Capstone: digestion, locomotion and physiology in a changing world

The earlier lessons treated physiological systems one at a time. Real animals have to run them all at once, on a limited energy budget, in environments that change. This capstone lesson brings the course together around three linked themes. First, how animals obtain and process the energy and nutrients that pay for everything else. Second, what it costs to move, and how body size and mode of locomotion shape that cost. Third, how physiology determines where animals can live and how they respond to a warming, acidifying and oxygen-poor world, the field of conservation physiology. The lesson ends with the ethical and legal framework for research on animals, which every physiologist must understand.

Feeding and digestion

Animal guts are tubes through which food passes in one direction, broken down mechanically and chemically, absorbed, and the residue eliminated. Their design reflects diet. Carnivores, whose food is easy to digest and rich in protein, tend to have short, simple guts. Herbivores face a harder problem. Plant cell walls are made of cellulose and other polysaccharides that no animal enzyme can break down efficiently (BIOL-340 described their structure), so herbivores rely on symbiotic microbes, bacteria, archaea, protists and fungi, that ferment fibre into short-chain fatty acids such as acetate, propionate and butyrate, which the host absorbs and uses for energy.

Herbivores house their microbes in one of two places. Foregut fermenters, including ruminants such as cattle, deer, moose, caribou and bison, ferment food in a large, chambered stomach before it reaches the small intestine. The rumen is a fermentation vat that can hold over 100 litres in a cow. Ruminants regurgitate and rechew their food, chewing the cud, which breaks particles down further, and a filter between the rumen and the rest of the stomach holds back large particles until they are small enough to pass. Microbes that wash out of the rumen are themselves digested in the true stomach and small intestine, providing high-quality protein. Ruminants can even recycle urea to the rumen, where microbes use its nitrogen to make protein, an advantage on poor diets. The price is methane: rumen archaea convert hydrogen from fermentation to methane, wasting 2 to 12 per cent of the dietary energy and making ruminants a significant source of a potent greenhouse gas.

Hindgut fermenters, such as horses, rabbits, beavers and many rodents, ferment food in an enlarged caecum and colon after the small intestine. They can process large amounts of low-quality food quickly but lose the microbial protein in their feces, a problem rabbits and many rodents solve by coprophagy, eating special soft fecal pellets to pass them through the gut a second time. Herbivorous birds such as grouse and ptarmigan, which live through northern winters on buds and twigs, have long paired caeca. The hoatzin of South America is the only bird known to be a foregut fermenter.

Guts are flexible. When energy demand rises, during lactation, cold exposure or migration preparation, many animals enlarge their digestive organs and eat more. Meadow voles exposed to cold increase the mass and length of their intestines within weeks. Migratory shorebirds such as red knots and bar-tailed godwits do the reverse before long flights: they shrink their guts and livers, which are heavy and of no use in flight, and enlarge their flight muscles and hearts, then rebuild the gut after landing. Bar-tailed godwits fly non-stop from Alaska to New Zealand, more than 11,000 km in about eight to nine days, burning fat and some protein from their own organs. These changes illustrate phenotypic flexibility, the reversible adjustment of an adult's organs to current demands.

The cost of locomotion

Moving costs energy, and the cost depends on the mode of locomotion and on body size. Physiologists compare animals using the cost of transport, the energy needed to move one unit of body mass over one unit of distance, usually expressed in joules per kilogram per metre. For running, C. Richard Taylor and colleagues found in 1982 that the net cost of transport, the energy used above resting metabolism, is nearly independent of speed within a gait and falls with body mass to about the −0.3 power: a mouse uses more than twenty times as much energy per kilogram to cover a metre as a horse. Swimming is the cheapest form of locomotion, because water supports the body against gravity; flying is intermediate, more expensive per unit time but very cheap per unit distance because birds and bats travel fast.

# Cost of transport (COT) versus body mass for running, flying and swimming
# Approximate allometric equations from comparative compilations (Schmidt-Nielsen 1972;
# Taylor et al. 1982; later reviews). Values in J per kg per m; rounded, for illustration.
eqs = {"running": (10.7, -0.32), "flying": (3.6, -0.31), "swimming": (1.1, -0.38)}

def cot(mode, M):
    a, b = eqs[mode]
    return a * M ** b

print("mass (kg)    running   flying   swimming   (J/kg/m)")
for M in (0.01, 0.1, 1.0, 10.0, 100.0, 1000.0):
    print(f"{M:9.2f}   {cot('running', M):7.2f}  {cot('flying', M):7.2f}   {cot('swimming', M):7.2f}")

# energy for a 600 kg moose to walk 10 km and a 30 g mouse to run 1 km
for name, M, km in (("moose, 10 km", 600, 10), ("mouse, 1 km", 0.03, 1)):
    E = cot("running", M) * M * km * 1000
    print(f"{name}: about {E / 1000:.0f} kJ above resting metabolism")

mass (kg)    running   flying   swimming   (J/kg/m)
     0.01     46.71    15.01      6.33
     0.10     22.36     7.35      2.64
     1.00     10.70     3.60      1.10
    10.00      5.12     1.76      0.46
   100.00      2.45     0.86      0.19
  1000.00      1.17     0.42      0.08
moose, 10 km: about 8289 kJ above resting metabolism
mouse, 1 km: about 1 kJ above resting metabolism

The equations give orders of magnitude, not precise values for any species, but they explain many patterns. Small animals pay dearly to travel and tend to have small home ranges; large animals can afford long migrations. Caribou of the Porcupine herd travel more than 1,000 km a year between wintering ranges and calving grounds on the Arctic coastal plain. Salmon migrate hundreds of kilometres upriver without feeding. Within a gait, animals choose speeds that minimize cost: horses on treadmills switch from walking to trotting to galloping at speeds that keep cost near its minimum, and freely moving horses choose those speeds. Elastic energy storage in tendons, as in the hopping of kangaroos and the running of horses, lowers the cost further, a theme introduced in lesson 6.

Physiology sets the limits of where animals live

Every species has a range of conditions within which it can survive, grow and reproduce, and its physiology largely sets that range. Thermal tolerance is the best studied. For ectotherms, performance, such as running speed, growth rate or aerobic scope, rises with temperature to an optimum and then falls steeply, giving a thermal performance curve. The critical thermal maximum (CTmax) is the temperature at which an animal loses coordinated movement in a standardized warming test; the critical thermal minimum (CTmin) is its cold equivalent. The difference between an animal's CTmax and the maximum temperature it experiences in its habitat is its warming tolerance, and the difference between its optimum and its habitat temperature is its thermal safety margin.

A broad pattern has emerged from comparative studies. Tropical ectotherms, which live in warm, stable climates, often have narrow thermal tolerances and are already living close to their upper limits; temperate ectotherms experience more variable temperatures and have wider tolerances and larger safety margins. Curtis Deutsch and colleagues argued in 2008 that, despite smaller expected warming in the tropics, tropical insects may suffer more from climate change than temperate ones because their safety margins are smaller. Marine ectotherms, which cannot easily escape to cooler microhabitats, tend to fill their potential thermal ranges more completely than terrestrial ones, and their ranges are shifting poleward faster.

# Warming tolerance and thermal safety margin for three invented ectotherms
# (all values illustrative, degrees Celsius)
species = [
    # name,                    CTmax, T_opt, habitat mean summer max
    ("tropical forest lizard",  38.0,  33.0,  32.0),
    ("temperate prairie lizard", 44.0, 35.0,  30.0),
    ("cold-water stream fish",  29.0,  16.0,  21.0),
]
print("species                     warming tolerance   safety margin   after +3 degC")
for name, ctmax, topt, hab in species:
    wt, tsm = ctmax - hab, topt - hab
    wt3, tsm3 = wt - 3.0, tsm - 3.0
    flag = "above optimum" if tsm3 < 0 else "below optimum"
    print(f"{name:27s} {wt:8.1f}            {tsm:6.1f}        WT {wt3:4.1f}, TSM {tsm3:5.1f} ({flag})")

species                     warming tolerance   safety margin   after +3 degC
tropical forest lizard           6.0               1.0        WT  3.0, TSM  -2.0 (above optimum)
temperate prairie lizard        14.0               5.0        WT 11.0, TSM   2.0 (below optimum)
cold-water stream fish           8.0              -5.0        WT  5.0, TSM  -8.0 (above optimum)

In this illustrative comparison, the tropical lizard has only a small safety margin, and 3 °C of warming pushes its habitat temperature above its optimum. The temperate lizard retains a comfortable margin. The cold-water fish is already living above its optimum in summer and is closest to danger, a pattern that matches field observations of brook trout and Atlantic salmon, which seek cold-water refuges, such as groundwater seeps and tributary mouths, when rivers warm in summer, and suffer mortality in heat waves.

Oxygen, temperature and aquatic animals

Hans-Otto Pörtner proposed that the thermal tolerance of aquatic ectotherms is set by their capacity to supply oxygen, the hypothesis of oxygen- and capacity-limited thermal tolerance (OCLTT). As water warms, oxygen demand rises with metabolic rate (lesson 2) while oxygen content falls (lesson 9), so aerobic scope narrows and eventually disappears. Supporting evidence comes from Pacific salmon in the Fraser River of British Columbia: Erika Eliason, Anthony Farrell and colleagues showed in 2011 that the temperatures at which aerobic scope peaked in different sockeye populations matched the river temperatures each population historically encountered during its upstream migration, and that populations with tougher migrations had larger hearts and better cardiac performance. In unusually warm years, migrating salmon die in large numbers. The OCLTT hypothesis does not fit all animals equally well; some species maintain aerobic scope up to temperatures close to lethal limits, and the generality of the idea is debated.

Oxygen itself is declining in many waters. Warming reduces oxygen solubility and strengthens stratification, while nutrient runoff fuels algal blooms whose decomposition consumes oxygen. Seasonal dead zones form each summer in the northern Gulf of Mexico, at the mouth of the Mississippi, and the deep waters of the Gulf of St. Lawrence have lost a large share of their oxygen over the past century, with recent measurements showing levels low enough to harm cod and other bottom-dwelling species. Fish respond to hypoxia by increasing ventilation, raising hemoglobin oxygen affinity, reducing activity and, if they can, moving away; prolonged hypoxia reduces growth and reproduction.

Ocean acidification

About a quarter to a third of the carbon dioxide released by human activity has been absorbed by the oceans. Dissolved carbon dioxide forms carbonic acid, so ocean surface pH has fallen by about 0.1 units since pre-industrial times, roughly a 30 per cent increase in hydrogen ion concentration, and the concentration of carbonate ions has fallen. Animals that build shells or skeletons of calcium carbonate, such as oysters, mussels, corals, pteropods and sea urchins, find calcification harder when carbonate saturation falls, and larval stages are particularly vulnerable. In 2007 and 2008, oyster hatcheries in Oregon and Washington suffered mass larval die-offs that were traced to upwelling of corrosive, low-pH water; hatcheries now monitor seawater chemistry and buffer their intake water. Fish face acid–base challenges too, compensating for raised carbon dioxide by accumulating bicarbonate, and some studies have reported effects on behaviour and sensory function, although several high-profile results on reef fish behaviour have not been replicated, a reminder that physiological claims need careful, reproducible evidence.

Conservation physiology

Conservation physiology, a term formalized by Steven Cooke and colleagues in 2013, applies physiological knowledge and tools to conservation problems. Examples include using glucocorticoid measurements to assess the impact of human disturbance (lesson 7), designing fishways whose water velocities match the swimming abilities of migrating fish, setting temperature thresholds for fisheries closures, and predicting which species and populations are most vulnerable to climate change from their thermal tolerances. Cooke's group at Carleton University and colleagues have used physiology to reduce the mortality of fish caught and released by anglers and in commercial bycatch, for example by limiting air exposure and handling time. Physiological traits can also guide reintroductions, translocations and captive breeding programs.

Ethics and the law of animal research

Much of what is known about animal physiology comes from experiments on living animals, and some of it from experiments that caused pain or death. The ethics of animal research rest on the Three Rs, set out by William Russell and Rex Burch in 1959: replacement of animals with non-animal methods where possible, reduction in the number of animals used, and refinement of procedures to minimize pain and distress. Field physiology raises its own issues, from the stress of capture and tagging to the effects of devices on behaviour and survival. All research on vertebrates in Canadian and American universities and government laboratories must be reviewed and approved in advance by an animal care committee.

In Canada, oversight rests mainly on the Canadian Council on Animal Care (CCAC), an independent body founded in 1968 that sets national guidelines and policies and assesses institutions. CCAC certification is not itself a federal law, but compliance is a condition of funding from the federal research councils, CIHR, NSERC and SSHRC, so in practice all publicly funded research follows it. Each institution's animal care committee reviews protocols and assigns them to categories of invasiveness from A (no vertebrates) to E (procedures that cause severe pain near or above the pain tolerance threshold of unanesthetized conscious animals). Several provinces, including Ontario under its Animals for Research Act, have their own legislation. The CCAC's guidelines cover all vertebrates and cephalopods. According to CCAC figures published in October 2025, about 3.7 million animals were used in science at certified institutions in 2024, of which fish made up about 46 per cent and mice about 32 per cent. Federal amendments to the Food and Drugs Act in 2023 banned the testing of cosmetics on animals in Canada, and amendments to the Canadian Environmental Protection Act the same year committed the government to promoting alternatives to animal testing.

Looking back over the course

The course began with the idea of homeostasis and the cost of regulation, and those two ideas run through every topic. Thermoregulation, osmoregulation, the control of breathing and circulation, and endocrine feedback are all ways of holding internal conditions steady, and each has a price in energy, water or risk. Body size, through scaling, shapes metabolic rate, heart rate, cost of transport and the feasibility of torpor. Physical laws, Fick's law of diffusion, Poiseuille's law, Henry's law, the Nernst equation and the principles of countercurrent exchange, constrain every design, and evolution has found remarkably similar solutions to them in unrelated animals, from the countercurrent exchangers of gills, kidneys and flippers to the convergent hemoglobins of high-altitude mice and birds. Understanding these principles lets physiologists predict how animals will respond to new conditions, which has never been more important than in a rapidly changing world.