What is life? Part 1 : Why the question matters


This is the first of a three-part essay entitled “What is Life?”.

  • Part 2: Details of a major new scientific understanding of life emerging from the addition of several principles of systems sciences – self-organization in dissipative systems, autopoiesis, emergence, symbiogenesis and Gaia theory – to existing knowledge from cell/molecular biology.
  • Part 3: Cognition and consciousness,
    and why life necessarily had to evolve before consciousness


Part 1 : Why the question matters

What is life? is surely one of the oldest questions.  We live.  We – people, birds, flowering plants, even algae glowing in the oceans at night – differ from steel, rock, inanimate matter.  We are alive.  But what does it mean to live, to be alive, to be a discrete being at once part of the universe but separated from it by our skin?  What is life?”

Lynn Margulis & Dorion Sagan, What is Life?


“Finally, I hold that the quest for an answer to the riddle, ‘What is Life?’ is one of the grand themes that resonate through the scientific conversation of this century …. That riddle embraces and transcends the subject matter of all the biological sciences, and much of physical science as well.  A physics that has no place for life is as impoverished as would be a biology not informed by chemistry.  The study of life as a natural phenomenon, a fundamental feature of the universe, must not be allowed to slip into the black hole of departmental tribalism.”

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


“The guiding story for this planetary era will place the origin of our species, our human history, and questions about our existence today within the sweeping narrative that recounts how Earth and its commonwealth of life have together made Gaia – the living system born of creative collaboration, the great process that makes possible our lives and all we see around us.  The Gaian story weaves human existence back into this ancient drama, showing how we are rooted in the Earth and the entire cosmic history that preceded it.  It tells us that our lineage was born through the dynamism of an evolutionary epic that is still being written.”

Dianne Dumanoski, The End of the Long Summer:
Why We Must Remake Civilization to Live on a Volatile Earth


In part 1 of this essay, I explain why there is a need for humans to understand not just ‘who’ we are, but also what we are and how we function at cellular and molecular levels, an understanding that has been greatly enhanced by advances in the systems sciences during the last few decades.

I am NOT suggesting that every one – or even most – should memorize the details of the citric acid cycle, DNA replication and protein synthesis, let alone the map of cell metabolism.  But I am asserting that more humans need now to understand – at least conceptually – what the phenomenon of life is and how it works at a cellular level.  We need to understand more of what happens inside us at the level of DNA, cell membranes, ribosomes, enzymes, energy flows and ATP.  In my biology courses for non-scientists, I offer students that broad conceptual understanding rather than excruciating detail better suited for cell biologists or biochemists.

Why do humans need to understand this now? For multiple reasons. First, without that knowledge, we are missing a beautiful, awe-inspiring story – as artistic, poetic and spiritual as it is scientific – about what we really are as living entities, how we function, how and why we evolved, and our role on Earth and in the universe.

Without that knowledge and the inspiration to which it leads, we cannot fully understand, appreciate and respect our relationship to other species, including the unfairly maligned microbes that are so important to life at every scale, with which we share most features of metabolism.

Without that knowledge, we are in danger of succumbing to an obsolete view of ourselves  as “mechanisms” or “machines”, which is in large part responsible – wrote Margulis, Sagan and Dumanoski — for the planetary predicament in which we now find ourselves: our centuries-long efforts to control the machine for our own use is backfiring on us in the form of a dangerously disrupted planetary metabolism, one symptom of which is climate change.  [For readers who wish to understand more about the problematic aspects of the mechanistic metaphor, I have added an end note containing explanatory excerpts from the three books quoted at the beginning of this essay.]

It is very important to understand – as I will make clear in part 2 of this essay – that living systems are emphatically not machines, but self-organizing, self-regulating and self-maintaining systems that owe their existence to energy gradients.  Indeed, this is one of the greatest contributions of systems sciences to biology: we are being led away from the mechanistic or “machine” metaphors of life towards conceptualizations that are much more organic and awe-inspiring while still being material.  (That is, even though the systems view is not mechanical, it is not mystical, either, but solidly grounded in the laws of physics and chemistry.  Note that these ideas may contribute to new spiritual views of existence without being mysterious or mystical.  More on this below.)

I offer these ideas from four decades of experience as a student and teacher of cell biology, physiology, ecology, evolution, and non-equilibrium thermodynamics (NET).  Those sciences offer us wondrous stories about our world: how light from the sun is transmuted within photosynthetic creatures into chemical energy, stored in the bonds of molecules, that flows into cells of the beings that consume them; how – with the help of biological  catalysts called enzymes - that energy is extracted from those molecules and invested into ATP (adenosine triphosphate) that powers virtually every process of our lives.

Knowing – grokking (to borrow a word from author Robert Heinlein) – these things has contributed greatly to not only my understanding of life, but to my wonder and awe of what I am, of how the forces of nature unconsciously produce me and every other living thing.  And that adds to my love of myself, friends and loved ones, other species, and nature as Gaia.

I  have seen that wonder and awe spring forth in others,  also.  For example, when I offer a creative, conceptual image-driven lecture (stripped of most dry, daunting details) about complex processes that occur inside of living cells, students are regularly awe-struck by the elegant beauty of structure and process; jaws often drop as awareness sinks in.

One of my favorite examples is the story of how electrons extracted in the citric acid cycle cascade down a series of molecules called the electron transport chain which pump protons that flow through a molecular “turbine” called ATP synthase to generate ATP.  It is material worthy of the best special effects that film makers have to offer. Upon seeing such elegant complexities, one advanced student would often say, with a smile on his face, “You’ve got to be making this up!”

Such experiences motivate me to argue that, starting at an early age, we need to cultivate our understanding, wonder and awe of life, of what and how we are, to put daily life – its beauty, trials, tribulations and soap operas – into a context of other species and planetary processes.  That humans, especially in the developed western world, are so consumed by fashion, cell phones, sports, politics and economics to the near exclusion of a fascination about what occurs inside of all of us is tragic.  It, also, contributes to a dangerous lack of understanding of Gaia, the name that James Lovelock and Lynn Margulis give our planetary-scale metabolism and homeostatic (self-regulating) system.

Why is an understanding of Gaia important? Because during this century, large-scale abrupt climate change is going to collapse civilization as we know it, forcing a major restructuring of human social systems. As Dianne Dumanoski points out in her book The End of the Long Summer, climate change is but a symptom of a much larger problem: the disruption of our planetary-scale metabolic and homeostatic system – Gaia – which is effectively life at a planetary scale.

As a result, the road ahead is going to be rough. As James Lovelock explains in his book, The Revenge of Gaia, by the end of the century, climate change will probably reduce the human population from a maximum of around 7 – 8 billion – slightly more than now – to … far fewer, most living in the far northern latitudes. (See my essay, “Why large-scale climate change (probably) cannot be stopped, and we must, thus, increase our adaptability”.)

Therefore, as Dianne Dumanoski asserts, we need a new “cultural map”, a new set of ideas and principles to guide us as we enter a new planetary era, a time of collapse and a transition into what is next.   [And as I'm fond of adding, it's not an apocalypse; it's an adventure!   Attitude is important.]   We need to replace our current outdated map based on the notions of progress and growth.  At the core of the new map, she argues, is a new, more accurate scientific and metaphorical understanding of Gaia as a planetary-scale metabolism and homeostasis – that is, a planet-sized life form.

But we cannot grok what that means even conceptually, let alone in detail, without some understanding of our own metabolism and homeostasis.  To understand Gaia, you need to understand your life, your metabolism, your homeostasis, then scale up the concepts.

Finally, we live – at least for now – in an electronic age with a global-scale “nervous system” called the Internet (metaphorical because it really only connects humans, not the full  system) within which anyone can advance any idea as “truth” regardless of how ridiculous and ungrounded.

For example, ideas are often advanced that life can be explained by quantum theory, or is a result of a fifth force, a life force, or even a mysterious elan vital not explainable by science.  Those are inaccurate and misleading explanations of life based more in religion and superstition than science.

Therefore, it is important that as humans move into the future, we carry the most accurate scientific concepts about life at all scales – from cellular to planetary — as a foundation of our cultural map, lest we fall into the trap that Carl Sagan wrote about in his book, The Demon Haunted World: Science as a Candle in the Dark. He feared that humans will fall into another dark age underpinned by superstition and dangerously misleading understandings of life and nature.

However, I am not suggesting that scientific answers to the question “What is Life?” should replace answers that are more poetic or artistic, but instead that they should supplement and inform them in a meaningful way.  Indeed, as a student once pointed out to me, understanding these ideas helps one understand the spiritual dimension of life – the notion that we are part of something larger than ourselves – without faith in a sentient deity.  These concepts do not prevent belief in a deity, but for those of us who are not religious, they circumvent the need for one while allowing a spiritual component to one’s life.

So with all of that as motivation for this question, I follow in the footsteps of my favorite biology mentor, Lynn Margulis, who published a book in 1995 with Dorion Sagan entitled What is Life? about what we have learned about the answer to that question since it was first asked by physicist Erwin Schrodinger in his book of that same title in 1944.  Many of the concepts that I employ in part 2 of this essay are addressed in that wonderful book.


Here is a supplemental end note about the problematic aspects of the mechanistic metaphor for those  who wish to understand that issue more deeply. The first two sets – from Margulis and Sagan, and Franklin Harold, respectively – address philosophical and logical issues with the metaphor  as it applies to living systems. The third set from Dianne Dumanoski relates the issue directly to our planetary crisis.

Lynn Margulis  & Dorion Sagan, What is Life? from chapter 1
[Note: they reject both animism and mechanism.]

“If you wish to, you can reach for a glass of water or snap this book shut. From the experience of willing our bodies to move came animism: the view  that winds come and go, rivers flow, and celestial bodies guard the heavens because something inside each wills  the movement. In animism all things, not only animals, are seen to be inhabited by an inner, animating spirit. Formalized  in polytheistic religion, the multiplicity of gods – a moon god, Earth god, sun god, wind god, and so on – was replaced in Islam, Judaism, and Christianity by a single god who crafted the world. Winds and rivers and celestial bodies lost their will, but living organisms – especially humans – retained  theirs.

“Finally, the last outpost of animism – living organisms – yielded to the philosophy of mechanism. Motion need not imply any inner consciousness; the program  could have been ‘built in’ by a creator. Wind-up toys and automated models of the solar system suggested to their inventors that even living things may be constructable from lifeless mechanisms, subtle concealed springs, tiny unseen pulleys, levers, cogs, and gears. Comparing flowing blood to a hydraulic system, English physician William Harvey (1578 – 1647) discovered circulation of the blood. Scientists sleuthed out the world’s secret mechanisms, part of an overall design. Natural history revealed the world to be a giant mechanism made according to the mind of  an omnipresent, omnipotent god.

“Isaac Newton (1642-1727) became the high priest of mechanism. A devoted student of alchemy, scripture and the occult, Newton made unparalleled innovations in optics, physics, and mathematics. In doing so he helped bridge the gap from medieval cosmos to the modern one. Explaining the motions of the planets with a new law of gravity, Newton’s equations showed that the world of the heavens and that of Earth were one and the same; the force that kept the moon in orbit was also the force that thuds an apple to the ground. So revealing were Newton’s discoveries of ‘laws’ governing the entire universe  that to some it seemed he had – in Kepler’s words – ‘glimpsed the mind of God’. Inspired by Newton’s analyses, Pierre-Simon de Laplace (1749-1827) speculated that, with sufficient information, the entire future of the universe, even the most minute human action, could be predicted. Far from being moved by hidden spirits, the celestial bodies now seemed to be under the governance of pre-existent mathematical laws. Divine intervention became increasingly superfluous. God did not  need to fiddle with creation. He had crafted it to last. The cosmos worked itself.

“With a grasp of gravitation’s cosmic sweep, scientists were spurred to explore phenomena once considered beyond human comprehension. Electricity and magnetism, sound and color, radiation and heat, explosion and chemical change were all described with an eye to their underlying unity. Optical instruments, telescope and microscope, presented formerly unseen worlds of the very far and the very near. Experiment and criticism replaced blind acceptance of classical authority and divinely revealed truth. Scientists coaxed nature to yield some of her most private secrets. Oxygen’s role in fire, lightning as electrical discharge, gravity as the invisible force causing the tides and attracting the moon into Earth’s orbit – one by one nature laid down her cards.

“Under the spell of the mechanical worldview, the ancient alchemical dream of shaping nature to human will became technological reality. After centuries of humans meddling with steamy concoctions in a Faustian quest to be godlike, then a 1953 discovery seemed to reveal the very secret of life. Life was chemical and the material basis of heredity was DNA, whose helical and staircase-like structure made clear how molecules copied themselves. Indeed, the ‘aperiodic crystal’ that Schrodinger had predicted was uncannily similar  to the double helix …. Replication was no longer beholden to a mysterious ‘vital principle’; it was the straightforward result of interacting molecules. The description of how DNA fabricated a copy of itself out of ordinary carbon, nitrogen, and phosphorous atoms was perhaps the most spectacular of all mechanism’s successes. But paradoxically, this success born of self-directed minds seemed to portray life – including the scientists themselves – as the result of atoms involuntarily interacting according to changeless and inviolable chemical law.

“Between these two extremes – the entire universe as alive, and the living organism as chemical and physical machines – lies the panorama of opinion. But is there not something wrong with both the mechanization of life and the vitalization of matter?
“The world as a vast machine fails to account for our own self-awareness and self-determination because the mechanical worldview denies  choice. Mechanisms, after all, don’t act; they react. And mechanisms, moreover, don’t come into existence on their own. The assumption that the  universe is a mechanism implies that it was made according to some human-like design – that is, by some living creator. In other words, successful as it is, the scientific mechanistic worldview is deeply metaphysical; it is rooted in religious  assumptions.

“The animistic view of the cosmos as a huge organism is also flawed. It blurs the distinctions among what is living, what is dead, and what has never been alive. If everything were alive, there would be no interest in – and scientists never would have discovered the replicative chemistry of – life.

“We thus reject mechanism as naïve and animism as unscientific. Even so, life, as an emergent behavior of matter and energy, is best known by science. Schrodinger was correct in advocating a search for physio-chemical underpinnings of life. So are Watson and Crick and other physicists and molecular biologists who hail the structure of DNA  as a key to life’s secrets. Like an uncoiling spring pushing the soft gears of life, DNA copies itself as it directs the making of proteins that together form the leopard’s  spots, the spruce tree’s cone, and living bodies in general. Understanding how DNA works may be the greatest scientific breakthrough in history. Nonetheless, neither DNA nor any other kind of molecule can, by itself, explain life.”


Franklin Harold, The Way of the Cell, from chapter 10

“Wander the corridors of a biology building to eavesdrop on the residents, and you’ll find them preoccupied with nuts and bolts. We argue about the mechanism of photosynthesis, of embryonic development  or even of evolution. We speak earnestly of the ‘machinery of life,’ of biological ‘ building blocks, ‘ of traits ‘hard-wired’ in the ‘blueprint’; and we prepare students for careers in the new manipulative  science, particularly in ‘genetic engineering’. Even medicine, that most humane of arts, seems to be turning into a science of spare parts, plastic or molecular. Isak Dinesen caught the mood early: ‘What is man, when you come to think upon him, but a  minutely set, ingenious machine for turning with infinite resourcefulness the red wine of Shiraz into urine’.

“A machine, Webster informs us, is ‘an assembly of parts that transmit force, motion and energy to one another in some predetermined manner and to some desired end’. It is a stretch, but seemingly not  an excessive one, to apply this definition to living things: chemical machines, whose object is to make two where there was one before. The metaphor carries immense heuristic power. It conjures up  a system of interacting parts with well-defined functions, joined together in service to a greater whole; of energy supporting useful work, and of powers emerging in the machine as a whole that were not present in the isolated parts. Every time we announce the unraveling of another mechanistic puzzle, we pay tribute to the metaphor of the machine: mechanisms are a real feature of living beings. Besides, the metaphor resonates with our deepest conceptions about the way things are. For three hundred years now, scientists have perceived the world through the eyes of Descartes and especially of Newton: a universe of  particles moving in fields of force, whose behavior is fully determined by the overarching laws of physics. For those who subscribe to this viewpoint, biology is little more than a collection of special cases that must be accommodated within the general framework; no deep mysteries there.

“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 [autopoietic systems; see part 2.]. Unlike machines, which reflect their maker’s intentions, organisms are ‘natural purposes’.”


Dianne Dumanoski, The End of the Long Summer, from chapter 8

“By the second half of the seventeenth century, as this atomism combined with the widespread fascination with such complex autonomous machines as clocks, a new image of nature emerged. Mother Nature – a living, active, creative, self-integrating organic whole – vanished as such leading philosophers as the French mathematician Rene Descartes, who also played a key role in the revival of atomism, rejected the randomness of the classical Greek version of this  material philosophy, asserting rather that this mechanical order behaved predictably according to laws ordained by God, now characterized as a clockmaker who had set the physical world in motion and then withdrawn from the operation. This notion of mechanism embraced everything; thus he regarded even the human body and  animals as no different from a clock or other ‘automata’. This extreme stance led him to make some preposterous-sounding claims: He denied that animals possess souls, minds or sensation, writing that ‘there is nothing in the whole  of nature which cannot be explained in terms of purely corporeal causes totally devoid of mind and thought.’ Descartes further declared that animals do not  feel pain, because they lack understanding; what appears to be pain is really only a mechanical response, which Cartesians likened to the scream of a pipe organ when a key is pressed. Although this bold assertion flies in the face of common sense and the natural empathy most people experience, it helped to justify the practice of experimenting on still-living animals – vivisection – to advance physiological  research, which as an exciting frontier of science in this period.

“This image of world as machine is the deep metaphor at the heart of  modern culture and, ‘despite many reformers,’ Mary Midgley notes, ‘Descartes still rules.’ Seeing the world through the metaphor of the machine does not mean that we take it as literally as Descartes and fail to see the difference  between a human body and a clock, rather the machine worldview lives on in our culture’s long-standing assumption that living things, which may look dazzlingly complex to the eye, are in reality simple. The atomistic vision – which denies that they whole has its own unity and integrity, so it is no greater than the sum of its aggregated parts – has justified reductionism in scientific investigation and the modern notion of the primacy of  self, which has fostered an increasingly radical and socially corrosive individualism. In the machine world, the parts are the fundamental reality and priority – whether these parts are ‘selfish genes’ in evolutionary theory or the individual in the social-construct theory of liberal democracies. Yet from a commonsense perspective, it is clear that society and the culture precede and shape the individual and that an organism is not just a vehicle for the perpetuation of ‘selfish genes’. Our  culture reads the world so naturally through the metaphor of the machine, it does not strike us  the least bit bizarre to describe the human body as ‘a beautiful machine,’ as a television exercise program did, or two title a popular science  book on evolution and ecology The Machinery of Nature, or to describe the human brain as a twenty-first-century automaton – a computer with hardware and software.

More than three centuries later, this basic modern premise about the simple, orderly nature of reality persists, and though modern physics has moved beyond this type of materialism, a good part of science still approaches the world with the atomistic [I.e, reductionist], mechanistic assumptions laid out by Descartes, Boyle, and others in the Scientific Revolution. Scientists pursuing the human genome project proceeded on the mechanistic expectation that they would find the ‘secret of life’ by mapping the genetic sequences. They assumed that analyzing the parts, the reductionist approach advocated by Descartes, would give them the ‘program’ that makes a person. No doubt the most stunning discovery at the end of this effort has been how little the genetic sequence of DNA reveals about the process that creates an organism. Contrary to expectations that have driven molecular biology since Watson and Crick described the double helix of DNA in 1953, life’s secrets have proved complex rather than simple.

“The revolutionary change that launched the modern era’s radical cultural experiment involved two distinct steps: first, the demotion of Nature into mindless mechanism; second, the bold elevation of humanity vis-a-vis the larger world. Bacon reflects this immodest view of humans when he begins his Refutation of Philosophies with the declaration: ‘We are agreed, my sons, that you are men. That means, as I think, that you are not animals on hind legs, but mortal gods.’ The  upshot was the creation of a yawning chasm between humans and the rest of life. In this dualistic vision, humans, who appeared to verge on divinity, stand starkly opposed to a Nature reduced to malleable matter. Bacon faults the natural magicians of the Renaissance – alchemists and other scientific forebears who studied nature and conducted experiments in the hope of directing natural forces toward human ends – for being too restrained n their collaborative approach to nature. With the new technologies, men could have the power ‘not only to bend nature gently, but to conquer and subdue, even shake her to her foundations.’ Even though his scientific utopia proposed an essentially mechanistic approach to solving problems by breaking them down into parts, Bacon’s writings are full of violent, vivid, sexually charged metaphors in which he often personifies Nature as a recalcitrant woman. [Note: Bacon was also an Attorney General who prosecuted witches.] Promising that the new science would bring about ‘the masculine birth of time,’ he declares, ‘I am … leading you to Nature with all her children to bind her to your service and make her your slave.’ Guided by this overweening ambition, moderns have pursued an extreme, aggressive, grandiose notion of dominion – Dominion with  a capital D.

“The image of the world as a machine meshed well with Bacon’s program to regain Eden by extending human control over nature. Transforming animals, plants, and natural systems into automata did more than banish bothersome  scruples and reverence; it made the enterprise of science and the dream of human control seem possible. Machines after all,are human creations and are by design under human control. Unlike a living nature, machines do not change in unpredictable ways. If the world is imagined as a giant clock, that suggests it is simple, orderly, predictable, fully comprehensible, and open to manipulation. By taking a machine apart, it is possible to understand fully how it works. The Eden that Bacon aimed to recover bore little resemblance to visions of a peaceable kingdom where the lion lies down with the lamb and humans live in democratic fellowship with the animals. In Bacon’s version, the recovery of Eden did not promise a return to some original harmony, but rather the attainment of absolute power. This is Eden as empire rather than garden – a realm where humans, who are emphatically not a part of nature, would rule as foreign tyrants over alien subjects. Fantasies of omnipotence, autonomy, and human apotheosis have been the fevered ‘dreams of reason,’ as Rene Dubos put it, and the shaped the modern cultural map as much as the ‘death of nature’.”

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