What is Life? 2: Complexity Sciences

Update 10.24.20. This essay is now undergoing substantive revision, including (re)addition of images for illustration. Revisions will likely require a week. After that, I intend to produce a video explaining the essay in a "live", narrated format.


“The great virtue of systems thinking is not that it predicts the facts of life, but that it blurs the crisp line which divides the organic world from the inorganic. There is nothing mystical or unnatural about complexity, self-organization, emergence and wholes that are greater than the sum of their parts. These are properties of a large and diverse category of physical systems; even sand piles do it. Organisms remain special, of course, thanks to their autopoietic character. But when organisms are seen as complex dynamic systems of a peculiar sort, the difference between the organic and inorganic seems just a little less daunting. One feels encouraged to wonder just how autopoietic entities might have emerged from the much larger category of complex dynamic systems, and here energetics hold the most promising clues.”

Franklin Harold, The Way of the Cell:
Molecules, Organisms & the Order of Life


On the face of it, the question – What is life? - should not be difficult to answer. After all, we're alive, right? Surely we know what it means to be “alive”. Yet in this essay, I'm going to explain why: 1) most people – including most contemporary biologists - cannot answer this question concisely and completely from a scientific perspective, but, 2) an answer is emerging from within the systems or network sciences that is fully consistent with the principles of physics and chemistry, but extend the idea well beyond their purview.

Part 1 of this essay - why the question matters - is here.

Background : Why the mechanistic sciences cannot define life

During the nineteenth and twentieth centuries, chemists and biologists worked diligently to understand life. Theodor Schwann, Matthias Schleiden and Rudolf Virchow laid the foundations for cell theory in the mid-nineteenth century, along with Gregor Mendel's seminal work on genetics, and Charles Darwin's theory of natural selection about how life evolved. Based on Mendel's work, genetics evolved as a discipline in the first decades of the twentieth century.

[caption] Diagram of the citric acid cycle, electron transport chain & chemiosmosis in a mitochondrion

In the 1940's, Albert Szent-Györgyi and Hans Krebs deciphered the core of metabolism: the citric acid cycle. (Krebs won the Nobel prize for his work.) In the 1950s, James Watson and Francis Crick - using Rosalind Franklin's X-ray crystallography data - inferred the structure of DNA. Then, we learned how cells synthesize proteins guided by information coded in DNA, and how most ATP is produced in mitochondria by chemiosmosis (another Nobel). Most recently, DNA sequencing has allowed us to “map” the human genome.

After all that, surely we know what life is from a scientific perspective, right? Apparently not. Case in point: in an ironic twist, even though biology is “the study of life”, glossaries of contemporary high school and college biology texts do not include the word “life”! Instead of a concise definition, those texts describe life – but do not define it - using a set of characteristics or properties allegedly demonstrated by cells and organisms: highly ordered structures, material exchanges with their environment, response to stimuli, reproduction, adaptation to their environment, etc.

Yet those properties do not unambiguously define life. For example, mules are hybrids between horses and donkeys that (usually) cannot reproduce, but they are just as alive as you are. Likewise, fire exchanges gases with the atmosphere, and crystals are ordered, but neither are alive in the same sense as leopards and lilies.

Even contemporary dictionaries do not unambiguously define life. For example, here's a typical definition from the Cambridge Advanced Learners Dictionary: “The period between birth and death; the experience or state of being alive”. That is not a useful definition for two reasons. First, at both cellular and organismal levels, there is no break between birth and the previous life that gave birth. In cell division, one living cell divides into two, so that life is continuous. In animal birth, one organism produces living sperm, another living eggs, which fuse to form a zygote, the first cell of a new organism; death does not enter that process. Second, the definition references the very concept it claims to define. Simplifying, one could write, “Life is the state of life”. Word games.

[caption] For centuries, biologists have compared life forms to machines.

So, why is it so difficult for contemporary biologists to define life? Because most of them are not framing the question correctly. The majority of biologists today are “mechanistic reductionists”. Treating life forms as machines, they attempt to understand life by reducing cells and organisms to their parts. Their premise is, if one can understand the parts, then one will understand the whole. According to that premise, if one dissects life into smaller and smaller pieces, eventually one will find the source of life dwelling among the parts.

As a university undergraduate in the early 1970's, I was told by my academic adviser – a biologist – that if I wanted to understand life, then I had to take courses in physics and chemistry, because ultimately, he said, life is - or will be - explained by physics and chemistry.

That was not merely his opinion; he was promoting the 'corporate' line of science. All scientists at that time, and many today, contend that biology is a “soft science”, whereas physics and chemistry are “hard sciences”, and that life will ultimately be explained by physics and chemistry alone. I intuited then that they were wrong, and I now know that they are wrong. This essay will help explain why.

In his eloquent book The Way of the Cell – the finest book about cellular biology ever written that should be required reading for every biologist, and that I use in my Life 3 course – Franklin Harold offers this about what sciences are relevant to understand life:

“This is actually a genuine philosophical puzzle, one version of the question whether biology can ultimately be ‘reduced’ to chemistry and physics or is an autonomous science with principles of its own ... There is more to life than just molecular mechanisms. From the chemistry of macromolecules and the reactions that they catalyze, little can be inferred regarding their articulation into physiological functions at the cellular level, and nothing whatever can be said regarding the form of development of those cells. It therefore seems to me self-evident that the quest for the nature of life cannot be conducted exclusively on the biochemist’s horizon. We must also inquire how molecules are organized into larger structures, how direction and function and form arise, and how parts are integrated into wholes.”

Whence came the argument that life is a machine that can be understood by studying the parts? Ultimately from the seventeenth century philosopher and mathematician Rene Descartes. In his day, clocks where still the only machines, and were seen as the model for not only living systems but the entire universe, which was deemed to be a clockwork mechanism.

But this machine metaphor is still employed today in disciplines ranging from mechanical engineering - where it is appropriate - to biology - where it is not appropriate. For example, automobile engines are composed of fuel and water pumps, fuel injectors, spark plugs, pistons, crank shafts and myriad other parts. Understanding the parts and how they are connected leads to a reasonable understanding of how the engine works.

[caption] A model of DNA, considered (incorrectly) by some "the molecule of life"

Following suit, biologists have for three centuries sought the secrets of life by dissecting organisms into smaller and smaller parts - organs, tissues, and cells – the latter of which are pulverized in test tubes to study their molecules - sugars, fats, proteins and DNA. The latter molecule – DNA - is often labeled “the molecule of life”, as if it is the secret of life.

But the “secret” of life is not DNA any more than the secret of an automobile engine is the cam shaft or the spark plugs. No single molecule is the secret of life. (Even if one were to try to identify the most important molecule in a living system, it would probably be ATP, not DNA.) Neither are light, electricity nor chemical energy, even though all play a role in life. Instead, as I explain below, life is a property of an entire network of tightly linked or coupled molecules and forces.

A definition of life

So, with that as background, here is my definition of life, based in principles of systems sciences, specifically emergence theory, non-equilibrium thermodynamics (about energy gradients and fluxes), and autopoiesis theory.

Life is an emergent property of autopoietic, dissipative systems.

In the following sections, I'll explain in introductory fashion what that means. Once those terms are understood, they lead to a rational yet intuitive understanding – both rational and intuitive - of the concept of life, simple enough to be taught to high school students yet applicable anywhere in the universe.

A much more thorough understanding is offered in my courses and seminars (and/or the texts upon which they are based). For example, in my introductory courses about basic principles of systems sciences, each concept – emergence and emergent properties; dissipative systems and self-organization; and autopoiesis - is addressed with an entire lesson (about 2.5 hours each), which are further enhanced by other topics not included in this essay. I also offer entire advanced courses about each topic that have been completed by dozens of students.

For an even more thorough explanation of life, we would also need to add concepts from nonlinear dynamics (in particular, the edge of chaos), fractal geometry, symbiogenesis and geophysiology (Gaia theory). But those will be addressed in separate essays.

The focus of this essay is the definition provided above, which captures the essence, the core, of an answer to the question, "what is life?".

Emergence & emergent properties

Life is not explained by any single molecule or group of molecules, nor by any specific form of energy. Instead, life is an emergent property, that is, a property that manifests or 'emerges' from the interactions among all of the parts of the living system, both matter and energy.

Emergence is a science studying and formalizing the ancient adage that the whole is greater than a sum of the parts. When parts of a system or network interact, properties emerge that are not fully explained from knowledge of the parts alone. Yet emergence is not mystical; emergent properties are consistent with the properties of the parts and with the laws of physics and chemistry. We can also explain and understand it - and even make predictions about it - using mathematical and computer models, a hallmark of science.

[caption] Chlorophyll

A simple example of an emergent property is the green color of chlorophyll molecules – produced by plants and algae that sequester the energy of sunlight in the chemical bonds between the atoms of sugar molecules. The green color emerges from the way that chlorophyll as a whole – as a linked network of atoms - absorbs red and blue frequencies of the light spectrum, but reflects green. That is, the color is a result of the structure of the entire molecule, not of its component atoms, none of which are green.

If one dissects chlorophyll, breaking the bonds (chemical linkages) between its atoms, the green color goes away because – again - none of its component atoms are green. Therefore, the “green-ness” of chlorophyll is more than a sum of its parts; it is an emergent property, and its explanation must include linkages among parts.

The concept of emergence is also demonstrated by the irony that in taking living systems – cells and organisms - apart, seeking life, biologists destroy the very property they seek to understand; a dissected organism will die. That is because the key to understanding life does not not reside in the parts, but in the connections or linkages between the parts.

Thus, as most systems scientists will argue, to borrow a phrase from mathematics, reductionism is necessary but not sufficient to understand life. To it, we must add a systems or network perspective that examines living systems as wholes.

Dissipative systems & self-organization

This section explains the forces that power life. The ideas discussed herein belong to a sub-discipline of the systems sciences called non-equilibrium thermodynamics, the science of energy gradients.

Living systems are composed of extremely complex and complicated networks of tightly-linked molecules – represented by the concept of metabolism, the networks of tens of thousands of different kinds of molecules and the reactions among them that occur in all living cells. Here is a “map” of metabolism summarizing the work of hundreds of thousands of chemists, biochemists and cell biologists during the last century.

Only a few relatively small molecules are imported into each cell as raw material: simple sugars (like glucose); fatty acids, mono- and triglycerides (fats); amino acids; nucleic acids (the components of DNA and RNA); some simple molecules like H2O, O2 and some inorganic salts and metals as ions (e.g., Na, Cl, K, Ca, Fe, Mg, Mn). From those relatively simple raw materials, the much more complex molecules of life are produced – complex carbohydrates, lipids (fats), proteins, DNA, RNA, chlorophyll, cytochromes, and co-enzymes like ATP, NAD and FAD (electron transporters).

The previous paragraph contains an important point that bears repeating and that is directly related to another topic discussed later in this essay, autopoiesis (discussed in the next section): the huge majority – nearly all - of the complex molecules of life – carbohydrates, lipids, proteins, nucleic acids and co-enzymes – are not imported into cells fully formed, but are produced in cells from smaller raw materials that were imported.

For example, your cells do not directly utilize the DNA and proteins from animals or plants in your diet. Instead, you break them down – digest them - into their component parts and import those simple molecules into your own cells (via your blood) where they are reassembled into your own proteins, RNA and DNA. (Your DNA, RNA and proteins have a different sequence of component parts than those of the organisms that you consumed as food.) This is one of the major characteristics of living systems: they build themselves from raw materials imported from outside themselves.

So how does this production of larger molecules occur? The production of large molecules from small ones will not occur spontaneously in vitro (in a test tube). For example, amino acids in a test tube will not spontaneously assemble themselves into proteins, and nucleic acids like adenine, cytosine, guanine and thymine will not spontaneously assemble into the double helix of DNA. How are simple molecules like mono-saccharides, amino acids and nucleic acids organized into the much more complex molecules that make up living systems and account for their function, growth and repair?

In short, what powers the organization of life?

The answer is energy gradients. A gradient is a graded change – from high to low - in the magnitude, amplitude or size of some physical quantity – matter or energy - in space. Metaphorically, one can think of gradients as hills: “more” stuff – energy or matter - is “uphill”, less stuff is “downhill”. Just like water flows downhill instead of up, matter and energy flow “downhill”, that is, "down" a gradient, from higher to lower concentration.

As energy flows from source to sink, the gradient is “dissipated”. For example, think of a fire in a wood stove. The fire generating heat and light is “uphill”, the outer edges of the room it is in are “downhill”. Heat (and light) always – always, with no exceptions - flows from uphill (high concentration) to downhill (lower concentration). The same is true for matter, which always moves from higher to lower concentration “down” a diffusion gradient, but not in reverse (unless it is "pumped" using an energy source).

[caption] An energy gradient. Left: high energy concentration. Right: low energy concentration.

The latter fact – that energy always flows down a gradient, and never up – is an empirical observation – a law - that is at the core of the most famous law in science: the second law of thermodynamics, which dictates that energy always flows down a gradient and that gradients are eventually degraded, that energy is dissipated – dispersed or scattered - in the process, to the point where there are equal amounts of energy in all parts of the space in question. That is, to a point where no more gradient exists. More on that state in a moment.

[caption] Degraded energy gradient with equal amounts of energy in all parts of the space.

Furthermore, when high quality energy (also called “free energy”) – like electromagnetic energy (e.g., light, microwaves, ultraviolet) or chemical energy or kinetic energy - performs work, the high quality, free energy is ultimately converted to heat, mostly low temperature, which is considered “waste” energy because it is least able to perform useful work, and is that into which other forms of energy eventually degrade. Furthermore, the degradation is “one-way”: once energy degrades into heat, it will not transform back into a higher quality form of energy. That is, total energy is conserved, but energy quality is not.

In their book Into the Cool: Energy Flow, Thermodynamics and Life – which is the best and most accessible introduction to non-equilibrium thermodynamics available for educated lay readers – authors Eric Schneider and Dorion Sagan use the following metaphor to explain the second law: nature abhors gradients. They are not implying that nature as a whole makes rational choices to degrade gradients in the same way that you would open a window to dissipate excess heat from a room; it does not. But the automatic process of gradient reduction dictated by the second law makes it appear as if it does.

In addition, and importantly, some some ingenious natural processes called self-organizing systems or dissipative systems have emerged in the universe to accelerate gradient reduction, including the evolution of life. More about that shortly.

When an energy gradient is degraded or dissipated – that is, the gradient no longer exists, but equal amounts of energy (or matter) exist in all parts of the space under consideration – the resulting condition is called thermodynamic equilibrium. For example, when the fire in a wood stove goes out and heat is equally dispersed in the room so that there is no remaining gradient, then the room has reached thermodynamic equilibrium (at least with respect to the heat and light that was emanating from the stove). So, we can say that as long as the wood stove is burning, the room is far from equilibrium.

At the end of a chemical reaction, when the energy of reactants has been dissipated in the production of products plus some waste heat, then chemical equilibrium - a special case of thermodynamic equilibrium - has been reached, and no more net change occurs in the system. Thermodynamic equilibrium in a living system – when there are no energy gradients to power that system - is death. Likewise, as long as we are alive, we are far from equilibrium – or FFE - systems. (A scientifically accurate get well card could read, “Get well soon! Avoid thermodynamic equilibrium!")

The latter point deserves repetition: all complex self-organizing systems – including life forms – are "far from equilibrium" (FFE) systems. They may exist in a dynamic steady state, where energy input (as high quality, free energy) equals energy output (as low quality, waste heat). But when they reach thermodynamic equilibrium, they lose their structural and functional integrity. (Note: steady state is sometimes called "dynamic equilibrium" or "quasi-equilibrium"; but to avoid confusion with the fundamentally different thermodynamic equilibrium, I prefer the term steady state. So do physiologists.)

When simple (or complex) molecules are exposed to an energy gradient of the right kind of energy – specific to each kind of system - they self-organize into either progressively more complex behaviors (the larger the gradient, the more complex the behavior or dynamics), or – if the proper catalysts are present – into more complex molecules that also have more complex behaviors. Again, one of those more complex behaviors is the property we call life which occurs in special kinds of dissipative systems.

The reason for this is simple: more complex systems - that is, systems with more complex behaviors – degrade or dissipate energy gradients more effectively than simple systems. This is because self-organization requires work – the movement of matter – and work requires energy. In fact, energy is generally defined most simply as “the capacity to do work”. Thus, work dissipates energy according to the second law.

So, self-organization – the spontaneous and natural emergence of organization, including life forms – is effectively mandated by the second law of thermodynamics which specifies that gradients are always dissipated.

I will provide examples below. But first, this point deserves to be stressed: self-organization to more complex behavioral (dynamical) states acts to dissipate an energy gradient more effectively so that the second law is satisfied more efficiently.

That deserves repeating, because creationists and advocates of intelligent design - creationism masquerading as science, a pseudoscience - fail to grasp this principle: self-organization to more complex states - including living systems - does not violate the second law; instead, it is driven – even mandated - by the second law.

Thus, the late Ilya Prigogine, founder of non-equilibrium thermodynamics and self-organizing science, who won a Nobel prize for his work, named self-organizing complex systems dissipative systems, systems that maintain their structural integrity by dissipating energy gradients. (This is related to a very profound scientific and philosophical explanation for why life has evolved, but that is a topic for another essay.)

(Note: The term “self-organization” is somewhat a misnomer because the energy causing the organization comes from "outside" the system, that is, outside the “self”. But the meaning of the term is that organization occurs inside the system - the "self" - as the energy flows through it down the gradient.)

Some of the simplest forms of self-organization are vortices or whirlpools. For example, water draining from a sink, tub or toilet self-organizes into a vortex in order to dissipate the kinetic energy (via the gravitational force) more effectively. If one disrupts the vortex with one's hand, the water drains more slowly.

[caption] Convection "cells" in silicon oil in a dish heated from below; these cells are vertically oriented, with hot fluid flowing up in the dark center and down in the lighter collar. The six odd-shaped cells were caused by an imperfection in the bottom of the dish.

Another simple example of self-organization is convection (Benard) cells that emerge when a fluid – liquid or gas - is exposed to a heat gradient. For example, above a critical threshold of heat gradient, oil in a dish heated from below will spontaneously “self-organize” into rolling currents as heated fluid rises to top (where heat is dissipated to the air), then cooler fluid flows downward. Convection patterns become progressively more complex with larger heat gradients: first horizontal “rolls” appear; then, vertical hexagonal “cells” (see image); then, spirals, and finally spirals inside of spirals.

Convection cells in Earth's atmosphere, called Hadley cells - driven by energy from the sun that is converted to heat when it strikes dark objects on the surface - rise into the upper troposphere (the lower layer of atmosphere where weather happens), dissipating heat into the stratosphere and from there into space. Along with the Coriolis force resulting from Earth's spin, such convection cells drive the movement of the atmosphere in our climate system.

[caption ] Unstirred BZ reaction manifesting ultra-slow motion concentric circles spreading from centers as if waves spreading from pebbles dropped into a pool.

More complex self-organizing systems require higher quality chemical energy that dissipates as heat. One is the Belousov–Zhabotinsky (BZ) reaction. When one stirs a mixture of a few relatively simple chemical compounds, it switches between different colors (oxidation states) in a precise clock-like manner. (Hence, they are called "chemical clocks"; see below.) If unstirred, the reaction mixture can produce remarkable visual patterns that become progressively more complex in larger chemical gradients - slow motion concentric circles (image), spirals and pinwheels - until chemical equilibrium is reached.

In the BZ reaction, the energy driving self-organization is not heat, as in convection cells, but chemical energy, a form of electromagnetic energy stored in and released from chemical bonds in the reagents of the mixture, doing the work of self-organization and being converted into heat. The BZ reaction is an example of a much-studied category of reactions called “chemical clocks” that include the citric acid cycles that help power your cells, and your heart's natural pacemaker that rhythmically stimulates heartbeat. Importantly, these kinds of reactions were not understandable from a mechanistic perspective. When Boris Belousov first reported them in the 1950's, no one would believe that they existed.

Far more complex and interesting examples of self-organizing, dissipative systems are biological cells and organisms like you. Self-organization of all living systems is powered by either light (photosynthetic organisms) or chemical energy from simple inorganic compounds (for certain types of bacteria) or from complex organic compounds – sugars, fats, proteins, etc - ingested as food by many bacteria, protoctists, all animals and fungi. The energy in those food molecules is then extracted by breakdown (often but not always by oxidation in the citric acid cycle, electron transport chain and chemiosmosis), then temporarily stored in tiny molecular “batteries” called ATP for use in virtually every process of life.

I often pause and reflect on the fact that we – all life forms, including humans - are self-organizing, dissipative systems. We are not machines. We make ourselves; machines do not. We did not require a “maker”; we made ourselves. This is a source of wonder that humans would do well to explicitly acknowledge as we re-write the stories of our cultural maps for the twenty first century and beyond in a way that promotes our awe and reverence for the large living system of which we are a part: Gaia, our living Earth. Our survival as a species depends on that.

A brief review

In the last two sections, I have addressed two of the three components of a definition of life. I have explained that life is an emergent property of certain types of self-organizing, dissipative systems. But what distinguishes living and non-living dissipative systems? Are vortices, convection cells and BZ reactions alive? The answer is no. The feature that distinguishes living from non-living dissipative systems is autopoiesis.


Dissipation of energy gradients fuels the emergence of life in some dissipative structures, but that does not fully define or explain life. That is, although the main force powering life is the electromagnetic force - as light driving photosynthesis and as energy in the chemical bonds of food - that force alone is not life.

Instead, as I will explain in this section, the final component of a definition of life is a process called autopoiesis occurring in some – but not all - dissipative systems. (Note: the explanation of autopoiesis begins in an abstract way. But later in this section, I will relate this concept directly to cell biology that will make it much more concrete.)

Lynn Margulis emphasizes that life is not a "thing" but a dynamic process. She wrote, “Life is not a noun, but a verb.” That is, life is neither a molecule, a force or an energy – which are nouns - but a process, which makes life a verb.

The word autopoiesis (pronounced "auto-po-ee-sis") was coined by Chilean biologists Humberto Maturana and Francisco Varela. (Philosopher Gregory Bateson independently described the same phenomenon, but he named it “the pattern that connects”.) Autopoiesis means "self-making", from “auto” (self) and “poiesis”, which means "creation" or "production" and shares a root with “poem” and “poet”.

In his book The Web of Life, Fritjof Capra wrote that autopoiesis is “… a set of relations among processes of production.” That is, nodes in an autopoietic system are not static parts, but instead each node is itself a production process. A more complete definition of autopoiesis is, a network pattern in which the function of each component is to participate in the production or transformation of other components in the network, so that the network continually makes itself. That is, all components of an autopoietic network are produced by other components in the network using matter and energy from outside the system. Thus, an autopoietic system is organizationally closed, but thermodynamically open.

Biologist Gail Fleischacker specified three criteria that define autopoietic systems:

1. self-organization [that is, they are dissipative systems]; their parts are generated inside the system from imported matter and energy 2. self-maintenance and self-repair 3. self-bounding via the production of unambiguous physical/chemical boundaries, like cell membranes or the skin of animals

Autopoiesis distinguishes living from non-living dissipative systems. Vortices, convection cells and chemical clocks self-organize – they are dissipative systems - but they do not maintain and repair themselves and – most importantly - they do not form unambiguous physical-chemical boundaries.

Likewise, machines are not autopoietic; their operation dissipates energy, but they are not self-organizing systems in the same way that convection cells and biological cells are because they do not produce and repair themselves, at least outside of science fiction tales like Terminator. Francisco Varela argued that the third criterion - self-boundedness - is the key distinguishing autopoietic from non-autopoietic but “autonomous” systems that demonstrate one or two of the first two Fleischacker criteria. He argued that corporations and cities are autonomous – self-organizing and self-maintaining, but not autopoietic because, 1) they do not produce their own components (people can and do migrate, and many complex components must be imported), and 2) they do not have self-produced, unambiguous boundaries.

In The Way of the Cell, Franklin Harold writes in chapter 10 – entitled, “So, what is life?” - about Immanuel Kant.

“Well then, what is wrong with the assertion that a cell – E. coli, say, or a ciliate – is just a particularly intricate and ingenious machine? The fault is that the claim begs the central issue. If a cell is just another machine, what is the basis for the distinction that has been drawn from ancient times between objects that are alive and those that are not? After all, what we seek to understand is not what these two categories have in common, but what sets them apart! The answer came in the eighteenth century from the German philosopher Immanuel Kant, and turns on the existence of a special category of objects called organisms. In a machine, Kant said, the parts exist for each other but not by each other; they work together to accomplish the machine’s purpose, but their operation has nothing to do with building the machine. It is quite otherwise with organisms, whose parts not only work together but also produce the organism & all its parts. Each part is at once cause & effect, a means and an end. In consequence, while a machine implies a machine maker, an organism is a self-organizing entity. Unlike machines, which reflect their maker’s intentions, organisms are ‘natural purposes’.”

Later in that chapter, Harold expands on the concept by discussing the work of science philosopher Robert Rosen.

“For Rosen, the heart of biology is that it revolves around the pattern of connections between components, and that allows him to offer a solution to Schrödinger’s riddle: ‘A material system is an organism if, and only if, it is closed to efficient causation’. [Efficient causation refers to Aristotle's four levels of causation; see Into the Cool, chapter 20, for more on this.] That is, if f is any component of a living system and we ask what is the cause of f, the question has an answer within the system. This would obviously not be true of [a] bicycle, and only partially true of [a] candle or university. Actual organisms will be realizations of this general and abstract principle of organization. Note that Rosen, pursuing his quarry by formal logic, arrives at an insight remarkably like that attained by Maturana and Varela before him: living organisms are autopoietic systems: they make themselves.”

The concept of autopoiesis may seem quite abstract to new students. It remained somewhat vague to me for several years after I began to study it, trying to grok it, to give it meaning in the real world.

Finally, a statement in one of Lynn Margulis's books helped me translate the abstract concept of autopoiesis into biological reality. She wrote, "Metabolism is the biochemical manifestation of autopoiesis".

[caption] A small region of the metabolic map of chemical processes occurring in all living cells; at the center of this region is the citric acid cycle common to virtually all life forms.

As a biologist who has for decades studied and taught principles of cell biology – their structure, their function, their metabolism - that sentence washed away all lack of clarity about the concept; I instantly grokked it. Autopoiesis is a term that names the self-organization of imported (as food), simple molecules into thousands of kinds of complex molecules involved in metabolism – fats, proteins, DNA, RNA, and co-enzymes like ATP - and the exportation of waste as small, low-energy molecules and heat.

In turn, those molecules self-organize (powered by ATP) into more complex structures called organelles like mitochondria, chloroplasts, Golgi bodies, endoplasmic reticula, ribosomes, etc, each of which is a "production process". This also includes production of cell membranes (and in some cases, walls) - system boundaries - which occurs from inside a cell.

Furthermore, when autopoiesis stops, life stops. That is, death results from the cessation of autopoiesis, where upon a living system moves rapidly towards thermodynamic and chemical equilibrium.

[caption] Typical bacteria (prokaryotic cell)

Autopoiesis exists on four scales of size and complexity. The simplest autopoietic systems are bacteria which, although biochemically complex - they have a metabolism as complex as more complex eukaryotic or nucleated cells like yours - they are structurally very simple and at least 10 times smaller. Their only internal organelles are ribosomes. They do have a cell membrane, however, and often possess one or more external motility organelles called flagella. [caption id="attachment_1260" align="alignleft" width="150"] Typical eukaryotic cell.[/caption] A second, more complex level of autopoiesis is eukaryotic or nucleated cells such as those comprising protoctists, animals, fungi and plants. Eukaryotic cells, larger and far more complex than bacterial cells, evolved via a process of symbiosis or symbiogenesis among bacteria that occurred about 1.5 billion (1,500 million) years ago. Specifically, the mitochondria and chloroplasts evolved from symbiotic bacteria; they have their own DNA and ribosomes that are more similar to bacteria than to those of the larger cell.

The motility organelles of eukaryotic cells - undulipodia, often mistakenly called flagella - are also of bacterial origins; they are analogous to flagella but not homologous: that is, they perform the same function but have radically different structures and origins. Lynn Margulis has demonstrated that they almost certainly evolved from spirochete bacteria very early in eukaryotic cell evolution. (No trace of bacterial DNA has been found in them.)

The third level of autopoiesis is multicellular organisms – animals, plants and fungi -which are composed of second- and first-order autopoietic entities: eukaryotic cells and bacterial symbionts. Organisms maintain their chemical composition (and for some, like mammals and birds, their temperature) via system-level processes called homeostasis, often involving multiple, linked organ systems that are studied by the science of physiology.

The fourth and largest, most complex level of autopoiesis is Gaia, our living planet, technically a planetary-scale metabolism and homeostasis. It self-organized in the energy gradient produced by our sun during the last 4,000 million years. It has automatically maintained (via homeostasis) the temperature and chemical composition of its atmosphere - its boundary (which it created) - and oceans, repairing itself after major perturbations like asteroid strikes and gargantuan volcanic eruptions.

Finally, as I'll explain in part 3 of this essay, Maturana and Varela argue that autopoiesis is directly related to the phenomena of cognition (in all life forms) and consciousness (in some complex, multicellular organisms like humans). That is, like life, cognition and consciousness are also emergent properties of autopoietic, dissipative systems.

Conclusion: the definition revisited

So, let's look at the definition of life again. This time, it should be more meaningful, even if not completely second nature yet. With some reading and study in my courses, it becomes second nature.

Life is an emergent property of autopoietic, dissipative systems with self-organized critical (SOC) dynamics.

That is a definition worthy of a college-level biology textbook. Further, we can expect that life any where in the universe would be described in the same way.

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