Chapter 1: Introduction to Biology

Evolution

The diversity of life on Earth is a result of mutations, or random changes in hereditary material over time. These mutations allow the possibility for organisms to adapt to a changing environment. An organism that evolves characteristics fit for the environment will have greater reproductive success, subject to the forces of natural selection.

The Diversity of Life

The science of biology is very broad in scope because there is a tremendous diversity of life on Earth. The source of this diversity is evolution, the process of gradual change during which new species arise from older species.

Systematics

The study of organisms with the purpose of deriving their relationships

Property of Life: Regulation/Homeostasis 2

To function properly, cells require appropriate conditions such as proper temperature, pH, and concentrations of diverse chemicals. These conditions may, however, change from one moment to the next. Organisms are able to maintain internal conditions within a narrow range almost constantly, despite environmental changes, through a process called homeostasis.

Testing a hypothesis

To test a hypothesis, a researcher will conduct one or more experiments designed to eliminate one or more of the hypotheses. This is important. A hypothesis can be disproven, or eliminated, but it can never be proven.

Molecule

a chemical structure consisting of at least two atoms held together by a chemical bond. Many molecules that are biologically important are macromolecules

Scientific theory

a generally accepted, thoroughly tested and confirmed explanation for a set of observations or phenomena. Scientific theory is the foundation of scientific knowledge.

Scientific Method

a method of research with defined steps that include experiments and careful observation.

Example of the link between basic and applied research is the Human Genome Project

a study in which each human chromosome was analyzed and mapped to determine the precise sequence of DNA subunits and the exact location of each gene. (The gene is the basic unit of heredity represented by a specific DNA segment that codes for a functional molecule.) Other organisms have also been studied as part of this project to gain a better understanding of human chromosomes. The Human Genome Project relied on basic research carried out with non-human organisms and, later, with the human genome. An important end goal eventually became using the data for applied research seeking cures for genetically related diseases.

Hypothesis

a suggested explanation for an event, which can be tested. Hypotheses are generally produced within the context of a scientific theory.

The Bacteria

are another quite different group of single-celled organisms without nuclei. Both the Archaea and the Bacteria are prokaryotes, an informal name for cells without nuclei.

The Archaea

are single-celled organisms without nuclei and include many extremophiles that live in harsh environments like hot springs.

Science includes such diverse fields as

astronomy, biology, computer sciences, geology, logic, physics, chemistry, and mathematics

wolf. Each taxon name is capitalized except for species, and the genus and species names are italicized. Scientists refer to an organism by its genus and species names together, commonly called a scientific name, or Latin name. This two-name system is called

binomial nomenclature

The point where a split occurs in a tree, called a

branch point, represents where a single lineage evolved into distinct new ones. Many phylogenetic trees have a single branch point at the base representing a common ancestor of all the branches in the tree.

The methods of science include

careful observation, record keeping, logical and mathematical reasoning, experimentation, and submitting conclusions to the scrutiny of others.

Eukaryote

cells that do have membrane-bound organelles and nuclei.

Ecosystem

consists of all the living things in a particular area together with the abiotic, or non-living, parts of that environment such as nitrogen in the soil or rainwater.

The domain Eukarya

contains organisms that have cells with nuclei. It includes the kingdoms of fungi, plants, animals, and several kingdoms of protists.

A hierarchical system

has levels and each group at one of the levels includes groups at the next lowest level, so that at the lowest level each member belongs to a series of nested groups. An analogy is the nested series of directories on the main disk drive of a computer.

phylogenetic tree

is a diagram used to reflect evolutionary relationships among organisms or groups of organisms. The hierarchical classification of groups nested within more inclusive groups is reflected in diagrams. Scientists consider phylogenetic trees to be a hypothesis of the evolutionary past because one cannot go back through time to confirm the proposed relationships.

Phylogeny

is the evolutionary history and the relationships among a species or group of species.

Biology

is the science that studies life.

Macromolecule

large molecules that are typically formed by combining smaller units called monomers. An example of a macromolecule is deoxyribonucleic acid (DNA), which contains the instructions for the functioning of the organism that contains it.

In the 18th century, a scientist named Carl Linnaeus first proposed

organizing the known species of organisms into a hierarchical taxonomy.

Scientists call such trees

rooted, which means there is a single ancestral taxon at the base of a phylogenetic tree to which all organisms represented in the diagram descend from.

Prokaryote

single-celled organisms that lack organelles surrounded by a membrane and do not have nuclei surrounded by nuclear membranes

When two lineages stem from the same branch point, they are called

sister taxa, for example the two species of orangutans.

The current taxonomic system now has eight levels in its hierarchy, from lowest to highest, they are:

species, genus, family, order, class, phylum, kingdom, domain. Thus species are grouped within genera, genera are grouped within families, families are grouped within orders, and so on.

The group at each level is called a

taxon (plural: taxa).

Scientists now recognize three domains of life:

the Eukarya, the Archaea, and the Bacteria.

Homeostasis

the ability of an organism to maintain constant internal conditions.

Community

the set of populations inhabiting a particular area. For instance, all of the trees, flowers, insects, and other populations in a forest form the forest's community. The forest itself is an ecosystem.

Atom

the smallest and most fundamental unit of matter that retains the properties of an element. It consists of a nucleus surrounded by electrons. Atoms form molecules.

Hypothesis-based Science

while hypothesis-based science begins with a specific question or problem and a potential answer or solution that can be tested. The boundary between these two forms of study is often blurred, because most scientific endeavors combine both approaches. Observations lead to questions, questions lead to forming a hypothesis as a possible answer to those questions, and then the hypothesis is tested. Thus, descriptive science and hypothesis-based science are in continuous dialogue.

Viruses

(This requirement is why viruses are not considered living: they are not made of cells. To make new viruses, they have to invade and hijack a living cell; only then can they obtain the materials they need to reproduce.)

Taxonomy

(which literally means "arrangement law") is the science of naming and grouping species to construct an internationally shared classification system. The taxonomic classification system (also called the Linnaean system after its inventor, Carl Linnaeus, a Swedish naturalist) uses a hierarchical model.

Deductive reasoning

-Deductive reasoning or deduction is the type of logic used in hypothesis-based science. In deductive reasoning, the pattern of thinking moves in the opposite direction as compared to inductive reasoning. -Deductive reasoning is a form of logical thinking that uses a general principle or law to predict specific results. -From those general principles, a scientist can deduce and predict the specific results that would be valid as long as the general principles are valid. -For example, a prediction would be that if the climate is becoming warmer in a region, the distribution of plants and animals should change. Comparisons have been made between distributions in the past and the present, and the many changes that have been found are consistent with a warming climate. Finding the change in distribution is evidence that the climate change conclusion is a valid one.

Inductive reasoning

-Inductive reasoning is a form of logical thinking that uses related observations to arrive at a general conclusion. -This type of reasoning is common in descriptive science. -A life scientist such as a biologist makes observations and records them. These data can be qualitative (descriptive) or quantitative (consisting of numbers), and the raw data can be supplemented with drawings, pictures, photos, or videos. -From many observations, the scientist can infer conclusions (inductions) based on evidence. -Inductive reasoning involves formulating generalizations inferred from careful observation and the analysis of a large amount of data. - Brain studies often work this way. Many brains are observed while people are doing a task. The part of the brain that lights up, indicating activity, is then demonstrated to be the part controlling the response to that task.

Control

A control is a part of the experiment that does not change.

Property of Life: Adaptation

All living organisms exhibit a "fit" to their environment. Biologists refer to this fit as adaptation and it is a consequence of evolution by natural selection, which operates in every lineage of reproducing organisms.

Cells

All living things are made of cells; the cell itself is the smallest fundamental unit of structure and function in living organisms. Some organisms consist of a single cell and others are multicellular. Cells are classified as prokaryotic or eukaryotic.

Property of Life: Energy Processing

All organisms use a source of energy for their metabolic activities. Some organisms capture energy from the Sun and convert it into chemical energy in food; others use chemical energy from molecules they take in.

Population

All the individuals of a species living within a specific area are collectively called a population

A branch point with more than two groups illustrates a situation for which scientists have not definitively determined relationships.

An example is illustrated by the three branches leading to the gorilla subspecies; their exact relationships are not yet understood.

Organ system

An organ system is a higher level of organization that consists of functionally related organs.

Biosphere

At the highest level of organization, the biosphere is the collection of all ecosystems, and it represents the zones of life on Earth. It includes land, water, and portions of the atmosphere.

Basic Science

Basic science or "pure" science seeks to expand knowledge regardless of the short-term application of that knowledge. It is not focused on developing a product or a service of immediate public or commercial value. The immediate goal of basic science is knowledge for knowledge's sake, though this does not mean that in the end it may not result in an application.

In addition to the hierarchical taxonomic system, Linnaeus was the first to name organisms using two unique names, now called the binomial naming system.

Binomial names consist of the genus name (which is capitalized) and the species name (all lower-case). Both names are set in italics when they are printed. Every species is given a unique binomial which is recognized the world over, so that a scientist in any location can know which organism is being referred to.

Descriptive Science

Both types of logical thinking are related to the two main pathways of scientific study: descriptive science and hypothesis-based science. Descriptive (or discovery) science aims to observe, explore, and discover

Scientific Inquiry

Curiosity and inquiry are the driving forces for the development of science. Scientists seek to understand the world and the way it operates. Two methods of logical thinking are used: inductive reasoning and deductive reasoning.

Variable

Each experiment will have one or more variables and one or more controls. A variable is any part of the experiment that can vary or change during the experiment.

Property of Life: Regulation/Homeostasis 1

Even the smallest organisms are complex and require multiple regulatory mechanisms to coordinate internal functions, such as the transport of nutrients, response to stimuli, and coping with environmental stresses.

Single-celled organisms vs Multicellular Organisms

Even very simple, single-celled organisms are remarkably complex. Inside each cell, atoms make up molecules. These in turn make up cell components or organelles. Multicellular organisms, which may consist of millions of individual cells, have an advantage over single-celled organisms in that their cells can be specialized to perform specific functions, and even sacrificed in certain situations for the good of the organism as a whole.

Examples of Adaptation

Examples of adaptations are diverse and unique, from heat-resistant Archaea that live in boiling hot springs to the tongue length of a nectar-feeding moth that matches the size of the flower from which it feeds. Adaptations

Example of an organ system

For example vertebrate animals have many organ systems, such as the circulatory system that transports blood throughout the body and to and from the lungs; it includes organs such as the heart and blood vessels.

Example of a Population

For example, a forest may include many white pine trees. All of these pine trees represent the population of white pine trees in this forest. Different populations may live in the same specific area. For example, the forest with the pine trees includes populations of flowering plants and also insects and microbial populations.

A hypothesis must be testable to ensure that it is valid.

For example, a hypothesis that depends on what a bear thinks is not testable, because it can never be known what a bear thinks. It should also be falsifiable, meaning that it can be disproven by experimental results.

Limitations of Phylogenetic Trees

It is easy to assume that more closely related organisms look more alike, and while this is often the case, it is not always true.

Important note about sister taxa

It is important to note that sister taxa share an ancestor, which does not mean that one taxon evolved from the other. The branch point, or split, represents a common ancestor that existed in the past, but that no longer exists. Humans did not evolve from chimpanzees (nor did chimpanzees evolve from humans) although they are our closest living relatives. Both humans and chimpanzees evolved from a common ancestor that lived, scientists believe, six million years ago and looked different from both modern chimpanzees and modern humans.

Levels of Organization of Living Things

Living things are highly organized and structured, following a hierarchy on a scale from small to large.

Property of life: Reproduction (multi)

Many multicellular organisms (those made up of more than one cell) produce specialized reproductive cells that will form new individuals. When reproduction occurs, DNA containing genes is passed along to an organism's offspring. These genes are the reason that the offspring will belong to the same species and will have characteristics similar to the parent, such as fur color and blood type.

Examples of Branches of Biological Study

Molecular biology, microbiology, neurobiology, paleontology, zoology, botany, biotechnologists, ecologists, physiologists, etc.

Hypothesis Testing

Once a hypothesis has been selected, a prediction may be made. A prediction is similar to a hypothesis but it typically has the format "If . . . then . . . ."

Properties of Life

Order, sensitivity or response to stimuli, reproduction, adaptation, growth and development, regulation/homeostasis, and energy processing.

Property of Life: Order

Organisms are highly organized structures that consist of one or more cells. Even

Organisms

Organisms are individual living entities. For example, each tree in a forest is an organism. Single-celled prokaryotes and single-celled eukaryotes are also considered organisms and are typically referred to as microorganisms.

Property of Life: Growth and Development

Organisms grow and develop according to specific instructions coded for by their genes. These genes provide instructions that will direct cellular growth and development, ensuring that a species' young will grow up to exhibit many of the same characteristics as its parents.

Property of Life: Sensitivity or Response to Stimuli

Organisms respond to diverse stimuli.

Organs

Organs are collections of tissues grouped together based on a common function. Organs are present not only in animals but also in plants.

The Nature of Science

Science (from the Latin scientia, meaning "knowledge") can be defined as knowledge about the natural world.

Property of life: Reproduction (single)

Single-celled organisms reproduce by first duplicating their DNA, which is the genetic material, and then dividing it equally as the cell prepares to divide to form two new cells.

Organelles

Some cells contain aggregates of macromolecules surrounded by membranes; these are called organelles. Organelles are small structures that exist within cells and perform specialized functions.

Tissues

In most multicellular organisms, cells combine to make tissues, which are groups of similar cells carrying out the same function.

Applied Science

In contrast, applied science or "technology," aims to use science to solve real-world problems, making it possible, for example, to improve a crop yield, find a cure for a particular disease, or save animals threatened by a natural disaster. In applied science, the problem is usually defined for the researcher.

Another aspect of phylogenetic trees is that, unless otherwise indicated, the branches do not show length of time, they show only the order in time of evolutionary events. In other words, a long branch does not necessarily mean more time passed, nor does a short branch mean less time passed— unless specified on the diagram.

For example, in Figure 12.5, the tree does not indicate how much time passed between the evolution of amniotic eggs and hair. What the tree does show is the order in which things took place. Again, the tree shows that the oldest trait is the vertebral column, followed by hinged jaws, and so forth. Remember that any phylogenetic tree is a part of the greater whole, and similar to a real tree, it does not grow in only one direction after a new branch develops. So, for the organisms, just because a vertebral column evolved does not mean that invertebrate evolution ceased, it only means that a new branch formed. Also, groups that are not closely related, but evolve under similar conditions, may appear more similar to each other than to a close relative.

The Levels of Classification

For example, in the most inclusive grouping, scientists divide organisms into three domains: Bacteria, Archaea, and Eukarya. Within each domain is a second level called a kingdom. Each domain contains several kingdoms. Within kingdoms, the subsequent categories of increasing specificity are: phylum, class, order, family, genus, and species.

Example of Homeostasis

For example, many organisms regulate their body temperature in a process known as thermoregulation. Organisms that live in cold climates, such as the polar bear, have body structures that help them withstand low temperatures and conserve body heat. In hot climates, organisms have methods (such as perspiration in humans or panting in dogs) that help them to shed excess body heat.

Example of Regulation

For example, organ systems such as the digestive or circulatory systems perform specific functions like carrying oxygen throughout the body, removing wastes, delivering nutrients to every cell, and cooling the body.

Example of Sensitivity or Response to Stimuli

For example, plants can bend toward a source of light or respond to touch. Even tiny bacteria can move toward or away from chemicals (a process called chemotaxis) or light (phototaxis).

Examples of Binomial Names

For example, the North American blue jay is known uniquely as Cyanocitta cristata. Our own species is Homo sapiens.

The branch points and the branches in phylogenetic tree structure also imply evolutionary change. Sometimes the significant character changes are identified on a branch or branch point.

For example, the branch point that gives rise to the mammal and reptile lineage from the frog lineage shows the origin of the amniotic egg character. Also the branch point that gives rise to organisms with legs is indicated at the common ancestor of mammals, reptiles, amphibians, and jawed fishes.

If two closely related lineages evolved under significantly different surroundings or after the evolution of a major new adaptation, they may look quite different from each other, even more so than other groups that are not as closely related.

For example, the phylogenetic tree shows that lizards and rabbits both have amniotic eggs, whereas salamanders (within the frog lineage) do not; yet on the surface, lizards and salamanders appear more similar than the lizards and rabbits.

Scientific laws

Hypotheses are the day-to-day material that scientists work with and they are developed within the context of theories. Laws are concise descriptions of parts of the world that are amenable to formulaic or mathematical description.