Module 1 Introduction To Biology PDF

MODULE 1: INTRODUCTION TO BIOLOGY WHY IT MATTERS: INTRODUCTION TO BIOLOGY Why learn about biology and its principles? One night while she was scrolling through her social media feeds, Cristina saw that her brother had linked to an article about some of the world’s weirdest...

MODULE 1: INTRODUCTION TO BIOLOGY WHY IT MATTERS: INTRODUCTION TO BIOLOGY Why learn about biology and its principles? One night while she was scrolling through her social media feeds, Cristina saw that her brother had linked to an article about some of the world’s weirdest animals. As she paged through the article, Cristina became increasingly interested in the different features these animals had: some were eyeless, some were colorless, and others had even stranger features. Before Cristina could dig deeper into these animals, she got a message from her cousin Samuel. He’d sent a link to an article about genetically modified foods and the dangers they inherently contain. 5 Cristina was only halfway through reading the first paragraph of the article when Samuel sent her another article: this one lauding the paleo diet and its benefits. Cristina started to read the article, but before she got too far, she remembered that she had a paper due the next day. She made a mental note to come back to the Figure 1. The pangolin (also known as the articles from her cousin, and she scaly anteater) is a unique animal. It bookmarked the animals article. walks on just its hind legs and uses its front claws to tear open termite mounds. Though Cristina might not realize it, she’s just been presented with three different biological questions. How did these animals develop such unique characteristics? Are GMOs dangerous? Are extreme diets (like the paleo diet) beneficial? Cristina still has to come to her own conclusions and make her own choices, but having an understanding of biology will help her make the best choices she can. Licensing & Attributions CC licensed content, Original Why It Matters: Introduction to Biology. Authored by: Shelli Carter and Lumen Learning. Provided by: Lumen Learning. License: CC BY: Attribution CC licensed content, Shared previously Scaly Anteater. Authored by: David Brossard. Located at: https:// ic.kr/p/dqrpWk. License: CC BY-SA: Attribution-ShareAlike CHARACTERISTICS OF LIFE 6 What you’ll learn to do: List the de ning characteristics of biological life Biology is the science that studies life, but what exactly is life? This may sound like a silly question with an obvious response, but it is not always easy to define life. For example, a branch of biology called virology studies viruses, which exhibit some of the characteristics of living entities but lack others. It turns out that although viruses can attack living organisms, cause diseases, and even reproduce, they do not meet the criteria that biologists use to define life. Consequently, virologists are not biologists, strictly speaking. Similarly, some biologists study the early molecular evolution that gave rise to life; since the events that preceded life are not biological events, these scientists are also excluded from biology in the strict sense of the term. From its earliest beginnings, biology has wrestled with these questions: What are the shared properties that make something “alive”? And once we know something is alive, how do we find meaningful levels of organization in its structure? LEARNING OUTCOMES List the properties of life Order the levels of organization of living things Properties of Life All living organisms share several key characteristics or functions: order, sensitivity or response to the environment, reproduction, growth and development, regulation, homeostasis, and energy processing. When viewed together, these characteristics serve to define life. Order 7 Organisms are highly organized, coordinated structures that consist of one or more cells. Even very simple, single-celled organisms are remarkably complex: inside each cell, atoms make up molecules; these in turn make up cell organelles and other cellular inclusions. In multicellular organisms (Figure 1), similar cells form tissues. Figure 1. This female monarch butterfly Tissues, in turn, collaborate to represents a highly organized structure create organs (body structures with consisting of cells, tissues, organs, and organ systems a distinct function). Organs work together to form organ systems. Sensitivity or Response to Stimuli Organisms respond to diverse stimuli. For example, plants can bend toward a source of light, climb on fences and walls, or respond to touch (Figure 2). Even tiny bacteria can move toward or away from chemicals (a process called chemotaxis) or light (phototaxis). Movement toward a stimulus is considered a positive response, while movement away from a stimulus is considered a negative response. Figure 2.The leaves of this sensitive plant (Mimosa pudica) will instantly droop and fold when touched. After a few minutes, Watch this video to see how plants the plant returns to normal. respond to a stimulus—from opening to light, to wrapping a tendril around a branch, to capturing prey. 8 Reproduction Single-celled organisms reproduce by first duplicating their DNA, and then dividing it equally as the cell prepares to divide to form two new cells. Multicellular organisms often produce specialized reproductive germline cells that will form new individuals. When reproduction occurs, genes containing DNA are passed along to an organism’s offspring. These genes ensure that the offspring will belong to the same species and will have similar characteristics, such as size and shape. Growth and Development Organisms grow and develop following specific instructions coded for by their genes. These genes provide instructions that will direct cellular growth and development, ensuring that a species’ young (Figure 3) will grow up to exhibit many of the same characteristics as its parents. Figure 3. Although no two look alike, Regulation these puppies have inherited genes from both parents and share many of the same characteristics. Even the smallest organisms are complex and require multiple regulatory mechanisms to coordinate internal functions, respond to stimuli, and cope with environmental stresses. Two examples of internal functions regulated in an organism are nutrient transport and blood flow. Organs (groups of tissues working together) perform specific functions, such as carrying oxygen throughout the body, removing wastes, delivering nutrients to every cell, and cooling the body. Homeostasis 9 In order to function properly, cells need to have appropriate conditions such as proper temperature, pH, and appropriate concentration 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, Figure 4. Polar bears (Ursus maritimus) through homeostasis (literally, and other mammals living in ice-covered regions maintain their body temperature “steady state”)—the ability of an by generating heat and reducing heat loss organism to maintain constant through thick fur and a dense layer of fat internal conditions. For example, an under their skin. organism needs to regulate body temperature through a process known as thermoregulation. Organisms that live in cold climates, such as the polar bear (Figure 4), have body structures that help them withstand low temperatures and conserve body heat. Structures that aid in this type of insulation include fur, feathers, blubber, and fat. In hot climates, organisms have methods (such as perspiration in humans or panting in dogs) that help them to shed excess body heat. 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 (photosynthesis); others use chemical energy in molecules they take in as food (cellular respiration). 10 Figure 5. The California condor (Gymnogyps californianus) uses chemical energy derived from food to power flight. California condors are an endangered species; this bird has a wing tag that helps biologists identify the individual. Levels of Organization of Living Things Living things are highly organized and structured, following a hierarchy that can be examined on a scale from small to large. The atom is the smallest and most fundamental unit of matter. It consists of a nucleus surrounded by electrons. Two or more atoms are joined together by one or more chemical bonds to form molecule. Many molecules that are biologically important are macromolecules, large molecules that are typically formed by polymerization (a polymer is a large molecule that is made by combining smaller units called monomers, which are simpler than macromolecules). An example of a macromolecule is deoxyribonucleic acid (DNA) (Figure 6), which contains the instructions for the structure and functioning of all living organisms. Some cells contain aggregates of macromolecules surrounded by membranes; these are called organelles. Organelles are small structures that exist within cells. Examples of organelles include mitochondria and chloroplasts, which carry out indispensable functions: mitochondria produce energy to power the cell, while chloroplasts enable green plants to utilize the energy in sunlight to make sugars. All living things are made of cells; the cell itself is the smallest fundamental unit of structure and function in living organisms. (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 the reproductive 11 mechanism of a living cell; only then can they obtain the materials they need to reproduce.) Some organisms consist of a single cell and others are multicellular. Cells are classified as prokaryotic or eukaryotic. Prokaryotes are single- celled or colonial organisms that do not have membrane-bound nuclei or organelles; in contrast, the cells of eukaryotes do have membrane- bound organelles and a membrane- bound nucleus. In most multicellular organisms, Figure 6. All molecules, including this cells combine to make tissues, DNA molecule, are composed of atoms. (credit: “brian0918″/Wikimedia Commons) which are groups of similar cells carrying out similar or related functions. Organs are collections of tissues grouped together performing a common function. Organs are present not only in animals but also in plants. An organ system is a higher level of organization that consists of functionally related organs. Mammals have many organ systems. For instance, the circulatory system transports blood through the body and to and from the lungs; it includes organs such as the heart and blood vessels. 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. All the individuals of a species living within a specific area are collectively called a population. For example, a forest may include many pine trees. All of these pine trees represent the population of 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 community is the sum 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. An ecosystem consists of all the living things in a particular area together 12 with the abiotic, non-living parts of that environment such as nitrogen in the soil or rain water. At the highest level of organization (Figure 7), the biosphere is the collection of all ecosystems, and it represents the zones of life on earth. It includes land, water, and even the atmosphere to a certain extent. Check Your Understanding Answer the question(s) below to see how well you understand the topics covered in the previous section. This short quiz does not count toward your grade in the class, and you can retake it an unlimited number of times. Use this quiz to check your understanding and decide whether to (1) study the previous section further or (2) move on to the next section. 13  PRACTICE QUESTION From a single organelle to the entire biosphere, living organisms are parts of a highly structured hierarchy. 14 Figure 7. The biological levels of organization of living things are shown. From a single organelle to the entire biosphere, living organisms are parts of a highly structured hierarchy. (credit “organelles”: modification of work by Umberto Salvagnin; credit “cells”: modification of work by Bruce Wetzel, Harry Schaefer/ National Cancer Institute; credit “tissues”: modification of work by Kilbad; Fama Clamosa; Mikael Häggström; credit “organs”: modification of work by Mariana Ruiz Villareal; credit “organisms”: modification of 15  work by “Crystal”/Flickr; credit “ecosystems”: modification of work by US Fish and Wildlife Service Headquarters; credit “biosphere”: modification of work by NASA) Which of the following statements is false? a. Tissues exist within organs, which exist within organ systems. b. Communities exist within populations, which exist within ecosystems. c. Organelles exist within cells, which exist within tissues. d. Communities exist within ecosystems, which exist in the biosphere. Answer Statement b is false: populations exist within communities. An interactive or media element has been excluded from this version of the text. You can view it online here: https://courses.lumenlearning.com/wmopen-nmbiology1/?p=1053 Licensing & Attributions CC licensed content, Original Introduction to Characteristics of Life. Authored by: Shelli Carter and Lumen Learning. Provided by: Lumen Learning. License: CC BY: Attribution CC licensed content, Shared previously Biology. Provided by: OpenStax CNX. Located at: http://cnx.org/contents/[email protected]. License: CC BY: Attribution. License Terms: Download for free at http://cnx.org/contents/[email protected] Monarch Butter y. Authored by: Sid Mosdell. Located at: https://www. ickr.com/photos/sidm/4813666686/. License: CC BY: Attribution fresh litter. Authored by: Magalie LAbbe. Located at: https:// ic.kr/p/9yeYXd. License: CC BY-NC: Attribution-NonCommercial Mimosa pudica. Authored by: Frank Vincentz. Located at: https://commons.wikimedia.org/wiki/File:Mimosa_pudica_01_ies.jpg. License: CC BY-SA: Attribution-ShareAlike Polar Bear. Authored by: David. Located at: https:// ic.kr/p/4fsyGe. License: CC BY: Attribution Public domain content Young California condor (Gymnogyps californianus) ready for ight. Provided by: US Fish and Wildlife Service. Located at: https://en.wikipedia.org/wiki/File:California-condor.jpg. License: Public Domain: No Known Copyright TAXONOMY 16 What you’ll learn to do: Describe classi cation and organizational tools biologists use, including modern taxonomy Viewed from space, Earth offers no clues about the diversity of life forms that reside there. The first forms of life on Earth are thought to have been microorganisms that existed for billions of years in the ocean before plants and animals appeared. The mammals, birds, and flowers so familiar to us are all relatively recent, originating 130 to 200 million years ago. Humans have inhabited this planet for only Figure 1. Our planet the last 2.5 million years, and only in the last 200,000 years have humans started looking like we do today. When faced with the remarkable diversity of life, how do we organize the different kinds of organisms so that we can better understand them? As new organisms are discovered every day, biologists continue to seek answers to these and other questions. In this outcome, we will discuss taxonomy, which both demonstrates the vast diversity of life and tries to organize these organisms in a way we can understand. LEARNING OUTCOMES Explain the diversity of life Explain the purpose of phylogenetic trees Explain how relationships are indicated by the binomial naming system 17 The Diversity of Life Biological diversity is the variety of life on earth. This includes all the different plants, animals, and microorganisms; the genes they contain; and the ecosystems they form on land and in water. Biological diversity is constantly changing. It is increased by new genetic variation and reduced by extinction and habitat Figure 2. Life on earth is incredibly degradation. diverse. What Is Biodiversity? Biodiversity refers to the variety of life and its processes, including the variety of living organisms, the genetic differences among them, and the communities and ecosystems in which they occur. Scientists have identified about 1.9 million species alive today. They are divided into the six kingdoms of life shown in Figure 3. Scientists are still discovering new species. Thus, they do not know for sure how many species really exist today. Most estimates range from 5 to 30 million species. Figure 3. Known life on earth. Click for a larger image. VIDEO REVIEW 18  Watch this discussion about biodiversity: An interactive or media element has been excluded from this version of the text. You can view it online here: https://courses.lumenlearning.com/wmopen-nmbiology1/?p=1066 Literally, the word biodiversity means the many different kinds (diversity) of life (bio-), or the number of species in a particular area. Biologists, however, are always alert to levels of organization, and have identified three unique measures of life’s variation: 19  The most precise and specific measure of biodiversity is genetic diversity or genetic variation within a species. This measure of diversity looks at differences among individuals within a population, or at difference across different populations of the same species. The level just broader is species diversity, which best fits the literal translation of biodiversity: the number of different species in a particular ecosystem or on Earth. This type of diversity simply looks at an area and reports what can be found there. At the broadest most encompassing level, we have ecosystem diversity. As Leopold clearly understood, the “cogs and wheels” include not only life but also the land, sea, and air that support life. In ecosystem diversity, biologists look at the many types of functional units formed by living communities interacting with their environments. Although all three levels of diversity are important, the term biodiversity usually refers to species diversity! Scale of Biodiversity Diversity may be measured at different scales. These are three indices used by ecologists: Alpha diversity refers to diversity within a particular area, community or ecosystem, and is measured by counting the number of taxa within the ecosystem (usually species). Beta diversity is species diversity between ecosystems; this involves comparing the number of taxa that are unique to each of the ecosystems. Gamma diversity is a measurement of the overall diversity for different ecosystems within a region. Bene ts of Biodiversity Biodiversity provides us with all of our food. It also provides for many medicines and industrial products, and it has great potential for developing new and improved products for the future. Perhaps most importantly, biological diversity provides and maintains a wide array of 20 ecological “services.” These include provision of clean air and water, soil, food and shelter. The quality—and the continuation— of our life and our economy is dependent on these “services.” AUSTRALIA’S BIOLOGICAL DIVERSITY The long isolation of Australia over much of the last 50 million years and its northward movement have led to the evolution of a distinct biota. Significant features of Australia’s biological diversity include: A high percentage of endemic species (that is, they occur nowhere else): over 80% of flowering Figure 4. The short-beaked echidna is plants endemic to Australia. This animal—along with the platypus and three other species over 80% of land of echidnas—is one of the five surviving mammals species of egg-laying mammals. 88% of reptiles 45% of birds 92% of frogs Wildlife groups of great richness. Australia has an exceptional diversity of lizards in the arid zone, many ground orchids, and a total invertebrate fauna estimated at 200,000 species with more than 4,000 different species of ants alone. Marsupials and monotremes collectively account for about 56% of native terrestrial mammals in Australia. Wildlife of major evolutionary importance. For example, Australia has 12 of the 19 known families of primitive flowering plants, two of which occur nowhere else. Some species, such as the Queensland lungfish and peripatus, have remained relatively unchanged for hundreds of millions of years. Phylogenetic Trees 21 In scientific terms, the evolutionary history and relationship of an organism or group of organisms is called phylogeny. Phylogeny describes the relationships of one organism to others—such as which organisms it is thought to have evolved from, which species it is most closely related to, and so forth. Phylogenetic relationships provide information on shared ancestry but not necessarily on how organisms are similar or different. Phylogenetic Trees Scientists use a tool called a phylogenetic tree to show the evolutionary pathways and connections among organisms. A phylogenetic tree is a diagram used to reflect evolutionary relationships among organisms or groups of organisms. Scientists consider phylogenetic trees to be a hypothesis of the evolutionary past since one cannot go back to confirm the proposed relationships. In other words, a “tree of life” can be constructed to illustrate when different organisms evolved and to show the relationships among different organisms (Figure 5). 22 Figure 5. This phylogenetic tree was constructed by microbiologist Carl Woese (See inset below) using genetic relationships. The tree shows the separation of living organisms into three domains: Bacteria, Archaea, and Eukarya. Bacteria and Archaea are organisms without a nucleus or other organelles surrounded by a membrane and, therefore, are prokaryotes. (credit: modification of work by Eric Gaba) A phylogenetic tree can be read like a map of evolutionary history. Many phylogenetic trees have a single lineage at the base representing a common ancestor. Scientists call such trees rooted, which means there is a single ancestral lineage (typically drawn from the bottom or left) to which all organisms represented in the diagram relate. Notice in the rooted phylogenetic tree that the three domains—Bacteria, Archaea, and Eukarya—diverge from a single point and branch off. The small branch that plants and animals (including humans) occupy in this diagram shows how recent and minuscule these groups are compared with other organisms. Unrooted trees don’t show a common ancestor but do show relationships among species (Figure 6). 23 Figure 6. An unrooted phylogenetic tree CARL WOESE AND THE PHYLOGENETIC TREE 24 In the past, biologists grouped living organisms into five kingdoms: animals, plants, fungi, protists, and bacteria. The organizational scheme was based mainly on physical features, as opposed to physiology, biochemistry, or molecular biology, all of which are used by modern systematics. The pioneering work of American microbiologist Carl Woese in the early 1970s has shown, however, that life on Earth has evolved along three lineages, now called domains—Bacteria, Archaea, and Eukarya. The first two are prokaryotic groups of microbes that lack membrane-enclosed nuclei and organelles. The third domain contains the eukaryotes and includes unicellular microorganisms together with the four original kingdoms (excluding bacteria). Woese defined Archaea as a new domain, and this resulted in a new taxonomic tree (Figure 5). Many organisms belonging to the Archaea domain live under extreme conditions and are called extremophiles. To construct his tree, Woese used genetic relationships rather than similarities based on morphology (shape). Woese’s tree was constructed from comparative sequencing of the genes that are universally distributed, present in every organism, and conserved (meaning that these genes have remained essentially unchanged throughout evolution). Woese’s approach was revolutionary because comparisons of physical features are insufficient to differentiate between the prokaryotes that appear fairly similar in spite of their tremendous biochemical diversity and genetic variability (Figure 7). The comparison of homologous DNA and RNA sequences provided Woese with a sensitive device that revealed the extensive variability of prokaryotes, and which justified the separation of the prokaryotes into two domains: bacteria and archaea. 25 Figure 7. These organisms represent different domains. The (a) bacteria in this micrograph belong to Domain Bacteria, while the (b) extremophiles (not visible) living in this hot vent belong to Domain Archaea. Both the (c) sunflower and (d) lion are part of Domain Eukarya. (credit a: modification of work by Drew March; credit b: modification of work by Steve Jurvetson; credit c: modification of work by Michael Arrighi; credit d: modification of work by Leszek Leszcynski) 26 Taxonomy Taxonomy (which literally means “arrangement law”) is the science of classifying organisms to construct internationally shared classification systems with each organism placed into more and more inclusive groupings. Think about how a grocery store is organized. One large space is divided into departments, such as produce, dairy, and meats. Then each department further divides into aisles, then each aisle into categories and brands, and then finally a single product. This organization from larger to smaller, more specific categories is called a hierarchical system. In the eighteenth century, a scientist named Carl Linnaeus first proposed organizing the known species of organisms into a hierarchical taxonomy. In this system, species that are most similar to each other are put together within a grouping known as a genus. Furthermore, similar genera (the plural of genus) are put together within a family. This grouping continues until all organisms are collected together into groups at the highest level. 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 (Figure 8). 27 Figure 8. This diagram shows the levels of taxonomic hierarchy for a dog, from the broadest category—domain—to the most specific—species. Click for a larger image. The kingdom Animalia stems from the Eukarya domain. For the common dog, the classification levels would be as shown in Figure 8. Therefore, the full name of an organism technically has eight terms. For 28 the dog, it is: Eukarya, Animalia, Chordata, Mammalia, Carnivora, Canidae, Canis, and lupus. Notice that each name is capitalized except for species, and the genus and species names are italicized. Scientists generally refer to an organism only by its genus and species, which is its two-word scientific name, in what is called binomial nomenclature. Each species has a unique binomial nomenclature to allow for proper identification. Therefore, the scientific name of the dog is Canis lupus. It is important that the correct formatting (capitalization and italics) is used when calling an organism by its specific binomial. The name at each level is also called a taxon. In other words, dogs are in order Carnivora. Carnivora is the name of the taxon at the order level; Canidae is the taxon at the family level, and so forth. Organisms also have a common name that people typically use, in this case, dog. Note that the dog is additionally a subspecies: the “familiaris” in Canis lupus familiaris. Subspecies are members of the same species that are capable of mating and reproducing viable offspring, but they are considered separate subspecies due to geographic or behavioral isolation or other factors. Check Your Understanding Answer the question(s) below to see how well you understand the topics covered in the previous section. This short quiz does not count toward your grade in the class, and you can retake it an unlimited number of times. Use this quiz to check your understanding and decide whether to (1) study the previous section further or (2) move on to the next section. An interactive or media element has been excluded from this version of the text. You can view it online here: https://courses.lumenlearning.com/wmopen-nmbiology1/?p=1066 29 Licensing & Attributions CC licensed content, Original Introduction to Taxonomy. Authored by: Shelli Carter and Lumen Learning. Provided by: Lumen Learning. License: CC BY: Attribution CC licensed content, Shared previously Biology. Provided by: OpenStax CNX. Located at: http://cnx.org/contents/[email protected]. License: CC BY: Attribution. License Terms: Download for free at http://cnx.org/contents/[email protected] Biodiversity. Provided by: CK-12. Located at: http://www.ck12.org/biology/Biodiversity/lesson/Biodiversity-BIO/?referrer=featured_content. License: CC BY-NC: Attribution-NonCommercial Conserving Australia's biological diversity. Provided by: Australian Government, Department of the Environment and Energy. Located at: https://www.environment.gov.au/sustainability/education/publications/conserving-australias-biological-diversity-teachers-notes. License: CC BY: Attribution Long-beaked Echidna. Authored by: Jaganath. Located at: https://commons.wikimedia.org/wiki/File:Long-beakedEchidna.jpg. License: CC BY-SA: Attribution-ShareAlike Scale of Biodiversity. Provided by: Wikipedia. Located at: https://en.wikipedia.org/wiki/Measurement_of_biodiversity#Scale. License: CC BY- SA: Attribution-ShareAlike Taxonomic hierarchy of the domestic dog. Authored by: Veronica Amaku. Provided by: Houston Community College. Located at: http://www.hccs.edu/. License: CC BY-SA: Attribution-ShareAlike dog. Authored by: ccbarr. Located at: https:// ic.kr/p/dAsmE. License: CC BY: Attribution Coyote. Authored by: Ariel Matzuk. Located at: https:// ic.kr/p/7HfK28. License: CC BY: Attribution Fox. Authored by: Jans Canon. Located at: https:// ic.kr/p/bw9swB. License: CC BY: Attribution Lion at Franklin Park Zoo in Boston. Authored by: Corey Leopold. Located at: https:// ic.kr/p/4Zu4fA. License: CC BY: Attribution HUMAN WOMAN. Authored by: matt smith. Located at: https:// ic.kr/p/cantD. License: CC BY-SA: Attribution-ShareAlike Coiled Snake. Authored by: Seattleye. Located at: https:// ic.kr/p/4VK5ud. License: CC BY: Attribution Paramecium / Trichocysten - Opalblau. Authored by: Picturepest. Located at: https:// ic.kr/p/dqbAxg. License: CC BY-SA: Attribution- ShareAlike Tree. Authored by: Sheila in Moonducks. Located at: https:// ic.kr/p/8Jtz9Q. License: CC BY-SA: Attribution-ShareAlike Fungi. Authored by: Nick Bramhall. Located at: https:// ic.kr/p/8KLrgq. License: CC BY-SA: Attribution-ShareAlike Biodiversity Diagram. Provided by: Alberta Biodiversity Monitoring Institute (ABMI). Located at: https://www.abmi.ca/home/biodiversity/what-is-biodiversity.html. License: CC BY: Attribution All rights reserved content Biodiversity - from The Wild Classroom. Authored by: Rob & Jonas Filmmaking Tips. Located at: https://youtu.be/vGxJArebKoc. License: All Rights Reserved. License Terms: Standard YouTube License Public domain content EPIC Earth Image. Provided by: NASA. Located at: http://www.nasa.gov/image-feature/nasa-captures-epic-earth-image. License: Public Domain: No Known Copyright Collapsed tree Labels. Authored by: TimVickers, SVG conversion by User_A1. Located at: https://commons.wikimedia.org/wiki/File:CollapsedtreeLabels-simpli ed.svg. License: Public Domain: No Known Copyright INTRODUCTION TO THE BRANCHES OF BIOLOGY What you’ll learn to do: Identify the main branches of biology 30 While this course provides a broad introduction to the science of biology, higher level study of the subject quickly breaks down into a vast number of sub-disciplines (e.g., microbiology, immunology, neurobiology, anatomy and physiology). Specialists in these different fields of biology include doctors, nutritionists, pharmacologists, botanists, astrobiologists, and many many more. Figure 1 In this section, we’ll learn about the different paths you can take as you study the science of life. LEARNING OUTCOMES Identify the main branches of biology The scope of biology is broad and therefore contains many branches and sub-disciplines. Biologists may pursue one of those sub-disciplines and work in a more focused field. For instance, molecular biology and biochemistry study biological processes at the molecular and chemical level, including interactions among molecules such as DNA, RNA, and proteins, as well as the way they are regulated. Microbiology, the study 31 of microorganisms, is the study of the structure and function of single- celled organisms. It is quite a broad branch itself, and depending on the subject of study, there are also microbial physiologists, ecologists, and geneticists, among others. FORENSIC SCIENCE Forensic science is the application of science to answer questions related to the law. Biologists as well as chemists and biochemists can be forensic scientists. Forensic scientists provide scientific evidence for use in courts, and their job involves examining trace materials associated with crimes. Interest in Figure 2. This forensic scientist works in a forensic science has increased in DNA extraction room at the U.S. Army the last few years, possibly Criminal Investigation Laboratory at Fort Gillem, GA. (credit: United States Army because of popular television CID Command Public Affairs) shows that feature forensic scientists on the job. Also, the development of molecular techniques and the establishment of DNA databases have expanded the types of work that forensic scientists can do. Their job activities are primarily related to crimes against people such as murder, rape, and assault. Their work involves analyzing samples such as hair, blood, and other body fluids and also processing DNA (Figure 2) found in many different environments and materials. Forensic scientists also analyze other biological evidence left at crime scenes, such as insect larvae or pollen grains. Students who want to pursue careers in forensic science will most likely be required to take chemistry and biology courses as well as some intensive math courses. Another field of biological study, neurobiology, studies the biology of the nervous system, and although it is considered a branch of biology, it is also recognized as an interdisciplinary field of study known as neuroscience. Because of its interdisciplinary nature, this sub-discipline 32 studies different functions of the nervous system using molecular, cellular, developmental, medical, and computational approaches. Paleontology, another branch of biology, uses fossils to study life’s history (Figure 3). Zoology and botany are the study of animals and plants, respectively. Biologists can also specialize as biotechnologists, ecologists, or physiologists, to name just a few areas. Biotechnologists apply the knowledge of biology to create useful products. Ecologists study Figure 3. Researchers work on excavating dinosaur fossils at a site in Castellón, the interactions of organisms in Spain. (credit: Mario Modesto) their environments. Physiologists study the workings of cells, tissues and organs. This is just a small sample of the many fields that biologists can pursue. From our own bodies to the world we live in, discoveries in biology can affect us in very direct and important ways. We depend on these discoveries for our health, our food sources, and the benefits provided by our ecosystem. Because of this, knowledge of biology can benefit us in making decisions in our day-to-day lives. The development of technology in the twentieth century that continues today, particularly the technology to describe and manipulate the genetic material, DNA, has transformed biology. This transformation will allow biologists to continue to understand the history of life in greater detail, how the human body works, our human origins, and how humans can survive as a species on this planet despite the stresses caused by our increasing numbers. Biologists continue to decipher huge mysteries about life suggesting that we have only begun to understand life on the planet, its history, and our relationship to it. For this and other reasons, the knowledge of biology gained through this textbook and other printed and electronic media should be a benefit in whichever field you enter. Check Your Understanding 33 Answer the question(s) below to see how well you understand the topics covered in the previous section. This short quiz does not count toward your grade in the class, and you can retake it an unlimited number of times. Use this quiz to check your understanding and decide whether to (1) study the previous section further or (2) move on to the next section. An interactive or media element has been excluded from this version of the text. You can view it online here: https://courses.lumenlearning.com/wmopen-nmbiology1/?p=5054 Licensing & Attributions CC licensed content, Original Introduction to the Branches of Biology. Provided by: Lumen Learning. License: CC BY: Attribution CC licensed content, Shared previously Upulie Divisekera. Authored by: Department of Foreign A airs and Trade. Located at: https:// ic.kr/p/SvZLj9. License: CC BY: Attribution Biology. Provided by: OpenStax CNX. Located at: http://cnx.org/contents/[email protected]. License: CC BY: Attribution. License Terms: Download for free at http://cnx.org/contents/[email protected] THE PROCESS OF SCIENCE What you’ll learn to do: Describe biology as a science and identify the key components of scienti c inquiry Like geology, physics, and chemistry, biology is a science that gathers knowledge about the natural world. Specifically, biology is the study of life. The discoveries of biology are made by a community of researchers who work individually and together using agreed-on 34 methods. In this sense, biology, like all sciences, is a social enterprise like politics or the arts. The methods of science include careful observation, record keeping, logical and mathematical reasoning, experimentation, and submitting conclusions to the scrutiny of others. Science also requires considerable imagination and creativity; a well-designed Figure 1. Biologists may choose to study experiment is commonly described Escherichia coli (E. coli), a bacterium that as elegant, or beautiful. Like is a normal resident of our digestive tracts but which is also sometimes responsible politics, science has considerable for disease outbreaks. In this micrograph, practical implications and some the bacterium is visualized using a science is dedicated to practical scanning electron microscope and digital applications, such as the prevention colorization. (credit: Eric Erbe; digital colorization by Christopher Pooley, of disease (see Figure 1). Other USDA-ARS) science proceeds largely motivated by curiosity. Whatever its goal, there is no doubt that science, including biology, has transformed human existence and will continue to do so. Figure 2. Formerly called blue-green algae, the (a) cyanobacteria seen through a light microscope are some of Earth’s oldest life forms. These (b) stromatolites along the shores of Lake Thetis in Western Australia are ancient structures formed by the layering of cyanobacteria in shallow waters. (credit a: modification of work by NASA; scale-bar data from Matt Russell; credit b: modification of work by Ruth Ellison) 35  LEARNING OUTCOMES Compare inductive reasoning with deductive reasoning Describe the process of scientific inquiry Describe the goals of basic science and applied science Scienti c Inquiry One thing is common to all forms of science: an ultimate goal “to know.” 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. 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. 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 forecast specific results. From those general principles, a scientist can extrapolate and predict the specific results that would be valid as long as the general principles are valid. 36 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. 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, 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. Hypothesis Testing Biologists study the living world by posing questions about it and seeking science-based responses. This approach is common to other sciences as well and is often referred to as the scientific method. The scientific method was used even in ancient times, but it was first documented by England’s Sir Francis Bacon (1561–1626) (Figure 3), who set up inductive methods for scientific inquiry. The scientific method is not exclusively used by biologists but can be applied to almost anything as a logical problem-solving method. The scientific process typically starts with an observation (often a problem to be solved) that leads to a question. Let’s think about a simple problem that starts with an observation and apply the scientific method to solve the problem. One Monday morning, a student arrives at class and quickly discovers that the classroom is too warm. That is an observation that also describes a problem: the classroom is too warm. The student then asks a question: “Why is the classroom so warm?” 37 Recall that a hypothesis is a suggested explanation that can be tested. To solve a problem, several hypotheses may be proposed. For example, one hypothesis might be, “The classroom is warm because no one turned on the air conditioning.” But there could be other responses to the question, and therefore other hypotheses may be proposed. A second hypothesis might be, “The classroom is warm because there is a power failure, and so the air conditioning doesn’t work.” Once a hypothesis has been selected, a prediction may be made. A prediction is similar to a Figure 3. Sir Francis Bacon is credited hypothesis but it typically has the with being the first to document the scientific method. format “If... then....” For example, the prediction for the first hypothesis might be, “If the student turns on the air conditioning, then the classroom will no longer be too warm.” 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. An example of an unfalsifiable hypothesis is “Botticelli’s Birth of Venus is beautiful.” There is no experiment that might show this statement to be false. 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. Science does not deal in proofs like mathematics. If an experiment fails to disprove a hypothesis, then we find support for that explanation, but this is not to say that down the road a better explanation will not be found, or a more carefully designed experiment will be found to falsify the hypothesis. 38 Scientific inquiry has not displaced faith, intuition, and dreams. These traditions and ways of knowing have emotional value and provide moral guidance to many people. But hunches, feelings, deep convictions, old traditions, or dreams cannot be accepted directly as scientifically valid. Instead, science limits itself to ideas that can be tested through verifiable observations. Supernatural claims that events are caused by ghosts, devils, God, or other spiritual entities cannot be tested in this way. 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. A control is a part of the experiment that does not change. Look for the variables and controls in the example that follows. As a simple example, an experiment might be conducted to test the hypothesis that phosphate limits the growth of algae in freshwater ponds. A series of artificial ponds are filled with water and half of them are treated by adding phosphate each week, while the other half are treated by adding a salt that is known not to be used by algae. The variable here is the phosphate (or lack of phosphate), the experimental or treatment cases are the ponds with added phosphate and the control ponds are those with something inert added, such as the salt. Just adding something is also a control against the possibility that adding extra matter to the pond has an effect. If the treated ponds show lesser growth of algae, then we have found support for our hypothesis. If they do not, then we reject our hypothesis. Be aware that rejecting one hypothesis does not determine whether or not the other hypotheses can be accepted; it simply eliminates one hypothesis that is not valid (Figure 4). Using the scientific method, the hypotheses that are inconsistent with experimental data are rejected. In practice, the scientific method is not as rigid and structured as it might at first appear. Sometimes an experiment leads to conclusions that favor a change in approach; often, an experiment brings entirely new scientific questions to the puzzle. Many times, science does not operate in a linear fashion; instead, scientists continually draw inferences and make generalizations, finding patterns as their research proceeds. Scientific reasoning is more complex than the scientific method alone suggests. 39  PRACTICE QUESTION Your friend sees this image of a circle of mushrooms and excitedly tells you it was caused by fairies dancing in a circle on the grass the night before. Can your friend’s explanation be studied using the process of science? Answer In theory, you might try to observe the fairies. But fairies are magical or supernatural beings. We have never observed them using any verifiable method, so scientists agree that they cannot be studied using scientific tools. Instead, science has an explanation supported by strong evidence: “fairy rings” result when a single colony of fungus spreads out into good habitat over a period of many years. The core area is clear of mushrooms because the soil nutrients have been partly depleted there. This idea can be evaluated with repeated observations over time using chemical soil tests and other verifiable measurements. Basic and Applied Science The scientific community has been debating for the last few decades about the value of different types of science. Is it valuable to pursue science for the sake of simply gaining knowledge, or does scientific 40 PRACTICE QUESTION 41 42  Figure 4. The scientific method is a series of defined steps that include experiments and careful observation. If a hypothesis is not supported by data, a new hypothesis can be proposed. In the example below, the scientific method is used to solve an everyday problem. Which part in the example below is the hypothesis? Which is the prediction? Based on the results of the experiment, is the hypothesis supported? If it is not supported, propose some alternative hypotheses. 1. My toaster doesn’t toast my bread. 2. Why doesn’t my toaster work? 3. There is something wrong with the electrical outlet. 4. If something is wrong with the outlet, my coffeemaker also won’t work when plugged into it. 5. I plug my coffeemaker into the outlet. 6. My coffeemaker works. Answer The hypothesis is #3 (there is something wrong with the electrical outlet), and the prediction is #4 (if something is wrong with the outlet, then the coffeemaker also won’t work when plugged into the outlet). The original hypothesis is not supported, as the coffee maker works when plugged into the outlet. Alternative hypotheses may include (1) the toaster might be broken or (2) the toaster wasn’t turned on. knowledge only have worth if we can apply it to solving a specific problem or bettering our lives? This question focuses on the differences between two types of science: basic science and applied 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. 43 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. Some individuals may perceive applied science as “useful” and basic science as “useless.” A question these people might pose to a scientist advocating knowledge acquisition would be, “What for?” A careful look at the history of science, however, reveals that basic knowledge has resulted in many remarkable applications of great value. Many scientists think that a basic understanding of science is necessary before an application is developed; therefore, applied science relies on the results generated through basic science. Other scientists think that it is time to move on from basic science and instead to find solutions to actual problems. Both approaches are valid. It is true that there are problems that demand immediate attention; however, few solutions would be found without the help of the knowledge generated through basic science. One example of how basic and applied science can work together to solve practical problems occurred after the discovery of DNA structure led to an understanding of the molecular mechanisms governing DNA replication. Strands of DNA, unique in every human, are found in our cells, where they provide the instructions necessary for life. During DNA replication, new copies of DNA are made, shortly before a cell divides to form new cells. Understanding the mechanisms of DNA replication enabled scientists to develop laboratory techniques that are now used to identify genetic diseases, pinpoint individuals who were at a crime scene, and determine paternity. Without basic science, it is unlikely that applied science would exist. Another 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; an individual’s complete collection of genes is his or her genome.) Other organisms have also been studied as part of this project to gain a better understanding of human chromosomes. The 44 Human Genome Project (Figure 5) 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. While research efforts in both basic science and applied science are usually carefully planned, it is important to note that some discoveries are made by serendipity, that is, by means of a Figure 5. The Human Genome Project was a 13-year collaborative effort among fortunate accident or a lucky researchers working in several different surprise. Penicillin was discovered fields of science. The project was when biologist Alexander Fleming completed in 2003. (credit: the U.S. Department of Energy Genome accidentally left a petri dish of Programs) Staphylococcus bacteria open. An unwanted mold grew, killing the bacteria. The mold turned out to be Penicillium, and a new antibiotic was discovered. Even in the highly organized world of science, luck— when combined with an observant, curious mind—can lead to unexpected breakthroughs. Reporting Scienti c Work Whether scientific research is basic science or applied science, scientists must share their findings for other researchers to expand and build upon their discoveries. Communication and collaboration within and between sub disciplines of science are key to the advancement of knowledge in science. For this reason, an important aspect of a scientist’s work is disseminating results and communicating with peers. Scientists can share results by presenting them at a scientific meeting or conference, but this approach can reach only the limited few who are present. Instead, most scientists present their results in peer-reviewed articles that are published in scientific journals. Peer-reviewed articles 45 are scientific papers that are reviewed by a scientist’s colleagues, or peers. These colleagues are qualified individuals, often experts in the same research area, who judge whether or not the scientist’s work is suitable for publication. The process of peer review helps to ensure that the research described in a scientific paper or grant proposal is original, significant, logical, and thorough. Grant proposals, which are requests for research funding, are also subject to peer review. Scientists publish their work so other scientists can reproduce their experiments under similar or different conditions to expand on the findings. The experimental results must be consistent with the findings of other scientists. There are many journals and the popular press that do not use a peer- review system. A large number of online open-access journals, journals with articles available without cost, are now available many of which use rigorous peer-review systems, but some of which do not. Results of any studies published in these forums without peer review are not reliable and should not form the basis for other scientific work. In one exception, journals may allow a researcher to cite a personal communication from another researcher about unpublished results with the cited author’s permission. Summary Biology is the science that studies living organisms and their interactions with one another and their environments. Science attempts to describe and understand the nature of the universe in whole or in part. Science has many fields; those fields related to the physical world and its phenomena are considered natural sciences. A hypothesis is a tentative explanation for an observation. A scientific theory is a well-tested and consistently verified explanation for a set of observations or phenomena. A scientific law is a description, often in the form of a mathematical formula, of the behavior of an aspect of nature under certain circumstances. Two types of logical reasoning are used in science. Inductive reasoning uses results to produce general scientific principles. Deductive reasoning is a form of logical thinking that predicts results by applying general principles. The common thread 46 throughout scientific research is the use of the scientific method. Scientists present their results in peer-reviewed scientific papers published in scientific journals. Science can be basic or applied. The main goal of basic science is to expand knowledge without any expectation of short-term practical application of that knowledge. The primary goal of applied research, however, is to solve practical problems. PRACTICE QUESTIONS A suggested and testable explanation for an event is called a ________. a. hypothesis b. variable c. theory d. control Answer A suggested and testable explanation for an event is called a hypothesis. Give an example of how applied science has had a direct effect on your daily life. Answer Answers will vary. One example of how applied science has had a direct effect on daily life is the presence of vaccines. Vaccines to prevent diseases such polio, measles, tetanus, and even the influenza affect daily life by contributing to individual and societal health. Check Your Understanding Answer the question(s) below to see how well you understand the topics covered in the previous section. This short quiz does not count toward your grade in the class, and you can retake it an unlimited number of times. 47 Use this quiz to check your understanding and decide whether to (1) study the previous section further or (2) move on to the next section. An interactive or media element has been excluded from this version of the text. You can view it online here: https://courses.lumenlearning.com/wmopen-nmbiology1/?p=4638 Licensing & Attributions CC licensed content, Shared previously Concepts of Biology. Provided by: OpenStax CNX. Located at: http://cnx.org/contents/[email protected]. License: CC BY: Attribution. License Terms: Download for free at http://cnx.org/contents/[email protected] Practice Question (Scienti c Inquiry). Provided by: Open Learning Initiative. Located at: https://oli.cmu.edu/jcourse/workbook/activity/page? context=434a5c2680020ca6017c03488572e0f8. Project: Introduction to Biology (Open + Free). License: CC BY-NC-SA: Attribution- NonCommercial-ShareAlike PUTTING IT TOGETHER: INTRODUCTION TO BIOLOGY Biology is the study of life. As we’ve learned, this field covers a broad scope of subjects. As you progress through this course, you’ll gain the knowledge you need to make informed decisions. Let’s think back to the articles Cristina encountered at the beginning of this module: how could a knowledge of biological principle help with her understanding of each article? THINK BACK Cristina read an article about some of the world’s weirdest animals. By learning about evolution and natural selection, Cristina could begin to see the different evolutionary reasons behind the extreme features some animals have. For example, the aye-aye, a mammal native to Madagascar, has evolved to have an extra long middle finger, which it 48  can use to dig grubs out of trees. We’ll learn more about how these types of traits are selected for in Module 12: Theory of Evolution. The next article Cristina read talked about GMOs (genetically modified organisms) and the risks they have. In order to truly understand potential risks of genetically modified foods, Cristina will need to first understand the science behind these foods. How are GMOs created? We’ll learn more about this in the Module 13: Modern Biology. Cristina then looked at an article about the paleo diet. In order to survive, humans require specific nutrients. While we won’t get into too much depth about nutrition in this course, we will learn about different biological macromolecules in Module 3: Important Biological Macromolecules. These macromolecules include categories you may recognize, like proteins, lipids (more commonly called fats), and carbohydrates. In that module, we’ll learn about the roles these molecules play in our bodies—we’ll learn the essential functions they perform. With this knowledge, Cristina could better decide what she should or shouldn’t remove from her diet. As you can see in Cristina’s example, biology is all around us—after all, you’re a living human being! In this course, we’ll learn about key biological principles that can help you live your life the best you can. Licensing & Attributions CC licensed content, Original Putting It Together: Introduction to Biology. Authored by: Shelli Carter and Lumen Learning. Provided by: Lumen Learning. License: CC BY: Attribution 49