Origin story

 

They still push the chemical self replication model which has zero hope of realization.

I contend that self replicating dark matter processors came first.  This is a much less daunting problem.  What is nifty is that the processor can also signal a molecule to be attracted to another nearby molecule and thus combine.  This is necessary in order to fabricate third tier life forms and certainly to animate them.

A 3D self replicating processor would be like the wonderful game of Life created by Conway.  Better yet it would fill the universe itself.  Our challenge is to actually create such a processor.  I do not think it is beyond us.

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Origin story

Perched on the cusp between biology and chemistry, the start of life on Earth is an event horizon we struggle to see beyond

Detail of Sunrise III (1936-37), by Arthur Garfield Dove. Gift of Katherine S Dreier to the Collection Société Anonyme/Yale University Art Gallery

Natalie Elliot

is an assistant professor at St John’s College in Santa Fe, New Mexico, and a science writer. Her writing has appeared in The New Atlantis and Parallax. She lives in Santa Fe and New York.

4,000 words

Edited by Pam Weintraub

https://aeon.co/essays/physics-and-information-theory-give-a-glimpse-of-lifes-origins

How did life originate? Scientists have been studying the question for decades, and they’ve developed ingenious methods to try to find out. They’ve even enlisted biology’s most powerful theory, Darwinian evolution, in the search. But they still don’t have a complete answer. What they have hit is the world’s most theoretically fertile dead end.

When scientists look for life’s origins, they usually work in one of two directions. They work backwards in time through the record of organisms that have lived on Earth, or they work forward from one of the many hypothetical prebiotic worlds in which life could have emerged.

When they work backwards, they travel through the fossil record, and through the branches of genetic relationships between species. They also look for geochemical signatures that mark life’s presence in the distant past. Somewhere at the end of the line lies life’s oldest ancestor. This ancestor has acquired a name: LUCA, the last universal common ancestor. It also has a hypothetical nature and place in the biological order of things: LUCA is a microorganism or group of microorganisms from which all life on Earth descends. Though scientists, such as the molecular biologist William Martin of Heinrich Heine University in Düsseldorf, and his team, have been able to infer some part of LUCA’s genetic profile, they don’t have a complete portrait. They also can’t see beyond LUCA: LUCA isn’t necessarily the first life, and scientists can’t see what other life forms could have cropped up before it. Ultimately, LUCA is the living system that scientists identify to say that, at least once, somewhere, spontaneously, life got its start on Earth.

To emphasise that any life before LUCA is currently unknowable, scientists call LUCA a phylogenetic event horizon. Phylogeny is the study of genetic relationships between species over evolutionary time; it allows scientists to trace the history of life. The term ‘event horizon’, in contrast, hails from astrophysics, and refers to the threshold around a black hole. Beyond this threshold, escape velocity surpasses the speed of light. Since nothing can travel through space faster than the speed of light, there’s no way to witness any event that takes place there. So too with LUCA: it marks a biological boundary beyond which no observer can see. Since there’s no record for phylogenetic analysis to work upon before LUCA, scientists can’t follow the biological record there.

Where to go from here?

It’s in the face of phylogenetic limits that scientists are peering into the deep past, nonetheless, and theorising hypothetical beginnings anew. In the 1920s, for example, the Soviet biochemist Aleksandr Oparin and the British-Indian scientist J B S Haldane independently began to develop theoretical models of life’s chemical origins, asking how life could have emerged from the stuff of early Earth. In the 1950s, the American chemists Stanley Miller and Harold Urey began to test those hypotheses in the lab by attempting to show that with basic chemicals of early Earth, they could generate simple biomolecules.

First, they created an environment made of gases that they thought were present in the Earth’s early atmosphere. Then they ran an electrical current through them to simulate lightning. Thus stimulated, their primordial soup produced a set of simple biomolecules, including amino acids, the basic building blocks of life.

The Miller-Urey experiment suggested that experimentalists could generate some of the conditions of early life in the lab. Yet the effort was riddled with difficulty. For one, Miller and Urey weren’t able to simulate conditions that caused those simple building blocks to form complex biomolecules such as nucleotides, or even more complex biomolecules such as proteins and nucleic acids, which are essential to life. And later, scientists theorised that Miller and Urey were wrong about the very environment they envisioned. Since then, no one has brewed up life spontaneously from the elementary chemicals of Earth’s primordial soup, and the number of possible theoretical worlds in which life got its start has only proliferated. To anyone watching, it might seem like we’d need a set of parallel universes to test all of the alternatives.

Whatever path scientists have taken to look for life’s origins, most look to the ideas of Charles Darwin, in his book On the Origin of Species (1859), to help them answer crucial questions in the field. Though Darwin didn’t think that the science of his day could explain life’s origins directly, many of his ideas became integral to the advancement of the field. Darwin’s metaphorical tree of life, for example, depicts the descent of species over evolutionary time, and initiated the phylogenetic hunt for LUCA. Darwin’s remark in On the Origin of Species that ‘probably all the organic beings which have ever lived on this Earth have descended from some one primordial form, into which life was first breathed’ led his contemporaries to embrace the idea that life on Earth has a single origin. His speculation, in his letter to the botanist J D Hooker in 1871, that life might have formed in some ‘warm little pond with all sorts of ammonia & phosphoric salts, – light, heat, [and] electricity’, spawned a massive body of experiments exploring life’s primordial soup.

Scientists have reached deep into the evolutionary past only to extend far beyond it

Most significantly, Darwinian natural selection has helped researchers develop hypotheses for thinking about the process by which chemicals organise themselves into living forms. Natural selection, the process that shapes evolution, tells us that, as populations reproduce and change, those species best adapted to their environment survive. Many researchers think that natural selection can also explain the process by which inanimate matter begins to organise itself into living forms. If new species emerge by natural selection, then there might be prebiotic chemical precursors that become capable of evolution – perhaps evolution marks the beginning of life.

Using Darwin’s theory to bridge the gap between chemistry and biology involves ‘thinking about chemical evolution in a new way’, says Chris Kempes, a theoretical physical biologist at the Santa Fe Institute. The fact that contemporary researchers are doing this thinking reveals how versatile evolutionary theory is. Strikingly, in 1994, NASA adopted a Darwinian definition to guide the search for life in the Universe: ‘Life,’ according to that definition, ‘is a self-sustaining chemical system capable of Darwinian evolution.’

As scientists have stretched the theoretical reach of Darwinian evolution, some have asked if we need to move beyond it. For Kempes, evolution is an invaluable law for investigating life’s origins, but it might not be all we need: ‘Evolution is one law,’ he says, ‘but there might be others.’ For Jeremy England, a physicist at Georgia Tech in Atlanta, Darwinian evolution explains the transformation of life on Earth, but we would do well to embrace a more universal theory to understand why matter spontaneously organises itself into life. Indeed, scientists tackling the hard problem of life’s origins have reached deep into the evolutionary past only to extend far beyond it. In the process, they’ve begun to view life in surprising new ways.

Is life easy or hard? The question contains a paradox in the study of life’s origins that has been with us from the time when Darwin inadvertently reignited the quest.

In the late-19th century, life looked like an easy thing. It seemed to crop up all over the place, especially out of decaying matter. Maggots on meat or mice in grain suggested that the spontaneous generation of life was neither rare nor singular. Enter Darwin’s contemporary, the French biologist Louis Pasteur, who was intent on proving this view wrong. To do so, Pasteur isolated sterile organic media to show that nothing living emerges from them. In turn, he made it seem like life was an extremely hard thing – it almost looked impossible. The effect was to deter many of his contemporaries from investigating the question of life’s origins altogether.

Yet if, as Darwin’s contemporaries increasingly believed, life didn’t always exist on Earth, then it had to emerge spontaneously at least once. But how? In the mid-20th century, while Miller and Urey were attempting to divine life from chemical soup, a figure from a different theoretical universe became enamoured of the challenge. This was the physicist Erwin Schrödinger, who helped to move origins-of-life research out of the soup and into molecular genetics.

In his paper ‘What Is Life?’ (1944), Schrödinger explained that he was fascinated by life because it seemed to act distinctly from ‘any piece of matter’ that physicists and chemists study. It’s not that life isn’t subject to the laws of physics – its material is governed by the same laws as everything else. It’s that life seems surprising in light of the laws of physics. In closed physical systems, entropy increases over time: statistically speaking, matter becomes more disordered because there are more possible ways for it to be disordered than there are for it to be ordered. In living systems, something different is true: over time, order and complexity increase. Schrödinger wanted to explain how this fact might arise.

Shannon’s notion of information as a measure of surprise has helped researchers theorise life’s emergence

Aside from entertaining the idea that we might need another law or a concept such as negative entropy to explain living things, Schrödinger thought that an explanation might be found by determining how life perpetuates itself by replication. The way that structures form, copy themselves, change, and pass those changes on to produce increasingly complex structures might be explained by understanding what he called the ‘hereditary substance’. He thought that what most needed understanding was the ‘most essential part of a living cell ­­– the chromosome fibre’, which, he argued, was analogous to an ‘aperiodic crystal’. Something like this structure, he suggested, could be the mechanism of heredity and the source of life’s ability to perpetuate order and complexity.

While the hunt for the hereditary substance rolled along, another figure offered a second key theoretical idea. This was the mathematician Claude Shannon, the founder of information theory. In his seminal article ‘A Mathematical Theory of Communication’ (1948), Shannon sought to explain the basic structure of communication and demonstrate how information could be encoded and transmitted in binary form. For Shannon, information is a measure of uncertainty or surprise. We might think that information is simply the stuff of communication but, from Shannon’s perspective, information was communication about uncertainty – the more uncertainty or surprise, the more information we receive. To the degree that information is a system of encoding and decoding, of course, it lies at the core of molecular genetics. But more recently, Shannon’s notion of information as a measure of uncertainty or surprise has helped researchers theorise life’s emergence – the great surprise that so puzzled Schrödinger.

Schrödinger’s hereditary principle inspired James Watson and Francis Crick who, with the help of the chemist Rosalind Franklin’s data and research, discovered the double-helix structure of DNA. As they point out in the concluding lines of their landmark paper ‘Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid’ (1953), DNA could be regarded as a key copying mechanism for all of life. As they write: ‘It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.’

Just over a month later, they published a second paper, called ‘Genetical Implications of the Structure of Deoxyribonucleic Acid’ (1953). There they remark that the hereditary material seems also to transmit information. In their words: ‘it therefore seems likely that the precise sequence of the bases is the code which carries the genetical information.’ Watson and Crick didn’t take entirely seriously much of the computational or cybernetic thinking about information that animated Shannon’s theoretical world, comments the zoologist and historian of science Matthew Cobb. But they seemed to share a sense that information was key to understanding any system of encoding and decoding.

Watson and Crick’s discovery was, of course, profoundly significant for evolutionary biology in general, and for molecular biology in particular. But what was its significance for origins-of-life research?

With a mechanism for replication, scientists began to explore the idea that early life, if not the first life, began with the onset of replication. There was one problem, however: DNA couldn’t be the first self-replicator – it couldn’t have emerged spontaneously through the chemicals of early Earth. Once it’s formed, DNA carries the information required for making proteins which do much of the functional work of life, from structuring cells to transmitting signals between organs. DNA also relies on specific kinds of proteins called enzymes in order to catalyse reactions that allow it to copy itself. But proteins weren’t present on early Earth, and they require DNA for their production. If neither DNA nor self-replicating proteins came first, what molecules began the process of replication?

In the 1960s, scientists began to consider that one candidate for this process might be ribonucleic acid, or RNA. In living organisms, RNA helps DNA convert its information to the functional products made possible by proteins. For many years, RNA was known simply as the messenger for transcribing the information in DNA so that its code could be translated into functional proteins. Early experiments on RNA, however, began to suggest that, unlike DNA, RNA might be able to perform not one but two functions essential to replication. Scientists knew that, like DNA, RNA could carry information; what they started to see is that, like enzymes, it could also catalyse chemical reactions. In the 1980s, the molecular biologist Sidney Altman and the chemist Thomas Cech, with their respective teams of researchers, made an advancement in this respect: independently, they demonstrated that RNA molecules can act like enzymes that catalyse reactions.

Not long after the discovery of this catalytic property of RNA, scientists began to embrace more broadly the idea of the ‘RNA world’ – a world in which RNA was an early life form capable of catalysing the replication of its own information. RNA world was beset by a number of problems, however. For one, even though experimentalists could show that RNA could act like an enzyme, they typically relied on external enzymes to get the process of replication started. Furthermore, many scientists now think that RNA is so unstable that it couldn’t continue to catalyse reactions and evolve in the extreme temperatures of prebiotic Earth.

In recent years, RNA world has therefore met with some rival theories about Earth’s first replicators. In 2017, for example, the scientists Elizaveta Guseva, Ken A Dill and Ronald N Zuckermann proposed a theory that protein-like molecules might have been the first replicators.

Challenges to RNA world are but one indication that scientists are far from a consensus about life’s chemical origins. In fact, the lack of consensus seems to be driving scientists to return to hypothetical beginnings and develop radical new hypotheses.

Others have begun to think more systemically, thermodynamically, universally about how life emerged

One attempt to theorise life’s origins anew came into focus around 20 years ago, when the physicist Freeman Dyson proposed in his book Origins of Life (1999) that we develop a two-origins hypothesis to explain the two processes essential to early life: metabolism and replication. Dyson adapted the groundbreaking work of the microbiologist Lynn Margulis, who discovered that early cellular life combines at least two different organisms to form the nucleated cell.

For Dyson, the experimental primordial soup world inaugurated by Miller and Urey could help scientists understand early metabolism. RNA world offered possible insight into the process of replication: ‘the first [metabolic] beginning must have been with molecules resembling proteins and the second beginning [replication] with molecules resembling nucleic acids.’ He likened the former to computer hardware and the latter to software – hardware, he argued, must come first, but both are essential to the machine. Recalling Shannon, Dyson said that the origin of life is the origin of an information-processing system.

Since Dyson, others have begun to think differently too – more systemically, more thermodynamically, more universally – about how life might have emerged.

David Baum, a botanist and experimental biologist at the University of Wisconsin-Madison, emphasises that in order to understand life’s chemical origins we must do justice to the immense complexity of prebiotic chemical systems. As he explains:

One of the frustrations for the origins of life field is that people often present it as a single problem, but it’s not. It’s a whole series of separate problems. It wasn’t that life suddenly jumped over this transition from random chemistry to systems with genetics and cells and so forth.

In origins-of-life experiments within the genetic realm, Baum explains, two phenomena are key. First, there is templating: ‘the idea that a molecule with a certain sequence of building blocks can feedback to increase indirectly the generation of that exact sequence.’ This process resembles informational systems and might be something that experimentalists can recreate. The second phenomenon is translation, which entails ‘understanding how an RNA molecule can speak to and control the sequence of a protein molecule’. This, by comparison, ‘is complicated, fascinating, and well beyond the scope of experiments right now’.

While Baum is careful to point out our current experimental limits, he’s far from hopeless about the prospects for studying life’s origins in the lab. In the end, he says, anyone doing experiments ‘must believe that life is not such a rare thing’. Still, this is not to say that life is a simple thing: ‘in evolution easy stuff happens, but once in a while, the easy stuff accumulates in a weird sequence to generate something really unexpected.’ It seems possible to Baum that the laws of the Universe necessarily generate life, but the particularities of how chemicals become living systems remain unpredictable. We might say that the early chemistry of life is full of Shannon information – full of surprises.

The physicist England sees things another way. For him, life isn’t a surprising thing at all: it follows naturally from the laws of physics. In his hypothesis, called ‘dissipation-driven adaptation’, the laws of the Universe generate the ordered structure we call life. His theory addresses Schrödinger’s challenge to explain why life doesn’t follow the path of matter in closed systems toward greater entropy, and why it instead becomes more ordered and complex over time. As England explains in a lecture in 2014, and in his forthcoming book, in non-equilibrium systems with a powerful source of energy, such as the Sun, matter necessarily forms structures that help dissipate energy. For living things, one of the most efficient ways to organise in order to dissipate energy is to reproduce. In accordance with England’s theory, life forms increase in complexity not only because they are subject to Darwinian evolution, but also, more fundamentally, because they must improve at dissipating energy. According to England: ‘Thinking about evolution in the language of physics allows us to identify new ways by which adaptations can emerge that do not necessarily require a Darwinian mechanism.’

For other scientists, such as Eric Smith at the Earth-Life Science Institute in Tokyo, studying life’s origins means turning to the biosphere as a whole – the complex biological system, he says: ‘carries the true nature of the living state’. For Smith, the evolutionary frame for origins-of-life research often leads scientists to focus on the origin of the organism. This impedes broader thinking about living systems. To understand life and its origins, Smith argues, we must look to the organisational and chemical structures that underpin life itself.

Meanwhile, physicists such as Sara Walker of Arizona State University say that, to understand life, we need to return more directly to first principles. For Walker, a key principle that we need to understand is information – and we need to understand it far more generally than did early geneticists. As she says: ‘There is a physics of information that governs living systems.’ At the moment, we don’t understand information well enough, but if we begin to understand how information interacts with matter, we will be much closer to explaining life.

As the evolutionary frame for origins-of-life research has expanded and frayed, so too has the definition of life. Once scientists start thinking about prebiotic chemicals spontaneously organising, the boundaries between living and nonliving begin to blur. For some researchers, such as the evolutionary biologist David Krakauer, challenges to the definition of life are welcome. According to Krakauer, the focus on the replication of forms that we call living things prevents us from thinking biologically about the fascinating array of emergent systems before us – things we wouldn’t say are alive.

Hamlet is alive, and computer viruses and cultural networks might rightly be considered life forms

There is an obsession with origins – and the idea that you can’t divorce the generality of the principle from the origin of the principle, Krakauer says. And that’s a mistake. It would be like saying that Johannes Gutenberg invented moveable type for replicating the Bible, so it can be used only for Bibles. But it’s useful for lots of kinds of books. Likewise, while Schrödinger was interested in reliable replication in the context of chemistry, who’s to say that Gutenberg’s context – print – doesn’t look to the same principle. Krakauer thinks that origins-of-life scientists would do well to seek out general principles of life and replication rather than focusing solely on the historical nature of life’s emergence on Earth.

In the close of ‘What Is Life?’, Schrödinger takes a surprising turn that seems to anticipate this reconsideration of life. To do so, he ventures into the realm of human consciousness. In this section of the paper, Schrödinger harkens back to the Upanishads to suggest that individual consciousness is nothing more than a canvas for gathering memories. When those memories fade, we don’t experience any kind of death, he says. Even if a hypnotist were to erase all of one’s memories, Schrödinger says, one wouldn’t lose one’s personal existence. The content of those memories, moreover, is alive: ‘the protagonist of a novel you are reading is probably nearer to your heart, certainly more intensely alive and better known to you’ than a version of your younger self. Since the world generates continual living content for the canvas of consciousness, there’s never any ‘loss of personal existence to deplore. Nor will there ever be.’

Krakauer shares many of Schrödinger’s views. He thinks that there are many forms of life – that Hamlet, for example, is alive, and that computer viruses and cultural networks might rightly be considered life forms, too. He also thinks that we don’t yet understand the principles of life. I asked Krakauer whether he thought that Schrödinger, in these closing reflections, was a mystic or provocateur or something else. He said that Schrödinger was interested in understanding consciousness and that he wasn’t being mystical with his suggestions. As Krakauer explained: ‘Schrödinger was struggling to find the principles that would unify cultural evolution with organic evolution.’ In short, he, too, was seeking broader principles of life.

When we look at the work in origins of life from the time of Darwin on, we see that the field is astonishingly resilient – perhaps not unlike the emergent life systems that it studies. When it hits a dead end, it spontaneously reconceives of itself. The theoretical frameworks that animate its research have adapted Darwin’s thinking in myriad ways, and now they’re moving beyond Darwin into new theoretical frames.

These frames make us pay attention to life in different ways. When we recognise the universal ways that matter organises and replicates; when we entertain the possibility that the transmission of information across computational and cultural systems can mark the emergence of life; when we turn to the biosphere as a living system, we begin to look for life in places that often seem inanimate. We look for signs of life in the outer planets or in the interstices of rocks and ice; or we see life replicating in the iterative tapestries of culture. We look for ways that life surprises us. It almost seems as though life emerges precisely when our ideas about it begin to conform to the phenomenon that we are attempting to conceive.