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August 2016
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ESSAY: LINDISFARNE CAFE - Lean Forward, Stand Back:

The Worldview of Lynn Margulis (Scientist)

“In the arithmetic of life, One is always Many.” – Lynn Margulis

Lynn Margulis in the Yucatan, Photo by Amarella Eastmond

Lynn Margulis, biologist and Distinguished Professor of Geosciences, composed a grand and powerful view of the living and the non-living. Integrating the work of obscure Russian scientists, DNA pulled from cell organelles, computer-generated daisies, and the hindguts of termites, her vision was wider in scope and more profound in depth than any other coherent scientific world view. At the time of her death on November 22nd, 2011, it was and is a vision that remains misunderstood and misconstrued by many scientists.

Margulis possessed an uncanny ability to lean forward and see the smallest inhabitants of the Earth, to hover there and then leap back at the speed of thought to conceptualize the entire planet. Lean forward, then stand back. This inner movement, this seeing from soil to space, marked a unique scientific endeavor.

This perspective was earned only through walking through diverse areas of study–geology, genetics, biology, chemistry, literature, embryology, paleontology. Fields that are sometimes separated by an untraversed distance at universities: They are housed in separate buildings which may as well be different worlds. In Margulis, they found agreement and discussion with each other; they were reconnected, just as they are intrinsically connected in nature.

Margulis's journey led her to emphasize in all her scientific work two phenomena: the fusing of distinct beings into a single being, symbiosis; and the interaction of organisms and their environments to create relational “loops” that lead to regulation of many Earth systems, Gaia Theory.

Taken separately these concepts have the ability to redefine, respectively, how we understand organisms and the environment. Taken together, they can redefine our consciousness.

After the Earth was born, give or take a few hundred million years, there were bacteria. Bacteria were here first and are with us still, comprising a major part of the biosphere. They are unseen with the naked eye, they lack nuclei (for this reason, they are called prokaryotes - pro = before,  karyon = nucleus). Their forms were legion and their metabolisms were (and continue to be) strange.

Where life could exist, it did exist in these tiny forms. One of these forms,  thermoplasma, was an amorphous blob. It enjoyed heat and sulfur. The bacteria was quite fond of the stuff we now associate with the devil.

Another bacterium was the spirochete. Familiar to us now as the type of bacteria that cause syphilis and Lyme disease, the spirochete is a curl of an organism; a tremulous and crooked line with no front or back. Margulis studied these strange beings through literature and microscope. From some corner of her intellect, they called to her.

Spirochete, Courtesy of University of California, Berkeley

The thermoplasmid and spirochete of early Earth were neighbors and, in a sense, enemies. Each one would try, when it encountered the other, to consume it. This was a popular notion at the time: meet and consume. Soon enough, encounter after encounter between the two beings led to an unprecedented event: The beings came together to eat each other and decided on marriage instead.

Just what changes happened to cause this friendly ingestion is still unknown.  What is known is that the spirochete didn’t digest the thermoplasmid and the thermoplasmid did not digest the spirochete. 

As Margulis was fond of saying, “1 + 1 = 1.” 

There was a union of the two, resulting in an entirely new being. They were inseparable, literally. The thermoplasmid had a rotor now, and the spirochete had a “head.” A head and a tail: for the first time, beings had direction

Cultural philosopher William Irwin Thompson examines this emergence in his book, Coming into Being. It isn’t that spirochetes couldn’t pursue a coordinate beforebut the asymmetricality of the new, combined entity resulted in a new way of being, completely without reference in the history of life. One end, distinct in form, ingested the food; the other end did the rowing. Both absorbed the nutrition. 

This was a giant step in the evolution of consciousness, and is echoed by all true evolutions in consciousness: The rise of a new way of being, inconceivable to the world that came before.

And soon, other mergers were taking place. Soon, oxygen-breathing bacteria were incorporated by endosymbiosis into this being. Where once oxygen was poison, now it flowed through without harm.

Cyanobacteria, green and photosynthetic, were incorporated in some of these cells as well. Both these symbioses remain visible todayas the mitochondria in all cells (the oxygen-breathing bacteria that became mitochondria) and chloroplasts in plant and some animal cells (the cyanobacteria that led to chloroplasts).

These are ancient partnerships that have never dissolved and which continue to pulse with rhythm, and our existence depends upon them. Human cells reflect these unions, and we breathe plant-respired oxygen.

Margulis, inspired by the work of little-known biologists, revealed and proved these mergers for us. At first, her work was rejected and scoffed at. It did not fit the still-dominant neo-Darwinian paradigm that tells us all evolutionary novelty comes from natural selection acting on genes and the gradual accumulation of random genetic mutation. 

But eventually these symbioses were accepted because they could not be ignored. In a stunning display of reluctance, despite mounting evidence, the spirochetal origin of the undulipodium (sometimes incorrectly called or mistaken for the “flagellum,” though the undulipodium and flagellum are not similar either chemically or structurally) is still contested and sometimes dismissed.

What is unquestionable: bacteria make up the living architecture of our bodies.

They evolved into our cells, and also remain “free-living” in our digestive system. Their spiraling remnants are in our gums, our brains. This means our physical selves are universes composed of the movements, biological agreements, and interactions of these beings.

What can this mean for the individual?

“Identity is not an object; it is a process with addresses for all the different directions and dimensions in which it moves...” Margulis once stated with her colleague Ricardo Guerrero.

And what happens when we are notes, songs, and the notes again?  What happens when we shift our perspective and see that we are cells made out of cells?

        Spirochetes become Undulipodia

As above, so below and as below so above. Margulis, somewhere in the middle, decided to thoughtfully occupy both positions. “Why does everybody agree that atmospheric oxygen...comes from life, but no one speaks about the other atmospheric gases coming from life?” she asked.

Bacteria created a whole other host of these gases, as Margulis knew well from her work. After she found scientist James Lovelock, they worked on making those processes known. Their collaboration resulted in Gaia Theory, which was a disciplinary symbiosisthe theoretical expression of Margulis’s interdisciplinary life.

Gaia is the work of the relational loops of push and pull between bacteria, other organisms, and the environment. The clouds, the atmospheric gases, the pH and salinity of the ocean, and other Earth systems express the “dialogue” between the organisms and the Earth. This dialogue is Gaia Theory. Particularly relevant to these relational (often called “feedback”) loops are the smallest living beings, the bacteria. 

In this dialogue between organisms and earth, the information yielded from and received by the bacteria and environment is absolutely crucial to the existence of life on this planet. Remove the bacteria and everything dies. The world becomes a Mars or a Venus, overtaken by harshness or billowing clouds so thick that everything is obscured. No direction-creating spirochetes and thermoplasma, no respiring green cyanobacteria, no purpose or breath, and there is no biosphere, for they are its regulators.

The science behind Gaia, particularly the science in Lovelock’s formulations, is complex and detailed, not guesswork.  But Lovelock came up with an understandable and accesible metaphor in the form of a computer program called Daisyworld. Daisyworld is not the “proof” of Gaia: Lovelock and his colleague Andrew Watson devised the program to see if living and environmental factors could theoretically interact without intention. This was a rebuff to the many criticisms that Gaia had to act through some sort of new age benevolence.  This view might be acceptable in spiritual circles, but is damning in scientific ones, and so: Lovelock’s little model.

In Daisyworld, there are black daisies, which absorb the sun’s heat, and white daisies, which reflect heat. Both flowers grow and produce offspring, and both have the same thresholds for life and growththey cannot grow at a low temperature and die at too high a temperature. The black daisies, which absorb heat, grow faster in cooler conditions, since the heat accumulates in their petals. White daisies, which reflect the heat, need warmer conditions to produce more offspring and thrive. The sun that shines on Daisyworld is dynamic. It grows in luminosity over millions of years.

Here is Margulis, quoted at length to make clear the results:

“Without any extraneous assumptions, without sex or evolution, without mystical presuppositions of planetary consciousness, the daisies of Daisyworld cool their world despite their warming sun,” Margulis writes. “As the sun increases in luminosity, the black daisies grow, expanding their surface area, absorbing heat, and heating up their surroundings. As the black daisies heat up more of the surrounding land surface, the surface itself warms, permitting even more population growth. The positive feedback continues until daisy growth has so heated the surroundings that white daisies began to crowd out the black ones. Being less absorbent and more reflective, the white daisies begin to cool down the planet...Despite the ever-hotter sun, the planet maintains a long plateau of stable temperatures.”

Many additional factors have been added into subsequent Daisyworld models.  The little world has always displayed a deep relationship between species selection and planetary temperature regulation.

The environment could no longer be seen as a tyrant, lording over selection; it was now a co-evolving field. And all the organisms on the planet are connected by this vast system of regulation and dynamism.  “Gaia,” Margulis’s former student Greg Hinkle said, “is just symbiosis as seen from space.”

Nothing 20 kilometers up or down on the Earth escapes the pulse of collectivity.  Indeed, no action or process is untouched by it, even the action of evolution itself.

Margulis’s answer to evolution was a logical extension of her work: Evolution happened through symbioses and Gaia. That symbiosis caused evolutionary innovation was readily observable in microorganisms, in large part because of Margulis’s work.

But neo-Darwinists such as Richard Dawkins still refused to accept it as true in the case of multicellular organisms, and thus tried and continue to try to discredit the theory.

Unfortunately for them, it’s not so simple: Gaia processes are real and observable (and sometimes referred to as “biogeochemistry,” a term more acceptable to mainstream science). Furthermore, the five kingdoms (bacteria, protoctists, fungi, plants, animals) of life are all touched by symbiosis. 

The bacteria are the symbionts. The protoctists (mistakenly called “protozoa”but they are not animals, so the “zoo” in the word is a misnomer) readily display symbioses. Indeed, symbiogenesis has been observed in the lab. An amoeba population, accidentally infected with bacteria, was observed over long periods of time, and soon enough, the infecting bacteria could not be removed from the infected amoeba without killing the organism.

Since 99.9% of all organisms on the planet are microbial beings, if we’re talking about evolution, we must be talking about microbes. Richard Dawkins himself admitted as much in a recent debate with Margulis at Oxford, when he said he could not claim to know much about life since he knew very little about bacteria.

Animals, plants and fungi readily display symbiotic mergers as well.  It’s not just that all eukaryotic (nucleated) cells are the products of symbiosis. All animals have symbiotic partners in their guts. Remove these symbionts and the animals die. Because of the disparity in size, we have trouble thinking of a rabbit as a symbiont with bacteria, but it is.

Margulis, this time with son and co-author, Dorion Sagan, presents it this way in their book of strange, otherworldly brilliance, Acquiring Genomes:

Darwin’s question about how species originate may be rephrased as: ‘What is passed from parent to descendant that we detect as evolutionary novelty?’  A straightforward answer is, ‘Populations and communities of microbes.'

I call the book’s brilliance “strange” and “otherworldly” because in it, a new view of the world rises to the surface. Acquiring Genomes, along with another of Margulis and Sagan’s books, Microcosmos show us a bacterial view of the world. Bacteria exchange their genes laterally. This means they don’t pass their genomic information only when they reproduce (though this can happen), but also through their existence. Bits of their genomes float in and out of their bodies and into other bacteria. This wasand ishappening all the time. The web of life created by such gene transfers is unbelievably complex and can even be baffling.

Along with the many detailed examples of bacterial mergers at varying levels of cellular complexity, the world revealed by Acquiring Genomes is also a world of mating between distinct phyla (a classification just below “kingdom”e.g. creatures of different phyla vary wildly from one another). This phenomenon, which should not be possible according to scientific orthodoxy, has been shown by UK scientist Don Williamson. 

Again, Margulis’s work has been contested, but she and Williamson have collected vast amounts of data and evidence, including live examples demonstrated in physician and writer Frank Ryan’s The Mystery of Metamorphosis

Many people dismissed Margulis for this large-scale sexual symbiosis, through which genomes are transmitted from one totally different being to another; but most of them have not looked deeply into Williamson’s work, and certainly not his live samples, preferring instead to dismiss without real investigation. Margulis was working on this project at the time of her death, and it remains to be seen whether or not other scientists will champion WIlliamson. Like much of Margulis’s work, it requires the uncommon ability to question basic assumptions to even understand the phenomena.

Mixotricha paradoxa

All her efforts and ideas, those accepted and those still controversial, led Margulis to sharply criticize the standard neo-Darwinist theory of evolution.

It’s not that she didn’t understand it, as some of her critics liked to claim.  Margulis has examined natural selection and genetic mutation carefully. In fact, Gaia theory is an intense examination of natural selection, since Gaia’s processes of regulation are the “natural selectors.” The push and pull of the biota (the total sum of all organisms) and the inorganictheir weaving and separations, their gestures of relationshipset the framework of regulation.  There is no need to be vague about “fitness” and just what the environment “selects” with Gaia in the picture.  Instead, there is something to aim forexploring Gaia’s processes of regulations.

But Gaia, the natural selector, does not create from the top-down alone.  While natural selection can refine all beings, no new species have been shown to arise from the natural selection plus random genetic mutation model. The difference between refinement and speciation is one that confounds and also confuses neo-Darwinists, who cart out example after example of refinement as proof of their theories, not realizing that they are still not indicating true speciation. Darwin himself did this by using dog breeding as evidence for his theory. Alfred Russell Wallace, who co-discovered evolution and whose view differs from Darwin’s in significant ways, referred to this as “unnatural selection” and was keen to note that it could not represent real evolutionary change.

Symbiogenesis may not prove to be the beginning and end of evolution. After all, it does not explain why forms are expressed in the way that they are (e.g. Why should similar gene sets express themselves in one creature as feathers and in another as spores?). These laws of nature remain to be revealed, but have been pursued in innovative ways by thinkers as disparate in time and field as Johann Wolfgang von Goethe (who thought of certain forms as having a “blueprint” of archetypal reality which bloomed into specific forms) and Brian Goodwin (who looked at evolution as a movement of physical and mathematical laws). What is definite is that the merging of beings is key, and symbiogenesis offers a clearly observable alternative to the consistent but woefully incomplete neo-Darwinian paradigm.

The neo-Darwinists were equally critical of Margulis’s work, some going so far as to say she was “corrupted by fame”presumably the slight fame she achieved after she popularized the endosymbiotic origin of cell organelles.   Anyone who knew Margulis laughed at such accusations. She worked in a small lab with a few dedicated graduate students: The lab was small in part because she resisted funding from corporate and governmental agencies that she thought would damage the integrity of her work. Once, she dismissed a potential funder for wanting her to do work whose content could not be disclosed to the public.  “If it’s not public, it’s not science,” she said, and hung up the phone on tens of thousands, possibly millions, of dollars.

The graduate students were dedicated because she practiced science for science’s sake, and was fond of quoting quantum physicist and philosopher David Bohm, who said, “Science is the search for truth...whether we like it or not.”  The truth was Margulis’s concern, not popularity, not big money, and certainly not fame.

Many neo-Darwinist concerns circled nervously around words like “Gaia” and “cooperation” (which Margulis did not like to use). They were, perhaps rightly, concerned that these terms were ripe for religious appropriation. But Margulis herself was outspoken against such mishandling of her research.

Some new-agers love to grasp symbiosis as signifying “altruism” between organisms. But it’s much more complex than thatthere is something “in it” for every symbiont, just as a state beneficial in some way arises out of each symbiosis.  Terms like “altruism” had no scientific value, because they are too single-minded to describe the phenomenon.

New age thinkers also use Gaia as a blanket term. They’ve appropriated it to mean that the Earth is a living organism. Or they refer to Gaia as a “goddess.” This turns Gaia into a sort of Stepford planet by containing its complexity in a simple and inadequate metaphor. This no more grasps reality than “selfishness” does our genes.

Margulis expressed her solution to the error once by saying, “Gaia is not merely an organism.”

The Earth is beyond stale conception. It is more magnificent and active than we can imagine. Gaia is object and process. Gaia houses volcanos and every book, every word on volcanos ever written, and at the same time is those volcanos. It is where our greatest loves live, and where every human heartbeat has ever rhythmically pulsed.  In this new understanding, that something can pulse with life and yet be beyond our concepts of living, those concepts begin to change.

If Gaia is conscious, it possesses a consciousness of a different magnitude, probably of a different order all together.

Richard Dawkins and his pre-cursors like John Maynard Smith, as well as other neo-Darwinist thinkers, could not and cannot understand this lesson: this complexity is impossible to incorporate in a linear and reductive understanding.

Part of their failure lies in a misunderstood version of cause and effect that plagues science.  At a certain level of complexity, somewhere just above a billiard ball clanking into a another billiard ball, cause and effect begins to change its shape.  This change may be realthat is, it may actually shift in its laws and patterns in natureor it may be imagined. In other words, it may demand a different sort of thinking.  Effectively it doesn’t matter, since we need to contend with the shift in our thinking. To encompass complex systems with our thinking, we must imagine a model that is less like “cause-effect” more like “being-manifestation.”  That is, multiple layers and numerous agents of forces unconsciously conspire together, and their conspiring is so intermingled, that it is simultaneously cause and effect, and thus beyond both.  For example, the being, or process of Gaia manifests itself as an unstable, constantly correcting level of oceanic salinity.  One cannot be said to cause the other, since the oceanic salinity interacts so deeply with the beings and environs from which it arises. Symbiosis and biological forms demand the same sort of thought.

A week before Margulis died, she and I spent a few days together. She expressed again and again her misgivings about Dawkins and his theories. Indeed she talked more about disproving neo-Darwinism than any other scientific project. Perhaps this was because I was interested in hearing about it, but it was clear to me that the battle between her and Dawkins wasn't merely a scientific disagreement.

She viewed this clash as intimately intertwined with her work and a deep motivator of it. Disproving the false theory of evolution and getting the academy to admit her work was correct was one of her biggest projects because it would have been a triumph of the true spirit of science: in which an old theory gave way to a new and richer one. Because she loved real science, far from being a footnote in her life, the clash was one of her highest concerns.

 At the time of her death, Marguliswith her handful of graduate students and a clutch of international scientists as collaboratorswas researching cures for Lyme disease and reassessing how treatable syphilis is (both Lyme and syphilis come from spirochetes, which Margulis probably knew more about than any other scientist); she was also writing a book on Emily Dickinson. Her projects often had the unsettling side-effect of forcing us to reexamine our most cherished presumptions. In other words, she was a true materialist whose work produced spiritual effects.

“In the arithmetic of life, One is always Many. Many often make one, and one, when looked at more closely, can be seen to be composed of many,”  said Margulis and Guerrero.  Being able to move from one perspectival state to the next--this is a sort of mental phase transition that is necessary to understand life, evolution, and the environment. It is the sort of thinking Goethe advocated, a thinking whose movement mirrored the movement of life itself. 

Margulis grasped this before us. She has done more than any other scientist in recent history to expand and explain this. It isn’t always easy to grasp her thinking, nor to rise to the challenges of it.  It is much easier to dismiss complexity and reduce ourselves to smaller ideas. 

It remains our choice to catch up with what Margulis and her life’s work have set in motion. To do so, we must continue to bring together the many fields of knowledge she embodied.  Biologists must talk to physicists, virologists must talk to geologists, cosmologists must talk to microbiologists, and scientists must talk to non-scientists.  This motion of meeting and exchanging ideas, if we act with it, will evolve our thinking.


Asikainen, C. E. and Krumbein, W. E., edts., 2011, Chimeras and Consciousness: Evolution of the Sensory Self.  Cambridge:  MIT Press.

Capra, F., 1996, The Web of Life: A New Scientific Understanding of Living Systems.  New York: Doubleday.

Margulis, Lynn, 1998, Symbiotic Planet: A New Look at Evolution. New York: Basic Books.

Margulis, L. and Sagan, D., 2002, Acquiring Genomes: A Theory of the Origin of Species. New York: Basic Books.

Ryan, F., 2011.  The Mystery of Metamorphosis: A Scientific Detective Story.  White River Junction: Chelsea Green

Sapp, J., 1994, Evolution by Association: A History of Symbiosis. New York:  Oxford University Press.

Thompson, W.I., 1998, Coming into Being: Artifacts and Texts in the Evolution of Consciousness.  New York:  St. Martin’s.

Thompson, W.I., edt., 1991, Gaia 2: Emergence: The New Science of Becoming. Great Barrington:  Lindisfarne.

Thanks to the students of Margulis Lab.

Lynn Margulis and Andre Khalil

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Andre Khalil, Contributing Writer


Andre Khalil is a writer, an anthroposophist, and a lecturer. He's been a college English instructor, a gay adult film actor, and a bookstore clerk.  He runs a Rudolf Steiner spiritual science discussion group at his home in San Francisco. He recently finished his first play, The Contradiction, which is in rewrites for production. He's currently working on a podcast series featuring discussions with leading thinkers in science, art, cultural criticism, and spirituality. Contact him for lectures, more information, or just to say hello at:
Or visit his blog connerhabib.wordpress.com


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