Introduction to Ecology: Systems, Evolution, and the Scientific Method

Searching for Life at the Bottom of the Ocean

• Early 1800s Hypotheses:     * Scientists hypothesized that deep ocean waters were devoid of life.     * Scientific Basis: Sunlight cannot penetrate to depths greater than $275\,m$. Without sunlight, photosynthesis is impossible. This implies no plants or algae can exist to serve as a food source.     * Secondary Factors: Extreme pressures and cold temperatures were also believed to contribute to the absence of deep-sea biological activity.     * Hypothesis Context: Given that ocean depths can exceed $10,000\,m$, logic suggested the deepest areas remained lifeless.
• The HMS Challenger Expedition (1873):     * Scientists aboard the British research ship HMS Challenger sampled the Atlantic Ocean floor using a "dredge"—a large, heavy, open-sided box suspended by long ropes.     * Discovery: Sampling at depths of up to $4,572\,m$, the team discovered nearly $5,000$ previously unknown species.     * Scientific Impact: This discovery forced the rejection of the earlier hypothesis that life could not exist beyond the penetration of light.
• Post-Discovery Hypotheses (Marine Snow):     * Scientists initially hypothesized that deep-sea life was sustained by particles originating in surface waters.     * Marine Snow: A steady descent of tiny particles produced by the death and decomposition of organisms living near the surface.     * Whale Falls: Occasional large biological inputs provided by the carcasses of massive organisms like whales.
• Submersible Discoveries (1970s):     * Small manned submarines allowed direct observation of the ocean floor.     * Hydrothermal Vents: Openings in the ocean floor that release hot water plumes containing high concentrations of sulfur compounds and mineral nutrients.     * Diversity found: Hydrothermal vent communities included tubeworms, clams, crabs, and fish, with biological density rivaling the most diverse places on Earth.
• Chemosynthesis Definition and Process:     * The amount of energy provided by "marine snow" was insufficient to support the rich life of hydrothermal vents.     * Mechanism: Bacteria use energy from chemical bonds, combined with carbon dioxide ($CO_2$) to produce organic compounds.     * Comparison: This is similar to photosynthesis where plants use sunlight and $CO_2$.     * Tubeworm Symbiosis: Organisms such as $Tevnia\,jerichonana$ (tubeworms) can grow to more than $2\,m$ in length. They lack a digestive system but house vast numbers of chemosynthetic bacteria in specialized organs. The worms capture sulfide gases and $CO_2$ from the water for the bacteria, which in turn provide organic compounds as food for the worms.

The Hierarchy of Ecological Systems

• Definition of Ecology: The word is derived from the Greek oikos, meaning "house." It is the scientific study of the abundance and distribution of organisms in relation to other organisms and environmental conditions.
• Darwin’s Perspective: In On the Origin of Species (1859), Charles Darwin compared interactions among species to the interactions between consumers and businesses in human economic systems, referring to them as the "economy of nature."
• Ernst Haeckel (1870): The German zoologist gave the word "ecology" its broader modern meaning: "investigation of the total relations of the animal both to its organic and to its inorganic environment."
• Ecological Systems (General): Biological entities that have their own internal processes and interact with external surroundings.
• Levels of the Ecological Hierarchy:     * Individuals: The most fundamental unit of ecology. Every individual has a membrane or covering across which it exchanges energy and materials with the environment. This boundary separates internal processes from external resources.     * Species: Historically defined as a group of organisms that naturally interbred and produced fertile offspring. Current research shows no single definition fits all organisms (e.g., ring species, asexual clones, or horizontal gene transfer in bacteria).     * Populations: Individuals of the same species living in a particular area. Boundaries can be natural (continents) or political (state lines).         * Five Properties of Populations: 1. Geographic range (distribution); 2. Abundance (total number); 3. Density (number per unit area, e.g., $1\,bear/100\,km^2$); 4. Change in size (increases/decreases); 5. Composition (makeup by age, gender, or genetics).     * Communities: All populations of species living together in a particular area. Interaction types include predation and mutualism (e.g., pollinators and plants). Boundaries are often indistinct; for example, the transition from Douglas fir ($Pseudotsuga\,menziesii$) to subalpine fir ($Abies\,lasiocarpa$) on a mountain slope in Colorado.     * Ecosystems: One or more communities interacting with nonliving physical and chemical environments (water, air, sunlight, nutrients). Focus is on the movement of energy and matter.         * Energy Flow: Typically originates from the Sun, is converted by producers, through consumers (herbivores, carnivores), and eventually leaves Earth as radiated heat.         * Matter Cycling: Matter (Carbon, Oxygen, Hydrogen, Nitrogen, Phosphorus) cycles within and between ecosystems through pools like living organisms, the atmosphere, water, and rocks.     * Biosphere: The highest level, including all ecosystems on Earth. Distant ecosystems are linked by wind and water currents and the movement of organisms (migrating birds, whales, fish).

Biological and Physical Governing Principles

• Law of Conservation of Matter: Matter cannot be created or destroyed, only changed in form. For example, carbon in gasoline is converted to $CO$, $CO_2$, and $H_2O$ during combustion.
• First Law of Thermodynamics (Law of Conservation of Energy): Energy cannot be created or destroyed, only converted. Living organisms must obtain energy to grow, maintain bodies, and replace energy lost as heat.
• Dynamic Steady State: Occurs when gains and losses in an ecological system are in balance, maintaining constancy.     * Examples: Mammal body temperature (heat loss vs. metabolic gain); Population size (Births + Immigration vs. Deaths + Emigration).
• Evolution Principles:     * Phenotype: An attribute of an individual (behavior, morphology, physiology).     * Genotype: The set of genes an individual carries.     * Evolution: A change in the genetic composition of a population over time.     * Natural Selection: A change in gene frequency due to differential survival and reproduction based on phenotypes.     * Darwin's Conditions for Natural Selection:         1. Individual organisms vary in their traits.         2. Parental traits are inherited by offspring.         3. Variation in traits causes differences in fitness (survival and reproduction).     * Adaptation: Characteristics of an organism that make it well-suited to its environment (e.g., desert animal kidney function).

Diverse Roles of Organisms

• Major Groups:     * Bacteria: Prokaryotes. Key roles in nitrogen assimilation, chemosynthesis (e.g., at vents using $H_2S$), and anaerobic decomposition in muck soils. Cyanobacteria (blue-green algae) are major aquatic photosynthesizers and cause algal blooms.     * Protists: Mostly single-celled eukaryotes (Algae, slime molds, protozoans). Algae range from micro-organisms to kelp up to $100\,m$ long. Parasitic protists include $Plasmodium$ (malaria) and $Trypanosoma\,brucei$ (sleeping sickness).     * Plants: Multicellular photosynthesizers.         * Standard Roles: Rooted in soil, using leaves to capture light.         * Epiphytes: Air plants (some orchids) that grow on other plants to reach humid air.         * Carnivorous Plants: Venus flytraps ($Dionaea\,muscipula$), sundews, and pitcher plants use invertebrates for extra nutrients in low-nutrient soils.         * Parasitic Plants: Dodder (stangleweed) sucks nutrients from other plants; some orchids parasitize fungi.     * Fungi: Consist of threadlike ¨C56C. They digest food externally via secreted acids/enzymes. Key decomposers. Symbiotic mutualists include ¨C57C (with plant roots) and ¨C58C (fungi and algae/cyanobacteria).     * ¨C59C Consumers. Predators ($Puma\,concolor$), Herbivores ($Bison\,bison$), Parasites ($Dermacentor\,albipictus$/Winter tick).

• Species Interactions Summary:

  Type of Interaction	Species 1	Species 2
  Predation / Parasitoidism	$+$	$-$
  Parasitism	$+$	$-$
  Herbivory	$+$	$-$
  Competition	$-$	$-$
  Mutualism	$+$	$+$
  Commensalism	$+$	$0$

Habitat and Niche

• Habitat: The physical setting where an organism lives (e.g., stream, lake, desert, tropical rain forest). Distinguished by dominant vegetation or physical traits like depth or water flow.
• Niche: The range of abiotic and biotic conditions an organism can tolerate. It includes what the organism does (e.g., specialized diet).     * Example: European corn borer ($Ostrinia\,nubilalis$) feeds on corn ($Zea\,mays$); Colorado potato beetle ($Leptinotarsa\,decemlineata$) feeds on potato leaves ($Solanum\,tuberosum$).

The Scientific Method in Ecology

• Hypothesis Types:     * Proximate Hypothesis: Addresses "how" an organism responds (immediate physiology/hormones).     * Ultimate Hypothesis: Addresses "why" (fitness costs and benefits).
• Experimental Design Units:     * Manipulative Experiment (Treatment): The factor being varied.     * Control: A manipulation including all aspects except the factor of interest.     * Experimental Unit: The specific object to which the manipulation is applied.     * Replication: Repeating the experiment multiple times for reliability.     * Randomization: Assigning units to treatments so each has an equal chance of assignment.
• Case Study (Marquis and Whelan, 1994): Tested if birds reduce insect herbivores on white oak trees. Birds were excluded with cages. Results showed caged trees had twice the insect density and twice the leaf tissue loss compared to controls.
• Alternative Methods:     * Microcosms: Simplified systems attempting to replicate essential features in a lab or field setting.     * Mathematical Models: Sets of equations representing hypothesized relationships (e.g., global carbon cycling or disease transmission).

Analytical Tools: Means and Variances

• Mean ($\overline{x}$): The average value of collected data ($E[x]$).
• Variance Overview: Indicates the spread of data around the mean. High overlap between two data spreads suggests less confidence that samples are truly different.
• Variance of the Population ($\sigma^2$):     * $\sigma^2 = E[x^2] - [E(x)]^2$
• Sample Variance ($s^2$): Used when only a portion of the population is measured.     * $s^2 = \frac{n}{n-1} [E(x^2) - [E(x)]^2]$
• Practice Problem Calculation (Uncaged Trees - Insect Abundance):     * Data: $4, 3, 2, 4, 2$.     * $n = 5$.     * Mean per tree ($E[x]$): $\frac{4+3+2+4+2}{5} = 3$.     * Mean of squared values ($E[x^2]$): $\frac{4^2+3^2+2^2+4^2+2^2}{5} = \frac{16+9+4+16+4}{5} = \frac{49}{5} = 9.8$.     * $s^2 = \frac{5}{5-1} \times (9.8 - 3^2) = 1.25 \times (9.8 - 9) = 1.25 \times 0.8 = 1$.

Human Influence and the California Sea Otter

• History of the Sea Otter ($Enhydra\,lutris$):     * Hunted to near extinction in the 1700s and 1800s.     * Small population rediscovered in the 1930s off central California.     * Protected status led to growth to several thousand by the 1990s.
• Ecological Impact of Otters:     * They eat sea urchins, which eat kelp. More otters lead to less urchins and more kelp.     * Kelp provides habitat for fish and a harvestable resource for humans (fertilizer, pharmaceuticals).
• Population Declines (1990s):     * Aleutian Islands: Killer whales ($Orcinus\,orca$) shifted to preying on otters as their usual prey (seals, sea lions) declined due to heavy commercial fishing of fish stocks.     * Morro Bay, California (2010): Mass mortality from brain inflammation caused by parasites $Toxoplasma\,gondii$ and $Sarcocystis\,neurona$.     * Source of Parasites: Opossums ($Didelphis\,virginiana$) and domestic cats. Parasites enter the ocean via runoff and cat litter flushed down toilets. Small marine snails (a non-preferred otter food) accumulate the parasites. When preferred food like abalone is scarce, otters eat snails and become infected.
• Global Challenges: Human population exceeds $7\,billion$. Greenhouse gases like $CO_2$ from fossil fuel combustion absorb infrared heat and radiate it back to Earth, causing global warming.