Civilization101Blueprint

Biology

Life from the cell up: the human body, microbes and immunity, inheritance and epidemics. Each result with what it lets you do and who first found it.

Home: First aid and surgery, Level 0 · Triage, level 1 of 2 in its track. Serves 11 steps across 3 subjects.

Every number a carer, a breeder or a health authority acts on comes from biology. An adult is about 30 trillion human cells carrying about as many bacteria (Sender, Fuchs and Milo, 2016). The heart moves the body's 5 litres of blood round once a minute at rest. One case of measles infects up to 18 people (WHO).

This page gives the results the rest of the site depends on, in the order each needs the last: cells and energy, the human body, microbes and immunity, inheritance, populations and epidemics, and the modern tools. Part 2 is a map of the body for the first-aid guide and the vital signs, not a medical course. Formulas use the notation of mathematics.

At a glance: what builds on what

Each part uses the ones above it.

PartResultsWhat depends on it
1 · Cells and energyCell theory, diffusion, photosynthesis, respiration, enzymesMicroscopy, crop yields, fermentation, food energy
2 · The human bodyDirections and quadrants, organ systems, skeleton, circulation, airway, gut and kidneys, nerves, energy needsFirst aid, surgery, nursing, rations
3 · Microbes and defenceBacterial growth, killing by heat, immunity, vaccinesFood safety, sterilising, vaccination
4 · InheritanceMendel's ratios, DNA, the genetic code, Hardy–Weinberg, inbreeding, response to selectionSeed saving, livestock breeding, inherited disease
5 · Populations and epidemicsNatural selection, logistic growth, the ten-per-cent rule, R₀, the SIR modelFisheries, grazing, antibiotic resistance, outbreak control
6 · Biology as engineeringPCR, sequencing, gene editing, mRNA vaccines, protein structureDiagnosis, vaccines, crop and drug design

Part 1Cells and energy

Cells, and why they are small

Every living thing is one cell or many. A bacterium is 1–2 µm long and most human cells 10–30 µm (1 µm is a thousandth of a millimetre). The naked eye resolves about 0.1 mm, so seeing cells takes a lens of 200× or more: a bead microscope gives it.

Cell theory and the surface-to-volume limit
AV=4πr243πr3=3r

All living things are made of cells, and every cell comes from a cell. A cell feeds through its surface, which grows as r² while its needs grow with its volume, r³: double the radius and each unit of volume gets half as much surface. A large organism is therefore many small cells, not one big one.

Use: Explains why the agents of infection went unseen until lenses of 200× and more, and why germ theory had to wait for the microscope.

First: Hooke named the cell in Micrographia, 1665 (Gutenberg). Schleiden (plants, 1838) and Schwann (animals, 1839) made all life cellular, and Virchow added omnis cellula e cellula, 1855 (Mazzarello, 1999).

Diffusion: Fick's law
J=−Ddcdx,t≈x22D

A dissolved substance moves down its concentration gradient: the flux J is the diffusion coefficient D times the gradient. The time to cover a distance x grows as x². Oxygen in water at body temperature crosses 1 µm in under a millisecond, 1 mm in about 3 minutes and 1 cm in about 5 hours.

Use: Diffusion alone serves no tissue more than about a millimetre from its supply. That is why the body needs a heart and a branching network of vessels, and why the lungs and the gut are built from huge, thin surfaces.

First: Adolf Fick, 1855 (Annalen der Physik).

Baker's yeast, Saccharomyces cerevisiae, through a school microscope's 40× objective: oval cells about 5 µm long, unstained. A bead microscope shows the same cells. Baking yeast cells under 40x microscope objective · 2023-01-02 22:03:33 · ~delta · CC BY-SA 4.0 · Commons ↗

Photosynthesis, respiration and enzymes

Plants store sunlight as sugar. Every cell, plant or animal, burns sugar back to carbon dioxide and water to make ATP, the molecule that powers the cell. Enzymes make both happen at the temperature of a leaf or a body.

Photosynthesis
6CO2+6H2O⟶lightC6H12O6+6O2

Green plants, algae and some bacteria build sugar from carbon dioxide and water using light, storing about 2,870 kJ in each mole of glucose and giving off oxygen. At most 4.6 % of the sunlight falling on a C₃ crop (wheat, rice, potatoes) can end up as biomass, and 6 % for a C₄ crop (maize, sorghum, sugarcane); fields over a season get well below that.

Use: Sets the ceiling on food from land. A field's yield is the sunlight it receives times this efficiency, and water, nutrients and the length of the season decide how near the ceiling it gets (holding fertility).

First: Ingenhousz showed in 1779 that plants restore air only in light. Calvin, Benson and Bassham traced the path of carbon with ¹⁴C, 1946–1954 (Nobel Prize 1961). The limits: Zhu, Long and Ort, 2008.

Respiration and ATP
C6H12O6+6O2⟶6CO2+6H2Oabout 30 ATP per glucose

Cells burn glucose back to carbon dioxide and water and capture the energy as about 30 molecules of ATP per glucose (older books say 36–38). Without oxygen, yeast turns glucose into ethanol and muscle into lactate, for 2 ATP.

Use: Food energy follows from it: 1 g of carbohydrate or protein gives about 17 kJ (4 kcal), 1 g of fat about 37 kJ (9 kcal). The oxygen-free route makes bread, beer, yoghurt and silage (fermentation).

First: Mitchell's chemiosmotic theory, 1961, explained how the energy is captured (Nature; Nobel Prize 1978). The yield of about 30 follows from the measured ratios of ATP made per oxygen used (Hinkle, 2005).

Enzymes: the Michaelis–Menten rate
v=Vmax[S]Km+[S]

An enzyme speeds one reaction by millions of times at body temperature. Its rate v rises with the concentration of its substrate [S] until every enzyme molecule is busy, at Vₘₐₓ; Kₘ is the concentration that gives half that rate. Each enzyme works fastest over a narrow range of temperature and pH, and most are destroyed by heating above about 60 °C.

Use: Why vegetables are blanched before freezing (to stop their own enzymes), why a mash for brewing is held at a set temperature (fermentation), and why a body temperature above 40 °C is an emergency.

First: Michaelis and Menten, 1913 (English translation, Johnson and Goody, 2011).

Leaf cells of a moss (Plagiomnium affine) under a light microscope: each cell is a box of cell wall packed with green chloroplasts, where photosynthesis happens. Plagiomnium affine laminazellen · created 01.11.2006 · Kristian Peters -- Fabelfroh · CC BY-SA 3.0 · Commons ↗

Part 2The human body

Directions, and the four quarters of the belly

Anatomy describes everything from the anatomical position: standing, facing forward, arms at the sides, palms forward. Left and right always mean the patient's own.

The abdomen is divided into four quadrants by lines through the navel. Pain is reported, and organs found, by quadrant:

  • Right upper: liver and gallbladder. Gallstone pain sits under the right ribs.
  • Left upper: stomach and spleen. A blow to the lower left ribs can burst the spleen and bleed into the belly.
  • Right lower: appendix and the start of the large bowel; right ovary. Appendicitis pain often starts round the navel and settles here.
  • Left lower: the last part of the large bowel; left ovary.
Illustration, not a photograph The abdomen divided (a) into nine regions and (b) into four quadrants by lines through the navel. Quadrants are what is used in first aid and when describing pain. Abdominal Quadrant Regions · 2013-06-03 · OpenStax · CC BY 3.0 · Commons ↗
TermMeansExample
Anterior / posteriorFront / backThe breastbone is anterior to the heart
Superior / inferiorTowards the head / the feetThe diaphragm is inferior to the lungs
Medial / lateralTowards / away from the midlineIn the anatomical position the thumb is lateral
Proximal / distalNearer to / farther from where a limb joins the trunkA tourniquet goes proximal to the wound
Superficial / deepNear / far from the surfaceThe femoral artery is deep in the thigh but superficial in the groin
Belly pain that needs a surgeonPain that becomes constant and stays in one place; a belly that is rigid, or hurts more when a pressing hand is lifted away; vomiting with no stool or wind passed; or fever with pain in one quadrant. These are the signs of appendicitis, a burst gut or a blocked bowel, which kill within days without an operation.

The eleven organ systems

The body is described as eleven systems working together. The numbers are for a healthy adult of about 70 kg.

Illustration, not a photograph Organ systems of the body, 1 of 2: integumentary (skin), skeletal, muscular, nervous, endocrine and cardiovascular, each with its main organs and jobs. Organ Systems I · 2013-04-05 00:41:42 · Connexions · CC BY 3.0 · Commons ↗
Illustration, not a photograph Organ systems of the body, 2 of 2: lymphatic, respiratory, digestive, urinary, and the male and female reproductive systems. Organ Systems II · 2013-04-02 22:16:35 · Connexions · CC BY 3.0 · Commons ↗
SystemMain organsJobNumbers that matter
IntegumentarySkin, hair, nailsBarrier; holds water in; sheds heat by sweatingAbout 1.8 m² of skin; sweating can lose more than a litre an hour in hard work in heat
SkeletalBones, cartilage, jointsSupport and protection; marrow makes blood cells206 bones in an adult, about 270 at birth before many fuse
MuscularMore than 600 skeletal musclesMovement, posture, heatSkeletal muscle is 38 % of body mass in men and 31 % in women (Janssen, 2000)
NervousBrain, spinal cord, nervesSensing, control, thought86 billion neurons (Azevedo, 2009); the brain is 2 % of body mass and uses about 20 % of its energy at rest
EndocrinePituitary, thyroid, pancreas, adrenal glands, ovaries, testesChemical messages (hormones) carried in the bloodInsulin and glucagon hold blood glucose between about 4 and 8 mmol/L
CardiovascularHeart, arteries, veins, capillaries, bloodCarries oxygen, fuel, heat and wasteAbout 5 L of blood (70 ml per kg); the heart pumps about 5 L a minute at rest
Lymphatic and immuneLymph nodes, spleen, thymus, bone marrow, white cellsReturns tissue fluid to the blood; fights infectionA swollen, tender node drains the infected area: armpit for the arm, groin for the leg
RespiratoryNose, throat, larynx, windpipe, lungsTakes in oxygen, gives off carbon dioxideAbout 480 million alveoli (Ochs, 2004); 0.5 L a breath at rest
DigestiveMouth, oesophagus, stomach, intestines, liver, pancreasBreaks food down and absorbs itAbout 5 m long in life; an absorbing surface of about 32 m², not the tennis court still printed (Helander and Fändriks, 2014)
UrinaryKidneys, ureters, bladder, urethraFilters the blood; sets its water and saltThe kidneys filter about 180 L of plasma a day and return all but 1–2 L
ReproductiveOvaries, uterus; testesMakes eggs, sperm and sex hormones; carries a pregnancyPregnancy lasts about 40 weeks from the first day of the last period (childbirth)

The skeleton and the spine

206 bones: 80 in the skull, spine, ribs and breastbone, 126 in the limbs and the girdles that hold them.

  • Spine: 7 neck (cervical) vertebrae, 12 thoracic (one for each pair of ribs), 5 lumbar, then the sacrum and the coccyx, each fused from several. The spinal cord ends at the first or second lumbar vertebra in an adult; below that run only nerve roots.
  • Arm: humerus; radius (thumb side) and ulna; in each hand 8 carpals, 5 metacarpals and 14 phalanges.
  • Leg: femur, the longest and strongest bone; kneecap (patella); tibia (shin) and fibula; in each foot 7 tarsals, 5 metatarsals and 14 phalanges.
  • Joints: hinge (elbow, knee, fingers), ball and socket (shoulder, hip), pivot (the top of the neck; the forearm turning), and fixed seams (sutures) in the skull.

A broken femur can hide 1–1.5 litres of blood in the thigh, and a broken pelvis several litres: treat either as bleeding as well as a fracture. Splinting is in the first-aid guide.

Illustration, not a photograph The adult skeleton from the front, with the main bones named: skull, spine, ribs and breastbone, shoulder girdle, arm and hand, pelvis, leg and foot. Human skeleton front en · 2007-01-03 · LadyofHats Mariana Ruiz Villarreal · Public domain · Commons ↗
Illustration, not a photograph The spine from behind and from the side: 7 cervical, 12 thoracic and 5 lumbar vertebrae, then the sacrum and coccyx. The four curves, seen from the side, are normal. 715 Vertebral Column · 2013-04-19 23:03:55 · OpenStax College · CC BY 3.0 · Commons ↗
Suspected neck or back injuryAfter a fall from height, a dive into shallow water or a heavy blow to the head, treat the spine as broken: keep the head in line with the body and move the person only to open the airway or escape danger. An open airway still comes first. An injury at or above the third neck vertebra can stop breathing, because the diaphragm's nerve leaves the cord at C3, C4 and C5.

Heart, blood and circulation

Blood runs two circuits in series. The right side of the heart pumps it through the lungs; the left side, with the thicker wall, pumps it round the whole body at about five times the pressure. Four valves keep it moving one way. Arteries carry blood away from the heart, veins bring it back.

  • Blood: about 70 ml per kg of body weight. Red cells, 4–6 million in every cubic millimetre, carry oxygen on haemoglobin and live about 120 days; white cells fight infection; platelets and clotting proteins plug leaks. Plasma, the straw-coloured fluid, is about 55 % of the volume.
  • Blood loss: an adult barely notices losing 15 % (about 750 ml). At 30–40 % (1.5–2 litres) the pulse races, the skin is cold and pale and the person becomes confused; more than 40 % is immediately life-threatening. Stopping it is in the first-aid guide.
  • Pulses are felt where an artery runs over bone near the skin: the wrist on the thumb side (radial), the neck beside the windpipe (carotid), the inner upper arm (brachial, used for infants), the groin crease (femoral). If you cannot find it at the wrist, try the neck.
  • Blood groups: a transfusion of the wrong ABO group can kill. Group O red cells can be given to anyone in an emergency, Rh-negative O to girls and women who may later become pregnant; each person's group must be tested and matched before a planned transfusion. Landsteiner found the groups in 1901.
Cardiac output: Harvey's argument
Q=f×V≈70 min−1×70 ml≈5 L/min

The heart's output Q is its rate f times the volume V of each beat. At rest the whole blood volume goes round about once a minute; in hard exercise the output rises four- to fivefold.

Use: A fast, weak pulse means a small volume per beat, from bleeding or dehydration, being made up by rate: lay the person flat, keep them warm and look for the loss (shock). Harvey's arithmetic proved the circulation: the heart sends out more blood in half an hour than the body holds, so the same blood must go round.

First: William Harvey, De motu cordis, 1628, chapter 9 (English translation, Gutenberg).

Flow and the fourth power: Poiseuille's law
Q=πr4ΔP8ηL

Steady flow Q through a tube rises with the fourth power of its radius r and falls with its length L and the viscosity η of the fluid. At the same pressure difference ΔP, halving the radius cuts the flow sixteenfold.

Use: Why a partly blocked artery starves the muscle beyond it, and why fluid or blood is given fast through a short, wide cannula, never a long thin one.

First: Hagen, 1839, and Poiseuille, 1840–1846 (Sutera and Skalak, 1993).

Illustration, not a photograph The heart cut open, seen from the front, so the patient's right is on the left. Blue: blood from the body enters the right atrium and is pumped to the lungs. Red: blood from the lungs enters the left atrium and the thick-walled left ventricle pumps it into the aorta. Four valves keep it moving one way. Diagram of the human heart (cropped) · 2006-06-02, 07:02 · Wapcaplet · CC BY-SA 3.0 · Commons ↗
Blood cells under a scanning electron microscope, false-coloured: a red cell (left, a dimpled disc about 7.5 µm across), a platelet (centre) and a white cell (right). Red White Blood cells · 21 September 2004 (original up · Electron Microscopy Facility at The National Cancer Institute at Frederick (NCI- · Public domain · Commons ↗
Taking the pulse at the wrist: two fingertips, not the thumb, on the thumb side of the inner wrist. Count for 30 seconds and double it. Radial pulse · 13 April 2004 (according to Ex · U.S. Air Force Staff Sgt. Jeanette Copeland · Public domain · Commons ↗
Illustration, not a photograph Where a pulse can be felt: an artery running close to the skin over bone. The radial (wrist) and carotid (neck) are used most; the brachial (inner upper arm) in infants. 2110 Pulse Sites · OpenStax College · CC BY 3.0 · Commons ↗

Airway and lungs

Air passes from the nose or mouth through the throat (pharynx), the voice box (larynx) and the windpipe (trachea) into two main bronchi, which branch about 23 times down to some 480 million alveoli. There, less than a thousandth of a millimetre of tissue separates air from blood.

  • The tongue blocks the airway of an unconscious person lying on their back. The head tilt and chin lift, and the recovery position, exist to stop that.
  • The right main bronchus is wider and steeper than the left, so an inhaled object or vomit usually goes into the right lung.
  • The diaphragm does most of the work of breathing. Its nerve, the phrenic, leaves the spinal cord at C3–C5.
  • Volumes: about 0.5 litre a breath and 12–18 breaths a minute at rest (vital signs); the lungs hold about 6 litres when full. A pulse oximeter reads 95–100 % in a healthy person at sea level.
  • Carbon monoxide binds haemoglobin more than 200 times as tightly as oxygen does. From charcoal braziers, stoves and engines in closed rooms it kills without warning or breathlessness, and a pulse oximeter reads it as oxygen.
Illustration, not a photograph The airway and lungs: nose, throat, voice box and windpipe, then the bronchi branching into each lung, ending in the alveoli (inset), where blood picks up oxygen. The diaphragm below does most of the work of breathing. Respiratory system complete en · 2007-12-13 · LadyofHats, Jmarchn · Public domain · Commons ↗

Gut, liver and kidneys

  • Gut: food takes 1–3 days from mouth to anus. The small intestine absorbs nearly all the nutrients and most of the water; the large intestine takes back the rest of the water and holds the gut bacteria.
  • Liver: the largest internal organ, about 1.5 kg. It stores glucose as glycogen, makes bile and the clotting proteins, and breaks down alcohol and most drugs and poisons. That is why an overdose of paracetamol or a meal of death cap mushrooms kills through liver failure days later (poisons).
  • Kidneys: each holds about a million filtering units, nephrons (200,000 to more than 2.5 million in different people; Bertram, 2011). Together they filter about 180 litres of plasma a day and return all but 1–2 litres. Less than 0.5 ml of urine per kg an hour, under about 400 ml a day for an adult, means too little fluid or failing kidneys.
Oral rehydration: salt rides in with sugar
Na+ 75+Cl− 65+glucose 75+K+ 20+citrate 10=245 mmol/L

The gut wall carries sodium and glucose across together, and water follows them. That carrier keeps working in cholera and the other diarrhoeas that make the gut pour water out, so a drink of the right salt and sugar strength replaces losses that would otherwise kill within hours. The WHO formula, in millimoles per litre, totals 245.

Use: Treats the dehydration of diarrhoea without a drip. The home recipe is 1 litre of safe water, 6 level teaspoons of sugar, ½ level teaspoon of salt (wound care and first aid). Measure, never guess: too much salt is dangerous in small children.

First: Crane described the sodium–glucose carrier in 1960–1961; trials in Dhaka and Calcutta proved oral rehydration between 1968 and 1971; the reduced-osmolarity formula has been recommended by WHO and UNICEF since 2003 (WHO).

Illustration, not a photograph The digestive tract from mouth to anus, with the liver, gallbladder and pancreas that empty into it. The appendix hangs from the start of the large intestine, low on the right. Digestive system diagram en · 2006-12-17 · Mariana Ruiz, Jmarchn · Public domain · Commons ↗
Illustration, not a photograph The kidneys and urinary tract from the front: 1 urinary system, 2 kidney, 3 renal pelvis, 4 ureter, 5 bladder, 6 urethra, 7 adrenal gland, 8 renal artery and vein, 9 inferior vena cava, 10 aorta, 11 common iliac artery and vein, 12 liver, 13 large intestine, 14 pelvis. The left kidney (right of picture) is drawn cut open. Urinary system · 2010 · Jordi March i Nogué [1] · CC BY-SA 3.0 · Commons ↗

Brain, nerves and hormones

  • Central nervous system: the brain and the spinal cord. Neurons lost there are not replaced, so damage is usually permanent. A cut nerve in a limb can regrow at about 1 mm a day.
  • Nerves: 12 pairs of cranial nerves serve the head, and one of them, the vagus, the heart and gut. 31 pairs of spinal nerves leave between the vertebrae, each serving a band of skin and a set of muscles, which is how the level of a spinal injury is read from where feeling stops.
  • Signals run along nerves as electrical impulses at up to about 120 m/s, and pass between cells as chemicals.
  • Hormones give slower control. Insulin and glucagon hold blood sugar. Thyroid hormone sets the body's pace and needs iodine: goitre and the brain damage of iodine deficiency in childhood are prevented by iodised salt. Adrenaline readies the body for effort.
  • The brain runs almost entirely on glucose. Anyone confused, drowsy or fitting who may have low blood sugar (a diabetic, a drinker, a starving or sick child) and who can still swallow should be given sugar.
Illustration, not a photograph The nervous system: brain and spinal cord (the central nervous system) and the nerves that branch from them to every part of the body, with the main nerves of the arm and leg named. Nervous system diagram-en · 2014-10-26 · Medium69, Jmarchn · CC BY-SA 4.0 · Commons ↗

Energy, weight and thinness

How much food a person needs, and how to tell from a scale, a tape and a ruler when they are getting too little. The nutrients that run short first are in preventing deficiency disease.

Energy needs: basal rate times activity
E=BMR×PALBMR=15.1W+692(men)BMR=14.8W+487(women)

A day's energy need E is the basal metabolic rate (the body at rest) times a physical activity level. For adults aged 18–30, BMR in kilocalories a day from weight W in kilograms is given above; older adults have their own lines. PAL is 1.40–1.69 for a sedentary life, 1.70–1.99 for an active one and 2.00–2.40 for hard physical work. A 60 kg man doing farm work needs about (15.1 × 60 + 692) × 2.1 ≈ 3,350 kcal (14 MJ) a day.

Use: Ration planning: multiply by people and days, and turn it into food at about 3,500 kcal per kg of dry grain, so about 1 kg of grain a day for that farm worker.

First: FAO, WHO and UNU, Human energy requirements, 2004, tables 5.2 and 5.3 (FAO).

Body mass index
BMI=mh2

Mass in kilograms divided by the square of height in metres. For adults WHO counts under 18.5 as underweight, 18.5–24.9 as normal, 25 or more as overweight and 30 or more as obese; under 16 is severe thinness.

Use: Screens adults for hunger or excess with a scale and a tape. It misleads in very muscular people, in pregnancy and in children. For a child from 6 months to 5 years, measure the mid-upper-arm circumference instead: under 115 mm is severe acute malnutrition.

First: Quetelet proposed the ratio in 1835 (MacTutor); Keys named it the body mass index in 1972 (Journal of Chronic Diseases).

Part 3Microbes and defence

How fast microbes grow, and what kills them

Most bacteria that cause disease grow fastest at 30–40 °C, slowly in a refrigerator and not at all above about 60 °C. Their numbers multiply, and heat kills them by a fixed fraction a minute: both rules work in powers, which is why a little time makes so much difference. The micro-organisms guide gives the weak point of each organism.

Bacteria double
N=N0×2t/g

Growing bacteria divide at a steady doubling time g: about 20 minutes for E. coli at 37 °C with food. Ten doublings make a thousandfold increase; one cell becomes a million in under 7 hours.

Use: Behind the food-safety rules: keep cooked food out of 5–60 °C, eat or chill it within 2 hours, and reheat it until steaming hot (WHO Five keys to safer food; preserving the harvest).

First: Monod measured and described bacterial growth, 1949 (Annual Review of Microbiology).

Heat kills in tenfold steps: the D-value
N=N0×10−t/D

At a fixed temperature every D minutes of heating kills 90 % of the organisms still alive. Each organism, and each kind of spore, has its own D. Spores of Clostridium botulinum survive boiling and have a D of about 0.2 minutes at 121 °C, so canning is designed for 12 tenfold reductions: the 'botulinum cook' of about 3 minutes at 121 °C at the centre of the can.

Use: Why low-acid food needs a pressure canner at 116–121 °C while acid food (pH below 4.6) needs only boiling water (preservation guide), and why surgical instruments are sterilised in steam at 121 °C for at least 15 minutes: boiling kills bacteria and viruses but not spores.

First: Bigelow showed that heat kills at a logarithmic rate, 1921 (Journal of Infectious Diseases); Esty and Meyer measured the botulinum spores that the 12-reduction rule is built on, 1922 (Journal of Infectious Diseases).

Immunity and vaccines

The body defends itself in two layers.

  • Innate: skin, mucus, stomach acid, fever, and white cells that engulf any invader within hours. It acts the same against every germ and learns nothing.
  • Adaptive: lymphocytes that make antibodies and killer cells matched to one germ. The first meeting takes 1–2 weeks to answer; afterwards memory cells answer within days, often for life, which is why most people catch measles only once.
  • A vaccine gives that first meeting safely: a killed or weakened germ, a piece of one, an inactivated toxin (tetanus, diphtheria) or, since 2020, the mRNA instructions for one of its proteins. Most need several doses; WHO's schedule for tetanus is six doses through childhood and adolescence. Storing and giving them is in antibiotics and vaccines.

Milestones: Jenner's cowpox vaccination, 1796, published 1798 (Gutenberg); Pasteur's rabies vaccine, 1885; smallpox declared eradicated in 1980, the only human disease ended so far (WHO); rinderpest, a cattle plague, eradicated in 2011; mRNA vaccines from 2020, built on Karikó and Weissman's modified RNA (2005).

A childhood vaccination. Health becomes a public system rather than a private accident. Young girl about to receive a vaccine in her upper arm (48545990252) · 2019-08-01 00:00 · SELF Magazine · CC BY 2.0 · Commons ↗

Part 4Inheritance

Genes, DNA and the code

Traits pass from parents to children as genes: stretches of DNA written in four letters and read three at a time into proteins. A person carries two copies of most genes, one from each parent. The human genome, read end to end without gaps in 2022, is 3.055 billion letters long and holds about 20,000 genes that code for proteins (Nurk et al., 2022).

Mendel's ratios
Aa×Aa⟶1AA:2Aa:1aa

Each parent passes on one of its two copies of a gene, at random. Crossing two carriers gives 1 : 2 : 1 by gene and 3 : 1 by appearance when A is dominant. Genes on different chromosomes sort independently, so two traits together give 9 : 3 : 3 : 1. Mendel's peas: 5,474 round seeds to 1,850 wrinkled, 2.96 : 1.

Use: Predicts what a cross will give and how many generations it takes to fix a trait, and explains why a hidden defect appears when relatives breed (securing seed and breeding stock).

First: Gregor Mendel, Versuche über Pflanzen-Hybriden, read 1865, published 1866 (English translation, Wellcome Collection).

DNA: the double helix
[A]=[T],[G]=[C]

DNA is two strands wound in a helix and held together by base pairs: adenine with thymine, guanine with cytosine. Each strand therefore fixes the other, so a cell copies its DNA by separating the strands and building a new partner for each.

Use: The basis of every genetic test, of paternity and forensic matching, and of PCR and sequencing.

First: Chargaff found the equal ratios, 1950 (Experientia). In 1953 came Franklin and Gosling's X-ray evidence (Nature) and Watson and Crick's model (Nature).

The genetic code
43=64 codons⟶20 amino acids+stop

Each three letters of messenger RNA, a codon, names one amino acid or 'stop'. Four letters in threes give 64 codons for 20 amino acids, so most amino acids have several. Nearly every living thing uses the same code, which is why a bacterium given the human gene can make human insulin.

Use: Lets a gene be read as the protein it makes; behind insulin, vaccines and enzymes made by microbes (biology as engineering).

First: Crick, Barnett, Brenner and Watts-Tobin showed the code is read in threes, 1961 (Nature); Nirenberg and Matthaei read the first word the same year, UUU for phenylalanine (PNAS).

Carriers, inbreeding and selection

Three results turn Mendel's rules into numbers for a whole population: a village, a herd or a field of seed.

Hardy–Weinberg
p2+2pq+q2=1

If a gene has two forms with frequencies p and q, so p + q = 1, and mating is random, the population holds p² of one type, 2pq carriers and q² of the other, unchanged from one generation to the next.

Use: Counts the carriers nobody can see: if 1 child in 2,500 is born with a recessive disease, q = 1/50 and about 1 person in 25 carries it. Marriage between cousins raises the risk because both parents are more likely to carry the same rare gene.

First: G. H. Hardy (Science, 1908) and, independently, the physician Wilhelm Weinberg, 1908.

Inbreeding and the effective population size
Ne=4MFM+FΔF=12Ne

A breeding group of M males and F females loses variation like an ideal group of size Nₑ, which is set mostly by the scarcer sex. Each generation it becomes ΔF more inbred. One bull with 25 cows gives Nₑ ≈ 3.8: about 13 % more inbreeding every generation.

Use: FAO's minimum for keeping a breed is Nₑ = 50, ΔF = 1 % a generation: for example 25 males and 25 females, or 14 males and 116 females (FAO, 2013). Use several sires, bring in unrelated ones, and save seed of cross-pollinated crops from many plants (livestock, seeds).

First: Sewall Wright, Evolution in Mendelian populations, 1931 (Genetics).

The breeder's equation
R=h2S

The gain R in the next generation is the selection differential S (how far the chosen parents are above the average) times the heritability h², the share of the trait's variation that is inherited. Milk yield and growth rate have h² of about 0.2–0.4; fertility and resistance to disease often under 0.1.

Use: If the animals kept for breeding average 10 kg heavier at a year old than the flock, and h² = 0.3, their offspring will average about 3 kg heavier. A trait with low heritability improves faster through better feed and care than through selection.

First: Jay Lush, Animal Breeding Plans, 1937 (Hill, 2014).

Part 5Populations and epidemics

Natural selection

Variation, inheritance and unequal survival are enough: the forms that leave more offspring become common. Selection by breeders, by antibiotics and by pesticides follows the same arithmetic.

Selection changes a population
Δp≈sp(1−p)

A form of a gene at frequency p whose carriers leave a fraction s more offspring rises by about s p (1 − p) a generation: slowly while it is rare, fastest at 50 %, slowly again near 100 %. Bacteria can divide every hour, so their resistance evolves thousands of times faster than any change in us.

Use: Antibiotic resistance is selection: each course kills the susceptible bacteria and leaves the resistant. Resistant infections directly caused about 1.14 million deaths in 2021 (GRAM, 2024). Give antibiotics only for bacterial infection, at the full dose, and never to make livestock grow (antibiotics).

First: Darwin and Wallace, 1858 (Linnean Society); Darwin, On the Origin of Species, 1859 (Gutenberg). The arithmetic: Haldane, Fisher and Wright, 1924–1932 (Wright, 1931).

Population growth and harvest

Unchecked, a population grows exponentially (e and growth). With limited food and space it levels off at a carrying capacity K.

Logistic growth and the largest sustainable harvest
dNdt=rN(1−NK)MSY=rK4at N=K2

Growth is fastest at half the carrying capacity, so the most that can be taken year after year, the maximum sustainable yield, is rK/4, from a stock held near K/2. Take more and the stock shrinks, its growth falls and the catch collapses.

Use: Sets the take from a fish pond, a fishery, a hunted herd or a woodlot. A lake that holds at most 10,000 fish, growing at r = 0.5 a year when sparse, yields at most about 1,250 a year from a stock kept near 5,000. Because r and K are never known exactly, take less than that (fish ponds).

First: Verhulst, 1838 (MacTutor); the maximum sustainable yield, Schaefer, 1954.

The ten-per-cent rule
En≈E0×0.1n

About a tenth of the energy at one feeding level reaches the next; the rest is spent on living. After n steps up a food chain, a tenth to the nth power is left.

Use: A field feeds far more people as grain than as meat from animals fed that grain. Livestock add food rather than cost it where they eat what people cannot: grass on land that cannot be cropped, and kitchen and crop waste.

First: Lindeman, 1942 (Ecology); a mean of 10 % from 48 aquatic food webs, Pauly and Christensen, 1995 (Nature).

Epidemics

An outbreak grows while each case infects more than one other person, and dies out when each infects fewer. Isolation, clean water and vaccination all work by pushing that number below one (the health authority).

The reproduction number and herd immunity
R=R0(1−v)vc=1−1R0

R₀ is the number of people one case infects where nobody is immune. Immunising a fraction v cuts it to R₀(1 − v). Once v passes the critical fraction 1 − 1/R₀, each case infects fewer than one and outbreaks die out.

Use: Measles, with up to 18 infections per case (WHO), needs about 95 % of people immune: two doses for nearly everyone. A disease with R₀ = 2 is stopped at 50 %. Babies too young to vaccinate are protected only by the immunity around them.

First: The threshold, Kermack and McKendrick, 1927; R₀ in Ross's and Macdonald's work on malaria, 1911–1952 (Heesterbeek, 2002).

The SIR model
dSdt=−βSINdIdt=βSIN−γIdRdt=γI

A population of N people is split into susceptible S, infectious I and recovered R. β is the rate of infecting contacts, 1/γ the time a case stays infectious, and R₀ = β/γ. The epidemic peaks when the susceptible share falls to 1/R₀ and ends with some people never infected.

Use: Shows why early action counts: halving contacts halves R₀ and can turn a growing outbreak into a shrinking one, and isolating cases sooner does the same by shortening 1/γ. It can be stepped forward a day at a time on paper (the derivative).

First: Kermack and McKendrick, 1927 (Proceedings of the Royal Society A; MacTutor).

Part 6Biology as engineering

Reading, copying and writing DNA

Since the 1980s biology has been a technology: genes are copied, read, edited and written. These tools need a laboratory, reagents and a cold chain, and each one changed what a health service or a breeder can do (biology as engineering).

PCR: copying DNA by doubling
N=N0×2n,230≈1.07×109

The polymerase chain reaction heats DNA to about 95 °C to part its strands, cools it to 50–65 °C so short primers bind on either side of the target, then lets a heat-proof polymerase copy it at 72 °C. Each cycle doubles the target: 30 cycles, about an hour, make a billion copies from one.

Use: Detects a germ from a few copies of its DNA or RNA (the COVID-19 test), matches a person or an animal, and supplies DNA for sequencing.

First: Kary Mullis's method, first published by Saiki and colleagues, 1985 (Science); Nobel Prize 1993.

A row of DNA sequencers. Biology becomes something you can read and then write. DNA-Sequencers from Flickr 57080968 · 2005-10-27 · Flickr user jurvetson · CC BY 2.0 · Commons ↗
ToolSinceWhat it doesSource
Sequencing a human genome2001Reads every letter of a person's DNA. The cost per genome at NHGRI's sequencing centres fell from about US$95 million in 2001 to about US$500 in 2022NHGRI
The complete genome2022All 3.055 billion letters of a human genome, with no gapsNurk et al.
CRISPR–Cas9 gene editing2012Cuts DNA at an address set by a 20-letter guide RNA, so a gene can be removed or rewritten; Nobel Prize 2020Jinek et al.
mRNA vaccines2020Carry the code for one protein of a virus; the body makes the protein and learns to fight it. Designed within days of a virus's genome being readKarikó et al.
Protein structure prediction2021AlphaFold predicts a protein's shape from its sequence; its open database holds over 214 million predicted structures. Nobel Prize 2024Jumper et al., Varadi et al.

Build the gear

Where to go next

This page covers what you are most likely to meet. It is not a field guide, and on identification that difference can kill you. These are the works that go further — chosen because they can be held offline.