Imagine you’ve just been handed the keys to a time machine. Heart thumping with that mix of wonder and nerves, you step inside, set the dial to “just before the origin of life on Earth,” and hit the switch. The machine shudders, hums, and when the door swings open, you’re not met by lush forests or living things, but by a world raw and untamed.
Before you stretches a planet sculpted by raw geology: barren rock formations, sprawling oceans, and a thick, swirling atmosphere heavy with volcanic gases. The air is dense and hot, saturated with chemicals spewed from relentless eruptions that reshape the landscape. Lightning crackles across the sky, and meteorites occasionally streak through the clouds.
And yet, in this most unlikely Eden, something stirs: life, or at least the whisper of it. In tiny, hidden pockets, perhaps a warm little pond or a sunlit tide pool, an improbable oasis emerges. Through a process scientists call chemical evolution, molecules link arms, shuffle, and in their own strange rhythm, take a step toward life. Against every odd, the lifeless begins to flirt with the living, with simple molecules combining in ever more complex ways, assembling into something entirely new: the first living cells. But it’s no miracle, nor is there a designer—no direction, no top-down meaning—just the outcome of chemistry, physics, and chance at work. It’s just nature, rolling dice with time.
If nature is a closed loop—self-sufficient, self-organising, and self-explaining, then all events result from nature’s own mechanisms that are themselves without ‘mindful’ or ‘transcendent’ explanations. It’s not just that every phenomenon can be explained by natural mechanisms; these mechanisms are also fully capable of explaining themselves without any need for higher, non-material explanations. On this view, the rise of life needs no intelligent cause or purposeful direction. But press your finger on that story, lean in a little closer, and the surface starts to crack.
*This is part one of our upcoming book. More details will be provided.
Exploring the Great Divide: Life and Non-life
One of the biggest challenges in talking about the origin of life is figuring out exactly when non-living matter crosses the line and becomes alive. Where is that threshold—the moment a handful of molecules wakes up and turns into something living? What do we even mean by “alive”? The answer isn’t a clean one. There’s no tidy, universal definition we can all shake hands on. We reach instinctively for traits like reproduction, evolution, metabolism, and the exchange of genetic information, but even these leave us in uncertainty, making it even harder to have a straightforward conversation about how life truly began.
I remember being taught back in school that the shift from non-life to life was this smooth, linear step, that the first living things were so basic you could barely tell them apart from the lifeless matter around them. Looking back, that naive story was misleadingly reductive. Even the most ancient lifeforms we know of, so-called “simple” cells, reveal astonishing levels of complexity. Geneticist Michael Denton paints a vivid picture of the divide between life and non-life, declaring:
“It represents the most dramatic and fundamental of all the discontinuities of nature. Between a living cell and the most highly ordered non-biological systems, such as a crystal or a snowflake, there is a chasm as vast and absolute as it is possible to conceive.”
Denton illustrates this by pointing to the smallest bacterial cells, which weigh less than a trillionth of a gram, yet are akin to a “veritable micro-miniaturised factory containing thousands of exquisitely designed pieces of intricate molecular machinery, made up altogether of 100 thousand million atoms, far more complicated than any machine built by man and absolutely without parallel in the non-living world.”
What’s truly astonishing, almost eerie and weird, is the consistency that molecular biology has uncovered in the inner workings of all life. No matter where you look on the “tree of life”, the same molecular choreography unfolds: DNA, RNA, and proteins form a universal trio that helps drive cellular activity. These components perform remarkably similar functions in every organism, from bacteria to humans. The genetic code itself is interpreted in a nearly identical way across the living world, and even the ribosomes, those tiny “workshops” that churn out proteins, share a surprising uniformity in their size, structure, and components, no matter the type of cell.
So, how should we make sense of this uniformity? Does it whisper of a single origin, a primordial ancestor from which all life descends? Or does it hint at some deeper, universal design? Maybe it’s both. After all, these two ideas aren’t mutually exclusive. One thing, however, is clear: the fact that most living organisms are built on the same biochemical foundation suggests that these biological principles arose early in the history of life on Earth. Nobel Prize-winning biochemist Jacques Monod supports this view, stating:
“We have no idea what the structure of a primitive cell might have been. The simplest living system known to us, the bacterial cell… in its overall chemical plan is the same as that of all other living beings. It employs the same genetic code and the same mechanism of translation as do, for example, human cells. Thus, the simplest cells available to us for study have nothing ‘primitive’ about them… no vestiges of truly primitive structures are discernible.”
In an intriguing way, cells demonstrate a form of ‘stasis’. Bruce Alberts, the President of The National Academy of Sciences of the USA, notes that “we have always underestimated cells.” He’s right. The entire cell can be imagined as a bustling city. Inside its boundaries, a network of pathways links countless neighbourhoods, each doing their own thing. Large protein complexes work like delivery trucks or maintenance crews, moving supplies, sending messages, and keeping everything running smoothly. But this city isn’t rigid or predictable, its inner life is constantly shifting, with molecules weaving in and out of interactions in a lively manner. It’s a city with a pulse to it. It is hard for us to get any kind of grasp of the seething, dizzyingly complex activity that occurs inside a single living cell. It’s mind-boggling.
So, what about the first cell? It makes sense that the very first cell was nowhere near this complex, probably just a humble protocell, slowly evolving until it could finally copy itself. Nature has the ability to work wonders, and that given the amount of time available, what seems impossible starts to look inevitable. This is where abiogenesis comes in. It’s a theory of chemical evolution that suggests that life began from non-living matter through self-organising natural processes. When you think about the immense span of time stretching across Earth’s history, the idea feels intuitive: an extraordinary transformation unfolding slowly but surely over millions of years.
The Birth of Life: Understanding Abiogenesis
One way to make sense of evolution is to split it into two tales: chemical and then biological. They’re connected, but not the same story. Biological evolution, driven by processes like natural selection and genetic variation, requires self-replicating entities capable of mutation and adaptation. Chemical evolution, however, is the earlier story of how the first self-replicating molecule arose. For this reason, we shouldn’t confuse chemical evolution with its biological successor. Applying concepts from biological evolution (like neo-Darwinism) to chemical evolution is generally premature.
Put simply, chemical evolution describes how simple, lifeless chemical compounds on early Earth, governed by the basic rules of physics and chemistry and influenced by random factors such as molecular distribution and chance reactions, gradually combined to form the essential building blocks of life, eventually leading to the first self-replicating biological forms.
But how? Back in the 1920s, two scientists named Alexander Oparin and J.B.S. Haldane, independently proposed that the early Earth had a “reducing” atmosphere rich in gases like methane, ammonia, hydrogen, and water vapour, but without free oxygen. This environment, where molecules gain electrons or hydrogen, was ideal for creating organic molecules. As Earth cooled from its molten origins, conditions also became better suited for organic chemistry, with various energy sources being abundant: Lightning crackled across the sky, thunder created shockwaves, geothermal vents belched heat, and ultraviolet sunlight bathed the surface. These forces catalysed reactions in the oceans and atmosphere, steadily building up amino acids and other organic molecules. Over time, these organic substances accumulated, especially near hydrothermal vents or tidal pools, where dynamic physicochemical conditions created the suitable environment for their concentration. This process gave rise to a dense, nutrient-rich “prebiotic soup”, a promising broth for life.
Within this primordial soup, simple organic molecules linked up to form longer chains called polymers. Next came protocells, which are primitive bubble-like structures with lipid membranes, able to hold their internal chemistry apart from the world outside. Despite their simplicity, these protocells were resilient enough to withstand Earth’s harsh early conditions. As protocells evolved, they grew more complex and eventually gained the ability to self-replicate. Within protocells, certain RNA molecules may have begun to catalyse their own replication, leading to the first rudimentary forms of genetic information transfer.
RNA, or ribonucleic acid, is a crucial biological macromolecule found in all living cells. It plays a key role in converting genetic information, regulating gene expression and catalyses biochemical reactions within cells. The RNA World Hypothesis (which we will get onto this later in the book) suggests that early forms of life relied on RNA both to store genetic information and to catalyse chemical reactions. This is because RNA molecules have the unique ability to act as both genes and enzymes (ribozymes), which could have allowed them to replicate themselves and catalyse other chemical reactions necessary for life. Over time, as these early life forms evolved, the system became more complex and efficient. DNA eventually took over as the more stable medium for storing genetic information, while proteins became the primary molecules for catalysis, energy conversion, and structural functions within cells. It makes sense that this transition would have been gradual, with RNA still playing a central role in processes like protein synthesis (through mRNA, tRNA, and rRNA) and regulation.
With the establishment of RNA and later DNA as genetic information carriers, and the development of protein synthesis machinery, early protocells evolved into “true” cells capable of replicating their genetic material. This moment marks the true beginning of biological evolution and, ultimately, the astonishing diversity of life we see today. Of course, what I’ve outlined here is a simplified telling of chemical evolution, but it still gives you a general gist to the supposed power of time, chance, and the fundamental laws of physics and chemistry in creating the wondrous world of life that surrounds us.
The Miller-Urey Experiment: Simulating Early Earth Conditions
Abiogenesis, which is the tale of how life emerged from simple inorganic compounds, has fascinated and frustrated scientists for decades. Is it solid science or hopeful speculation? Do we have real trail markers, or just whispers in the dark?
The good news is that we aren’t completely fumbling in the dark. We can test the waters of the primordial soup, so to speak. By recreating the conditions of early Earth in our labs, we can observe first hand whether the basic building blocks of life could have formed spontaneously. Still, turning back the clock a few billion years is no easy feat. We can’t be certain we’re recreating the exact conditions that existed on early Earth, which, of course, means our experiments come with a large degree of uncertainty. The more assumptions we make about the ancient world, the less certain we can be about our results.
Even so, real progress exists. In 1952, the scientific world was shaken by the now-famous Miller-Urey experiment. This study sought to identify a plausible chemical pathway that could transform the gases thought to make up early Earth’s atmosphere into amino acids, those tiny yet mighty molecules that form the building blocks of proteins and, ultimately, all living cells.
The experiment was the brainchild of chemist Stanley Miller, working under the mentorship of Harold Urey. Miller reported the “first laboratory synthesis of organic compounds under primitive Earth conditions.” His setup involved passing an electrical charge through a flask containing water vapour, methane, ammonia, and hydrogen but no oxygen, simulating the believed conditions of early Earth’s atmosphere and ocean. The electrified spark mimicked lightning storms. The result? Miller generated a variety of organic compounds, including amino acids. This was a huge breakthrough. It was the first laboratory demonstration that under the right conditions, some of the raw ingredients for life could emerge from non-living matter.
Building on Miller’s experiment, subsequent researchers have explored alternative energy sources that could have been present on prebiotic Earth to drive the synthesis of organic compounds. For instance:
- Heat experiments substituted Miller’s spark generator with a furnace to mimic the heat from volcanic activity.
- Ultraviolet experiments replaced the spark with UV light, exposing the primordial gases to short-wavelength UV radiation, akin to the sun’s rays reaching an early Earth with a much thinner atmosphere.
- Shockwave experiments subjected the gases to brief, intense heat followed by rapid cooling, emulating the effects of shockwaves from thunder or meteorite impacts.
Amazingly, each approach churned out amino acids, some more efficiently than others, with telling differences in the types of organic molecules produced. The message, however, was clear: Multiple, commonplace energy sources could have driven the steady accumulation of essential biological precursors in early oceans.
Taken together, the Miller–Urey work and its successors sketch a coherent picture: the primordial seas could have been stocked with organic compounds. From that ancient pantry, nature could sift, accumulate, and concentrate a workable “prebiotic soup”, which then leads to the next long project: turning those simple molecules into the first living systems.
Fast-forwarding to 2009, John Sutherland and his team at the University of Manchester made significant progress in understanding how the basic components of RNA, believed to be one of the first genetic molecules, could have formed spontaneously from simple chemicals. They demonstrated that ribonucleotides, the building blocks of RNA, could be synthesised from relatively simple starting materials, including cyanamide, cyanoacetylene, glycolaldehyde, and glyceraldehyde. Their work provided a plausible chemical pathway for the prebiotic formation of ribonucleotides, marking an important step toward understanding the origin of RNA.
A decade later, in 2019, Thomas Carell and his team took a different approach by simulating conditions of early Earth and successfully producing precursors to the four nucleobases of RNA from basic prebiotic chemicals. So the picture sharpens from both directions: Sutherland’s research focused on the direct assembly of RNA’s building blocks; Carell explored the origins of the nucleobases themselves.
Assessing the Validity of Chemical Evolution Theory
At this point, you’re probably thinking, “So far, so good. This sounds promising!” And you’re right, it does. But I’ve been generous. The real test of any scientific theory isn’t in how good it looks on paper, it’s in how it holds up when you start pokin’ and proddin’ at it. Playing devil’s advocate is how we make sure we’re not getting ahead of ourselves or overlooking potential errors. So, let’s put the famous Miller-Urey experiments under the microscope and examine the broader implications of their findings.
Challenging the Myth of the Prebiotic Soup
In the 1920s, Oparin and Haldane sold the scientific community a seductive vision: an ancient Earth where ammonia and hydrogen sulphide mixed in an oxygen-free atmosphere. This meant the early Earth was largely hospitable to chemical formation.
We ate it up. They became scientific legends.
But they were wrong. Fresh geochemical evidence has upended the popular myth of a cosy chemical cradle for the origin of life. Instead, it paints a picture of a far less hospitable Earth, forcing scientists back to the drawing board and challenging some long-held assumptions about the conditions that gave rise to life.
One persistent, underappreciated problem is the inherent dilution processes prevalent in both the ancient atmosphere and the early oceans. Chemical evolution relies on polymerisation, where simpler molecules (monomers), like amino acids, connect to form long organic chains called polymers. However, in a water-rich environment like the ocean or a hypothetical prebiotic soup, the odds of polymerisation occurring are particularly low. According to researchers like Jeffrey Bada and Steven Cleaves, who studied “the origin of biologically coded amino acids”, both Earth’s oceans and atmosphere would have scattered life’s building blocks too thinly for significant chemical reactions to take place. Astrobiologist Paul Davies echoes the concern, suggesting that if a “prebiotic soup” ever existed on Earth, it was likely so weak and watered-down that the chances of crucial chemical reactions taking place were slim to none. Imagine trying to build a sandcastle at the beach while waves keep washing away your progress, that’s what polymerisation faces in water. As the U.S. National Academy of Sciences explains, “Two amino acids do not spontaneously join in water. Rather, the opposite reaction is thermodynamically favoured.” In other words, water doesn’t play nice; hydrolysis (the breakdown of polymers into monomers) is thermodynamically favoured over condensation (the formation of polymers from monomers).
Faced with this dilution dilemma, origin-of-life researchers have been exploring ways nature might have fought back. The idea is that some special spots on early Earth could have acted like concentration zones, gathering life’s essential molecules and giving them a better shot at reacting with one another. These include evaporating pools in coastal regions, microscopic water channels within ice formations, adsorption onto mineral surfaces, thermal gradients in porous rocks, and hydrothermal vent systems. These environments could theoretically provide conditions for concentrating organic molecules, though experimental evidence supporting their effectiveness remains limited, and each proposed mechanism must account not only for the concentration of molecules but also for maintaining conditions suitable for complex chemistry. Take tidal pools, for instance. As water evaporates, molecules can get packed into tighter spaces, improving their chances of combining. But tidal pools also face wild shifts in pH and temperature, which can destabilise molecules and increase the risk of hydrolysis. In ice environments, while liquid water veins between ice crystals can concentrate molecules through freezing-induced exclusion, the low temperatures significantly reduce molecular collision rates and reaction speeds. Then there are mineral surfaces, such as clays, which can gather organic molecules by attracting them through adsorption and electrostatic forces. But here, the problem is that the molecules tend to bind too tightly, a process called over-adsorption, which can restrict their movement and prevent them from forming longer chains.
Then there’s the energy problem, which is a classic double-edged sword. On the one hand, energy is absolutely necessary to organise molecules into complex structures. On the other hand, too much raw energy can be downright destructive. The energy sources available on early Earth, like UV radiation from the Sun, volcanic heat, or lightning strikes, weren’t exactly gentle tools. Sure, they might have sparked critical reactions, but they were just as likely to obliterate their own handiwork. For example, research led by chemist Jeffrey Bada has shown that ultraviolet light, while able to spark certain life-essential syntheses, tends to break down the same molecules as quickly as it makes them. The story is much the same with volcanic and geothermal energy. Research by Johnson and Li (2018) in the Journal of Prebiotic Chemistry found that vents can indeed help synthesise important biomolecules like amino acids. But there’s a catch, those same vents often get so hot and unstable that they destroy the molecules before they can participate in further reactions.
Lightning stories fare no better. The famous Miller-Urey experiment once wowed the world by demonstrating that electrical discharges could synthesise amino acids and other organic molecules from simple gases. But a more recent 2024 study published in the Proceedings of the National Academy of Sciences titled “Mimicking lightning-induced electrochemistry on the early Earth”, revisits the classic Miller-Urey experiments with a focus on both the synthetic and degradative pathways of complex organic molecules under simulated lightning conditions. Their findings suggest that while electrical discharges can help form essential biomolecules, they are just as likely to break these molecules down again. The creation and destruction go hand in hand, painting a picture where every chemical step forward is threatened by immediate erasure.
What complicates matters further is how these scenarios are recreated in the lab. Experimental setups typically isolate and control one energy source at a time, for practicality’s sake. But this controlled approach doesn’t reflect the ever-changing environment of early Earth, where multiple forces like lightning, UV radiation, and volcanic activity acted simultaneously and unpredictably. As Dr. Ian Fry aptly puts it, the disconnect between controlled laboratory conditions and the reality of these raw, multifaceted and interdependent energy conditions makes our grasp of chemical evolution fundamentally incomplete.
Adding to the disconnect, scientists often rely on “traps” in the lab: clever strategies to protect newly formed molecules from annihilation by the same energies that produced them. While this selective control helps scientists preserve reactions in the lab, nature does not discriminate; it offers no inherent protective measures to shield emerging organic molecules from the destructive impacts of those same environmental energies. These carefully controlled settings don’t replicate the unpredictable conditions of early Earth, and this gap is important to keep in mind when we try to draw conclusions about what these experiments might tell us.
To summarise, here is what I consider the key problems with the ‘prebiotic soup’ hypothesis as the cradle for the emergence of life on Earth:
- Destructive Interactions: The various forms of energy on early Earth would likely have resulted in damaging interactions that could have significantly diminished, if not entirely consumed, essential precursor chemicals. This constant cycle of creation and destruction could have significantly slowed down, or even halted, chemical evolution.
- Dilution Problems: The envisioned “prebiotic soup” was likely too dilute to support direct polymerisation. This dilution issue challenges the feasibility of achieving the necessary concentrations of organic molecules for life’s precursors to form and evolve.
- Lack of Geological Evidence: There is a conspicuous absence of concrete geological evidence supporting the existence of an “organic soup” on the primitive Earth, despite extensive research.
- Experimental Limitations: Laboratory experiments designed to recreate the conditions of early Earth and explore the origins of life frequently fall short of capturing the complex, dynamic, and often chaotic nature of our planet’s nascent ecosystems. These models fail to simulate the delicate balance between the constructive roles of energy sources in synthesising organic molecules and their destructive potential. The use of traps and other methodologies in these experiments, intended to protect synthesised organic products from degradation, does not reflect the unshielded conditions of the natural world.
Early Earth’s Atmosphere: Not So Welcoming After All
Here’s the thing about oxygen: it’s essential for life today, but it would’ve been a buzzkill for assembling life’s first building blocks billions of years ago. Even trace amounts in the air could have choked off the formation of organic molecules. Why? Oxygen creates oxidising conditions that both hinder their formation and accelerate their breakdown. That’s why origin-of-life experiments often leave oxygen out: in a low-oxygen, reducing environment, molecules like amino acids actually have a fighting chance to form and stick around.
But here’s the twist: early Earth wasn’t the pure “zero-oxygen” world Oparin and Haldane imagined. It’s likely that small amounts of free oxygen showed up much earlier than once thought, this is shown through oxidised minerals, photochemical pathways that split water compounds, and rock records that only make sense if a little O2 was around. A study published in the journal Science in 2007 found that certain iron formations from 2.5 billion years ago could only have formed if there was some free oxygen in the atmosphere. A 2014 Nature paper pushed that timeline back further, finding traces of oxygen in 3‑billion‑year‑old Australian rocks. And perhaps most striking, isotopic studies of sulphur published in Geochimica et Cosmochimica Acta, points to the presence of oxygen around 3.8 billion years ago.
This paints a far more complex picture of Earth’s atmosphere during its formative years. The presence of oxygen would have made early Earth less conducive, or even detrimental, to the emergence of life. It’s no longer as simple as “no oxygen, no problem.”
Moreover, the Miller-Urey experiments originally assumed that Earth’s early atmosphere was primarily made up of methane, ammonia, and hydrogen. That seemed reasonable in the 1950s. By the 1980s, though, geochemical evidence suggested a less reducing, more CO2‑ and N2‑dominated atmosphere. As one article put it bluntly:
“No geological or geochemical evidence collected in the last thirty years favours an energy-rich, strongly reducing primitive atmosphere (i.e., hydrogen, ammonia, methane, with no oxygen). Only the success of the Miller laboratory experiments recommends it.”
Fast-forward to the 1990s, and the gap between the classic Miller-Urey experiment and our evolving understanding of early Earth grew wider. By 1995, Science declared that the portrait of the early atmosphere painted by the Miller-Urey experiment bore little resemblance to reality. This sentiment was reinforced in 2008, when the journal reported, “Geoscientists today doubt that the primitive atmosphere had the highly reducing composition Miller used.” Unfortunately, this body of evidence doesn’t favour the original hypothesis but implies that chemical evolution was probably less plausible than the Miller-Urey experiments initially suggested.
The Indispensable Role of Human Intervention
Another thorny issue is that while the Miller-Urey experiment and those that followed aimed to recreate the conditions for life’s spontaneous emergence on Earth, they were anything but “spontaneous”. They were meticulously designed and tightly controlled by scientists, which is a far cry from the unpredictable prebiotic Earth.
Take ultraviolet (UV) light, for example. In origin-of-life research, scientists use UV light to simulate the sun’s radiation and its potential effects on chemical evolution. However, they often cherry-pick specific types of UV light, usually shorter wavelengths, because longer ones can be destructive to organic compounds. Nature doesn’t filter like that. On the early Earth, prebiotic chemicals would have been exposed to the full UV spectrum, helpful and harmful alike. Lab setups that filter out the rougher end of the spectrum, then, give us a far rosier picture than what chemistry in the real world would have faced.
Then there’s the issue of using other energy sources like heat, electrical sparks (to simulate lightning), and shock waves. But real lightning? It unleashes temperatures hot enough to obliterate fragile compounds. Real volcanic heat? Fierce, patchy, and short-lived—unlikely to sustain a steady conveyor-belt of synthesis. Simulated energy sources deliver just the right nudge under just the right conditions, but this control is anything but natural. And that points to the deeper problem. The lab, by necessity, is an intelligently controlled box. Early Earth was not. The prebiotic Earth was a dynamic and unstable environment: oceans in constant motion, shifting weather systems, and a complex interplay of chemicals interacting in innumerable and unpredictable ways. Reactions in that world wouldn’t have sat quietly in isolation—they’d have overlapped, clashed, and short-circuited each other. Why assume chemical reactions will behave the same way isolated in a lab as they would in the dynamic, complex prebiotic environment? Scientists describe this interplay as the “Concerto Effect,” in which chemical reactions do not occur in isolation but instead overlap, amplify, and interfere with one another in complex and often unpredictable ways. Within a primordial probiotic environment, such interactions likely produced disruptive consequences that impeded or even prevented the synthesis of more complex molecular assemblies.
So here’s the tension: To make these experiments work, scientists must carefully adjust the conditions—tweaking variables like atmospheric composition, energy inputs, and reaction isolation—to “coax” reactions toward a desired outcome. In doing so, they unintentionally introduce an element of design into a system meant to represent prebiotic Earth. This intelligent “nudge,” while necessary to get results, raises some big philosophical questions. Whenever researchers direct a reaction sequence or impose particular constraints upon a chemical system that are foreign to the system they are attempting to model, aren’t they effectively introducing an element of information and foresight into that system? If the laboratory result requires intelligent nudges to succeed, how much of what we’re really seeing is chemistry, and how much is an overarching intellectual order?
These origin-of-life experiments, while teaching us a ton about possible chemical pathways that could have contributed to life, also show how much we rely on intelligent input to make biologically relevant chemistry happen.
The Challenge of the Spontaneous Assembly of Life’s Essential Chemicals
For argument’s sake, let’s grant the idea that early Earth really did harbour a rich prebiotic “soup” brimming with organic molecules. The real puzzle isn’t whether those ingredients existed, it’s how they ever assembled into the first spark of life. After all, in the absence of a living biological agent, molecules don’t exactly have ambitions. They don’t naturally decide to band together and “evolve” toward becoming alive. Molecules are indifferent to the whole concept of life.
Yes, once life appears, organisms exploit chemistry with astonishing skill, hijacking reactions to survive, grow, and replicate. But without life already in the picture, we don’t see random molecules spontaneously self‑assembling into anything remotely like a living cell.
That’s where chemist James Tour steps in. A renowned Rice University professor and one of the most cited minds in chemistry and nanotechnology, Tour has made a career of spotlighting this very problem. As a synthetic chemist, his argument is blunt: Despite decades of effort, the leap from simple molecules to an autonomous, self‑replicating cell remains unsolved, which makes a spontaneous origin of life look increasingly unlikely. To say the least, I have spent a fair chunk of time listening to him, and six recurring issues stand out, though I would argue that there’s some overlap among them:
1. Chirality: The Left-Hand, Right-Hand Fiasco
One of the most curious quirks of biology is something called chirality, or molecular handedness. Think of hands: left and right are mirror images, but a left hand won’t fit a right glove. Many biomolecules work the same way, amino acids, sugars, and lipids come in left- and right‑handed forms, but life shows a strict bias: proteins use left‑handed (L) amino acids, and nucleic acids use right‑handed (D) sugars. That uniformity isn’t trivia, it’s essential for precise molecular recognition and function; flipping a single amino acid’s handedness can derail protein folding and activity.
Rewind to early Earth and the picture gets messy. Ordinary chemistry tends to produce equal mixes of left and right. In a racemic soup, the odds of randomly chaining 100 purely L‑amino acids is 1 in 2¹⁰⁰, and even one D‑amino acid incorporated into a protein chain can disrupt the protein’s proper folding, rendering the protein unfunctional. Since proteins do most of the heavy lifting in cells (like speeding up reactions or building structures), this precision is critical.
So, how did chemistry on early Earth manage to only use left-handed amino acids and right-handed sugars? Various hypotheses have been proposed to address the chirality problem: polarised light selection, mineral-catalysed asymmetric synthesis, or amplification of statistical fluctuations. Yet even under carefully controlled conditions with purified reagents, optimal pH, precise temperatures, and specialised catalysts, synthetic chemists still struggle to replicate the flawless homochirality that life achieves so effortlessly. The best laboratory attempts produce modest enantiomeric excesses, far from the near-perfect homochirality required for functional proteins and nucleic acids.
But the problem runs deeper. It’s not sufficient to merely have the correct handedness; molecules must also link up with precise regiochemistry (the right connection points) and achieve the proper stereochemistry (exact three-dimensional orientations). Each of these requirements creates a specifications pyramid that multiplies the improbability of this occurring randomly. If today’s cutting edge science struggles to reproduce the razor-sharp uniformity of nature, then why are we confident that, somehow, a “primordial soup”, without any intelligent directing force acting on it, supposedly managed it billions of years ago?
2. Selection mechanisms: The Bootstrap Paradox
Building even the most rudimentary protocell takes a surprising degree of molecular precision. It’s not enough to have the right ingredients, you also need them lined up in exactly the right order, orientation, and timing. Take something as “simple” as a phospholipid membrane. To get one, fatty acid chains have to be matched with the correct head groups, the right chirality, and specific chain lengths. Miss any of those details, and you don’t end up with a stable membrane at all—you get leaky, fragile bubbles that collapse long before they can host any meaningful chemistry.
And the challenge goes well beyond membranes. Functional nucleotides depend on coupling the correct nitrogenous base to the right sugar in the exact stereochemical configuration, followed by phosphorylation at the proper position. Slip up on any one of those and you get either a defective nucleotide or an inhibitory molecule that actively disrupts subsequent chemistry. In the lab, getting this right takes tightly controlled conditions, purified reagents, and stepwise protocols—luxuries no plausible prebiotic setting could consistently offer. To then rebuttal this with the idea that simple physical forces like electrostatics or hydrophobic interactions could serve as adequate “selectors” fundamentally misunderstands the nature of biological specificity. While these forces certainly influence molecular behaviour, they operate indiscriminately. Electrostatic attraction doesn’t distinguish between a productive nucleotide addition and a chain-terminating analog, both carry similar charges. Hydrophobic effects can drive membrane formation, but they’re equally happy to incorporate membrane-disrupting molecules alongside functional lipids.
True biological selection means telling apart molecules that look chemically similar but act very differently. That calls for recognition systems able to judge not just immediate fit, but downstream function. In life, that discrimination rests on pre-existing information-rich structures, proteins that recognise specific molecular features, or nucleic acids that “encode” selection criteria. And there’s the bootstrap problem: Suppose, for the sake of argument, there were “selectors” in that ancient environment, something choosing the right molecules. Those selectors represent exactly the kind of specified complexity that selection mechanisms are supposed to explain. Who, then, selected the selectors? It’s a loop—selectors would need other selectors to choose them, and so on.
There’s also the error issue, and prebiotic chemistry operates under constraints that make error correction virtually impossible. Unlike biological systems with sophisticated proofreading mechanisms, primitive chemical systems offer no “undo” function. When an incorrect amino acid incorporates into a growing peptide chain, or when a wrong nucleotide adds to an extending RNA molecule, the error typically becomes permanent. Energetically speaking, removing errors often costs more than a prebiotic setting can pay.
That sets up a failure mode. As chains get longer, errors pile up fast. A hypothetical prebiotic system might successfully assemble short, functional sequences occasionally, but maintaining fidelity over the dozens or hundreds of steps required for meaningful biological function becomes statistically out of reach. Each error not only ruins that particular molecule, but often produces inhibitory products that interfere with subsequent attempts.
Living systems beat this by preserving fidelity in inherited information—DNA sequences that reliably guide molecular structures and processes. This memory allows organisms to build on past successes and avoid repeating failures. Prebiotic systems don’t have that advantage: no durable record of success, no accumulation of working “recipes,” and nothing to stop the same destructive errors from recurring. A single misplaced chemical can derail the entire assembly, and once a faulty unit is incorporated, correcting it is rarely simple and often impossible. It’s like a sculptor at work: one wrong strike can shatter the piece. Without memory, each molecular attempt begins from scratch (assuming it does begin again), facing the same overwhelming odds.
Ultimately, the selection problem reduces to an information problem. Successful molecular selection requires biological information that specifies which components to choose, in what order to assemble them, and how to verify correct assembly. This information must be sufficiently detailed to distinguish between thousands of chemically similar but functionally distinct possibilities, robust enough to maintain fidelity across multiple generations, and accessible enough to guide actual chemical processes.
3. Purification: The Leaky Bucket Problem
Purification is the quiet precondition of life. Before genes, before enzymes, before metabolism as we know it, something had to sort what helped from what harmed. Early twentieth‑century thinkers like Alexander Oparin and J. B. S. Haldane imagined a world where chemistry gradually organised itself, and the mid‑century Miller–Urey experiments populated the idea that simple organics could have been present. But the problem soon shifted from making molecules to keeping the useful ones apart from the junk. Life, even in its most tentative forms, needed a way to concentrate, protect, and steward fragile chemistry long enough for selection to get a foothold. Impurities cripple prebiotic reactions because chemistry, unlike biology, lacks enzymes to select the desired reactants from a messy mixture, making laboratory success with pure reagents a poor guide to plausibility.
That is where membranes enter the story. Back in the 1920s, Russian biochemist Alexander Oparin proposed that life began when organic molecules became organised into what he called “coacervates”—droplets that could concentrate chemicals and create distinct internal environments. It was a prescient insight, though Oparin couldn’t have imagined just how sophisticated these biological boundaries would turn out to be.
The real breakthrough came in the 1970s when scientists like David Deamer began studying how simple lipid molecules behave in water. They discovered that under the right conditions, molecules could arrange themselves into hollow spheres called vesicles, creating natural “bags” that could, in theory, house the chemistry of early life.
Our modern cell membranes are far more than just molecular bags. The lipid bilayer itself acts like a selective wall, letting water and small molecules pass through while blocking larger, potentially harmful compounds. But the real magic happens with the embedded proteins that act as molecular bouncers. These protein channels and pumps don’t just passively filter; they actively transport molecules against concentration gradients, maintain electrical potentials, and even communicate with other cells.
Scientists have made impressive strides in recreating simpler versions of these membrane systems. Pier Luigi Luisi’s group has shown that basic vesicles can form from simple fatty acids, creating compartments that grow, divide, and even compete with each other. Jack Szostak’s laboratory has demonstrated that these primitive membranes can selectively allow certain molecules to pass through while retaining others, which is a crucial property for any proto-cell.
But while these experiments show that basic compartmentalisation is possible, they’re still light-years away from the sophisticated purification that any cell relies on. Modern membranes don’t just leak selectively; they actively pump, sort, and process thousands of different molecules simultaneously. No laboratory experiment has come close to replicating this suite of functions without borrowing heavily from existing biological systems.
Faced with this complexity, researchers have proposed various “stepping stone” scenarios for early purification systems. Günter Wächtershäuser suggested that mineral surfaces around hydrothermal vents could have acted as primitive filters, concentrating organic molecules while excluding harmful compounds. Others have pointed to clay particles, which can selectively bind certain organic molecules, or to environmental cycles that might concentrate key ingredients through repeated drying and wetting.
These ideas sound reasonable in principle, but mineral surfaces that attract useful organic molecules are equally welcoming to destructive contaminants. Simple fatty acid membranes may form protective bubbles, but they leak like sieves, shedding the very ingredients they’re meant to safeguard. Mechanisms like mineral catalysts, flimsy membranes, and metal ions by themselves don’t get us far. Without the help of sophisticated transport proteins—which depend on genetic information—the level of selective purification life requires has never been shown to emerge through any spontaneous processes.
Just picture the Goldilocks scenario: mineral surfaces filter and concentrate the right molecules, lipid vesicles form at just the right moment to encapsulate them, and replication begins before the whole system degrades. This molecular choreography would need to happen under conditions that suit RNA stability, lipid chemistry, and mineral interactions simultaneously, while maintaining precise pH levels and temperatures that don’t destroy the very molecules you’re trying to protect. Laboratory researchers can achieve each of these steps individually with careful control and intervention. But no natural environment has been shown to spontaneously orchestrate this entire symphony of events.
This brings us to the heart of the paradox: Life’s purification systems rely on sophisticated proteins reading and acting on genetic information, yet that very information couldn’t have lasted without purification in the first place. It’s a biological Catch‑22, and the idea that such a finely tuned purification system arose spontaneously strains plausibility.
4. Chemistry is fragile: Too Hot, Too Cold, Too Dead
Chemistry is exquisitely sensitive to context, even minor deviations in temperature (often within 5-10°C), pressure changes of just a few atmospheres, or pH shifts of 0.5 units can completely redirect reaction pathways or halt them entirely. Left uncontrolled, variables such as temperature, pressure, solvent, light, pH, mineral surfaces, and even trace gases can send reaction networks down side paths, stall them, or cause them to congeal into tar-like mixtures, and the more steps involved, the faster control slips away. Building complex molecules becomes exponentially more difficult as these environmental factors drift from their optimal ranges. The sobering reality is that chemistry is exquisitely fragile, requiring levels of control that seem at odds with the environments where life supposedly began.
Consider the formation of peptides. For amino acids to link together, they must undergo condensation reactions where water molecules are systematically removed. This process faces a substantial energy barrier that typically requires specific catalysts to overcome. In living cells, aminoacyl-tRNA synthetases and ribosomes, powered by ATP hydrolysis, drive these reactions with remarkable efficiency. Strip away this cellular assistance, however, and peptide bond formation becomes a rare and inefficient process, making meaningful protein assembly virtually impossible on prebiotic timescales.
The challenge extends beyond mere synthesis. Many organic molecules suffer from inherent instability, readily degrading when exposed to ultraviolet radiation, prolonged contact with water, or temperature fluctuations. The very compounds essential for life’s emergence must somehow persist long enough in relatively hostile environments to undergo subsequent reactions and self-assemble into increasingly complex structures. As mentioned earlier, it’s because of this that modern biochemistry laboratories are tightly controlled. Gerald Joyce’s so-called “self-replicating” RNA enzymes work only under laboratory perfection: precise buffers, temperatures controlled within 2°C, purified substrates, and zero metal contamination. David Deamer’s membrane experiments demand lipid concentrations that dwarf anything geological processes could realistically produce. Most revealing is Jack Szostak’s protocell work (the field’s crown jewel), which creates dividing vesicles only when spoon-fed pre-made fatty acids and nucleotides.
To be successful, scientists meticulously monitor molecular behaviour under varying conditions, adding catalysts or inhibitors as needed, adjusting parameters in real-time, and guiding reactions toward desired outcomes. This level of micromanagement has yielded impressive results. Researchers have successfully created basic membrane structures, simple vesicles, specialised molecular modules that perform specific tasks, and even biomimetic compartments that mimic cellular organelles. But every step is observed, measured, and fine-tuned because if the environment isn’t controlled, even the slightest oversight can derail experiments, producing failed reactions or unwanted byproducts that must be painstakingly separated and discarded.
The gap between carefully creating functional components and a cohesive living cell remains enormous. A cell represents far more than the sum of its molecular parts, it requires a whole network of interdependent processes, regulatory mechanisms, error-correction systems, and energy management protocols that must all coordinate with each other. System biologists call this “autocatalytic closure”—each subsystem depends on products from the others, creating circular dependency problems that resist stepwise assembly.
Now, if assembling even fragments of cellular “machinery” demands such precise conditions in a tightly controlled laboratory, how could the precursor molecules of life have spontaneously formed and organised within the environments of the early Earth? The idea of complex, multi-step chemical pathways unfolding unaided near volcanic vents, in tidal pools, or within mineral matrices—without guidance or regulation—strains credibility. To accept spontaneous abiogenesis requires a whole lot more faith than many scientists care to admit.
5. Specificity: When One in a Trillion Isn’t Good Enough
As my old biology teacher once told me: Specificity matters. Proteins don’t just “work” because amino acids are strung together. They function because particular amino acids are arranged in the right sequences that allow the chain to fold into highly specific three‑dimensional shapes.
And the odds? They’re mind‑bending. Take a relatively modest protein of 150 amino acids. The number of possible sequences is about 20150. From that astronomical landscape, biophysicists Pei Tian and Robert B. Best dug into the question in their 2017 Biophysical Journal study, How Many Protein Sequences Fold to a Given Structure? A Co‑evolutionary Analysis. Looking at ten different protein domains, they estimated that only about one sequence in somewhere between 1024 and 10126 folds into anything even remotely functional. The rest? They either flop into a useless tangle, clump together, or worse—misfold into the toxic amyloid fibrils linked with Alzheimer’s, Parkinson’s, and Huntington’s diseases.
But here’s the puzzle: how do you arrive at the right sequence in the first place? In modern cells, this requires an intelligent and coordinated system that includes:
- Transfer RNAs ferrying specific amino acids.
- Aminoacyl‑tRNA synthetases (complex proteins themselves) attaching the correct amino acid to each tRNA.
- Ribosomes that read mRNA and stitching amino acids together.
- Chaperone proteins shepherding the chain into its correct fold.
- Quality‑control systems, spotting and eliminating misfolded products.
Each of these is a case study in molecular engineering, and each would need a plausible origin story in any serious theory of life’s beginnings. The RNA World hypothesis tries to sidestep this by proposing that RNA came first, doing double duty as both genetic material and catalyst. But this still doesn’t solve the problem; it just moves it. RNA faces its own serious hurdles that we will discuss more later on. For now, James Tour, who has spent decades making complex molecules in the lab, stresses the point that even building short RNA chains requires careful controls, pure reagents, and intricate protection/deprotection steps. The idea that 40–80‑nucleotide ribozymes, which is the bare minimum for catalytic function, spontaneously assembled on the early Earth? He calls it synthetic chemistry fantasy.
Of course, the fundamental issue running through all this is explaining the information. Biology doesn’t just need molecules, it needs specified molecules. Not just any sequence, but the right sequence—whether for proteins, RNA, or DNA, whether for folding, catalysis, or metabolism. At every stage, from atomic bonds up to cellular networks, the requirement for specification intensifies.
And here’s Tour’s challenge to the field: chemists know how difficult it is, even in pristine labs with modern equipment, to make these molecules and capture their specificity. So to hear theoretical biologists claim they formed unguided in a chaotic prebiotic soup, with impurities and side reactions, stretches scientific plausibility. For him, it’s not enough to invoke “emergence” or “self‑organisation.” Until we can show real, testable chemical pathways that produce functional biomolecules under conditions resembling early Earth, the origin‑of‑life story remains, at best, a speculative sketch.
6. The Role of Time in Life’s Origins: Friend or Foe?
When we talk about life’s beginnings, it may feel intuitive to respond: “It only had to happen once, over hundreds of millions, or even billions, of years.” The assumption is that if you wait long enough, the right molecules will eventually appear, organise, and evolve into primitive life.
But what if time isn’t always on our side?
In chemistry, especially when forming complex molecules, time can actually work against you. Nobel Laureate Richard Roberts has noted that synthetic reactions don’t come with an off-switch. In a prebiotic world, without some kind of intervention, reactions would keep running until the reactants were gone or until external conditions disrupted them. Once the “right” molecules formed, there’d be nothing to stop the chemistry from continuing, using them up or producing a messy mix of by-products.
As a synthetic chemist, Tour draws on the gritty realities of the lab and argues that when it comes to organic chemistry, time isn’t your friend—it’s your enemy. Molecules tend to fall apart when left unchecked. This is what Tour calls the stability problem. Take RNA, for instance. Under favourable lab conditions, a large quantity might have a half-life of 100 days. But shrink that down to a single strand that might randomly form in a prebiotic soup, and its lifespan collapses. A short RNA molecule of 600 nucleotides would last only about four hours before degrading. Proteins face a similar dilemma. A modest polypeptide of 200 amino acids floating in water breaks down in around 13 days. Yet functional proteins usually need not hundreds, but even thousands of amino acids lined up.
Chemists in the lab compensate for this with constant replenishment of purified materials. But in a prebiotic world, there is no hand topping up the reactants once they’re consumed. Over millions of years, even promising chemistries would simply run out of fuel with no obvious way to start over.
In labs, chemists can fine-tune conditions to get specific outcomes. But in a natural setting, it’s not clear that such control is present. Reactions just keep going, often overshooting, drifting into chemical dead-ends, or producing complex tangles that render the resulting molecules useless. Even simple tasks become monumental. For example, linking two amino acids together sounds easy—but reactive side chains, present in about half of the 20 standard amino acids, interfere with the process. Once these cross-links form in the wrong place, as Tour puts it, “game over.”
And so the paradox emerges. We tend to think of time as the great enabler, the resource that makes the improbable possible. But when it comes to life’s chemical beginnings, too much time may actually be the enemy. Instead of giving the right molecules more opportunities to assemble, it gives them more chances to fall apart, drift, or clog the process with chemical noise. Time, left unchecked, tangles the chemistry rather than clarifies it, which is why Tour argues that beneath biology lies an information paradox that needs to be explained.
Tour’s Conclusion
Given the extraordinary complexity required in molecular sequencing, the exact conditions necessary for chemical reactions, and the intricate array of functional structures that must align in the processes leading to the origin of life, it becomes increasingly difficult to support the idea that life emerged spontaneously. The leap from non-living matter to living organisms demands a staggering level of control, order and precision, something that purely unguided natural processes seem unlikely to accomplish on their own. Even with our most advanced technology and intelligent intervention, we have yet to successfully replicate all the steps required for biological life, which raises doubts about the likelihood of a purely naturalistic explanation for life’s origin.
Entropy, Information, and the Unresolved Challenge of Life’s Origins
In 1944, physicist Erwin Schrödinger posed a deceptively simple question that would haunt biologists for decades: “What is Life?” His answer was equally puzzling: living things, he suggested, feed on “negative entropy,” creating order by consuming the disorder around them. This insight cuts to the heart of an interesting question on the origin-of-life: how do complex biological macromolecules, like DNA and proteins, form spontaneously in an environment subject to entropy?
Entropy is a physics idea about disorder. It is the universe’s way of reminding us that nothing lasts forever. It’s a term from physics that describes how everything, from a carefully built sandcastle to a star in the cosmos, tends to move from order to disorder. This idea comes from the second law of thermodynamics, which tells us that the total entropy (or disorder) of the universe always increases over time. In other words, the universe “prefers” messiness. Energy spreads out, systems become less efficient, and even the most stable structures eventually break down.
This concept was shaped by scientists like Sadi Carnot, Rudolf Clausius, and Ludwig Boltzmann. Carnot first noticed that no machine could be perfectly efficient, some energy is always lost as useless heat. Clausius later introduced the term “entropy” in 1865, from the Greek word for “transformation,” while Boltzmann connected entropy to probabilities, showing there are far more ways for particles to arrange themselves in a disordered state than in an orderly one. At its heart, entropy explains why things fall apart, why life feels so delicate, and why perfection seems so fleeting.
How does this universal drift toward disorder relate to the origin of life? The question is simple: How could life’s essential macromolecules, which are highly ordered structures, arise from simpler, more disordered precursors like amino acids, sugars, and phosphates, in a universe that trends towards increasing entropy (disorder)?
The answer lies in a surprising twist: while the second law of thermodynamics says that the total entropy of the universe must always increase, local pockets of order can form, as long as the overall entropy still climbs. This idea is captured by the term “negative entropy,” or “negentropy.” Though it may seem counterintuitive, systems can become more ordered when they are part of a larger, open system that exchanges energy and matter with the environment.
Think about ironing a wrinkled shirt. You’re imposing order by smoothing out the fabric, which reduces its entropy. But this doesn’t break any natural laws because the energy you use, both from your body and the hot iron, releases heat and increases disorder elsewhere. So, while the shirt becomes more orderly, the total entropy of the entire system (you, the iron, and the room) still goes up.
This same principle might help explain how life’s first molecules formed. Early Earth was an “open system,” meaning it constantly received energy inputs from external sources like sunlight, lightning, and geothermal heat. These energy flows could drive localised decreases in entropy, allowing simpler molecules like amino acids and sugars to assemble into more complex macromolecules, such as proteins or RNA. Essentially, raw energy acted like a cosmic ironing board, temporarily countering the natural pull toward disorder and enabling the building blocks of life to come together.
Of course, there are still challenges. Earth’s ability to foster local order is always temporary, as it depends on a constant influx of energy. This raises doubts about whether it could sustain the conditions long enough for the origin of life. Regardless, the popular census is that steady energy flow meant that there were likely some environments that could hold just the right conditions for favouring chemical complexity.
Still, we shouldn’t overreach. Energy can generate patterns of order, but this is not the same as the highly specific and dynamic organisation we observe in living systems.
Think about DNA. It’s not just the molecule’s structure that matters, what makes DNA extraordinary is the information it carries. Its double-helix structure, famously described by Watson and Crick, is functionally optimised for this purpose. The sequence of its four nucleotides forms a molecular “code” that provides templates for building proteins. DNA’s primary role is to act as a durable, high-density information storage medium for the genetic “recipes” that must be interpreted, edited, and executed by the intricate cellular parts that surround it.
Let’s compare three cases:
Think about a salt crystal. At first glance, it seems impressive, sodium and chloride ions arranged in a perfectly ordered, repeating pattern. No matter where you look, it’s the same predictable structure: sodium, chloride, sodium, chloride. This kind of arrangement is orderly and impressive, no doubt, but it doesn’t carry much information. Once you understand the basic rule—sodium alternates with chloride—you’ve cracked the code. There are no surprises, no deeper meaning. It’s all repetition. Orderly? Yes. Full of information? Not so much.
Now imagine a heap of random polymers, and in this case, they’re all mixed up with no particular order or pattern. Sure, the polymers themselves are complex molecules, but because they’re arranged randomly, there’s no real functional organisation. So, while the system is complex, it lacks any meaningful information.
Biological life, on the other hand, hits the sweet spot where order and complexity come together in a way that creates information. Scientists often call this “specified complexity.” Back to our example of DNA: its sequence of bases (adenine, thymine, guanine, and cytosine) isn’t just random, nor is it repetitive like the salt crystal. Instead, these bases are arranged in a specific order to provide template information for the cell to make proteins.
In part, this is what sets life apart from mere chemistry. A salt crystal might be beautifully ordered, but it doesn’t actually do anything. A chaotic jumble of polymers might be complex, but it doesn’t hold the information for anything useful. DNA, and life in general, combines the best of both worlds. It’s ordered enough to be functional and structured, but complex enough to carry functional information.
But here’s the real puzzle: can energy, even when focused and filtered by natural processes, actually create information? Order—Yes, maybe. Repetition—Possibly. But information, that’s a different beast altogether. Edward Steele and his thirty-two co-authors, across eleven countries, in ‘Progress in Biophysics and Molecular Biology,’ tackled this very question, and concluded:
“The transformation of an ensemble of appropriately chosen biological monomers (e.g., amino acids, nucleotides) into a primitive living cell capable of further evolution appears to require overcoming an information hurdle of super astronomical proportions, an event that could not have happened within the time frame of the Earth except, we believe, as a miracle. All laboratory experiments attempting to simulate such an event have so far led to dismal failure.”
Thermodynamics can nurture pockets of order, but it also sets limits on how much “coding work” nature can do on its own. In other words, you might get some structure, but you won’t get the kind of organised information that life needs. Negative entropy might explain how some order forms, but just as a gold bar cannot emerge from a lump of coal regardless of the energy or effort applied, information cannot be derived from mere negative thermal entropy. Bricks might be necessary to build a house, but a house won’t self-assemble without a plan. Similarly, regardless of negative entropy, amino acids or nucleotides won’t spontaneously form functional proteins or RNA without a “drive” or “ambition,” and existing information to use in the first place.
That’s the crux of the limit. An open system with steady energy helps, but it doesn’t explain the jump to functional, coded complexity that we observe in living systems. Amino acids in a warm pond or by a vent won’t assemble into a cell just because the energy, conditions—even endless time—are “right”. Something more is needed, something nature, on its own, seems ill-equipped to supply. In part two, we’ll dig into that “something” in detail.
The Hurdle of Self-Replication in Life’s Origin
Self-replication remains one of the most perplexing puzzles in science. It’s the ultimate leap from chemistry to an evolving world of biology. Without self-replication, life as we know it couldn’t exist, yet there is so much about this process we don’t understand.
Abiogenesis claims that life started through unguided chemical reactions that, against all odds, produced a simple self-replicating molecule. That first replicator would have kicked off biological evolution. Natural selection, random mutations, and environmental pressures would have done the rest, slowly transforming that primordial replicator into the first cellular organisms.
But here’s the rub: self-replication isn’t simple. It’s a marvel of precision and coordination. James F. Kasting, a scientist renowned for his work in planetary habitability, pointed out the difficulties in his book How to Find a Habitable Planet. He mentioned that “the origin of a self-replicating molecule, which is capable of undergoing Darwinian evolution, is currently one of the most fundamental problems in science and one that is largely unsolved.” Biologist Eugene Koonin echoed this, highlighting that current theories offer intriguing leads but fail to explain how the first efficient RNA replicase or translation system could have emerged:
“Despite considerable experimental and theoretical effort, no compelling scenarios currently exist for the origin of replication and translation, the key processes that together comprise the core of biological systems and the apparent pre-requisite of biological evolution. The RNA World concept might offer the best chance for the resolution of this conundrum but so far cannot adequately account for the emergence of an efficient RNA replicase or the translation system.”
When a cell replicates, it doesn’t just split in half. It undergoes a highly coordinated in-house engineering process. The cell expands, constructs a replica within its own membrane, and then partitions itself, releasing a new cell into its surroundings. This ensures accuracy, protects the process from outside disruption, and keeps components from diffusing away. To help you imagine, visualise this process as a car expanding its frame to accommodate a second car, assembling the new components within this protected space, and then constructing a dividing wall to release a fully functional, identical car on the road beside it. It sounds like science fiction, but it captures the core idea: A true self-replicating system must autonomously find, acquire, and process materials, generate energy and have feedback and quality control mechanisms.
How could something so intricate arise spontaneously? Even DNA and RNA can’t self-replicate without help. They rely on each other and an array of cellular machinery. Geneticist Michael Denton explains such a feat:
“What we would be witnessing would be an object resembling an immense automated factory, a factory larger than a city and carrying out almost as many unique functions as all the manufacturing activities of man on earth. However, it would be a factory which would have one capacity not equalled in any one of our most advanced machines, for it would be capable of replicating its entire structure within a matter of a few hours. To witness such an act… would be an awe-inspiring spectacle.”
Richard Dawkins claimed in The Selfish Gene that “a molecule that makes copies of itself is not as difficult to imagine as it seems at first, and it only had to arise once.” Yes, just imagine. The idea of such a self-replicating entity arising spontaneously demands a great deal of imagination. Eric H. Anderson captures this dilemma well:
“The accumulated evidence, taken together, strongly suggests that self-replication lies at the end of a very complicated, deeply integrated, highly sophisticated, thoughtfully planned, carefully controlled engineering process… The abiogenesis paradigm, with its placement of self-replication as the first stage of development, is fundamentally flawed at a conceptual level. It is opposed to both the evidence and our real-world experience and needs to be discarded.”
Conclusion—Beyond Naturalism
The conventional story of life’s genesis—that tidy, domino-line of chemical events—feels incomplete. The usual take on abiogenesis tends to skip the tough questions, leaning hard on naturalism as the only “scientific” way to see it. That’s where we go wrong. Somewhere along the line, we let a philosophical assumption—not born of science itself—set the rules for what counts as scientifically “acceptable.” And in doing so, we’ve left a big piece of the origin-of-life story untold.
While we haven’t yet fully explored alternative theories, such as the RNA World Hypothesis, or the intricacies of molecular self-assembly (though we absolutely will in the next chapter), the point here is simple: the field of chemical evolution is anything but settled. To treat it as a done deal is to miss the real, ongoing debates—debates that press hard against the notion that life just sprang up from lifeless matter. It’s not that the more we learn, the gap steadily narrows, and a naturalistic explanation comes into view; it’s that the deeper we dig, the gap widens, and a purely naturalistic framework feels less and less plausible.
Plenty of leading scientists are open about the gaps. Theoretical biologist Stuart Kauffman puts it bluntly: “Anyone who tells you that he or she knows how life started on the earth some 3.45 billion years ago is a fool or a knave. Nobody knows.” Likewise, Jack W. Szostak, a Nobel laureate, stated that “It is virtually impossible to imagine how a cell’s machines, which are mostly protein-based catalysts called enzymes, could have formed spontaneously as life first arose from non-living matter… Thus, explaining how life began entails a serious paradox.” Harvard chemist George Whitesides admitted, “Most chemists believe, as do I, that life emerged spontaneously from mixtures of molecules in the prebiotic Earth. How? I have no idea… We need a really good new idea.” Elsewhere, he states: “I don’t understand how you go from a system that’s random chemicals to something that becomes, in a sense, a Darwinian set of reactions that are getting more complicated spontaneously. I just don’t understand how that works.” Antonio Lazcano, a renowned theoretician, noted in his Origin of Life entry in the Springer Encyclopedia of Astrobiology that: “A century and a half after Darwin admitted how little was understood about the origin of life, we still do not know when and how the first living beings appeared on Earth.” James Tour provided a similar statement: “based on what we know of chemistry, life should not exist anywhere in the universe. Life’s ubiquity on this planet is utterly bizarre, and the lifelessness found on other planets makes far more chemical sense.”
So, what do we do with this uncertainty? We acknowledge it. We accept that we need to broaden our perspective.
Imagine a nanotech device that generates energy, processes information, and runs other essential functions. Outside biology, we’d take that level of complexity and efficiency as evidence of a directed, intentional origin. When we look at cells, with their purposeful structures and coordinated processes, we often see signs that feel like intentionality: foresight, coordination, directed outcomes. Intelligent Design advocates argue that, based on our everyday experience, the advanced organisation and information handling in cells points to some form of intentional cause. That appearance could be an illusion, and we should keep that in mind, but it might also be a clue.
For instance, consider if scientists were to build a cell from scratch in a lab, would that disprove a purpose-driven emergence? Arguably, it would demonstrate the very principle: complex life requires intelligent assembly. Bringing a non-random origin into origin-of-life discussions can seem unconventional, even taboo, especially in mainstream science which leans on naturalistic assumptions. Still, I get the appeal of the design argument; it’s a common-sense read of the data. That being said, ideas about intelligent design have their own problems and are often oversimplified in popular discussion. In this book’s conclusion, I’ll offer a different kind of teleological model, one that departs from the usual framing. The aim here is simply to recognise the limits of what we know and give ourselves permission to explore other models. As we move to part two of this book, I simply ask that you consider these alternative ideas with an open mind, which doesn’t mean you have to necessarily accept them, I just hope you will entertain them.
