The Origin and Nature of Life on Earth: The Emergence of the Fourth Geosphere 1st Edition

In this stunning, magisterial, and surprisingly wide-ranging book, Eric Smith and Harold Morowitz approach the origin of life from first principles and bring together knowledge from astrophysics, geochemistry, biochemistry, information theory and statistical mechanics to show how all the hints and constraints we know so far about life’s start and the universal patterns of life we’ve found compel us to adopt a new framework to understand life: life is a complex series of non-equilibrium phase transitions driven by a persistent geochemical redox potential.First, Smith and Morowitz argue that the ecosystem is the correct level to view the phenomenon of life and how it integrates with the rest of the planet’s geochemistry. It is only there that one can see the closed, robust nature of life. In every ecosystem from hydrothermal vents to rainforests, the ecosystem as a whole takes in inorganic inputs and free energy and builds biomass using a conserved core set of metabolic reactions. These core reactions give us many hints to the context of where and how life began suggesting the primary role of hydrothermal vents and of autocatalytic chemical networks.Next, Smith and Morowitz examine the physical conditions that were present before life began and ask the question: what stress was present in the non-living world that could have compelled the phenomenon of life into existence? Any non-equilibrium process (of which life is the most complex example) requires energy and a barrier to keep that energy from dissipating away too quickly. Smith and Morowitz take the physicist’s view and list many possible energy sources present on or around the early Earth and the barriers that could have maintained them. For example, they point out that the sun uses gravitational potential energy to drive nuclear fusion and the barrier to dissipation is the low probability of having a fusion collision which is set by the weak force!They then review the geophysical and geochemical processes that take place in the mantle, the crust and the atmosphere and describe the redox states of minerals in the mantle and how the atmosphere on the surface is held at a more oxidized state by hydrogen escape. (This chapter is the most in-depth and best introduction to the field of geochemistry that I’ve ever read.) The reduced state of the mantle and the oxidized state of the atmosphere turns the Earth into a giant redox battery (which has precisely the right energy difference to run the organic reactions of life) with the barrier being the crust itself and hydrothermal vents acting to concentrate this diffuse redox energy to specific points on Earth.Smith and Morowitz then present the core metabolic reactions that are universal to all life. This set of reactions creates a closed feedback loop and the whole loop (and most of the steps) are energetically favorable in a reduced hydrothermal vent environment. The core processes of life want to happen spontaneously at vents! Patterns and structure in core metabolism also reveal many more hints as to the key steps life needed to pass through on its journey to “lift itself off the rocks”. The evidence is fascinating and compelling, but there’s too much to adequately summarize here.Throughout the book, Smith and Morowitz argue that the most important question is not how were the organic precursors to life synthesized, but instead how was the selectivity of chemical reactions robustly maintained? There are many proposed reaction pathways to produce the building blocks of life, but the problem is that these pathways make many more products than the ones life uses and these unwanted products would starve the early reactions of life from getting enough input material. Bringing the questions of selectivity and robustness to center stage immediately suggests that one could use the tools of information theory and phase transitions to make progress.Information theory studies the storage and communication of information and deals with things like error-correcting codes that help you preserve information if you’re sending it through a noisy channel. Studying phases of matter has yielded a mathematical framework to understand how qualitatively different macroscale behavior (like ice or water) can result from the same fundamental building blocks and interactions (H2O molecules and electromagnetic interactions). Error correction in message transmission and the maintenance of some system in a particular phase require that only certain configurations of message or system can be selected. Furthermore, we know that the stability of a phase and the efficacy of message transmission mean that such selectivity can be robust.The authors then give an introduction to the broad and successful field of phase transitions and describe how ideas from information theory fit into understanding what a phase really is. This introduction leads to the math necessary to understand dynamic phase transitions in out of equilibrium chemical networks (which is close to what we’d want to understand life!) and includes a fantastic introduction to the modern viewpoint of how the universe formed as a cascade of phase transitions starting with the quark-gluon plasma right after the Big Bang to nucleons to neutral atoms to chemistry to eventually, after every symmetry has been frozen, superconductivity.Finally, Smith and Morowitz bring all these ideas together and describe how they conceptualize “the nature of the living state”. Central are the ideas of robustness and modularity. They recount a parable about two watchmakers who are trying to build complex watches and are both interrupted every few minutes. One builds the watch in a very complex way so that it only works if all the pieces are in place and falls apart if the watchmaker leaves halfway through. The other watchmaker builds his watch out of self-contained modules which are each stable on their own. His progress remains when he is interrupted. The second watchmaker is able to finish his watch much faster than the first. We can see that modularity gives us a way of preserving a complex system against perturbations and of building more complex structures without the whole system becoming unmanageable or unstable. The modularity of life is evident everywhere one looks and is returned to again and again throughout the book.Modularity links with another idea that Smith and Morowitz emphasize: why can physics theories work at all if we don’t know the underlying building blocks of the world? The answer actually comes from the study of phases and is closely related to modularity. Matter in a certain phase can be described by an “effective theory” within that phase that allows us to ignore laws of the universe that act outside the regime of that phase. For example, the laws of chemistry don’t really apply when the world is too hot and atoms are ionized into plasma. The cascade of freezing transitions that matter undergoes itself represents a type of modularity and robustness. One phase lets us have molecules, we can then use molecules as the building blocks for minerals, which can then be used as the building blocks for more complex structures. Although much work remains, Smith and Morowitz see similar ideas present in how life self-organized into such a hierarchical and modular form (although in life’s case, it remained fully out-of-equilibrium unlike the phase transitions for matter mentioned above).Overall, this was one of the most profound and thought-provoking books I’ve ever read. It provides a solid foundation for those who are sufficiently motivated to reach the forefront of the current discussions on the origin of life. It also provides tools and ideas that have shaped how I understand the world more generally. I learned so much from this book! As a warning, the book assumes comfort with several branches of science (geology, chemistry and physics) and is rather dense at parts, but the book is laid out in a modular enough way that one should be able to find those parts of the book they are most interested in. It’s not light reading, but the insights in this book are totally worth the effort for those interested in the origin of life!

I have been following the material coming out of the Santa Fe Institute for decades, but somehow I missed this 2016 publication when it first came out, and only discovered it in 2019. But what a discovery! The Origin and Nature of Life on Earth: The Emergence of the Fourth Geosphere is an intellectual feast. It is full of challenging ideas, novel perspectives and grand unifying principles. It is a physicist’s approach to life’s origin, and it is glorious.For the remainder of this review, I’ll refer to the book as TFG, standing for The Fourth Geosphere.Like everything coming out of the Santa Fe Institute, TFG is quite multidisciplinary. While I have some background in organic chemistry, evolutionary biology and physics, my fluency in those fields was inadequate to make the book an easy read. Quite the contrary: I read it through twice over a period of a year, emailed the primary author for clarifications and wrote out a long form summary. Finally, on the principle that the best way to understand anything is to try to explain it, I composed my own, popular-science level version of the text. (That book is published as Spontaneous Order and the Origin of Life.)The theory of the origin of life expounded in TFG falls in the general category of Metabolism-First theories, an approach proposing that evolution in chemical networks preceded RNA replication. Its central claim is that the energy processing mechanism found in all living things, metabolism, is continuous with the flows of energy and chemistry in the early geochemical environment. From this perspective, RNA and its precursors arose only later, after geochemistry had attained a certain level of spontaneous organization.This is the viewpoint underlying Jeremy England’s All Life is on Fire, and Nick Lane’s The Vital Question, both excellent books that are well worth reading. Unlike these and other versions of Metabolism-First, however, TFG is a comprehensive presentation that grounds itself in universal principles and carries its idea forward through all phases of biosphere development. It has several moving parts, all intertwined, and each one fascinating. I will try to introduce each of them here.TFG begins by asking the reader to shift level of abstraction. Rather than focus on individual organisms and lineages, as is common in evolutionary biology, it elevates its perspective as high as an orbiting space station, and evaluates the biosphere as a planetary process. From this perspective, the particular organisms that compose the biosphere at any period in history, whether they are archaea, trilobites or wildebeest, matters little. Regardless of particular components, the biosphere as a whole functions as a planetary energy processing system. It creates pathways for high energy electrons to flow “downhill” that would not exist on an Earth devoid of life. The complex, ordered and evolving realm of living things is thus viewed as an apparatus to facilitate electron flow.The biosphere can thus be regarded as a fourth geosphere, one of independent planetary significance alongside the lithosphere, atmosphere and hydrosphere. Lest one suspect that the biosphere is insignificant compared to those other geospheres, consider that the biosphere is responsible for creating Earth’s oxygen environment. It is no slight, trivial thing.In the modern biosphere, most of the high energy electrons transduced through chemistry originate via photosynthesis, the process that oxygenated our atmosphere. However, photosynthesis was a secondary development that arose after life was well underway. Metabolism-First proposes that the original source of high energy electrons powering the biosphere are those found in the upwelling chemicals of sub-oceanic hydrothermal vents. These drove the first generation of life into existence, the chemotrophic organisms that still exist in vent environments today. Later, photosynthetic organisms plugged a new source of electrons into that pre-existing metabolic engine, while leaving that engine largely intact.Metabolism, the energy processing pathways utilized by life, is to a surprising extent universal. With certain informative partial exceptions, all lifeforms utilize variations of a single chemical cycle, the TCA cycle, to both build up and break down biomass. Besides being nearly universal, TCA is also central. It is at once the starting point for all biosynthesis and the endpoint of all chemical breakdown utilized for energy production. TFG proposes that metabolism is continuous with pre-life geochemistry: the means by which electrons found a way to move downhill in hydrothermal vents initiated reaction patterns that were later consolidated by Darwinian evolution.The initial chemical stages leading to the biosphere can regarded as a process similar to that of a lightning bolt, although operating over a much longer time scale and utilizing chemical networks rather than a plasma channel. As many scientists have noted, when there is an unresolved energy differential in a system, that system has a tendency to reorganize in such a way as to resolve the differential. Electrons concentrated in a thundercloud are driven to return to ground by strong electrical forces, but they cannot immediately do so because air is an excellent insulator. Ionized air, however, conducts electricity well, and lightning is initiated by poorly understood processes that ionize a small area of physical space. Electrons flow into that region, producing heat, which further ionizes air, allowing more electron to flow, producing more heat and more ionization. In short order, electron flow cuts a plasma channel through the atmosphere, in the form of a bolt of lightning.The process by which a minute area of ionized atmosphere leads to accelerating ionization can be regarded as a form of autocatalysis. An autocatalyst (broadly speaking) is something that creates more of itself. Fire is another example. The term, however, was invented to describe processes in chemistry. In Metabolism-First, chemical autocatalysis was a primary process initiating biosphere formation.The story goes like this: Electrons in upwelling magma reside at a higher energy level than those in the oceanic fluids that magma encounters. This yields an energy differential that, like the electrons in a thundercloud, has no efficient means of resolution. A small quantity of electrons would nonetheless flow downhill through ambient geochemistry. It is a peculiarity of the non-oxygenated vent environment that downhill electron flow favors the formation of molecules containing multiple carbons. (In the modern, oxygenated environment, such “anabolism” requires energy, but that was not originally the case.) As the initial, limited electron flow elaborated a variety of organic chemicals, autocatalytic reaction pathways arose.An autocatalytic chemical reaction pathway is one where chemical products of that pathway enhance the rate of reactions that produce them. This positive feedback effect channels an exponentially increasing total flow of energy and matter through the autocatalytic network.As chemical synthesis driven by electron energy increased, random chemistry led to the discovery” of new and more efficient autocatalysts. These “better” autocatalysts would “outcompete” less efficient ones, yielding a form of natural selection in mere chemistry. Eventually, stable, cyclic forms of autocatalysis arose, and this was the recognizable beginning of the biosphere.Readers of Jeremy England will recognize that this description is reminiscent of the concept of dissipative adaptation, in which systems reorganize to enhance energy flow by increasing energy dissipation. It is tempting to generalize from the findings in non-equilibrium thermodynamics utilized by England and others to conclude that the chemical reorganization just described was driven by the same processes. However, none of the theorems utilized in non-equilibrium thermodynamics can as yet address flows of chemicals in networks. Without disagreeing on the thermodynamics of dissipative adaptation, TFG focuses instead on the kinetics of autocatalysis. The result is a theory grounded in phase transitions. Indeed, phase transitions are the central idea of the book, but the chapter that addresses it in detail, chapter 7, is difficult to follow. It was initially a desire to understand this difficult idea that caused me to write my own popular science “translation.”Simply put, phase transitions moving in the cooling direction, such as from liquid to ice, result in increased local order. They do so by means of cooperative effects between individual elements that autocatalyze their way into a sudden change of state. The result of a completed cooling-direction phase transition is a new substance made from the same matter but possessing altogether different properties, and residing at a state of decreased local entropy. The grand underlying idea of TFG is that the biosphere came into a being as a series of phase transitions within the reaction space of organic chemistry, leading to steadily increasing levels of order and information density.Note that Darwinian selection itself is a form of autocatalysis, because a mutation that produces an incrementally more successful organism causes more of itself to be produced as that organism’s descendants flourish. Thus, one primary thesis of this book can be boiled down to Darwinian selection is autocatalytic, but it was not the only selective autocatalytic process involved in the origin of life.This is a very grand idea, and it is one not yet entirely fleshed out. And yet, if one follows the argument intuitively, it leads to shivers and glimmers of understanding, a deep intellectual frisson. (Caveat: beautiful ideas that cause intellectual shivers are not necessarily true.)There are several conceptual stages between phase transitions in the manner of water becoming ice and those hypothesized to have formed the biosphere. Phase changes in solid matter are called equilibrium phase transitions. When they occur in more dynamic, non-equilibrium environments, they are called non-equilibrium phase transitions. The initiation of a lightning bolt and the formation of a hurricane are both examples of such non-equilibrium phase transitions.The above two categories of transition occur in the context of energy release. However, in recent decades it has become clear that phase transitions are a much more general phenomenon, occurring in such widely dispersed areas as bird flock behavior, game theory problems, economic recessions, social dynamics, traffic patterns and many others. Similar mathematics underlies all these processes.Utilizing the phase transition paradigm, one can see continuity between the stages of matter condensation in the early universe, the formation of planets, autocatalysis in hydrothermal vents and the successive grand transitions of biogenesis. The biosphere, seen in this way, is a “merely” a novel state of matter.TFG sees phase transitions in the formation of the several layers of metabolism, the development of RNA replication, the creation of a universal genetic code, and the movement from prokaryote to eukaryote to multicellularity to superorganismal structures. It is indeed a cosmic viewpoint.A related concept is that of modularity; in particular, TFG proposes that phase transitions naturally lead to the creation of successive modules stacked within one another, each one having achieved stability before the next one occurs. Modularity has been an interest of biologists for decades, and TFG provides an explanation for its occurrence and functionality via ideas drawn from the field of control theory.One specific idea that often dominates discussion of TFG is in fact offered only tentatively by the authors. This is the proposition that the reverse TCA cycle, still seen in certain anaerobic prokaryotes, was the primordial energy transmission cycle; that it arose as an optimum in geochemistry. Chapters 4 and 6 of the TFG promote this idea in detail, while at the same time admitting it may be problematic. Those chapters, in a sense, are more important for the system of reasoning they develop than for specific claims. They outline a research program: When analyzing the biosphere, look for islands of stability linked by narrow bridges.One fascinating chapter, Chapter 5, analyzes regularities in the genetic code to hint at pre-code processes. This discussion illustrates that replication is not an on-off mechanism. Early RNA copying and protein translation from RNA would have been highly inaccurate, leading to suites of outcomes rather than single chemicals. Analysis of the stages of this process illustrate a continuous gradient between chemical autocatalysis in networks and increasingly accurate replication processes. Only after a long period of development did precise translation “precipitate out,” initiating modern Darwinian selection. This coincides with the development of true individuality, a unique feature of the type of matter organization found in the biosphere, although one that is itself subtle and multilayered.It should be noted that Metabolism-First is not the dominant view of the origin of life. That distinction goes to the RNA World hypothesis. TFG can be regarded as an extended argument against the idea that RNA replication was the initial step in biosphere formation. One may describe this as “replication-first,” “genetic-first,” “control-first” or “individuality-first.” TFG agrees that at some point RNA replication took on a dominant role. However, it argues (to my mind effectively) that RNA could not form in sufficient quantities to produce any meaningful effect until its precursors were present in high and stable concentrations. In turn, this requires that their production was part of a stable, energy-driven chemical network. Precursors of RNA would in this view have arisen first as autocatalysts, emerging out of the network of primeval metabolism, increasing their own concentration by facilitating the reactions that produced them. Only after high levels of nucleotides were sustained in this way could RNA formation and replication become a significant process. Even then, true individuality could emerge only after the onset of precise transcription and translation, which, as already noted, came into being after many intermediate stages lacking such precision.An awe-inspiring consequence of the TFG analysis is that, under appropriate conditions, the origin of life might be a deterministic process. One way to say this is that “the early Earth was unstable, and it relaxed into life.” Lightning bolts are inevitable once enough charge has built up, even though their exact paths owe a great deal to chance. A rock on top of a mountain will eventually fall; water in an alpine lake will find its way to the sea; and any planet with plate tectonics and a liquid ocean will tend to create a biosphere.TFG is a complex text, not always ideally organized, and often difficult to follow. And yet, for those who take the time to read it, it will yield tremendous intellectual challenges and rewards.Steven Bratman, author of Spontaneous Order and the Origin of Life.

This is an excellent scientific text, offering a comprehensive review of empirical results and analysis with an introduction to large-deviations theory (LDT), and some suggestion to how it might apply to origin of life. Yet these two aspects of the book don't seem married so well, and the presentation of LDT can be very arcane. Clearly the authors assume the reader has been exposed to statistical mechanics and is comfortable with advanced mathematics. This is alright if you feel comfortable, but for other readers not exposed to such topics (likely from a biological background) this section (chapter 7) should unfortunately be skipped or skimmed over. It is such a compelling perspective though, and a mathematical framework which can be beneficial to biological science, that it misses the point in being so arcane: this should be an interdisciplinary text, succeeding elsewhere in this regard. Chapters 3-6 are impressive in their content and presentation, introducing the reader to geophysics and chemistry, the structure of metabolism, patterns in energy cycles and the genetic code, and a succinct presentation on a possible chronology of events in abiogenesis. Chapter 7 is impressive in content, but disappointing in presentation. Chapters 1-2 and 8 give necessary binding to the text, the last chapter offering some intriguing insights, more so if one gets through Chapter 7. Finally, the book offers an impressive bibliography. It is worth getting for Chapters 3-6 - they are clearly presented and provide an excellent framework to understand patterns in cellular biology and it's possible histories. Chapter 7 is great if comprehendable, and this is the main flaw of the book.