Understanding Biology: From Cells to Ecosystems - Prof. Thomas Abbott, Study notes of Biology

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Chapter 1 Exploring Life Lecture Outline Overview: Biology’s Most Exciting Era  Biology is the scientific study of life.  You are starting your study of biology during its most exciting era.  The largest and best-equipped community of scientists in history is beginning to solve problems that once seemed unsolvable.  Biology is an ongoing inquiry about the nature of life.  Biologists are moving closer to understanding:  How a single cell develops into an adult animal or plant.  How plants convert solar energy into the chemical energy of food.  How the human mind works.  How living things interact in biological communities.  How the diversity of life evolved from the first microbes.  Research breakthroughs in genetics and cell biology are transforming medicine and agriculture.  Neuroscience and evolutionary biology are reshaping psychology and sociology.  Molecular biology is providing new tools for anthropology and criminology.  New models in ecology are helping society to evaluate environmental issues, such as the causes and biological consequences of global warming.  Unifying themes pervade all of biology. Concept 1.1 Biologists explore life from the microscopic to the global scale  Life’s basic characteristic is a high degree of order.  Each level of biological organization has emergent properties.  Biological organization is based on a hierarchy of structural levels, each building on the levels below.  At the lowest level are atoms that are ordered into complex biological molecules.  Biological molecules are organized into structures called organelles, the components of cells. Lecture Outline for Campbell/Reece Biology, 7th Edition, © Pearson Education, Inc. 1-1  Cells are the fundamental unit of structure and function of living things.  Some organisms consist of a single cell; others are multicellular aggregates of specialized cells.  Whether multicellular or unicellular, all organisms must accomplish the same functions: uptake and processing of nutrients, excretion of wastes, response to environmental stimuli, and reproduction.  Multicellular organisms exhibit three major structural levels above the cell: similar cells are grouped into tissues, several tissues coordinate to form organs, and several organs form an organ system.  For example, to coordinate locomotory movements, sensory information travels from sense organs to the brain, where nervous tissues composed of billions of interconnected neurons —supported by connective tissue—coordinate signals that travel via other neurons to the individual muscle cells.  Organisms belong to populations, localized groups of organisms belonging to the same species.  Populations of several species in the same area comprise a biological community.  Populations interact with their physical environment to form an ecosystem.  The biosphere consists of all the environments on Earth that are inhabited by life. Organisms interact continuously with their environment.  Each organism interacts with its environment, which includes other organisms as well as nonliving factors.  Both organism and environment are affected by the interactions between them.  The dynamics of any ecosystem include two major processes: the cycling of nutrients and the flow of energy from sunlight to producers to consumers.  In most ecosystems, producers are plants and other photosynthetic organisms that convert light energy to chemical energy.  Consumers are organisms that feed on producers and other consumers.  All the activities of life require organisms to perform work, and work requires a source of energy.  The exchange of energy between an organism and its environment often involves the transformation of energy from one form to another.  In all energy transformations, some energy is lost to the surroundings as heat. Lecture Outline for Campbell/Reece Biology, 7th Edition, © Pearson Education, Inc. 1-2  Our thoughts and memories are emergent properties of a complex network of neurons.  This theme of emergent properties accents the importance of structural arrangement.  The emergent properties of life are not supernatural or unique to life but simply reflect a hierarchy of structural organization.  The emergent properties of life are particularly challenging because of the unparalleled complexity of living systems.  The complex organization of life presents a dilemma to scientists seeking to understand biological processes.  We cannot fully explain a higher level of organization by breaking it down into its component parts.  At the same time, it is futile to try to analyze something as complex as an organism or cell without taking it apart.  Reductionism, reducing complex systems to simpler components, is a powerful strategy in biology.  The Human Genome Project—the sequencing of the genome of humans and many other species—is heralded as one of the greatest scientific achievements ever.  Research is now moving on to investigate the function of genes and the coordination of the activity of gene products.  Biologists are beginning to complement reductionism with new strategies for understanding the emergent properties of life—how all of the parts of biological systems are functionally integrated.  The ultimate goal of systems biology is to model the dynamic behavior of whole biological systems.  Accurate models allow biologists to predict how a change in one or more variables will impact other components and the whole system.  Scientists investigating ecosystems pioneered this approach in the 1960s with elaborate models diagramming the interactions of species and nonliving components in ecosystems.  Systems biology is now becoming increasingly important in cellular and molecular biology, driven in part by the deluge of data from the sequencing of genomes and our increased understanding of protein functions.  In 2003, a large research team published a network of protein interactions within a cell of a fruit fly.  Three key research developments have led to the increased importance of systems biology. 1. High-throughput technology. Systems biology depends on methods that can analyze biological materials very quickly and produce enormous amounts of data. An Lecture Outline for Campbell/Reece Biology, 7th Edition, © Pearson Education, Inc. 1-5 example is the automatic DNA-sequencing machines used by the Human Genome Project. 2. Bioinformatics. The huge databases from high- throughput methods require computing power, software, and mathematical models to process and integrate information. 3. Interdisciplinary research teams. Systems biology teams may include engineers, medical scientists, physicists, chemists, mathematicians, and computer scientists as well as biologists. Regulatory mechanisms ensure a dynamic balance in living systems.  Chemical processes within cells are accelerated, or catalyzed, by specialized protein molecules, called enzymes.  Each type of enzyme catalyzes a specific chemical reaction.  In many cases, reactions are linked into chemical pathways, each step with its own enzyme.  How does a cell coordinate its various chemical pathways?  Many biological processes are self-regulating: the output or product of a process regulates that very process.  In negative feedback, or feedback inhibition, accumulation of an end product of a process slows or stops that process.  Though less common, some biological processes are regulated by positive feedback, in which an end product speeds up its own production.  Feedback is common to life at all levels, from the molecular level to the biosphere.  Such regulation is an example of the integration that makes living systems much greater than the sum of their parts. Concept 1.3 Biologists explore life across its great diversity of species  Biology can be viewed as having two dimensions: a “vertical” dimension covering the size scale from atoms to the biosphere and a “horizontal” dimension that stretches across the diversity of life.  The latter includes not only present-day organisms, but also those that have existed throughout life’s history. Living things show diversity and unity.  Life is enormously diverse.  Biologists have identified and named about 1.8 million species. Lecture Outline for Campbell/Reece Biology, 7th Edition, © Pearson Education, Inc. 1-6  This diversity includes 5,200 known species of prokaryotes, 100,000 fungi, 290,000 plants, 50,000 vertebrates, and 1,000,000 insects.  Thousands of newly identified species are added each year.  Estimates of the total species count range from 10 million to more than 200 million.  In the face of this complexity, humans are inclined to categorize diverse items into a smaller number of groups.  Taxonomy is the branch of biology that names and classifies species into a hierarchical order.  Until the past decade, biologists divided the diversity of life into five kingdoms.  New methods, including comparisons of DNA among organisms, have led to a reassessment of the number and boundaries of the kingdoms.  Various classification schemes now include six, eight, or even dozens of kingdoms.  Coming from this debate has been the recognition that there are three even higher levels of classifications, the domains.  The three domains are Bacteria, Archaea, and Eukarya.  The first two domains, domain Bacteria and domain Archaea, consist of prokaryotes.  All the eukaryotes are now grouped into various kingdoms of the domain Eukarya.  The recent taxonomic trend has been to split the single- celled eukaryotes and their close relatives into several kingdoms.  Domain Eukarya also includes the three kingdoms of multicellular eukaryotes: the kingdoms Plantae, Fungi, and Animalia.  These kingdoms are distinguished partly by their modes of nutrition.  Most plants produce their own sugars and food by photosynthesis.  Most fungi are decomposers that absorb nutrients by breaking down dead organisms and organic wastes.  Animals obtain food by ingesting other organisms.  Underlying the diversity of life is a striking unity, especially at the lower levels of organization.  The universal genetic language of DNA unites prokaryotes and eukaryotes.  Among eukaryotes, unity is evident in many details of cell structure.  Above the cellular level, organisms are variously adapted to their ways of life. Lecture Outline for Campbell/Reece Biology, 7th Edition, © Pearson Education, Inc. 1-7  She has also collected volumes of quantitative data over that time.  Discovery science can lead to important conclusions based on inductive reasoning.  Through induction, we derive generalizations based on a large number of specific observations.  In science, inquiry frequently involves the proposing and testing of hypotheses.  A hypothesis is a tentative answer to a well-framed question.  It is usually an educated postulate, based on past experience and the available data of discovery science.  A scientific hypothesis makes predictions that can be tested by recording additional observations or by designing experiments.  A type of logic called deduction is built into hypothesis-based science.  In deductive reasoning, reasoning flows from the general to the specific.  From general premises, we extrapolate to a specific result that we should expect if the premises are true.  In hypothesis-based science, deduction usually takes the form of predictions about what we should expect if a particular hypothesis is correct.  We test the hypothesis by performing the experiment to see whether or not the results are as predicted.  Deductive logic takes the form of “If . . . then” logic.  Scientific hypotheses must be testable.  There must be some way to check the validity of the idea.  Scientific hypotheses must be falsifiable.  There must be some observation or experiment that could reveal if a hypothesis is actually not true.  The ideal in hypothesis-based science is to frame two or more alternative hypotheses and design experiments to falsify them.  No amount of experimental testing can prove a hypothesis.  A hypothesis gains support by surviving various tests that could falsify it, while testing falsifies alternative hypotheses.  Facts, in the form of verifiable observations and repeatable experimental results, are the prerequisites of science. We can explore the scientific method.  There is an idealized process of inquiry called the scientific method. Lecture Outline for Campbell/Reece Biology, 7th Edition, © Pearson Education, Inc. 1-10  Very few scientific inquiries adhere rigidly to the sequence of steps prescribed by the textbook scientific method.  Discovery science has contributed a great deal to our understanding of nature without most of the steps of the so- called scientific method.  We will consider a case study of scientific research.  This case begins with a set of observations and generalizations from discovery science.  Many poisonous animals have warning coloration that signals danger to potential predators.  Imposter species mimic poisonous species, although they are harmless.  An example is the bee fly, a nonstinging insect that mimics a honeybee.  What is the function of such mimicry? What advantage does it give the mimic?  In 1862, Henry Bates proposed that mimics benefit when predators mistake them for harmful species.  This deception may lower the mimic’s risk of predation.  In 2001, David and Karin Pfennig and William Harcombe of the University of North Carolina designed a set of field experiments to test Bates’s mimicry hypothesis.  In North and South Carolina, a poisonous snake called the eastern coral snake has warning red, yellow, and black coloration.  Predators avoid these snakes. It is unlikely that predators learn to avoid coral snakes, as a strike is usually lethal.  Natural selection may have favored an instinctive recognition and avoidance of the warning coloration of the coral snake.  The nonpoisonous scarlet king snake mimics the ringed coloration of the coral snake.  Both king snakes and coral snake live in the Carolinas, but the king snake’s range also extends into areas without coral snakes.  The distribution of these two species allowed the Pfennigs and Harcombe to test a key prediction of the mimicry hypothesis.  Mimicry should protect the king snake from predators, but only in regions where coral snakes live.  Predators in non–coral snake areas should attack king snakes more frequently than predators that live in areas where coral snakes are present.  To test the mimicry hypothesis, Harcombe made hundreds of artificial snakes. Lecture Outline for Campbell/Reece Biology, 7th Edition, © Pearson Education, Inc. 1-11  The experimental group had the red, black, and yellow ring pattern of king snakes.  The control group had plain, brown coloring.  Equal numbers of both types were placed at field sites, including areas where coral snakes are absent.  After four weeks, the scientists retrieved the fake snakes and counted bite or claw marks.  Foxes, coyotes, raccoons, and black bears attacked snake models.  The data fit the predictions of the mimicry hypothesis.  The ringed snakes were attacked by predators less frequently than the brown snakes only within the geographic range of the coral snakes.  The snake mimicry experiment provides an example of how scientists design experiments to test the effect of one variable by canceling out the effects of unwanted variables.  The design is called a controlled experiment.  An experimental group (artificial king snakes) is compared with a control group (artificial brown snakes).  The experimental and control groups differ only in the one factor the experiment is designed to test—the effect of the snake’s coloration on the behavior of predators.  The brown artificial snakes allowed the scientists to rule out such variables as predator density and temperature as possible determinants of number of predator attacks.  Scientists do not control the experimental environment by keeping all variables constant.  Researchers usually “control” unwanted variables, not by eliminating them but by canceling their effects using control groups. Let’s look at the nature of science.  There are limitations to the kinds of questions that science can address.  These limits are set by science’s requirements that hypotheses are testable and falsifiable and that observations and experimental results be repeatable.  The limitations of science are set by its naturalism.  Science seeks natural causes for natural phenomena.  Science cannot support or falsify supernatural explanations, which are outside the bounds of science.  Everyday use of the term theory implies an untested speculation.  The term theory has a very different meaning in science. Lecture Outline for Campbell/Reece Biology, 7th Edition, © Pearson Education, Inc. 1-12