Chapter 1: Exploring Life

Biologists explore life from the microscopic to the global scale w Each level of biological organization has emergent properties. Biological organization is based on a hierachy of structural levels, each level building on the levels below it.

HIERARCHY OF BIOLOGICAL ORGANIZATION w Molecules (built of many atoms to perform a function) w Organelle (conglomerate of molecules which work together to perform a process) w Cell (many organelle working together to form a living unit) w Tissue(groups of cells forming a functional unit)

Hierarchy continued w Organ (many tissues forming a specialized center for a body function) w Organism (many organs forming functional multicellar life) w Populations: all individuals of a species living within a specific area w Communities: The entire array of organisms inhabiting a particular ecosystem w Ecosystems: Includes both biotic and abiotic factors w Biosphere: All the environments on Earth that are inhabited by life.

Ecosystems The biosphere Organisms Populations Communities Cells Organelles Molecules Tissues Organs and organ systems Cell 1 µm Atoms 10 µm 50 µm

A Closer look at Ecosystems w Ecosystem Dynmaics Producers and consumers The dynamics of an ecosystem include two major processes: Cycling of nutrients, in which materials acquired by plants eventually return to the soil The flow of energy from sunlight to producers to consumers

Energy Conversions w Activities of life require work w Work depends on sources of energy w Energy exchange between an organism and environment often involves energy transformations w In transformations, some energy is lost as heat w Energy flows through an ecosystem, usually entering as light and exiting as heat

LE 1-4 Sunlight Ecosystem Heat Chemical energy Consumers (including animals) Producers (plants and other photosynthetic organisms)

A Closer Look at Cells w The cell is the lowest level of organization that can perform all activities of life w The ability of cells to divide is the basis of all reproduction, growth, and repair of multicellular organisms w Brief_History_of_Cells.asf Brief_History_of_Cells.asf

LE µm

The Cell’s Heritable Information w Cells contain DNA, the heritable information that directs the cell’s activities w DNA is the substance of genes w Genes are the units of inheritance that transmit information from parents to offspring

w Each DNA molecule is made up of two long chains arranged in a double helix w Each link of a chain is one of four kinds of chemical building blocks called nucleotides

Two Main Forms of Cells w Characteristics shared by all cells: Enclosed by a membrane Use DNA as genetic information w Two main forms of cells: Eukaryotic: divided into organelles; DNA in nucleus Prokaryotic: lack organelles; DNA not separated in a nucleus

LE 1-8 Membrane Cytoplasm EUKARYOTIC CELL PROKARYOTIC CELL DNA (no nucleus) Membrane 1 µm Organelles Nucleus (contains DNA)

Concept 1.2: Biological systems are much more than the sum of their parts w A system is a combination of components that form a more complex organization w Cells, organisms, and ecosystems are some examples of biological systems

The Emergent Properties of Systems w With each step upward in the hierarchy new properties emerge. Each level must work for the whole to work. Disrupt one part of a molecule and the organ will cease to function properly. Diabetes

The Power and Limitations of Reductionism w In order to study an organism we break down the whole into its individual parts. w But when broken down the organism no longer functions. w Biology balances the reductionist strategy with understanding emergent properties.

Systems Biology w Systems biology seeks to create models of the dynamic behavior of whole biological systems w An example is a systems map of interactions between proteins in a fruit fly cell w Such models may predict how a change in one part of a system will affect the rest of the system

LE 1-10 CELL Nucleus Cytoplasm Outer membrane and cell surface

Systems Biology w The ultimate goal of systems biology is to model the dynamic behavior of whole biological systems.

w Systems biology uses three key research developments: High-throughput technology: methods to generate large data sets rapidly Bioinformatics: using computers and software to process and integrate large data sets Interdisciplinary research teams

Feedback Regulation in Biological Systems w Regulatory systems ensure a dynamic balance in living systems w Chemical processes are catalyzed (accelerated) by enzymes w Many biological processes are self- regulating: the product regulates the process itself

w In negative feedback, the accumulation of a product slows down the process itself e.g lac operon w In positive feedback (less common), the product speeds up its own production e.g. partrition Animation: Negative Feedback Animation: Negative Feedback Animation: Positive Feedback Animation: Positive Feedback

LE 1-11 Enzyme 1 A A B B C C D D D D D D D D D D D Enzyme 2 Enzyme 3 Negative feedback Enzyme 1

LE 1-12 W Enzyme 4 W X X Y Y Z Z Z Z Z Z Z Z Z Z Enzyme 5 Enzyme 6 Positive feedback Enzyme 4 Enzyme 6 Enzyme 5 Z Z Z Z Z Z Z Z Z

Grouping Species: The Basic Idea

w Taxonomy is the branch of biology that names and classifies species into a hierarchical order w Kingdoms and domains are the broadest units of classification

TAXONMONY: GROUPING SPECIES w 3 Domains of life Bacteria Archaea Eukarya

BACTERIA w Contains part of the old Moneran Kingdom but now is called the Eubacteria kingdom w Most diverse and widespread prokaryotes

ARCHAEA w Prokaryotic but live in extreme environments w Molecular evidence indicates that they have many things in common with the Eukarya.

EUKARYA w Contains all eukaryotes w Kingdoms Fungi Protista Plantae Animalia

LEVELS OF CLASSIFICATION w DOMAIN w KINGDOM w PHYLUM w CLASS w ORDER w FAMILY w GENUS w SPECIES

LE 1-14 Ursidae Ursus Carnivora Mammalia Chordata Animalia Eukarya SpeciesGenus Family Order Class Phylum KingdomDomain Ursus americanus (American black bear)

UNITY IN THE DIVERSITY OF LIFE w THE HUGE NUMBER OF SPECIES OF LIFE ON THIS PLANET GIVES US DIVERSITY w YET THERE IS MUCH THESE ORGANISMS HAVE IN COMMON. ESPECIALLY IN THE LOWER LEVELS OF ORGANIZATION EG. DNA

LE 1-16a Cilia of windpipe cells Cilia of Paramecium 15 µm 5 µm

LE 1-16b Cilia of windpipe cells Cilia of Paramecium Cross section of cilium, as viewed with an electron microscope 0.1 µm

 Concept 1.4: Evolution accounts for life ’ s unity and diversity w The history of life is a saga of a changing Earth billions of years old

w The evolutionary view of life came into sharp focus in 1859, when Charles Darwin published On the Origin of Species by Natural Selection w “Darwinism” became almost synonymous with the concept of evolution

w The Origin of Species articulated two main points: Descent with modification (the view that contemporary species arose from a succession of ancestors) Natural selection (a proposed mechanism for descent with modification) Some examples of descent with modification are unity and diversity in the orchid family

Natural Selection w Darwin inferred natural selection by connecting two observations: Observation: Individual variation in heritable traits Observation: Overpopulation and competition Inference: Unequal reproductive success Inference: Evolutionary adaptation

LE 1-20 Evolution of adaptations in the population Differences in reproductive success Overproduction and competition Population of organisms Hereditary variations

w Natural selection can “edit” a population’s heritable variations w An example is the effect of birds preying on a beetle population

w Natural selection is often evident in adaptations of organisms to their way of life and environment w Bat wings are an example of adaptation Video: Soaring Hawk Video: Soaring Hawk

The Tree of Life Many related organisms have similar features adapted for specific ways of life w Such kinships connect life’s unity and diversity to descent with modification w Natural selection eventually produces new species from ancestral species w Biologists often show evolutionary relationships in a treelike diagram [Videos on slide following the figure]

LE 1-23 Large ground finch Large cactus ground finch Sharp-beaked ground finch Geospiza magnirostris Geospiza conirostris Medium ground finch Geospiza fuliginosa Small ground finch Woodpecker finch Camarhynchus psittacula Large tree finch Medium tree finch Cactus ground finch Geospiza difficilis Cactus flower eaters Geospiza scandens Seed eater Ground finches Seed eaters Tree finches Common ancestor from South American mainland Insect eaters Bud eater Warbler finches Mangrove finch Geospiza fortis Cactospiza pallida Small tree finch Camarhynchus pauper Camarhynchus parvulus Green warbler finch Gray warbler finch Certhidea olivacea Certhidea fusca Vegetarian finch Platyspiza crassirostris Cactospiza heliobates

Video: Albatross Courtship Ritual Video: Albatross Courtship Ritual Video: Blue-footed Boobies Courtship Ritual Video: Blue-footed Boobies Courtship Ritual Video: Galapágos Islands Overview Video: Galapágos Islands Overview Video Galapágos Marine Iguana Video Galapágos Marine Iguana Video: Galapágos Sea Lion Video: Galapágos Sea Lion Video: Galapágos Tortoise Video: Galapágos Tortoise

So….. What is life?

So…..What is life?

THEME 10 : Science, Technology, and Society

w Concept 1.5: Biologists use various forms of inquiry to explore life w Inquiry is a search for information and explanation, often focusing on specific questions w The process of science blends two main processes of scientific inquiry: Discovery science: describing nature Hypothesis-based science: explaining nature

Discovery Science w Discovery science describes nature through careful observation and data analysis w Examples of discovery science: understanding cell structure expanding databases of genomes

Types of Data w Data are recorded observations w Two types of data: Quantitative data: numerical measurements Qualitative data: recorded descriptions

Induction in Discovery Science w Inductive reasoning involves generalizing based on many specific observations

Hypothesis-Based Science w In science, inquiry usually involves proposing and testing hypotheses w Hypotheses are hypothetical explanations

The Role of Hypotheses in Inquiry w In science, a hypothesis is a tentative answer to a well-framed question w A hypothesis is an explanation on trial, making a prediction that can be tested

LE 1-25a Hypothesis #1: Dead batteries Hypothesis #2: Burnt-out bulb Observations Question

LE 1-25b Hypothesis #1: Dead batteries Hypothesis #2: Burnt-out bulb Test prediction Test falsifies hypothesis Prediction: Replacing batteries will fix problem Prediction: Replacing bulb will fix problem Test prediction Test does not falsify hypothesis

Deduction: The “If…then” Logic of Hypothesis-Based Science w In deductive reasoning, the logic flows from the general to the specific w If a hypothesis is correct, then we can expect a particular outcome

A Closer Look at Hypotheses in Scientific Inquiry w A scientific hypothesis must have two important qualities: It must be testable It must be falsifiable

The Myth of the Scientific Method w The scientific method is an idealized process of inquiry w Very few scientific inquiries adhere rigidly to the “textbook” scientific method

w In mimicry, a harmless species resembles a harmful species w An example of mimicry is a stinging honeybee and a nonstinging mimic, a flower fly A Case Study in Scientific Inquiry: Investigating Mimicry in Snake Populations

LE 1-26 Flower fly (nonstinging) Honeybee (stinging)

w This case study examines king snakes’ mimicry of poisonous coral snakes w The hypothesis states that mimics benefit when predators mistake them for harmful species w The mimicry hypothesis predicts that predators in non–coral snake areas will attack king snakes more frequently than will predators that live where coral snakes are present

LE 1-27 Scarlet king snake Eastern coral snake Scarlet king snake Key Range of scarlet king snake North Carolina Range of eastern coral snake South Carolina

Field Experiments with Artificial Snakes w To test this mimicry hypothesis, researchers made hundreds of artificial snakes: An experimental group resembling king snakes A control group resembling plain brown snakes Equal numbers of both types were placed at field sites, including areas without coral snakes After four weeks, the scientists retrieved the artificial snakes and counted bite or claw marks The data fit the predictions of the mimicry hypothesis

LE 1-28 (a) Artificial king snake (b) Artificial brown snake that has been attacked

In areas where coral snakes were present, most attacks were on brown artificial snakes. In areas where coral snakes were absent, most attacks were on artificial king snakes. LE 1-29 % of attacks on artificial king snakes % of attacks on brown artificial snakes Field site with artificial snakes 83% North Carolina South Carolina 17% 16% 84% Key

Designing Controlled Experiments w Scientists do not control the experimental environment by keeping all variables constant w Researchers usually “control” unwanted variables by using control groups to cancel their effects

Theories in Science w A scientific theory is much broader than a hypothesis w A scientific theory is: broad in scope general enough to generate new hypotheses supported by a large body of evidence

Model Building in Science w Models are representations of ideas, structures, or processes w Models may range from lifelike representations to symbolic schematics

LE 1-30 From body From lungs Right atrium Left atrium Right ventricle Left ventricle To lungs To body

The Culture of Science w Science is an intensely social activity w Both cooperation and competition characterize scientific culture

Science, Technology, and Society w The goal of science is to understand natural phenomena w Technology applies scientific knowledge for some specific purpose

w Concept 1.6: A set of themes connects the concepts of biology w Biology is the science most connected to the humanities and social sciences w Underlying themes provide a framework for understanding biology

Table 1.1 Review of Ten Unifying Themes in Biology

Table 1.1 Review of Ten Unifying Themes in Biology (continued)

THE END

SCIENCE IS A PROCESS OF INQUIRY THAT ICLUDES REPEATABLE OBSERVATIONS AND TESTABLE HYPOTHESIES w DISCOVERY SCIENCE INDUCTIVE REASONING w HYPOTHETICO-DEDUCTIVE REASONING DEDUCTIVE REASONING HYPOTHESIS

DISCOVERY SCIENCE AND INDUCTIVE REASONING w GENERALIZATION THAT SUMMARIZES MANY CONCURRENT OBSERVATIONS. E.G. “ALL ORGANISMS ARE COMPOSED OF CELL” BASED ON CENTURIES OF OBSERVATIONS.

THE SCIENTIFIC METHOD AND DEDUCTIVE REASONING w HYPOTHESIS: A TESTABLE EXPLAINATION w DEDUCTIVE REASONING THE “IF…THEN” LOGIC

IDEALIZED VERSION OF THE SCIENTIFIC METHOD w OBSERVE w FORMULATE QUESTION w HYPOTHESIZE w PREDICT w TEST w REPEAT

CONTROLLED EXPERIMENT w COMPOSED OF 2 GROUPS CONTROL GROUP (STAYS THE SAME) EXPERIMENTAL GROUP CREATED BY CHANGINE 1 VARIABLE

A THEORY w A THEORY IS A BROAD HYPOTHESIS. w IT IS BACKED UP BY EXTENSIVE AND VARIED OBSERVATIONS AND DATA. w USUALLY IT TIES TOGETHER A NUMBER OF SEEMINGLY UNRELATED OBSERVATIONS AND EXPERIMENTAL RESULTS. w E.G. NEWTON’S LAWS

SCIENCE IS A SOCIAL PROCESS w SCIENTISTS READ JOURNALS, SHARE INFORMATION AND PUBLISH THEIR FINDING FOR OTHER SCIENTISTS TO READ. w THEY CHECK AND VALIDATE PUBLISHED FINDINGS.

TECHNOLOGY w A DEVELOPMENT THAT SOLVES A PROBLEM w NOT ALL ARE SCIENCE RELATED E.G. PRIMITIVE TOOLS w TECHNOLOGY HAS SOLVED MANY PROBLEMS BUT AT THE SAME TIME HAS CREATED OTHERS.

Figure 1.8 Regulation by feedback mechanisms