This document is a excerpt from John Turner Scott’ book Purpose and Desire, with a few personal additions (the reader will easily recognize them, after my insistence on “changing life strategies from individualistic to cooperative). This is a very long text, very scientific and probably not easy to read. But for those who are passionate about science, especially biology, it is fascinating and extremely insightful for understanding of what drives the adaptation (and hence the evolution of Life): the cognition and intentionality of the living beings. It is insightful for the understanding of what we have to do in our turn to adapt to the immediate future.

The reader is warned that the whole book Purpose and Desire is a plea for a new scientific understanding and, as a result, the author is often in controversy with the dogmatic, reductionist view of the materialistic science.

The whole idea of this appendix is to break the spell of the old scientific perspective that living things are devoid of free will, that evolution is devoid of direction and life is meaningless, that we are all predetermined by forces beyond our control. Nothing more false! The honest scientific perspective shows that the intentionality and desire of living beings are the main drivers of the evolution of life on this planet. Intentionality, being oriented toward collaboration (we have to co-live together as the only way to live), makes us all interconnected and inter-dependent.

Our society is in a major social and ecological crisis precisely because it is based on a profoundly misleading understanding, that sets separation and competition as the foundation of our society.


On one side is the ebullient and engaging Will Provine telling me: “There are no gods, no purpose, no goal-directed forces of any kind. There is no ultimate foundation for ethics, no ultimate meaning to life, and no free will for humans, either.”

On the other side, Francis Crick says to me that: “[reductionist science has shown you that] your joys and your sorrows, your memories and your ambitions, your sense of identity and free will, are in fact no more than the behavior of a vast assembly of nerve cells and their associated molecules.”

Standing in front of me, the relentless Richard Dawkins informs me: “The universe we observe has precisely the properties we should expect if there is, at bottom, no design, no purpose, no evil, no good, nothing but blind, pitiless indifference.”

And, standing behind me, the dangerous Daniel Dennett hectors me: “No matter how impressive the products of an algorithm [natural selection], the underlying process always consists of nothing but a series of individually mindless steps succeeding each other without the help of any intelligent supervision.”

I asked myself: What if intentionality is real? Furthermore, what if intentionality is not only real, but is actually the most important attribute of life? Could we then be scientists true to our calling if we ignored it? What if the distinctive attributes of life truly are intentionality, purposefulness, and the wants and desires of living beings? How could we possibly understand Life if we deliberately ignored those attributes?

To be “scientists” (meaning materialist/reductionist scientists), it seems that the first thing we must do is put on blinders to ideas like purposefulness, intentionality or guiding intelligence. But what if these ideas are central to the phenomenon we are studying – life itself? We force ourselves into a Hobson’s choice on the matter: accept intentionality and purposefulness as real attributes of life, which disqualifies you as a scientist, or become a scientist and dismiss life’s distinctive quality from your thinking.

I have come to believe that there is something presently wrong with how we generally think about life, its existence, its origins, and its evolution. It’s bad enough that we are somehow forced into making the Hobson’s choice described above. What’s worse is that being forced to make the choice actually stands in the way of our having a fully coherent theory of life, in all its aspects, most notably its evolution. In other words, this bias is now obstructing the scientific progress. This is tragic, because there is nothing in the nature of the science of life per se that forces the choice to be made. The problem traces its beginning to the early twentieth century, when biology sold its soul, committing the practitioners of the science of life wholesale to the premises of mechanism and materialism.

I argue in this book that agency is where the distinction can be reliably drawn. The cauliflower can be construed as a collection of intention-driven agents that go about purposefully building a cauliflower. To say that a cauliflower exists because, in some deep sense, it wants to exist might strain credulity as well, but with a squint and a hope, we can almost see how it could be true.

In a nutshell, this is where the crisis of biology looms, because our prevailing modes of thinking about life – the triumphant confluence of mechanism and materialism – do not deal well with the concept of agency – that ineffable striving of living beings to become something, of adaptation – what actually drives the evolution and adaptation of living beings, of coherence/well-designess of the living systems.

Philosophically fencing those things off, as much of the modern science has done, has brought the science of life to the brink of its crisis. What is at stake is a coherent theory of life. The manifestations of living beings: (intentionality, agency, desire, purposefulness, tenacity, creativity – in a word, self-hood) are important to all these unresolved questions. A coherent theory of life will help us to build fairer human societies in coherence with the planetary ecosystems and also, will help individuals to find a better meaning for their life and better understanding how to commune and cooperate with other individuals.

We have to find meaningful answers to questions like these: What brings forth a self? What drives the adaptation and evolution of living beings? What informs the tendency toward increasingly larger wholes? What inspires the creativity of selves?

I claim that there are such answers and the path that will lead us to them is the proper understanding of the phenomenon of homeostasis.

What precisely do we mean by metabolism?

A termite is not a noun as much as it is a verb. It is a highly ordered stream of matter and energy, which takes the ephemeral form of a termite, that is continually built up as fast as it breaks down. What about their mound? Well, that too is more of a verb than a noun. The mound is highly ordered and dynamic: rain and wind strips it of nearly a quarter ton of soil each year, which the termites must assiduously replace, grain by grain, just as the myriad cells in a termite’s body must do with every atom that flows through them. And the soil grains are replaced in a highly specified way that sustains the mound’s functionality. What, then, is the difference between termite and mound? A mound can be perceived as an extended organism.

Do we have a coherent theory of evolution?

I intend to argue that the answer to this question might actually be “no.” Part of the reason for this is that we don’t have a good Darwinian explanation for what life is in the first place. If that weren’t enough, Darwinism is also having a hard time explaining what an organism is, or why life seems to tend toward “organism-like” assemblages, or why living things are actually well-designed.

The problem for modern biology is that we lack a coherent theory of adaptation. To illustrate, consider how a recent textbook of evolution put it: “Adaptations are the products of natural selection, while adaptation is the response to natural selection.” This demonstrates, in one short and elegantly crafted sentence, that our conception of this core evolutionary idea is essentially meaningless. What is adaptation? The product of natural selection! What is natural selection? The outcome of adaptation! This type of reasoning is known as a tautology, which is ranked as one of the main logical fallacies. Yet there it is…

The tautology somehow needs to be resolved. But how? One is tempted to say that more research will clear it up eventually, given enough time and money to fund the quest. I’m doubtful that will work, however, for the obstacle to resolving the tautology is not that we know too little, but that we aren’t thinking properly about what we do know. In short, the obstacle is largely philosophical: the stumbling block of our materialist worldview is the purposefulness that is inherent in the phenomenon of adaptation. To see adaptation at work is to witness a phenomenon rife with purpose, intentionality and striving. But even more: the purpose, intentionality and striving are oriented toward higher levels of mutual consistency with the environment (meaning with all the other participants which constitutes your environment). Life is not an individualist striving, but is a cooperative one. Life is synergy, cooperation, mutual consistency – all for creating conditions conducive to Life.

I propose, for all the obvious evidence around us, that the main driver of Life (to survive) to be translated to cooperate or even better, to be a functional part of your ecosystem. Actually, these are just two aspects of the same holarchic reality: a holon striving to maintain its integrity (to survive) is fulfilling its functional role in the greater holon it is part of (to be a functional part of your ecosystem). Therefore, we can discern a first principle that drives adaptation and evolution: to be a functional part of of the environment you are part of (and in the end, the Great Circle of Life). This is actually the only way for you to survive.

As we look at holon’s inner environment, its adaptation and evolution are oriented toward increasing the efficiency and coherence of this inner environment (its intensive homeostasis). As we look at holon’s outer environment, the adaptation and evolution are oriented toward increasing the efficiency and coherence of this outer environment (its extensive homeostasis). In the end, this outer environment is Gaia, the Great Circle of Life.

Don’t forget that what we call “inner environment” for a level of organization – be it a cell or an organism, are “outer environment” for other levels of organization: The inner environment of an organism is the outer ecosystem of its cells. But a cell, in its turn, it is an outer environment for its smaller constituent living beings, the organelles.

Each level of organization is a level of being. And these beings commune, cooperate, co-evolve together to bring forth a higher level of being, characterized by its own homeostasis. So, how these higher levels of cooperation and integration are created? This is not a blind process, the inevitable outcome of some physical laws. A higher level of coherence is the outcome of intentionality of the living beings engaged in this process of evolution as their only way to survive and thrive.

The cooperation of living beings to reshape their outer environment to become more conducive to their well-being is the main way in which living beings adapt and evolve. It is rather through reshaping their environment (see extended organism and niche construction concepts) rather than adapting to it that living beings survive and thrive. Adaptation is about cognition and intentionality, communication and cooperation, creativity and inspiration. What inspires living beings in this amazing act of co-creation? I found a very good answer to this question by reading the book “Spiritual Intelligence” by Danah Zohar. John Turner also introduce an amazing concept: tele-symbiosis. Symbiosis is not only about direct-symbiosis, but tele-symbiosis: larger scale of symbiosis that are coordinated by “larger patterns of communication and cognition” that are able to inform the system in a very coherent way. The Gaia’s ability to create and maintain conditions conducive to life is a good case of tele-symbiosis. The same with what we call inner-calling, inspiration, insight, revelation or spiritual intelligence. All living beings are able to communicate, exchange information, learn and improve their correlation with the whole. And we all – Gaia, the polar bears, you and me – are learning how to better deal with our challenges.

Such things do not sit well in the old metaphysics of biology, which regards phenomena like purposefulness, intentionality, consciousness or inspiration as illusory. For a biologist to treat them as something real is therefore a modern heresy, and those who advocate it suffer the fate that heretics often do: they are cast mercilessly from the altar. Yet disposing of a heretic does not make the uncomfortable question go away. And the uncomfortable question is this: what if phenomena like intentionality, purpose, and intelligence are not illusions, but are quite real – are in fact the central attributes of life? How can we have a coherent theory of life, if we shunt these phenomena to the side? In search for a coherent theory of life, our first step is to understand better what homeostasis is. I call it Biology’s Second Law.


Biology’s Second Law has a name: homeostasis, defined as “a state of internal constancy that is maintained as a result of active regulatory processes.” The concept is central for the science of physiology. For example, our body temperatures are tightly regulated, and so we speak of body temperature homeostasis and the mechanisms that underlie the body’s “thermostat.” The same can be said for a myriad of other functions, such as regulation of water in the body (water-homeostasis), of salts (salt-homeostasis), or of the blood’s acidity (blood ph-homeostasis). This anodyne description of homeostasis doesn’t really do the concept justice. Homeostasis stands today as one of the least understood and most widely trivialized concepts in modern biology.

If homeostasis is the foundational principle of physiology, we should have a pretty good idea of what it works. But we don’t, and the obstacle is clear: we perceive the relations between living beings as mechanical, when there are actually negotiations oriented toward cooperation (simply, because the cooperation is sustainable in long term, being the only one that could build and maintain a Circle of Life, and by far it brings evolutionary advantages to cooperators). When physiologists speak of homeostasis, their reflex is to perceive it through the materialist lens, as the organism is mechanism-like. This invites the question: is life mechanism-like?

The credit for the concept of homeostasis goes to physiologist Claude Bernard (1813–1878): “The constancy of the internal environment is the condition for a free and independent life.” Bernard did not phrase his aphorism as an invitation to discover a mechanism of life. Rather, his aphorism is a statement of the nature of life.

Homeostasis is not the outcome of life. Homeostasis is the Life’s principle. The question that Bernard is inviting us to explore is the “why” rather than the “how” of life. Why should body temperature be regulated? Why there is life in the first place? Why there is symbiosis in the first place? Why living processes interconnect and create larger scale living processes?

“Why” questions can evoke meaningful answers. The focus on “why” is what makes homeostasis a profound idea. Its “how” dimension is simple, but its “why” dimension could reinvent our society and literally reorient our lives and our meaning of life. Its “why” implications are deeply subversive for the assumptions about mechanistic life that presently reign.

If we want to have a coherent theory of Life – a more meaningful understanding of who we are and how to evolve as a species further – we have to change our metaphysical basis and offer us a different lens to look at life afresh. If we want a more meaningful, free and purposeful life for us as individuals, we have to choose a metaphysics that allows meaning, intentionality and purposefulness in the first place!

The most striking thing about life is how robust it is in the face of perturbation. Homeostasis is a form of dynamic equilibrium, persistent but flexible; resilient and adaptable. This is the essential nature of homeostasis: it is life as a persistent dynamic equilibrium. The self-adjusting confluence of forces is precisely what living beings do as a matter of routine. It is what distinguishes the living from the inanimate world. Whereas the static equilibrium of stones did not require any effort to maintain, work has to be continually done to sustain a dynamic equilibrium.

Unfortunately, the mystery of homeostasis has been corralled and tamed behind the dogmatic fence of materialism, concerned only with the “how”, not the “why.” We are called to focus only on the cogs and gears, but when we do so, we strip away the soul of Life.

A short incursion into a historical debate about Life

The modern sciences of life cannot be properly understood without an appreciation of vitalism. Vitalism poses a basic questions: is life a special phenomenon, unlike any other in the universe? If your answer is “yes,” you are a vitalist, whether you want to admit it or not.

The rub comes with how the second question – what makes it so? – is answered. Traditionally, that answer took the form of what we may call essentialism: life is special because it is imbued with a special vital essence. Life exists because this vis essentialis infuses and animates otherwise inanimate matter. This perspective predates the Hippocratic physicians, whose medical philosophy derived from the still more ancient doctrine of humors: systems of opposing forces, like the lightness of air versus the heaviness of earth, or the heat of fire versus the cold of water.

Life is a state of harmony suspended in a matrix of diametrically opposed forces, with the balance mediated by the vis essentialis. To the Hippocratic physicians, health was a state of balance and harmony.

By the eighteenth century, vitalism had become the subject of vigorous debate between competing European schools of academic medicine. What emerged from this debate was a radical transformation of vitalist thought from an “essentialist” vitalism (vis essentialis) to a “process” vitalism (vis mediatrix). With the rising tide of Enlightenment, the whole doctrine of vital essences could not stand up long under such scrutiny. In short, vis essentialis died because it was a scientific dead end. The vis mediatrix was one of many designated hitters brought in to fill the roster. But these couldn’t stand long either, for the same reasons that did in vis essentialis – hard to be grasped and quantified by materialistic science.

In a remarkable anticipation of the superorganism idea, Théophile de Bordeu drew a parallel between the coordinated behavior of a swarm of bees and a living body. If bees in a swarm were separate bodies, physically disconnected from one another, how could any putative vis mediatrix flow between them? And if there was no vis mediatrix, how were the behaviors of the individuals mediated to produce the hive’s “organism-like” behavior? Bordeu’s little thought experiment not only called into question the very idea of a vis mediatrix, it opened the door to a new and powerful metaphor for understanding life: its functionality and evolution. This was the metaphor of life as an assemblage of many little lives, of organisms as collections of inter-dependent “little lives” that, through a process of negotiation and mutual accommodation, produced the coherent organism. This was a new way to think about Life. It was not about the vital essence that formed the organism, but the process, the negotiation and mutual accommodation of the organism’s “many little lives”.

An understanding of the chemical workings of life would enable physiologists to meet their prime scientific obligation: to make the workings of life’s antecedent intelligible. But physiologists could never forget that it is the antecedent, life’s unique nature. Bernard expressed it this way: “Physicists and chemists cannot take their stand outside the planet (cannot perceive the harmonious whole of the planet), thus they study bodies and phenomena in separation, without trying to integrate them functionally into the whole of the planet. But physiologists are seeing the organisms wholes: they must take account of the harmony of these wholes. Physicists and chemists can reject the final causes of the bodies and phenomena they study; while physiologists are inclined to acknowledge the harmony and coherence of an organism as a final cause, all of whose partial actions are interdependent and mutually generative.” Here we see the elements of XIX-century process-vitalism – the notion of the organism as a harmonious whole comprising “many little lives”, along with the emphasis on the processes of mutual accommodation that under-girded the principal “fact on the ground”: the integrated, coherent, and harmonious organism.

If life is a unique phenomenon of nature, what is it that makes it distinct? To Bernard, life was irreducibly unique, and what set it apart was homeostasis. This is where we encounter the modern misconception about homeostasis: it is not a statement of rational mechanism; rather, it is a profoundly vitalist idea.

Bernard’s conception of homeostasis traces its roots back to the previous century’s fertile turmoil over essentialist versus process vitalism. Among the eighteenth-century vitalists was a growing difference of opinion on what an organism’s “many little lives” were. Some thought they were the innumerable cells of the body. Some thought they were the organs of the body. And some, like Bordeu, saw the “many little lives” existing at multiple scales (holarchy). Despite this, there was a broad consensus among the process vitalists that life’s distinct quality emerged from the negotiation and accommodation of the organism’s innumerable “little lives” to one another. One of the outward signs (what we might today call an emergent property) of this ongoing mutual accommodation was adaptation. Organisms can exist in a variety of circumstances and respond in adequate ways to ensure their continuing “good fit” to whatever environment they are in. This is the meaning of adaptation: a tendency of living things to “apt function”, to have an aptitude to persist in the face of a whimsical environment.

Bernard’s novel take on the “many little lives” metaphor was to internalize the phenomenon of adaptation. The persistence of a life in the face of environmental perturbation had to involve a certain independence from the environment. Thus, body temperature would be steady even as outside temperature could vary. There had to be a process of mutual accommodation operating within the body that mirrored the adaptation of the body itself to the variable external environment. Just as the body was immersed in an external environment, so were the body’s “many little lives” immersed in an internal environment, the organism itself. The adaptation to the external environment for an organism as a whole means a renegotiation of the relations between cells inside the organism.

Bernard sought to untangle this mutual accommodation that brings forth the homeostasis of the internal environment. This is what process-vitalism is all about: life as the mutual accommodation of many little lives”. Bernard’s approach to experimental medicine cannot be understood independently of the larger motivation behind his work: to vindicate a profound truth about life, that life is a special quality, that chemistry might be a tool for studying life but it is not life itself.

Bernard’s story is that of the double-edged sword of the Hobson’s choice that sits at the heart of modern biology, which we may now rephrase: can one be a scientist and a vitalist at the same time? Modern biology’s answer to this is “no.” To be a scientist who studies life, you must also be a materialist. You emphatically should not be a vitalist. Claude Bernard stands as a striking refutation of this assertion. When we are confronted with someone like Bernard, two things commonly happen. We might find that an ideological narrative begins to assume precedence over the complicated truth. If Bernard was a brilliant practitioner of the experimental arts, then his vitalism becomes simply inconceivable and cannot be part of the narrative. This is an essentially political dynamic, a dynamic that promote purposely this dogmatic materialist science. This narrative that support the materialist science is enforced through political means. The same was the transformation of Bernard’s vitalist conception of homeostasis in the materialist clockwork homeostasis.

There was a tectonic shift in the metaphysical universe that began in the latter XIX-century and built for several decades into the XX. In the end, our modern attitudes toward the value and reach of science came to be cemented into place, setting modern biology on its materialistic trajectory.

A little about epistemology

Epistemology is about how we come to know and understand the world. How we perceive the world? As a meaningless mechanism or an emergent space of meaning? If we think it is a mechanism, then the understanding comes from drilling down to the tiny details and reductive understanding, thus toward materialism. In the second case we are searching for meaning, for principles that are meaningful to orient our life. The Story of Life – a biological approach to the meaning of human life – makes sense, because we are life too and the same principles that are organizing the life around us should be also applied to our social life. Scientific endeavor is oriented to search for principles that pervade and organize the living world. Whatever it is this organizing principle, it will be literally a meta-physical one, meaning beyond the mere physical.

On the question of life, these opposed viewpoints swept like tides through the eighteenth and nineteenth centuries, trending one way, then the other, from the rational to the romantic then back, from the vitalist to the mechanist then back, endlessly surging but never seeming to settle on a “right” answer. Bernard’s form of vitalism pointed a way out of this state – a middle path that was not quite mechanism and not quite vital essence, but an extraordinarily fruitful synthesis. Unfortunately, biology in the XX-century did not follow Bernard’s insight.

There’s a phrase for this as well: epistemic closure, where everyone simply agrees that we will think only one way about the universe – one form of epistemology – and not bother to engage other ways. Epistemic closure implies a kind of closed-mindedness and it can become a dogma. Those living within an epistemically closed world become engrossed in their self-referential universe. Mental blindness is followed by intellectual pathology. Among those pathologies is fractiousness, with intellectual energy directed to ever smaller problems or questions. In the sciences, we prefer to call this “specialization” rather than narcissism, but the dynamic is the same no matter what we call it: highly learned people coming to know more and more about less and less, until they know everything about nothing at all. Faced with this proliferation of “biological specializations”, it is reasonable to ask: is there such a thing as a coherent science of life anymore? Another common pathology of epistemic closure is an increasing reliance on politically enforced orthodoxy. Narcissism demands that everyone admire the same thing, with unpleasant consequences for those who demur. The means to enforce orthodoxy can range from credentialing systems that ensure that only “right” thinkers are allowed to think professionally (which describes the modern university system), to sustaining agreed-upon myths by ridicule or expulsion of those who depart from the “correct” thinking, to exercising naked political power over dissidents through governments and courts of law. The end-point, as it was for Narcissus himself, is isolation and alienation – of scientist from artist or theologian, of scholar from public, of the science of life from the phenomenon of life itself.

Once Friedrich Nietzsche declared in 1882 that God was dead, something had to fill the gap, and scientists came rushing in. This was the rise of scientism – science now as God – with claims to be the sole legitimate basis for thinking about all aspects of the world. What followed was the rise of “scientific” theories of history, economics, sociology, education, politics etc. This was the era of the technocrats, of rule by the credentialed over the incompetent uncredentialed, all inspired by the phantasm of politics, economics and even morality that could be made scientific, rational, predictable and therefore controllable… Among the casualties was the novel form of XIX-century vitalism championed by Bernard and many others. The story of how Bernard’s fundamentally vitalist conception of homeostasis became transformed into its modern anodyne, tamed form of mechanism – a clockwork homeostasis – illustrates the most pernicious feature of epistemic closure: its ever-increasing reliance on ideological narratives, rather than evidence, to sustain it.

Despite the physiological chemists’ efforts to get us all to look away, that nagging problem of the “many little lives” that had obsessed the process vitalists kept popping up. In the early XX century Lawrence Joseph Henderson, for example, showed how regulation of the blood’s acidity involves a cooperative interaction between nearly every organ and cell type in the body. Henderson’s contemporary, Walter B. Cannon, saw the same propensity in the regulation of blood sugar, stress or any adaptive response to a changing environment. He coined a single elegant word to capture it – homeostasis. Also, the more philosophical side of Bernard’s legacy of homeostasis pop up here and there as eructations of the old vital essence: élan vital, entelechy, omega point etc.

4. The clockwork homeostasis and its inadequacy for the phenomenon of life

Cybernetics found its inspiration in biology’s self-regulating systems, Perhaps cybernetics could go beyond merely imitating homeostasis and solve the very problem of living homeostasis itself? And so was born the notion of homeostasis as the outcome of a negative feedback control machine. The clockwork homeostasis of Norbert Wiener and his many acolytes was adopted into the biological family.

Thanks to Norbert Wiener and his formulas, one could, in principle, predict the behavior of any cybernetic system from the system’s measurable parameters of operation: the sensitivity of the sensors, the responsiveness of the controllers, the time lags between sensing and response. If body temperature was controlled by a cybernetic controller, then Wiener’s mathematical formulas should enable one to calculate the specific response of body temperature to known perturbations. That opened the door to some “real science”: one could predict the behavior and see experimentally how close the agreement was between predicted behavior and reality. Invariably, these experiments showed encouraging agreement with the cybernetic model, but also some significant departures. What, then, should a “real” (that is, a reductionist) scientist do? Do we question whether the beautiful model is a reliable facsimile of the real system at work, or do we tweak the model to make it behave “properly,” that is, more like the observed behavior? Invariably, tweaking the model was the preferred choice, which meant generating a more complex cybernetic model that, it was hoped, could more precisely model the actual behavior. And again, invariably, these new models produced some agreement, and new discrepancies, which necessitated more complex models, which led to new discrepancies, and… You got the idea. This endless tweaking and fixing of the purported cybernetic machinery of thermo-regulation proliferated into baroque assemblages of multiple controllers, sensors, and effectors distributed throughout the nervous system and body, all arising ad hoc as explanatory needs multiplied.

Now, one can convincingly argue that this is nothing to be troubled over. Are not organisms extraordinarily complex? Would not we then expect their cybernetic control systems to be commensurably complex? And is it not perfectly natural that the “proper” scientific trajectory should be to ever more complex cybernetic models until they ultimately match the complexity of the thing being modeled? For the scientist working today, this logic is sound and compelling. But models can be a siren song, particularly if the model is beautiful, and this can lead scientists into an unreal realm where the model supersedes the thing it seeks to explain. There certainly is historical precedent for this, for it was this very cycle of seduction, disappointment, and requital that drove and sustained for centuries the unreal Ptolemaic picture of the geocentric solar system. Slight discrepancies in the motions of planets and stars could be fixed by just adding one orbital epicycle here, but that’s not quite right, so just another epicycle there will fix the problem, and so forth and so on. These accumulated fixes and tweaks made for a remarkably accurate model for the motions of the heavenly bodies, even as they made the Ptolemaic model physically absurd.

The search for the clockwork thermostat has led to ever more complex and sophisticated cybernetic models, until the clockwork thermostat finally converged on the ultimate complexity of the “many little lives” metaphor. Rather than nerve cells and sensors serving as dedicated components in neural “circuits” that are wired together into a well-tuned cybernetic computer, there are innumerable little conversations, spreading of gossip and vague rumors. Individual nerve cells seem to be homeostatic agents unto themselves, capable of sensing temperature, making comparisons, and even bringing about a degree of self-maintenance of temperature on their own. Just as Henderson and Cannon had been led by their studies back to the “many little lives” metaphor, there too has the cybernetics of thermoregulation been led. There is no master thermostat; every cell is a “-stat” of some sort. The steady temperature of the body somehow emerges from the endless conversations/negotiations between these innumerable many little “- stats.”

But the metaphor of the clockwork homeostasis runs into trouble when it ventures beyond the simple models for cybernetic temperature regulation. The endothermic homeothermy (that describes our own form of temperature homeostasis) actually is rare among the animals. It is found mainly among mammals and birds, but for the rest of the animal kingdom, a broad diversity of body temperature “styles” prevails, ranging from just drifting along with the temperature of the environment to actively seeking thermal comfort. Among these diverse styles of thermoregulation is a body temperature that is determined not by internal heat generation, as it is in mammals and birds, but by the clever exploitation of external sources of heat. Creatures that regulate their body temperatures in this way were long called “cold-blooded,” but this is a misrepresentation. Many lizards, for example, can maintain impressively high and steady body temperatures through the day. Where a mouse in the cold morning might burn through its food reserves to warm its body, a lizard might spend the early morning hours sunning itself on a rock, capturing solar heat to offset its body’s heat loss to the cool morning air. Once the lizard’s body has warmed sufficiently, it may begin making forays into cool parts of its territory to find food, cooling as it forages. When it starts feeling too cold, the lizard might then find a sun fleck to soak up a bit of heat to warm its body, then go off into the cool to forage some more. By shuttling all day between hot spots and cool spots, warming up a little now, cooling a little then, again and again, the lizard can keep its body within a narrow band of temperatures. In short, a supposedly “cold-blooded” lizard not only can be “warm-blooded,” it can be remarkably adept at regulating its temperature behaviorally.

The behavioral dimension of lizard thermoregulation throws a spanner into the cogs of clockwork homeostasis. It’s well-illustrated by the matter of fever. Lizards that have a bacterial infection also develop fevers, and their fevers are simultaneously like and unlike the fevers of endothermic homeotherms such as ourselves. Whereas a febrile homeotherm drives up its body temperature by ramping up its heat production, a lizard develops a “behavioral fever” that is brought about by adjusting its shuttling schedule so that it spends proportionally more time in warmer environments and less time in cooler environments than it would if it were healthy. The febrile lizard’s body temperature oscillates around a higher value than a healthy lizard’s does. We can imagine that the lizard has a “behavioral thermostat” that has been turned up by fever, just as in a febrile rat. There’s a subtle problem with this analogy, because the notion of a cybernetic “controller” becomes blurred when the thermoregulation is behavioral.

A cybernetic thermostat is an attractive metaphor when it is the physiology of the body that is being driven by the cybernetic machine. There, the cybernetic machine holds the whip in its hand (that’s why it’s called a controller, after all). When I have a fever, I have no choice in what my body temperature is. It simply is what it is; my body temperature is controlled by the machine running my body, set at whatever the machine says, irrespective of time of day, how I’m feeling, what I’ve recently eaten, and so forth. This is not the case with behavioral fever, nor is it, as we shall see, the case for behavioral thermoregulation in general. A febrile lizard has a high body temperature because, in some sense, it wants to have a high body temperature, and it acts on this desire in a way that is impossible for me to do. In what sense, then, is the lizard’s brain “thermostat” driving its body temperature in the same way my brain “thermostat” supposedly does?

Things get fuzzier still when we explore how lizards maintain their body temperatures in the real world. There, body temperature is not just physiology; it is a broader ecological problem because the body temperature affects nearly all aspects of how the lizard fits into its environment: its adaptation, in a word. A lizard’s body temperature affects how fast it can move, how big its territory is, how intelligent it is, how successful it is at catching prey, how effectively it digests its food, and how successfully it reproduces. What temperature the lizard maintains is therefore the result of a careful balancing of benefits against cost. Some of these are so-called opportunity costs. When a lizard basks on a rock, it is forgoing opportunities to catch food, to find mates, and to fend off rivals. There is also frank risk. Because good sun-basking sites are often well-exposed sites, this makes the lizards that use them conspicuously visible and susceptible to being snatched up by a predator. What temperature a lizard maintains will therefore be determined by a balance sheet of sorts. If, for example, sunny spots are abundant, as they might be in an open desert, the risk of predation that accrues to sun-basking in any one spot is low: every place in an open desert is equally visible, so there is small additional risk to basking in a particularly nice spot. Opportunity costs might be similarly low: a lizard lying on a rock in an open desert landscape can easily keep a watchful eye out for potential danger. The balance sheet can change quite a bit for lizards living in more sheltered environments. If you live near some woods, take a walk through them and look around as if you were a lizard looking for a place to bask in sunlight. In a typical forest, suitable basking spots are limited to the scarce flecks of sunlight that stream between gaps in the forest canopy. Now try to take the lizard’s-eye view of how to maintain a particular body temperature. The scarcity of suitable basking spots boosts the frank risks to a basking lizard because this makes any prospective predator’s job easier. If the predator wants lunch, it just needs to find a sun fleck, hang around there, and the probability will be high that a tasty lizard will take the chance and try to bask there: dinner is served. There are also increased opportunity costs. When sun flecks are scarce, the lizard must leave a large territory unpatrolled while it takes time out of its day to bask. Furthermore, there appears to be little genetic variation that accounts for the different body temperatures maintained by lizards inhabiting different environments. It appears, then, that lizards actively take stock of their environments and determine what temperature they will sustain based upon a perceived matrix of costs/benefits/risks. The point I’m trying to make is that the body temperature of a lizard is not so much the outcome of a machine regulating it, but is a kind of cognitive state. This is where things begin to get even more metaphysically hairy for the metaphor of the clockwork homeostasis, because it opens the door to that anathema of modern biology, intentionality.

In The Tinkerer’s Accomplice, I argued that cognition and intentionality are flipsides of the same underlying phenomenon of homeostasis. Cognition involves forming a coherent mental image of the “real world”, and the coherence of that mental image depends upon a homeostatic brain. Intentionality is the obverse of this: intentionality is the reshaping of the real world to conform to a cognitive mental image. This also depends upon a homeostatic brain. In short, all homeostasis involves a kind of wanting, an actual desire to attain a particular state, and the ability to create that state. The nexus of strivings and desires in a lizard might be completely alien and inaccessible to the strivings and desires in ourselves, but they are no less strivings and desires all the same.

A clockwork vision of homeostasis cannot ever hope to capture this dimension of the problem, because in what way can a thermostat “want” to achieve a particular temperature in the same way a lizard might “want” to do the same? (The “thermostat” is the lizard itself, the organism as a whole or, better said, the individuality, the self that bring forth around him the organism.)

5. Cognition and Intentionality

Cognition and intentionality are flipsides of the same underlying phenomenon of homeostasis. Cognition involves forming a coherent mental image of the “real world”, and the coherence of that mental image depends upon a homeostatic brain. Intentionality is the obverse of this: intentionality is the reshaping of the real world to conform to a cognitive mental image. Homeostasis involves a kind of wanting, a desire to attain coherence with the outer environment. But from where comes the ability (for cooperation and innovative behavior) to create that state?

As Darwin himself conceived it, natural selection was primarily a theory of evolution driven by adaptation. Without adaptation, natural selection cannot work. Darwinian evolution therefore relies upon a coherent theory of adaptation. Physiology has in its pocket a robust theory of adaptation: It is the Bernardian concept of homeostasis, the tendency of living processes to cohere and thus to create larger and larger scale coherence.

The path to a coherent theory of life and evolution depends upon a coherent theory of adaptation. For a coherent theory of adaptation we have to make sense of cognition, intentionality, cooperation and even creativity or inspiration.

Living systems have to be aware of their surroundings, to be aware of what they are, to make judgements and assessments, to face confusions, to choose, to take decision, to take risks, to hope, to cooperate, to imagine better ways, to strive toward a particular state, to be able for innovative behavior. Materialist scientists reject this solution, because it is metaphysically inconvenient. The modern synthesis of the natural selection reduces evolution to the operation of a machine, and it is impossible to attribute purpose and desire to machines. Therefore, there can be no purpose and desire in evolution, as the Four Horsemen of the Apocalypse try to mislead us.

Like his contemporaries, Lamarck’s thinking was influenced by the growing conception of the organism as “many little lives”. Lamarck sought vital principles that could unify our understanding of the universe, from mineralogy to the weather to life itself. Lamarck proposed that living systems are uniquely imbued with at least two vital forces. One is “the force that tends perpetually toward larger scale of complexity and coherence”. Lamarck’s second vital force was the “adaptive force.” Within the individual, adaptive force modifies the body to help it meet unpredictable environmental circumstances. If fur becomes thicker in the winter, if skin becomes darker under the sun, if muscles become stronger under strain, this is the adaptive force at work. Both the complexifying and adaptive forces were the mainstays of the vitalist thinking of Lamarck’s day, and his thinking in this regard was not original with him. Lamarck’s real intellectual innovation was to propose that these forces could apply to lineages of organisms as much as they applied to individual organisms: Not only were developing embryos marked by an ever-increasing complexity through time, the lineages of successive generations of embryos were as well. Thus, the complexifying force could act across generations too. Similarly, if the adaptive force could be invoked to fit an organism more aptly to a new set of circumstances, so too could the adaptive force operate over many generations to bring about an ever more apt fit of a lineage to a long-standing change of environment. If burrowing shrews lost their eyes to become moles, if shrews grew wings to become bats, if panthers grew lithe and supple to become cheetahs, this was the adaptive force working across generations. Put them both together, and you have a theory of evolution: of lineages becoming ever more complex and ever more well-adapted through the lineage’s history. Lamarck’s adaptive force looks a lot like homeostasis, properly understood.

The main point about Lamarck is that he was proposing a radical connection between adaptation in individuals and adaptation in lineages. Why not a step further: connection between adaptation/evolution in individuals/lineages and the adaptation/evolution of other species – co-evolution? Why not a co-evolution between biota and its inorganic environment? Lamarck has been the object of caricature, because his idea of a unified theory of adaptation is inconvenient to the modern narrative.

Comparative anatomy compares the forms of different species with one another: how a horse’s hoof is like a mouse’s hand, for example. Comparative anatomy is something we force modern students of biology to endure because it teaches them valuable lessons about homology. For Cuvier, comparative anatomy provided the evidence for his own theory of adaptation, which he called the “conditions for existence”, meaning those conditions within an organism that would serve apt function. His logic went something like this: to survive and reproduce, an organism had to be objectively capable of surviving and reproducing; to do that, all the parts of the body had to work well together. These were Cuvier’s conditions for existence: a coherent organization of the organism. If all parts of an animal had to function well together to meet the conditions for existence, a change of one part by itself would violate those conditions. There would have to be specific correlated changes (mutually-consistent) to ensure that the organism’s conditions for existence could be met as the body changed. Furthermore, not just any correlation would do: they have to be in concordance to better serve a specific function.

There was an important point to Cuvier’s idea: the correlation of parts is a clear example of the organism’s “many little lives” working out their mutual-consistency within the context of the well-functioning organism. Just as Bernard saw homeostasis as a fundamental property of living things, Cuvier saw the same in his conditions for existence. The specific correlations that had to exist for the animal to be well-adapted betokened a fundamental body-intelligence. All the parts had to know, in a deep sense, how to fit in with one another, and to be capable, again in some deep sense, of working out a consistency with the other parts that carried their own sense of knowledge and striving toward a destiny. At root, the “many little lives” metaphor was a statement of life as fundamentally a cognitive and intentional phenomenon.

What about Darwin? Did he not leave all that vitalist theorizing behind? Well, not really… It’s worth remembering that Darwin spent his formative years in an intellectual milieu that was similar to Lamarck’s and Cuvier’s and that was animated by the central question of nineteenth-century scientific vitalism: how did the well-constructed, coherent, and adaptable organism come to be? His novel thinking has to be understood in the broader context of XIX century debates over the nature of adaptation. On the English side of the Channel, the notion of a marvelously designed living world had long planted its foot in the English school of natural theology, championed by a long line of thinkers from John Ray to William Derham to Thomas Malthus and culminating in the vivid apologetics of the great William Paley (1743–1805). Darwin knew this tradition well but came into it sideways, as he did with so much of his thinking. He had come to know and admire Paley’s thought and work when he was ensconced as a young man at Christ’s College, Cambridge. Charles Darwin was part of an extended family of free thinkers and liberals, part of the new professional elite that grew up during the Industrial Revolution. Charles’s grandfather, Erasmus, had studied medicine at Leiden, which was involved in the tumult over the transformation of vitalism that was roiling the eighteenth-century European schools of medicine. Consequently, there were many close connections between the medical schools at Leiden and Edinburgh. Charles’s father, Robert, had also studied medicine at both universities, and he certainly would have been familiar with the doctrines of scientific vitalism that were emerging there. Much of the history of evolutionary thought can be understood as an ongoing argument between two competing visions of nature: Romantic idealism and Enlightenment rationalism. Vitalism, and the insistence on the ineffable nature of the organism, was a reflection of the Romantic, as was the whole notion of natural theology as it applied to natural history. The tension between Romantic idealism and Enlightenment rationalism twined itself through the Darwin family tree. Erasmus Darwin was a free thinker and admirer of the more Romantic tendencies of the voluble French. From his grandfather, Charles became familiar with the radical concepts of species transformation streaming in from France: Erasmus had speculated about evolution and natural selection in several of his works, including his epic Zoonomia. Erasmus Darwin was also no friend of mechanism, as can be seen in his preface to Zoonomia: “It happened, perhaps unfortunately for the inquirers into the knowledge of diseases, that other sciences had received improvement previous to their own; whence, instead of comparing the properties belonging to animated nature with each other, they, idly ingenious, busied themselves in attempting to explain the laws of life by those of mechanism and chemistry, forgetting that animation was life’s essential characteristic.” The two core ideas of Darwin’s theory bear the unmistakable stamp of XIX-century vitalist thought. Success in the struggle for existence boils down to apt function (physiological adaptation), which draws inspiration from Lamarck’s adaptive force applied to lineages. Homology, cited by Darwin as strong evidence that lineages could evolve through gradual modification of existing parts, drank deeply from Cuvier’s notion of the correlation of parts and the mutual consistency of the organism’s “many little lives”.

What works now works because there is (was) an intention to make it work!

Agency seems to be a very large part of what living systems do, and agency seems to extend down to life at its infinitesimal scale. I will make a bald assertion: bacteria (or any living system, for that matter) can be agents because they are cognitive beings. (How about at the largest scale: ant-hill, bee-have or Gaia? Gaia is a living system for sure: is She a cognitive being?)

Now, before going any further, I need to insert a disclaimer: I am using “cognition” in the broadest possible sense to mean the mapping of information about the external environment onto the cell’s internal workings. That said, I confidently say that bacteria are cognitive agents because they have embedded in their membranes a suite of cognitive mapping tools. These are in the form of protein receptor molecules that respond to environmental conditions and alter the catalytic landscape within the cell. Cognitive mapping is a universal phenomenon of life. Intentionality is fundamentally the flip side of cognition, and you cannot really have one without the other. Cognitive mapping is invariably connected to engines that do work to modify the environment toward a particular – a purposeful – end. In the case of the spirochete, the purposeful end is to sustain the ordered flow of electrons and matter through it so as to sustain the evanescent form of the spirochete. This is intentionality at work. Every living system has intentionality. An agent could change its location or construct an environment that is more suitable to its physiology. Life is an intentional phenomenon.

But we cannot stop here because this fundamental cognitive dimension has brought to the fore a challenging, unavoidable question about the nature of evolution: what exactly drives it forward? Is it forward-looking intentionality that strides confidently into the future, intending to stand rather than simply to die. No longer are we stuck in the bleak landscape of the 4 Horsemen where there is no purpose, desire, intention or meaning. From where we stand, we begin to see a landscape where those essential attributes of life – purposefulness, desire, intentionality, intelligence etc. can once again re-enchant our understanding of life.

6. What is the relation between an organism and an individual?

The first difficult problems we will try to tease apart are individuality and the nature of the organism. But why this rises so “difficult problems”? For us, usually, the discrete individual is the central fact of existence and of our relationship to the world. An organism is the autonomous, coherent, integrated, adaptable, responsive, intentional, intelligent stream of matter, energy and information that is wrapped up in the pretty package of the individual.

This raises an interesting question: are organisms and individuals the same thing? Am I an organism because I am an individual? Or vice versa? As you delve into the matter, though, the equivalence of individual and organism begins to look a little iffy. Without understanding the relation between the two, how can we point to an evolutionary origin of either? If we define the organism, as we commonly do, as a tangible individual comprising a multitude of genetically related cells functioning together as an autonomous whole, then the organism came onto the scene rather late in the evolution of life on Earth. We see them finally emerging only around 600 million years ago (the beginning of the Cambrian). Before that, Earth was a prokaryotic planet, teeming with bacteria. Bacteria are obviously cells, but could we say these were organisms? Cells are autonomous living systems, like organisms are after all; but a swarm of bacteria seems too amorphous to qualify as an organism as we commonly conceive it. Then again, we reflect upon the community of sulfur-breathing bacteria and spirochetes. In nature, bacteria usually live in layered mat communities, like those ancestors of the eukaryotes did, and this habit seems to have stretched all the way back to the origin of the bacteria. Microbial mats mimic some of the specialized functions of the organs in the body of a more conventionally defined organism. Could microbial mats be construed as organisms, then? Perhaps they could, if we were willing to stretch the definition. Could microbial mats be individuals? It would be difficult to go that far.

The presumed equivalence of organism and individual gets muddier the deeper we look. A striking feature of the evolution of life on Earth is the emergence of a variety of “organism-like” systems, that is, many individuals that coordinate their lives in ways that make them look and behave like organisms. The microbial mat is one example. Another would be “symbiotic organisms” such as lichens, which bring together 3 kingdoms of life (fungi, algae and cyanobacteria) into such close association that a lichen looks, behaves and acts as if it were an individual organism. The best example of an organism-like system is the social insect colony, which, since Théophile de Bordeu, has been likened to a “superorganism”. The social insect swarm exhibits many of the same traits as organisms: coherence, adaptability, collective responsiveness, and even, intentionality.

I’m afraid our confusion is not yet complete. Turning back to look in the mirror, the “I” that seems so unequivocally “me” begins to lose focus as I contemplate that “I” am more of an “us”! The assemblage of cells that is my body is populated by ten times as many alien cells – bacteria, yeasts, and fungi – as “my” own cells, and these alien riders carry in them a hundred times more genes than the ones I inherited from my parents. So, who I am: only “my cells” or the whole functional ensemble? “I” would not function or even be the same “I” in their absence. What, then, is “I”? Am “I” an organism, or an organism-like system, or something else?

At this point, the long-assumed equivalence of organism and individual becomes very strained indeed. So, we’ve worked ourselves again into a bit of a muddle. It’s important that the muddle be resolved, because the origin of the multicellular organism – and by implication, the individual – has been tagged as one of the “major evolutionary transitions” in the history of life on Earth. It implies that we understand the relationship between organism and individual. Again, can we say honestly that we do? I can’t. We are confused about the nature of the organism, its supposed equivalence to the individual, and what has compelled both into being.

What are the organisms? What are the individuals? How did organisms evolve? How did individuality evolve? Did they evolve simultaneously, or separately to a degree? Is there a theory to explain the origin of both?

The individuals are Life’s unique expressions that embody its qualities: self-hood, autonomy, agency, intentionality, purposefulness, creativity etc. The relations between individuals reveal other life qualities: cooperation and communication, joy and love, trust and courage. Also, the relations between individuals and the Whole reveals other life qualities: being inspired, being connected and yearning to be connected, hope.

Gaia – the former molten rock – is now a symphony and a dance of billions of individuals. Each individual is an expression of Gaia. But these expressions of Life are all selves, aware of themselves. So, what is the root of selves, of individuals, of individuality? What is the relation between an organism and an individual?

Gaia is an organism-like organization brought forth by the interaction of billions of individuals. Each organism (actually organism-like system) is an individual made by billions of individuals. Where can we draw a sure line delimiting an organism? I am an individual. But “my” organism is not limiting at “my” cells. Also, my organism is not limiting at my skin, because my very life is coming from the Great Circle of Life. I am part of a bigger organism. Gaia is my true organism. So, who I am? An expression of life of my body, delimited by my skin? Or I am an expression of Life as The Great Circle of Life? The answer is our choice!

Here is where homeostasis might provide a lifeline. Claude Bernard conceived of the organism as a well-regulated inner environment that is demarcated from an outer environment. The organism is the process of homeostasis. That process might take different forms, but in all instances, a successful homeostatic process is one that sustains the form most reliably in the changing environment. Homeostasis is persistence and persistence is fitness.

This is quite a different conception of the organism. It is an intriguing conception, because it allows us a new way to explore the relationship between the individual – ultimately the agent of evolution – and the organism-like symbiotic system.

7. Extended Organism. Adaptive interfaces

What separates an organism by its outer environment is something we will call an adaptive interface, which hosts/protects the inner homeostasis. At its most fundamental level, the cell membrane can be an adaptive interface, but adaptive interfaces exist at many different scales.

No matter what the scale, an adaptive interface comprises numerous processes that do work to power the flux of materials across the interface, that is, between the milieu intérieur and the ambient environment. Homeostasis is the outcome when these material and energy fluxes are managed in a way that sustains the internal environment, even if the ambient conditions change. Homeostasis boils down to what happens at this interface, or more precisely what happens across the interface.

Let me illustrate with a simple example where the adaptive interface is the cell membrane. Cells closely manage the salt content of their internal environments, in particular, the concentrations of sodium chloride and potassium chloride. Within a cell, in a cell’s milieu intérieur, potassium is abundant, but sodium is sparse. The opposite conditions prevail in the cell’s ambient environment: sodium is abundant, while potassium is sparse. Large differences in concentration of the two salts therefore exist across the cell membrane, made possible because machines in the cell membrane, called sodium-potassium ATPases, do work to drive sodium across the membrane out of the cell while simultaneously drawing potassium in. The activity of these so-called ion pumps is regulated together with ion “channels” that allow both sodium and potassium to diffuse across the cell membrane: sodium leaking into the cell, and potassium leaking out. High potassium levels within the cell can be sustained only because work is being done to pump potassium in across the membrane at a rate sufficient to offset potassium’s leakage out through the potassium channel. Homeostasis is therefore a balancing act between ion pumps and channels that, if functioning together, produces a steady composition of the cell’s milieu intérieur, even as the salts are flowing continuously through the cell, and even if the salt composition of the external environment changes. The adaptive interface of the cell membrane is the pivot point of this balancing act. The interface is adaptive because it gauges the work it must do by the demands of an uncertain ambient environment.

So far, this has been a conventional description of homeostasis, an operational definition Claude Bernard would have been quite comfortable with. It’s important to note that this is an intensive definition of homeostasis, it is focused on the milieu intérieur, which is only one side of the cell’s adaptive interface. What Bernard did not see was that physiology could also be extensive: any modification of the cell interior necessarily affects the environment outside the cell as well. Every potassium ion pumped into the cell depletes the external environment of one potassium ion. Every sodium ion pumped out of the cell enriches the external environment by one sodium ion. Therefore, homeostasis is necessarily both intensive and extensive: it can be no other way. Homeostasis, indeed all physiology, cannot be confined to an internal environment. All homeostasis must be extended homeostasis that encompasses both internal and external environments.

It is fair to ask whether extended homeostasis should ever be de facto relevant to anyone’s thinking. Here’s why the question is important. It’s fine to argue from first principles that something exists, but its importance to the “real world” may be minuscule. A single cell floating in the ocean and pumping potassium into itself will not appreciably change the ocean’s concentrations of potassium. There’s just too much potassium there for the cell’s internal homeostasis to make much of a dent in its external environment. But even if the effects of some purported extended homeostasis on the external environment might be negligible, the phenomenon still will have some impact, somewhere. The impact could be on the work of homeostasis, which the cell itself must pay. Energy must be expended to pump that potassium in against the high concentration already there. That energy cost will vary depending upon the potassium concentration outside the cell, and that might vary in both magnitude and time. This means that homeostasis imposes energy costs that are driven by the inhospitability or unruliness of the external environment. To the cell, such costs are not negligible, even if the effects on the external environment might be negligible. If those costs are large or unpredictable, this may mean that less energy is available for the cell’s reproduction or persistence. Some fitness premium should therefore accrue whenever those costs can be reduced or otherwise brought better under the cell’s control.

What, then, is a cell to do if the environment changes, or somehow imposes higher costs for homeostasis than the cell is capable of mobilizing? More to the point, what is a cell lineage to do if it is to persist? There is a solution which life seized upon often: transforms/tames the external environments behind new adaptive interfaces.

The kidney provides a useful example for how this works. The kidneys manage the water and salt composition of the body’s extracellular fluids, in which the body’s cells bathe. The kidneys are made up of a complex suite of tubules, which themselves are made up of sheets of cells folded into the tubules. This sheet of cells, called an epithelium, comprises a new adaptive boundary. The kidneys pull off the trick of managing the salt and water content of the body’s extracellular fluids by managing the flux of salts and water across the tubular epithelium. Now let us ask: what in this example is milieu intérieur and what is ambient environment? The answer is not self-evident. To Bernard, the milieu intérieur would be the extracellular fluid. But the cells of the body would beg to differ: to them, the milieu intérieur is the cytoplasm and the extracellular fluid is the ambient environment. The cells of the kidney tubule, for their part, agree with Bernard. To them, the milieu intérieur is the extracellular fluid, and the ambient environment is the fluid contained inside the tubule. From the perspective of the kidney as a whole, though, the milieu intérieur is the fluid within the tubule. Even though the interior of the kidney tubule is topologically external to the body, that is, it is contiguous with the ambient environment, what comes out of the tubule at the urethra is quite different from what initially shows up in the tubules. This makes the kidneys an adaptive interface.

Which is milieu intérieur and which is ambient environment is defined by which of several nested adaptive interfaces we are talking about. The costs of homeostasis that burden the cells of the body are now borne largely by the cells in the tubule epithelium, which have enfolded the tubule’s external environment into an internalized environment. The costs of homeostasis for the tubule epithelium, in turn, are eased by the kidney folding the tubule’s “external” environment into a new internalized environment of the kidney. The tubule represents the extended homeostasis of the cell. The kidney represents the extended homeostasis of the tubule. What comes out of all this serial nesting of adaptive interfaces and internalized environments is the organism. The organism is the sum of the extended homeostasis of its subsidiary parts. The logic of this “extended organism” need not stop at the organism conventionally defined. Earthworms, for example, modify soils to provide themselves with the essentially aquatic environments for which their own kidneys suit them. In this instance, the modified soil is part of the earthworm extended organism: it is an adaptive interface between the harsh desiccating environment and the earthworm’s essentially aquatic kidneys. Similarly, social insect colonies build nests, some of them of stunning complexity, that function as adaptive interfaces between a now internalized nest environment and the external environment. The logic of the extended organism extends to all organism-like systems. Organisms at any scale – cell, organism, society – are properly extended organisms, continually working to draw the environment into a conspiracy of extended homeostasis. The conspiracy is vast and diffuse, and it is limited in its reach only by the confines of the biosphere itself. (Gaia – the ultimate extended organism, the ultimate large scale of extended homeostasis)

The extended organism concept treats the organism as a focus of homeostasis rather than as a collection of genes. The individual can include all the microbial riders that populate its body. It can include his/her brotherhood. It can encompass the whole planet. I am the extended homeostatic “me”.

The extended organism idea seems to dissolve whatever equivalence there might be between organism and individual. “I” am no longer only an autonomous individual, but a super-organism, a part of something larger than me that effectively sustains “my” life. “I”, of course, includes the multitude of genetically diverse microbial riders, but also the numerous other living systems that extend outward from “me”, at multiple scale sheltered by multiple adaptive interfaces: the farmers who grow my food, the soil microbes that help the farmers, the rivers that provide me water, the mountains, the clouds, the winds that nourish those rivers etc… The whole planet is, in the end, my truly extended organism. I am the Planet! But even the planet can not sustain its homeostasis without Sun. In the end, the whole Universe is my extended organism!

In this tangled web of physiological conspiracies, the individual that is “me” seems to dissolve away into the vast collective “we”. But this conclusion is not the whole story. If it will be the whole story, for sure will be unsatisfying on many levels, not least because it conflicts with what seems to be another insistent fact of nature: the individual exists. I know I am an individual. That is as incontrovertible a fact to me. If we are led to a conclusion that seems to negate this fact, either the argument itself is wrong, or there is more of the argument yet to follow. There is more, and the “more” of the argument is homeostasis, properly understood, which leads us to a new conception of the organism, as well as a new conception of the relationship between individual and organism. (This is about holarchy: different levels of being, different levels of individuality.)

Let us return to the “ant-mound model” of homeostasis: mass flow (sand into the mound) is coupled to energy flow (the work needed to organize the inflowing sand) to produce a specified dynamic equilibrium (the ephemeral ant mound). The mass and energy flow parts of this definition are covered by well-established physical principles, like conservation of energy and mass. The “specified” part is more problematic, because it prompts the question “specified by what?” The extended organism, defined as a focus of homeostasis, is actually a cognitive and learning organism. Homeostasis involves coupling information about the state of the internal and external environment on the sides of an adaptive boundary to the matter and energy flows across that adaptive boundary. The individual is the cognitive being that has a sense of itself as something distinct from its environment. It is reasonable to argue that cognition is a property of all living systems, including the physiological unity that is Gaia – the planetary living organism.

What conclusions may we now draw about evolution and adaptation? When we define individuals as cognitive entities, we are also defining them as intentional entities. And here is our startling conclusion: evolution becomes a phenomenon driven largely by the intentions of the cognitively individual actors. It is the striving of cognitive individuals that reach into the future. Perhaps most important, the organisms and individuals are reunited into a cognitive whole that both lives with desire and evolves with purpose.

8. Life emerged as an intentional system

There is another large question looming. How did life come to be?

There is no good answer for this, but that should not stop us from asking whether, in light of our new way of thinking about evolution, driven by purpose and desire, at least a plausible explanation is possible.

The mystery of life origin is unsolved because it is unsolvable!

It is certainly not solvable by direct evidence or observation. Being curious apes, we peel back as many pages of life’s history as we can, hoping to see what’s printed on that first page. We know from the likely age of the oldest microbial fossils that life was thriving on Earth by 3.8 billion years ago. We know that the Earth at that time was stumbling out from under an extended period of devastating meteorite bombardment. It was hot and there was no oxygen in the atmosphere. Dimly outlined on those early pages, like some ancient palimpsest, we can discern traces of some important milestones: prokaryotes cells from the beginning, eukaryotes cells appearing about two billion years ago, embryogenesis and complex organisms about a billion years after that. But first page of the Book of Life will remain for ever a mystery!

Throughout the XX-century, both theories tied their fortunes to the miracles of the prebiotic chemistry of auto-catalytic sets of molecules and the spontaneous self-organization. The prebiotic chemistry and physics had provided both grounds upon which many ingenious theories for the spontaneous origin of life have been built. These have brought us ever so close to the origin, but never quite to the starting point, at least not without having to verge uncomfortably into miraculous thinking, the same reliance on miracles that sustains creationists.

The default response to such problems has been to invoke the magic power of time: given enough of it, even highly improbable events, like the spontaneous and simultaneous origin of an enzyme and gene, might be expected to happen at least once. But fossil traces of early life are pointing to a surprisingly rapid emergence of life from the prebiotic Earth. On the basis of known times when the Earth could have cooled sufficiently to support life, and the subtle evidence of Earth’s incipient life, the transition appears now to be incredible short. There may even have been multiple origins of life only to be wiped out by an asteroid impact or some other catastrophe and replaced by the next glowing coal fanned into life. That makes the origin of life a very fast proposition: a blink of a geological eye. The conclusion is inescapable: something beyond mere chance seems to have drawn life into being. But what could that something be?

After many decades of effort, where do we stand on the question: how did life emerge from nonlife? Perhaps, the time is ripe for thinking about it another way!

There’s one very large problem with looking to the small scale for life to emerge, and that is the relentless scourge of the small scale: diffusion. To us, large creatures accustomed to perceiving the world at a large scale, diffusion is a weak force. At the small scales where we imagine life to have emerged, however, diffusion is literally an explosive phenomenon, scattering everything before it into oblivion. How could proto-life ever have managed to survive in such an environment, let alone evolve into life? It’s nearly impossible to imagine, and this is why every theory that imagines life to have emerged from the “bottom up” has come up short. This leads me to a strange thought: What surrounds me is not quite a complex world of things, but a complex cascade of energy. If life is the expression of the organizing principle of homeostasis, then the origin of life is tantamount to the this principle too.

Homeostasis demands certain things, among them at least rudimentary forms of cognition and intentionality. This leads to the very strange thought that the origin of life is tantamount to the origin of cognition and intentionality. So, cognition and intentionality had to have actually preceded the origin of cellular life.

We can rescue this idea from the loony bin by defining cognition very broadly and generally, as informing a state or process about its environment. Our own very complex cognition should not blind us to the fact that cognition can be framed even in very simple systems, like individual cells, or even simpler. The nerve cells that underlie our own cognitive systems are certainly cognitively aware, but they are cognitively aware in a very different and highly circumscribed way from the large-scale cognitive phenomena in which they participate. An individual nerve cell is cognitively aware of the fluid environment in the brain in which it bathes, and of the chemical signals flung at it by the myriad other nerve cells communicating their own cognitive states, and very likely many other features of its little world. Outside of brains, individual cells are cognitive entities in the same way. A photosynthetic algal cell maps the presence or absence of light onto its encapsulated catalytic milieu, altering the cell’s physiology in accordance with its environment. Similarly, intentionality can be defined very broadly. Intentionality can be construed as the coupling of cognition to metabolic engines that can shape the world to conform to a cognitive map. Brains produce a very complicated intentionality. If I have a cognitive vision of my office being organized in a particular way, I can do the work to bring my office into conformity with that cognitive map. When my office degrades into inevitable chaos, I do the work again to conform it to that cognitive vision of an orderly office. There is no reason to suppose that this kind of intentionality cannot operate at different scales of life. The microbial mat, for example, is the large-scale emergence of a constructed environment that reflects the awareness of each species of microbe of its local environment, and the reshaping of that environment to bring it into conformity with the microbe’s internal cognitive map of what its surroundings should be.

The origin of life invites us to think differently about the nature of life and its distinction from the material world. Specifically, thinking of life as chemistry or simple mechanism has led us ultimately to a dead end. Confronted with this hurdle, we are forced to turn the problem upside down. In so doing we are drawn to think about life as a global phenomenon, driven by the emergence of homeostasis and the cognitive capabilities that implies. Life shapes its world according to its desires and striving toward homeostasis. Life emerged as an intentional system.

The problem of purpose and desire is thorny enough for life as it exists, but it becomes an enormously more difficult proposition when it comes to evolution. Individuals may have purpose and desire. We know this of ourselves, undeniably, and we can guess pretty well that we see purpose and desire in fellow humans. But individuals die, leaving only their lineages to evolve. What role could desire possibly play there, when desires must die with the individual feeling them? Or do their desires really die? Lamarck thought that the ineffable forces that drove purpose and desire in individuals could transmit through lineages.

9. The adaptive landscape or Niche construction

The trophic-dynamic concept. It reflected Hutchinson’s conception of the niche as an ongoing transaction of matter and energy between an organism and its environment. His concept of the niche is one of the most influential concepts in the history of ecology. The metaphor of the Hutchinsonian niche makes us think in specific ways about the world: If a species of flying insectivore exists, then it exists because a lineage has evolved to “fill” the “flying insectivore niche.” If you have a warbler that gleans insects from leaves, it is because a lineage of warblers has evolved to fill the “avian gleaner niche”. If one finds two species of flying insectivore, it is because two lineages have divided the “flying insectivore niche” effectively between them: swifts occupy a “diurnal flying insectivore niche,” and bats occupy a “nocturnal flying insectivore niche,” for example. The metaphor of the Hutchinsonian niche even provides a handy explanation for the phenomenon of convergence: Success in occupying the “flying insectivore niche” presupposes certain things, such as high maneuverability in flight; ways to range, track, and intercept prey; the means to sweep up the unlucky meal once it’s intercepted. And so the lineages of both bats and swifts converge on these necessities, albeit from different starting points. Both have wings and systems of other airfoils that make for high maneuverability while flying. Both use echolocation and sound to track and home in on their prey, and both have brains modified in similar ways to provide the needed computational power for turning sound into landscapes. This use of the niche metaphor provides satisfying and internally consistent answers, but it ultimately muddies the waters rather than clarifies them:

Evolution has now become a striving of organisms toward disembodied and abstract ideals (niches) that draw lineages toward them as strongly as any Platonic Ideas. This tendency to crypto-Platonism arises from a presumption about the role the environment plays in the transaction between organism and environment that is the Hutchinsonian niche. The presumption is that the environment is just there, like gravity or sunlight, and that organisms either adapt to it or they don’t. From there, it’s a short hop to the proposition that lineages either adapt to the environment or not.

In the “real” world, however, organisms not only draw energy and materials from the environment, they actively remodel the environment to channel matter and energy toward them. Earthworms modify soils to help with their water balance; termites build massive mounds from soil that functions as colony’s “lungs”; beavers dam streams to promote an environment conducive to their well-being etc. These are examples of organisms not just “fitting into” niches, but actively building them. Now you have an entirely different way to think about adaptation and evolution. The adaptive landscape is under the control of the organisms supposedly adapting to it.

Now, it becomes an open question: what is adapting to what? The challenge of niche construction theory to modern Darwinism is serious. Where the challenge is most strenuous is how niche construction theory admits the phenomenon of agency back into evolutionary thought. With agency comes intentionality and purposefulness. Niche construction theory melds the organism and environment into a coherent theory of adaptation and evolution.

To illustrate this problem, let’s ask a basic question: why are there flying animals? The trivial answer is because animals have evolved to fly. Could it be that birds fly because, in a deep sense, the ancestors of birds wanted to fly? They wanted to glide from tree to tree. This could make evolution at root a phenomenon of cognition, of intentionality, of purpose, of desire.

From biology is a missing a fundamental ingredient: the living organism that is marked by purpose and desire. Without that missing ingredient, modern evolution is just a magnificent wooden bird in the cuckoo clock that is no more alive than the cogs and springs and bellows that move it.

10. Epilogue: evolution, purpose and desire

The crisis of our scientific paradigm will be averted, when biology becomes re-enchanted. My candidate for the re-enchanting of biology is Claude Bernard’s homeostasis: the relentless striving of living systems for self-sustenance (hence coherence inside and outside). Properly understood, homeostasis is life’s fundamental property, what distinguishes it from non-life. In short, homeostasis is life.

It is a first principle that stands on its own and does not derive from any process associated with life. What drives the course of evolution is life’s striving for persistence. The striving is driven by a cognitive sense of self, even down to the smallest bacterium, even preceding the emergence of life itself. A deep intelligence is at work in life and it cannot be denied.

Science objective value comes from its practice of querying nature itself for answers to what nature is. This is what makes science distinctive as a philosophy of nature. I don’t think I would find much disagreement on this point. Where things begin to get dicey is the relationship of science with the broader culture: no matter how ardently it is desired, science cannot really hold itself apart from the culture in which it is embedded. This is not a claim for dominance of culture over science. In the best liberal tradition, science can be a powerful voice to shape culture, but there is no escaping that science’s metaphysical assumptions are also shaped by culture. The crisis for biology right now is one of alienation: of the alienation of the science of life from life itself, but more alarmingly, of the alienation of science from the broader culture. But there is a middle path to follow, which I have argued in this book means coming to grips with life’s truly distinct nature – its purposefulness, its intentionality, and its distinctive intelligence. Failing to do this will only cast us deeper into the shadows of irrelevance.