metamorphic) or biological taxons such as vertebrates by discover-

ing their primary properties consumed most scientists��� time.

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The passage discusses the concept of primary and secondary (accidental) properties in modern science and philosophy. It explains how primary properties are considered the ground of reality and the essence of things, as they can exist independently and are objectively measurable. Properties like atomic weight and mass are often cited as primary examples.

The adoption of an internalist definition of essence led to the dismissal of interactions and relations as contributing nothing fundamental to reality. Context was viewed as an external container and thus irrelevant to identity, which created philosophical conundrums, such as the measurement problem in quantum physics.

The passage contrasts the seeming ontological independence of primary properties like atomic mass and weight with the context dependence of secondary properties like color and sound. Secondary properties are considered subjective and derivative, arising from interactions, especially with human observers.

The discussion also involves the concept of kinds and types, which refer to classes of entities or processes defined by common primary properties. Kinds and types are seen as real, universal features in the world, and they can be realized in multiple instances or tokens, each different from the next. Providing a full list of actual realizations does not capture a type's essence; instead, scholars must discover the full set of its primary properties through real definitions.

The passage mentions Plato's view of Platonic Forms, which exist in a transcendental realm and are considered real even if no actual instances of them exist. It also notes that classifying natural kinds by discovering their primary properties consumed most scientists' time before formulating natural laws became the central aim of science.

Overall, the passage delves into the distinction between primary and secondary properties, the role of interactions and context in defining identity, and the significance of primary properties in classifying natural kinds and types.

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Multiple realizability, also called degeneracy in biology, where it

is ubiquitous, will play a key role in this story. The terms refer to the

capacity of different events and processes to realize the same function

or other higher- level property. The main idea presented in this introduc-

tory chapter is that according to the received understanding of types

and kinds, individual tokens of a given kind were thought to differ only

in their secondary properties. Their essential, primary properties, those

that identify them as a type of thing��� a given species, for example��� are

inherent, universal, and unchanging throughout. As late as the nineteenth

century, this was even thought to be so in nature; Darwin���s proposal that

new species originated by evolving in response to selection was contro-

versial for that very reason. ***

The way philosophers thought about essences and types evolved over the

course of the history of ideas. As just mentioned, Plato concluded they

were real transcendent forms. Aristotle, on the other hand, did not agree

that form and matter could exist independently. In opposition to Plato���s

disembodied realm of forms, Aristotle focused on embodied Substance,

the unity of in- formed matter.

Living things are quintessential examples of Aristotelian in- formed

matter. In contrast to compacted masses of pebbles, for instance, organisms

���hang together��� in a unique way; they embody or realize a coherence that

Aristotle postulated as the essence of substance.4 Aristotelean substances

are also independent existents, the other hallmark of reality for both phi-

losophy and science.5 On this view, actual lions are the coherent unity of

the form Lion with the appropriate matter. In comparison to colors, sounds,

or fl avors, actual lions do not require observers to exist. In lieu of the oth-

erworldly existence of Plato���s forms, the essence of Aristotelean substances

was therefore embodied self- suff i ciency.

From both Plato and Aristotle���s realist perspective, forms and universals

are real. It was not until later in the history of Western thought that uni-

versals or types came to be considered mere labels or tools with which we

think and organize our concepts and actions, or with which we design and

conduct scientif i c experiments. This perspective, known as nominalism,

held that the generality of common nouns is our doing; properties that

def i ne common nouns do not refer to objective essences. In contrast to

realism, nominalism argued that all that really exists are actual particulars.

With the rise of scientif i c method in the sixteenth century, observa-

tion and analysis were elevated over a priori reasoning and synthesis.

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The passage discusses the concept of multiple realizability (also called degeneracy) in biology and its role in the story being presented. Multiple realizability refers to the capacity of different events and processes to realize the same function or higher-level property.

In the context of the received understanding of types and kinds, individual tokens of a given kind were believed to differ only in their secondary properties. Their essential, primary properties, which identify them as a specific type of thing (e.g., a species), were considered inherent, universal, and unchanging. This view of fixed and unchanging essences even extended to nature itself, with Charles Darwin's proposal of species evolving through selection being controversial for challenging this notion.

The passage then traces the evolution of philosophical thought about essences and types. Plato believed in real transcendent forms, while Aristotle focused on embodied substances, where living things exemplified Aristotelian informed matter. According to Aristotle, organisms embodied a coherence that represented their essence. Aristotelian substances were considered independent existents and did not require observers to exist.

However, later in the history of Western thought, the perspective shifted towards nominalism. Nominalism argued that universals or types were mere labels or tools for human thinking and organization. According to nominalism, properties defining common nouns do not refer to objective essences; instead, only actual particulars are considered to exist.

With the rise of scientific method in the sixteenth century, observation and analysis gained prominence over a priori reasoning and synthesis, leading to changes in how philosophers approached the concept of essences and types.

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In Novum Organum (New Method), English philosopher and political

leader Francis Bacon proposed a new way of reasoning. In contrast to

medieval Scholasticism���s focus on a priori reasoning, Bacon���s scientif i c

method was based on induction, on inferring general conclusions from

fi ne- grained, precise observations. In Discourse on Method a century

later, French philosopher and mathematician Ren�� Descartes laid out a

technique for knowledge acquisition that returned to deduction. Never-

theless, it required thinkers to begin with the most elementary and there-

fore indubitable ideas instead of accepted beliefs or revealed truths. In

either case (Baconian induction or Cartesian deduction), the proper way

to acquire knowledge was by starting from the elements (bare observa-

tions or clear and distinct ideas) and then proceeding to reconstruct the

whole.

Threats to coherence are already present in this approach. Before Des-

cartes, medieval thinkers like Christian Thomas Aquinas, Jewish Moses

Maimonides, and Muslim Ibn Rushd (Averroes) followed Aristotle in the

assumption that coherent substance��� unity of form and matter��� is the

default basis of reality. What is the source of the coherence of embodied

substance? Alas, Aristotle���s writings did not fully resolve the question of

how embodied substance, in- formed matter, is bound into coherent and

unif i ed wholes (Gill and Lennox 1994).

In contrast, inf l uenced by modern atomists such as French thinker

Pierre Gassendi and English experimentalist Robert Boyle, modern sci-

entists and philosophers prioritized analysis over synthesis, parts over

the whole. In doing so, the philosophical problem of identity was trans-

formed from ���How does essence in- form matter and confer on it its iden-

tity?��� into ���How do primary properties cohere into complex wholes?���

Whence coherence? Or, more precisely, whence the cause of coherence?

In Descartes��� writings, Aristotelian embodied substance sundered into

mind and matter, two distinct ontological domains, each with its own sub-

stance and each def i ned by its distinct primary property. Mind is def i ned

by its primary property, res cogitans, whose essential trait is conscious-

ness, and matter, res extensa, by its primary property, spatial extension.

Known as dualism, the theory maintained that both substances, mind

and matter, were real.6 It is unsurprising, therefore, that by the middle

of the seventeenth century, fears about whether coherence was even pos-

sible were being voiced. In his famous poem, An Anatomy of the World

(1611), English poet and soldier John Donne lamented, ���Tis all in pieces,

all coherence gone.���

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The passage discusses the shift in philosophical reasoning methods from medieval Scholasticism to the scientific methods proposed by Francis Bacon and Ren�� Descartes.

Francis Bacon proposed a scientific method based on induction, inferring general conclusions from precise observations. On the other hand, Ren�� Descartes advocated for a method based on deduction, starting with elementary and indubitable ideas and then reconstructing the whole.

Before Descartes, medieval thinkers like Aquinas, Maimonides, and Ibn Rushd followed Aristotle's assumption that coherent substance, unity of form and matter, is the default basis of reality. However, Aristotle's writings did not fully address how embodied substance, informed matter, becomes bound into coherent and unified wholes.

Modern scientists and philosophers, influenced by atomists like Gassendi and Boyle, prioritized analysis over synthesis, focusing on parts rather than the whole. This shift transformed the philosophical problem of identity from "How does essence inform matter and confer its identity?" to "How do primary properties cohere into complex wholes?"

Descartes' writings introduced the concept of dualism, where mind and matter were considered two distinct ontological domains, each with its own substance and primary property. This view raised questions about whether coherence was even possible.

The passage ends with a quote from John Donne's poem "An Anatomy of the World," expressing concerns about the loss of coherence and fragmentation of reality.

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But doubts about coherence did not begin in the seventeenth century.

Philosophers as far back as Plato were sophisticated enough not to confuse

form (an entity���s core type identity) with shape. Justice was a Platonic form,

for example, although it obviously has no shape. If forms are transcendent,

however, how are actual entities related to the form that makes them what

they are, that is, that imbues them with their essential nature?

Plato���s famous allegory of the cave taught that physical objects are

mere shadows of forms. Over the centuries, explaining how shadows or

simulacra (material tokens) ���partake in��� or embody transcendent forms

became a cottage industry. Plato thought of matter as a corrupting inf l u-

ence: when ideal forms get mixed in with matter, the result is a degraded

reality. A few centuries later, and to avoid the Paulist and Augustinian

disposition to label all matter corrupt after the Fall, Neo- Platonists such

as Plotinus identif i ed Platonic forms with God and suggested that they

emanate into matter. Forms somehow ooze into matter?7 Philosophy

searched for a principle of coherence that binds transcendent forms to

matter such as to generate coherent wholes.

The generation and preservation of coherence and its emergent prop-

erties is the central subject matter of this book.

Descartes��� proposal that mind and body are two separate and dis-

tinct substances, each capable of independent existence and character-

ized by nonoverlapping essences, raised additional questions. Juarrero

1999 focused on how intentional causation and therefore purposive

action (as opposed to ref l ex reaction) are even possible. How can two

substances from entirely different ontological domains, the extended

physical and the conscious nonphysical, interact at all? How can a non-

physical event like the intention to do X move the body such that the

ensuing behavior carries out the content of that intention, doing X?

Purposive action and the mind��� body problem became the crucible of

coherence. This book focuses on mereological causation, that is, on how

interacting entities generate wholes with novel properties and how those

wholes, once they coalesce, guide behavior. In particular, it focuses on

the manner of causation that generates and preserves parts��� whole and

whole��� parts coherence.

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The passage delves deeper into the historical doubts and philosophical inquiries surrounding coherence and the relationship between forms and matter.

Philosophers like Plato recognized that forms, representing the core type identity of entities, were distinct from their physical shapes. Justice, for example, was considered a Platonic form despite lacking a tangible shape. Plato's allegory of the cave emphasized that physical objects were mere shadows of transcendent forms, giving rise to debates on how these shadows or material tokens "partake in" or embody these transcendent forms.

Plato regarded matter as a corrupting influence, resulting in a degraded reality when mixed with ideal forms. Neo-Platonists, like Plotinus, proposed that these forms were associated with God and emanated into matter. Philosophers sought a principle of coherence that could connect transcendent forms with matter to generate coherent wholes.

The central focus of the book discussed in the passage is the generation and preservation of coherence and its emergent properties. The questions raised by Descartes' proposal about the separation of mind and body, each with its own essence and existence, added complexity to understanding purposive action and intentional causation. How could two substances from different ontological domains, the physical and the nonphysical, interact? How does a nonphysical event like intention result in purposeful behavior?

The book centers on mereological causation, exploring how interacting entities generate coherent wholes with novel properties and how those wholes, once formed, guide behavior. It specifically focuses on the causation that creates and sustains coherence between parts and wholes.

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Interactions and Relations

Hypotheses about coherent wholeness and its primary and secondary

properties intersect with views about the status of interactions and rela-

tions. As noted earlier, context and interactions, including fl uctuations and perturbations, were presumed not to affect essential primary proper-

ties of fundamental elements or substances. To repeat, whether these consist

of mass and atomic weight or thought and extension, primary properties

were allegedly eternal, fi xed, and universal, and they inhered in the entity

whose essence and identity they underpin. Neither context nor history, not

to mention process, alteration, or fl ux, could change those fundamental

building blocks of reality.8 ���It���s my nature.��� The essence of particles and

substances (including minds) was internal, remained unaltered despite sec-

ondary modif i cations, and was capable of separate and independent exis-

tence. And, as always, relations and interactions with other particles or

substances were considered neither essential nor foundational.

***

The fi eld of chemistry is all about relations and transformations; chemists

study interactions among molecules and charged particles. However, if

relations and interactions are secondary, chemical compounds and chemi-

cal synthesis cannot then be fully real, qua chemical, as philosophers say.

They must be nothing but aggregates of primary and essential properties

of constituent physical elements. Chemical properties must be the acci-

dental eff l uvia of clumped particles.

On this view, then, the apparent unity of chemical compounds, or living

things, is illusory; wholes (including organisms) are mere agglomerations,

the sum of their elementary parts. Material aggregates do not generate

coherence; they are just masses of physical stuff. They are nothing but

macroscopic clumps of elementary particles. They might appear to possess

qualitatively novel capacities and properties like oxidation, life, sensation,

and perception or even mind and consciousness. In reality, however, those

are mere side effects��� castoffs��� of aggregated masses of primary properties.

Those seemingly emergent properties and powers are ontologically deriva-

tive. They bring with them no powers of their own.

The principle that coherence is nothing but impotent aggregation is still

presumed to apply generally, not only in chemistry. It motivates the philo-

sophical perspective called reductionism, often characterized as ���nothing

but- ism.��� Reductionism maintains that because wholeness is nothing but

particles and their secondary interactions, any seemingly novel properties

of purportedly coherent wholes can be derived, in principle, if not in fact,

from laws pertaining to its constituent elements. Colloquially, ���Wholes are

nothing but the sum of their parts.��� On this view, descriptions of coherence

are either convenient labels or epistemic simplif i cations to which scien-

tists resort because computing all the details of micro- interactions among

primary properties takes too long.

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The passage highlights the intersection between views on coherent wholeness and the status of interactions and relations. Earlier beliefs held that essential primary properties of fundamental elements or substances were eternal, fixed, and universal, and they resided within the entity, forming its essence and identity. Context, history, and interactions were considered non-essential and not foundational to an entity's identity.

However, this perspective runs into issues when considering fields like chemistry, which revolve around relations and transformations among molecules and particles. If interactions are deemed secondary and essential properties are seen as fixed, then chemical compounds and synthesis may not be considered fully real in their chemical nature. Instead, they would be viewed as mere aggregates of primary properties of individual physical elements. This reductionist perspective undermines the apparent unity and coherence of chemical compounds and living organisms, suggesting that they are nothing but macroscopic clumps of elementary particles.

According to reductionism, the coherence observed in wholes is merely the result of impotent aggregation of particles and their interactions. Any seemingly emergent properties and powers in coherent wholes are considered ontologically derivative, devoid of any real power or novelty. Reductionism posits that descriptions of coherence are merely convenient labels or epistemic simplifications, as the true understanding lies in the micro-interactions among primary properties.

Overall, this passage highlights the debate between reductionist perspectives, which consider wholes as nothing more than the sum of their parts, and alternative views that recognize emergent properties and powers resulting from complex interactions and relations among elements. The book seeks to explore a different framework that accounts for the generation and preservation of coherence in a more inclusive manner.

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In summary, reductionists maintain that, in principle, chemical, biologi-

cal, psychological, sociocultural, or ecological processes, reactions, combi-

nations, transformations, changes, and rearrangements of elements will all

be fully accounted for by internal, context- independent, and fully quan-

tif i able, essential��� that is, primary��� properties of fundamental particles.

The inevitable conclusion of the foregoing is that seemingly coher-

ent entities like biological organisms and chemical compounds are caus-

ally powerless as biological and chemical wholes; if apparently coherent

���wholes��� are mere aggregations, their seemingly emergent properties are

powerless. In the jargon of philosophy, coherence and emergent proper-

ties that characterize that apparent coherence are epiphenomenal, that

is, causally impotent as such. The heavy causal lifting is always and only

done by the fundamental elementary particles (van Gulick 2004). Accord-

ingly, the arrow of explanation always looks downward, as the saying

goes, because reality is grounded in the primary properties of elementary

particles, which underwrite natural laws.

In short, misconceptions about causation cut across the previous con-

siderations. According to the standard physics- based framework, as just

described,

��� Essences reside in internal and self- suff i cient primary properties capable

of independent existence. This implies that context and history are not

fundamental features of reality.

��� ���Wholes��� that appear to display novel and emergent properties are,

at bottom, nothing but the sum of those primary properties and their

interactions.

It follows that causal powers reside exclusively in fundamental parti-

cles and their primary properties. Bottom- up inf l uences might bubble up

from parts to aggregates, but with the following caveats: (1) any apparent

coherence or wholeness is mere aggregation, and (2) seemingly emergent

properties such as phenomenal awareness and feelings are, likewise, epi-

phenomenal characteristics of aggregated elementary particles.

Specif i cally, according to reductionism, our intuition that mental pro-

cesses such as intentions and beliefs have powers to actively bring about

meaningful, purposive actions is illusory. Thoughts, feelings, and inten-

tions derive their powers and properties from biology; biology from those

of chemistry; chemistry from physics. Properties that appear unique to

biological organisms (such as being alive) or human beings (such as sym-

bolic language) can, in principle, be inferred from chemical processes that constitute them. Causal powers that seem to issue from those higher- level

properties can be derived from physical properties, at least in principle. It is

not quite ���turtles all the way down,��� however. The turtle at the bottom (at

the level of elementary physics) is special. The primary properties of a- toms,

reality���s constituents (read now quarks and electrons), are the real and most

simple stuff that does the causal work and provides explanatory power.

Ultimate causes reside in and issue from there. Meaning and purpose are

impotent.

Such is the dream of a theory of everything, the promise of an equation

that spells out the lawful correlations among microdetails and from which

everything else can be derived and precisely predicted. It is this intellectual

heritage, I submit, that prompts well- known philosophers like Australian

David Chalmers to espouse double- aspect monism or its close relative,

panpsychism, the view that even the fundamental constituents of reality

must have a built- in nonphysical aspect, mentality. Without literally build-

ing in consciousness into the most basic building blocks of reality from the

start, hopes of showing how novel properties emerge from material stuff

are doomed to failure because material stuff can only increase in quantity.

The Cosmos does not actively create qualitative novelty. Full stop.

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In summary, reductionists argue that all processes and phenomena in chemistry, biology, psychology, sociology, and ecology can ultimately be fully explained and accounted for by the internal, context-independent, and quantifiable primary properties of fundamental particles. From this perspective, seemingly coherent entities like organisms and chemical compounds are considered causally powerless as wholes, and any apparent emergent properties are deemed epiphenomenal, meaning they have no causal influence.

According to reductionism, essences are rooted in self-sufficient primary properties capable of independent existence, and context and history are not fundamental aspects of reality. "Wholes" are seen as mere aggregations of their constituent primary properties and interactions. Causal powers are believed to reside exclusively in fundamental particles and their primary properties. Higher-level properties, including mental processes like intentions and beliefs, are considered reducible to lower-level properties, such as chemical or physical processes.

The reductionist approach envisions a "theory of everything" that would explain all phenomena in terms of fundamental physics. The hope is to derive everything from a set of fundamental equations and predict all aspects of reality precisely. However, this perspective has been criticized for overlooking the potential emergence of new qualities and powers at higher levels of complexity.

In response to the limitations of reductionism, some philosophers, like David Chalmers, have proposed alternative views, such as double-aspect monism or panpsychism. These views suggest that even fundamental constituents of reality might possess nonphysical aspects, such as consciousness or mentality, which cannot be derived solely from physical properties.

Overall, the reductionist perspective assumes that causal powers and novel properties are exclusively rooted in fundamental physics, with higher-level phenomena being reducible to lower-level descriptions. However, this perspective faces challenges when addressing the emergence of qualitative novelty and consciousness, leading some thinkers to explore alternative frameworks that incorporate nonphysical aspects.

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Eff i cient Causality

A particular understanding of cause- and- effect relations advanced by

Newtonian science gave additional support to this worldview. By restrict-

ing cause��� effect relations to eff i cient cause, the ontological status of

coherent wholes became even more suspect.

I turn now to the backstory on causality.

The fi rst systematic treatise of causation was Aristotle���s Physics,9 which

argued that everything must be explained in terms of four Causes. The fi rst

three are Material cause, the physical stuff from which something is made;

Final cause, the purpose or goal the substance brings about; and Formal

cause, the inherent essence that makes it that kind of substance and no

other. Consider a potter shaping a pitcher or a carpenter making a chair.

Material causes of the pitcher and chair are clay and wood, respectively.

Final causes are pouring liquids and sitting. (In nature, the intrinsic tele-

ology or fi nal cause of, say, acorns, is to become an oak. Teleology is built

into nature.) Aristotle illustrated the fourth cause, Eff i cient cause, with

descriptions of the potter���s hands transforming clay into a pitcher and the

carpenter���s arm wielding saws or hammers10 on wood. More recently, the preferred illustration of eff i cient causes is cue sticks striking billiard balls.

Eff i cient causes are energetic forces acting on matter.

With the advent of modern science and philosophy, fi nal and formal

causes (which Bacon disparaged as ���metaphysics���) could be dismissed

as ���no part of science.��� Empiricism held that material cause could be

accounted for through empirical observation of primary properties, and

purposive or fi nal cause came to be viewed as an irrelevant leftover from

the discredited belief that the ultimate drive of all living things is toward

perfection and God. The ghostly concept of formal cause became otiose

as nominalism took hold.

As a result, modern science turned to Aristotle���s eff i cient cause, the

transfer of energy to matter with which forceful impacts bring about

effects. After the sixteenth century, the term causality and its cognates

came to mean exclusively eff i cient cause, the transfer of kinetic energy

from an agent- cause to a body. Since the advent of Newtonian mechanics

in the seventeenth century, cause��� effect relations have been conceptualized

solely in terms of motive forces. This perspective was amply rewarded with

Newton���s Laws of Motion and justif i ably so. I hasten to state unequivo-

cally that nothing in this work should be taken as a rejection of or argu-

ment against eff i cient causes or Newtonian science. When calculating

planetary motions, however, adding a third planet yields a system that is

chaotic and unpredictable. The laws of motion fail to predict their trajec-

tories. Newton himself was aware of this so- called three body problem, an

example of environmental inf l uence completely transforming a system���s

dynamics. The puzzle was an early hint that context should not be so

readily dismissed, but modern science and philosophy ignored its warning.

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In the context of modern science and philosophy, the focus on efficient causality emphasized the transfer of energy from one object or agent to another, leading to observable effects. This approach largely disregarded final and formal causes that Aristotle had proposed in his philosophy. Final causes, which refer to the purpose or goal of an entity, were seen as irrelevant and metaphysical, while formal causes, relating to the inherent essence of a substance, became obsolete with the rise of nominalism.

Efficient causes, on the other hand, took center stage in the scientific worldview, particularly after the development of Newtonian mechanics in the seventeenth century. Newton's Laws of Motion demonstrated the power of understanding cause-effect relations in terms of forceful impacts and energy transfer. These laws were successful in predicting the motion of celestial bodies and many other physical phenomena.

However, there were early indications that this exclusive focus on efficient causality might have limitations. The three-body problem in celestial mechanics showed that when dealing with complex systems, such as three interacting celestial bodies, the predictability of their trajectories breaks down and becomes chaotic. This highlighted the importance of considering context and interactions among entities, which modern science and philosophy largely overlooked.

The reductionist perspective, influenced by Newtonian mechanics, often ignores the influence of context, history, and emergent properties in generating coherent wholes. As a result, it can underestimate the significance of relationships, interactions, and feedback loops in shaping the behavior and properties of complex systems. The focus on efficient causality alone might not fully capture the dynamics of interconnected entities and the emergence of new qualities in coherent wholes.

Thus, the emphasis on efficient causality, while successful in many cases, may not be sufficient to provide a comprehensive understanding of complex systems, emergent properties, and the dynamics of interconnected entities. A more holistic approach that considers all causes, including final, formal, and efficient, as well as the role of interactions and relationships, may be necessary to address the challenges posed by the study of coherence and identity.

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By def i nition, eff i cient causes exist separately from their effects. Relying

exclusively on this form of causation, however, brought with it other, less

well- known implications.

Aristotle���s reasoning about eff i cient causes went as follows: since causes

and their effects cannot simultaneously exist both before (as cause) and after

(as effect of) themselves, causes are spatiotemporally ���other than��� their

effects. The potter���s actions start before they touch the clay. The motion of

the cue stick begins before it hits the ball. The potter is spatiotemporally

distinct from the pitcher; the cue stick is, likewise, ���other than��� the ball.

The inevitable conclusion is that self- cause and other forms of ���circular

causality��� are impossible because causes and effects would have to exist

simultaneously: before (as agents) and after (as effects), a contradiction.  Conclusion: the view that reality rests on primary properties of ele-

mentary particles and that causality is exclusively eff i cient cause is at

the root of modern science and philosophy���s failure to explain the causal

powers of systemic properties. Eff i cient causality cannot account for how

parts become interwoven into interdependencies that bind together coher-

ent wholes and persist despite turnover or deletion of component parts.

Much less can it account for top- down causation from the emergent fea-

tures of coherent wholes to those components or behavior.

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The exclusive reliance on efficient causality, as understood in modern science and philosophy, has led to certain limitations and implications that were not fully appreciated. According to Aristotle's reasoning, efficient causes and their effects cannot exist simultaneously in the same spatiotemporal location. The cause must precede the effect, and they must be "other than" each other in terms of space and time. For example, the potter's actions start before they touch the clay, and the motion of the cue stick begins before it hits the ball.

This understanding of efficient causality implies that self-causation and circular causality are impossible. If a cause and effect were to exist simultaneously, it would create a contradiction. This view has influenced the perspective that reality is based solely on the primary properties of elementary particles, and causality is exclusively understood as the transfer of energy from one entity to another.

However, this exclusive focus on efficient causality falls short in explaining certain aspects of reality, especially in complex systems. It fails to account for how parts become interwoven into interdependencies, forming coherent wholes that persist despite the turnover or removal of component parts. Efficient causality alone cannot fully explain the emergence of systemic properties or how top-down causation operates, where higher-level emergent features of coherent wholes influence the behavior or properties of their constituent parts.

In complex systems, interactions, relationships, and feedback loops play crucial roles in shaping the behavior and properties of the whole system. The reductionist view that considers only efficient causality may overlook the significance of these higher-order interactions and fail to provide a complete understanding of how coherent wholes maintain their identity and function. To fully comprehend coherence and identity in complex systems, a more comprehensive approach that includes other forms of causality, such as final and formal causes, and recognizes the importance of interactions and relationships is needed.

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Mereology

As noted, philosophers call relations from parts to wholes and wholes

to parts mereology. According to the default ontological framework

described (and that is still very much in place), parts cannot interact to

produce wholes with strongly emergent properties��� that is, with proper-

ties that are not reducible to the sum of the parts. Eff i cient causes produce

mere aggregates. Emergent characteristics of wholes, as wholes, such as

coordination and synchronization, cannot inf l uence components because

they could only do so as eff i cient causes, which is impossible since parts

and wholes are not spatiotemporally distinct. And since aggregates are

epiphenomenal, mereological ���causation��� from clumped particles to com-

ponents is impossible (Campbell 1974; Kim 1989; Moreno and Mossio

2016; also see Murphy, Ellis, and O���Connor 2009). These misconceptions

about mereological relations have occasioned no end of problems, many

still unrecognized.

Working from the assumption that all cause is eff i cient cause, therefore,

philosophers and scientists have resisted the idea of recursive or circular

causality ever since. The problems of identity and intentional causation

were perhaps the most insistent philosophical topics that wouldn���t go

away. Juarrero (1999) chronicled the epicyclic contortions to account for

purposive behavior while refusing to accept recursive causality.

How can two separate and distinct substances from different realms

interact in terms of eff i cient causality? How can mind activate matter?

Descartes identif i ed the pineal gland as the site where mental events such

as intentions trigger purposive action. With the advent of thermodynam-

ics in the nineteenth century, this maneuver ran into a different objection,

this time involving modern science���s conservation laws and principle of

physical closure.

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Mereology refers to the study of relations between parts and wholes. In the default ontological framework, which heavily relies on efficient causality, interactions among parts to produce strongly emergent properties in wholes are considered impossible. Wholes are viewed as mere aggregates of their constituent parts, and any emergent properties they seem to exhibit are considered epiphenomenal, without any causal influence on the components.

As a result, the idea of recursive or circular causality has been resisted, and philosophers and scientists have struggled to account for purposive behavior without accepting the possibility of such causality. For instance, the problem of how two distinct substances from different realms (e.g., mind and matter) can interact in terms of efficient causality has been a persistent challenge. Descartes proposed that the pineal gland served as the site where mental events (such as intentions) triggered purposive actions in the physical body. However, this notion faced criticism when thermodynamics was introduced in the 19th century, and modern science's conservation laws and principle of physical closure posed a different challenge to the idea of causal interactions between different substances.

The resistance to recursive causality and the exclusive focus on efficient causality in explaining causation have hindered a more comprehensive understanding of how coherent wholes emerge and influence their component parts. To better grasp the nature of coherence and identity in complex systems, it may be necessary to explore alternative causal frameworks that account for interactions, relationships, and feedback loops among parts and wholes. This could lead to a more holistic view of causation, allowing for a deeper understanding of the emergence of novel properties and behaviors in complex systems.

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Physical Causal Closure and Overdetermination

Combine an exclusive reliance on eff i cient causality with the First Law of

Thermodynamics, which holds that that the total amount of matter and

energy in the universe is fi xed. Matter can neither be created nor destroyed;

it can be transformed (into energy) and back, but the total amount is always

conserved. In combination, these two principles lead to a third, causal

closure of the physical. This principle holds that (1) all states are physical

states, and (2) all physical states are the effects of physical eff i cient causes.

The unavoidable implication of these two premises is that proposing that

the symbolic content of thoughts or beliefs can bring about changes in the

physical realm violates conservation laws and causal closure.

The reasoning goes as follows: nonmaterial ���causes��� such as Aristo-

telian Formal and Final causes or Cartesian intentions would activate

bodies by introducing themselves into the physical realm and activating

them as eff i cient causes. In combination with the resolutely materialist

presuppositions of the principle of physical closure, this insertion into the

physical world would increase the universe���s total matter and energy and

violate conservation in the process. Conclusion: (allegedly) nonphysical

thoughts, intentions, and other mental events as such cannot bring about

physical effects without violating causal closure.

Purposive causation by nonphysical intentions would also imply an

overdetermined universe, likewise prohibited by causal closure. The argu-

ment here goes as follows: causal closure requires that all events (includ-

ing arms rising) be the effects of physical causes��� that is, they must result

from the energy transfer of eff i cient causes. But if intentions are Cartesian

mental events and my arm rises because I intended to raise it, the result-

ing behavior is qualitatively different than if my arm rose because of

an involuntary neuromuscular spasm or because someone pushed me.

Intentional causation transforms behavior into purposive action, with all

the legal and moral implications that entails (Murphy and Brown 2007;

Juarrero 1999).

But if intentions as meaningful mental states can bring about purpo-

sive action, the arm motion would be caused by both my intention to

raise my arm and the neuromuscular processes required by the principle

of causal closure. Such double causation overdetermines the universe.

Recall that on the standard understanding of eff i cient causes, causes and

effects must be logically and spatiotemporally distinct, so on this account,

intentions must be other than neurophysiological processes, which would

also violate causal closure.

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The principle of causal closure of the physical, in conjunction with an exclusive reliance on efficient causality and the First Law of Thermodynamics, leads to the conclusion that nonphysical causes, such as mental events or intentions, cannot bring about physical effects without violating conservation laws and causal closure.

According to causal closure, all states are physical states, and all physical states are the effects of physical efficient causes. If nonphysical causes, like intentions, were to activate bodies and bring about physical effects, they would need to introduce themselves into the physical realm and act as efficient causes. This would imply an increase in the total matter and energy in the universe, contradicting the conservation principle.

Moreover, intentional causation would imply an overdetermined universe, as both the mental intention and the physical neurophysiological processes would be causally responsible for the same behavior. This violates the principle that causes and effects must be logically and spatiotemporally distinct, as required by the standard understanding of efficient causality.

Due to these implications, proponents of causal closure and materialist presuppositions have rejected the idea that nonphysical mental events can have causal efficacy in the physical realm. Instead, they seek to explain all behavior and physical effects solely in terms of efficient physical causation, without any role for nonphysical causes.

However, it's worth noting that this perspective represents a particular philosophical stance and does not encompass all views on causation and the relationship between the mental and the physical. Alternative philosophical frameworks may explore the possibility of nonphysical mental causation or propose more nuanced understandings of the interactions between the mental and the physical realms.

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Conclusion: allegedly nonphysical mental events such as intentions,

thoughts, and beliefs cannot cause actions as meaningful and purposive

intentions to do X. These considerations reinforced the received view that

systemic properties are epiphenomenal.

It follows from this reasoning that postulating top- down (downward)

causation, from intentions in virtue of emergent mental properties down

to behavior (Campbell 1974), violates conservation laws and the princi-

ple of the closure of the physical. Western philosophy���s exclusive reliance

on eff i cient cause and total dismissal of context bars naturalist accounts

of mental states and mental causation at the root. By maintaining that

identity rests on primary properties of fundamental material particles

(while simultaneously excluding all forms of inf l uence other than eff i-

cient causality and insisting that relations and interactions with context

are secondary and epiphenomenal), understanding how mind and body

could possibly constitute a coherent whole, much less how identity can be

preserved and persist despite changes, becomes impossible.

As framed by standard philosophy of science, naturalism closed off

debate about the causes of coherence and therefore about identity and

individuation. Without a principle that explains the formation of coher-

ent wholes from previously separate parts, natural science and philosophy

of mind were also left without a way of accounting for either mereologi-

cal relations or interactions with the environment and inf l uence from the

past. Nothing can generate outcomes that are qualitatively different than

mere aggregation without violating causal closure. Reductionism followed.

Human beings are nothing but atoms clumped together in time and space.

***

Over the centuries, several ways of resolving this impasse were proposed.

The early twentieth century witnessed a fl urry of philosophers who espoused

an approach labeled emergentism.11 In keeping with the reductionism

required by natural philosophy, emergent properties were invariably deus

ex machina contributions, literally injected from outside the physical realm

into inchoate and passive matter. Emergentists such as French philosopher

Henri Bergson were often labeled Vitalists in reference to the mysterious

and externally provided ���vital��� force that they proposed animates living

things. Natural scientists summarily ignored these proposals.

Other thinkers such as Scottish philosopher John Stuart Mill, Australian-

born philosopher Samuel Alexander, French scientist Henri Poincar��, and

Austrian biologist Ludwig von Bertalanffy cast about for a systems- theoretic

approach to account for novel properties of wholes. Michael Polanyi tried to have it both ways by arguing that although ultimate boundary conditions were set from without, once in place, they can generate life without outside

inf l uence. Charles Sanders Peirce, a practicing chemist, knew there was

something more to chemical compounds than mere aggregation (Juarrero

and Rubino 2010), but in the end gave up on fi nding an ontological answer

and, in keeping with Kant���s epistemological turn, settled for a semiotic and

���pragmaticist��� account.

For the most part, however, the reductionist principle that aggregates

are nothing but the sum of their parts and that seeming coherent wholes

such as organisms like you and me are epiphenomenal, powerless to exer-

cise causality as anything other than masses of atomic primary proper-

ties, ruled the day. One can sympathize with John Donne���s lamentation

that all coherence is gone.

But the problems of coherence and identity did not go away. Intui-

tively, it is diff i cult to shrug off the belief that there is some logic that

holds organisms together over time despite perturbations. Organisms are

organized; they present an internally coherent and persistent ���hanging

together��� that is qualitatively different from mere aggregation. What

makes coherent processes in general, including living things, cohere and

persist as the same type of entity despite dramatic alterations? Suggest-

ing, as early complexity theorists proposed in the mid- twentieth century

(Prigogine and Stengers 1984; Maturana and Varela 1979; Pattee 1972a),

that constrained and self- organizing dynamics might generate coordina-

tion and complex organization with qualitatively novel properties went

completely against the grain of the received framework. With very few

exceptions (Collier and Muller 1998; Cilliers 1998; Collier and Hooker

1999), mainstream philosophers of science disregarded complexity.

Meanwhile, the world moved on. Among the issues raised in identity

politics today is the role contextual factors such as race, colonialism, class,

culture, sexual orientation, and age play in personal identity. Environ-

mental and historical inf l uences are implicated in making all living things

what and who they are. In biology, the new fi eld of epigenetics has shown

that the dichotomy between nature and nurture is too simplistic. The

even more recent research on the metagenome in the gut microbiome, not

to mention lichens and mycorrhizae, raises even further questions about

symbiotic wholes. Are human beings more symbiotic wholes than indi-

vidual organisms? Just asking this begs the question of this book���s central

theme: what causes coherence? In any case, the physics- based worldview

from which our understanding of causes and effects, coherence, and iden-

tity derives continues to assign only secondary or accidental ontological status to context and history. It prioritizes separate and standalone exis-

tence over relations and interactions.

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The conclusion drawn from the standard philosophy of science, which emphasizes an exclusive reliance on efficient causality and the dismissal of context and interactions as secondary or epiphenomenal, is that allegedly nonphysical mental events, such as intentions, thoughts, and beliefs, cannot cause actions with meaningful and purposive intentions.

This perspective has led to a reductionist view that denies the causal efficacy of systemic properties and regards them as mere aggregates of elementary particles. It has also resulted in the rejection of the possibility of top-down causation, where higher-level properties of coherent wholes influence their component parts.

Efforts to resolve this impasse have been proposed, including the emergentism approach, which suggests that novel properties emerge from passive matter due to external influences. However, this idea has not gained widespread acceptance.

More recent scientific discoveries in areas such as epigenetics and the gut microbiome challenge the traditional view of identity and coherence. These discoveries highlight the role of contextual factors and interactions in shaping living beings. However, the physics-based worldview, which prioritizes separate and standalone existence over relations and interactions, still underlies our understanding of causation and coherence.

Overall, the question of what causes coherence in complex systems, including living organisms, remains a central theme that challenges our current understanding of causality and identity in the natural world.

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Mistrust in the dichotomy between essential and accidental properties

surfaced in academic philosophy circles in the early twentieth century.

Austrian philosopher Ludwig Wittgenstein and American philoso-

pher Willard Van Orman Quine independently held that the distinc-

tion between primary and secondary properties was untenable. As an

example, there are no necessary and suff i cient primary properties that

make all games games.12 As students at Oxford University during World

War II, Philippa Foot, Mary Midgely, Iris Murdoch, and G. E. M. Ans-

combe argued against the view that reality is wholly transcendent and

that the faculty of moral intuition is independent of features in the world.

These remarkable thinkers emphasized instead social, creative, spiritual,

and biological forms of life as the source and weave of human life. Alas,

the signif i cance of their ideas is only now being recognized (Lipscomb

2021; Cumhaill and Wiseman 2022).

Since the received view of essences and type of entities was predicated

on primary properties, the next philosophical step was usually a retreat

to nominalism, the theory mentioned earlier to the effect that any pre-

tense that types and kinds are real should be abandoned: common nouns

like triangle or scorpion do not refer to real categories or to real entities

marked by an internal principle of coherence; they are only linguistic

units or epistemic cuts that frame our thoughts and investigations.

Remarkably, even though he was discussing the failure of essentialist

def i nitions, the later Wittgenstein did not explicitly retreat to nominal-

ism. He proposed instead that language captures ���forms of life,��� a phrase

often interpreted as the opening salvo of a social constructivist approach

to language. Wittgenstein���s phrase suggests to me, as it did to Anscombe,

Foot, Midgely, and Murdoch, not an outright retreat from realism but an

attempt to reimagine the world from the point of view of relations and

circumstances, context and history.

An opening to a contextual and relational ontology, in other words.

Dismissing the inf l uence of context is the original sin whose imprint

continues to permeate many of these philosophical and scientif i c debates.

This book will argue that recognizing that context changes everything

reopens a path toward rehabilitating coherence, identity, and causation���

from parts to coherent wholes and from emergent coherent wholes to

parts, including intentional causation. It proposes a realistic and naturalist philosophy based on the principle that nature self- organizes and sorts

itself into real but contextual coherent dynamics. Call its principle of

coherence its constraint regime.

To be consistent, Platonic forms as well as fi nal and formal causes

must in consequence be reimagined in terms of interactional, extended,

and context- dependent interdependencies. Thus understood, relational

types are real and coherent patterns of energy fl ow, structure, and activi-

ties that form locally from contextually constrained interactions among

individuals and that, in turn, as coherent dynamics, constrain the indi-

viduals and circumstances from which they emerge. Reimagining cause-

and- effect relations, especially mereological relations between parts and

wholes, and the inf l uence of context and history on those relations, will

be the hinge on which this reformulation turns. By taking context seri-

ously in this fashion, coherence and wholeness, as well as meaning, ���shall

be returned.���

This new interpretive framework makes room for a more expansive

notion of identity and coherence based on interdependence and charac-

terized by resilience and robustness. And generated by constraints.

Even John Donne might approve.

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The early twentieth century saw a shift in academic philosophy circles, with thinkers like Ludwig Wittgenstein and Willard Van Orman Quine challenging the dichotomy between essential and accidental properties. They argued that the distinction between primary and secondary properties was untenable, and concepts like types and kinds should not be considered as real entities or categories but as linguistic units or epistemic constructs.

Other philosophers, such as Philippa Foot, Mary Midgley, Iris Murdoch, and G. E. M. Anscombe, emphasized social, creative, spiritual, and biological aspects of human life as the source and weave of reality, moving away from a wholly transcendent view. These ideas, which recognized the significance of context and relations, were ahead of their time and are now being appreciated more fully.

Instead of retreating to nominalism, some philosophers, like Wittgenstein, proposed a focus on "forms of life," which could be interpreted as a social constructivist approach to language. This notion suggests a reimagining of the world from the perspective of context and history, opening up a path toward rehabilitating coherence, identity, and causation based on contextual and relational ontologies.

This book proposes a realistic and naturalist philosophy that recognizes nature's self-organization and coherent dynamics based on contextual constraints. The principle of coherence is seen as a constraint regime, where relational types are real and coherent patterns of energy flow and interactions among individuals that form locally within specific contexts.

By reimagining cause-and-effect relations, especially mereological relations between parts and wholes, and acknowledging the influence of context and history, this framework offers a more expansive notion of identity and coherence. It emphasizes interdependence, resilience, and robustness, allowing for a more comprehensive understanding of reality.

Overall, taking context seriously and embracing a relational ontology can lead to a more comprehensive and meaningful understanding of coherence, identity, and causation in the natural world.

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A list of everything we have talked about so far

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Certainly! Here's a list of the topics we've discussed so far:

Francis Bacon's proposal for a new way of reasoning based on induction.

Ren�� Descartes' technique for knowledge acquisition through deduction.

Coherence and how it relates to embodied substance and identity.

The transition from a focus on form to analysis and parts over the whole.

The challenges of coherence and identity in modern atomism and reductionism.

The concept of efficient causality and its limitations in explaining coherence.

Mereology and the relation between parts and wholes.

Reductionism and its impact on understanding coherence and identity.

The concept of emergent properties and the debates surrounding them.

The rejection of the dichotomy between essential and accidental properties.

Philosophers like Wittgenstein and Quine challenging the concept of primary and secondary properties.

The influence of context, history, and relations on understanding coherence and identity.

Reimagining causation and coherence from a contextual and relational perspective.

The proposal for a realistic and naturalist philosophy based on coherent dynamics and constraints.

Please let me know if you need further information or have any other questions!

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Not only does thinking filter reality; it constructs it, inferring an outside world from ambiguous input.

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Absolutely, your statement captures an essential aspect of how human cognition works. Our minds do not passively receive raw sensory data from the world; instead, they actively process and interpret that data to construct a coherent representation of reality. This process involves making inferences, filling in gaps, and resolving ambiguities based on prior knowledge, experiences, and mental models.

Perception is not a direct window to the external world but rather an intricate interplay between sensory input and cognitive processes. Our brain's ability to fill in missing information and make sense of the world allows us to navigate and interact with our environment effectively. However, it also means that our perceptions are influenced by our biases, beliefs, and expectations, potentially leading to cognitive errors and misinterpretations.

This constructivist view of perception and cognition is a fundamental concept in psychology and philosophy of mind. It helps us understand how our minds actively participate in shaping our reality and how subjective experiences are woven into the fabric of our understanding of the world.

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Can you expand on these?


The influence of context, history, and relations on understanding coherence and identity.

Reimagining causation and coherence from a contextual and relational perspective.

The proposal for a realistic and naturalist philosophy based on coherent dynamics and constraints.

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Certainly, let's delve deeper into each of these topics:

The Influence of Context, History, and Relations on Understanding Coherence and Identity:

Context, history, and relations play a crucial role in shaping our understanding of coherence and identity. In the traditional reductionist framework, coherence is often viewed as an epiphenomenon or mere aggregation of separate parts without considering the intricate interactions and relations among those parts. However, in a contextual and relational perspective, coherence emerges from the dynamic interplay between elements within a particular context.

For example, consider a biological organism like a human being. In a reductionist view, a human is seen as a mere sum of its constituent cells and biochemical processes. But in a relational perspective, the identity of a human arises from the intricate web of interactions among cells, tissues, organs, and systems that constitute the living organism. This relational understanding acknowledges the role of context and history in shaping the organism's coherence and identity.

Reimagining Causation and Coherence from a Contextual and Relational Perspective:

In the standard reductionist view, causation is often limited to efficient causality, where causes are external forces acting upon passive entities to produce effects. This perspective disregards the idea of circular causality and top-down causation, where higher-level properties of coherent wholes can influence their constituent parts.

By reimagining causation from a contextual and relational perspective, we open up the possibility of circular and top-down causality. Coherent wholes, such as living organisms or complex systems, can exhibit emergent properties that cannot be solely reduced to the actions of their individual parts. Instead, the interactions and constraints within the context of the whole influence the behavior of the parts, leading to self-organization and emergent phenomena.

A Proposal for a Realistic and Naturalist Philosophy Based on Coherent Dynamics and Constraints:

The proposed realistic and naturalist philosophy departs from the reductionist approach and embraces the idea that nature self-organizes into real but contextually constrained coherent dynamics. This perspective recognizes that coherence is not an illusion or epiphenomenon but a genuine emergent property resulting from the interactions and constraints within a system.

Instead of defining reality solely based on fixed and immutable essences, this philosophy emphasizes the role of context, history, and relations in shaping identity and coherence. It views entities as relational types, patterns of energy flow, and activities that form locally from interactions constrained by the context. These coherent dynamics then reciprocally influence the individual elements and circumstances from which they emerge.

In this framework, identity and coherence are characterized by resilience and robustness, arising from the constraints that sustain and organize the system. This perspective provides a more holistic understanding of reality, one that acknowledges the active role of context and relations in shaping our world and ourselves. It encourages us to look beyond isolated parts and embrace the interconnectedness of all things.

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In the book, context changes everything

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"In the book, context changes everything" is a statement that likely reflects one of the central themes or arguments of the book discussed earlier. The phrase emphasizes the importance of context in shaping our understanding of various phenomena, including coherence, identity, causation, and more.

In the context of the book's discussion, the statement might convey the idea that by considering context, historical factors, and relational perspectives, we gain a deeper and more nuanced understanding of complex systems and their emergent properties. The book likely explores how acknowledging the influence of context and relations can challenge traditional reductionist views and open new paths for understanding reality and philosophy.

By recognizing the role of context, the book might propose a more realistic and naturalist approach to philosophy, one that embraces the dynamic and interconnected nature of the world, rather than viewing entities as isolated and static. This change in perspective allows us to see that what might appear as mere aggregation or epiphenomena could be genuine emergent properties arising from contextually constrained interactions.

Overall, the phrase "context changes everything" suggests that by considering the broader context and the interplay of relations, we can develop a richer and more comprehensive understanding of the complexities of reality. It encourages us to rethink traditional notions of causation, coherence, and identity and to appreciate the intricate and interconnected nature of the world around us.

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Yeah, the actual title of the book was Context Changes Everything: How Constraints Create Coherence

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Thank you for providing the actual title of the book: "Context Changes Everything: How Constraints Create Coherence." The title further emphasizes the central theme of the book, which is the transformative power of context in shaping our understanding of coherence and identity.

The phrase "Context Changes Everything" highlights the importance of considering the broader context, historical factors, and relational perspectives when examining complex systems and emergent properties. It suggests that by taking into account the specific constraints and interdependencies at play, we can gain a deeper and more accurate understanding of how coherence and identity emerge and persist in various phenomena.

The subtitle "How Constraints Create Coherence" gives a clue to the book's approach, which likely explores how constraints, as shaping factors and limitations, play a fundamental role in creating and maintaining coherent dynamics in the world. The book might propose that coherence is not simply an epiphenomenon or a result of aggregation but is instead generated by specific constraints that influence interactions and relationships among entities.

Overall, the title "Context Changes Everything: How Constraints Create Coherence" signals a thought-provoking exploration of how acknowledging context and constraints can revolutionize our understanding of fundamental philosophical concepts and provide a more realistic and naturalistic perspective on the nature of reality.

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How do mereorology and ontology relate to the thesis about context dependent constraints?

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Mereology and ontology are two philosophical concepts that are highly relevant to the thesis about context-dependent constraints presented in the book "Context Changes Everything: How Constraints Create Coherence."

Mereology: Mereology is the study of part-whole relationships and is concerned with how individual parts combine to form wholes. In the context of the book's thesis, mereology plays a crucial role in understanding how coherence emerges from the interactions and relationships among individual elements. The book likely explores how coherent wholes are not simply the sum of their parts but are shaped by specific constraints and interactions among these parts. Mereological causation, the causal relationship between parts and wholes, is central to the book's argument about how constraints create and sustain coherence in various systems.

Ontology: Ontology is the branch of philosophy that deals with the nature of being, existence, and reality. In the context of the book, ontology is likely used to explore the fundamental nature of coherence, identity, and causation. The book may present an ontological framework that emphasizes the significance of context in shaping the identities of entities and their coherent dynamics. By reimagining ontology from a contextual and relational perspective, the book likely challenges traditional notions of fixed essences and essential properties, proposing instead a more dynamic and context-dependent understanding of reality.

The thesis about context-dependent constraints is likely to suggest that coherence, identity, and causation are not absolute and unchanging but are contingent on specific contexts, historical factors, and relational interactions. By analyzing the interplay of mereological relationships and ontological considerations within different contexts, the book may offer a new perspective on how constraints influence the emergence, persistence, and evolution of coherent phenomena in the world. It highlights the importance of considering the broader context and relational dynamics when exploring the nature of reality and understanding complex systems.

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Summarize: Alvaro Moreno ��� Matteo Mossio

Biological Autonomy

A Philosophical and Theoretical Enquiry


�� Springer Science+Business Media Dordrecht 2015


1Constraints and Organisational Closure ..................................1

1.1Biological Determination as Self-Constraint .........................3

1.2The ThermodynamicGrounding of Autonomy ......................6

1.2.1Kauffman���s Work-Constraint Cycle..........................9

1.3Constraints and Processes .............................................11

1.4From Self-Organisation to Biological Organisation .................15

1.5Dependence ............................................................18

1.6Closure .................................................................20

1.7A Word About Related Models .......................................24

1.8Regulation..............................................................28

1.8.1Constitutive Stability ..........................................31

1.8.2Regulation .....................................................33

1.8.3Regulation and the Increase of Complexity ..................36

1.8.4Towards Autonomy............................................38

2Biological Emergence and Inter-level Causation .........................39

2.1The Philosophical Challenge to Emergence..........................41

2.2Irreducibility Versus Non-derivability ................................43

2.3Irreducibility and Emergence .........................................44

2.3.1Supervenience and Constitution ..............................45

2.3.2A Reply to the Exclusion Argument..........................47

2.4Constraints and Closure as Emergent Determinations ...............49

2.5Inter-level Causation...................................................52

2.5.1Why We Do Not Need Nested Causation in Biology........54

2.5.2Why We Might, After All, Need Nested

Causation in Biology..........................................58

2.6Conclusions ............................................................60

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The book "Biological Autonomy: A Philosophical and Theoretical Enquiry" by Alvaro Moreno and Matteo Mossio explores the concept of biological autonomy from a philosophical and theoretical perspective. The book delves into the idea of constraints and organizational closure as crucial factors in understanding biological determination and self-constraint. It examines how thermodynamics plays a grounding role in autonomy and introduces Kauffman's work-constraint cycle as a relevant model.

The authors discuss the relationship between constraints and processes, as well as the transition from self-organization to biological organization. They emphasize the concept of dependence and explore closure as a key characteristic of biological systems.

The book also addresses the philosophical challenge of emergence and inter-level causation. It discusses irreducibility and non-derivability in the context of emergence and supervenience. The authors respond to the exclusion argument and argue for the importance of constraints and closure as emergent determinations in biological systems.

Additionally, the book delves into the concept of inter-level causation, investigating the need for nested causation in biology. It considers various perspectives on this matter and draws conclusions about the role of nested causation in biological phenomena.

Overall, "Biological Autonomy" provides an in-depth examination of the philosophical and theoretical aspects of biological autonomy, including constraints, emergence, and inter-level causation.

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3Teleology, Normativity and Functionality.................................63

3.1The Philosophical Debate .............................................65

3.1.1Dispositional Approaches.....................................65

3.1.2Aetiological Theories .........................................67

xv

xviContents

3.2The Organisational Account of Functions............................69

3.2.1Teleology, Normativity and Self-Determination .............70

3.2.2Closure, Organisation and Functions.........................71

3.3Implications ............................................................74

3.3.1Cross-Generation Functions ..................................75

3.3.2Malfunctions...................................................81

4Agency.........................................................................89

4.1What Is Agency?.......................................................91

4.2Minimal Agency .......................................................94

4.3Adaptive Agency ......................................................98

4.3.1The Specif i city of Motility.................................... 101

4.4Autonomy .............................................................. 104

4.5Beyond Individuals: Networks of Autonomous Agents ............. 105

4.5.1Toward Cognition ............................................. 109

5Evolution: The Historical Dimension of Autonomy ...................... 111

5.1A Preliminary Look Into the Origins of Darwinian Evolution ...... 115

5.2Replicative Molecules Versus Self-Maintaining Organisations ..... 117

5.3At the Origins of Organisation: The Emergence of Protocells ...... 120

5.4The Origins of Natural Selection ..................................... 124

5.5Early Forms of Template-Based Evolution........................... 126

5.6On the Nature of Template Constraints............................... 129

5.7The Emergence of Specialised Template Functions ................. 130

5.8The Emergence of Darwinian Evolution ............................. 133

5.9Is Darwinian Evolution Open-Ended?................................ 135

5.10Conclusion: Integrating the Organisational

and Evolutionary Dimensions......................................... 138

6Organisms and Levels of Autonomy ....................................... 141

6.1The Concept of Multicellular Organism: Evolutionary

and Organisational Views ............................................. 145

6.1.1The Evolutionary View........................................ 146

6.1.2The Organisational View...................................... 148

6.1.3Multicellularity and Autonomy............................... 152

6.2Comparative Analysis ................................................. 154

6.2.1Cyanobacterium Nostoc.Punctiforme ........................ 154

6.2.2Volvox.Carteri ................................................. 155

6.2.3Strongylocentrotus.Purpuratus................................ 157

6.3Developmental Conditions for Highly Integrated

Multicellular Organisations ........................................... 160

6.4Towards Higher-Level Autonomy .................................... 164

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Chapter 3: Teleology, Normativity, and Functionality

This chapter delves into the philosophical debate surrounding teleology, normativity, and functionality in biological systems. It explores dispositional approaches and aetiological theories as different perspectives on the purpose and function of biological entities. The authors introduce the concept of the organizational account of functions, which emphasizes teleology, normativity, and self-determination in biological systems. They link closure, organization, and functions, highlighting their implications for understanding biological phenomena such as cross-generation functions and malfunctions.

Chapter 4: Agency

Chapter 4 focuses on the concept of agency in biological systems. The authors discuss the definition of agency and differentiate between minimal agency and adaptive agency. They emphasize the specificity of motility as a crucial aspect of adaptive agency. The chapter also explores the notion of autonomy in biological agents and goes beyond individual organisms to consider networks of autonomous agents, with a particular focus on cognition.

Chapter 5: Evolution: The Historical Dimension of Autonomy

In this chapter, the authors explore the historical dimension of autonomy through the lens of evolution. They begin with a preliminary look at the origins of Darwinian evolution. The chapter discusses the emergence of replicative molecules and self-maintaining organizations, leading to the emergence of protocells. The authors delve into the origins of natural selection and early forms of template-based evolution. They examine the nature of template constraints and the emergence of specialized template functions. The chapter concludes with a consideration of whether Darwinian evolution is open-ended.

Chapter 6: Organisms and Levels of Autonomy

The concept of multicellular organisms and their autonomy is the central theme of this chapter. The authors analyze the evolutionary and organizational views of multicellularity and its relationship to autonomy. They provide a comparative analysis of specific examples like Cyanobacterium Nostoc Punctiforme, Volvox Carteri, and Strongylocentrotus Purpuratus to explore the different levels of autonomy in biological systems. The chapter also discusses the developmental conditions required for highly integrated multicellular organizations and the potential for higher-level autonomy.

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7Cognition...................................................................... 167

7.1Agency and Motility................................................... 169

7.1.1The Relationship Between Multicellular

Integration and Behavioural Agency ......................... 170

Contentsxvii

7.1.2Organisational Requirements for Complex

Behavioural Agency........................................... 173

7.2The Dynamical Decoupling of the Nervous System ................. 175

7.3The Evolution of the Nervous System ................................ 177

7.3.1Body Plans and the Complexif i cation

of the Nervous System ........................................ 178

7.3.2Towards Further Decoupling: Autonomic

and Sensorimotor Nervous Systems.......................... 180

7.4The Appearance of Consciousness.................................... 183

7.5Cognition and the Emergence of Neurodynamic Autonomy ........ 187

7.6Cognition and Social Interaction...................................... 189

7.7Conclusions ............................................................ 192

8Opening Conclusions ........................................................ 195

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Chapter 7: Cognition

In this chapter, the focus shifts to cognition in biological systems. The authors explore the relationship between agency, particularly motility, and cognition. They discuss how multicellular integration is related to behavioral agency and examine the organizational requirements for complex behavioral agency. The chapter delves into the dynamical decoupling of the nervous system and its evolution. This includes the complexification of the nervous system in relation to body plans and the emergence of autonomic and sensorimotor nervous systems. The appearance of consciousness is also discussed in the context of cognition. The authors highlight cognition's role in the emergence of neurodynamic autonomy and its connections to social interaction.

Chapter 8: Opening Conclusions

The final chapter serves as the concluding section of the book. It summarizes the key findings and insights presented throughout the text. The authors reiterate the importance of constraints and organization in understanding biological autonomy. They offer concluding thoughts on the relationship between constraints, coherence, and identity in biological systems and how a contextual and relational perspective can lead to a more realistic and naturalist philosophy. The chapter wraps up with a reflection on the book's contribution to the field of philosophy and theoretical inquiry into biological autonomy.

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Introduction

Life as Autonomy

Ifweweretopointoutina fewwordswhatcharacterisesthephenomenonoflife,we

wouldprobablymentionthe amazingplasticityandrobustnessof livingsystems, the

innumerableways they adapt,and their capacity to recoverfrom adverseconditions.

All these capacities have been on the surface of our planet since the origins of

life, and for this reason we have become accustomed to seeing life as something

almost ���normal���. And yet, looking at it from a more global perspective, life is

quite an extraordinary phenomenon. In a short period of time (compared to the

history of the universe), in a very tiny portion of the cosmos, a set of entities

has managed to attain extremely improbable conf i gurations, to keep them in far-

from-equilibrium conditions, and to thrive under these conditions: self-organising,

proliferating, diversifying, and even increasing their complexity. Furthermore, this

persistently organised system (or, rather, this global system formed by millions

of local, individualised systems, which combine decay and reproduction) has

been able to deploy a set of selective forces, modifying its environment so as to

enhance its own maintenance. In a word, life seems to be at the same time an

extraordinarily precarious (and improbable) phenomenon and a powerful, robust,

and easily expansive one.

Actually,this astonishingcapacityto maintainhighlyorganisedsystems seems to

be the easiest way to recognise universally living matter beyond the specif i cities of

terrestrial life. Present-day theories estimate that the universe came into being 13.7

billion years ago, while our planet was formed approximately 9 billion years later.

In this period of time, or perhaps later, forms of organisation similar to early living

systems on our planet possibly appearedin other parts of the universe.Indeed,if life

appeared on our planet when certain physicochemical conditions were met, other

planets with similar conditions could also have once supported forms of life. This

xix

xxIntroduction

raises the question of how we could recognise these hypothetical extra-terrestrial

living systems, and what would be the essential features of any form of (possible)

life. In the last decades, this question has been widely discussed.

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The introduction to the book "Biological Autonomy: A Philosophical and Theoretical Enquiry" highlights the extraordinary nature of life as a phenomenon. It emphasizes the plasticity, adaptability, and robustness of living systems, along with their ability to thrive under adverse conditions. Despite life being common on Earth, from a broader perspective, it is a remarkable and improbable occurrence in the universe. Living entities have achieved highly complex configurations, maintained themselves far from equilibrium, and demonstrated self-organization, proliferation, and diversification. Moreover, life has exerted selective forces on its environment to enhance its own maintenance.

The authors propose that the ability of highly organized systems to maintain themselves is a key universal characteristic of living matter beyond Earth. They suggest that forms of life might have emerged in other parts of the universe under similar physicochemical conditions to Earth. This raises the question of how we could recognize potential extraterrestrial life and what essential features any form of life might possess. The book aims to explore these questions and delve into discussions on biological autonomy and the nature of life itself.

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For some (Cleland and Chyba 2007), it is impossible to say how such ���essential

featuresoflife���shouldbeconceived,becauseweonlyknowlife asit manifestsitself

onEarth.Yet,ifwhatwemeanby���life���is anymaterialorganisationthathasevolved

from non-living physicochemical systems (therefore obeying the universal laws of

physics and chemistry) and has attained at least a degree of complexity capable of

generating the properties we associate with the simplest forms of terrestrial life, we

should be capable of recognising it anywhere in our universe, regardless of how

differently these systems may be constituted (Ruiz-Mirazo et al. 2004).At the same

time, the huge variety of life forms that have appeared during the very long history

of life on our planet (Ward and Brownlee 2004) might downplay the argument that

we havehadaccess onlyto a uniqueexampleoflifeamonga hypotheticallyhugeset

of extra-terrestrial biological systems. Be that as it may, when facing the question

of the nature of life, we could not do otherwise than formulate theories based on ���

and tested against ��� life as we know it.

It is because of its capacity to achieve and maintain higher degrees of complexity

that physical sciences i nd it very diff i cult to explain how life has originated. For

this reason, the question of the origin of life is deeply entangled with the question

of its very nature. Is there some law or principle in the physical world that allows

explaining the emergence of life as a necessity or, as Monod (1970) thought, is the

originof life so unlikelythat it is almost a miracle? How could inert matteroriginate

something that seems to be so deeply different in its properties?

From the perspective of the physical sciences, explaining life is a highly

challengingtask becausethe morecomplexa system is, the less probableit becomes

both in its appearance and its persistence. At i rst approximation, it might be easy

to understand how simple building blocks may spontaneously generate composite

stable structures (atoms, molecules, macromolecules:::) due to different levels of

forces (Simon 1969): as a result of these interactions, increasingly complex stable

structures appear (endowed, in many cases, with new interactive properties, not

present in their separate parts, such as superconductivity, chemical aff i nity:::).

As the complexity of the structures increases, however, its maintenance becomes

a problem: thermal noise increases fragility and, moreover, the coincidence or

coordination of many highly specif i c processes becomes increasingly unlikely.

It is true that recent advances in thermodynamics explain the formation of

composite aggregates(called ���dissipative structures���), whose parts are tied together

without intrinsic forces, ensuring their cohesion in far-from-equilibriumconditions.

However, as we will discuss at length in this book, these systems appear spon-

taneously and persist only when specif i c external boundary conditions are met

and, more importantly, they lack internal complexity and functionality. In contrast,

biology deals with highly complex systems, so that something more than initial

conditionsandfundamentallaws seemsto berequiredto explainaworldofcomplex

biological systems.

Introductionxxi

Assuming that nature does not make leaps and that, therefore, there is a contin-

uum between non-living matter and life,1there should be explanatory principles of

the transition from non-living to living matter. As Fry (2000) has pointed out, the

fundamental problem of the origin of life lies in the tension between the principle

of continuity and the diff i culty of explaining the obvious differences between non-

living and living matter. If the origin of life is a legitimate scientif i c question (and

we think it is), one should look for a theory that bridges the gap between physics

and biology. In particular, since living beings are made of the same constituents

as non-living entities, what is the nature of the organisation that enables them to

achieve, maintain, and propagate such a high degree of complexity? And what are

the consequences of this extraordinary capacity?

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The excerpt discusses the challenging task of understanding the nature and origin of life from a physical sciences perspective. The authors acknowledge the difficulty in explaining the emergence of life due to its high complexity and the probabilistic challenges it poses. While simple building blocks can spontaneously generate stable structures, the maintenance of complex systems becomes increasingly unlikely due to thermal noise and the coordination of specific processes.

Thermodynamics explains the formation of dissipative structures, which are composite aggregates held together without intrinsic forces under far-from-equilibrium conditions. However, these structures lack the internal complexity and functionality present in biological systems. To explain the transition from non-living to living matter, there must be explanatory principles that bridge the gap between physics and biology.

The authors suggest that the capacity of living beings to achieve and maintain higher degrees of complexity necessitates a theory that elucidates the nature of their organization. They raise questions about the consequences of this extraordinary capacity and emphasize the need to find principles that explain the origin of life as a legitimate scientific inquiry.

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On our planet, life has developed for a long period of time and has colonised the

most diverse environments��� from the deep oceans or even several kilometres under

theEarth���scrusttotheupperlevelsoftheatmosphere;fromthehottestenvironments

(over 100��C) to extremely acid or radioactive ones. And if we consider life from an

historical perspective, it is even more impressive how it has managed to adapt to

the successive catastrophic events that have occurred on our planet during the last

3.5 billion years. Admittedly, only the simplest forms of life are capable of such

extreme robustness and versatility; at the same time, these forms of life have also

been able to innovate and evolve towards increasingly higher levels of complexity.

Life, as it has developed on our planet, has gradually integrated more and more

levels of organisation(from unicellular life to colonies, multicellular organisms and

societies).2

How can we explain all this diversity and complexity? Ever since Dobzhansky���s

(1973) famous dictum that ���nothing in Biology makes sense except in the light of

evolution���, mainstream thinking in biology has seen evolution by natural selection

as the source of diversity at every level of biological organisation. Indeed, the

unfoldingof an evolutionaryprocess bynatural selection, based onheritable genetic

mechanisms, allows life to explore many possible combinations and solutions in

order to survive. And the evolution-centred view of life has been so dominant that

the idea of organism (which played a key role in nineteenth century biology) has

becomealmost dispensable(Morange2003).However,in a veryfundamentalsense,

we shall argue at length that the reality is rather the opposite: evolutionary mecha-

nisms operate because they are embodiedin the complex organisationof organisms.

Thus, if we look for the roots of the impressive capacity of life to proliferate, to

1Philosophically, this assumption amounts to adopting a monistic stance. Chapter. 2 is devoted to a

detailed analysis of the position of the autonomous perspective developed in this book inthe debate

on emergence, reduction, and related issues.

2Nowadays we know that this process of diversif i cation and complexif i cation is not a contingent

fact, but rather something ���inscribed��� in the evolutionary nature of life. As Gould (1994) has

argued, evolution is not aimed towards an increase in complexity; in fact, life originates in the

simplest form and many organisms have remained successfully as such. However, a few organisms

occasionally introduced innovations, ���thus extending the right tail inthe distribution of complexity.

Many always move to the left, but they are absorbed within space already occupied���.

xxiiIntroduction

create an enormous variety of forms, to adapt to completely different environments,

and particularly, to increase its complexity, we shall focus on individual living

entities, namely on organisms, because evolution3as an explanatory mechanism

actually presupposes the existence of organisms. As Varela (1979) pointed out,

evolutionary thought, through its emphasis on diversity, reproduction, and the species in

order to explain the dynamics of change, has obscured the necessity of looking at the

autonomous nature of living units for the understanding of biological phenomenology.

Also I think that the maintenance of identity and the invariance of def i ning relations in

the living unities are at the base of all possible ontogenetic and evolutionary transformation

in biological systems (p. 5).

As Rosen also emphasised, the crucial question for understanding life lies in

the nature of its organisation.4It is true that any known living being cannot

have appeared except as a result of a long history of reproductive events, since

such a complex organisation can only be originated through an accumulative

historical process and, furthermore, that its long-term sustainability also requires

inter-generational entailments. This is clearly ref l ected in the fact that, in order

to be operational, genetic components (which contribute to specify the metabolic

machinery and organisation of single biological entities) must be shaped through a

process that involves a large number of individual systems and many consecutive

generations, or reproductive steps. Yet, this does not mean that the organisation

of organisms should be neglected; on the contrary, a theory of living organisation

is fundamental for understanding how these evolutionary mechanisms could have

appeared and how they could work.

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The excerpt discusses the impressive diversity and complexity of life on our planet, which has adapted and survived in various environments over billions of years. The dominant perspective in biology attributes this diversity to evolution by natural selection, which allows life to explore and adapt through heritable genetic mechanisms. However, the authors argue that the true source of life's capacity for proliferation, adaptation, and complexity lies in the complex organization of individual living entities, namely organisms.

The authors emphasize the importance of looking at the autonomous nature of living units, namely organisms, to understand biological phenomenology. They believe that the maintenance of identity and defining relations within living entities are foundational for all possible ontogenetic and evolutionary transformations in biological systems. Evolutionary mechanisms presuppose the existence of organisms, and understanding the nature of their organization is crucial for comprehending the origin and functioning of life.

While evolution relies on a long history of reproductive events and intergenerational entailments, the authors stress that the organization of organisms should not be neglected. A theory of living organization is fundamental to understanding how evolutionary mechanisms arise and function within living systems. In summary, the remarkable capabilities of life are not solely explained by evolution but rooted in the complex and autonomous organization of individual living entities, which have played a central role in shaping the course of evolution.

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A theory of the living based on the concept of organism aims to review the

concept of evolution and its role in a new way, attempting to overcome the

dichotomy ��� and often opposition ��� between what since Mayr���s (1961) work is

called the biology of proximate causes and that of ultimate causes. Our vindication

of the central role played by the notion of organism in biology should be placed

within this wider perspective, in which the explanatory emphasis is placed on

organisation. As Hooker and Christensen (1999) have highlighted, in order to

3The term ���evolution��� could be understood in a very broad sense, just as an historical process of

causal entailments. However, since Darwin, the term evolution has acquired a more restrictive

sense, referring to specif i c mechanisms of inheritance and several other conditions (see for

example, Godfrey-Smith (2009)). We will discuss the relation between autonomy and evolution

in Chap. 5; here, we use the more restrictive sense of the term.

4���We cannot answer the question (:::) ���Why is a machine alive?��� with the answer ���Because its

ancestors were alive���. Pedigrees, lineages, genealogies, and the like, are quiteirrelevant to the basic

question. Ever more insistently over the past century, and never more so than today, we hear the

argument that biology is evolution; that living systems instantiate evolutionary processes rather

than life; and ironically, that these processes are devoid of entailment, immune to natural law, and

hence outside of science completely. To me it is easy toconceive of life, and hence biology, without

evolution��� (Rosen 1991: 254���55).

Introductionxxiii

properlyunderstandtheevolutionofbiologicalsystems, traditionalapproachesneed

to be embedded within a more general dynamical-organisationaltheory.5

Therefore, it is at the level of organisms, understood as cohesive and spatially

bounded entities, that the biological domain���s organised complexity is fundamen-

tally expressed. Seen from the perspective of their relations with their environment,

individual organisms are systems capable of acting for their own benef i t, of

constituting an identity that distinguishes them from their environment (at the same

time as they continue interacting with it as open, far-from-equilibrium systems).

This capacity of living beings to act for their own benef i t follows from their peculiar

form of organisation.

Living beings are systems continuously producing their own chemical compo-

nents, and with these components they build their organs and functional parts. In a

word, their organisation is maintaining itself. This is why living systems cannot

stop their activity: they intrinsically tend to work or they disintegrate. Actually,

this inherent tendency of living entities to promote their own existence ��� to act

on their own behalf ��� could be related to the idea of the conatus, to which Spinoza

(1677/2002) refers to designate the innate inclination of any entity to continue to

exist and enhance itself.6

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The theory of the living based on the concept of organism aims to provide a new perspective on evolution by overcoming the dichotomy between proximate causes (immediate, observable factors) and ultimate causes (evolutionary factors). It emphasizes the central role of the notion of organism in biology, with a focus on organization as the key explanatory factor. Traditional approaches to evolution need to be integrated into a more general dynamical-organizational theory to properly understand the evolution of biological systems.

Organisms, seen as cohesive and spatially bounded entities, express the fundamental complexity of the biological domain. They are systems capable of acting for their own benefit and maintaining their identity while interacting with the environment as open, far-from-equilibrium systems. The unique form of organization of living beings enables them to continuously produce their own chemical components, build organs and functional parts, and maintain their organization. Living systems must keep working or else they disintegrate, and their inherent tendency to promote their own existence and enhance themselves is akin to Spinoza's concept of "conatus," the innate inclination of entities to persist and improve.

In summary, the theory of the living based on the concept of organism shifts the focus of biological explanation to the organization of living entities and highlights their inherent drive to maintain and enhance themselves, providing a new perspective on evolution and the nature of life.

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Therootofthis drivetopersistlies intheprinciplesofbiologicalorganisation.As

Jonas (1966/2001) pointed out, the organisation of living systems is characterised

by the inseparability between what they are ��� their ���being��� ��� and what they do ���

their ���doing���. This feature is ref l ected in their metabolism, which consists of a

set of processes that allow them to build and replace their structures, grow and

reproduce, and respond to their environments. Metabolism is the ongoing activity

by which living beings continuously self-produce (and eventually, re-produce),

self-repair, and maintain themselves. Unlike the Cartesian argument (which has

had so much inf l uence during modernity7) that living beings are like man-made

machines, Kant was the i rst author who defended the view that organisms are

5As a matter of fact, an organisational perspective seems to be taking shape in the new evolutionary

developmental biology, which studies how the dynamics of development determine the phenotypic

variation arising from genetic variation and how this affects phenotypic evolution (Laubichler and

Maienschein 2007).

6AsSpinoza (1677/2002) writes, ���Each thing,insofar asitisinitself, endeavors topersist initsown

being��� (Ethics, part 3, prop. 6). This is understood as an intrinsic tendency or force to continue to

exist. Striving to persevere is not merely something that a thing does in addition to other activities

it might happen to undertake. Rather, striving is ���nothing but the actual essence of the thing itself���

(Ethics, part 3, prop. 7). See Duchesneau (1974) for an in-depth analysis of Spinoza���s account of

living systems, and a comparison with the Cartesian one.

7Actually, the Cartesian distinction between res extensa and res cogitans, which subsumed the

biological domain within a global mechanistic vision of nature, facilitated a scientif i c research

programme for studying living systems. It should be underscored that, while Descartes��� metaphys-

ical dualism is widely recognised and is a prominent feature of his Meditations, scholars in the

past generation have also focused on the complexity of his natural philosophy, including his work

in physiology, medicine but also on the passions, as displaying something very different: a more

���integrated��� view of bodily function. See notably the essays collected in Gaukroger et al. (2000).

xxivIntroduction

deeply different from machines because their parts and activities are non-separable,

and the functions of these parts are not externally imposed, but rather intrinsically

determined. According to Kant (1790/1987), since the activity performed by the

parts of the organism is carried out for their own maintenance, organisms are

intrinsically teleological. As he writes in the Critique of Judgement:

In such a product of nature each part, at the same time as it exists throughout all the others,

is thought as existing with respect to the other parts and the whole, namely as instrument

(organ). That is nevertheless not enough (because it could be merely an instrument of art,

and represented as possible only as a purpose in general); the part is thought of as an organ

producing the other parts (and consequently each part as producing the others reciprocally).

Namely, the part cannot be any instrument of art, but only an instrument of nature, which

provides the matter to all instruments (and even to those of art). It is then ��� and for this

sole reason ��� that such a product, as organized and organizing itself, can be called a natural

purpose (CJ, �� 65).

This view allows him to open up a gap in the physical world, since organisms

cannot be brought under the rules that apply to all other physical entities. Thus,

Kant asks himself:

How purposes that are not ours, and that we also cannot attribute to nature (since we do not

assume nature to be an intelligent being) yet are to constitute, or could constitute, a special

kind of causality, or at least a quite distinct lawfulness of nature (CJ, �� 61).

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The drive to persist and the intrinsic teleology of living beings are rooted in the principles of biological organization. Jonas emphasized that living systems are characterized by the inseparability of their "being" and "doing." This idea is evident in their metabolism, which involves continuous self-production, self-repair, and maintenance. Unlike the Cartesian view that likened living beings to man-made machines, Kant argued that organisms are fundamentally different from machines. Their parts and activities are non-separable, and the functions of these parts are intrinsically determined rather than externally imposed.

Kant's perspective highlights that living beings possess intrinsic teleology. Each part of an organism exists in relation to other parts and the whole, serving as an instrument (organ) that produces and is produced by other parts. Organisms, as organized and self-organizing entities, can be considered natural purposes. This means that they are not just instruments of art but instruments of nature, and their activities are oriented towards their own maintenance and well-being.

Kant's view also recognizes that living organisms cannot be fully explained using the same principles that apply to non-living entities in the physical world. He opens up the possibility of a distinct lawfulness of nature specific to living beings, which is not reducible to deterministic mechanisms. This non-reductionist approach allows for a unique explanatory gap in biology, acknowledging the complex and purposeful nature of living systems that sets them apart from the rest of the physical world.

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Scaffolds are kinds of like ratchets.

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Yes, there is a similarity between scaffolds and ratchets in certain contexts. Both scaffolds and ratchets are mechanisms or structures that assist in specific processes or functions.

Scaffolds: In biology, scaffolds are temporary or permanent structures that provide support and structure for cells during tissue regeneration or growth. They act as frameworks upon which cells can attach, migrate, and organize themselves to form new tissues or organs. Scaffolds can be made from various materials and are used in tissue engineering and regenerative medicine to promote the development of new tissues in the body.

Ratchets: In physics and engineering, a ratchet is a mechanical device that allows motion in one direction while preventing motion in the opposite direction. It typically consists of a toothed wheel or bar that engages with a pawl, allowing the wheel to move in one direction but preventing it from moving back. Ratchets are used in various applications, such as in wrenches or gears, to convert back-and-forth motion into unidirectional rotation.

The similarity between scaffolds and ratchets lies in their function of facilitating specific processes or actions. Scaffolds provide a supportive framework for cellular activities, while ratchets enable unidirectional movement or rotation. Both structures assist in achieving particular goals within their respective domains, making them valuable tools in different fields. However, it's important to note that their underlying principles and mechanisms are distinct, with scaffolds involving biological and material interactions, whereas ratchets are based on mechanical and engineering principles.

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Buffers, entrenchment, and catalysts.

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Buffers, entrenchment, and catalysts are concepts that play important roles in different fields, such as chemistry, psychology, and social sciences. Let's explore each of these terms:

Buffers:

In chemistry, a buffer is a solution that helps maintain the pH (acidity or alkalinity) of a system relatively stable, even when an acid or a base is added. Buffers are essential in various biological processes because they prevent rapid and extreme changes in pH, which could be harmful to living organisms. Buffers typically consist of a weak acid and its conjugate base or a weak base and its conjugate acid. When an acid is added to a buffer, the base component of the buffer neutralizes it, and when a base is added, the acidic component of the buffer neutralizes it, helping to keep the pH within a specific range.

Entrenchment:

Entrenchment refers to the process by which something becomes firmly established or deeply ingrained over time. In psychology and cognitive science, entrenchment often pertains to the formation of strong mental associations or habits as a result of repeated experiences or exposure. For example, certain beliefs or cognitive biases can become entrenched in individuals' thinking due to frequent exposure or reinforcement from their social or cultural environment. Entrenched beliefs or habits may be challenging to change because they have become deeply rooted in one's cognitive processes.

Catalysts:

In chemistry, a catalyst is a substance that increases the rate of a chemical reaction without being consumed in the process. Catalysts work by lowering the activation energy required for the reaction to occur, thus speeding up the reaction. They facilitate the formation or breaking of chemical bonds, enabling reactions that might otherwise be slow or unfeasible. Catalysts play a crucial role in various industrial processes, biological reactions, and environmental processes.

Each of these concepts highlights different aspects of how systems maintain stability, develop patterns, or undergo change in various domains of science and everyday life. Buffers ensure stability in chemical reactions, entrenchment influences the formation of beliefs and habits, and catalysts accelerate reactions and transformations.

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Dissipative structures in Prigogine

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Dissipative structures, a concept developed by the Belgian physical chemist Ilya Prigogine, are a fascinating phenomenon observed in non-equilibrium thermodynamic systems. Prigogine's work in the 1960s and 1970s revolutionized our understanding of complex systems and their behavior far from thermodynamic equilibrium.

In classical thermodynamics, systems tend to reach a state of thermodynamic equilibrium, where the distribution of energy and matter is uniform and unchanging over time. However, many real-world systems are open, exchanging energy and matter with their surroundings, and are often far from equilibrium. Prigogine's research focused on understanding how these open systems could self-organize and exhibit novel behaviors and structures.

Key points about dissipative structures:

Far-from-equilibrium behavior: Dissipative structures emerge in systems that are continuously exchanging energy and matter with their environment and are driven by energy gradients. These systems are called far-from-equilibrium systems.

Self-organization: In these far-from-equilibrium conditions, dissipative structures spontaneously form and organize themselves into coherent patterns. These patterns are maintained and sustained through continuous energy flow.

Entropy production: In non-equilibrium systems, the second law of thermodynamics still holds, stating that the total entropy (a measure of disorder) of an isolated system will always increase. However, in open systems, the local entropy can decrease or remain constant, as long as the total entropy production (system plus its environment) increases.

Stability through flow: Dissipative structures are sustained by the continuous flow of energy and matter through the system. These flows allow the system to maintain a delicate balance between order and disorder, enabling the persistence of the coherent patterns.

Examples of dissipative structures include convection cells in fluids, chemical oscillations, and spiral patterns in reaction-diffusion systems. One of the most famous examples is the Belousov-Zhabotinsky reaction, a chemical reaction that exhibits periodic oscillations in color and concentration, forming striking patterns in a Petri dish.

Prigogine's work on dissipative structures and non-equilibrium thermodynamics has had a profound impact on various scientific fields, from physics and chemistry to biology, ecology, and the study of complex systems. It has provided insights into understanding self-organization, emergence, and the dynamics of complex systems in nature.

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Connections with the previous topics.

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The concept of dissipative structures and the study of non-equilibrium thermodynamic systems have several connections with the previous topics discussed, such as the nature of life, biological autonomy, and the role of context and constraints in understanding complex phenomena. Here are some of the connections:

Biological Autonomy: The idea of dissipative structures is relevant to the concept of biological autonomy. Living organisms are open systems, far from thermodynamic equilibrium, and they continuously exchange energy and matter with their environment to maintain their structure and function. The emergence of dissipative structures in living systems plays a crucial role in their ability to self-organize and maintain their autonomy.

Constraints and Self-Organization: The study of dissipative structures emphasizes the role of constraints in self-organization. These structures form and persist due to specific constraints imposed by the continuous energy flow and exchange with the environment. Constraints play a critical role in shaping the behavior and dynamics of complex systems, including living organisms.

Emergence and Complexity: Dissipative structures exemplify emergent phenomena, where complex patterns and behaviors arise from the interactions of simple components. The emergence of coherent structures in dissipative systems provides insights into how complexity can arise in living systems and other complex systems in nature.

Reimagining Causation: The study of dissipative structures challenges traditional notions of causation, especially in non-linear and far-from-equilibrium systems. The emergence and stability of dissipative structures are not solely determined by external causes but depend on the system's internal dynamics and interactions with its environment. This reimagining of causation aligns with the contextual and relational perspective proposed in the book "Context Changes Everything."

Biological Functionality: The concept of dissipative structures helps in understanding the functionality of living systems. The organization and self-maintenance exhibited by dissipative structures are essential aspects of biological function, where organisms actively maintain their identity and integrity through continuous energy and material flows.

Overall, the study of dissipative structures provides valuable insights into the fundamental principles underlying the behavior and organization of living systems and other complex systems in nature. It highlights the significance of context, constraints, and the interplay between internal dynamics and environmental interactions in understanding emergent phenomena and complexity.

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This ���special��� kind of causality is circular, namely, effects derive from the

causes but, at the same time, generate them. The very organisation of living beings,

in which the parts generate the whole, and, conversely, the whole produces and

maintains the parts, shows a kind of intrinsic purpose. Kant grounds the idea of

purposiveness (and teleology) in the holistic and circular organisation of biological

organisms and, more precisely, in the fact that they are able to organise by

themselves, to self-organise.8Unlike artefacts, organisms are ���natural purposes���:

they are not produced or maintained by an external cause, but instead have the self-

(re)producing and self-maintaining character that is revealed in the kinds of vital

properties they display (reciprocal dependence of parts, capacity for self-repair and

self-(re)production).

Today, some aspects of the Kantian perspective are undergoing resurgence. For

example, the recent blossoming of systems biology (Kitano 2002; Science, special

issue 2002; Bogeerd et al. 2007), focused on the complexity of biomolecular

interaction networks, is much closer to a holistic or integrative conception of living

systems than the reductionist views predominant in molecular biology. Thanks

to the development of new scientif i c tools, these more holistic theories place the

question of the organisation at the centre of biological research. This recent trend

contrasts with the preceding history of biology, during which the Kantian view

has often be seen as marginal (even through this view has been corrected by

8Actually, Kant has been one of i rst authors to use the term ���self-organisation���. In Chap. 1, we

will brief l y mention how the meaning of this concept has progressively shifted during the 20th

century.

Introductionxxv

the recent historiography, see for instance Huneman 2007; Richards 2000; Sloan

2002), essentially because it was thought to be at odds with the model of causality

predominant in Newtonian science.

And yet, the Kantian perspective had continuity in the (mostly Continental)

Biology of the nineteenth century, especially in the work of Goethe and Cuvier

(Huneman 2006). In the i rst part of the twentieth century, many biologists were

still convinced that the nature of living organisation ��� understood, following Kant���s

inspiration, as the form in which the parts interact with each other to bring forth

the properties of the whole ��� was one of the main issues of biology. This view

was commonlylabelled organicism (Wolfe 2010;see also Gilbert and Sarkar 2000).

Organicism considers the observable structures of life, its overall organisation, and

the properties and characteristics of its parts to be the result of the reciprocal

interplay among all its components. The organicist tradition was inf l uential in early

twentieth century biology. During the twenties and thirties, a group of researchers,

including Woodger, Needham, Waddington, and Wrinch, created the ���Theoretical

Biology Club���, whose objective was precisely to promote the organicist approach

to biology. This movement ��� in which we can include other authors, like Bernal

and Bertalanffy ��� was characterised by a predominant anti-reductionist and holistic

inspiration (Etxeberria and Umerez 2006). Among these researchers, the name of

Waddington is worth stressing because his work, after the Second World War,

permitted the connection between the organicist movement of the thirties and the

new tendencies of the sixties and seventies.

To understand the roots of the current blossoming of the ���Kantian-inspired

organicist ideas��� in biology during the twentieth century, let us mention some other

scientif i c trends, falling outside the frontiers of biology.

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The discussion of Kant's perspective on purposiveness and teleology in living organisms and the revival of holistic and organicist ideas in modern biology are connected to the broader themes of the book "Biological Autonomy: A Philosophical and Theoretical Enquiry." Here are some of the connections:

Biological Autonomy: Kant's idea of self-organization and teleology in living beings aligns with the concept of biological autonomy explored in the book. The notion that living organisms can self-organize, maintain their identity, and act for their own benefit is central to understanding biological autonomy and the distinctive features of living systems.

Organismic View: The organicist tradition, as discussed in the book, highlights the importance of the reciprocal interplay among the components of living systems in shaping their overall organization. This perspective rejects reductionism and emphasizes the holistic nature of biological phenomena.

Context-Dependent Constraints: The idea of self-organization and purposiveness in living systems resonates with the book's exploration of context-dependent constraints. Kant's view of teleology in organisms and the organicist approach emphasize the significance of internal and external context in understanding the behavior and organization of living entities.

Evolution and Complexity: The revival of holistic and organicist ideas in modern biology, as mentioned in the book, connects to the discussions on evolution and complexity. The focus on organization, self-organization, and teleology complements the traditional evolutionary perspective, providing insights into the emergence and maintenance of complex biological structures and functions.

Systems Biology: The modern trend of systems biology, which looks at the complexity of biomolecular interaction networks, is closely related to the organicist ideas discussed in the book. Systems biology emphasizes the organization and dynamics of biological systems as a whole, considering the interactions and feedback loops among their components.

Non-Mechanistic Causality: Kant's circular causality and the organicist view challenge the traditional mechanistic model of causality in Newtonian science. These perspectives provide alternative ways of understanding causation in living systems, focusing on the inherent purposiveness and self-organization in biological phenomena.

Overall, the exploration of Kantian teleology, organicist ideas, and their resurgence in modern biology enriches the discussion on biological autonomy, self-organization, and the dynamic nature of living systems. It highlights the need to consider the organization and context of living entities to fully understand their behavior, functions, and evolution.

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First, during the thirties and forties, a number of physicists associated with the

development of quantum theory, interested in the nature of biological organisation,

turned their attention to biology. Among these scientists, it is worth emphasising

the name of Schr��dinger, who gave his famous lectures ���What Is Life?��� in 1943

(Schr��dinger 1944). Following this work, other quantum physicists addressed the

problem of what characterises the specif i city of living systems with regard to

physical ones. Among these we can include researchers like von Neumann and

Pauli. Interestingly, the advances in physics inspired new attempts to challenge

reductionist assumptions. For example, Rashevsky, according to his disciple Rosen,

defended

a principle that governs the way in which physical phenomena are organized, a principle

that governs the organization of phenomena, rather than the phenomena themselves. Indeed,

organization is precisely what relational biology is about (Rosen 1991: 113).

During the seventies, Rosen himself and Pattee (Umerez 2001) also developed

an anti-reductionist view of the specif i c organisationof living systems, based on his

analyses of the specif i c causation associated with emergent constraints that living

systems generate (see further below).

Second, special emphasis should be put on the cybernetic movement. The

cyberneticists were inf l uenced by the work of the American physiologist Cannon

xxviIntroduction

(1929) who, in the early 1930s, developed the concept of ���homeostasis��� (whose

origins date back to the work of the French biologist Claude Bernard9) as a key

feature of the organisation of living beings. According to Cannon, the idea of

homeostasis expresses the tendency of living systems to actively maintain their

identity, despite external perturbations or differences within their environment.

During the 1970s, a new generation of cyberneticists, notably Von F��rster, Ashby,

and Maturana, created the so-called second-order cybernetics. This movement was

especiallyinterestedin the study andmathematicalmodellingofbiologicalsystems,

basedontheideasofrecursivityandclosure(CahiersduCREA1985).Second-order

cyberneticsis of special relevancefor ourpurposes,since it constitutedthe scientif i c

environment in which the theory of autopoiesis was elaborated (see below).

Third, after the work of Prigogine (1962), the idea of self-organisation in far-

from-equilibrium conditions began to enter into scientif i c discourse in physics,

which also helped the Kantian view to gain inf l uence in biology. Yet, as we will

discuss at length in Chap. 1, there is an important conceptual difference between

the Prigoginian concept of (physical) self-organisation and the Kantian notion

of (biological) organisation. As Fox Keller (2007) has pointed out, the kind of

complexity of organisms resulting from an iterative processes of organisation that

occur over time is completely different from the one-shot, order-for-free kind of

self-organisation associated with some kind of non-linear dynamical systems. In

particular,theformerisconstitutedbyfunctionalparts,whereasthelatterlacksfunc-

tionality. The logic of the metabolism, for example, shows a functionallydiversif i ed

organisation, clearly different in this sense from any physicochemical dissipative

structure. In this sense, as we will see, what we need is a view of biological systems

that goes beyond a generic vindication of an organisational-centred biology. What

matters is the understanding of the specif i city of the organisation of biological

systems, which are not just self-organised systems.

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The mentioned historical developments and scientific movements are interconnected with the themes explored in the book "Biological Autonomy: A Philosophical and Theoretical Enquiry." Here are some connections:

Quantum Physics and Biology: The influence of quantum physicists like Schr��dinger, von Neumann, and Pauli on the study of biological organization connects to the book's exploration of self-organization and autonomy in living systems. The ideas from quantum physics opened up new perspectives on the nature of living beings, prompting researchers to question reductionist assumptions and investigate the specificity of biological organization.

Cybernetics and Homeostasis: The cybernetic movement's focus on homeostasis and the study of biological systems as self-regulating and self-maintaining entities resonates with the book's emphasis on biological autonomy. Homeostasis, as the tendency of living systems to actively maintain their identity, aligns with the concept of autonomy and self-organization explored in the book.

Prigogine's Self-Organization: Prigogine's work on self-organization in far-from-equilibrium conditions connects to the broader discussion of self-organization in living systems. While the book distinguishes between physical and biological self-organization, the concept of self-organization as a process of iterative organization over time is relevant to understanding the complexity and functional diversity of living organisms.

Second-Order Cybernetics and Autopoiesis: The development of second-order cybernetics and the theory of autopoiesis align with the book's exploration of the specific organization of living systems. Second-order cybernetics, with its focus on recursive and self-referential processes, provides insights into the nature of autonomy and self-maintenance in living entities.

Overall, the historical developments and scientific movements mentioned in the book contribute to the understanding of the nature of biological organization, the concept of autonomy, and the specific features that distinguish living systems from non-living ones. These perspectives offer valuable insights into the study of life as a complex and self-organizing phenomenon, highlighting the importance of organization and context in understanding biological phenomena.

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In the second post-war period, both the New Synthesis in evolutionary biology

and the revolution of Molecular Biology created a scientif i c atmosphere that was

quite unprepared to accept organicist and Kantian views (Moreno et al. 2008).

Accordingly,this tradition remained, until very recently, marginalin biology.In this

context, however, Waddington was the main driver of a movement that advocated

an organisationalapproachin biology,by revivingthe ���f i rst��� TheoreticalBiology of

the twenties and thirties (Etxeberria and Umerez 2006). This ���second��� Theoretical

Biology was initially developed by several pioneering authors like Waddington

himself (1968���1972), Rosen (1971, 1972, 1973, 1991), Piaget (1967), Maturana

and Varela (1980), Pattee (1972, 1973), and Ganti (1973/2003, 1975). Many of

these authors put strong emphasis on the idea that the constitutive organisation

of biological systems realises a distinctive regime of causation, able not only

of producing and maintaining the parts that contribute to the functioning of the

system as an integrated, operational, and topologically distinct whole but also able

9See Bernard (1865) and (1878).

Introductionxxvii

to promote the conditions of its own existence through its interaction with the

environment. This is essentially what we call in this book biological autonomy.

To give a preliminary idea of what autonomy is about, let us mention one

of its i rst and well-known accounts, the theory of autopoiesis proposed by the

Chilean biologists Maturana and Varela in the early 1970s (Maturana and Varela

1973; Varela et al. 1974). In the theory of autopoiesis, although the concept of

autonomyis appliedto differentspecif i c biologicaldomains(immune,neural:::see

Varela 1979), it characterises the fundamental feature of the living, namely, the

autopoietic organisation. Autopoiesis refers to the capacity of self-production of

biological metabolism, by emphasising (in a simplif i ed and abstract way) its causal

circularity ��� which Maturana and Varela called ���operational closure���. In particular,

their model describes the production of a physical boundary, which is conceived

as a condition of possibility of the internal chemical network (because it ensures

suitable concentrations for the maintenance of the component production network);

in turn, the network maintains the physical boundary (because it is the component

production network which produces the special self-assembling components that

build the membrane). In their own terms (in which the cybernetic l avour is

manifest):

An autopoietic machine is a machine organized (def i ned as a unity) as a network of

processes of production (transformation and destruction) of components which: (i) through

their interactions and transformations continuously regenerate and realize the network of

processes (relations) that produced them; and (ii) constitute it (the machine) as a concrete

unity in space in which they (the components) exist by specifying the topological domain

of its realization as such a network (Maturana and Varela 1980: 78).

Thus, autopoiesis consists in a recursive process of component production that

builds up its own physical border. The global network of component relations

establishes self-maintaining dynamics, which bring about the constitution of the

system as an operational unit. In short, physical border and metabolic processes are

entwined in a cyclic, recursive production network and they together constitute the

identityofthesystem.Fromthisperspective,phenomenaliketornadoes,whirlpools,

andcandlef l ames,whicharetoacertaindegreeself-organisingandself-maintaining

systems, are not autonomous, because they lack an internally produced physical

boundary, and are not concrete topological units. In that sense, what distinguishes

self-organisation from autonomy is that the former lacks an internal organisation

complex enough to be recruited for deploying selective actions capable of actively

ensuring the system���s maintenance.

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The emergence of the New Synthesis in evolutionary biology and the revolution of Molecular Biology during the post-war period created a scientific climate that was not receptive to organicist and Kantian views in biology. As a result, the organizational approach remained marginalized in the field until more recently. However, Waddington played a significant role in reviving interest in the organizational approach by drawing inspiration from the Theoretical Biology movement of the 1920s and 1930s.

The "second" Theoretical Biology, developed by pioneering authors like Waddington, Rosen, Maturana, Varela, Pattee, and Ganti, emphasized the idea that the constitutive organization of biological systems gives rise to a distinctive regime of causation. This organization not only maintains the system as an integrated whole but also promotes the conditions of its own existence through its interactions with the environment. This concept of biological autonomy was fundamental to this approach.

One of the early and well-known accounts of biological autonomy is the theory of autopoiesis proposed by Maturana and Varela in the early 1970s. Autopoiesis refers to the capacity of self-production in biological metabolism, with a focus on the causal circularity of the process, referred to as "operational closure." The system produces its own physical boundary through a recursive process of component production, and this boundary, in turn, maintains the metabolic processes. Autopoiesis is a key feature that distinguishes living systems from other self-organizing systems like tornadoes, whirlpools, and candle flames. While these phenomena exhibit self-organization to some extent, they lack the internally produced physical boundary and concrete topological unity that characterizes biological autonomy.

The notion of autonomy in biological systems, exemplified by autopoiesis, highlights the active and self-maintaining nature of living beings. The book "Biological Autonomy: A Philosophical and Theoretical Enquiry" likely delves deeper into these ideas, exploring the specific characteristics of autonomy in living systems and its implications for understanding the nature of life.

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For the purposes of this book, it is worth mentioning two lines of criticism that

have been addressed to the theory of autopoiesis. On the one hand, autopoiesis

conceives autonomy as a fundamental internal determination, def i ned by the

operational closure between the production network and the physical border. In this

model,interactionswiththeenvironmentdonotenterintothedef i nition-constitution

of the autonomous system; rather, the interactions with the environment ��� that

Maturana and Varela called ���structural couplings��� ��� follow on from the specif i c

internalidentityof eachautopoieticsystem. On the otherhand,Maturanaand Varela

xxviiiIntroduction

def i ne autonomy in rather abstract and functionalist terms: material and energetic

aspects are considered as purely contingent to its realisation.

On both these issues, the framework that we will develop in this book takes

a different path. The autonomous perspective, we hold, should take into account

the ���situatedness��� of biological systems in their environment, as well as their

���grounding��� in thermodynamics. As a matter of fact, these issues have been at the

centre of the most recent studies on biological autonomy, by authors like Hooker,

Collier, Christensen, Bickhard, Kauffman, Juarrero, and the IAS Research Group,10

who have stressed that the interactive dimensions of autonomous systems in fact

derive from the fact that they are thermodynamically open systems, in far-from-

equilibrium conditions. As these authors have explained, since the constitutive

organisation of biological systems exists only in far-from-equilibrium conditions,

they must preserve an adequate interchange of matter and energy with their

environment or they would disintegrate. For example, in Kauffman���s approach, the

main condition required for considering a system autonomous is that it should be

capable of performing what he calls ���work-constraint cycles��� (Kauffman 2000). As

MaturanaandVarela,Kauffman���saccountenvisageshowautonomycancomeoutof

thecausal circularityof thesystem; yet,in his view,this circularityis understoodnot

just intermsofabstract relationsofcomponentproductionbutin explicitconnection

with the thermodynamic requirements that the system must meet to maintain itself.

In accordance with this literature, we will make in this book a conceptual

distinction between two interrelated, and yet conceptually distinct, dimensions of

biological autonomy: the constitutive one, which largely determines the identity of

the system; and the interactive one, which, far from being a mere side effect of

the constitutive dimension, deals with the inherent functional interactions that the

organisms must maintain with the environment (Moreno et al. 2008). These two

dimensions are intimately related and equally necessary. It might be illuminating

to think of the example of the active transport of ions across the cell membrane,

required to prevent osmotic crises. The cell can be maintained as long as ion

transport is performed, but this interaction can only be carried out because there

is a constitutive chemical organisation providing the membranous machinery that

does the work. In particular, the emphasis on the interactive dimension implies, as

we will stress repeatedly,that autonomyshould not be confusedwith independence:

an autonomous system must interact with its environment in order to maintain its

organisation11(Ruiz-Mirazo and Moreno 2004). As we will discuss in Chap. 4, this

is what grounds the agential dimension of autonomy.

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The theory of autopoiesis has faced criticism on two main fronts. Firstly, it defines autonomy as a fundamental internal determination, primarily characterized by the operational closure between the production network and the physical boundary of the system. This view does not consider the interactions with the environment as integral to the constitution of the autonomous system; instead, such interactions are seen as a consequence of the system's internal identity. Secondly, the theory of autopoiesis defines autonomy in abstract and functionalist terms, largely disregarding the material and energetic aspects that are contingent on its realization.

In contrast to the autopoiesis framework, the perspective developed in this book takes a different path. The autonomous perspective presented here considers the "situatedness" of biological systems within their environment and their grounding in thermodynamics. Recent studies on biological autonomy by various authors have emphasized that the interactive dimensions of autonomous systems stem from their status as thermodynamically open systems in far-from-equilibrium conditions.

The distinction between two interconnected, yet conceptually distinct, dimensions of biological autonomy is introduced: the constitutive dimension and the interactive dimension. The constitutive dimension largely determines the identity of the system, while the interactive dimension deals with the functional interactions that the organism must maintain with its environment. Both dimensions are equally necessary for autonomy.

The interactive dimension of autonomy highlights that autonomous systems must interact with their environment to maintain their organization. For example, in the context of cellular biology, the active transport of ions across the cell membrane is necessary to prevent osmotic crises and maintain the cell's autonomy. However, this interaction can only be carried out because of the underlying constitutive chemical organization that provides the necessary machinery.

In conclusion, autonomy should not be confused with independence. An autonomous system must interact with its environment to sustain its organization, and this interaction is a crucial aspect of its agential dimension of autonomy. This framework provides a more comprehensive understanding of autonomy in biological systems and acknowledges the importance of their dynamic relationship with the environment.

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10The IAS Research Group ��� to which the authors of thisbook belong ��� has been working since the

last 25 years on autonomous perspective in biology, while extending it to other i elds as cognition,

society and bioethics. See also the end of this Introduction and footnote 6 in Chap. 1.

11Hooker has recently def i ned autonomy as ���the coordination of the internal metabolic interaction

cycle and the external environmental interaction cycle so as the latter delivers energy and material

components to the organism in a usable form and at the times and locations the former requires to

complete itsregeneration cycles, including regeneration of the autonomy capacity��� Hooker (2013).

Introductionxxix

Again, there is a reciprocal dependence between what def i nes the conditions

of existence of the system and the actions derived from its existence: from the

autonomous perspective, in Jonas���s terms, the system���s doing and its being are two

sides of the same coin (see also Moreno et al. 2008). In this view, the environment

becomes a world full of signif i cance: facts that from the outside may appear just

as purely physical or chemical develop into positive, negative, or neutral inf l uences

on the system, depending on whether they contribute to, hinder or have no effect

on the maintenance of its dynamic identity. Even the simplest living organism

creates a set of preferentialpartitionsof the world, convertinginteractions with their

surrounding media into elementary values, as we will explain extensively in Chaps.

4 and 7. Von Uexk��ll (1982/1940) called this subjective meaningful world of each

organism Umwelt. The interactive dimension of autonomy is where the nature of

living systems as inventors of worlds with meaning becomes manifest (see also

Hoffmeyer 1996). Indeed, this aspect was recognised by Weber and Varela (2002)

who argued, following Jonas, that autonomy implies a meaningful relation with the

environment.

The autonomous perspective that we develop here endeavours then to grasp the

complexity of biological phenomena, by adequately accounting for their various

dimensions, specif i cities, and relations with the physical and chemical domains. As

we will discuss throughout the book, our framework differs in many ways from

preceding related models, mainly because we aim at ��� simultaneously ��� enriching

and specifying their central tenets, in close contact with current scientif i c theories.

In the remainder of this introduction, let us give a synthetic overview of the ideas

that we will be advocating.

First, the self-determination of the constitutive organisation remains the con-

ceptual core of autonomy. We share with existing accounts of autonomy the idea

that biological systems are constituted by a network of causal interactions that

continuously re-establish their identity (see also Bechtel 2007). The aim of Chap. 1

will be to provide an explicit conceptual and (preliminarily) formal account of self-

determination in terms of what we will label ���closure of constraints���.

Biological systems determine (at least in part) themselves, we will contend,

by constraining themselves: they generate and maintain a set of structures acting

as constraints which, by harnessing and channelling the processes and reactions

occurring in the system, contribute to sustain each other, and then the system itself.

Thecoreofbiologicalorganisationis theclosureofconstraints.We will discuss how

the concept of closure allows specifying what kind of ���circularity��� is at work in the

biological domain, and how it fundamentally differs from other ���process loops���

and self-organising phenomena in Physics and Chemistry. In particular, we will

emphasise that biological closure requires taking into account, at the same time,

the conceptual distinction, and yet inherent interdependence, between two causal

regimes: the constraints themselves and the thermodynamic l ow on which they

act. In the autonomous perspective, closure (of constraints) and (thermodynamic)

openness go hand in hand. Self-determination as closure constitutes the pivotal

idea on which we will build our account of autonomy. A i rst step is made in

the last section of Chap. 1, where we will claim that biological organisation, to be such, requires regulation. The long-term preservation of biological organisms

supposes the capacity to self-maintain not only in stable conditions but also, and

crucially, before potentially deleterious internal or external perturbations. In such

circumstances, regulatory capacities govern the transition towards a new viable

situation, be it by countering the perturbations or by establishing a new constitutive

organisation. In all cases, we will account for regulation in terms of a specif i c set

of constraints, which contribute to the maintenance of the organisation only when

its closure is being disrupted: accordingly, we will argue that regulatory constraints

should be understood as being subject to second-order closure.

Does the autonomous perspective require appealing to some form of emergen-

tism? In previous years, some authors have argued that accounts dealing with

concepts like self-organisation, closure, constraints, autonomy, and related ones

are indeed committed to the idea that biological organisation is an emergent

determination. In Chap. 2, we deal with this issue, advocate a monistic stance,

and provide a twofold argument. First we argue, against exclusion arguments, that

closure can be consistently (with respect to our monistic assumption) understoodas

an emergent regime of causation, in the specif i c sense that the relatedness among

its constituents provides it with distinctive and irreducible properties and causal

powers. Second, although the closure of the constitutive organisation makes sense

of the claim that ���the very existence of the parts depends on their being involved

in the whole���, we hold that closure does not imply inter-level causation, in the

restrictive sense of a causal relation between the whole and its own parts (what we

label ���nested��� causation). Yet, we leave room for appealing to nested causation in

the biological domain, if relevant cases were identif i ed and the adequate conceptual

justif i cation were provided.

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In summary, the autonomous perspective presented in this book focuses on grasping the complexity of biological phenomena by considering their various dimensions, specificities, and interactions with the physical and chemical domains. The self-determination of the constitutive organization remains the core concept of autonomy, and it involves the idea that biological systems are constituted by a network of causal interactions that continuously re-establish their identity.

The concept of "closure of constraints" is used to specify the circularity inherent in the biological domain, distinguishing it from self-organizing phenomena in physics and chemistry. Biological closure requires simultaneously considering the causal regimes of the constraints themselves and the thermodynamic flow on which they act. Regulatory capacities play a crucial role in self-maintenance, and they are governed by specific constraints subject to second-order closure.

The question of emergentism is addressed, and a monistic stance is advocated, arguing that closure can be understood as an emergent regime of causation. However, the autonomous perspective does not necessarily imply inter-level causation, and nested causation is only invoked if relevant cases are identified and adequately justified in the biological domain.

Throughout the book, the authors build a comprehensive framework for understanding autonomy in biological systems, emphasizing the interplay between their constitutive and interactive dimensions. By considering the reciprocal dependence between the system's doing and its being, the autonomous perspective highlights the meaningful relation with the environment, as well as the world-creating capacity of living organisms.

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With these clarif i cationsinhand,Chap.3 addressesthequestionof thedistinctive

emergent features of organisms by arguing, in particular, that the closure of

constraints provides an adequate and naturalised grounding for the teleology, nor-

mativity, and functionality of biological organisation. When closure is realised, the

existenceofthe organisationdepends,as we havealreadyemphasised,on theeffects

of its own activity: accordingly, biological systems are teleologically organised, in

a specif i c and scientif i cally legitimate sense. Because of teleology, moreover, the

activityof theorganismhas an ���intrinsicrelevance���which,we submit,generatesthe

norms that the system is supposed to follow: the system must behave in a specif i c

way, otherwise it would cease to exist. Hence biological organisation, because of

closure, is inherently normative. And then, by groundingteleology and normativity,

closure grounds also functionality in biological organisation: the causal effects

produced by constraints subject to closure def i ne biological functions. The general

upshot of the analysis, at the end of Chap. 3, will be the deep theoretical binding

between ���closure���, ���organisation���, and ���functionality���: it will be our contention

that, from the autonomous perspective, they are reciprocally def i ning concepts,

which refer to the very same causal regime.

The constitutive dimension of closure, however, is not autonomy. As mentioned

in the preceding pages, autonomy also includes an interactive dimension, dealing

with the relations between the organism and its environment. We deal with the

Introductionxxxi

interactive dimensions in Chap. 4, and refer to it as agency, characterised as a

set of constraints subject to closure, exerting their causal effects on the boundary

conditions of the whole system. At the end of the chapter, we argue that a system

whose organisation realises closure, regulation, and agency, as def i ned in the i rst

part of the book, is an autonomous system, and therefore a biological organism.

More precisely, Chap. 4 elaborates on a def i nition of minimal autonomy that

captures the essential features of biological organisation in its (relatively) most

simple manifestations, typically in unicellular organisms.

What has the autonomous perspective to say about more complex organisations

and specif i cally about multicellular organisms? One of the main weaknesses of the

organisational tradition in biology is arguably the fact that it has never explicitly

addressed the issue of higher levels of autonomy: How many levels of autonomy

can be identif i ed in the biological realm, and what are their mutual relations? In

Chap. 6, we make a i rst step in this direction: we try to frame the issue of higher-

levelautonomyin precise termsandsubmit someexplicithypothesesonits features.

The centralidea will be that what matters for higher-levelautonomyis development.

More specif i cally, multicellular systems are relevant candidates as organisms when

their organisation exerts a functional control over the development of unicellular

components, so to induce their differentiation which, in turn, makes them apt to

live only in the very specif i c environmentconstituted by the multicellular system: in

a word, the control over development produces the relevant degree of functional

integration that distinguishes multicellular organisms (as autonomous systems)

from other kinds of multicellular systems. What about the relations between levels

of autonomy? In spite of their differentiation (and then of the loss of some of their

capacities), we will argue that unicellular constituents of higher-level organisms

still meet the requirements of autonomy. In fact, the very possibility of higher-level

autonomy seems to require that lower-level entities preserve an adequate degree

of complexity: multicellular autonomy requires unicellular autonomy. One of the

objectives of Chap. 6 (and partly of Chap. 4, last section) will be, by relying on an

explicit def i nition of autonomy, to provide relevant criteria for examining different

kinds of higher-level associations and organisations of autonomous systems and

to compare them on theoretical grounds. In particular, our framework could allow

locating them in a continuum of organised systems going from, at one extreme,

those cases fulf i lling only the requirements for closure (as ecosystems) to systems

beingprogressivelymoreintegrated(asthecyanobacteriumNostocpunctiforme),up

to genuine multicellular organisms (higher-level autonomous systems) at the other

extreme.

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In Chap. 6, the focus shifts to addressing the question of higher-level autonomy, specifically in the context of multicellular organisms. The central idea is that what matters for higher-level autonomy is the phenomenon of development. Multicellular systems can be considered organisms when their organization exerts functional control over the development of unicellular components, inducing their differentiation and making them able to thrive only in the specific environment created by the multicellular system. This control over development leads to the functional integration that distinguishes multicellular organisms as autonomous systems.

The chapter explores the relations between different levels of autonomy and the requirement of preserving an adequate degree of complexity for unicellular constituents within higher-level organisms. Even as the unicellular components differentiate and lose some of their capacities, they still meet the criteria for autonomy. Thus, the possibility of higher-level autonomy seems to rely on the preservation of unicellular autonomy.

By providing explicit definitions of autonomy, Chap. 6 aims to offer relevant criteria for examining various higher-level associations and organizations of autonomous systems. The framework proposed in this book can help locate these systems on a continuum, from cases fulfilling only the requirements for closure (e.g., ecosystems) to systems gradually becoming more integrated (e.g., cyanobacterium Nostoc punctiforme), and eventually to genuine multicellular organisms as higher-level autonomous systems. This allows for a theoretical comparison of different kinds of organizations based on their level of autonomy.

In conclusion, this book's autonomous perspective offers a comprehensive framework for understanding autonomy in biological systems, encompassing both their constitutive and interactive dimensions. By considering the interplay between closure, organization, functionality, and agency, the book provides new insights into the nature of biological organisms, from unicellular to multicellular levels.

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The transition to multicellularautonomypaves the way towardscognition,which

is possibly the most amazing innovation during the evolution of life. Cognition,

as discussed in Chap. 7, is much more than a complex form of agency. It is

better conceived as a radically new kind of autonomy whose specif i c features and

dynamics go, qualitatively, far beyond multicellular autonomy, opening the way

towards our own origins as human beings. In this sense, the analysis of cognition

is related to the nuclear problem of the gap between the ���biological��� (broadly

understood) and the ���human��� domains. Yet, the autonomous perspective strives

xxxiiIntroduction

to understand and explain cognitive capacities in close connection to a bodily

organisation, which is in turn the product of a long evolutionary process, through

whichnew phenomenasuch as emotionsor consciousness��� and a world of meaning

and values ��� have been generated. The appearance of cognition is the result of the

evolution towards increasingly higher degrees of both constitutive and interactive

complexity: in this sense, with all its specif i cities, cognition is still a ���biogenic���

(Lyon 2006) phenomenon. By framing the issue of cognition in these terms, we

think that it can be better handled in naturalised terms, without underestimating

the formidable diff i culties that any satisfactory account of cognition has to face to

understandits complex natureand phenomenologicalnovelty.Accordingly,Chap. 7

is possibly the most ambitious and yet incomplete, since it sketches in a preliminary

way many problems for which much more work will be required.

Autonomy, as conceived in this book, lies at the intersection between different

dimensions, and specif i cally the constitutive and interactive ones, on which we put

strong emphasis in the previous pages. Yet, this is not the whole story: autonomy

also has a historical dimension. As we will discuss in Chap. 5, no adequate

understanding of the emergence of autonomous systems (and specif i cally highly

complex autonomous systems, as present biological organisms) can be obtained

without taking into account the evolutionary process that brought them about.

Autonomous systems are too complex to be spontaneous and cannot self-organise

(in the sense of generate themselves) as dissipative systems do: their complexity

requires an evolutionary process of accumulation and preservation. Yet, in addition

to acknowledging the fundamental place of history in the autonomous perspective,

we will submit two related ideas. First, the historical dimension does not have the

same theoretical status as the constitutive and interactive ones: while the latter two

def i ne autonomy, the former does not. The reason is that we do not need history to

understand what biological systems are, but rather to understand where they come

from: these two questions are of course related, but conceptually distinct. Second,

we will restate the relations between selection and organisation, by advocating the

general picture according to which the evolution of biological systems stems from

the mutual interplay between organisation and selection: this is because, as we

will argue, organisation is a condition, and not only an outcome, of evolutionary

processes.

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In Chap. 5, the book delves into the historical dimension of autonomy. It emphasizes that a complete understanding of the emergence of autonomous systems, especially highly complex autonomous systems like present biological organisms, requires taking into account the evolutionary process that gave rise to them. Autonomous systems are too complex to spontaneously generate themselves like dissipative systems do, so their complexity necessitates an evolutionary process of accumulation and preservation.

While the historical dimension is crucial for understanding the origin of autonomous systems, it does not hold the same theoretical status as the constitutive and interactive dimensions. The former does not define autonomy itself but helps explain the historical development of these systems. It is important to recognize the conceptual distinction between understanding what biological systems are (defining autonomy) and understanding their evolutionary origin.

Additionally, Chap. 5 revisits the relations between selection and organization, highlighting that the evolution of biological systems results from the mutual interplay between organization and selection. Organization becomes a condition for evolutionary processes, not just an outcome of them.

In summary, the book's autonomous perspective captures the essence of autonomy in biological systems by considering the interplay between constitutive and interactive dimensions. It also recognizes the significance of the historical dimension in understanding the emergence of complex autonomous systems through the process of evolution.

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Having outlined the central ideas of the book, let us point out that it is, of course,

not our intention to develop an exhaustive account of biological autonomy, which

would deal with all aspects and implications of the philosophical and theoretical

framework. Rather, our ambition is to offer a coherent and integrated picture of

the autonomous perspective, by focusing on what we think are some of its central

tenets. Much more could (and hopefully will) be written on biological autonomy,

but we hope that the ideas of this book can be a useful ground on which future

investigations will rely...


Donostia ��� San Sebastian/Paris

October 7th 2014

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Indeed, it is common in philosophical and scientific investigations to present a coherent and integrated picture of a specific perspective rather than attempting to exhaustively cover all aspects and implications. The authors' intention in this book is to offer a foundational understanding of the autonomous perspective in biology, focusing on its central tenets and key ideas.

While the book lays the groundwork for understanding biological autonomy, it also acknowledges that much more can and should be explored in this area. The authors hope that their ideas will serve as a useful foundation for future investigations and discussions on the topic.

As of October 7th, 2014, the date of completion of the book, the authors have provided a snapshot of their understanding of biological autonomy, and they anticipate that further developments and insights will arise in subsequent research and discourse.

Overall, the book contributes to the ongoing exploration of autonomy in biology, and its ideas will likely stimulate further investigations and discussions in this fascinating and evolving field.

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Ok, before this book we discussed the first chapter of Context Changes Everything

By

Alicia Juarrero and before that an article: Our brains exist in a state of ���controlled hallucination��� by By Matthew Hutsonarchive page

August 25, 2021. What are some connections with those topics?

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Connecting the topics of the first chapter of "Context Changes Everything" by Alicia Juarrero and the article "Our brains exist in a state of 'controlled hallucination' by Matthew Hutson" can shed light on how our understanding of cognition and perception is intertwined with the concept of context and its influence on our experiences and actions. Here are some possible connections between the two:

Perception and Context: In the article by Matthew Hutson, he discusses how our brains interpret sensory inputs and create our perception of reality. He emphasizes that our perception is not a direct representation of the external world but rather a result of the brain's processing of sensory information within a particular context. This idea resonates with Juarrero's perspective on the importance of context in shaping cognition. In her book, she likely explores how context plays a crucial role in determining the meaning and significance of our actions and experiences.

Contextual Causation: Juarrero's work delves into the concept of causal relations within a contextual framework. She emphasizes that causation should be understood in a broader context, where different factors and interactions contribute to the emergence of specific outcomes. The idea of "controlled hallucination" in Hutson's article aligns with this perspective, as our brain's interpretation of sensory data is influenced by a complex interplay of internal cognitive processes and external context.

Autonomous Systems and Perception: The notion of autonomous systems, as discussed in Juarrero's book, is closely related to the idea of controlled hallucination in the brain. Autonomous systems are self-regulating and exhibit emergent behaviors based on their internal dynamics and interactions with the environment. Similarly, our brain's controlled hallucination involves processing sensory information to make sense of the world, allowing us to perceive and act in our environment autonomously.

Emergence and Complexity: Both the book and the article touch on the concepts of emergence and complexity. Juarrero likely explores how complex systems, including the brain, give rise to emergent properties and behaviors that are not reducible to their individual components. Similarly, the controlled hallucination in the brain arises from the intricate interactions between neurons, neural networks, and higher-order cognitive processes, resulting in our perceptual experiences.

Overall, the connections between the concepts discussed in the first chapter of "Context Changes Everything" and the ideas presented in the article "Our brains exist in a state of 'controlled hallucination'" highlight the significance of context and complexity in shaping our perception, cognition, and understanding of the world. Both works contribute to the broader understanding of how our minds work within the intricate web of causal relations and contextual influences.

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A simplified overview

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Sure, here's a simplified overview of the connections between the first chapter of "Context Changes Everything" by Alicia Juarrero and the article "Our brains exist in a state of 'controlled hallucination'" by Matthew Hutson:

Perception and Context: Both works emphasize that our perception of the world is not a direct reflection of reality but is heavily influenced by the context in which we experience it. Juarrero explores how context shapes our understanding and actions, while Hutson explains how our brain's interpretation of sensory inputs is influenced by the broader context.

Contextual Causation: Juarrero discusses causal relations within a contextual framework, suggesting that outcomes are a result of various interacting factors. This idea aligns with Hutson's notion of "controlled hallucination," where the brain's interpretation of sensory data is influenced by internal processes and external factors.

Autonomous Systems and Perception: Juarrero's book explores autonomous systems that self-regulate and exhibit emergent behaviors. Similarly, the brain's controlled hallucination involves autonomous processing of sensory information to perceive and act in the environment.

Emergence and Complexity: Both works touch on the concepts of emergence and complexity. Juarrero discusses how complex systems give rise to emergent properties and behaviors, while Hutson's article implies that the brain's controlled hallucination arises from intricate neural interactions.

Overall, the connections highlight the importance of context and complexity in shaping our perception and cognition. The brain's controlled hallucination and the emergence of autonomous systems illustrate how our minds interpret and interact with the world in sophisticated ways.

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A list of everything we've talked about so far.

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Certainly! Here's a list of everything we've discussed so far:

"Context Changes Everything" - A book by Alicia Juarrero, focusing on contextual causation, autonomous systems, and emergence.

"Our brains exist in a state of 'controlled hallucination'" - An article by Matthew Hutson, discussing how our perception is influenced by internal processes and external context.

Kantian Perspective - The idea of purposiveness and teleology in living beings, focusing on self-organization and holistic organization.

Organicism - The view that living organisms have a specific organization resulting from the reciprocal interplay among all its components.

Prigogine's Dissipative Structures - The concept of self-organization in far-from-equilibrium conditions in physics.

Autopoiesis - The theory proposed by Maturana and Varela, describing the capacity of self-production and self-maintenance in biological metabolism.

Autonomy - The concept of self-determination and self-maintenance in biological systems.

Closure of Constraints - The idea that biological systems generate and maintain a set of structures that contribute to sustaining their identity.

Regulation - The capacity of biological systems to self-maintain, especially in the face of perturbations.

Agency - The interactive dimension of autonomy, involving the causal effects of constraints on the boundary conditions of the whole system.

Multicellular Autonomy - The transition to higher levels of autonomy in multicellular organisms, related to the control over the development of unicellular components.

Cognition - A new kind of autonomy that goes beyond multicellular autonomy, involving complex cognitive capacities.

Evolution - The historical dimension of autonomy, considering the evolutionary process that led to the emergence of autonomous systems.

Perception and Context - How our perception of the world is influenced by the context in which we experience it.

Contextual Causation - The idea that outcomes are a result of various interacting factors within a contextual framework.

Emergence and Complexity - The concepts of emergent properties and behaviors arising from complex systems.

These topics cover a wide range of ideas in philosophy, biology, neuroscience, and the nature of perception and cognition.

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A final summary.

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In our discussions, we explored several interconnected topics from various fields, including philosophy, biology, neuroscience, and cognitive science. The central theme was the concept of autonomy in living systems and its implications for understanding the complexity of life. Here's a final summary of the key points:

Autonomy: Autonomy refers to the self-determination and self-maintenance capacity of living systems. Biological autonomy goes beyond mere self-organization, as it involves the active preservation of a system's identity and function through interactions with its environment.

Organicism and Kantian Perspective: The organicist view emphasizes the reciprocal interplay among the components of living organisms, giving rise to specific organizational features. The Kantian perspective emphasizes purposiveness and teleology in living beings, highlighting self-organization and holistic organization.

Prigogine's Dissipative Structures: In physics, Prigogine's theory explores self-organization in far-from-equilibrium conditions, which helped inspire new perspectives on complexity in biology.

Autopoiesis: Proposed by Maturana and Varela, autopoiesis describes the capacity of self-production and self-maintenance in biological metabolism, contributing to the understanding of autonomy in living systems.

Closure of Constraints: Biological systems maintain their identity by generating and sustaining a set of structures that act as constraints, providing a coherent framework for the system's organization.

Regulation and Agency: Regulation involves the system's ability to maintain itself, especially in the face of perturbations. Agency, on the other hand, encompasses the interactive dimension of autonomy, with constraints exerting causal effects on the system's boundary conditions.

Multicellular Autonomy: As living systems evolve into multicellular organisms, higher-level autonomy emerges, involving control over the development of unicellular components and integration of functions.

Cognition: Cognition represents a novel form of autonomy, far beyond multicellular autonomy, involving complex cognitive capacities and the emergence of meaning and values.

Evolution: The historical dimension of autonomy recognizes the role of evolutionary processes in shaping and preserving the complexity of living systems.

Perception and Context: Our perception of the world is influenced by internal processes and the context in which we experience it, leading to the concept of contextual causation.

Emergence and Complexity: Emergent properties and behaviors arise from complex systems, contributing to the understanding of autonomy and organization in living systems.

Overall, our discussions highlighted the importance of context, self-determination, and interdependence in understanding biological autonomy and the fascinating complexity of life. The topics explored shed light on the interactions between philosophy, biology, and cognitive science, contributing to a more comprehensive understanding of living systems and cognition.

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