You Are Nature: Rethinking What It Means to Be Human

Who do you think you are?

If you look down at your hands, you must see human skin, seemingly defining a bounded body. Yet beneath the surface, biology tells a fundamentally different story. You are not an isolated individual, a discrete organism surrounded by an external environment you may call nature. You are a walking, breathing ecosystem, a compound organism forged through billions of years of biological cross-talk, genomic mergers, and microbial partnerships.

What we are is a result of where we come from

Evolution, from Darwin to molecular phylogenetics

More than a century and a half ago, Darwin realized that species were not fixed, that they diverged from common ancestors and became specific to an environment, to a niche. They diversified, forming the shape of an evolutionary tree. That was the new story of macroscopic life, and it deeply changed our sense of self, laying a first brick of understanding of our continuity with the rest of the living realm.

Then came the science of making evolutionary trees by using DNA as molecular evolutionary clocks: molecular phylogenetics. In the late 1950s and 1960s, Crick, Zuckerkandl and Pauling proposed reading molecules as records of the evolutionary past. In 1977, Woese and Fox, using ribosomal RNA as a molecular clock, scrutinized the evolution of the microcosm and discovered a whole new form of life in the microscopic world alongside bacteria and eukaryotes (organisms made of cells with a true nucleus, including all animals, plants and fungi). There was a third domain: archaea. But it’s what came next that revolutionized the perception of the human identity.

Endosymbiosis – the workhorse of our every cell is an engulfed ancient microbe

Virtually every human cell relies on mitochondria, the organelles acting as microscopic powerhouses that run the Krebs cycle to generate ATP, the biological energy currency of life. Mitochondria are shaped like bacteria, they possess their own distinct DNA, they replicate independently via bacterial-style binary fission, and they mirror the structure of ancient prokaryotes. These organelles are different from the others: they keep a small genome of their own, separate from the DNA in the cell nucleus, and they replicate themselves, just like bacteria.

As proposed by evolutionary biologist Lynn Margulis in 1967 (here) and later confirmed by genetic evidence, eukaryotic life arose through endosymbiosis: a mutually beneficial relationship that happened by internalization of a cell by another cell. Roughly 1.5 billion years ago, an ancestral host cell engulfed an oxygen-breathing bacterium. Instead of digesting the microbe, they formed a permanent, synergistic alliance. The host provided food and protection, and the internalized bacterium turned sugar into a great quantity of energy: over 15 times the yield of the earlier biological technology, fermentation. This symbiosis provided a quantum leap in terms of available energy, which gave rise to complex life. In time, the internalized bacteria shed DNA they no longer needed, and became what we call today mitochondria. This story is beautifully told in Microcosmos, 4 billion years of microbial evolution, by Lynn Margulis and her son Dorion Sagan.

We do not merely live alongside microbes: our very cells are a blend. They are microbial chimaeras. Since then, we humans have no choice but to recognize ourselves, and every living eukaryote – every plant, fungus and animal – as compound beings.

“Life did not take over the globe by combat, but by networking” - Lynn Margulis.

Lynn Margulis’s work uncovered a major motor for novelty in life: variation doesn’t only come from minor mutations, but from the acquisition of whole genomes.

And the consequence is that the evolutionary pattern is not a tree, but a web: the branches fuse. Life is intertwined.

Are your genes purely yours?

When you think of what you are, your pure self, you can turn to your genes, your DNA, protected in the shape of chromosomes in the nucleus, into the core of your cells. That must be pure, right?

Well, let’s start with a short detour in the world of microbial genetic information. Bacteria transmit genes in two ways: vertically, when a mother cell splits into two identical daughter cells, or horizontally, when two cells exchange genes, usually in the form of round portions of DNA called plasmids. This is called horizontal gene transfer (HGT), and happens constantly in the microscopic world. E. coli, the most studied bacterial species in the lab, appears to have acquired 18% of its genome by horizontal gene transfer (Lawrence and Ochman, 1998). And an analysis covering over 57,000 gene families from 190 bacteria and archaea showed that at least two thirds of all genes had arrived horizontally at some point in their ancestry (Dagan and Martin, 2007). Nature evolves through interconnectedness rather than isolated branches.

In microbial life, naming species and even strains is extremely difficult, so dynamic is the extent of their swaps.

Eric Alm’s group found HGT to be very common in the human microbiome too, especially among microorganisms inhabiting the same body sites (Smillie et al., 2011).

“These analyses indicate that recent HGT frequently crosses continents and the Tree of Life to connect the human microbiome globally in an ecologically structured network” — Eric Alm.

Everything is connected.

Back in 1970, Jones and Sneath had observed that genes could cross boundaries between species and genera. They wrote that “barriers between species might begin to fall”, and in 1983 Sonea and Panisset argued that bacteria exchange genes so freely that they act as one global community. Genome studies have since shown that HGT reaches beyond bacteria into eukaryotes: about 8% of the genes of bdelloid rotifers appear to have been acquired from bacteria and other non-animal sources (Flot et al., 2013). Bacterial DNA has been reported in human cells too.

“Everyone agrees that puppies are individuals, owls are individuals, humans are individuals, until you consider the disquieting molecular facts. We are mosaics, not individuals.” — David Quammen, from The Tangled Tree

The viral DNA that made natural birth possible

The sequencing of the whole human genome led to some conundrums and unanswered questions. Why do we carry so much “junk” DNA? What are these similar repetitive sequences found in humans, opossums, monkeys, and frogs? Scientists finally understood. Big Aha moment. Viruses.

Sapp reckons that 8% of the human genome consists of remnants of retroviruses that have invaded our lineage (Sapp, 2009; Constantin et al., 2025). Thierry Heidmann from Gustave Roussy found such retroviruses to code for syncytin, a protein so important that mice whose syncytin genes were removed by bioengineering (knocked out) present structural defects in the placenta and can’t give birth. Heidmann understood that the “domesticated” viral genes turned out to be key for two mammalian functions: forming a syncytium between the mother and the fetus to let nutrients and gases seep in and waste seep out, and suppressing the immune reaction that would otherwise expel the fetus as non-self (Heidmann et al., 2009 and 2011). The capability to carry the next generation internally that all mammals share seems to be a trait acquired by viral infection!

“Without viruses, we wouldn’t be born.” – Camille Heisserer, Marc-André Selosse and Jean-Michel Drezen, in Beneficial viruses for plants and animals.

The Microbiome and the Holobiont

Our body is constituted of roughly 30 trillion human cells containing the same 20,000 or so genes that encode what has been thought of as our unique human DNA. It is at the same time home to an estimated 38 trillion bacteria, which make up most of the microbiome and colonize every niche of our gut, skin and mucosa (Sender et al., 2016). Because this microbiome comprises a variety of different species, it brings to the table of your being somewhere between 1 and 4 million genes (Qin et al., 2010). Genetically speaking, even without speaking of your viral ancestry, you’re barely 1% “purely” human. But then, isn’t humanhood defined by its nature as a community?

These microbes are not mere hitch-hikers: they co-evolved with us. We were born in their midst, literally, and this relationality created our physiology: we learnt to welcome the presence of non-virulent microbes by establishing immune tolerance, and they helped us switch off inflammatory pathways. They brought to the table of our digestion a great number of enzymes and largely contribute to the degradation and energy harvest in the gut, leading to the very efficient recovery of 95 to 99% of the energy contained in our food, and to the conversion of fiber into short-chain fatty acids used to feed the cells lining the gut surface. The biochemical cross-talk between our physiology and the microbes is so much of a part of us that when the gut microbial richness is depleted, due to a course of antibiotics, hyper-sterilization, lifestyle, or diet, our body starts to malfunction.

We need exposure to a variety of microbes coming from our parents, from food, from soils, from animals, to prime our immune system, to turn down the inflammation and regulate the gut-brain axis, to produce the signals needed for our metabolism. This is why the exposure to Old Friends (Rook et al., 2003) is so much a part of becoming complete, functioning ecosystems. We no longer speak of “individuals” but of “holobionts”: holos for whole and biont for unit of life.

Ancient wisdom that already questioned boundaries

We usually consider that there is a separation between ourselves and nature, between our species and others, between the living and the inert. We see water in the glass as inert, mineral, non-living. Yet, when we drink it and it becomes a part of our cells and our metabolism, is there a precise moment it becomes living?

This question can be asked of every molecule of our body, from the air we breathe in and out to the food we eat and excrete, the iron from the rock that becomes the heart of hemoglobin, to the hair we wear or cut.

There is always continuity, in time and space.

The nature of everything contains the nature of everything else. A flower could not be a flower if it didn’t have its ancestors, its microbiome to help it access water, nutrients, and regulate its stress, its soil to anchor onto and absorb nutrients and water from, sun to power its photosynthesis, and the insects that made its flowerness evolve for pollinators to land. A flower includes all of the cosmos that made it possible. It is made of all the non-flower elements, as Buddhist mindfulness teaches. This is the essence of non-self: not that we don’t exist, but we don’t exist as separate beings.

When we look at a cloud above the mountain and think “this is nature”, let us ask: when this cloud becomes rain, and the rain becomes drinking water, and the drinking water becomes you, do you feel that you are the continuity of nature? That there is no separation?

In the Buddhist tradition, the Diamond Sutra, whose copy from 868 CE is the oldest dated printed book known, invites us to reconsider four notions:

• there is no separate self
• there is no species separation: human beings are not separate from other species
• there is no life / inert separation: we inter-are with the inert on the planet too
• there is no life / death separation: we go beyond our lifespan (there are aspects of us that were there before our birth, and some that will continue after our death)

Modern science, through genetics and the understanding of microbiomes, now echoes these perspectives. The human species includes countless other species, from the ancestors of mitochondria, to microbiomes populating every corner of our gut, skin and surfaces, to the viruses that made us mammals. There is no separate self, we are multitudes, and everything that constitutes us is literally nature coming in and out of us, from the air we breathe to the water we drink and the food we eat. We are stardust, we are nature, like everything else on the Blue Marble.

Conclusion: A reintegrated sense of self

Microbes are the best teachers for an expanded understanding of our identity: they challenge our need for boundaries and illustrate how deeply and thoroughly everything is connected.

Instead of individuals, we see ourselves as holobionts. We truly are ecosystems, permeated by nature and permeating nature. Interestingly, holobiont literacy was recently shown to increase the sense of nature connectedness (Robinson et al., 2026). Indeed, embracing ourselves as ecosystems moves us away from germophobia and motivates increased contact with nature, both conceptually and concretely. More nature connectedness is also associated with pro-environmental behaviour (Mackay and Schmitt, 2019) and psychological well-being (Barragan-Jason et al., 2023).

If you’ve read all the way, congratulations - you’re likely to have increased your feeling of connection with nature, willingness to spend time outdoors and get exposure to Old Friends and their wide-ranging benefits for your immune and nervous system.

But then, if you’re already nature, where do you need to go? Here’s an idea.