How Can Anything Be Half-Alive?

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.

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.

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.

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).

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.

The Littlest Genome and the Question of Life

By Doug Marman and Alan Rayner

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

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.

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.

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.

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.

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.

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 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.

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.

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.

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.

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