This is a course in the physiology of animals, or, to use a common phrase, how animals work.
Animals are, in one sense, machines, and the aim of the science of physiology is to understand how these machines function—what drives them, how they operate, the interaction of the various systems they comprise, and the physical and chemical constraints on how they work.
Animals are also organisms, and this course is intended to help you understand how animals work as integrated units, i.e. as organisms. We will be concerned with how organisms’ various components work to keep an animal alive, with how these are coordinated, and how the various types of animals, despite their disparate evolutionary histories, solve common physiological problems, sometimes in remarkably innovative ways.
This course is intended for the upper-division biology student. It is also a good course for graduate students and practicing professionals looking for a brush-up course in animal physiology. I presume that you come into this course with the background in chemistry, physics, mathematics and biology that can be reasonably expected of a senior biology student. The course consists of about five hours of video clips, parceled into six lectures. This is the first module of four similar courses. This module covers respiration. Subsequent modules cover blood and circulation; digestion and metabolism; and heat and water balance. All four comprise one semester of a two-semester course in animal physiology.
Physiology is a science marked by many divisions. The question we want to explore here is whether there is a unified set of principles that can cover all the different kinds of physiologies that are out there.
KW: reductionism; Ernest Rutherford; thermodynamics;
Thermodynamics is a set of principles that unifies all the different kinds of physiology. Physiology is governed by three principles. The first is the law of conservation of energy, or the first law of thermodynamics.
KW: thermodynamics; first law; conservation of energy;
Even though energy is conserved as is transformed from one form into another, the conversion is not perfect. Any work producing transaction inevitably involves a certain loss of heat. This is the second law of thermodynamics, or the law of increasing entropy.
KW: second law of thermodynamics; entropy; Sadi Carnot; Rudolf Clausius; salt balance; ATPase; potassium; sodium;
There is a third law of thermodynamics that defines the concept of temperature. Rather than a temperature scale set on arbitrary limits, like the freezing or boiling points of water, the third law of thermodynamics allows us to set a thermodynamic temperature that properly describes what temperature is, namely an energy density.
KW: third law of thermodynamics; thermodynamic temperature; Kelvin temperature; Celsius temperature;
The three laws of thermodynamics were formulated for so-called closed thermodynamic systems. Closed thermodynamic systems are those in which energy can neither enter nor leave, but this does not describe the typical thermodynamics of living systems. These are so-called open thermodynamic systems in which energy flows through the system and create order in the process.
KW: open thermodynamic system; closed thermodynamic system; salt balance; equilibrium; dynamic;
The general definition of physiology we see can be found in thermodynamics, in particular the thermodynamics of open systems, which energy flow is. In this light physiology is the study of the dynamics of systems that spontaneously create order and sustain it.
KW: homeostasis; dynamic disequilibrium; super organisms; scalability; free energy; entropy reduction;
KW:glucose; oxidative phosphorylation; ATP; glycolysis; Krebs cycle; electron transport; electron flow; oxidation potential; carbon dioxide; water; oxygen;
Glucose can be oxidized either aerobically, that is in the presence of oxygen, or anaerobically, that is, in the absence of oxygen. Even though the two are related, they are two different types of oxidation reduction reaction. In the absence of oxygen glucose is fermented, while in the presence of oxygen, glucose is oxidized. There’s a fundamental distinction between these two types of breakdown processes. Glycolysis, the principle reaction in the absence of oxygen is a fermentation reaction, while the breakdown of glucose in the presence of oxygen is the phenomenon of respiration.
KW: respiration; fermentation; glycolysis; electron acceptor; oxidation-reduction; redox potential; NAD; electron shuttle;
KW: redox potential; oxidation potential; metabolic power; electronegativity;
KW: redox potential; mitochondrion; superoxide; oxygen radical; super oxide dismutase; metalloprotein; hydrogen peroxide; peroxisome; peroxidase;
KW: prokaryotes; eukaryotes; evolution; symbiosis; symbiogenesis; mitochondrion; flagellum;
The evolution of animals first required the evolution of the eukaryotic cell. The evolutionary origins of the eukaryotic cell, and the ability to effectively manage oxygen is the end result of a process called symbiogenesis; which stands out as a radically different theory of evolution.
KW: prokaryotes; eukaryotes; symbiogenesis; endosymbiosis; Lynn Margulis; mitochondrion; organelle; photosynthesis; oxygen;
Oxidative metabolism requires that oxygen be delivered to the cells at the correct rates, and that carbon dioxide be removed to the environment, also at a similar rate. These rates are determined by the chemical stoichiometry of glucose oxidation. Ultimately this is determined by the animals energy demand, its metabolic rate.
KW: oxidative metabolism; glucose; oxygen flux rate; carbon dioxide flux rate; metabolic rate; stoichiometry;
KW: partial pressure; atmospheric pressure; gas mixture; small fraction; ideal gas law; Dalton’s law of partial pressure; energy density; altitude;
Oxygen and carbon dioxide ultimately must dissolve in water to be able to flow from the environment to the cells. This is true whether the animal lives in air or water. We need to be very clear about what governs the solubility of gases, which is quantified by Henry’s law.
KW: Henry’s law; Bunsen solubility; molar flux rate; oxygen; carbon dioxide; nitrogen; temperature; ideal gas law; gas constant; gas constant;
Partial pressure is often used as a measure of gas concentration, but this can be misleading, particularly when the gas makes the transition from the gaseous phase into the aqueous phase. This confusion can be cleared up by realizing what pressure is, it’s a measure of the energy density of gas molecules.
KW: partial pressure; energy density; phase change; gaseous phase; aqueous phase; gas concentration;
KW: carbon dioxide; carbonic acid; bicarbonate; weak acid; apparent solubility; acid dissociation constant; pH; anion ratio;; Henderson-Hasselbalch equation;
Delivering oxygen to the cell, and taking carbon dioxide away, as well as most of the exchange steps for these gases involves the process of diffusion. Diffusion is governed by Fick’s law, which is a fundamental component of a general theory of respiratory gas exchange.
KW: diffusion; Fick’s law; diffusion coefficient; oxygen; nitrogen; diffusion barrier; shape factor;
KW: diffusion; Fick’s law; bird’s egg; porosity; egg membranes; chorioallantois; pores; partial pressure; diffusion barrier;
KW: diffusion; Fick’s law; bird’s egg; porosity; egg membranes; chorioallantois; pores; partial pressure; diffusion barrier;
KW: Fick’s law; diffusion; diffusion coefficient; air; water; circulatory system; insect; dragonfly; Permian; Mesozoic; atmospheric oxygen concentration;
KW: Fick’s law; diffusion; diffusion coefficient; air; water; circulatory system; insect; dragonfly; Permian; Mesozoic; atmospheric oxygen concentration; trachea; tracheole;
KW: diffusion; tracheal system; insect; mixed diffusion solubility pump; discontinuous respiration; carbon dioxide; oxygen; water vapor; mitochondrion; spiracle; carbon dioxide;
KW: bubble gill; Richard Ege; tracheal respiration; insect; diving bell spider; back swimmer;
KW: bubble gill; surface tension; pressure; law of Laplace; radius of curvature; partial pressure; solubility; instability;
KW: bubble gill; surface tension; pressure; law of Laplace; radius of curvature; partial pressure; solubility; instability; gill factor; oxygen; nitrogen;
KW: bubble gill; surface tension; pressure; law of Laplace; radius of curvature; partial pressure; solubility; instability; plastron gill; water boatman; cuticle hair; meniscus;
Most gas exchange organs of animals bring together two streams of fluid: an extra stream of fluid, either air or water, which is called the ventilation stream, and an internal fluid, blood, which is known as the perfusion stream. These represent so-called convection – diffusion – convection exchangers, more compactly expressed as ventilation – perfusion exchangers.
KW: respiratory gas exchange; gill; lung; convection; diffusion; ventilation; perfusion; heart;
A ventilation – perfusion gas exchanger requires a different level of analysis than diffusion gas exchangers. In diffusion, gas exchange is analyzed by Fick’s law. Ventilation and perfusion involves another mode of analysis, embodied in what is called the Fick principle.
KW: respiratory gas exchange; Fick principle; ventilation; perfusion; oxygen flux; arteriovenous difference; volume flow rate; oxygen consumption;
Any physiological oxygen delivery system has to be able to match the delivery of oxygen, calculated with the Fick principle, with cellular demand for oxygen, or metabolic oxygen consumption. Sometimes, changes in demand are more rapid than the circulatory system can deliver. In these cases, a reserve capacity of blood becomes vital.
KW: respiratory gas exchange; Fick principle; ventilation; perfusion; oxygen consumption; oxygen flux; arteriovenous difference; oxygen reserve capacity; venous oxygen concentration;
KW: respiratory gas exchange; fish gill; countercurrent exchange; ventilation; perfusion; gill arch; gill filaments; pharyngeal cavity;
The fish gill employs what is called a countercurrent exchange system, in which the flows of blood and water run anti-parallel to one another. Countercurrent exchange is best understood by comparing it with a so-called co-current exchanger system, in which the two fluids run parallel with one another. This analysis reveals that countercurrent exchange can extract a greater proportion of gas from the ventilated fluid, even though both gas exchangers rely simply on diffusion to bring about the exchange.
KW: respiratory gas exchange; fish gill; countercurrent exchange; co-current exchange; ventilation; perfusion; diffusion; efficiency;
Gills are ventilated by a complex two-phase pump known as the bucco-pharyngeal pump, which operates in two phases. The first phase is powered by a complicated motion of the jaw, which expands the buccal cavity of the mouth. The second is a complicated motion of the operculum, which expands the opercular cavity behind the gills. The result is a continuous one-way flow of water across the gills.
KW: respiratory gas exchange; fish gill; ventilation; bucco-pharyngeal pump; buccal cavity; opercular cavity; operculum; jaw; mandible; hyomandibular bone; quadrate bone; maxillary bone;
The function and design of gas exchangers like the fish gill are best understood by the equation known as the ventilation perfusion ratio. The ventilation perfusion ratio is derived from the Fick principle, and combines it with the principle of conservation of mass to yield a very powerful equation which embodies the interplay between fluid flow, storage capacity, and extraction efficiency of gas exchangers.
KW: respiratory gas exchange; ventilation perfusion ratio; metabolic rate; Fick principle; solubility; partial pressure difference; conservation of mass;
The ventilation/perfusion ratio provides a powerful tool for analyzing the design of gas exchange organs, because conservation of mass demands that the ventilation / perfusion ratio must always tend towards a value of 1. This means that a change of one term of the ventilation perfusion ratio must be accompanied by compensatory changes in the other terms.
KW: respiratory gas exchange; ventilation perfusion ratio; conservation of mass; solubility coefficient; oxygen demand; Bunsen solubility;
The ice fish inhabits the Antarctic, and it has no hemoglobin in its blood. This fish can tell us quite a bit about ventilation, perfusion and gas exchange.
KW: respiratory gas exchange; hemoglobin; Bunsen solubility; oxygen; ventilation; perfusion; ventilation/perfusion ratio; ice fish
Hemoglobin is a metalloprotein that is involved in respiratory gas exchange, particularly oxygen. It is built around iron, which reversibly exchanges oxygen with the surroundings.
KW: respiratory gas exchange; hemoglobin; porphyrin; heme; iron; copper; embryonic hemoglobin; oxygen binding; carbon monoxide; blood cell size;
The dissociation curve is a useful tool for quantifying the dynamics of oxygen exchange in respiratory pigments.
KW: respiratory gas exchange; hemoglobin; oxygen affinity; dissociation curve; saturation; p50; myoglobin; sigmoid; cooperativity;
The Fick principle governs diffusion gas exchange. Hemoglobin enters into the analysis by decoupling oxygen exchange from partial pressure.
KW: respiratory gas exchange; Fick principle; Bohr shift; oxygen affinity; acidification; blood acidity; apparent solubility; beta;
The dissociation curve for hemoglobin is sigmoid, which indicates a complex change of affinity as hemoglobin become saturated. This is unusual among respiratory pigments.
KW: respiratory gas exchange; dissociation curve;, sigmoid; cooperativity; myoglobin; oxygen binding; affinity; fetal hemoglobin; adaptation; evolution; Bohr shift;
The animal kingdom has many different respiratory pigments besides hemoglobin. The common features of these various pigments points to an interesting evolutionary origin of these remarkable pigments.
KW: respiratory gas exchange; hemerythrin; hemocyanin; chlorocruorin; respiratory pigment; iron; copper; evolution; metalloprotein; oxidation reduction potential;
Hemoglobin does more than transport oxygen. It also plays a significant role in transporting carbon dioxide about the body.
KW: respiratory gas exchange; carbon dioxide; hemoglobin; bicarbonate; acidification; carbamino; chloride shift; carbonic anhydrase; anti-port;
Hemoglobin is a combination of protein and metal. The composition of the protein part, the globin, affects hemoglobin’s oxygen binding kinetics. This means that hemoglobin binding kinetics is subject to adaptation by natural selection.
KW: respiratory gas exchange; evolution; adaptation; body size; Bohr shift; Delta p50; p50; Allometric scaling; mouse; elephant; specific metabolism; capillary density; diffusion;
I am a Professor of Biology at the State University of New York College of Environmental Science and Forestry in Syracuse, New York.
I am a physiologist by training but with a deep interest in the interface of physiology, ecology, adaptation and evolution. You can read some of my thoughts in two books I have published: The Extended Organism: The Physiology of Animal-Built Structures (2007) and The Tinkerer's Accomplice: How Design Emerges from Life Itself (2007), both published by Harvard University Press. I have completed a third book, Purpose and Desire: Biology's Second Law, which I hope will be published soon.
My current research focuses on the problem of emergent physiology in social insect colonies. specifically the mound building termites of southern Africa.