The Fallacy of Complexity

Posted on April 18, 2017 by Doug Marman

By Doug Marman

Even the simplest organisms are amazingly complicated. This is why scientists who focus on the origin of life often study complexity. They try to find ways that intricate patterns can emerge from simple algorithms. They hope that this will give us clues on how cellular life evolved. This is a fallacy.

The mistake comes from confusing complexity, in general, with the specific kind of intricacies we find in living things. There is so much vague thinking about this subject that many scientists think that generating any kind of complexity can help solve the mystery of life. Countless hours have been wasted on this pursuit.

Professor Sharon Glotzer talks with some engineering students. Photo from University of Michigan.

A recent article raises this issue again. “A ‘Digital Alchemist’ Unravels the Mysteries of Complexity” describes the fascinating work of Sharon Glotzer and her 33-person team, at the University of Michigan.

Glotzer uses computer simulations to study emergence — the phenomenon whereby simple objects give rise to surprising collective behaviors. “When flocks of starlings make these incredible patterns in the sky that look like they’re not even real, the way they’re changing constantly — people have been seeing those patterns since people were on the planet,” she said. “But only recently have scientists started to ask the question, how do they do that? How are the birds communicating so that it seems like they’re all following a blueprint?”[1]

Glotzer specializes in the way inert shapes can naturally align to create surprisingly complex patterns.

For example, if you have a room full of spheres, all the same size, they will naturally assemble into a simple lattice pattern. You only need to shake them gently and they will fall into this simple repeating pattern. What Glotzer discovered is that if you start with other shapes, such as pyramids, made from triangles on all sides, they produce quasi-crystalline patterns that never repeat. Simple shapes can produce surprisingly complex patterns.

Glotzer sees this as a potential new insight into the origin of life. She said:

Most scientists think that to have order you need chemical bonds — you need interactions. And we’ve shown that you don’t. You can just have objects that, if you just confine them enough, can self-organize… So it’s a completely different way to think about life and increasing complexity… I know because I’ve done this, that I can take a bunch of objects and put them in a little droplet and shrink the droplet a little, and these objects will spontaneously organize. So maybe that phenomenon is important in the origin of life, and I don’t think that’s been considered.

This insight about the patterns created by different shapes is valuable for the work that Glotzer does: creating new materials through molecular engineering. Unfortunately, it isn’t going to helps us solve the mystery of the origin of life because it displays the wrong kind of complexity.

This simple mistake happens far too often. It is time to kill this fallacy.

The reason that even smart scientists fall for this error is that they really don’t understand organic life. They can’t explain how even the simplest cells survive. Physics and chemistry don’t give us the tools needed to illuminate the secret of life.

What happens when we face something unknown, something we don’t understand? We naturally compare it to things that we know. That is why scientists keep trying to see if mechanical reactions can explain life.

Unfortunately, this doesn’t help, for a simple reason: Life is complicated in a special way that machines can’t achieve. Once you see this, you will realize why all of the games with computer algorithms, looking for ways to create complexity, are a waste of time.

To understand this, let’s start with one of the best introductions to this problem and how it relates to the origin of life. In Richard Dawkin’s book, “The Blind Watchmaker,” he asks:

So, what is a complex thing? How should we recognize it? In what sense is it true to say that a watch or an airliner or an earwig or a person is complex, but the moon is simple?[2]

Dawkins takes us down this path to show that we have to throw away many of the simplest ideas about complexity if we want to get at what really matters. For example, the moon is simple because it is one homogeneous thing, like a bowl of milk or the endless sands in the Sahara desert. Dawkins suggests that we need a system with many different elements. That is the kind of complication we are looking for.

However, this isn’t enough. A mountain, like Mont Blanc, is made up of many different types of rocks. And every area of Mont Blanc is truly unique and distinct from every other, making it far from simple. But this doesn’t resemble the patterns we find in organisms.

Mont Blanc, the highest mountain in the Alps. Photo from Wikipedia.

He then asks if we can get closer to the mystery of life by looking at probabilities. What if we say something is complex only if it has an arrangement of many different elements in a way that is highly improbable?

[I]f you take the parts of an airliner and jumble them up at random, the likelihood that you would happen to assemble a working Boeing is vanishingly small. There are billions of possible ways of putting together the bits of an airliner, and only one, or very few, of them would actually be an airliner. There are even more ways of putting together the scrambled parts of a human.

This approach to a definition of complexity is promising, but something more is still needed. There are billions of ways of throwing together the bits of Mont Blanc, it might be said, and only one of them is Mont Blanc. So what is it that makes the airliner and the human complicated, if Mont Blanc is simple?[3]

In other words, the complexity we are looking for can’t be found by just throwing things together. We need to see something more than just an accumulation of parts.

This shows why Glotzer’s discovery is not going to help. She researches the results of tossing things together. Yes, they can make amazing patterns that never repeat, which are fascinating, but it is still just a pile of parts. By itself, this pile doesn’t do anything special.

Therefore, it isn’t the improbability of a non-repeating pattern that we are looking for. We need something more. As Dawkins says:

If we see a plane in the air we can be sure that it was not assembled by randomly throwing scrap metal together…[4]

Intentional flight requires a different type of complexity. A plane allows people to travel around the world. That is what jumps out at us. Jets can’t be created by just throwing things together and hoping that something special is going to emerge.

But this is where I part ways with Richard Dawkins, because even this isn’t the kind of complexity we are looking for in living creatures. Why? Because planes are designed and constructed by human beings from a plan, from a blueprint. On the other hand, multicellular creatures, such as animals, fish, even trees and plants, develop from single cells, into complex bodies, made up of many organs that work intricately with each other. We don’t see the same thing in even the most sophisticated machines.

Can we explain the difference between the complexity of machines and organisms? Let’s look.

Planes don’t grow from seeds. That’s one difference. Here is another, plants and animals are not assembled by outsiders.

Airliners don’t seek for food or fuel on their own, while creatures are able to overcome incredible obstacles to find nutrition. Jets don’t develop unique ways of defending themselves from predators. And planes don’t reproduce by mating with other aircraft, or by dividing into two.

Organisms clearly show us a different kind of complexity than machines. Scientists keep trying to treat creatures as if they are sophisticated machines, but the metaphor fails in important ways. For example, biologists have been forced to abandon the old idea that DNA contains a blueprint for constructing the body of animals. It simply doesn’t work.

When DNA was first discovered, biologists expected to find one gene for every protein and enzyme needed in the human body. Once they mapped the whole genome, however, they found that there aren’t even close to enough genes to pull this off.

Every gene is involved in multiple roles. They also need to work with countless other genes. Many times, parts of one gene are used with parts from another, to get what is needed. And genes are turned on and off from outside the DNA.

Look at trees. They don’t follow a blueprint or a plan. That’s why the branches, leaves, and seeds emerge spontaneously at different places, making each tree unique. The blueprint idea simply doesn’t work as an explanation. This is one of the many failed attempts to compare living things to machines.

So we need to find a different kind of complexity than we see in machines. How do we describe this difference? Here is one way: You can’t take a creature apart to study how all of its organs and cells work together. If you try to do this, you will kill it.

That leads us to an even bigger difference: If a bird dies, it can no longer fly or search for food. Its body is just as complex as it was the moment before it died, but now it no longer hops on its feet, flaps its wings, or sings.

Robert Rosen’s description of complexity brings us closer to the mystery of life that we are searching for: A living organism is a system that cannot be fully explained by reducing it to its parts because it can only live when its parts work in a relationship with each other as a whole.

Rosen puts it this way:

It has turned out that, in order to be in a position to say what life is, we must spend a great deal of time in understanding what life is not. Thus, I will be spending a great deal of time with mechanisms and machines, ultimately to reject them, and replace them with something else. This is in fact the most radical step I shall take, because for the past three centuries, ideas of mechanism and machine have constituted the very essence of the adjective ‘scientific’; a rejection of them thus seems like a rejection of science itself.

But this turns out to be only a prejudice, and like all prejudices, it has disastrous consequences. In the present case, it makes the question ‘What is life?’ unanswerable; the initial presupposition that we are dealing with mechanism already excludes most of what we need to arrive at an answer. No amount of refinement or subtlety within the world of mechanism can avail; once we are in that world, what we need is already gone.[5]

This helps us see the enigma of life more clearly. This is the puzzle we need to solve. Now that we understand the mystery we are up against, it is easy to see why most discussions about complexity and the origin of life completely miss the point. Complex mechanisms and chemical reactions are not enough. Even random events won’t help because the puzzle we need to solve is to explain what makes living things alive.

No one has found a mixture of chemicals that alters its course, avoids threats, or replenishes itself. Chemical reactions simply stop when the energy driving them runs out. Then where does the remarkable desire for life come from?

A crystal, a candle flame, a hurricane, or a Bénard cell does not seek resources when the material conditions for continued catalysis runs out; they cease. Living things do so until all options are exhausted. Some of the simplest organisms engage in surprisingly elaborate behaviors to forestall cessation.[6]

How did a self-organizing, autocatalytic chemical system come to persist in such a way that it could be described as self-preserving…? We do not know. Moreover, we do not appear to be overly concerned that we do not know. The answer cannot be, it just did.[7]

One way to make this point even clearer is by distinguishing between “self-ordering” systems and the kind of organization that we see in living organisms, where cells and organs form responsive relationships, as they work with each other toward a common goal.

Self-ordering should not be confused with self-organization.[8]

A flame on a candle, the vortex that forms in tornados and hurricanes, and crystalline shapes are all examples of self-ordering. They are all the result of physical dynamics that can be explained with physics and chemistry.

No truly sophisticated function has ever arisen from self-ordered states.[9]

Living organizations are different. They require relationships between responsive life forms. For example, human beings work together for a common purpose. Cells and organs work together as a whole. And flocks of starlings fly together as a group. These types of living organizations can’t be explained by simple cause and effect mechanisms or principles of chemistry.

Swarm of starlings. Photo from Wikipedia.

What Glotzer is talking about is clearly self-ordering, not self-organizing. Glotzer’s work is fascinating, but there is no great mystery in the way objects self-order and arrange themselves. This isn’t going to help us solve the enigma of life. Even a well-planned blueprint isn’t enough.

Living organizations and living organisms have a special form of complexity that can never be fully understood by taking them apart.

[1] Natalie Wolchover quotes Sharon Glotzer, “A ‘Digital Alchemist’ Unravels the Mysteries of Complexity,” Quanta Magazine, March 8, 2017.

[2] Richard Dawkins, The Blind Watchmaker (New York: W. W. Norton & Company, 1986), p. 6.

[3] Richard Dawkins, The Blind Watchmaker (New York: W. W. Norton & Company, 1986), p. 7.

[4] Richard Dawkins, The Blind Watchmaker (New York: W. W. Norton & Company, 1986), p. 8.

[5] Robert Rosen, Life Itself: A Comprehensive Inquiry into the Nature, Origin, and Fabrication of Life (New York: Columbia University Press, 1991), p. xv-xvi.

[6] Lyon, “To Be or Not To Be: Where Is Self-Preservation in Evolutionary Theory?” Major Transitions, p. 106.

[7] Ibid., p. 122.

[8] Abel DL, Trevors JT. Self-Organization vs. Self-Ordering events in life-origin models. Physics of Life Reviews. 2006;3, page 211. Also available from http://lifeorigin.academia.edu/DrDavidLAbel.

[9] Abel, DL. Life Origin, A Scientific Approach, edited for the non-scientist. Available from http://lifeorigin.info/whats-the-difference-between-self-ordering-and-self-organizing.html – _ENREF_21

How Can Anything Be Half-Alive?

Posted on August 22, 2016 by Doug Marman

By Doug Marman and Alan Rayner

(This article has also been published on BestThinking.com: https://www.bestthinking.com/articles/science/biology_and_nature/genetics_and_molecular_biology/how-can-anything-be-half-alive-)

A new understanding of biology shows that life originates in a community and that individuality evolves when beings work together.

Cells that spawned all of life on our planet appear to have lived in hydrothermal vents. Image courtesy of NOAA.

Recently, we published a paper showing a new way of looking at the foundation of life: as a relationship between a lifeform and its habitat. If we use this lens, the origin of life suddenly makes a lot more sense.

Now here comes a new study that’s been reported in The NY Times, Smithsonian.com, The Christian Science Monitor, Independent and others, that identifies the genetic makeup of the cells from which all life on this planet descended. These mother cells are called the “Last Universal Common Ancestor” (LUCA). But the microbiologists who reported this news went on to say that it appears as if LUCA was only “half-alive.” How can anything be half-alive?

The scientists made this claim for a reason, because they see DNA as a building block of life. You see, a cell’s structure and function is dependent on proteins, and the genes in DNA guide the manufacturing of proteins. This allows a cell to build its own body. But LUCA was missing the genes needed to create crucial proteins. In other words, its genome was incomplete. So it appears that LUCA was dependent on its surroundings to supply the necessary materials.

Does this mean it was half-alive? No. All living things depend on their neighborhood, as we showed in our previous article. No lifeform is an island because life doesn’t belong to it alone. Living is a relationship—a continual give-and-take—between organisms and other living creatures in the world around them. This is why their bodies are porous and fluid. The expressions of other life forms nourish us, and the wastes and breaths we expel are food for others. Being alive is a shared experience.

The problem is that we don’t have a scientific explanation for what living is. And since we don’t understand how it works, we revert to old lenses. This is why many who study the origin of life look for cause-and-effect reactions learned from physics and chemistry, even though it’s clear that this approach falls short. Using the wrong lens, unfortunately, can also distort the picture.

Saying that LUCA was half-alive makes no sense. It’s like saying a woman with an unfertilized egg cell is half-pregnant and she becomes fully pregnant only when she gets the necessary ingredients from a sperm cell. That’s ridiculous. There is no such thing as being half-pregnant. There is no such thing as being half-alive. And there is no such thing as independent living because all creatures depend on others to thrive.

Complete independence would only be possible if a creature, by itself, created everything it needed to be alive. That’s impossible. Why? Because living means gathering and using energy, and nothing can create all of the energy it needs, by itself.

Where does energy come from? For life on Earth, our sun is the main source, but long ago the heat within our planet was also an important element. The molten core created deep sea ‘hydrothermal vents,’ and this is where LUCA appears to have survived.

However, this doesn’t tell us fundamentally where energy originates. To understand this, we can’t use the traditional physics that we learned from Isaac Newton, where external forces move lifeless matter. Instead, we must turn to quantum mechanics, which shows us that what physicists call ‘forces’ emerge from invisible, shared exchanges between ‘particles’.

Different types of relationships between particles lead to different types of energy.[1] For example, electricity and magnetism are the result of particles forming mutual one-on-one relationships with each other. Organisms display the same trait. Even we, as human beings, feel the power of attraction and repulsion when meeting people. We call it ‘chemistry’.

A second type of relationship leads to an attraction that pulls groups of particles to work together. The bodies of protons and neutrons are formed this way, when three quarks begin spinning as a unified group. And the bodies of atoms are held together by the attraction that emerges from the protons and neutrons that form the nucleus. Physicists call this the strong force. The same unification occurs with living things. We experience the added energy when people work together as a community. And the camaraderie we feel with co-workers is the same feeling of inclusiveness that pulls cells together to work as a body. This is why we see a relationship between living things and their habitats at the heart of every ecosystem.

Therefore, life is expressed through relationships.

All lifeforms live as members of a community. Painting by Alan Rayner.

This insight paints an inspiring new picture of how the first cells came into existence. There was never a time when ‘lone wolf’ bacteria lived in an empty, inert world because the world we live in is just as much alive with energy as we are. Our desire to live emerges from our relationships with a living environment. This means that the process of evolution is not something that happens to individuals—it is the community and their relationships that evolve.

Imagine being the only person in the world. You have no friends, family, or anyone to talk to. Would you ever want to develop a new business? Would you feel the need to learn how to read or write? Does it matter how much money you have?

Now think about what you look forward to when waking up in the morning. Isn’t your involvement with other living beings most important? Relationships are the medium of life.

Once we see that this is the essence of living, we have a new lens that reveals deeper truths behind the story of life.

For example, it helps us understand how life developed before genes existed. As we showed in our previous article, if you remove DNA from a cell, the cell will continue living for a while. It can’t reproduce, and it can’t replace or repair proteins, but it’s still alive. This proves that genes aren’t necessary for life to exist.

On the other hand, if you take DNA out of a cell—its habitat and home—it becomes a mere chemical compound. It doesn’t do anything special. In other words, DNA comes into life when it’s in the right ecosystem. If this is true, then this applies to all of the enzymes and proteins in a cell. That is why they respond to each other and the cell itself. They’re dynamic inhabitants of each other’s neighborhood and the shared space of the cell.

Where does the magic come from that pulls these molecules and atoms together to form a living organism? More than chemical actions and reactions are needed. A mutually inclusive relationship is required. This ‘quantum state’ is why cells work so closely together that they form our human bodies. It’s a natural phenomenon that emerges from group relationships when beings work for a common good.

According to quantum theory, these relationships can’t be explained by their individual components because they’re shared. When quantum particles become ‘entangled,’ an added dynamic exists between them that keeps them allied. This is why dissecting organisms will never show us how life works, because the shared exchanges in relationships are hidden from outsider eyes. Only those involved can feel the fluid cohesion aligning them.

We aren’t the source of our own life. We need oxygen, carbohydrates, fats, and proteins, all supplied primarily by photosynthetic bacteria and plants, in meat, fruit, and vegetables. Other life forms die for us to live, just as the death of our bodies is food for other organisms. How could human beings ever evolve if these other life forms didn’t evolve first?

Even today, life thrives near hydrothermal vents. Image courtesy of NOAA Okeanos Explorer Program.

Biologists are right to say that the first proto-cells—the cells that were not yet able to fashion all the proteins they needed to make their bodies—were dependent on the world around them. If a hydrothermal vent was the source, they were tethered to that vent. They weren’t free to roam elsewhere. Therefore, life was restricted before the necessary genes developed. But this doesn’t mean these proto-cells were half-alive. We have more mobility as human beings today, but we’re just as reliant on our ecosystem. We’ve simply replaced our dependence on a static source of power and materials for dependence on a dynamic neighborhood of cellular life.

This leads us to a question that has stumped biologists: What gave rise to life before cells began to reproduce? In other words, why did living things start creating progeny in the first place? If being alive is the only objective, then why would proto-cells give birth to children? It didn’t help them persist as individuals. In fact, reproduction is an energy-demanding process that requires life forms to expose themselves to risk rather than seal themselves off from the outside world.

Biologists often turn to Darwinism to explain the mysteries of biological life, but this can’t explain what happened before reproduction began and genes existed. Darwin’s theories offer no help in understanding the meaning of life.

But if we accept that life is a relationship between living things and their habitat, then we can see what’s missing from the puzzle: Reproduction develops stronger communities. Remember, proto-cells couldn’t survive on their own. They weren’t foolish enough to believe that they lived independently. They belonged within their neighborhood, like a tree is rooted within the earth.

In other words, they didn’t struggle to preserve their individual lives. They were participating in a shared adventure with others. That is the story of the origin of biological life on Earth.

No wonder they risked their lives and spent their hard-won energy and resources to produce offspring, because this was the only way they could sustain and build the community they were living in. Helping their community helped them blossom as well, strengthening the mutual relationship

Think of human experiences. Do you feel better when you lie, steal, and think only of your own desires? Or do you feel more empowered and healthier when contributing to a purpose larger than yourself? Psychologists have shown that working for families, friends, communities, and companies leads to psychological growth and maturity. Selfish individuals actually de-evolve. They regress psychologically.[2]

Biologists see the same thing. Parasites devolve. They lose genes over time, making them more and more dependent on their hosts.[3] Their lives get smaller. That’s the outcome of selfish living.

This all makes sense if living is a relationship between an organism and its habitat. The source of a creature’s life is the community it lives in, even for humans that are free to move around the planet. The more we work to make a healthier ecosystem—to enrich the world—the more we feel life-energy flowing through us. The reason is because energy flows through mutually inclusive relationships.

Therefore, the origin of cellular life needed more than a source of energy. It also required a place where communities of mutually dependent proto-cells could survive for long periods of time. Yes, they needed the right chemical elements, but they also needed other partial life forms, and they needed millions of years. Only then, as they co-evolved their community, could they start making the genes that would one day allow them to roam freely and spread across the globe. Stronger communities, working together, produced genes that would eventually give cells the freedom and ability to roam.

This reveals a fascinating insight: Individuality evolves when beings work together.

Hydrothermal vents create millions of tiny spaces just right for proto-cells. Reproduced with permission from Deborah S. Kelley and the Oceanography Society (Oceanography, Dec. 2007).

It turns out that deep sea hydrothermal vents were perfect environments for the origin of biological life, because they create millions of small cavities, just right for proto-cells to inhabit. Each cavity was a room with a built-in energy supply, as the warm chemistry flowed through it from the molten core. More importantly, the environment could protect a growing community of genetically incomplete cells. And these vents existed for millions of years.

So the process of life began long before LUCA. Communities grew and evolved gradually over millions of years before giving birth to organisms with mobility. Cellular life then eventually found a way of making their homes in virtually every nook and cranny, from the driest to wettest and coldest to hottest places on the planet.

The simplest expressions of living are in communities. This is and always has been the heart of life. This is why we grow as individuals when we work for the world we live in. We need our habitat and our habitat needs us. It’s a shared relationship—a quantum condition that is invisible to outside observers. We must be involved in this mutual exchange of life or we can’t live in this world. That’s why there is no such thing as being half-alive.

[1] Doug Marman, Lenses of Perception: A Surprising New Look at the Origin of Life, the Laws of Nature, and Our Universe (Washington: Lenses of Perception Press, 2016), p. 242-258.

[2] http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2743415/pdf/nihms115884.pdf

[3] Marman, Lenses of Perception, p. 376-378.

From The Nature of Business

Posted on August 3, 2016 by Doug Marman

What is life?? Let’s take a closer look shall we…
Once upon a time, not too long ago, I had the great pleasure of spending time with Dr Alan Rayner, a first rate scientist and former President of the British Mycological Society. Alan kindly contributed many insights to my book The Illusion of Separation, about how nature really works once we see beyond our acculturation.

This blog post is a guest post jointly written by Alan Rayner (author of NaturesScope) and Doug Marman (author of Lenses of Perception).

In March 2016, a group of biologists led by Craig Venter announced the creation of ‘independently’ living cells with the smallest genome. Their announcement was hailed as a milestone. The big lesson learned by the biologists is that no one can explain why almost one-third of the genes are needed for survival. However, hidden in the subtext of this study, we believe, is an even more important lesson: The most essential ingredient of life may not actually be genes or a substance of any kind, but rather a relationship.

Image of the new freely-living cells with the smallest genome. Image by: Tom Deerinck and Mark Ellisman of the National Center for Imaging and Microscopy Research at the University of California at San Diego.

In the experiment, the biologists started with bacteria that had the smallest genomes they could find. They then began deactivating genes one at a time, to see which ones were needed for survival. If the bacteria lived and kept reproducing, those genes weren’t necessary and were removed. After years of work, the genome was reduced to half its original size. Every remaining gene has been tested. None can be eliminated. Their goal is now to identify the role of the mystery genes. They hope this will give them a blueprint of what is needed for living cells to survive as independent entities.

But there’s more to the story. It turns out that many of the “unnecessary” genes could only be deleted after supplying the petri dish with key nutrients and eliminating potential dangers. As a result, the new cells can no longer survive in the wild because they’ve lost the ability to hunt for food and avoid threats.

Is it fair to say that these are independently living cells? Don’t they need the biologists to feed them and remove their wastes? This is where the story gets interesting.

[To read the rest of this post on The Nature of Business, go HERE.]

From Yahoo Finance News

Posted on July 26, 2016 by Doug Marman

The Fundamental Building Block of Life Is Not DNA, It’s a Relationship, According to a New Scientific Study

RIDGEFIELD, Wash., July 26, 2016 /PRNewswire/ — All origin-of-life theories have a problem: explaining the gap between chemistry and living cells. A new paper by Doug Marman and Alan Rayner offers a solution by posing that the source of life isn’t DNA, proteins, or any other kind of substance, but the relationship between a life form and its environment. This is consistent with quantum physics, where entangled relationships between particles produce states that can’t be reduced. This creates a bridge between particles and organisms.

“It sounds strange that a relationship would be fundamental,” said Marman. “But quantum theory shows that fundamental particles need relationships to exist in this world. No particle is an island; they are also wave-like. Every biologist knows that the same thing is true for living things: they need their habitat to survive. If we accept this relationship as fundamental, it changes the story of the origin of life and what it means to be alive.”

For example, a cell can survive for a while if its DNA is removed. But DNA is inert, a mere chemical compound, on its own. Therefore, DNA is involved in the process of life only when it’s in the right environment, a living cell. The same thing is true for the proteins and enzymes in a cell.

“It’s a theory that challenges some fundamental assumptions most scientists have been holding,” says Jonathan Reams, associate professor at the Norwegian University of Science and Technology, who has been following the discussion between Marman and Rayner that led to their study. “They are at the early stages of exploring the implications of the theory, but what I think many will find interesting is that their insights offer new possibilities for how to address many challenges in society today. I would encourage readers to imagine how they could use this theory in their own work and life.”

About the Authors:

Doug Marman is author of the recently published book: Lenses of Perception: A Surprising New Look at the Origin of Life, the Laws of Nature, and Our Universe. He was Chief Technology Officer of a $1.7B division of General Electric, co-founder of an artificial intelligence business, and inventor with over 30 patents. https://www.bestthinking.com/thinkers/doug-marman

Alan Rayner is a biological scientist, a former Reader in Biology at the University of Bath, and the author of seven academic books. Since spring 2000, he has been pioneering ‘natural inclusionality,’ a new philosophy of ecological and evolutionary diversity and sustainability, based on how we naturally live in the world. https://www.bestthinking.com/thinkers/science/biology_and_nature/ecology/alan-rayner

The Littlest Genome and the Question of Life

Posted on July 19, 2016 by Doug Marman

By Doug Marman and Alan Rayner

(This article has also been published on BestThinking.com: https://www.bestthinking.com/article/display/2677)

Let’s take a look at the experiment. The first thing you should know is that the new cells created by these biologists were NOT made from scratch. No one knows how to do that. Here’s what happened:

They started with bacteria that had the smallest genomes they could find. They began deactivating genes, one at a time, to see which ones were needed for survival. If the bacteria lived and kept reproducing, those genes weren’t necessary and were removed.

Progress was slow, but after many years the genome was reduced to half its original size. Every remaining gene has been tested. None can be eliminated. The biologists can explain what two-thirds of these genes do, but the other third remains a mystery. Their goal is now to identify the role of these mystery genes. They hope this will give them a blueprint of what is needed for living cells to survive as independent entities.

31% of the genes have an unknown function. Illustration by Thomas Shafee via Wikipedia.

But there’s more to the story. It turns out that many of the ‘unnecessary’ genes could only be deleted after supplying the petri dish with key nutrients and eliminating potential dangers. As a result, the new cells can no longer survive in the wild because they’ve lost the ability to hunt for food and avoid threats.

Is it fair to say that these are independently living cells? Don’t they need the biologists to feed them and remove their wastes? This is where the story gets interesting.

You see, the genomes of these cells may be tiny compared to other single-celled organisms, but they are still 200 times larger than the genomes of simple viruses. So they aren’t even close to the littlest genomes.

Outside of a cell, a virus shows no signs of life. Photo by Andrzej Pobiedzinski.

Viruses, however, are not considered independent life forms because they can’t survive outside a host cell. They need a host in which to live, and they need the genome of the host to reproduce. Viruses are nothing like the life forms that live outside of host organisms. That’s why the biologists wanted to study creatures that live on their own. But do they? Is true independent living even possible?

All organisms depend on their environment for energy, carbon, and mineral nutrients to grow and reproduce. No plant, animal, or microbe can survive without this supply. Cutting them off leaves them as inactive as a car without fuel. All biologists know this. But if we consider the implications of this deeply, it frames the question of life in a new way and it opens the door to a new explanation for how biological life may have emerged.

Trees create habitats that team with life. Painting by Alan Rayner, from Mycological Research, 102, 1441-1449.

For example, it shows that treating organisms as if they are self-contained entities, isolated from their neighborhood, is a profound mistake because life doesn’t belong to individuals alone. Life is a relationship between creatures and their environment.

We can’t separate life forms from the habitat they live in any more than we can remove our hearts from our bodies and expect them to keep beating without some external source of support. Organs stop functioning when they’re removed, just as we stop breathing if we’re taken out of the atmosphere created by other living organisms.

If this is right, then finding which genes are necessary for survival will not in itself explain how life works, because genes aren’t the cause.

Look at what happens when DNA or RNA are removed from cells. The cells can live on for a while, but DNA and RNA stop participating in life. They become inactive chemical compounds.

“Removed from the context of the cell, RNA does nothing functional in a biological sense.”[1]

But inside cells, DNA and RNA spring into life. Does this mean they are alive?

This doesn’t sound right if we think of life as something that belongs to individuals. Clearly DNA and RNA don’t possess life by themselves. But if life is a relationship between a life form and the world it is nourished by, then yes, DNA and RNA are involved in life when inside a cell.

This offers a new solution to the debate over viruses: Are they living organisms or just bits of inactive genetic material that activate when they’re in the right cells? Viruses show no signs of life outside of a host cell. But they truly do spring into life-as-a-relationship inside cells.

Seeds remain dormant until they are in the right habitat. Photo by Adyna

Seeds act the same way. If they land on fallow ground with no water, they remain dormant. They need a habitat that welcomes them, to develop.

Are seeds alive before the rain comes? If life is a dynamic, shared relationship between individuals and the world they live in, then we have good reason to say that while seeds are viable, as capsules of living potential, they do not truly come into life until they germinate.

Inactive existence, biologically, is completely different from thriving. The distinction between inert material and active living is the crucial mystery of life we are trying to understand. Seeing it as a relationship completes the picture.

For example, if genes become alive when they’re involved in the life of a living cell, the same can be said for all the other constituents of cellular life, not least the proteins whose two-way relationship with DNA is so central.

This opens a new door on the origin of life. Every day, biologists see the liveliness of enzymes, as they work for the benefit of the cells they belong to. Even atoms are involved, as seen by the way hydrogen moves through ‘proton pumps,’ guided by electrical charges, in a process that is necessary for the respiration of all organic life on planet Earth. In other words, life reaches all the way down, even to molecules and atoms, as long as they are in the right environment.

This shifts the puzzle of life to a new question: How do molecules act in such a directed way, as if they are following a plan? Physics and chemistry alone can’t explain it.

Some scientists propose that self-organizing, self-catalytic chemistry may be the key to explaining the origin of life, but this doesn’t get at the real problem. It doesn’t tell us how molecular reactions alone could ever create something with the ability to preserve life, find food, and avoid threats.

“Scientists don’t have any idea how chemical chain reactions could learn to change themselves or the world around them in order to survive… Why would a mixture of chemicals suddenly produce this behavior?”[2]

But what if cells move our muscles and keep our hearts pumping because they are devoted to us? We would then be the source of the plan they are following. The reason they dedicate themselves to us is because they depend on us. If we die, they die. Our survival is needed for their survival. And we are just as much in need of our cells and neurons to live. This is the relationship we are in. Living is a shared experience.

Which comes first? Photo by Subhadip Mukherjee.

Looking at life this way seems enigmatic. It brings to mind the paradox of the chicken and the egg. In this case we have to ask: Which comes first, a nourishing environment or the forms that spring into life and embody it? But this isn’t a paradox, because relationships don’t need cause-and-effect. They are mutual. They don’t belong to one person or the other, but both together. Once we see life as a relationship, the puzzle is solved. Eggs and chicken need each other. They can’t live independently.

This also resolves the mind-body question that has been hounding philosophers for centuries: How do we control our bodies? We just answered that. Our cells do all the work. No life force needed. They move our bodies toward food, away from threats, and into the adventure of life around us, because our life is their world. We depend on each other. Life is only possible when mind and body work together.

Can we explain how this works scientifically? Yes, we only need to turn to quantum mechanics. We find the same principles at work in the subatomic world. There we see that the force of attraction that holds quarks together and forms the bodies of protons emerges from relationships between quarks. Invisible exchanges between quarks create a shared attraction, a bond. The quarks then stop moving as independent particles. They start spinning as one.[3]

Cross section of a Jasmine leaf clearly shows the cells working together as one organism. Photo by Krzysztof Szkurlatowski.

Doesn’t this sound like cells acting together as one body? And doesn’t the force of attraction between quarks remind us of the attraction we feel in relationships? Something invisible passes between us and others, pulling us together. Our lives then move in synchrony with each other.

This is the nature of relationships. They’re delicate, like the meaning of a poem hidden between its lines. You can’t pull them apart to see what makes them tick. Dissecting organisms will never explain this mystery. It will never reveal the secret because the relationship is essential.

All of this leads us to a strange conclusion: The relationship of life reaches all the way down to fundamental particles, as long as they are involved in the right environment. Does this mean that quarks are also dedicated to us because their lives depend on us? That makes no sense. Quarks may form the bodies of protons, but those protons will continue to survive after we die. Is it only our cells that are bound to us in this way?

No. The key to understanding this is that we are not talking about inert existence, we are talking about participating in the experience of life. This is the only reason that cells are involved in a relationship with us. They don’t just need to exist; they need to live. This is what reaches all the way down.

Looking at life this way seems to be circular, as if it can’t be the full story, until we find the right lens to see it clearly. The authors can attest to this. Both of us took different paths to arrive at this same understanding, but now that we see that relationships are fundamental and can’t be broken down, we see the validity of it everywhere.

We need to stop treating organisms and cells as if they’re machines made up of components driven by external forces. If that is the lens we use, we will never see life as it is or experience what it means to belong to a living world. We will see only the inertness of things. Molecules then become mere objects moved around by chemistry.

Mechanisms can’t help us understand the vitality of life. Quantum mechanics has come to a similar conclusion: Cause-and-effect can’t explain the behavior of subatomic particles. We believe this is the issue that has been clouding our understanding of life.

In fact, the parallels between quantum behavior and biological life seem too strong to be coincidental.

Bee and flowers. Photo by Bruno Schievano.

For example, one of the most fundamental principles of quantum mechanics is that it is impossible to calculate what an individual particle will do next. We can make good statistical guesses, but there is no way to know the actual outcome because it isn’t determined by external influences alone. Mechanical reactions are not the cause.

Don’t we see this same amazing behavior with organisms? Bees and flowers may lead symbiotic lives, but which flower will the bee choose next? No equation can tell us.

The quantum world is stranger than fiction. You might think that every electron is attracted to every proton because they have opposite charges, but this isn’t true. The attraction is completely unpredictable when you look at individual particles. This proves that attraction and repulsion between charged particles are not caused by the electromagnetic force. In fact, the exact opposite is true. Relationships are the true source of all electrical and magnetic phenomena.[4]

Doesn’t this have a striking resemblance to the attraction and repulsion that creatures experience with each other when they bond? We call it ‘chemistry,’ but we aren’t drawn to others because of an external force. It isn’t a mechanical reaction. Attraction emerges. When it’s a shared experience, we accept it as real. This is the nature of relationships.

‘Entanglement’ is another mystery of the quantum world. This is the term used to describe the strange alignment that can form between particles without any physical connection. For example, two entangled electrons will spin in opposite directions, no matter how far apart they might be. How do they know which way the other is spinning? How do they stay aligned? Physicists have no answer. They only know that this is a relationship that reaches across space, as if the electrons share one combined state—a state that is more than the sum of its parts.

This also happens to be one of the most startling qualities of living things: They are more than the sum of their cells and DNA. Organs work together as a single body, as a shared state. In other words, our cells stay aligned because they’re entangled with each other and with us.

Swallowtail butterfly in its natural habitat. Photo by Dale Eurenius.

This brings us to one of the characteristic marks of life: its nested relationships. Genes inhabit cells; cells participate in the life of multicellular organisms; organisms live in communities; communities thrive in ecosystems; and ecosystems work together like organs in the biosphere. At the quantum level, we find quarks combining to form the bodies of protons and neutrons, and those protons and neutrons bond to make atoms.

In fact, one of the oddest anomalies in physics takes this to the lowest level. According to quantum theory, fundamental particles such as quarks and electrons should be dimensionless points. But every test shows that they inhabit a volume in space. The only way to get their equations to give the right answers is to treat the bodies of quarks and electrons as if they are formed by a ‘cloud’ of invisible ‘virtual’ particles.[5]

Thus, in each sphere of life we find individuals ‘entangled’ with a world larger than themselves. And each individual is composed of smaller forms that make up their bodies. This is why we see the nesting of forms all the way down to the level of particles. It comes from the relationship we’ve been talking about, between living things and their environment.

The closer you study these forms, the more permeable their boundaries look, because they’re never isolated from each other or their surroundings. They are inescapably living within the influence of each other.

This is the companionship that we see and experience when we open up to nature. Once this relationship sinks in, it transforms the way we think about the evolution of natural diversity and the place of human beings in this story. It reveals the importance of living co-creatively, sustainably, and compassionately, because we are involved in life together.

“Essentially I think this understanding becomes possible as soon as we STOP thinking of ourselves and others as autonomous, free-willed objects subjected to external administration and judgement, and START thinking of ourselves and others as dynamic inhabitants and expressions of our natural neighbourhood, living within each other’s mutual influence…

“Underlying this move is a simple but fundamental shift in the way we perceive all natural, tangible phenomena, including ourselves…”[6]

Living things all have bodies that are dynamic and permeable for a reason: They’re continually sharing and exchanging with the environment. It’s an amazing relationship, a wonderful dance of give and take that shapes organisms and the world around them. This is what makes life so remarkable.

Looking at it this way, the question—what is life—suddenly takes on a radical new meaning.

[1] Pamela Lyon, “To Be or Not To Be: Where Is Self-Preservation in Evolutionary Theory?” in The Major Transitions in Evolution Revisited, p. 112.

[2] Doug Marman, Lenses of Perception: A Surprising New Look at the Origin of Life, the Laws of Nature, and Our Universe (Washington: Lenses of Perception Press, 2016), p. 392.

[3] Doug Marman, Lenses of Perception: A Surprising New Look at the Origin of Life, the Laws of Nature, and Our Universe (Washington: Lenses of Perception Press, 2016), p. 248-258.

[4] Ibid, p. 239-247.

[5] Ibid, p. 462-465.

[6] https://www.bestthinking.com/articles/science/biology_and_nature/natural-companionship