Many people have a vague sense that the hypothesized origin of life, in the form of bacteria, sounds plausible. However, few people can fathom how the first eukaryotic cell, complete with nucleus, mitochondria and maybe chloroplast, came into being. This book presents the evidence that reveals the origins of all three DNA-containing organelles. In addition, this book will illustrate how DNA, a molecule that is 2 meters (6 feet) long, can fit into all cells' nuclei that are only about 2 microns (0.000002 meters) in diameter. Once eukaryotes evolved, the next obvious question is how multicellular organism could have evolved from simpler unicellular species. This book looks at multicellular algae as a case study on the origins of multicellularity.

All organisms are composed of cells, but what is the definition of a cell? Can size, shape or function be used to distinguish cells from non-living biological systems such as a virus? Whatever the definition of a cell is, it can probably be contradicted by cells with unusual characteristics. For example, there are cells as long as a giraffe's neck while others are smaller than a mitochondrion. Sometimes it is hard to know the difference between an animal and a plant cell. Despite their diversity of shapes and sizes, cells are small-most of the time. Why has natural selection favored small cells? Would it be possible for big organisms to have big cells? It would seem safe to say viruses are small, except some are quite large. In the end, this book will provide evidence that cells are difficult to characterize and define even though they are the foundation of all living things.

It is common for most people to mistakenly think that humans are the only species that can coordinate their behavior and build structures that protect them from the environment. Students of nature will think of birds building nests, but very few people know that bacteria are able to communicate and restructure their environment in complex ways that improve their ability to survive. This book presents experimental evidence of quorum sensing, biofilm formation, self-assembly of microbes into visible and mobile creatures. This book also examines the experimental evidence showing how bacteria can keep track of time and coordinate the behavior of an entire population. Individual cells, it turns out, are capable of functioning in ways that blur the distinction between unicellular and multicellular organisms.

Once the first cell arose on Earth, how did genetic diversity arise if DNA replication and cell division generate exact copies? The answer is that neither process is perfect and that changes do occur at each step. Some changes are small and subtle while others are large and dramatic. As DNA mutates, evolution of a population takes place. But when can someone determine if a single species has changed enough to be considered two separate species? How is a species defined and is this definition useful in the real world? Real biological data will be examined to confront and an-swer these questions. Finally, the book examines an example of evolution that takes place in humans on a regular basis-the mammalian immune system. White blood cells evolve rapidly to confront any substance that enters a body and is perceived as a threat. With each exposure, these cells get better and better at neutralizing the threat.

This book examines four examples of animal physiology that illustrate emergent properties in whole organisms. The first example shows how mammals coordinate the activity of all their cells using a daily rhythm. The second case explains an apparent contradiction that happens every time a woman gets pregnant and delivers a healthy baby-how the immune system tolerates a foreign tissue such as the fetus. The next case study in this book shows how bodies regulate the amount of fat using a complex in-teraction of proteins that function as a lipostat, a self-regulating fat maintenance system. Finally, the book provides an understanding of why some species live long lives while others die after very short lives, and under what conditions each situation is favored. What is evolutionarily adaptive about death? These four case studies provide sufficient evidence to understand how animals regulate many of their own metabolic functions.

This book will synthesize the concepts of selection against individuals in response to environmental change to illustrate how selection against individuals results in homeostasis at the population level. For instance, selection against the light phenotype of the peppered moth during the early part of the industrial revolution led to an increase of the dark phenotype, which was better camouflaged against the soot that accumulated on tree bark as a result of burning coal. Populations are shown to be regulated by feedback mechanisms, several of which are discussed here. Populations are regulated by extrinsic factors, such as competition and predation, and that lead to changes in intrinsic factors, such as reproduction. Changes in population density often lead to initiation of feedback mechanisms, such as changes in birth or death rates. In a final example, pollutants are shown to be a factor that can disrupt homeostasis of populations. In particular, populations of top predators, such as raptors, have suffered due to bio-magnification of toxins.

Organisms maintain homeostasis in a variety of ways. In the first part of this book, mammals are shown to regulate their body temperatures through homeostatic mechanisms. The data from thermoregulation experiments that demonstrated the role of neurons in body temperature homeostasis are examined. The second part of this book discusses how organisms allocate the limited energy that is available to them for survival, growth, or reproduction. Excess energy in individuals can translate to growth of populations: if enough remains after survival and growth, it can be allocated to reproduction. However, even closely related organisms may have different strategies for allocating resources that are dependent upon the environmental conditions in which they exist.

Animal behavior includes the exchange of non-heritable information between individuals of the same species. Animals exchange information for a variety of reasons, including mating, defense, and cooperation, and all of these situations will be discussed. This book will describe the functions of communication and information transfer between organisms and explain how animals communicate and find each other through use of different signals. The costs and benefits of using various signals will be evaluated, as will the costs and benefits of living in groups. Playback experiments and the comparative method are approaches used for understanding and interpreting signals used by organisms to communicate information to other members of the same species. Plants also communicate information between individuals, often for purposes of species identification during mating. Female reproductive structures in plants recognize pollen from members of the same species. Finally, the commonalities and differences between animal and plant communication will be identified

This book describes and analyzes genetic and environmental factors that cause variation in individuals and populations. Data will be used to evaluate the processes by which variation is generated in organisms and how variation affects natural selection. Genetic factors include mutation, independent assortment, crossing over, and recombination. Environmental factors include gradients and differences in abiotic conditions. Genotype frequencies can be used to determine allele frequencies and this information can be used to determine whether a population is evolving at a genetic locus. The Hardy-Weinberg equilibrium will be applied as a null model to make this determination. Non-Mendelian genetics can affect the evolution of viruses and reassortment in viruses will be used to illustrate another mechanism that generates variation in organisms and how this mechanism relates to rapid evolution of viruses and the need for annual flu vaccines.

What happens to a meal after it is eaten? Food consists primarily of lipids, proteins and carbohydrates (sugars). How do cells in the body process food once it is eaten and turned it into a form of energy that other cells can use? This book examines some of the classic experimental data that revealed how cells break down food to extract the energy. Metabolism of food is regulated so that energy extraction increases when needed and slows down when not needed. This type of self-regulation is all part of the complex web of enzymes that convert food into energy. Adding to this complexity is that all food eventually winds up as two carbon bits that are all processed the same way. This book will also reveal why animals breathe oxygen and how that relates to the end of the energy extraction process and oxygen's only role in the body. Rather than look at all the details, this book takes a wider view and shows how cellular respiration is self-regulating.

Properties of populations include age and spatial distribution, both of which emerge from actions and properties of individuals and can affect population dynamics, the changes in populations and metapopulations over time and space. The age structure of a population is described and analyzed to determine how it affects the growth of a population. The various aspects of spatial structure of populations, which also arise from characteristics and behaviors of individuals, are examined and used to develop the concept of a metapopulation. Finally, this book discusses how individuals perform behaviors that can lead to other properties observed at the population level, such as birds flocking. The advantages and disadvantages to flying in flocks are evaluated, as are the mechanisms by which flocks of birds are maintained and how they respond to an attack by a predator.

Three of the four major mechanisms of evolution, natural selection, genetic drift, and gene flow are examined. There are 5 tenets of natural selection that influence individual organisms: Individuals within populations are variable, that variation is heritable, organisms differ in their ability to survive and reproduce, more individuals are produced in a generation than can survive, and survival & reproduction of those variable individuals are non-random. Organisms respond evolutionarily to changes in their environment and other selection pressures, including global climate change. The importance of spatial structure of a population in relation to how it affects the strength of gene flow and/or genetic drift, as well as the genetic variation and evolution of populations, is shown. Gene flow tends to reduce variation between populations and increase it within populations, whereas genetic drift tends to reduce genetic variation, especially in small, isolated populations. The mechanisms of evolution can lead to speciation, which requires both time and genetic isolation of populations, in addition to natural selection or genetic drift.

This book identifies the commonalities between communication within a species and communication between species. Behavior and exchange of non-heritable information occurs between individuals of different species, in animals and plants, in order to exploit other species and compete for resources. Several examples of adaptations of one species to exploit the information passed between individuals of another species are given. This book describes how animals make decisions while gathering information and resources, selecting habitat, and interacting with potential competitors. Plants grow in response to nutrients in soil, which may require gene regulation in response to information in the environment. Information is also exhibited in biodiversity, in the number and types of species present, and this information is used by other organisms as they assess their surroundings. The information content of ecological systems changes when species are added or lost.

Pairwise and diffuse coevolution are defined, with examples that include mutualisms and predator-prey interactions. In any example of coevolution, the costs and benefits to both species involved in the interaction must be assessed in order to understand evolution of the interaction. Models to explain coral bleaching are examined in the context of a coevolutionary mutualism, as are the implications for the possible extinction of coral reefs. Data are examined in order to determine which model is best supported. Other examples of how evolution affects interactions and communities of organisms include adaptation to living in particular habitats and evolution to frequent and somewhat predictable disturbances. For the former, physiological adaptations possessed by some plants to live in low light conditions are described and assessed. Ecological disturbances are defined, and the role of disturbance on evolution of ecological systems is assessed through the use of data. Finally, how time and spatial scales affect disturbances and the evolutionary responses of organisms to disturbances are also examined.

This book describes how evolutionary history is studied using several well-known examples and also using evolutionary trees. Evolutionary trees are analyzed and used to explain adaptive radiations of orchids and the diversification of bats over geologic time. Evolutionary trees and genetic evidence is used to infer when and from what ancestors terrestrial plants evolved and invaded land. Specific adaptations of early land plants led to the evolution of terrestrial plants and their success on land. Evidence about the ancestors and habitats of humans is used to infer and analyze the evolution of the human family tree, whose populations were subject to the same forces of evolution to which other species are subject. Human evolution was not linear, involved offshoot species that did not survive, and took many thousands of years. In contrast, evolution can be seen in just a few years or less in other examples, and analysis of the evolution of mechanisms of pesticide resistance in insects will be used to illustrate this rapid evolution.

This book begins by describing what an individual organism is, comparing preconceptions of the individual to non-standard ways of thinking about individuals. Variation in what individuals are is described, using giant fungi, clonal trees and honey bee hives as examples. Individuals are thus shown to be emergent properties. Other emergent properties of individuals are also described. Classic experiments that elucidated the source of emotions in humans and other mammals are described. Emotions arise from the actions of the nervous and endocrine system and often include a variety of signals given to other individuals of the same or different species. In particular, this book focuses on fear and anger, two emotions that are closely related and often confused, but that have been well studied. In one final example of emergent properties of individuals, cooperative behavior is analyzed. The behaviors displayed by individuals that facilitate cooperation among individuals and why those individuals may actually cooperate instead of compete when acquiring resources or defending against predators are discussed.

Several genetic and pathogenic diseases are described to illustrate how diseases can and do disrupt normal molecular and cellular functions, and how those disruptions affect entire organisms. In the case of genetic diseases, how they arise and are maintained in populations is discussed. In the case of pathogenic and parasitic organisms, understanding their complex life cycles and their modes of transmission is critical to understanding their effects on individuals and how disease outbreaks occur in ecological systems. Communication between the pathogen and the host organism occurs in the course of infection and involves the disruption of normal cell function. Finally, epidemiology is briefly discussed, using the case of severe acute respiratory syndrome (SARS). Data are used to describe how the disease may have originated and evolved to infect humans, and how it spread relatively quickly and almost caused a global pandemic. Understanding how disease outbreaks occur in ecological systems is critical to controlling the spread of disease.

Population growth, dynamics, and blooms of bacterial, unicellular eukaryotes, and toxic algae are described in this book. Microbes are used to illustrate both exponential and logistic population growth. Microbes are also used to illustrate dynamics in other aspects of ecological systems, including nutrient cycling. The movement of nitrogen in ecological systems is largely affected by microbes, some of which have symbiotic relationships with legumes. The effects of the environment on the growth of microbes and the effects of the microbes on ecological systems are described in reference to nutrient cycles and harmful algal blooms. Populations of harmful algal can quickly grow and exceed carrying capacity, with resulting negative effects on other species, including humans.

Food webs, energy flow, indirect effects, and nutrient cycling are described as properties that emerge in ecological systems. Several of these properties are shown in this book to result from indirect effects and interactions between species and abiotic components of ecological systems. For instance, top predators affect organisms with which they do not directly interact, including plants and non-prey animals. In some other interactions, including competition, the nonliving components of ecological systems (the abiota) can alter the outcome of a biotic interaction. A limiting resource often results in competition, but varying environmental conditions allow for species coexistence. Finally, this book illustrates how energy flows in ecological systems, why it is rather inefficient, and how species interactions relate to homeostasis and emergent properties. In the course of that discussion, primary production, secondary production, and trophic levels are defined. Energy flow in ecological systems is tied to the carbon cycle.

Individual organisms contribute to nutrient cycling in ecological systems, which is shown to be a mechanism of homeostasis at that level. The phosphorus and nitrogen cycles are used to illustrate effects of changes in populations or communities on the cycling of these nutrients. Major disturbances such as deforestation and global climate change disrupt nutrient cycles and ecological system homeostasis. Data are examined to determine effects of deforestation on nutrient cycling. Increasing atmospheric carbon dioxide and global climate change are disrupting ecological systems' homeostasis, and several studies are used to show how this is happening, including changes in primary production, temperature and precipitation patterns. This book also discusses the role of individual species in filtering contaminants and pollutants from ecological systems.

Two systems illustrate how individual cells of an organ system function, communicate, and coordinate activities. The digestive system breaks down and absorbs nutrients, and some specialized cells break down and absorb nutrients. The case of parietal cells in the stomach and epithelial cells in the small intestine are used to describe how cells function as a unit within organ systems, coordinating activities and communicating with one another. The endocrine system of insects affects molting and metamorphosis, and specialized cells are also important in each of these processes within that organ system. The experiments that were devised to determine the role of hormones in insect molting and metamorphosis are described. Finally, stem cells are healthy components of several different systems in animal bodies and are described in relation to a disruption in function. In this breakdown of function, cancer cells, in contrast to stem cells, can abnormally affect cell cycle regulation.