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Biology studies living systems: how biological cells maintain themselves, how organisms develop and reproduce, and how evolution generates diversity. Its scales connect molecules, genes, biological cells, organisms and the interactions studied by ecology. These are complementary viewpoints: a protein's chemistry can explain a cellular mechanism, while evolution explains why inherited variants of that mechanism persist. See Clark, Douglas and Choi, Biology 2e: the science of biology.

Two organizing ideas make this immense subject navigable: shared cellular organization and descent with inherited modification. A neuron and a gliding bacterium differ dramatically in shape and behavior, yet both depend on a cell membrane and metabolism. Their differences become intelligible through specialization and evolution.

Keep observations separate from the mathematical models used to explain them. A measured membrane potential is evidence; an idealized two-state ion-channel gating equation proposes a mechanism. A mathematical model earns trust through predictions and comparisons with measurements. Its assumptions delimit its usefulness, and disagreement can reveal missing biology rather than a faulty measurement.

The goal of ecology is to explain where organisms live, how many there are, and how their interactions with one another and their surroundings change those patterns. Living partners include prey, predators and parasites; nonliving conditions include light, temperature and water. An ecosystem brings these interacting parts into one study system. See Clark, Douglas and Choi, Biology 2e, 44.1: the scope of ecology.

Start with an invented aquatic food web: photosynthetic algae feed zooplankton, which feed small fish, which feed large fish. That food chain has four feeding positions and three feeding arrows. Dead material also reaches decomposers through detritus, so the food web branches rather than forming a single ladder.

The appeal of ecology is that an organism's surroundings include other organisms that change those surroundings. Photosynthesis links light to living material; predation transfers that material between organisms; decomposers return its constituent chemical elements to forms that can be used again. These connections help explain why changing one part of an ecosystem can affect distant parts of its food web, although an arrow alone does not predict the size or even the direction of an indirect change. Population dynamics supplies quantitative tools when the question concerns changing counts.

In 1866, Ernst Haeckel's Generelle Morphologie der Organismen included a section titled Oecologie und Chorologie in volume 2, beginning on page 286. This places the terminology of ecology in an early systematic treatment of organisms and their relationships. See Haeckel, Generelle Morphologie der Organismen, volume 2 (1866), contents and p. 286. A later quantitative landmark is Raymond L. Lindeman's 1942 treatment of ecosystems through feeding relationships and energy flow. See Lindeman, The Trophic-Dynamic Aspect of Ecology, Ecology 23 (1942), 399–417.

Seed germination is renewed plant embryo activity and growth. Many germination assays score completion as radicle emergence, before seedling establishment. Seed imbibition precedes that endpoint; swelling alone is insufficient.^[ref]

Water, molecular oxygen and suitable temperature support germination; light sensitivity depends on the species and seed state. Neither illumination nor one particular temperature is universally required. Seed dormancy connects germination timing to ecology by delaying seedling establishment.^[ref]

The distinction matters when comparing propagation experiments: a treatment that increases radicle emergence need not improve later seedling survival. Define the endpoint before comparing treatments, then measure the later outcome separately.