Physics of Life 1. Thermodynamics

Overview of Lecture 2.

Thermodynamics takes place within the context of thermodynamic systems, which are systems in which energy and material are involved in transactions of some sort. The basic laws of thermodynamics are formulated with respect to such thermodynamic systems, of which there are two varieties. Closed thermodynamic systems are the most common, but life is inconsistent with close thermodynamic systems. Life takes place in so-called open thermodynamic systems, which have peculiar properties of their own.

The classical first three laws of thermodynamics apply to close thermodynamic systems. Open thermodynamic systems are governed by those classical laws, but there is in addition a fourth law. This fourth law is sometimes known as the law of dissipative systems. One of the peculiar behavior of dissipative systems is a transient orderliness that emerges from them. This transient orderliness is important to understanding the phenomenon of life, which is itself a form of transient orderliness.

Keywords: Physics of life; thermodynamics; open thermodynamic system; dissipative systems; Benard cell;

Open thermodynamic systems can occur at many scales, ranging from the molecular to the global. Different phenomena govern the behavior open thermodynamic systems at these different scales. At small scale, diffusion and Brownian motion are important driving phenomena, while at large scales, Brownian motion and diffusion are insignificant. This distinction becomes important when we speak of theories of the origin of life, which invariably examine life originating from small scales.

Review quiz for Section 2. Thermodynamic systems and life

Theories of the origin of life have drawn strongly from the so-called warm little pond scenario, which supposes that life originated at the molecular scale and then scaled up to cellular and higher levels of organization. The foundation for all of these theories is the so-called Oparin-Haldane hypothesis, which suppose that the origin of life was preceded by an extensive period of so-called prebiotic synthesis, which formed a week chemical soup of many of the precursors of living systems, like amino acids, nucleotides, and carbohydrates.

In the Oparin-Haldane hypothesis, the bridge between primordial soup and life involves encapsulation of life’s precursors into some kind of a proto-cellular structure that could protect incipient metabolic systems from the disruptive power of diffusion. These included small structures like coacervates, or microspheres produced by abiotically synthesized proteins.

The chemistry of life involves complex reaction sequences, in which the products of one reaction serve as a reactants for another. One of the classic examples of this is the oxidation of carbohydrates. This involves a complex suite of chemical transactions which must take place in order for a living system to extract usable energy from the oxidation of a fuel like glucose. To ensure these reaction systems work reliably, catalysts bias chemical reactions in various ways to ensure a reliable outcome. Here we look at the basic energetics of catalyzed versus non-catalyzed reactions.

Life is persistent, that is it sustains itself forward through time. Diffusion is a phenomenon that resists persistence. It is disruptive. The big challenge for the origin of life from the bottom up is to sustain persistent metabolic reactions in the face of the disruptive power of diffusion. Autocatalysis, that is reaction systems that feedback on and stimulate themselves are a form of metabolic persistence.

Classically, theories for the origin of life presume that either life is synonymous with the gene-so-called gene first theories-or that life originated with the emergence of complex and self-sustaining metabolic pathways-- so-called metabolism first theories. Gene first theories must propose that the first gene had to have been something quite different from what we now understand the gene to be. One of the most prominent gene first theories is so-called RNA world, in which the first gene was not DNA, but RNA.

Gene first theories like the RNA world do not really solve the problem of the origin of the gene, largely because it simply pushes the origin further back. Just as DNA had to have been preceded by an extended period of evolution, so to must RNA world have been. One of the ways that’s this paradox has been addressed is to conflate both metabolism and hereditary memory, but this faces challenges of its own. One of the more radical theories to address these challenges is the notion that the original organisms were not based upon carbon as present-day life is, but on silicon.

Keywords: Physics of life; thermodynamics; origin of life; clay crystals; genetic takeover; Cairns-Smith;

Review quiz for Section 3. Thermodynamics and the origen of life.

Overview of Lecture 4

All warm little pond scenarios for the origin of life presume that life originated from the molecular and scaled up. This poses a significant hurdle for incipient life, because the necessary persistence through time faces enormously disruptive power is at the hands of diffusion. Overcoming that hurdle means taking a different perspective on the origin of life, one that is informed by the thermodynamics of large-scale open thermodynamic systems. The earth is an open thermodynamic system, and it too has a metabolism, and then energy budget.

At large-scale, open thermodynamic systems exhibits a peculiar orderliness that is manifest in several ways. The large-scale patterns of oceanic and atmospheric circulation are an example of this. The important thing about open thermodynamic systems operating at large scale is that there is sufficient energy to overcome the disruptive power of diffusion at small scales. This is an important factor in considering the validity of warm little pond scenario is for the origin of life.

The large-scale orderliness of planetary open thermodynamic systems offers a means for persistent life to piggyback on the orderliness that emerges at large-scale. In other words the origin of life could have been a planetary phenomenon and scaled down rather than the other way around. Gaia theory offers a plausible mechanism for that to have happened, focused on the persistent disequilibrium that exists in atmospheres. The classic counterexample to the earth is that Mars could not be alive because its atmosphere is close to equilibrium. The Earth’s atmosphere, in contrast, is strongly out of equilibrium. Closer observations of the Martian atmosphere shows that there are instances in which the atmosphere is driven to a disequilibrium state, offering plausible evidence that such large scale disequilibrium could exist.

Martian methane shows that large-scale gradients of potential energy could be plausible evidence of the existence of life on Mars. Closer to earth, there are large-scale open thermodynamic systems that do support large-scale flows of matter and energy in ways that are consistent with life originating at large-scale. The most famous example of these are the hydrothermal vents that exist at seafloor spreading zones. The support a complex ecological community that shapes energy flow according to the fourth law of thermodynamics.

Overview of Lecture 5

Evolution is commonly supposed to be driven by natural selection of genes. This conception of evolution ignores the unique energetic attributes of life, namely its mobilization of matter and energy for persistent form and function: adaptation in a word. To have a coherent theory of evolution, we must take these into account, and redefine Darwinian fitness in energetic and thermodynamic terms.

An important complement of the energetic definition of fitness is the phenomenon of homeostasis. Homeostasis, broadly defined, is the persistence of form and function through time. There are specific criteria that must be met for this to happen, including work that must be done, which we call the metabolic rate. Metabolic rate is strongly affected by body size, and by the activity of living things as they function in their environments.

Metabolic rate is not simply a function of individual organisms. It can apply to collections of organisms as well. An important concept related to this is the so-called standing crop: how much biomass of a living system can be sustained by ongoing metabolic work? This is limited that only by the gross input of energy into a system, but by the degradation of energy into heat with every transaction of matter and energy. This structures ecosystems in a profound way.

Ecosystems are rife with transactions of matter and energy, most evident in the form of trophic networks, that is who eats whom. The energetics of these trophic networks are limited by the second law of thermodynamics. Every transaction of matter and energy between, and within, organisms, inevitably dissipate some proportion of energy into heat. This has profound effects on the relationships between trophic levels, that is between primary producers, like plants, primary consumers like herbivores, and secondary consumers like predators. We illustrate this using a simple ecosystem: the dune communities of the Namib Desert.

One can use thermodynamic principles to make predictions about how ecosystems are structured. These principles can extend even to extinct ecosystems. For example, there’s a question about whether dinosaurs were endothermic, that is warm-blooded creatures like mammals and birds. How can we answer such a question. We can do so by analyzing trophic networks of present-day communities of predators and prey. In present day endotherms, the standing crop of predator that can be sustained is considerably less than if the predators and prey were ectothermic. We explore this question in the context of extinct ecosystems, in particular the reptilian dominated ecosystems of the late Paleozoic and Mesozoic eras. Based upon ratios of predators and prey in these extinct ecosystems, it looks like dinosaurs were indeed endothermic.

Review quiz Section 5