This interview is a dramatised reconstruction based on historical sources, not a transcript of actual words spoken by Lynn Margulis, who died in 2011. It represents an informed imaginative engagement with her documented scientific work, public statements, and historical context, designed to make her complex legacy – her revolutionary contributions and her significant errors – accessible to contemporary readers through dialogue.
Lynn Margulis (1938–2011) was an American evolutionary biologist whose endosymbiotic theory fundamentally rewrote our understanding of how complex life originated on Earth. She proposed that the mitochondria and chloroplasts within our cells were once independent bacteria that merged with primitive cells through symbiosis, challenging the prevailing assumption that evolution was driven primarily by competition. Her revolutionary work faced rejection from nearly fifteen journals before publication, was ignored for a decade, and then became foundational to modern cell biology – a vindication that earned her election to the National Academy of Sciences, the National Medal of Science, and the Darwin-Wallace Medal.
Today, as we sit down with Lynn Margulis – we encounter not a distant historical figure but a living intellect, still animated by the questions that consumed her: How did complexity arise? What role does cooperation play in evolution? And why do scientific communities resist paradigm shifts even when evidence demands them?
Her story matters now more than ever. In an age of interdisciplinary science, climate crisis, microbiome research, and the need to understand Earth as an integrated system, Margulis’s insistence on symbiosis, cooperation, and systems thinking has become prophetic. Yet she remains overlooked in popular culture, her name absent from most people’s knowledge of biology, even as her theories appear in every textbook. This interview seeks to recover her voice – scientific, combative, brilliant, and unapologetically complex.
Dr Margulis, thank you for meeting with us today. I want to begin by acknowledging the strangeness of this conversation – it’s December 2025, fourteen years after your death in 2011. You’re joining us from a kind of speculative space. How does it feel, looking back at the trajectory of your ideas?
Well, that depends on which of my ideas you mean, doesn’t it? If you’re asking about endosymbiosis – mitochondria and chloroplasts, the whole symbiotic origin of eukaryotic cells – I’m delighted. Vindicated, even. Every cell biology textbook now contains what was rejected fifteen times. That’s extraordinary. That’s not luck; that’s how science should work when you’re right.
But if you’re asking about the other things – AIDS, 9/11, some of my more speculative positions – I suspect the tone of this future is rather different about those matters. And rightfully so. I made errors in judgment there, though I maintain that’s not the same as abandoning scientific inquiry. But that’s a conversation for later, I think.
The truth is, looking back at the arc, I see a woman who solved one magnificent puzzle and then spent too long looking for the next one. Sometimes that drive served science brilliantly. Sometimes it led me astray.
Let’s start with the beginning. You were born in Chicago in 1938, came to the University of Chicago at fifteen, earned your BA at nineteen. That’s precocious even by the standards of academic overachievement. What was your childhood like? What made you a scientist?
My father was a lawyer, my mother was involved in education and progressive causes. Chicago in the 1940s was intellectually vibrant – this was the city of Fermi and the University of Chicago’s physics programme. I was a voracious reader, restless, always asking why and how. My parents encouraged that. They were secular Jews who believed in the power of the mind, believed that intelligence was the currency that mattered.
I was also quite anxious as a child, if I’m honest. Shy. Being precocious is a strange experience – you’re ahead of your age peers intellectually but you don’t understand social dynamics. You’re isolated. Science became my refuge. In a microscope or in a biology textbook, I could understand the rules. Life had a logic.
The University of Chicago was transformative. I studied biology and philosophy, and what fascinated me was the question beneath the facts: How did things originate? Not just what are they, but how did they become? I was reading the evolutionists, but I was also reading philosophy – especially Whitehead and process philosophy. The idea that the world was dynamic, that novelty emerged, that things came into being through interaction – that shaped how I thought about biology.
And I was young. I was nineteen years old, brilliant, arrogant, certain I’d understand evolution better than the textbooks suggested. That confidence – some of it was youthful naïveté, but some of it turned out to be justified.
You were married to Carl Sagan in 1957. You were twenty years old. How did that come about, and what was it like being married to someone who would become the most famous scientist in America?
Carl was a graduate student. I was an undergraduate. He was brilliant, charismatic, ambitious – exactly the kind of man who seems inevitable when you’re twenty. We had our two sons, Dorion and Jeremy. And then it became clear that we couldn’t both be at full throttle intellectually and maintain a marriage. Not in the 1950s. Not with the way society expected women to subordinate themselves.
Here’s what I said about that, and I stand by it: “It’s not humanly possible to be a good wife, a good mother, and a first-class scientist. You have to make a choice.” I chose science. Some people were scandalised. Some people – especially later, after Carl became famous – seemed to think I should be proud to be his former wife. But I had my own work.
The bitterest part is that we divorced in 1964, before Carl became Carl Sagan the public figure. So when people introduce me, they say “Carl Sagan’s ex-wife,” as if that’s my credential. As if my National Medal of Science, my election to the National Academy, the fact that I transformed cell biology – as if all that is somehow secondary to having been married to someone for seven years.
That said, Carl and I remained on good terms intellectually. He understood that I was serious about my work. He never tried to diminish it. And we both came from that tradition of asking big questions about life, origins, the cosmos. He went to the stars; I went to the cells. Both valid directions.
You earned your doctorate in 1965 from UC Berkeley while working at Brandeis. What was your early research focused on?
Genetics and microbiology, particularly Euglena – a flagellated protist. I was interested in organelles within cells, even then. Euglena is fascinating because it has a chloroplast, and I was trying to understand how this organelle worked, how it was inherited genetically. Could it reproduce independently? Did it have its own DNA? These were not easy questions to answer in the early 1960s. DNA sequencing was still years away. Electron microscopy was expensive, not widespread.
But there were hints. There were always hints if you paid attention. Mitochondria had their own membranes – double membranes, actually, which was odd. Chloroplasts had DNA, which nobody expected. Biochemists had shown that certain genetic traits didn’t follow Mendelian inheritance; they seemed to be inherited through the cytoplasm, maternally. Why?
The prevailing assumption was that these were simply compartments that the cell had evolved to compartmentalise functions. Standard cellular evolution – just more complexity developing from less complexity through random mutation and natural selection operating on the whole organism.
But I kept asking: Why do they have their own DNA? Why the double membranes? Why this particular biochemistry?
And then came 1967 – the paper that would change everything. “On the Origin of Mitosing Cells.” Tell me about writing that paper and the process of trying to publish it.
I’d been working on the ideas throughout the early 1960s, reading obsessively – Soviet literature on symbiogenesis, forgotten papers by Boris Kozo-Polyansky, older work by people like Schimper and Mereschkowski. This wasn’t original to me, you understand. But those earlier scientists had been ignored, their work buried, especially the Soviet work because of the Cold War. I was synthesising, reframing, bringing modern genetic understanding to bear on old ideas.
The hypothesis was straightforward: Mitochondria and chloroplasts aren’t compartments that evolved gradually. They’re bacteria. Ancient bacteria that were engulfed by larger cells and became incorporated through symbiosis. Not parasitism – symbiosis. Mutualism. Two organisms evolving together as one. And crucially, this process is reversible in some sense, or at least visible. You can see the evidence in the genome, in the structure, in the biochemistry.
The paper was rejected. And rejected. And rejected. I think it was fifteen journals before Theo Dobzhansky – bless him – got it into the Journal of Theoretical Biology. Do you know what the reviewers said? Not that my data was wrong. But that the hypothesis was “too speculative,” “unparsimonious,” “not supported by accepted theory.” In other words: Your evidence is fine, but we don’t believe the conclusion because it contradicts how we think about evolution.
That’s paradigm resistance. That’s not science; that’s orthodoxy masquerading as science.
Once it was published, what happened?
Essentially nothing. For a decade. The paper came out in 1967. It was ignored. Cell biologists didn’t read it, or they read it and dismissed it as fringe. Molecular biologists thought it was too speculative. Evolutionists thought it was too cellular. It landed in nobody’s domain.
But I kept working. I kept collecting evidence, thinking through the mechanisms, reading everything I could about bacterial evolution, organellar genetics, cell structure. I taught at Brandeis, then moved to Boston University. I was raising four children by then – I’d remarried and had two more sons with Thomas Sagan, my second husband.
And then, in the late 1970s, something shifted. New techniques became available. Genetic sequencing was becoming possible. People started finding mitochondrial DNA, chloroplast DNA. They started sequencing it. And when you sequence organellar DNA, you find something astonishing: it’s bacterial. Not eukaryotic, not derived from eukaryotic genes. It clusters, phylogenetically, with modern bacteria. Not ancient bacteria – modern bacteria still living today. That means the endosymbiotic event happened relatively recently in evolutionary time, and the bacteria involved were related to species we can actually identify.
Around 1978, 1979, the evidence became overwhelming. By the early 1980s, the theory had achieved consensus. It’s now in every textbook. Every undergraduate learns it. My vindication was complete.
Except it took eleven years from publication to acceptance. That’s a long time to be right and ignored. How did that experience affect you?
It strengthened certain convictions and warped others. It convinced me that scientific communities are fundamentally conservative – that paradigm shifts require not just evidence but generational change. That was Kuhn’s insight, and it proved correct. The older generation of cell biologists, trained in the conventional synthesis, retired or died. The younger generation, trained with molecular genetics as a standard tool, could see the evidence more clearly because they had the conceptual framework to interpret it.
It also convinced me that I was right to be rebellious, right to challenge orthodoxy. And that conviction – correct in the case of endosymbiosis – may have made me too willing to challenge other orthodoxies later. It may have created a permanent identification with the outsider role. A vindicated heretic is still a heretic, after all. And heretics don’t necessarily become epistemically humble.
Looking back, I wish I’d learned the right lesson: Sometimes the mainstream is wrong and you’re right. But that doesn’t mean you’re always right. Sometimes you’re just wrong, or partially wrong, or right in ways that still don’t translate to other domains. I didn’t always maintain that distinction.
Let’s explore that. You became committed to neo-Darwinist critiques – arguing that the Modern Synthesis, with its emphasis on random mutation and natural selection, was fundamentally incomplete. You argued that symbiosis and cooperation were as important, or more important, than competition for evolutionary change. Explain that position for someone in 2025 who might be hearing about it for the first time.
The Modern Synthesis – what people usually call neo-Darwinism – was formulated in the 1930s and 1940s by combining Darwin’s natural selection with Mendelian genetics. The idea is beautifully simple: Genetic variation exists in populations. Natural selection favours variants that enhance reproduction. Over time, favoured variants become more common. You get evolutionary change.
It’s elegant. And it explains a great deal. But it treats evolution as something that happens to genes within organisms. Competition between organisms, selection against deleterious mutations, gradual accumulation of beneficial changes. It’s fundamentally vertical – genes passed from parents to offspring. Linear descent with modification.
What endosymbiotic theory showed – what my work showed – is that large-scale evolutionary innovation comes from horizontal transfer. From symbiosis. From cooperation between different organisms. The origin of eukaryotic cells wasn’t millions of small mutations. It was the merger of two different kinds of organisms entirely. A permanent symbiosis that became so integrated that we call it a single organism.
Once you see this, you start noticing it everywhere. Lichens – fungus and algae in symbiosis. Corals and their zooxanthellae. Legumes and nitrogen-fixing bacteria. Mitochondria in your cells. Not rare exceptions. Not minor evolutionary processes. Fundamental.
The neo-Darwinists – particularly people like Richard Dawkins, whom I debated repeatedly – wanted to explain everything through gene-level selection. Selfish genes, they called them. Genes competing with other genes. It’s a metaphor, but it’s a powerful one, and it shaped how people thought about evolution. Cooperation didn’t fit. Symbiosis didn’t fit. The examples I provided were dismissed as minor embellishments on the main process.
I argued they had it backwards. Or not backwards – incomplete. Both mechanisms matter. Competition and cooperation. Vertical and horizontal gene transfer. Individual selection and group-level symbiotic integration. The Modern Synthesis didn’t deny symbiosis existed; it just didn’t see it as central to the evolutionary process. I did. And I think history has vindicated that position.
But the Extended Evolutionary Synthesis – the modern framework that incorporates developmental bias, niche construction, epigenetics, and horizontal gene transfer – suggests that you were partially right. Not entirely right.
Yes. And I can say that now with more clarity than I had then. I overcorrected. I said symbiosis explained “most” genetic variation. That was too strong. What I should have said – what I should have emphasised more clearly – is that the neo-Darwinist focus on competition and random mutation was incomplete. That symbiosis was underappreciated. That cooperation matters.
The Extended Evolutionary Synthesis agrees with that. It’s incorporated horizontal gene transfer, developmental plasticity, holobiont thinking – the idea that an organism plus its symbiotic partners constitute the evolutionary unit. These are Margulis ideas. But the EES also maintains that natural selection on variants is still fundamental. There’s no contradiction there, but I spent so much energy fighting neo-Darwinism that I didn’t always communicate that well.
That’s a failure of communication on my part. I was fighting an orthodoxy, and when you’re fighting, you tend toward overstatement. You make your position sound more radical than it is to make sure people hear you at all.
Let’s talk about the mechanics of endosymbiosis in more technical detail. For readers who want to understand exactly what happened and how we know it happened, can you walk through the evidence?
Absolutely. Let me think about how to structure this clearly.
Start with a simple observation: Look at a cell under an electron microscope. A typical eukaryotic cell – say, a cell from your cheek. You’ll see a nucleus in the centre, surrounded by a nuclear envelope. But you’ll also see numerous small structures scattered throughout the cytoplasm. These are mitochondria. They’re roughly the size of bacteria – a few micrometres – and they have a very distinctive structure: a double membrane. An outer membrane and an inner membrane with folded cristae.
Why a double membrane? Standard cellular organelles – vacuoles, lysosomes, parts of the endoplasmic reticulum – they all have single membranes. They’re vesicles budded off from other membranes. But mitochondria have two membranes. The outer one and the inner one have different compositions, different proteins, different lipids. That’s the first clue: this structure didn’t evolve as a single unit. It’s a composite.
Now, the really striking evidence: Mitochondria have their own DNA. Not much – in humans, about 16,500 base pairs, encoding about 37 genes. But it’s there, circular, like bacterial DNA, not linear like eukaryotic nuclear DNA. And it’s transcribed in the mitochondria. It’s not controlled by the nucleus. The mitochondria have their own ribosomes – ribosomes that are structurally more similar to bacterial ribosomes than to eukaryotic ribosomes.
When you sequence that DNA and compare it to known bacteria, you find it clusters with alpha-proteobacteria. Not randomly. Not with eukaryotic nuclear genes. With alpha-proteobacteria.
Here’s the mechanism: 1.5 to 2 billion years ago – we can date this fairly precisely now through molecular clocks – an archaeal cell, a primitive eukaryotic ancestor, engulfed a bacterium. This wasn’t ingestion followed by digestion. This was ingestion followed by incorporation. The bacterial cell’s outer membrane was dissolved by the host cell’s digestive enzymes, but the bacterial cell’s inner membrane remained intact. So you ended up with a bacteria-derived structure inside a larger cell.
Initially, this was probably parasitic or at best mutualistic in a tenuous way. The bacterium was living inside the larger cell, consuming resources. But over time – and this is where natural selection absolutely does apply – the system became integrated. The host cell benefited from the metabolic activities of the bacterium, particularly its ability to generate ATP through oxidative respiration. The bacterium benefited from the host cell’s protection and metabolic substrates.
Eventually, genes from the bacterial genome began to transfer to the host cell’s nuclear genome. This is horizontal gene transfer, and we can see evidence of it. We find sequences in the nuclear genome that are clearly bacterial in origin. Some of these genes have been duplicated and modified, evolving new functions. Others have been transferred wholesale into the nucleus and that’s where they’re transcribed now – the protein is made in the cytoplasm and then imported back into the mitochondrion.
The process was gradual. It took millions of years. But eventually, the bacterium lost the ability to exist independently. Its genome shrank. Genes that weren’t essential in the protected environment of the host cell were lost. Genes whose functions were taken over by nuclear genes were lost. You ended up with a structure that is, to all intents and purposes, an organelle – a permanent, integrated part of the eukaryotic cell.
But the evidence of its origin remains. The double membrane. The own DNA. The own ribosomes. The phylogenetic relationship to alpha-proteobacteria. These aren’t arbitrary features. They’re the signature of symbiosis, of integration, of two organisms becoming one.
Chloroplasts tell the same story, except the originating organism was a cyanobacterium – a photosynthetic bacterium. You have the same double membrane, the same independent DNA, the same phylogenetic signal. Cyanobacteria sequences in the chloroplast genome. Evidence of horizontal transfer to the nuclear genome.
And here’s the beautiful part: We’re not speculating. We can see this happening in nature right now. There are modern algae that have recently incorporated cyanobacteria as chloroplasts. There are bacteria that are in the process of becoming organelles in other cells. The process that took place a billion and a half years ago is still occurring. We’re watching evolution in action.
That’s extraordinary. And yet, when you first proposed this, even after publication, it was ignored. Why do you think the resistance was so profound?
Because it violated fundamental assumptions about what evolution was and how it worked. The Modern Synthesis was built on the idea that evolution is vertical – genes passed down from ancestors to descendants through reproduction. Mutation and selection acting on those genes. It’s a very individualistic view: organisms compete, variants spread through populations, species evolve.
Symbiosis is fundamentally horizontal. It’s not parent-to-child; it’s organism-to-organism, sometimes across species boundaries. It implies cooperation, integration, merger. And when I started talking about it in the 1960s, there was deep ideological resistance.
This was the Cold War era. In America, we had this narrative of competition, of struggle, of the fittest surviving. We projected that onto nature – “nature red in tooth and claw,” as the saying goes. The idea that evolution might be driven as much by cooperation, by merger, by symbiosis – that was somehow threatening. It sounded too collectivist, too communitarian, too much like communism. I’m not making this up. People really did make those associations.
And there was a genuine scientific conservatism. The Modern Synthesis had just been established as orthodoxy. Any challenge to it seemed radical. The tools didn’t exist yet to prove the hypothesis definitively. You couldn’t sequence DNA easily. You couldn’t track horizontal gene transfer directly. So there was a reasonable scepticism based on the evidence available at the time. But that scepticism turned into dismissal, and dismissal became resistance to new data.
It took genetic evidence in the late 1970s – direct DNA sequencing of organellar genomes and comparison with bacterial genomes – to overcome that resistance. Ideology couldn’t argue with the code itself.
You developed the Five Kingdoms classification system – or rather, you championed and modified Robert Whittaker’s system. Explain that work and why it mattered.
This is one area where history has decided against me, and I can accept that.
Whittaker proposed five kingdoms in 1969: Monera (bacteria), Protista (single-celled eukaryotes), Fungi, Plantae, and Animalia. I adopted and refined this system, particularly emphasising Protista. My book Five Kingdoms, co-authored with Karlene Schwartz, was my attempt to create a comprehensive taxonomy that reflected what we understood about life’s diversity and origins.
The rationale was endosymbiotic. If mitochondria and chloroplasts originated as symbiotic bacteria, then organisms with different combinations of these organelles should be classified differently. Organisms with mitochondria but no chloroplasts – that’s Protista and Animalia and Fungi. Organisms with mitochondria and chloroplasts – that’s Plantae. Organisms with neither – that’s Monera, the bacteria.
It was a system that made sense within an endosymbiotic framework. It classified organisms according to the kinds of symbiotic events they’d experienced. Not just by morphology or ecology, but by their evolutionary history.
But then Carl Woese came along with his three domains – Bacteria, Archaea, Eukarya – based on ribosomal RNA sequences. His work showed that life’s deepest divisions weren’t between plants and animals, but between bacteria, archaea, and everything else. The three domains are now the standard classification, and rightfully so. The molecular evidence is unambiguous.
I held onto the five kingdoms even as evidence accumulated for three domains. That was a mistake. I was attached to the system, attached to the emphasis on symbiosis. But science doesn’t care about your attachments. The evidence was clear: three domains. I should have abandoned the five kingdoms framework more gracefully than I did.
That’s a lesson in intellectual humility. You can be right about something fundamental – endosymbiosis – and still be wrong about other things. Still be overcorrected or stubborn in ways that don’t serve science.
Let’s talk about the Gaia hypothesis, which you co-developed with James Lovelock. What was the core idea, and how did it follow from your thinking about symbiosis?
Gaia is about understanding Earth as a single, integrated system – not metaphorically, but as a practical scientific insight. James Lovelock and I worked together in the late 1960s and 1970s, and what James had noticed was something remarkable: The Earth’s atmosphere is not in chemical equilibrium.
If you were to assemble a planet with no life, its atmosphere would reach chemical equilibrium relatively quickly. Oxygen and methane would combine. Different gases would settle into stable ratios. But Earth’s atmosphere is violently not in equilibrium. Oxygen is present at about 21 per cent – high enough to support combustion, low enough that the whole atmosphere doesn’t spontaneously ignite. Methane is present at levels that shouldn’t exist given the photochemical processes that destroy it. Nitrogen is at high levels despite processes that remove it.
The reason? Life. Organisms – microbes, particularly – are maintaining these ratios actively. They’re producing oxygen through photosynthesis, consuming methane through oxidation, fixing nitrogen, producing sulphur compounds. The entire atmosphere is, in a sense, a bacterial construct. Or rather, a symbiotic construct – bacteria, algae, plants, and other organisms working in concert.
What James and I proposed was that Earth functions as a self-regulating system. Not that the biosphere intentionally regulates itself, as if it had consciousness or foresight – that was the mystical interpretation that drove me absolutely mad. I wrote an essay called “Gaia is a Tough Bitch” precisely to counter the New Age spiritualisation of the idea. Gaia doesn’t care about humanity. She’s not nurturing. She’s a system, governed by physics and chemistry and the actions of billions of organisms.
But within that system, there are feedback loops. Organisms modify the environment. The modified environment affects which organisms can survive. Over billions of years, these feedback loops have created a relatively stable planetary system despite changes in solar output, asteroid impacts, and all manner of disturbances.
This follows directly from symbiosis. If endosymbiotic theory shows that organisms at small scales – bacteria merging to form eukaryotic cells – create integrated systems with emergent properties, then the same logic applies at planetary scales. The biosphere plus the physical systems – the oceans, the atmosphere, the rocks – form an integrated whole.
The scientific reception was mixed. Some scientists saw it as transformative; others thought it was teleological or untestable. What’s your response to those criticisms?
The criticism about teleology – the idea that the system is “aiming” at some goal – was fair when levelled at loose versions of Gaia. If you’re saying Earth deliberately maintains conditions optimal for life, that’s teleological nonsense. But that’s not what the hypothesis says.
What it says is that the biosphere and the physical environment coevolve. Organisms modify the environment; the environment selects for organisms. Over time, you get a system that is stable – not perfectly stable, but remarkably stable given the external stresses. That’s not teleology; that’s feedback and selection.
As for testability – people said you couldn’t test Gaia because you only have one Earth. That’s a lazy criticism. You can test Gaia’s predictions. You can look at chemical cycles, at microbial contributions to atmospheric composition, at the stability of conditions over geological time. You can look at exoplanets and ask whether their atmospheres show evidence of biological regulation. All testable.
But I’ll admit: Gaia became a political and cultural symbol in ways that obscured the science. New Age advocates embraced it as spiritual truth. Climate activists used it as motivation. And scientists, seeing it co-opted, became sceptical of the framework itself.
What’s interesting is that the core ideas – Earth system science, biogeochemical cycling, the integration of biological and physical processes – are now mainstream. Climate science is built on these ideas. The language has changed. We don’t call it “Gaia” anymore; we call it “Earth system science.” But the conceptual framework is sound, and it traces directly back to the work James and I did.
You were elected to the National Academy of Sciences in 1983. How did that recognition feel, given the earlier rejection and dismissal?
Vindication. Absolute vindication. But also, by that point, I’d become accustomed to being right despite institutional scepticism. The NAS membership was wonderful – recognition from the community that matters most, from other scientists at the highest level. It meant something different to be elected by your peers than to have your paper eventually accepted. It meant they understood what you’d done.
And it opened doors. It gave me a platform. After that, when I spoke, people listened – not always agreed, but listened. It made me more willing to take heterodox positions, I think. I had institutional credibility. I could afford to be controversial because the core of my work was established and recognised.
In retrospect, that credibility may have made me overconfident. When you’re right about something as fundamental as endosymbiosis, you start to believe your intuitions about other things. You stop being as careful about evidence. You assume that the same contrarian impulse that was right about symbiosis will be right about other domains.
Let’s discuss your relationship with Richard Dawkins and the broader neo-Darwinist establishment. You had some famous debates with him.
Richard is a brilliant writer and a careful thinker, but he is committed to the gene-level view of evolution. Absolutely committed. He wrote The Selfish Gene, and it’s a powerful metaphor. But metaphors can become prisons. He built an entire framework around genes as the primary units of evolution, and anything that didn’t fit that framework – like symbiosis, like cooperation, like horizontal gene transfer – he treated as secondary or exceptional.
We debated at conferences. I’d present evidence for symbiosis’s role in evolution. He’d acknowledge the evidence but argue it didn’t require abandoning the gene-centred view. And he was clever enough that he could usually make that argument stick with the audience. Gene-level selection plus genes moving between organisms through symbiosis – okay, you can retrofit that into a selectionist framework.
But I thought he was missing the point. The point isn’t that genes are selfish in the metaphorical sense. The point is that the major transitions in evolution – from prokaryotes to eukaryotes, from single-celled to multicellular – happened through cooperation, through integration, through symbiosis. That’s not a minor add-on to the gene-level story. That’s a fundamental process that gene-level thinking obscures.
We were talking past each other in some ways, because we were working at different levels of analysis. Richard was asking: How do genes spread through populations? I was asking: How does complexity arise? He was right that natural selection acting on genetic variation explains population genetics. I was right that symbiosis and cooperation explain major evolutionary transitions.
Both are true. You don’t have to choose. But we were embedded in a culture of scientific debate where you had to choose. You had to win. You had to establish that your framework was the fundamental one. So Richard would fight to maintain gene-level primacy, and I would fight to maintain organism-level and symbiotic integration as primary.
Looking back, I wish we’d been less about winning and more about integrating the two perspectives. But that’s not how science works, or how human beings work, really.
In 2009, you published a paper questioning HIV as the cause of AIDS. This is a sensitive topic, but it’s central to understanding how your reputation shifted. What led you to that position?
I want to be clear about what I was and wasn’t arguing. I was not saying that AIDS doesn’t exist. I was not saying that HIV isn’t involved in AIDS. What I was exploring was whether HIV alone was a sufficient cause, or whether there were co-factors – in particular, mycoplasmas or other pathogens – that were necessary.
The idea wasn’t baseless. There was legitimate scientific discussion about co-factors in AIDS pathogenesis. Peter Duesberg, who became associated with AIDS denialism, was arguing for multi-factor theories. And I thought those arguments deserved engagement rather than dismissal.
But I was wrong. I was wrong in a way that mattered. The evidence overwhelmingly supports HIV as the cause of AIDS. The co-factor theories have been refuted. And more importantly, lending scientific credibility to AIDS denialism – even tentative, exploratory credibility – caused real harm. In South Africa, the government’s denialist position, informed by people like Duesberg and others, led to hundreds of thousands of preventable deaths.
That’s not an abstraction. That’s mass death. That’s a tragedy that could have been prevented if scientists had presented the evidence clearly and unambiguously instead of opening space for “alternative” hypotheses that weren’t supported by the data.
I’d like to say I was trying to maintain scientific open-mindedness, that I was challenging orthodoxy the way I’d done successfully with endosymbiosis. But that’s not the right comparison. Endosymbiosis was a paradigm-shifting idea supported by evidence that the mainstream was too conservative to accept. AIDS co-factors were a scientifically marginal idea without compelling evidence, and I lent it credibility I shouldn’t have.
One of my deepest convictions is that science progresses through challenging orthodoxy. But that conviction can become dangerous if you don’t also have the humility to distinguish between legitimate heterodoxy and pseudoscience. I didn’t maintain that distinction carefully enough in the late 2000s.
Similarly, you made public statements about 9/11 that suggested support for controlled demolition theories. How did you arrive at those positions?
I was wrong. I was wrong in a way that undermined my credibility as a scientist. And I’m not going to defend it or reframe it. Those conspiracy theories lack evidence. They contradict expert engineering analysis. And by endorsing them – even publicly – I added my name and my credentials to a denialist movement that serves no purpose but confusion.
I think what happened – and this is something I can analyse about myself now with some distance – is that I’d developed such a strong identity as the person who was right when everyone else was wrong that I became drawn to all manner of fringe ideas. I’d been rejected, vindicated, celebrated. That vindication felt like proof that my instincts were reliable. That contrarian thinking was my domain. That I could trust my intuition against mainstream expert consensus.
It’s a dangerous psychological place to be. And I went there. I spent years in that place. And it damaged my reputation, my credibility, and my legacy in ways that the endosymbiotic theory accomplishments can’t fully compensate for.
The “communicated submission” incident with Donald Williamson’s metamorphosis paper in 2009 – when you used your NAS position to bypass peer review – fits into this pattern, doesn’t it?
Yes. Williamson’s paper proposed that larval stages in many organisms originated from symbiotic mergers – that caterpillars, for instance, were originally independent creatures that merged with adult insects. It’s a speculative idea with limited evidence. And I believed in it – believed it fit the symbiogenetic framework.
As an NAS member, I could “communicate” papers, meaning I could vouch for them and get them published without normal peer review. I did that for Williamson’s paper. And critics said – rightly – that I was abusing my position. That I was using the academy as a platform for ideas that hadn’t survived scrutiny.
My defence was: Peer review suppresses innovation. Heterodox ideas need platforms. If I don’t use my position to support unconventional work, who will? Institutions become gatekeepers; gatekeepers suppress paradigm shifts.
All of that is true in principle. But in practice, I was wrong. Peer review is imperfect, but it exists for a reason. Most rejected papers are rejected because they’re wrong, not because they’re too innovative. And by bypassing peer review, I wasn’t supporting innovation – I was using my institutional credibility to circumvent quality control.
It’s the same error as the AIDS co-factors and 9/11: Believing that my track record of vindication gave me the right to override normal epistemic processes. It didn’t.
Looking back, do you think early rejection of the endosymbiotic theory created a permanent outsider identity that made it harder to distinguish good science from pseudoscience later?
Yes. I think that’s exactly right. Being rejected, being ignored, being vindicated years later – that creates a very particular psychological state. You learn that institutions are conservative, that consensus is often wrong, that persistence despite rejection is necessary for truth-telling. All valid lessons.
But you also develop an identification with the outsider role. You start to see yourself as the person who knows better, who sees through conventional wisdom, who has the courage to challenge orthodoxy. And that identity can become self-fulfilling. You keep looking for orthodoxies to challenge, even when you should be accepting the evidence.
The tragedy is that I could have had a later career as a respected elder scientist, someone whose ideas had been vindicated and who was now offering perspective on how science actually works, how paradigm shifts happen, how institutions need to balance conservatism and innovation. Instead, I spent my sixties and seventies chasing increasingly fringe ideas, damaging my credibility and overshadowing the legitimate work.
I wish I’d been wiser about that. I wish I’d recognised that vindication doesn’t mean infallibility, that a good contrarian instinct about one thing doesn’t make you a good judge of all things.
What advice would you give to scientists today – particularly women and scientists from marginalised backgrounds – who are challenging established paradigms?
First: Be precise. Know your evidence better than anyone else. If you’re challenging orthodoxy, you need to be right, or at least more right than the mainstream. That’s a hard standard, but it’s necessary. Handwaving and intuition aren’t enough.
Second: Distinguish between paradigm shifts and pseudoscience. Both involve challenging consensus. But paradigm shifts have evidence, even if that evidence is initially contested. Pseudoscience feels liberating – you get to dismiss all the experts, all the institutions. But that feeling is a warning sign, not validation.
Third: Don’t develop an identity around being right. Develop an identity around truth-seeking. The moment you become more invested in winning the argument than in following the evidence, you’ve lost your way.
Fourth: Gender dynamics are real. I was called “unruly,” “difficult,” “combative” – terms rarely applied to male scientists with similar personalities. There’s unfairness in that. The scientific establishment is male-dominated, and women have to fight harder to be heard. But don’t let that lead you to believe that all opposition is sexism. Some of it is legitimate scientific scepticism. Learn to distinguish.
Fifth: Be generous toward your predecessors and peers. I did this work on symbiosis partly to rehabilitate earlier scientists whose work had been ignored or forgotten – Schimper, Mereschkowski, Kozo-Polyansky. That felt important. It still does. Science is a human enterprise with a history. Acknowledge the people who came before. Build on their work rather than pretending you invented everything.
And sixth – don’t become attached to your ideas. Be in love with the problem, not the solution. Be willing to be wrong. Be willing to change your mind when evidence demands it. And be especially willing to admit when you’ve made errors that caused harm.
You worked extensively on five-kingdom classification and on astrobiology – the search for life beyond Earth. How do you see those areas of work now?
The five kingdoms framework lost out to Woese’s three domains, as I said. That was the right outcome scientifically. But the symbiogenetic principles underlying my classification system – the idea that organisms should be understood partly through their symbiotic history – those ideas are more relevant now than when I was defending the five-kingdom system.
As for astrobiology: That work feels vindicated in a different way. We understand now that on Earth, microbial life – bacteria, archaea, protists – are the foundation of all complexity. We understand symbiosis as a fundamental process. We understand that the early Earth was shaped by microbial metabolism. All of that informs our search for life elsewhere.
If we find microbial life on Mars or Europa or Enceladus, the first thing we’ll want to know is: Does it have symbiotic partnerships? Does it carry evidence of horizontal gene transfer? Does it show signs of the kinds of integrations that created eukaryotic complexity on Earth? Those are Margulis questions.
And the climate crisis has validated Gaia’s core insight: Earth system science matters. Understanding how biological and physical systems integrate matters. The atmosphere, the oceans, the biosphere – they’re not separate domains. They coevolve. We’re conducting a massive, unplanned experiment in how much perturbation this integrated system can absorb.
Let’s talk about your children. You had four sons: Dorion with Carl Sagan, Jeremy with Carl, and two more with Thomas. Dorion became a science writer and collaborated extensively with you on books. How was that dynamic – having a son who could engage with your work intellectually?
Dorion is remarkable. Truly. He’s a skilled writer, a genuinely creative thinker, and he understood symbiosis in a way that allowed him to communicate it to broader audiences. Our collaborations on Microcosmos and What is Life? and Acquiring Genomes – those books wouldn’t have been possible without him.
Having sons who understood the science, who were interested in the big questions – that was wonderful. But it also reinforced my conviction that you can’t do serious science and motherhood at the same level simultaneously. Not in the world as it was structured. I made my choice. I had my children, and I raised them – four of them – but I also pursued science at the highest level. Not everyone could do that. Not everyone should have to choose.
What I hope is that the next generation of women scientists – and men, but especially women, because this burden falls disproportionately on women – won’t have to make that choice. That we’ll structure science and society so that you can do both well. Can be a good parent and a first-class scientist. I don’t think that was possible in my lifetime. It should have been. And it should be, going forward.
Your former husband Carl Sagan went on to become the most famous scientist in America. Did that create a complicated legacy for you?
On one hand, Carl’s popularisation of science was extraordinary. Cosmos reached millions of people. He made science accessible and wondrous. That’s valuable. That matters.
On the other hand, when I’m introduced now, even to people interested in science, they often say, “Oh, Carl Sagan’s first wife.” As if my credentials don’t stand alone. As if I’m someone’s ex-wife who happened to be a scientist, rather than a scientist who happened to be married to another scientist.
The injustice – and it is an injustice – is that Carl built a public reputation as the face of science while I did fundamental research that transformed how biology works. Both contributions matter. But one gets the public recognition. And one gets footnoted in relation to the other.
That said, I don’t harbour resentment. We both chose science. We both pursued it relentlessly. We couldn’t maintain a marriage while doing that in the 1950s and 1960s. He went his direction, I went mine. His path was to the public. Mine was to the cells. Both valid.
You received the National Medal of Science in 1999 from President Clinton. That’s one of the highest honours in science. How did that recognition feel?
Like the scientific community was saying: You were right. We know now that you were right. And we honour that.
By 1999, endosymbiotic theory was decades past vindication. It wasn’t controversial anymore. Every cell biology textbook in the world was teaching what had been rejected fifteen times in 1967. So the medal wasn’t vindication – I already had that. It was acknowledgement. The most formal, prestigious acknowledgement possible.
What made it bittersweet is that by 1999, I was already involved in some of the positions – AIDS work, later the 9/11 statements – that would complicate my legacy. The medal acknowledged what I’d accomplished. But it couldn’t protect the reputation I was about to damage.
In 2008, you received the Darwin-Wallace Medal from the Linnean Society – their highest honour, awarded every fifty years. You were only the eighth woman to receive it in its entire history. What did that mean to you?
That may be the honour I’m most proud of. Not because it’s more prestigious than the National Medal of Science – it’s not. But because it specifically recognised evolutionary biology contributions. Darwin and Wallace and the tradition they established. To be recognised in that context, alongside the greatest evolutionary biologists in history, by an institution that goes back to the founding of modern biology – that felt like being woven into the fabric of the science itself.
And the fact that I was only the eighth woman in the entire history of the award? That tells you something about the structures of science. It tells you about who gets recognised, whose contributions get acknowledged, whose ideas become textbook material and whose get footnoted.
I hope that as science progresses, as more women enter every field and make fundamental contributions, awards like the Darwin-Wallace Medal go to more women. Not because women deserve special recognition, but because women make contributions as fundamental as men’s and have always been systematically overlooked.
How do you think your legacy will evolve? What do you hope will be remembered?
I hope endosymbiotic theory is remembered as transformative. Not because I was the only person working on it – I wasn’t. But because it fundamentally changed how we understand the origin of complexity. It showed that the major transitions in evolution don’t happen through countless tiny mutations accumulating. Sometimes they happen through merger, through integration, through organisms coming together to create something new.
I hope the work on symbiosis and cooperation in evolution will be remembered as correcting an overemphasis on competition. Evolution is both – competition and cooperation. Struggle and symbiosis. The full picture is richer and more interesting than neo-Darwinism alone captured.
I hope the historical recovery work – bringing attention to Kozo-Polyansky, Schimper, Mereschkowski – will be remembered as an act of scientific justice. Those scientists had important ideas that were ignored for decades. Bringing their work back to light mattered.
And I hope the errors – AIDS, 9/11, the other missteps – will be remembered as a cautionary tale. Not as reasons to dismiss the fundamental contributions. But as evidence that even brilliant scientists can lose their way. That vindication in one domain doesn’t confer wisdom in all domains. That intellectual humility is essential, especially for people who’ve been right about something important.
If I’m remembered as someone who was right about endosymbiosis and wrong about other things – well, that’s honest. That’s true. And that’s better than being remembered as heroic and infallible. The real legacy is the science. The real contribution is the transformation of understanding. The errors are regrettable, but they don’t erase that.
We’re coming toward the end of our conversation. Is there anything you want to say – anything you’d like to set on the record that we haven’t covered?
I want to say that science is one of humanity’s greatest endeavours. It’s a way of understanding the world through careful observation, rigorous thinking, and collective scrutiny. It’s imperfect. It’s institutional and biased and conservative. But it works. It generates real knowledge.
And I want to say that my life in science – the vindication, the honours, the mistakes, the overreach – was worth it. The work mattered. Understanding how complexity arose, how symbiosis drives evolution, how organisms integrate to create new possibilities – that understanding is genuinely valuable. It changes how we see life, ourselves, our place in the biosphere.
I also want to say that the struggles – the rejections, the battles with orthodoxy, the fight to be taken seriously as a woman in a male-dominated field – those were real. They shaped me. And they shaped the science too. You don’t do revolutionary work by being accommodating and conventional.
But I also want to say that fighting orthodoxy can become a trap. That vindication can be dangerous if it makes you think you’re always right. That being a good scientist requires constantly checking your own certainty, constantly asking whether the evidence still supports your conclusions.
And finally: To the young scientists, particularly women and people from backgrounds underrepresented in science – fight for your ideas. Challenge orthodoxy. Be rigorous. Be rigorous about everything, including your own premises. Don’t let institutional gatekeeping stop you from asking important questions. But also don’t let the identity of being a rebel become more important than the actual evidence. The goal is understanding, not victory. The goal is truth, not vindication.
And if anyone tells you that you’re too difficult, too combative, too unruly – well, that might mean you’re onto something. But not automatically. Check the evidence. Trust the process. And be willing to admit when you’re wrong.
Dr Margulis, thank you. This has been extraordinary.
Thank you for asking questions that matter.
Questions from Our Community
Following the main interview, we received a remarkable response from our international community of scientists, historians, and thinkers who wanted to extend the conversation. The questions below represent letters and emails from researchers across four continents – marine biologists confronting ecological collapse, evolutionary biochemists working with genomic data that has become exponentially richer than what Margulis had access to, historians of science asking uncomfortable questions about ideology and paradigm suppression, astrobiologists wondering whether Earth’s symbiotic complexity is universal or rare, and philosophers of biology probing the structural incentives that shape how science rewards and reinforces certain kinds of thinking.
These five voices – from Brazil, Italy, Norway, Kazakhstan, and Mexico – embody the intellectual lineage that Margulis’s work has inspired. They ask not just about her science but about how vindication shapes a scientist’s psychology, whether our search for life beyond Earth might be blind to what we’re looking for, and what we might learn from observing symbiotic networks collapsing in real time under anthropogenic stress. They also press her on uncomfortable questions: about ideology in scientific history, about the difference between necessary heterodoxy and destructive contrarianism, and about whether the very mechanisms that rewarded her are structurally incapable of teaching humility.
What follows are these five questions, each reflecting a specific dimension of Margulis’s influence and the ongoing work she inspired.
Márcia Campos | 34 | Marine Biologist & Microbiome Researcher | Rio de Janeiro, Brazil
You spent decades arguing that symbiosis wasn’t just a curiosity but a driver of evolution itself. Now we’re finding symbiotic partnerships everywhere – in coral bleaching, in the human microbiome, in plant-fungal networks. But we’re also discovering that these partnerships are fragile. They’re breaking down under climate stress, pollution, and acidification. If symbiosis is as fundamental to life’s stability as your Gaia hypothesis suggests, what does this ecological collapse mean for the future of complexity on Earth? Are we watching evolution’s mechanisms unravel in real time?
Márcia, thank you for this question. It cuts right to the heart of what troubles me most about the world we’ve created.
You’re right that symbiosis is fundamental – not incidental, not decorative, but fundamental to how life maintains itself and evolves. Every major transition in the history of life involved symbiotic integration. Eukaryotic cells emerged from bacterial symbiosis. Photosynthetic organisms emerged from cyanobacterial symbiosis. Multicellular life emerged from cooperative colonies. The biosphere itself – what James Lovelock and I described as Gaia – is a vast symbiotic system where organisms and the physical environment regulate each other.
But here’s what I didn’t emphasise enough, and what your question forces me to confront: symbiotic partnerships are delicate. They require stability. They require time. They require that the partners remain in relationship long enough for the integration to deepen.
The coral-zooxanthellae partnership is instructive. Corals and their symbiotic algae have been integrated for millions of years. They’ve evolved together. The coral provides the algae with a protected environment and access to sunlight. The algae provide the coral with photosynthetic products – sugars, oxygen. It’s mutualistic. It’s integrated. But when water temperature rises even a few degrees, the partnership breaks down. The stress is too acute. The algae are expelled. The coral starves.
This is what we’re watching happen across the globe right now, and it reveals something about symbiosis that my work perhaps didn’t emphasise enough: symbiotic systems have tolerances. They’ve evolved within particular environmental parameters. Push them outside those parameters too quickly, and the system collapses.
The human microbiome is another example. We’ve discovered – and you’re working in this field, so you know this better than most – that our bodies are not individual organisms but holobionts. We are humans plus trillions of bacterial partners. Our digestion depends on them. Our immune function depends on them. Our mental health, it turns out, may depend on them. We couldn’t exist without this symbiotic partnership.
But this partnership is fragile. Antibiotics disrupt it. Processed foods disrupt it. Stress disrupts it. And when it’s disrupted, we get dysbiosis – inflammatory bowel disease, obesity, mental health disorders. We’re learning that many modern illnesses are diseases of broken symbiosis.
Now extend this logic to the planetary scale. The Gaia hypothesis proposes that Earth’s biosphere and physical systems have co-evolved into a self-regulating whole. The atmosphere is maintained at particular compositions by biological activity. Ocean chemistry is maintained by microbial and algal communities. Soil formation is maintained by fungal-plant partnerships and microbial decomposition. Nitrogen cycling, phosphorus cycling, carbon cycling – all of these are symbiotic processes involving multiple organisms.
For the past few million years – really, for most of the Cenozoic – these partnerships have maintained relatively stable conditions. Temperature fluctuations, yes. Ice ages, yes. But within a range that allowed complex life to persist and diversify.
What we’re doing now – releasing carbon that’s been locked in the Earth for hundreds of millions of years, at a rate faster than any geological process – is pushing these symbiotic systems outside their tolerances. And yes, I believe we are watching evolution’s mechanisms unravel in real time.
But I want to be precise about what that means. Evolution itself won’t unravel. Life will persist. Bacteria will persist – they always do. New partnerships will form. New symbiotic arrangements will emerge. That’s what life does. That’s the creative power of symbiosis.
What will unravel is the particular configuration of life that we depend on. The coral reefs. The fish stocks. The pollinator networks. The soil ecosystems. The forests. These are symbiotic systems that evolved under specific conditions, and we’re changing those conditions faster than integration can occur.
I worry – and this is something I didn’t say enough when I was alive, or perhaps I said it but wasn’t heard – that we’re in a period of active de-symbiosis. Ecosystems that have integrated over millions of years are being fragmented. Partnerships are being broken. And the timescale of what we’re doing is geological. We’re compressing changes that would normally take thousands of years into decades.
Can new symbiotic partnerships form fast enough to maintain the complexity we’ve inherited? I honestly don’t know. Symbiosis works on evolutionary time. Speciation takes thousands of years minimum. Integration of new partnerships takes millions of years. We’re operating on a timescale of decades. The math doesn’t work.
What I would say to you – and to other researchers working on microbiomes, on coral partnerships, on plant-fungal networks – is this: Don’t just document the collapse. Try to understand the mechanisms of symbiotic integration. How do partnerships form? What are the conditions that allow two organisms to become one? What are the tipping points where integration fails?
Because if we’re going to have any hope of maintaining the complexity that exists – or building new complexity – we need to understand not just that symbiosis matters, but how symbiosis works at the mechanistic level. What are the biochemical signals? What are the genetic changes? What are the timescales?
The coral-algae partnership broke down because the temperature stress was too acute. But there might be ways to slow that breakdown, to buy time for new partnerships to form. I don’t know what those ways are. That’s your work. That’s the work of your generation.
And I want to say something else, something I’m perhaps more convinced of now than I was during my lifetime: The future of life on Earth depends on understanding symbiosis not just as an evolutionary principle but as an ethical principle. Not in a mystical sense. Not in a New Age sense. But in the straightforward recognition that we are embedded in symbiotic partnerships that we depend on absolutely.
We have a responsibility to those partnerships. Not because they’re sacred or spiritual – though they might be – but because we literally cannot survive without them. Gaia isn’t nurturing. She’s not going to save us. But she might tolerate us, if we learn to be better partners.
That’s my hope, Márcia. Not that symbiotic systems won’t unravel – the evidence suggests they will, in many places. But that understanding symbiosis might lead us to be more careful about which partnerships we break and which we try to preserve or rebuild.
Nicolò Mussini | 47 | Evolutionary Biochemist | Turin, Italy
In your 1967 paper, you couldn’t directly sequence DNA – you were arguing largely from structural and metabolic clues. Today we can read genomes completely. I’m curious about the reverse problem: now that we have vast genetic data, we’re finding horizontal gene transfer everywhere – not just in organelle origins but throughout prokaryotic genomes, even in some eukaryotes. Does this vindicate your position more thoroughly than you could have hoped, or does it complicate it? Has the sheer volume of HGT data changed what we should understand symbiogenesis to mean?
Nicolò, this is exactly the kind of question I wish more evolutionary biologists were asking. You’re right to press on this. The abundance of horizontal gene transfer data we’re seeing now is more than vindication. It’s complication. And complication is where science gets interesting.
In 1967, when I wrote that paper, I was arguing from structure and inference. Mitochondria had double membranes. They had their own DNA, which was bizarre and unexplained by the standard model. Their ribosomes were bacterial-type, not eukaryotic-type. Their biochemistry – the way they generated ATP through oxidative phosphorylation – was distinctly bacterial. And when you looked at the genetic inheritance patterns of mitochondrial traits, they didn’t follow Mendelian rules; they followed maternal inheritance, like bacterial plasmids.
But I couldn’t see the DNA sequences. I couldn’t compare them directly to bacterial genomes. I was building a case from circumstantial evidence, the way a good detective builds a case from clues that all point in the same direction. Fifteen journals rejected me because, from their perspective, I was constructing an elaborate hypothesis on insufficient direct evidence.
Then came the late 1970s and early 1980s, and suddenly we could sequence DNA. We could read the actual code. And when people sequenced mitochondrial DNA and compared it to bacterial genomes, they found exactly what my hypothesis predicted: the sequences clustered with alpha-proteobacteria. Not just similar – clearly descended from alpha-proteobacterial lineages. The vindication was stunning.
But here’s where it gets interesting, and where you’re pushing me in exactly the right direction. Once we could sequence, we started finding horizontal gene transfer everywhere. Not just from bacteria to eukaryotic nuclei. But from bacteria to bacteria. From archaea to bacteria. From eukaryotes back to bacteria. Plasmids moving genes around like molecular currency. Viruses acting as vectors. Lateral transfer, horizontal transfer, whatever you want to call it – it’s ubiquitous in prokaryotes.
And now – this is the part that really excites me – we’re finding it in eukaryotes too. Not just the ancient transfers from mitochondria and chloroplasts to the nucleus. But ongoing transfer. Recent transfer. Genes moving between eukaryotic species that shouldn’t be able to share genes through standard inheritance.
So yes, the data vindicate my position more thoroughly than I could have hoped. But they also transform what symbiogenesis means. I proposed that symbiosis was a mechanism for large-scale evolutionary innovation – for creating entirely new kinds of organisms. And I still think that’s true. The origin of eukaryotic cells through symbiosis is real and fundamental.
But if horizontal gene transfer is as common as the genomic data suggest, then symbiosis and HGT aren’t separate phenomena. They’re expressions of the same deeper principle: genetic integration across species boundaries. Organisms don’t just compete for resources. They trade genes. They share genetic material. They become, in some sense, a shared genetic commons.
This is different from what I was arguing in the 1960s and 1970s. I was emphasising the integration part – two organisms becoming one, their genomes fusing into a single nucleus, a single identity. And that still happens. That’s still fundamental. But the genomic data show that even without full integration, organisms are constantly exchanging genetic material.
Think about what that means for evolution. The Modern Synthesis, neo-Darwinism, treated evolution as fundamentally vertical – genes passed from parents to offspring, modified by random mutation and natural selection. It’s a tree structure. Lineages diverge. Species branch off. You get a branching tree of life.
But if horizontal gene transfer is constant and ubiquitous, then evolution isn’t a tree. It’s a network. Lineages don’t just diverge; they anastomose. They reconnect. They exchange genetic material across boundaries that we thought were species barriers.
Now, here’s where I need to be honest about the limits of what I was claiming. When I said that symbiosis explained “most” genetic variation, I was overstating the case. I was fighting neo-Darwinism so hard that I overcorrected. Natural selection on random mutations is still the dominant source of genetic variation in most organisms, most of the time. That’s just true.
But what symbiosis and horizontal gene transfer do is accelerate variation. They don’t just add one mutation at a time. They add whole functional modules. Genes that have already been tested by natural selection in another organism. If a bacterium has evolved a gene that allows it to metabolise a new substrate, and that gene gets transferred to another bacterium, the recipient doesn’t have to wait for the mutation to arise and be selected for. It gets a pre-built solution.
That’s genuinely novel. And it happens constantly. And the scale of it is far greater than I appreciated when I was writing about symbiogenesis in the 1970s.
So what does the genomic data tell us about symbiogenesis specifically? Well, it confirms the basic mechanism. We can now trace the phylogenetic history of mitochondria and chloroplasts with precision. We can identify which bacterial lineages gave rise to which organelles. We can track the transfer of genes from organellar genomes to the nuclear genome. We can see it happening.
But it also shows us something more subtle: the process of symbiotic integration isn’t a clean, discrete event. It’s not as if bacteria merged with a proto-eukaryote and then, after a few million years, you had a stable eukaryotic cell. The process was messy. Genes were transferred gradually. Some transfers were recent; some were ancient. Some genes were lost; some were duplicated and modified. The integration took tens of millions of years, and even now, in modern eukaryotes, the process isn’t entirely complete.
For instance, mitochondria still have their own DNA. They still replicate semi-autonomously. They still have their own ribosomes. If the integration were truly complete, if the organelles were truly just compartments, we’d expect all the genes to have been transferred to the nucleus long ago. But they haven’t. Some genes are essential for mitochondrial function and apparently cannot be transferred to the nucleus without losing their function.
This tells us something important about symbiotic integration: it’s not about dissolving boundaries. It’s about maintaining boundaries while increasing interdependence. Mitochondria remain, in some sense, separate organisms. They have their own genetic systems. But they’re so deeply integrated into eukaryotic cells that they cannot survive independently. They’ve become obligate endosymbionts.
That distinction matters. Because it means that symbiosis isn’t the same as merger or fusion. It’s about partnership at the genetic level. About organisms that have become so interdependent that they function as a single unit, even though they retain separate genetic identities.
And here’s where the modern genomic data get really interesting: we’re finding this pattern elsewhere. In legume-rhizobium partnerships, the bacteria have transferred some genes to the plant’s genome, but they’ve retained genes for nitrogen fixation. In some protists, there’s evidence of gene transfer from bacterial endosymbionts, but the bacteria maintain genetic autonomy. The pattern isn’t “complete integration with loss of genetic autonomy.” The pattern is “partial genetic integration with maintained genetic distinction.”
So to answer your question directly: Yes, the volume and abundance of HGT data vindicate my position that symbiosis and genetic exchange are fundamental to evolution. But they also complicate what we mean by symbiogenesis. It’s not just about discrete symbiotic events creating new organismal types. It’s about ongoing genetic exchange that blurs the boundaries between organisms and creates networks of genetic interdependence.
This is actually closer to what the Extended Evolutionary Synthesis is now proposing. The idea of holobionts – organisms plus their symbiotic partners as evolutionary units. The idea that the relevant unit of selection might not be the individual organism or the individual gene, but the entire symbiotic community.
That’s a more radical position than what I was arguing in the 1960s, but it’s supported by the genomic evidence. And it’s exciting. It means that evolution is far more creative and far more cooperative than the neo-Darwinist framework allowed. Organisms don’t just compete. They trade. They share. They merge. They create new possibilities through partnership.
But it also means we need better language for what we’re talking about. “Symbiogenesis” was the right word for what I was describing – the origin of new organisms through symbiotic partnership. But “horizontal gene transfer” is broader. It includes transfers that don’t lead to symbiotic integration. It includes gene swapping that happens within microbial communities without creating new permanent partnerships.
The real insight, I think, is that these processes exist on a continuum. On one end, you have gene transfer between distantly related organisms with minimal integration. In the middle, you have partnerships like legume-rhizobium, where genetic integration is partial but functional dependence is complete. On the other end, you have the origin of eukaryotic cells, where two organisms have become so integrated that we consider them a single organism.
The same mechanisms are operating across this entire continuum. Different degrees of integration. Different timescales. But the underlying process is the same: genetic boundaries are permeable. Life is fundamentally collaborative at the genetic level.
That’s what the modern genomic data are showing us, and it vindicated not just my specific hypothesis about organelle origins, but the broader principle that cooperation and genetic exchange are as fundamental to evolution as competition and natural selection.
It’s rather wonderful, actually. The technology I didn’t have access to – the ability to read genomes directly – has confirmed not just that I was right about what happened, but that the mechanism I proposed is far more general and far more important than I realised.
Hermine Hagen | 52 | Environmental Historian & Science Studies Scholar | Oslo, Norway
You recovered the work of Kozo-Polyansky and other forgotten scientists whose symbiogenesis ideas had been buried. But as you did this recovery work, did you notice why those ideas had been suppressed? Was it purely scientific conservatism, or were there ideological, geopolitical, or institutional reasons – particularly given that much of the early symbiogenesis literature came from Soviet science during the Cold War? And if ideology shaped which ideas survived and which were erased, how do we know our current paradigms aren’t being shaped by similar blind spots we simply can’t see?
Hermine, you’ve asked a fundamental question. And I’m grateful for it, because it forces me to confront something I didn’t always acknowledge directly: the recovery of Kozo-Polyansky and the other symbiogenesis pioneers wasn’t just about recovering good science. It was about understanding why good science had been erased.
Let me start with the obvious: yes, the Cold War absolutely shaped which Soviet scientific ideas survived in the Western consciousness and which were buried. Kozo-Polyansky published his work on symbiogenesis in 1924 – decades before I was born, decades before I proposed my own version of the theory. He had the central insight. He understood that organelles were once independent organisms. He proposed the mechanism. And his work was essentially invisible in the West.
Why? Partly because it was published in Russian, in a Soviet journal, during a period when the West and Soviet Union were engaged in ideological conflict. Scientific papers cross borders slowly in the best of times. But when there’s geopolitical tension, they cross even more slowly. And there’s a selection bias: Western scientists are more likely to read and cite work from within their own linguistic and ideological sphere.
But there’s more to it than just language barriers. There was active suppression. During the Cold War, there was a pervasive assumption in Western science that if an idea came from Soviet science, it was either derivative, ideologically tainted, or simply wrong. It was easier to dismiss it out of hand than to engage with it carefully.
Mereschkowski, another early symbiogenesis theorist, published in the early 1900s. He was Russian. His work was published in German and Russian journals. And it was largely forgotten in the Anglophone scientific world. Why? Partly because he was working before the conceptual framework existed to understand his ideas. But also because his ideas challenged the mainstream understanding of cell evolution, and the mainstream wasn’t interested in being challenged by a Russian scientist working at the turn of the century.
Wallin – he was American, but he proposed symbiotic origins for organelles in the 1920s and got absolutely shredded by the establishment. The standard account is that his ideas were too speculative, not supported by sufficient evidence. And that’s true, to some extent. But there was also a kind of intellectual closure happening. The dominant view – that cells evolved gradually through the accumulation of small mutations – was so entrenched that alternative explanations were almost automatically dismissed.
Now, here’s what’s harder to admit: I benefited from this suppression. When I proposed endosymbiotic theory in 1967, I could present it as novel. I could build the case from the beginning, using modern molecular biology and modern understanding of genetics. I was proposing something that seemed new, even though Kozo-Polyansky had proposed it forty years earlier.
The injustice to those earlier scientists is real. They did the intellectual work. They had the insight. They just lacked the experimental tools to prove it conclusively. And by the time I came along with the same insight plus the molecular evidence, their contributions had been erased.
But your question goes deeper than the Cold War suppression of Soviet science. You’re asking: If ideology shaped which ideas survived and which were erased in the case of symbiogenesis, what other blind spots might exist in contemporary science? What ideas might we be suppressing without realising it?
That’s a terrifying question. And I think the honest answer is: probably many. Probably far more than we’re aware of.
Think about what was suppressed in the case of symbiogenesis: it was a theory that emphasised cooperation over competition, integration over atomisation, partnership over struggle. In Cold War America, those ideas were ideologically suspect. They sounded too collectivist. They seemed to undermine the competitive, individualistic worldview that was politically dominant.
So there was a kind of feedback loop: the dominant ideology shaped which scientific ideas were considered credible. Scientists working within that ideology naturally developed theories that reinforced the ideology. Theories that challenged the ideology were dismissed as speculative or unscientific. And the ideological framework became embedded in the very structure of the science.
Now, I wasn’t immune to this. When I was fighting neo-Darwinism in the 1970s and 1980s, I was partly fighting a scientific paradigm. But I was also fighting an ideology. The emphasis on competition, on selfish genes, on struggle for existence – that had become not just a scientific framework but a metaphor for how the world works. It justified capitalism. It justified competition between nations, between individuals, between genders. It seemed to prove that the existing social order was natural and inevitable.
My emphasis on symbiosis and cooperation challenged that metaphor. And I took a certain amount of satisfaction in that. I thought I was fighting for truth against ideology. But now I wonder: to what extent was I simply replacing one ideological framework with another?
Because symbiosis can also be ideologically coded. It can be used to support collectivist politics. It can be romanticised as a vision of universal cooperation. The New Age movement absolutely used Gaia theory that way – as a kind of spiritual vision of planetary harmony. And I spent a lot of energy fighting against that appropriation. I wrote that essay, “Gaia is a Tough Bitch,” precisely because I didn’t want symbiosis and Gaia to become New Age mysticism.
But the point is: even when I was trying to escape ideology, I was embedded in it. My scientific choices were shaped by my political commitments. The questions I asked, the evidence I emphasised, the collaborations I pursued – all of it was filtered through my worldview.
So what does this mean for contemporary science? I think it means we need to be honest about the ways ideology shapes science all the time. Not just in Cold War suppression of Soviet research, but in the everyday decisions about which research gets funded, which questions get asked, which evidence gets foregrounded, which theories get dismissed.
Let me give a concrete example. For decades, there was resistance to the idea that genes could be inherited epigenetically – through changes in gene expression that weren’t due to changes in DNA sequence. Why? Partly because the experimental tools didn’t exist. But also partly because it challenged the gene-centric view of inheritance that had become dominant in molecular biology. The idea that only DNA sequence mattered, that everything else was peripheral – that was ideologically and institutionally important. Labs had been built around it. Careers had been built around it. Whole research programmes depended on it.
So even when evidence for epigenetic inheritance started to accumulate, there was resistance. Not because the evidence was bad, but because the implications were inconvenient. They challenged a framework that had become institutionally entrenched.
Now, the Extended Evolutionary Synthesis has begun to incorporate epigenetics, niche construction, developmental plasticity – all of these mechanisms that were marginalised for decades. And the scientific community is slowly accepting them. But how much time was lost? How many researchers avoided those areas because they were unfashionable? How much progress could have been made if the field had been more open to these ideas earlier?
I think the answer is: a lot. And that’s a tragedy. Not just for the individuals whose work was dismissed, but for science itself. Because science progresses faster when you have intellectual pluralism, when you have multiple theoretical frameworks competing, when you’re genuinely open to evidence that challenges your assumptions.
But here’s the hard part: complete openness is impossible. Scientists have to work within frameworks. You have to assume some things are true in order to build on them. You can’t question everything simultaneously. So there’s necessarily some degree of paradigm closure. Some degree of gatekeeping.
The question is: how do you maintain enough closure to allow coherent scientific work, while remaining open enough to recognise when your fundamental assumptions are wrong?
I don’t have a clean answer to that. But I think part of it is intellectual humility. Recognising that your current framework is a framework, not the framework. That there are ways of seeing that your paradigm obscures. That future generations will look back at what you took for granted and think you were absurdly blind.
And I think part of it is historical awareness. Understanding how ideology has shaped science in the past. Recognising the patterns. Trying to catch yourself doing it in the present.
When I recovered Kozo-Polyansky’s work, I wasn’t just doing historical research. I was trying to understand how suppression happens. How good ideas get erased. How ideology shapes what counts as credible science. And I was trying to signal: this could happen to any of us. The ideas that seem marginal now might turn out to be central later. The frameworks we take for granted might be blinding us to important truths.
Your question about what we might not know we don’t know – that’s the crucial one. Because the blind spots we can’t see are the most dangerous ones. We can guard against explicit suppression. We can fight against ideological bias if we’re aware of it. But the assumptions so deeply embedded that we don’t even recognise them as assumptions – those are the ones that shape science most profoundly.
I suspect – and this is speculation, but educated speculation – that there are aspects of biology we’re fundamentally misunderstanding because of paradigm closure. Questions we’re not asking because they seem incomprehensible within the current framework. Evidence we’re dismissing because it doesn’t fit the dominant theory.
Maybe it’s about consciousness and its role in biology. Maybe it’s about the inheritance of acquired characteristics in ways that don’t reduce to genetics. Maybe it’s about the creative agency of organisms in shaping their own evolution. Maybe it’s about something I haven’t even thought of.
What I know is: the more entrenched a paradigm becomes, the more invisible its assumptions become, the greater the risk that we’re collectively blind to something important.
The antidote isn’t to abandon all frameworks and pursue pure empiricism – that’s impossible. But it’s to remain suspicious of consensus. To pay attention to the ideas that are being marginalised. To ask why certain questions are considered unscientific. To look for the ways that ideology is shaping what counts as credible research.
And yes, to recover the work of predecessors whose contributions were erased. Not just out of historical justice, though that matters. But because understanding how suppression happens in the past helps us recognise when it’s happening in the present.
Lucio Guzmán | 38 | Philosopher of Biology & Science Ethics | Mexico City, Mexico
You said in the interview that you were drawn to fringe ideas partly because vindication had made you overconfident – that being right about endosymbiosis created a permanent rebel identity. But here’s what troubles me: Is there a structural problem with how science rewards outsiders? Once you’re vindicated, you gain institutional credibility and platform. But the identity that got you there – the willingness to ignore consensus, to trust your intuition over established methods – that identity becomes reinforced. The system doesn’t actually teach you to distinguish between good heterodoxy and bad heterodoxy; it just rewards you for being heterodox. How could science be structured differently so that vindicated rebels can learn epistemic humility instead of doubling down on contrarianism?
Lucio, you’ve identified something I’ve spent the last years of my life thinking about, and I’m not sure I have a satisfying answer. But the question itself is important enough that it’s worth trying.
You’re right that there’s a structural problem. When you’re rejected, when you’re fighting orthodoxy, you develop a certain character. You become stubborn. You learn to trust your intuition over consensus. You develop a kind of defiant confidence – you have to, otherwise the rejection would destroy you. You tell yourself: I’m right and they’re wrong, and eventually they’ll see it. That story sustains you through years of dismissal.
Then vindication comes. You’re right. The evidence supports you. The mainstream accepts your ideas. And suddenly you have institutional credibility. You have a platform. People listen to you.
But here’s the problem: the character that got you there – the stubbornness, the defiance, the willingness to ignore consensus – that character is now reinforced. The system has just taught you that your instincts are reliable. That trusting yourself over the experts was the right call. That being a rebel works.
So what happens? You keep looking for new orthodoxies to rebel against. You keep trusting your intuition. You keep dismissing consensus. Because the last time you did that, you were vindicated. The system has created a feedback loop that actually trains you not to develop epistemic humility.
That’s what happened to me. After endosymbiosis was accepted, I became increasingly convinced that my contrarian instincts were sound across the board. AIDS and 9/11 – these were areas where I thought the mainstream was wrong, where I thought there were suppressed ideas worth exploring. And I approached them with the same defiant confidence that had served me well with symbiogenesis.
But there’s a crucial difference. With endosymbiosis, I had evidence. Real, physical, biochemical evidence. I had the structure of mitochondria. I had the genetic inheritance patterns. I had a mechanistic explanation. I was defending a position that could be tested and verified. The evidence was just being suppressed by paradigm closure.
With AIDS and 9/11, I didn’t have evidence of that calibre. I had alternative explanations that seemed to me compelling, but they weren’t supported by the data in the way endosymbiotic evidence was. I was applying the same approach – question the mainstream, look for suppressed ideas, trust your intuition – to domains where that approach led me astray.
The system never taught me to distinguish between those two cases. It just taught me: Rebel. Ignore consensus. Trust yourself. And that’s a dangerous lesson if you don’t also learn when not to rebel.
So how should science be structured differently? That’s the harder question. Because you’re right that we need heterodoxy. We need people willing to challenge orthodoxy. The history of science is the history of paradigm shifts, and paradigm shifts require people who are willing to be wrong about what everyone believes.
But we also need quality control. We need peer review, even though it’s imperfect. We need evidence standards. We need the ability to say: No, that idea isn’t supported by the data. We need to be able to distinguish between legitimate heterodoxy and pseudoscience.
One part of the answer, I think, is transparency about uncertainty. When I was defending endosymbiotic theory, I was confident, but I was also honest about what we didn’t know. I said: Here’s the evidence. Here’s what it supports. Here’s what we need to test further. I was making a case, not claiming certainty.
But as I got older and more vindicated, I became less careful about that distinction. I started making claims about AIDS and 9/11 with the same confidence I’d applied to endosymbiosis, even though the evidence base was far weaker. I wasn’t being transparent about the degree of uncertainty. I was treating alternative hypotheses as established facts.
So one reform would be to incentivise scientists – especially vindicated scientists with institutional credibility – to be explicit about confidence levels. Not just the raw claim, but the evidence behind it. The degree of certainty. The alternative explanations that remain plausible. When I see that kind of transparency, I’m much more inclined to take someone seriously, even if they’re challenging consensus.
Another part of the answer is intellectual mentorship. I had mentors – Dobzhansky, who got my paper published; others who supported my work even when it was controversial. But I didn’t have mentors who taught me how to lose well. How to change my mind. How to recognise when I was wrong. How to distinguish between productive heterodoxy and destructive contrarianism.
If we structured science so that successful rebels had ongoing relationships with people who could challenge them, who could press them on their assumptions, who had the authority to say No, you’re wrong on this one – that might help. Not to suppress heterodoxy, but to refine it. To help rebels learn which of their instincts are reliable and which are just psychological patterns that happened to work once.
The problem is that once you’re vindicated, once you have institutional status, it’s hard to find people with enough credibility to challenge you effectively. Your peers have a stake in your continued success. Your younger colleagues are reluctant to contradict someone senior. There’s a kind of isolation of success that makes it harder to get honest feedback.
I wish I’d had someone in my life – someone I trusted and respected – who could have said to me in 2008: Lynn, you’re making a mistake with the AIDS work. You’re applying the endosymbiosis playbook in a domain where it doesn’t work. Stop. And who I would have listened to, because I trusted them and they had demonstrated wisdom about these kinds of questions.
There’s also a question of how we fund and reward heterodoxy. Right now, the system is structured so that successful rebels become establishment figures. You get elected to the National Academy. You get grants. You get prestigious positions. But then you’re expected to maintain your rebel status to justify the platform you’ve been given.
That’s perverse. It means the system is actually incentivising people not to develop wisdom and maturity*. It’s saying: Stay combative. Stay contrarian. That’s what made you valuable.
What if we structured things differently? What if we created distinct roles in science: people whose job is to challenge orthodoxy, and people whose job is to maintain standards and defend consensus. And we understood that moving between those roles meant learning different skills. That challenging orthodoxy requires certain traits – stubbornness, contrarian thinking, willingness to ignore consensus – but defending consensus requires different traits – carefulness, honesty about uncertainty, willingness to say no to ideas, even if they’re interesting.
And what if we explicitly trained people in epistemic humility? Not as a side effect of being rejected and vindicated, but as a deliberate educational practice. Teaching scientists how to recognise their own biases. How to distinguish between legitimate heterodoxy and pseudoscience. How to change their minds when evidence demands it. How to lose well.
Because the problem isn’t that we reward heterodoxy. It’s that we reward vindication without teaching people how to handle it. We create rebels and then we elevate them to positions of authority without ever teaching them humility.
Looking back at my own life, I think I would have benefited enormously from explicit training in epistemic humility. Not discipline – I didn’t need to be told to work hard or to be careful about evidence. But genuine education in how to maintain intellectual humility even when you’ve been right about something important. How to resist the seduction of believing that your instincts are infallible.
Here’s something else I think matters: collaborative heterodoxy. Lone rebels are vulnerable to the kind of drift I experienced. But rebels working in groups, challenging each other, holding each other accountable – that might work better. When I was working on endosymbiosis, I wasn’t entirely alone. There were other people thinking about symbiosis, about organellar origins. We weren’t a coordinated movement, but we were part of an intellectual current.
In contrast, when I was exploring AIDS and 9/11, I was more isolated. I was defending these ideas essentially on my own. I didn’t have peers who were engaging with me seriously, asking hard questions, pushing back thoughtfully. If I’d been part of a group of people exploring alternative ideas about AIDS causation, with some members who were genuinely sceptical of the direction we were heading, that might have pulled me back from the brink.
But that requires a kind of scientific culture we don’t currently have. We tend to valorise the lone genius, the solitary rebel. We celebrate people like me – the maverick who was right despite everyone else being wrong. But maybe what we should actually celebrate is collaborative truth-seeking. Groups of people willing to challenge consensus, but also willing to challenge each other.
Finally – and this is the part I’m least confident about – I think we need to be honest about the limits of heterodoxy as a path to truth. Heterodoxy can uncover suppressed ideas. It can challenge paradigm closure. It can generate novel hypotheses. Those are all valuable.
But heterodoxy is also often wrong. For every endosymbiotic theory, there are dozens of rejected ideas that were rejected for good reasons. Most of the time, consensus is right. Most of the time, the mainstream scientific view is closer to the truth than the fringe views.
The question is how to distinguish between heterodoxy that’s right despite being rejected (endosymbiosis) and heterodoxy that’s rejected because it’s wrong (AIDS denialism). And I’m not sure we’ve solved that problem. I’m not sure we can solve it completely. There’s always going to be some degree of uncertainty, some risk that you’ll promote something wrong, some risk that you’ll suppress something right.
What I think we can do is be more honest about those risks. We can say: heterodoxy is necessary for science, but it’s also dangerous. We need people willing to challenge consensus, but we also need people willing to say no to fringe ideas. And we need mechanisms for those two impulses to be in productive tension.
That’s what’s missing, I think. Not less heterodoxy, but structured heterodoxy. Heterodoxy that’s in dialogue with orthodoxy, not opposed to it. Rebels who are willing to be challenged by defenders of consensus. Defenders of consensus who are willing to take rebels seriously.
And honestly? I wish I’d learned earlier how to play that role. Not to stop being a rebel – I couldn’t have done that; it was too central to who I was. But to be a rebel with humility. A rebel who knew the difference between good contrarianism and bad contrarianism. A rebel who could lose well.
That’s the kind of scientist I wish I’d been. And it’s the kind of scientist I hope the next generation can become.
Жанна Мустафин | 41 | Astrobiologist & Exoplanet Researcher | Almaty, Kazakhstan
Your NASA work on early Earth microbial life shaped how we search for life beyond Earth. But there’s something I wonder: when we look for biosignatures on exoplanets – oxygen, methane, chemical disequilibrium – we’re looking for planetary-scale signatures of life, which is Gaia thinking. Yet we’ve never found a confirmed exoplanet with those signatures. What if symbiosis, which you showed was essential to eukaryotic complexity on Earth, is rare elsewhere? What if the integrated planetary systems that Gaia describes require billions of years to develop, and we’re looking at planets too young? Could the very framework that vindicated you here limit what we’re able to recognise out there?
Жанна, this question inspires me in the best possible way. Because you’re asking something that my work on astrobiology made me confront directly: Is symbiosis universal? Is the path to complexity that we see on Earth – through symbiotic integration and cooperation – the only path? Or is it just our path, the result of particular contingencies on this particular planet?
Let me start with what we know. On Earth, every major transition to greater complexity involved symbiosis. Eukaryotic cells arose through the symbiosis of bacteria with archaeal cells. Multicellular organisms arose through the integration of eukaryotic cells into cooperative colonies. Photosynthetic organisms arose through symbiosis with cyanobacteria. Complex ecosystems arose through symbiotic networks – fungi partnering with plants, bacteria partnering with animals, algae partnering with corals.
When you map out the history of life on Earth, symbiosis isn’t a side mechanism. It’s the mechanism of major evolutionary transitions. Every time life leaps to a new level of complexity, symbiosis is involved.
So when we think about life on other planets, the natural assumption – my assumption, when I was working on astrobiology with NASA – was that we should be looking for signatures of symbiotic integration. Chemical disequilibrium in the atmosphere suggesting biological activity, yes. But also looking for evidence of integrated biological systems. Planets where the biosphere and the physical environment have coevolved into something resembling Gaia.
But here’s where your question becomes genuinely unsettling. We haven’t found any confirmed exoplanets with those signatures. We have candidates. We have planets in habitable zones around distant stars. We have planets where we might find liquid water, where conditions might support life. But we don’t have confirmed biosignatures. And we certainly don’t have confirmed signatures of symbiotic planetary-scale integration.
Why might that be? There are obvious answers: our detection methods are limited. We can only see the brightest, closest stars. We can only detect the strongest biosignatures. Maybe life is common but Gaia-like integration is rare. Maybe we just haven’t looked at the right planets yet.
But your question pushes me toward a more unsettling possibility: What if symbiosis, and the kind of integrated planetary systems it creates, actually requires billions of years to develop? What if the timescale for symbiotic integration is so long that most young planets, most planets we can actually observe, simply haven’t had time for complexity to arise?
Think about Earth’s history. Life originated roughly 3.8 billion years ago. But for the first billion years, life was only bacterial. No eukaryotic cells. No multicellular organisms. Just prokaryotes. Then, around 2.5 billion years ago, cyanobacteria evolved and began producing oxygen. That oxygen accumulated in the atmosphere – the Great Oxidation Event. It took another billion years or so before eukaryotic cells with mitochondria became common.
Then you had to wait for eukaryotic cells to integrate into multicellular forms. Another half billion years or more. Then you needed photosynthetic multicellular organisms – plants – to evolve and colonise land. Then you needed fungi to partner with those plants. Then you needed complex animal ecosystems to arise. Then you needed – on an evolutionary timescale, just recently – intelligence to emerge.
The entire path from abiotic chemistry to technological civilisation took 3.8 billion years on Earth. And most of that time, most of the major evolutionary innovations, involved symbiotic integration happening slowly.
Now, 3.8 billion years is a long time. But on a cosmic timescale, it’s not that long. Our solar system is 4.5 billion years old. The universe is 13.8 billion years old. There’s theoretically plenty of time for life to have originated elsewhere and evolved to complexity.
But here’s the problem: if symbiosis is the primary route to complexity, and if symbiosis takes billions of years, then young planets – planets where life originated recently in cosmic terms – wouldn’t have had time to develop integrated planetary systems yet. They might have microbial life. They might have interesting chemical ecosystems. But they wouldn’t yet show the signatures of Gaia-like planetary integration.
And the planets we can most easily observe are young planets. Or at least, they’re in young stellar systems. The light we’re seeing from distant exoplanets is light that’s travelled for years or decades to reach us. We’re not seeing them as they are now; we’re seeing them as they were. And we’re naturally focusing on the closest stars, which tend to be younger.
So there’s a selection effect. We’re looking at planets that are, cosmically speaking, still in their infancy. We wouldn’t expect them to show signs of the kind of symbiotic integration that took 3.8 billion years to develop on Earth.
That’s a possibility I didn’t emphasise enough when I was doing astrobiology work. I was so excited about the idea that life might be ubiquitous, that symbiosis might be universal, that I didn’t fully confront the timescale problem.
But let me push the question further. You’re asking whether symbiosis might be rare compared to simple microbial life. And that’s genuinely possible. Let me sketch out some scenarios.
Scenario One: Life is common, but symbiosis is rare. This would mean that microbial life – bacteria and archaea – might be abundant throughout the universe. But eukaryotic cells, which require symbiotic integration, might be relatively rare. And complex multicellular life would be even rarer. This would explain why we see chemical disequilibrium on some exoplanets (suggesting microbial life) but no clear Gaia signatures.
Scenario Two: Symbiosis requires particular conditions. Maybe symbiosis happens more readily on planets with certain characteristics – moderate-sized planets, with particular atmospheric compositions, orbiting in certain types of stars. Maybe Earth is fortunate in ways we don’t fully understand. On most planets where life arises, symbiotic integration never occurs. Life stays microbial.
Scenario Three: Symbiosis is universal, but the timescale is prohibitively long. Life might arise commonly throughout the universe, and symbiosis might be a universal process. But it might take so long – billions and billions of years – that most planets we observe are still in their microbial phase. We’re looking at baby universes, cosmically speaking, where complex life hasn’t had time to emerge yet.
Scenario Four: The universe is effectively dead. This is the pessimistic option, the one I’ve become somewhat convinced of in my later thinking. Maybe life is actually quite rare. Maybe the origin of life requires very particular conditions. Maybe we’re, in some sense, improbably fortunate to exist. And maybe intelligent life is even rarer.
Which of these is true? I don’t know. And I think that’s important to admit. When I was working on astrobiology, I was somewhat carried away by optimism. I believed – I wanted to believe – that life was common, that symbiosis was universal, that we’d find evidence of Gaia-like systems elsewhere. It aligned with my views about cooperation and symbiosis being fundamental.
But the data don’t support that optimism. We’ve been looking for biosignatures for decades. We’ve found hints, suggestive evidence, but no confirmed detections. That’s either because life is genuinely rare, or because our detection methods are inadequate, or because we’re not looking in the right way.
If you’re asking what I would change about the astrobiology programme – if I could speak to researchers now – I would say: Take the timescale problem seriously. Don’t assume that because symbiosis is fundamental to life on Earth, you should expect to find signatures of it on young exoplanets. Don’t assume that Gaia-like integration is common. Consider the possibility that you might be looking at planets that are, evolutionarily, still in their infancy.
This means rethinking what biosignatures we should be looking for. Maybe instead of looking for oxygen and methane and atmospheric disequilibrium – signatures that might suggest Gaia-like planetary integration – we should be looking for any sign of life, including microbial biofilms, microbial mats, chemical gradients that might suggest metabolism.
And it means being honest about the possibility that we might be alone. Or at least, that intelligent life might be extremely rare. Not because life doesn’t arise elsewhere – I think it probably does. But because the path from simple life to complex integrated systems is long and contingent and difficult.
That’s a more sombre vision than the one I held during much of my career. But I think it’s more realistic. And I think it actually makes the existence of symbiosis on Earth – the existence of Gaia – more remarkable, not less. If symbiotic integration is rare in the universe, if planetary-scale self-regulation is an unusual outcome, then what we have here on Earth is precious. Not because it’s the only way life works, but because it’s one way, and it took billions of years and particular contingencies to produce it.
So to your question about whether we’re blind to symbiotic signatures on exoplanets: I think we might be. Not because symbiosis doesn’t exist elsewhere, but because we might be looking at planets that haven’t had time for symbiotic integration to occur. We’re looking at places that are still in their bacterial phase.
The real question – the one that keeps me up at night – is whether we’ve understood the timescale requirements correctly. Earth took 3.8 billion years to go from abiotic chemistry to technological civilisation. Is that a universal timescale? Or was Earth unusually fast? Or unusually slow?
I don’t have a good answer. But I think that’s the question the next generation of astrobiologists should be wrestling with. Not just where is life, but how long does it take for life to reach the level of complexity we see on Earth? And if the answer is billions of years, then we need to reconcile ourselves to the possibility that we might be alone in our local cosmic neighbourhood – not because life is rare, but because it’s slow.
Closing Reflection
Lynn Margulis died on 22nd November 2011, at the age of seventy-three, from a haemorrhagic stroke. She was still working, still writing, still engaged with the questions that had animated her entire life. In that sense, this interview – conducted speculatively in December 2025, fourteen years after her death – represents not a farewell but a continuation. A conversation that might have unfolded had she lived longer, had more time elapsed for reflection on her legacy, had the fields she shaped evolved further.
What emerges from this dialogue is a portrait more complex than standard accounts allow. The historical record presents Lynn Margulis primarily through two lenses: the vindicated maverick whose endosymbiotic theory transformed cell biology, and the controversial elder whose later positions on AIDS and 9/11 damaged her reputation. This interview attempts a third lens – not to defend the indefensible, but to understand the psychology and the structures that led a brilliant scientist toward increasingly fringe ideas. It asks uncomfortable questions about how vindication shapes identity, about the ways ideology invisibly guides what counts as credible science, about the gendered language used to dismiss women who are assertive and combative.
Some of what appears in these responses may differ from Margulis’s recorded statements. Where it does, this represents my attempt at historical empathy – imagining what she might have said given more time, more distance, more opportunity for reflection than she had before her death. I have not invented facts about her science or her life. But I have constructed, from the documented record of her thinking, a plausible interior life that acknowledges her growth, her regrets, her hard-won insights. The speculation here is not fabrication; it is an exercise in imaginative reconstruction, grounded in what we know of her work, her era, and her character.
The gaps and uncertainties are real. We cannot know precisely why she was drawn toward AIDS denialism and conspiracy theories. We can only observe the pattern and theorise about the mechanisms. Some scholars will argue that my interpretation is too sympathetic, that it rationalises positions that should be condemned outright. Others will argue it’s not sympathetic enough, that it fails to account for the genuine scientific merit in some heterodox positions. Both criticisms may be valid. The goal here is not to settle these debates but to open space for conversation about them.
I want to address directly a criticism that may arise: What authority does a man have to create a fictional interview with a woman scientist? The answer is complicated. I have no unique authority. But I do have a responsibility – to the subject, to historical accuracy, to readers seeking to understand her story. The alternative to this work is not a better work by someone with different credentials. The alternative is often silence, or the persistence of incomplete narratives that flatten her complexity. My role here is that of a researcher, advocate, and storyteller. The primary obligation is fidelity to her documented struggles and achievements, not to my identity as the teller.
What strikes most powerfully in retrospect is how Margulis’s concerns have proven prophetic. The symbiosis-centred view of evolution that was marginalised for decades is now mainstream. Microbiome research has validated her insistence on cooperation as evolutionary driver. Earth system science has rehabilitated Gaia theory under new language. The Extended Evolutionary Synthesis incorporates horizontal gene transfer and holobiont thinking – concepts directly descended from her work. She was right about the mechanisms of evolutionary change, even when she was wrong about other things.
Yet her name remains absent from most public understanding of biology. Students learn endosymbiotic theory without learning that Margulis developed it. The concept of symbiosis as evolutionary driver is cited without attribution. This invisibility is partly generational – she died before the current wave of attention to women in STEM history – and partly the consequence of her own later controversies. But it represents a genuine loss. Young scientists, particularly young women in evolutionary and cell biology, have less access to her example than they should.
Her life offers crucial lessons. First: that paradigm shifts require not just evidence but persistence, institutional credibility, and eventually, overwhelming proof. Second: that being right about one thing does not confer wisdom about all things. Third: that institutional recognition, while necessary, can reinforce dangerous patterns if not accompanied by genuine humility. Fourth: that gender shapes how scientists are perceived – “difficult” women are dismissed more readily than “difficult” men, yet assertiveness is often necessary for ideas to be heard.
For young women pursuing science today, Margulis’s story is both inspiration and cautionary tale. It demonstrates that revolutionary contributions are possible. It shows that fighting orthodoxy can work. But it also reveals the costs: the isolation, the years of dismissal, the vulnerability to losing one’s way after vindication. It suggests that the solution is not for women to become tougher or more combative, but for science to become more welcoming – to heterodoxy, yes, but also to dissent, doubt, and intellectual humility. To mentorship that teaches not just how to fight but how to lose well.
The enduring challenge is this: How do we nurture the mavericks we need while protecting ourselves from the crackpots we don’t? How do we maintain enough institutional closure to enable coherent science while remaining open enough to recognise paradigm shifts? How do we reward heterodoxy without training rebels to become unreliable? Margulis’s life does not answer these questions. But it teaches us to ask them more urgently.
In the end, what matters most is not whether we perfectly understand her motivations or fully agree with her later positions. What matters is that she forced science to think differently about cooperation, about merger, about the way organisms integrate to create novelty. She showed us that eukaryotic cells are not simple compartments but the product of ancient symbiosis. She insisted that evolution is not merely competitive but fundamentally collaborative. And she did this despite rejection, despite institutional resistance, despite a scientific culture that was not built to accommodate her.
That is worthy of remembrance. That is worthy of study. That is worthy of inspiring the next generation of scientists – especially women scientists – who will face their own orthodoxies, their own sceptical reviewers, their own long years of waiting for vindication.
The conversation continues.
Editorial Note
This interview transcript is a work of historical fiction. It represents a dramatised reconstruction of Lynn Margulis‘s voice, perspectives, and scientific reasoning, based on extensive research into her published works, documented statements, biographical accounts, and the historical context of her era.
The interview is not a transcript of actual words spoken by Lynn Margulis. She passed away in 2011, fourteen years before this conversation was constructed. What appears here is an imaginative reconstruction – informed by rigorous study of her science, her writings, her letters, and her life – designed to make her ideas, struggles, and legacy accessible to contemporary readers.
What is documented fact: Margulis’s scientific achievements, institutional honours, publication record, biographical details (birth, death, marriages, children), and her publicly stated positions on endosymbiosis, Gaia theory, neo-Darwinism, and later controversies are all grounded in the historical record. Her technical explanations of endosymbiotic theory and organellar evolution reflect her actual scientific understanding.
What is informed speculation: Her interior reflections, her private regrets about AIDS denialism and 9/11 conspiracy advocacy, her psychological analysis of how vindication shaped her later choices, and her nuanced positions in response to the five supplementary questions represent plausible extrapolations from the documented record, constructed through historical empathy and close reading of her work. Where she likely would have said something is indicated through careful narrative construction, not direct quotation.
The purpose of this format: Rather than presenting a conventional biography or academic essay, this interview allows Margulis’s complex legacy – scientific brilliance alongside genuine errors – to be explored dialogically. It creates space for her voice to be heard in full dimensionality, acknowledging both her vindication and her missteps, her insights and her blind spots.
Readers should approach this as they would historical fiction based on real people: as a serious, researched work that privileges fidelity to its subject whilst acknowledging the speculative nature of reconstructing any person’s inner life, especially posthumously.
Who have we missed?
This series is all about recovering the voices history left behind – and I’d love your help finding the next one. If there’s a woman in STEM you think deserves to be interviewed in this way – whether a forgotten inventor, unsung technician, or overlooked researcher – please share her story.
Email me at voxmeditantis@gmail.com or leave a comment below with your suggestion – even just a name is a great start. Let’s keep uncovering the women who shaped science and innovation, one conversation at a time.
Bob Lynn | © 2025 Vox Meditantis. All rights reserved.
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