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The goal of science is to help humans gain a deeper understanding of the world. In this, science is like the graphic arts, dramatic arts, music, literature, religion, philosophy, and other endeavors. How is science distinct from other ways of knowing? Two attributes stand out: 1) It focuses on quest...

The goal of science is to help humans gain a deeper understanding of the world. In this, science is like the graphic arts, dramatic arts, music, literature, religion, philosophy, and other endeavors. How is science distinct from other ways of knowing? Two attributes stand out: 1) It focuses on questions about the natural and physical world; and 2) It is grounded in evidence-based decision-making, and specifically in evidence that is measurable and verifiable. Science can be both a radical enterprise and a conservative one. The radical or extreme aspect is that nothing in science is ever viewed as completely certain. Every scientific idea, dataset, and conclusion is always open to questioning and testing. The conservative aspect of science is one that resists change. This stance is based on standards of evidence. Scientists are skeptical about new ideas and insights until they are supported by rigorous data. Specifically, new data or claims will not be widely accepted in science until three things occur: 1. The results are replicated. Replication takes two forms: the research group that originally performed a particular experiment or observational study needs to repeat it and get a similar or identical result, and other lab groups need to repeat the study and get similar or identical results. Until results are replicated, critics of the work are skeptical of the conclusions. 2. The results cannot be explained by a reasonable alternative hypothesis. For example, experiments have to be designed so that only one thing differs between the treatment groups and the control group. Then, if the results show that the groups respond differently to the treatment, the researchers can claim that the results were caused by the one thing that differed between them. Otherwise, critics of the work can claim that other factors caused the results. 3. The results are supported by more than one type of data or source of evidence. Like religion, politics, and other human endeavors, science can be used to elevate the human condition or cause great harm. Researchers are still working to acknowledge and confront past and current abuses of science. There is also an ongoing effort to improve systems for detecting and punishing cheaters. In both cases, two tools are important: 1.​ A culture that values integrity and trust, underlain by a commitment to "follow where the data lead;" and​ 2.​ The recognition that all work will be examined critically and rejected if it cannot be replicated or if data supporting other hypotheses are more convincing. Science: A human endeavor based on asking questions about the natural and physical world and answering them with measurable, verifiable evidence. Pseudoscience: A tradition that tries to explain or predict natural and physical phenomena but 1) does not rely on measurable, verifiable evidence, and 2) invokes mysterious or unnamed mechanisms rather than known physical mechanisms. Here are some ways to think about the distinction: ​ Science pursues questions that can be answered by measuring something, while religion pursues questions that cannot be answered by measuring something.​ ​ Scientific research is based on measurable evidence; religious belief and practice are based on faith. ​ A hypothesis is a proposed explanation for something that researchers have observed. ​ A prediction is a statement of an outcome that should occur if a hypothesis is correct. Hypotheses are testable because they make predictions. If the data that result from an experiment or observational study match the predictions made by a hypothesis, then the hypothesis is supported. But if the data don't match the predictions, then researchers have to reject the hypothesis as incorrect, or at least modify it and re-test it. When you are just starting out, though, it can be tricky to recognize the distinction between a hypothesis and a prediction. Here's one way to think about it: In an "if... then..." statement, the hypothesis is the "if" part and the prediction is the "then" part. For example, "If my tomatoes haven't germinated because they need more time, then I should start to see some seedlings emerging if I wait a few more days." A hypothesis is a cause; a prediction is an effect. Null hypothesis: A hypothesis that represents the "not" or "no-effect" contrast to the hypothesis being tested. Treatment (or experimental) group: A group that experiences experimental conditions that conform to the mechanism proposed in the hypothesis. Control group: A comparison group that represents the normal or no-treatment condition to contrast with groups that experience experimental manipulation. Controlled conditions: Aspects of an experimental design that are used in both control and experimental treatments to eliminate bias among treatments and reduce influence from confounding factors. Outcome variable: The variable that is measured in an experimental or observational study. It represents a quantity that is relevant to the hypothesis being tested. Independent variable (also known as the predictor or explanatory variable): A variable whose value does not depend on the value of another variable. Common examples include the treatment groups in an experimental study or time. Dependent variable (also known as the response variable): A measured quantity whose value depends on the value of another variable. Discrete variable: A quantity that can only take certain, discrete values. Continuous variable: A quantity that can take a continuous range of values. Scatterplot: A type of graph where individual datapoints from two continuous variables are plotted to assess whether the variables are correlated in any way. Histogram: A type of graph where a range of possible values is plotted along the x-axis and the frequency of datapoints in each interval in the range is plotted on the y-axis. Lecture 3 Ecology is the study of how organisms interact with each other and the environment. Ecology emerged as a distinct branch of the life sciences about 100 years ago, and has recently grown into a particularly high-profile discipline. Ecology allows us to understand the interrelations between things. Understanding microbiomes requires evolution and ecology. The biotic components of an environment are the organisms present—the ones that do the eating and competing and beneficial exchanging. The abiotic components are the non-living, physical aspects that impact those organisms, such as temperature, mineral nutrients, wind, soils, and water quantity and quality. Together, the biotic and abiotic conditions in an area define an ecosystem. In general, the abiotic components of a habitat define which organisms have the potential to live at that location. This is because each species has adaptations that allow it to tolerate or thrive in specific physical conditions. And in general, biotic interactions define which organisms actually live in that location. Some species may be excluded by competition or disease or by the absence of a species that it depends on to thrive. Organismal ecology focuses on how individuals of the same species interact with each other and the environment. The focus is often on animal and plant behavior, meaning how individuals take in information and change their activity in response. For both animals and plants, the questions of interest tend to revolve around food and sex. For animals, this means decisions about what to eat and who to mate with. For plants, this means seeking out the resources needed for photosynthesis and accomplishing pollination (or sperm transfer, in ferns and bryophytes). Individual: A single organism A population is defined as a group of individuals of the same species that live in the same area at the same time, and interact with each other via competition, cooperation, and/or sexual reproduction. The most fundamental questions about populations often focus on numbers, meaning whether the population is growing or declining and why. A species is defined as an evolutionary unit in nature. Species are comprised of one or more populations that evolve as a unit and share genetic and physical characteristics. At the species level, ecologists often study why—in terms of responses to biotic or abiotic factors—populations have evolved or are evolving. Ecological communities comprise the groups of species present in the same area at the same time. Community ecologists study how those species came to be found there and how they interact with each other. At the ecosystem level, most research in ecology focuses either on how changes in abiotic conditions change the communities present, or on how energy and matter flow through organisms and the physical environment. In this unit, we will generally move rom populations to communities to ecosystems to the biosphere. Exponential growth can occur when a new population gets started in a previously unoccupied area or when a population is recovering from a disaster, such as the reduction in the bison population in the late 1800s. Population can also grow rapidly when there are no limiting factors. But exponential growth cannot continue indefinitely, because as a population increases, the number of individuals per unit area—the population density—also increases. Geometric growth involves reproduction at regular time intervals. As density increases, the availability of food and other resources decreases and the prevalence of disease and predation increases. Finite rate of increase (λ): The growth rate over a defined time period usually one year for organisms that breed once per year. Instantaneous rate of increase (r): The growth rate at any moment. Exponential growth (or decay): A growth pattern produced when r (or λ) stays the same over time. Density-dependent growth: Population growth that is limited by density dependent factors such as disease, predation, and access to food or other resources. Carrying capacity: The population size that can be sustained over time in a particular habitat. In finite rate of increase: 𝜆 > 1 → growth 𝜆 < 1 → decline 𝜆 = 1 → equilibrium Exponential versus geometric growth. Similarities Both have an intrinsicgrowth rate Both show unlimited, rapid growth due to multiplication Both involve some rate of increase Differences Geometric growth is discrete, exponential growth is continuous Different interpretation of intrinsic growth rates Geometric growth “finite” - 𝜆 Exponential growth “instantaneous” - 𝑟 The larger values of 𝜆 = faster growth, smaller values of 𝜆 = slower growth Lecture 4 Recall that in ecology, a community refers to the collection of species that are found in the same place at the same time. But the species that are present in a community do more than just co-habit a place: They actively interact in ways that affect each others' distribution, abundance, and evolution. Community ecology is the study of those interactions. These layers are significant because humidity, wind, and other physical conditions vary among them. This means the types of plant food, and thus the fungi and animals present, also vary throughout the forest. Each layer can represent a distinct community within the larger community. In addition to providing food and physical structure in terrestrial habitats, plants provide a long list of ecosystem services, meaning goods and services that humans derive from the natural environment. Oxygen Virtually all of the oxygen in the atmosphere is formed during photosynthesis. For the past 400 million years, land plants have been responsible for the vast majority of all photosynthesis on Earth. Plants impact other important aspects of the atmosphere beyond just oxygen availability. For example, trees provide a canopy cover that increases humidity and moderates both wind and temperatures. Urban and suburban areas that have good tree cover are often considered attractive in part because of the role trees play in these ecosystems. Drinking Water Areas with a high diversity and density of plants tend to have much cleaner and more abundant ground and surface water than areas where the plant cover has been degraded. Healthy plant communities help prevent contaminants from roads, agricultural, or industrial activities from getting into water sources. Communities with rich plant life also tend to have cooler and thus moister soils because they are shaded, and rainfall and snowmelt do not run off and leave the community as readily. Soils Most of the organic matter that we see in rich and productive soils is derived from decaying plants—both shoots and roots. This organic matter is black or brown in color and is called humus. Accumulation of humus in soil is beneficial because the organic compounds in humus hold nutrients and prevent soil from becoming too porous or too compact. In addition to its role in soil health, humus plays an important role in carbon sequestration. Plant roots also bind soil particles together and prevent them from breaking off and eroding away when exposed to wind or water. Widespread removal or degradation of native plant communities is one of the major reasons why high levels of soil loss are occurring worldwide. Carbon Sequestration Trees and shrubs take carbon dioxide (CO2) from the air and sequester (store) it in woody stems and roots. Grassland plants also sequester large amounts of carbon in their extensive root systems and surrounding soil. As a result, large-scale tree planting and forest preservation are important elements in the long list of actions designed to reduce CO2 concentrations in the atmosphere and thus the impact of climate change. Physical, Mental, and Spiritual Health In the United States, the 20 top-selling prescription drugs all contain an active ingredient derived from a plant; 40% of all prescription drugs contain a plant product. Many of these plant-derived drugs have been used by indigenous people since time immemorial. Plants also support mental health. In one experiment, researchers randomly assigned vacant lots in the same urban area to one of three treatments: trash clean-up, "greening" accomplished by cleaning up trash and then planting grasses and trees, or no intervention. Before the interventions and then during the year following the interventions, the researchers had randomly selected local residents answer questions that created a score on a widely used Psychological Distress Scale. The data showed that people who lived near the greening treatments reported feeling less depressed and worthless and that their overall mental health was better. Studies in other contexts show that people heal faster from illness or injury and feel better when they are in plant-rich environments. One of the central tools in analyzing species distribution and abundance is the concept of the niche. In the life sciences, a niche is defined as the range of conditions a species lives in. A fundamental niche defines the locations where it is physically possible for a particular species to live. Before we move on, it's important to note that physical conditions can interact in ways that impact a species' fundamental niche. For example, water temperature directly impacts aquatic oxygen levels because cold water can hold more dissolved oxygen than warm water. each is found in a more limited range of conditions called the realized niche. This difference occurs because biotic interactions restrict where species are actually found. These biotic interactions can include:  ​ Predation or herbivory (literally, "plant eating") that eliminates a species from certain areas;​ ​ Diseases caused by parasites;​ ​ Mutualisms involving a strong and beneficial interdependence between two species; and​ ​ Competition for space, nutrients, water, nesting sites, or other resources. In the "fast" life history, individuals allocate most of their energy to reproduction. Lifespans are short because fast organisms expend relatively little energy on things like defending themselves against predation or herbivory and disease. In the "slow" life history, individuals allocate most of their energy to growth and maintenance. The contrast between fast and slow life history characteristics is relevant to the abiotic and biotic constraints on a species' niche. For example, plants that live fast and die young have relatively few traits that make them effective competitors for light, water, and nutrients in the soil. As a result, they tend to be found in areas where competing plants have been removed by flooding, fire, high winds, a catastrophic insect outbreak, or other disturbance. Fast plants are bad at competition, but well-adapted to coping with the high sunlight, low-humidity, and low-nutrient conditions of disturbed sites. Slow plants, in contrast, invest energy in building woody stems, extensive root systems, mycorrhizal associations, defense compounds, and other traits that make them effective competitors for light, water, and nutrients. Instead of being well-adapted to harsh physical conditions, their realized niche is more heavily influenced by biotic interactions. Ecosystem services: Goods and services provided to humans by the natural environment such as oxygen, high-quality and abundant water, productive soils, food and fiber, and recreational and spiritual resources. Humus: Soil organic matter originating in decaying plants roots, leaves, and stems. Niche: The range of conditions that a species lives in. Fundamental niche: The range of physical conditions that a species can tolerate, which define the types of habitats where a species can potentially occur. Realized niche: The range of physical conditions that a species actually occupies, given the constraints of biotic interactions such as predation, competition, disease, and mutualisms. Carrying capacity can limit population growth.determined by the resources available in that environment e.g., food, water, and habitat a form of density dependence Density -independent factors can cause fluctuations in population size. can increase or decrease the population size no clear pattern over time often are abiotic factors, due to random/unpredictable events Populations fluctuate in part due to environmental variability Changes in population size are linked to four key processes: birth, death, immigration, and emigration. inputs> outputs = growth Outputs > inputs = decline Inputs = outputs = dynamic equilibrium Lecture 5 Recall that a species' tolerance for abiotic conditions defines its fundamental niche. These physical conditions include high and low temperatures, atmospheric humidity and soil moisture, and other factors that are changing as average global temperature increases. It is reasonable to predict, then, that species are changing where they live based on changes in abiotic conditions. Recall that when a disturbance such as fire or flooding or a massive disease outbreak removes individuals, it changes the composition of the community. This is important because climate change is causing a significant increase in the size and intensity of some types of disturbance—especially forest fires and hurricanes and other storms. Not all of the species living in a particular community have the same fundamental niches. Rather, they can live in the same place because their fundamental niches overlap. But at any particular location, some species may be at the very limits of their tolerance while other species are in the conditions where they thrive best. So when physical conditions are modified due to climate change, it will not impact all of the species present in the same way. In many areas of the world, surburbanization, road construction, agricultural expansion, and other types of human development are converting large, contiguous regions of forest, grassland, or desert habitat into geographically isolated fragments. The phenomenon is called habitat fragmentation. One primary consequence of fragmentation is that it causes a large increase in the amount of "edge" habitat relative to the amount of "interior" habitat. After fragmentation occurs, trees that end up on a forest edge are exposed to intense sunlight and high winds. Increased light intensity increases temperatures and evaporation, while stronger winds increase dryness or topple trees outright. Fragmentation also reduces gene flow, or mixing of genetic information, in many or most of the species present. This is because individuals, including pollinators, can no longer travel freely throughout the habitat without exposing themselves to the danger of crossing a human-dominated part of the landscape. Life scientists define a keystone species as one that has a disproportionately large impact on the community it belongs to relative to its total biomass or the number of individuals present. To understand why keystone species can be so important, it's helpful to use the diagrams called food webs. A food web is a two or three-dimensional representation of what researchers call trophic relationships, or who eats whom. Your analysis should help make the definition of a keystone species come alive. The keystone in the arch shown below is small, but it is the element that holds the entire structure together. Human impacts on plant and animal communities vary widely, from traditional use of well-timed fires in North America and tree-farming in the Amazon to today's climate change, habitat fragmentation, and elimination or reintroduction of keystone species. But in many cases, humans are now actively working to regenerate entire communities from the ground up—from scratch. The work begins by planting carefully selected plants that are native to the region and rebuilding soils that have been lost to erosion, mining, or intense fires. In effect, humans can work to regenerate the bottom layer of a food web like the one you just analyzed. Disturbance: An event that removes biomass. Biomass: The total mass of living organisms in a specific area. Habitat fragmentation: The conversion of large, contiguous areas of native plant and animal communities to small fragments separated by tracts of human development. Keystone species: A species that has a disproportionately large impact on a community relative to its numbers. Food web: A diagram showing the trophic relationships among species in a community. Trade offs shape how organisms allocate limited resources. Abiotic factors can imit the distribution of a species, as well as biotic factors. Abiotic conditions help us to identify where organisms can potentially live, this is called the fundamental or potential niche. The range of tolerance refers to the range of environmental conditions within which an organism can survive, grow, and reproduce. Competition is a result of a realized niche. Competition can be interspecific - between two species or intraspecific - within a species Lecture 6 Recall that ecosystems are defined as the interacting biotic and abiotic components present in an area. When researchers analyze how ecosystems work, one of their most basic questions is about biomass production. More specifically, they initially focus on primary productivity, which in most ecosystems is defined as the amount of light energy captured by photosynthetic organisms. The total amount of primary productivity in an area is referred to as gross primary productivity, where "gross" means overall or total. It is usually measured as a rate and reported in units such as g/m2/year (grams per square meter per year). Much more frequently, however, you will see references to net primary productivity (NPP), which is defined as the primary productivity found in biomass. NPP is a fraction of gross primary productivity because only a portion of the chemical energy produced in photosynthesis is used to fuel growth and reproduction. In other words, not all of the sugars produced during photosynthesis end up in the nucleic acids, proteins, carbohydrates, and lipids that form the plant body. Plants have to use a significant portion of photosynthetic products for other activities that keep them alive but don't involve growth and reproduction. Researchers spend a lot of time and energy measuring and analyzing biomass and NPP for a simple reason: It contains the energy that every other organism in the community relies on to stay alive. If NPP is high, there are likely to be a large number of individuals of other species around interacting with each other in dynamic, complex ways. If NPP is low, species diversity is likely to be low and the ecosystem will be relatively simple in terms of the number of components and interactions. To analyze how energy flows through ecosystems, life scientists use several key concepts: ​ A food chain describes the sequence of organisms that eat each other in a particular ecosystem, starting with plants and other primary producers and moving to primary consumers that eat plants, to secondary consumers that eat primary consumers, to tertiary consumers that eat secondary consumers, and so on.​ ​ The distinct levels in a food chain are called trophic levels, from the Greek word root meaning nourishment. In aquatic ecosystems, and especially in marine environments, the biomass observed at each trophic level can display an array of patterns. In addition to the types of pyramids commonly observed in terrestrial ecosystems, researchers sometimes document "inverted pyramids" or "hourglass-shaped" relationships like this one, from a coral reef community: There is a strong contrast in the nature of primary producers in terrestrial versus aquatic ecosystems. The grasses, shrubs, and trees that dominate on land are large and long-lived, and much or most NPP is cellulose and lignin that can't be used by primary consumers. But in marine and freshwater environments, most primary producers are single-celled bacteria and algae that have extremely short lifespans and are readily eaten by primary consumers. In general, NPP is much higher in terrestrial environments than in aquatic environments. With exceptions like coral reefs, marshes, and estuaries (where rivers flow into the sea), NPP per unit area is low in aquatic systems. It is particularly low in what is far and away the most widespread ecosystem on Earth: the open ocean, meaning areas distant from coastlines. There is over 10 times as much open ocean as any other habitat on the planet, but it is essentially a desert in terms of NPP. In addition to being different in terms of overall productivity, the factors that limit NPP in terrestrial and aquatic ecosystems differ sharply. On land, NPP is usually limited by precipitation and temperature. Warmer, wetter regions have higher NPP than cooler, drier regions. But in aquatic habitats, productivity is usually limited by access to nutrients. Researchers have found one important aspect of energy flow that is common to aquatic and terrestrial ecosystems: the proportion of energy that gets transferred from biomass at one trophic level to the next is about 10%. This observation suggests that all organisms studied to date have to spend about the same proportion of the energy they have on staying alive versus growing or reproducing. Humans are having an array of impacts on NPP and the way that energy flows through ecosystems. For example, the amount of biomass present in different trophic levels of a coral reef varies with the amount of human disturbance, and in particular with how many sharks and other large fish are hunted for food. By removing biomass at the top levels, an episode of intense fishing for sharks can turn an inverted or hourglass relationship in biomass into a pyramid. Primary productivity: In most ecosystems, the amount of light energy captured by photosynthetic organisms. Gross primary productivity: The total amount of primary productivity in an area, often reported as a rate with units of g/m2/year. The rate at which energy is captured and assimilated by produces in a given area. Net primary productivity (NPP): The amount of primary productivity present in biomass, often reported as a rate with units of g/m2/year. The rate at which energy is assimilated by produces and converted into biomass in a given area. Human appropriation of net primary productivity (HANPP): The amount of primary productivity used by humans, often reported as a rate with units of gigatons of carbon per year. Exploitative competition refers to the indirect competition between individuals or species for limited resources within an environment. Interference competition reffers to direct interactions between individuals or species that impede the access of competitors to essential resources. Apparent competition occurs when two or mor eprey species are indirectly linked through a shared predator. Competitive exclusion principle states that if two species with identical niches compete, then one will inevitably drive the other to extinction What can happen whencompetitors overlap? 1)Temporary co-existence (at reduced carrying capacity): both species continue to live in the area but at lower numbers. 2) Competitive exclusion: one of the species dissapears from the area 3) Niche partitioning:both species continue to co-exist, but they diverge to occupy slightly different ecological niches within the shared habitat. Priority effects refer to the influence that the order and timing of species arrival have on a community Competitors may inhibit other species from establishing Disturbance events may impact the abundance of one species more than the other. Photosynthesis results in oxygen in aquatic environments and the atmosphere, carbon storage in plant tissues The niche is also the functional role of a species in an ecosystem. - Autotrophs Can produce their own food, primary producers ” Photoautotrophs use sunlight for photosynthesis Chemoautotrophs obtain energy by oxidizing inorganic substances (e.g., sulfur, ammonia) often found in extreme environments like deep-sea hydrothermal vents Heterotrophs must consume other organisms to obtain energy and nutrients. ​ Herbivores consume primary consumers ​ Decomposers break down organic matter from dead organisms Tertiary Consumers feed on secondary consumers Secondary Consumers omnivores or carnivores consume primary consumers Primary Consumers typically herbivores consume primary producers Lecture 7 Analyzing how energy flows in the form of biological macromolecules among organisms is a basic tool for the life scientists tasked with understanding how ecosystems work. But energy flows are primarily among organisms, whether dead or alive, and ecosystems encompass both the biotic and abiotic components of a region. One of the basic ways to answer these questions is to take a global view and observe how critically important key atoms and molecules cycle through abiotic and biotic ecosystem components. Answering these questions is important because humans are altering global nutrient cycles in massive and unprecedented ways. These changes have consequences for all organisms, including humans. Researchers study a wide array of key molecules and atoms, but here let's focus on just three: water, nitrogen, and carbon. Recent changes in the water, nitrogen, and carbon cycles are having enormous impacts on the world. ​ Nitrogen is essential for all organisms to stay alive, grow, and reproduce. Humans are adding massive amounts of usable nitrogen to habitats all over the world.​ ​ Most of the mass of living organisms consists of water and carbon. Access to water is essential for plants to conduct photosynthesis and create the NPP that other organisms depend on. Indeed, without water, there is no life at all.​ ​ It's no exaggeration to say that life is carbon-based. Carbon forms the skeleton of virtually every significant biological macromolecule. Changes in the carbon cycle are the root cause of the climate change occurring today. To study how water moves through and between ecosystems, researchers use data from weather stations throughout the globe. The figure below represents a simplified version of the water cycle with the most recent estimates for how water moves among four major compartments: the atmosphere over land, the atmosphere over the oceans, the land surface, and the world's oceans. The values given are in units of 1000 km3/year. Nitrogen atoms are enormously important to organisms for a simple reason: It takes a lot of them to build proteins and nucleic acids. And nitrogen is super-abundant on Earth. For example, 78% of the molecules in the atmosphere are molecular nitrogen, N2. Unfortunately, this form of nitrogen is useless to the vast majority of organisms—they cannot use it to synthesize the amino acids and nucleotides they need. For organisms to use nitrogen atoms from N2 to make the molecules they need, the nitrogen atoms have to be "fixed," meaning reduced. Recall that reduction refers to a gain of electrons. The diagram below represents a highly simplified version of the process of nitrogen fixation, starting from N2 and ending with ammonia (NH3). Lines indicate covalent bonds between atoms and dots indicate the positions of electrons in those bonds: You might be aware of one other major biological process that impacts the nitrogen cycle: A large number of bacteria and archaea species process various types of nitrogen-containing ions or molecules as food. Specifically, they use these molecules as electron donors or electron acceptors in cellular respiration. A particularly critical group of reactions called denitrification results in the release of N2 back to the atmosphere. In terms of understanding the nitrogen cycle, let's focus on three punchlines from this discussion: ​ Photosynthetic bacteria in the ocean called cyanobacteria fix large amounts of N2 and use those nitrogen atoms to grow and reproduce.​ ​ Nitrogen-fixing bacteria that live in association with the roots of pea-family plants and a few other species also remove large amounts of N2 from the atmosphere and use reduced nitrogen atoms to build proteins and nucleic acids.​ ​ Soil- and ocean-dwelling bacteria use nitrogen-containing molecules and ions in ATP production and release N2 to the atmosphere via denitrification. Humans are also having a major impact on the water cycle, but not as directly. How is carbon related to all of this? Evaporation and precipitation patterns are changing indirectly through human impacts on the carbon cycle. Massive releases of carbon dioxide (CO2) and other greenhouse gases from major sinks—via burning of coal, natural gas, and oil—and are causing average global temperatures to rise dramatically. The model below will help you understand the big picture regarding carbon's dynamics. The diagram summarizes researchers' current best estimates for the flux of carbon atoms into and out of distinctive compartments in the world's ecosystems. Flux is defined as the rate of movement. A couple of points to note as you analyze it: 1.​ Arrows that point up reflect processes that add carbon dioxide (CO2) to the atmosphere. In most cases these are oxidation reactions that act on reduced forms of carbon in biomass. (If you haven't studied biochemistry yet, don't worry about that last sentence.) "Land use change," for example, refers to human activities that convert forests and other habitats to farms or residential areas and result in a release of CO2.​ 2.​ Arrows that point down reflect processes that take carbon dioxide out of the atmosphere and place it into a different compartment. There are two main types: ​ Photosynthesis is a reduction process that "fixes" carbon atoms from CO2 into sugars and biological macromolecules in organisms.​ ​ The "Gas exchange" label that leads to marine environments indicates that CO2 from the atmosphere dissolves in the world's oceans. There, it reacts with water to form carbonic acid (H2CO3), which then dissociates into bicarbonate (HCO3-) and hydrogen (H+) ions. Sink: A long-term repository where a particular atom or molecule may remain for millions to hundreds of millions of years. Denitrification: A collection of metabolic processes in different bacteria and archaea species that results in the release of N2 as an end-product. Analogous reactions release N2 when biomass burns during wildfires. Flux: The rate that a substance moves—its direction and amount per unit time. Microplastics: two major sources 1.​ Small manufactured plastics 2.​ Breakdown of llarger plastic items Vocabular is important! must/never - absolute certainty with no exceptions likely /often/usually - a high chance or frequency but not certainty Not - meaning of the statement is flipped A limiting factor is any environmental or ecological factor that restricts the growth, distribution, or abundance of roganisms within that ecosystem Lecture 8 The rapid and global climate change that is occurring now is caused by human activities that disrupt the carbon cycle. Carbon dioxide (CO2) is released when humans burn coal, natural gas, and petroleum-based fuels, and methane (CH4) is released when those substances are extracted from the Earth and processed. Although neither CO2 or CH4 are abundant as a percentage of the atmosphere, both molecules are extremely efficient at absorbing solar radiation that is reflected from the Earth's surface. Instead of being lost to the upper atmosphere and outer space, the energy in the outgoing solar radiation stays in the atmosphere. This heats the air. As air temperatures rise, heat is also transferred to the oceans, raising their temperature as well. In essence, carbon on Earth exists in two forms: an oxidized form represented by CO2 and reduced forms in the C-C and C-H bonds that dominate nucleic acids, proteins, carbohydrates, lipids, and other biologically important molecules.When carbon atoms in CO2 are transferred to the C-H and C-C bonds in sugars during photosynthesis, it requires an input of energy in the form of sunlight. When carbon atoms in the C-H and C-C bonds of sugars are oxidized to CO2 during the controlled reactions of cellular respiration, energy is released. Your cells use this energy to synthesize the ATP that is keeping you alive right now. And when C-H and C-C rich organic molecules in fossil fuels are oxidized during the uncontrolled reaction we call burning, energy is also given off in the form of heat. We use this heat to move automobiles and airplanes, generate electricity, and warm our homes. A carbon sink is a long-term repository that keeps carbon dioxide out of the atmosphere, where it can affect climate. The most important carbon sinks store molecules derived from the partially decayed bodies of organisms that lived hundreds to hundreds of millions of years ago. Here are some examples of carbon sinks: ​ Peat consists of semi-decayed plant parts.​ ​ Coal is a carbon-rich rock that forms when peat is exposed to heat and pressure generated by sediment and rock layers deposited over it.​  ​ Petroleum, or crude oil, forms from the bodies of marine organisms that sink to the ocean floor after death, collect in large concentrations, and then are gradually transformed by exposure to heat and pressure generated by accumulating sediment and rock layers.​ ​ Methane, also called natural gas, often forms in petroleum deposits. In essence, the key carbon sinks on Earth are repositories of reduced carbon that originated in photosynthesis and occurred in the past—usually the distant past. To understand the nature of carbon sinks, it's essential to understand the nature of decay or decomposition. You may have noticed that the major sinks have their origins in partially decayed biomass. This is because if decay were complete, all of the reduced carbon in the biomass would all be oxidized to CO2. So what makes decomposition slow or stop? Let's walk through the logic: 1.​ When an organism dies, bacteria, archaea, fungi, and various types of single-celled eukaryotes begin harvesting biological molecules in the dead body and using them as food.​ 2.​ If oxygen is present, the organisms that do the decomposition use the sugars and other C-C and C-H rich molecules in dead bodies to do aerobic respiration. This means that that they synthesize ATP using oxygen as a final electron acceptor. But in oxygen-poor environments, only organisms that perform anaerobic respiration can continue the decay process. Anaerobic respiration uses a final electron acceptor other than oxygen.​ 3.​ Aerobic respiration is many times more efficient than anaerobic respiration. This means that given the same amount of food, aerobic organisms can generate much, much more ATP and grow much faster than anaerobic organisms can.​ 4.​ When oxygen is available, decay is fast. When oxygen is not available, decay is slow or can even stop altogether. Decay is also slow to nonexistent in cold environments, simply because the enzymes required for cellular respiration and ATP production can't function.​ 5.​ As a result, partially decayed biomass begins to accumulate in oxygen-poor or extremely cold environments. When negative feedback on climate change occurs, an event or process causes greenhouse gas concentrations in the atmosphere to drop, making climate change less extreme.​ When positive feedback on climate change occurs, an event or process causes even more greenhouse gases to be released into the atmosphere, making climate change even more extreme. Humans are disrupting the global carbon cycle by oxidizing massive numbers of carbon atoms that have been locked up in sinks. The result has been rapid increases in atmospheric CO2 concentration and in average air and ocean temperatures. Based on the data available to date, the current rate and amount of change in global climate is the most extensive since a 10 km-wide asteroid smashed into the Earth 65 million years ago and triggered a mass extinction. How is all this change affecting organisms? This question occupies the minds of thousands of researchers from all over the planet, and teams are documenting responses ranging from rapid evolutionary change to stark shifts in geographic distribution. The data on diatoms and Daphnia are an example of what researchers are calling phenological mismatch: changes in the timing of seasonal events that change the way two species interact. (Issues that involve feeding are referred to as trophic mismatches.) In this case, diatoms are starting to grow and reproduce earlier and earlier in the year, but Daphnia are coming out of their overwintering state and starting to feed and reproduce at about the same time. As a result, Daphnia have less food available and their peak population size should decline. This has wider ecological implications because Daphnia are the primary source of food for a diverse array of fish species. To get a feel for the variety of ways that a shift in phenology or other climate-change-related events can reverberate through ecosystems, consider two additional datasets on: (1) a heat wave in the Pacific Ocean that researchers called The Blob, and (2) changes in the life cycles of bark beetles in North America. The Blob Beginning in late 2013 and continuing until early 2016, a large expanse of the Pacific Ocean experienced the most extreme heat wave recorded to date. Water temperatures rose to up to 6°C (over 10ºF) over normal and stayed elevated. Oceanographers used color-coded "surface temperature anomaly" maps to visualize the extent of the warming from off the coast of California north to Alaska, with darker reds indicating higher temperatures. The results inspired the nickname "The Blob:" The Blob set off several different chains of events that are still impacting the ecosystems of the North Pacific Ocean today. One of these chains can be summarized as follows: 1.​ Normally, ocean currents bring nutrient-rich water from the ocean bottom to the surface. But the extremely warm surface waters and associated changes in winds during The Blob prevented this.​ 2.​ The lack of nutrients caused populations of primary producers to drop dramatically.​ 3.​ Fish that act as primary and secondary consumers either starved to death or lacked enough food to reproduce.​ 4.​ Bird and mammal species that eat fish either starved to death or lacked enough food to reproduce. The commercial fishing industry in the North Pacific, which provided jobs for tens of thousands of people, was virtually shut down. Researchers estimate that about one million common murres—an abundant fish-eating bird—died as a result of The Blob. Years later, the populations of many fish-eating birds and mammals, including the murres and orcas pictured below, have still not fully recovered. Bark Beetle Outbreaks Like plants and most other organisms, insects do not maintain their body temperature at a steady level. Instead, their body temps tend to track their surroundings closely. As a result, insects are exquisitely sensitive to changes in air and water temperature. This is important because insects are often the most important herbivores (plant-eaters) in terrestrial ecosystems, and because they provide food for many amphibians, reptiles, birds, and mammals. One of the damaging impacts of climate change on ecosystems involves a phenomenon known as an insect outbreak. These are events when a single species of insect explodes in numbers. In the case of herbivores like the spruce bark beetle and pine bark beetle, which burrow into spruce and pine trees and feed on phloem sap, the results can be devastating. In early research on how climate change was impacting phenology and species interactions, researchers noticed an increase in bark beetle outbreaks in the forests of Canada and the mountain states of the western U.S. Large tracts of spruce or pine forest were being killed, often in a single season. Follow-up studies showed that two things were happening: 1.​ Increased dryness and higher temperatures were reducing photosynthetic rates in trees, lowering their nutritional status and making them less able to synthesize and transport anti-herbivore defenses.​ 2.​ Warmer temperatures were accelerating bark beetle phenology enough that these herbivores could complete their entire life cycle in a single summer, instead of being spread out over two years. The increased probability of a one-year life cycle correlated directly with an increased probability of a population explosion. Carbon sink: A long-term repository for reduced carbon atoms (carbon atoms not in CO2). Negative feedback (in the context of climate change): An event or process that causes greenhouse gas concentrations in the atmosphere to drop, making climate change less extreme. Positive feedback (in the context of climate change): An event or process that causes even more greenhouse gases to be released into the atmosphere, making climate change even more extreme. Phenology: The study of the timing or seasonality of life events in organisms. Phenological mismatch: Changes in phenology that change the way that two species interact. The principle of ecologicalefficiency only a fraction of the energy and biomass at each trophic level is transferred to the next level some energy is always lost as heat or waste often ~10% of energy Is available for movement to the next trophic level crucial implications for ecological systems Productiviy: the rate at which energy is converted into organic matter Production - the biomass produced by organisms in an ecosystem over a given period of time Standing biomass - the biomass of produces present in an area at a particular moment in time 47 The water cycle Key fluxes Evaporation - the conversion of liquid water into water vapor Transpiration - the release of water vapor from plants through stomata Precipitation - the release of water from the atmosphere as rain, snow, sleet, or hail. Runoff - the movement of water over the land surface and into bodies of water such as rivers, lakes, and oceans. Percolation/infiltration - the process by which water seeps into the soil downward through pores and fractures. The carbon cycle is closely tied to the movement of energy Key processes of the carbon cycle: convert carbon dioxide from the atmosphere into organic carbon compounds through photosynthesis Consumers Consume organic carbon by feeding on plants or other organisms. During respiration both plants and animals release carbon dioxide back into the atmosphere as a byproduct of metabolic processes. When plants and animals die, their organic matter is broken down during decomposition Some organic carbon can become buried in sedimentary rock via sedimentation Diffusion is the passive movement of molecules from an area of high concentration to an area of low concentration the nitrogen cycle. The carbon cycle is closely tied to the movement of energy Key pools Atmosphere Biosphere Oceans Soil Sediment  Lithosphere (e.g., coal, oil, rocks) Key forms Carbon dioxide (CO2) Methane (CH4) Carbonates Living organic matter (complex) Dead/soil organic matter (complex) Key processes of the nitrogen cycle Nitrogen fixation - atmospheric nitrogen gas is converted into biologically usable ammonia Nitrification - biological oxidation of ammonia to nitrite and then to nitrate Ammonification - decomposition of organic nitrogen compounds (e.g., proteins, nucleic acids) into ammonia/ammonium ions Denitrification - reduction of nitrate and nitrite to nitrogen gas Assimilation/uptake – nitrates are taken up by the roots of plants Key pools: Atmosphere Soil Biosphere Sediments Aquatic reservoirs (dissolved inwater) Lithosphere (rocks) Key forms: Nitrogen gas Ammonia/ammonium Nitrate/nitrite Organic nitrogen Primary producers turn carbon dioxide into sugars Heterotrophs get energy/nutrients from biotic sources Consumers obtain carbon -Containing compounds through ingestion. Decomposers break down dead organic matter into their non-biological form. Lecture 9 The diversity of organisms that exist at a particular time and place can be measured in a variety of ways. For example, species richness is defined as a simple count of the number of species present. Species diversity, in contrast, is calculated as the number of species present weighted by how even the species are in terms of the relative abundance of individuals.Biodiversity can be measured by quantifying which species are present and in what numbers relative to each other. Life scientists also routinely consider other aspects of diversity in communities. Let's consider two examples: whether the species present are native or exotic, and whether they are diverse in terms of their ecological structure and function. Species are identified as native to a region if they are indigenous, meaning that they have lived there for a long time. As a result, native species are well-adapted to local physical conditions and have interacted extensively enough with other native species for coevolution to occur—meaning that native species have traits honed by competition, mutualism, predation, parasitism, or other interactions over long periods of time. Exotic species, in contrast, evolved elsewhere and were recently introduced to the region in question by humans. Although many of these introductions have little impact on communities and ecosystems, some are devastating. Invasive species, for example, are defined as exotic species that outcompete native species for space and other resources, in some cases taking over areas and eliminating native species entirely. When considering exotic versus native species, one key point is that biodiversity is more than just a list of species. Which species are present also matters. To drive this point home, consider data on what ecologists call functional groups. In the context of ecology, a functional group is a collection of species that have a distinctive structural or functional role in an ecosystem. Often these roles focus on how and when they use resources. The Importance of Plant Diversity When members of the general public think of biodiversity, they usually think about animals like lions and tigers and bears—what marketing people call "charismatic megafauna." (The term megafauna was inspired by the Greek word roots for "large animals.") But when life scientists think about biodiversity, they think about plants. This is because plant diversity is the key to the diversity of everything else, from the bacteria and fungi that decompose dead leaves and tree trunks to the millions of species of leaf-eating, sap-sucking, nectar-feeding insects that function as primary consumers to the large and beautiful mammals and birds and reptiles that get most of the screen time on television and social media. The key assumption here, which has now been supported by data, is that increased plant diversity leads to increased everything-else diversity. Productivity—meaning biomass production—is considered one of the most fundamental aspects of quality or "goodness" in an ecosystem. The reason is simple: the mass of living material that is produced provides the energy that every other organism in the ecosystem depends on. Productivity is usually measured as net primary productivity (NPP) and is expressed as the amount of aboveground biomass produced in a given amount of surface area per year. Researchers usually only report aboveground productivity because below-ground productivity (biomass of roots) is extremely difficult to measure, even if you kill the plants involved. When measured at small scales, productivity can be reported in units of grams per square meter per year. When measured at large scales, productivity can be reported as cubic meters of biomass per hectare per year. Productivity is really all about plant growth. Now the question becomes: does the presence of more species lead to more overall growth, even though the amount of sunlight, rain, and mineral nutrients hasn't changed? Researchers have taken two general approaches to assess how species richness impacts productivity: 1.​ Experimental approaches begin with establishing study plots, sowing seeds in each plot from a randomly assigned number of species—often ranging from 0 to about 12—letting the plants grow for 1-5 years, and then harvesting them to quantify aboveground biomass.​ 2.​ Observational studies measure the number of species present in study plots in intact environments, and then estimate the amount of biomass. n ecology, resilience is defined as the ability to recover from disturbance, and is considered a key aspect of stability. The issue of resilience has attracted a great deal of attention recently because climate change is disturbing ecosystems all over the globe. Biodiversity is valuable. It is also under threat—more so now than at any time in the past 65 million years. In fact, based on data on the current rates of species moving into threatened or endangered status or actually going extinct, researchers think that if present trends continue, the 6th mass extinction in the history of life is already occurring. It's a longstanding principle that to solve a problem, you have to understand what is causing it. In that spirit, let's explore six major reasons why the numbers of many or most non-human organisms are declining, starting with the most important. Threats to biodiversity Habitat Loss In another Readiness Reading, you may have seen data on the proportion of total global net primary production that is being used by humans. If so, you might remember that it has more than doubled over the past 100 years—increasing from about 7% in the early 1900s to about 15% in the early 2000s. When humans appropriate NPP, less is left for other organisms. Habitat fragmentation Climate change Species richness: The number of species present. Species diversity: The number of species present weighted by their evenness in terms of abundance. Coevolution: Adaptations that result from interactions between species over time, resulting in traits influenced by a history of competition, mutualism, feeding interactions, or disease. Exotic species: Species that are not native to a region but were introduced relatively recently by humans. Invasive species: Exotic species that outcompete native species for space and other resources. Functional groups: Groups of species that have distinctive structures and/or perform distinctive functions in communities. Resilience: The ability to recover from a disturbance.