BIO101 General Biology 1 PDF

NATIONAL OPEN UNIVERSITY OF NIGERIA FACULTY OF SCIENCES COURSE CODE: BIO101 COURSE TITLE: GENERAL BIOLOGY 1 1 Course Code & Course Title: BIO101: General Biology 1 Course Team Course Reviewer: Prof. Mohammed Bello Abdullahi Federal University, Kashere-Gombe Reviewed Content Editor: Dr. Maureen N. Chukwu National Open University of Nigeria Abuja Course Coordinator: Dr. Maureen N. Chukwu Department of Biological Sciences National Open University of Nigeria Reviewed: 2023 National Open University of Nigeria 2 © 2023 by NOUN Press National Open University of Nigeria Headquarters University Village Plot 91, Cadastral Zone Nnamdi Azikiwe Expressway Jabi, Abuja Lagos Office National Open University of Nigeria 14/16 Ahmadu Bello Way Victoria Island Lagos e-mail: URL: www.nou.edu.ng Published by National Open University of Nigeria Printed 2017 Reviewed 2023 All Rights Reserved 3 Course Guide Introduction GENERAL BIOLOGY I is a one semester, 16 Units course. It will be suitable to all students to take towards the core module of B.Sc. (Hons) Biological Sciences. It will also be suitable as an elective course for any student in Faculty of Sciences who does not want to complete an NOU qualification but want to learn about Biology. The course involves the study of Cell structure and organization, functions of cellular organelles, characteristics and classification of living things, chromosomes, genes their relationships and importance, general reproduction, interrelationships of organisms (competitions, parasitism, predation, symbiosis, commensalisms, mutualism, saprophytism); heredity and evolution (introduction to Darwinism and Lamarkism, Mendelian laws, explanation of key genetic terms), elements of ecology and types of habitat. Course Competencies This course aims to enable you to know/understand the basic concepts of ecology, life support and ecosystem. It will guide your understanding of various natural phenomena in the planet earth. Course Objectives The Comprehensive Objectives of the Course as a whole are to; 1. Explain cell structure and organizations, 2. Summarize functions of cellular organelles 3. Characterize living organisms and state their general reproduction 4. Describe the interrelationship that exists between organisms 5. Discuss the concept of heredity and evolution 6. Describe the basic elements of ecology and enumerate habitat types and their characteristics. Working Through this Course To successfully complete this course, you are required to read each study unit, read the textbooks and other materials provided. Reading the reference materials can also be of great assistance. Each unit has self –assessment exercise which you are advised to do. There will be a final examination at the end of the course. The course should take you about 8 weeks to complete. This course guide provides you with all the components of the course, how to go about studying and how you should allocate your time to each unit so as to finish on time and successfully Study Units The study units in this course are given below: BIO 101 GENERAL BIOLOGY I (2 UNITS) MODULE 1: INTRODUCTION TO BIOLOGY 4 Unit 1 Properties of Life Unit 2: The Diversity of life and its organization Unit 3: Introduction to Biological Inquiry Unit 4: Scientific Inquiry method Unit 5: Microscopy and the Cell Theory MODULE 2: STRUCTURE AND FUNCTIONS OF THE CELL Unit 1: Cell and Cell Components Unit 2: Cells Communication Unit 3: Tissues, Organs and Organ Systems Unit 4: Characteristics and Classification of Living Things Unit 5: The Study of Genes and Chromosomes Unit 6: Reproduction Process and Life cycles MODULE 3: INTERRELATIONSHIP BETWEEN ORGANISMS Unit 1: Interrelationship between organisms Unit 2: Heredity and Variation Unit 3: Introduction to Evolution Unit 4: Natural selection Unit 5: Elements of Ecology References and Further Readings You would be required to read the recommended references and textbooks as provided in each unit of the course. Presentation Schedule There is a time-table prepared for the early and timely completion and submissions of your TMAs as well as attending the tutorial classes. You are required to submit all your assignments by the stipulated date and time. Avoid falling behind the schedule time. Assessment There are three aspects to the assessment of this course. The first one is the in-text questions and the second is self-assessment exercises, while the third is the written examination or the examination to be taken at the end of the course. Review the exercises or activities in the unit by applying the information and knowledge you acquired during the course. The work submitted to your tutor for assessment will account for 30% of your total work. At the end of this course, you will have to sit for a final or end of course examination of about a two-hour duration and this will account for 70% of your total course mark. 5 How to get the Most from the Course In this course, you have the course units and a course guide. The course guide will tell you briefly what the course is all about. It is a general overview of the course materials you will be using and how to use those materials. It also helps you to allocate the appropriate time to each unit so that you can successfully complete the course within the stipulated time limit. The course guide also helps you to know how to go about your in-text questions and Self- assessment questions which will form part of your overall assessment at the end of the course. Also, there will be tutorial classes that are related to this course, where you can interact with your facilitators and other students. Please I encourage you to attend these tutorial classes. This course exposes you to Introductory Ecology, a sub-discipline and very interesting field of Biological Sciences. Online Facilitation Eight weeks are provided for tutorials for this course. You will be notified of the dates, times and location for these tutorial classes. As soon as you are allocated a tutorial group, the name and phone number of your facilitator will be given to you. The duties of your facilitator is to monitor your progress and provide any necessary assistance you need. Do not delay to contact your facilitator by telephone or e-mail for necessary assistance if You do not understand any part of the study in the course material. You have difficulty with the self-assessment activities. You have a problem or question with an assignment or with the grading of the assignment. It is important and necessary you attend the tutorial classes because this is the only chance to have face to face contact with your facilitator and to ask questions which will be answered instantly. It is also a period where you can point out any problem encountered in the course of your study. Course Information Course Code: BIO 101 Course Title: GENERAL BIOLOGY I Credit Unit: 2 Course Status: COMPULSORY Course Blub: This course is designed to enable the students to understand the basic concepts of ecology, life support and ecosystem. It will also guide their understanding of various natural phenomena in the planet earth. Semester: 2 SEMESTERS Course Duration: 13 WEEKS Required Hours for Study: 65 hours Ice Breaker Prof. Mohammed Bello Abdullahi is a Professor of Biology (Biodiversity and Environmental Management) in the Department of Biological Sciences, Federal University, Kashere-Gombe. He has been briefly in the Department of Biological Sciences, National Open University of Nigeria from 2017-2021 participating in all academic activities in the Department; examining, moderating 6 and facilitating courses such as; BIO101; BIO202; BIO204; BIO304 and BIO412, and seminars and practicals. Prof. Abdullahi's research interest covers phytosociology, climate change, ecological economics, ethnobotany, plant physiology, biodiversity and environmental management, and environmental toxicology. 7 Module 1: Introduction to Biology Module Structure In this module we will discuss about the properties, diversity and organization of life and the scientific method of inquiry: Unit 1 Properties of Life Unit 2: The Diversity of life and its organization Unit 3: Introduction to Biological Inquiry Unit 4: Scientific Inquiry method Unit 5: Microscopy and the Cell Theory Glossary End of the module Questions Module 1: Introduction to Biology Unit 1 Properties of Life Unit Structure 1.1 Introduction 1.2 Intended Learning Outcomes (ILOs) 1.3 The Study of Biology 1.4 The origin and nature of life 1.5 Properties of Life 1.6 Summary 1.7 References/Further Readings/Web Sources 1.8 Possible Answers to Self-Assessment Exercises 1.1 Introduction Biology is the science of life. All living organisms share several key properties such as order, sensitivity or response to stimuli, reproduction, adaptation, growth and development, regulation, homeostasis, and energy processing. Living things are highly organized following a hierarchy that includes atoms, molecules, organelles, cells, tissues, organs, and organ systems. Organisms, in turn, are grouped as populations, communities, ecosystems, and the biosphere. 1.2 Intended Learning Outcomes (ILOs) By the end of this unit, you will be able to: Define Biology Trace the origin of life Identify and describe the properties of life 1.3 The Study of Biology Earth provides few hints about the variety of life forms that inhabit it when viewed from space. Microorganisms are assumed to have been the first life forms on Earth, existing for billions of years before the emergence of plants and animals. Our familiar mammals, birds, and flowers are 8 all quite recent, having evolved 130 to 200 million years ago. Only in the last 300,000 years have humans begun to resemble the creatures we are today, despite the fact that humans have only been on this planet for the past 2.5 million years. The science that examines life is called Biology. What is life, exactly? Although it may seem like a frivolous question with a simple solution, it is difficult to define life. For instance, the study of viruses, which share some traits with living things but not all of them, is one area of Biology called virology. Viruses do not fit the criteria that scientists use to define life, despite the fact that they may assault living things, spread diseases, and even reproduce. In the past, the study of living things was limited to fields of pure science, such as botany and zoology, which together make up Biology. However, as time went on, other branches emerged. New technologies emerged in both applied and pure domains, giving rise to a highly expansive concept of science known as biological sciences. The field of biological sciences spans a wide range of topics, from the intricate interactions of chemical elements within living cells to the expansive ideas of ecosystems and planetary environmental changes. Additionally, it is interested in the physical traits and actions of both modern and extinct species. How did they come into being, and what relationships do they have with one another and their surroundings? The biological sciences deal with a close examination of the inner workings of the human brain, the make-up of our genes, and even how our reproductive system functions. Four problems have plagued biology from its earliest days: What characteristics unify things to be considered "alive"? How do the different living things work? How do we organise the various types of organisms so that we can better understand them in the face of the astounding diversity of life? And finally, how did this diversity develop and how is it maintaining itself is what biologists eventually aim to understand. Biologists are constantly looking for solutions to these and other issues as new creatures are found every day. Biology is the study of living things as a result. Because of this, biology is sometimes referred to as "life science." The term "systematic study of living beings or study of nature" refers to the biological sciences. The main focus of teaching life science is to enlighten students on the most recent advancements being made worldwide in the biological sciences. What are the four problems that plagued biology from its earliest days? Self-Assessment Exercises 1 1. What are the first forms of life that appeared on planet earth? 2. How many years ago did humans starts to inhibit the earth? 1.4 The Origin and Nature of Life The origin or emergence of life is one of the biggest and most significant emergent phenomena. Science is still divided on the enigma of life's beginning. It is difficult to give a definitive response to the question "what is life?" since we truly want to know why it exists. To put it another way, "we are really asking, in physical terms, why a given material system is an organism and not anything else." In order to respond to this why question, we must comprehend the potential origins of life. There are numerous hypotheses on the beginning of life. These various theories regarding the origin of life are highlighted in the following few sections. The following series of occurrences have occurred during the evolution of life on Earth. Single-celled organisms were the most basic species to first exhibit signs of life. These gave rise to more advanced, multicellular creatures. More cells exhibited cellular specialisation, meaning that some cells within the multicellular organism carried out certain activities, which meant that becoming more complex meant more than 9 just an increase in cell quantity. The evolution of organisms through millions or perhaps billions of years gave rise to the living entities we now refer to as plants and animals. Since most geologists, paleontologists, biologists, and even theologians agree on this basic timeline of events, one would infer that Moses, Aristotle, and Darwin were all sharp observers and naturalists who were capable of logically determining the most likely creation story. Most Scientists agree that our solar system formed around 4.5 billion years ago, and that time has passed since then. People who hold the six- day creationism theory are frequently referred to as creationists. Their approach to research is predicated on the idea that the Bible should be taken as a perfectly accurate account of everything it discusses. On the other side, Scientists apply what they refer to as the scientific method, which enables them to test theories and hypotheses and to create concepts and ideas. The origin of life on earth has been the subject of numerous explanations over the years. As a result, these theories each propose a different explanation for how life might have originated. Here are a few of them: 1. Idea of Special Creation: According to this theory, God, the All-Powerful, created all the many forms of life that exist today on planet Earth. Hypothesis of Spontaneous Generation: According to this theory, any type of non-living material could unexpectedly and spontaneously give rise to a living organism. Aristotle, a Greek philosopher, was one of the ardent supporters of spontaneous creation (384-322 BC). 2. The notion of catastrophe is merely a special case of the theory of special creation. It claims that God has created life on earth in several ways, each of which was preceded by a disaster brought on by a geological disturbance of some kind. This hypothesis holds that since every catastrophe wiped out all existing life, every new life form that was created was distinct from the preceding ones. 3. Cosmozoic Theory (Theory of Panspermia): In accordance with this theory, some organisms' highly resistant spores travelled to Earth from other heavenly bodies like meteorites. This idea was proposed by Richter in 1865 and supported by Arrhenius (1908) and other contemporary Scientists. The theory did not gain any support. This theory lacks evidence, hence it was discarded. 4. Theory of Chemical Evolution: This theory is also known as the physical-chemical hypothesis or the materialistic theory. According to this view, the chemical evolution that led to the origin of life on Earth probably took place over the course of 3.8 billion years. Two Scientists separately proposed this theory: A.I. Oparin, a Russian Scientist, in 1923 and J.B.S. Haldane, an English Scientist, in 1928. How do we best refer to the theory of physical-chemical hypothesis or the materialistic theory in Biology? Self-Assessment Exercises 2 1. What are the four prominent theories on the origin of life? 2. What is the thrust of the theory of Chemical Evolution? 1.5 Properties of Life All groups of living organisms share several key characteristics or functions: order, sensitivity or response to stimuli, reproduction, adaptation, growth and development, regulation/homeostasis, and energy processing. When viewed together, these eight characteristics serve to define life. Order Cells make up organisms, which are highly organised structures. It is amazing how intricate even extremely basic, single-celled organisms are. Molecules are made up of atoms inside each cell. Organelles or cell components are created from these. Multicellular creatures, which can have millions of individual cells, have an advantage over single-celled organisms in that they can 10 specialise their cells to carry out particular tasks and even sacrifice them in some circumstances for the benefit of the organism as a whole. How these specialised cells in creatures like toads combine to generate organs like the heart, lung, or skin. Sensitivity or Response to Stimuli Organisms react to a variety of stimuli. For instance, plants might sway in the direction of a light source or react to touch. Even very little bacteria can move in response to chemicals or light (a process known as chemotaxis) (phototaxis). Moving away from a stimulus is regarded as a negative response, but moving toward it is regarded as a good response. The plant returns to normal after a short while. Reproduction The genetic material, or DNA, of single-celled organisms is first duplicated, and then it is divided equally when the cell gets ready to divide into two new cells. Numerous species with more than one cell, or multicellular organisms, create specialised reproductive cells that give rise to new individuals. DNA containing genes is transferred to an organism's progeny during reproduction. Because of these genes, the progeny will be of the same species as the parents and will share traits like fur colour and blood type with them. Adaptation Every living thing displays a "fit" to its surroundings. This adaptability, as described by Biologists, is the result of evolution by natural selection, which affects every lineage of reproducing creatures. Examples of adaptations range from heat-resistant Archaea that can survive in steaming hot springs to a nectar-eating moth whose tongue length matches that of the flower it feeds on. The ability to survive and reproduce is improved by adaptations in the individual who is displaying them. Adaptations change with time. Natural selection drives the traits of individuals in a population to follow environmental changes. Growth and Development Genes encode specific instructions on how organisms should grow and develop. These genes give instructions for cellular growth and development, ensuring that the offspring of a species will develop into adults who share many traits with their parents. Regulation/Homeostasis Living organisms are complex and need various regulatory mechanisms to regulate internal processes like nutrition, transport, stimulus response, and stress management. Homeostasis, which is defined as a "steady state," is a generally stable internal environment needed to support life. For instance, organ systems like the digestive or circulatory systems convey oxygen throughout the body, remove waste, give nutrients to every cell, and cool the body, among other specific tasks. Cells need the right circumstances to function effectively, including the right temperature, pH, and chemical concentrations. These circumstances could, however, change at any time. By turning on regulatory systems, organisms are able to nearly constantly maintain homeostatic internal conditions within a small range, despite changes in their environment. For instance, many species use a mechanism called thermoregulation to control their body temperatures. Cold-adapted organisms, like the polar bear, have physical characteristics that enable them to survive extreme cold and retain body heat. In hot regions, species have mechanisms to assist them release extra body heat, such as perspiration in humans or panting in canines. By producing heat and preventing heat loss through their thick fur and a layer of dense fat under their skin, polar bears and other mammals that live in ice-covered areas keep their body temperatures stable. Energy Processing 11 All living things require a source of energy for their metabolic processes. Some species use chemical energy from molecules they consume, whereas others use chemical energy that is captured from the Sun and transformed into chemical energy in food. Evolution Mutations, or chance changes in hereditary material over time, are the cause of the diversity of life on Earth. These mutations give organisms the chance to adapt to a shifting environment. According to the laws of natural selection, an organism with traits adapted to its surroundings will reproduce more successfully. Why do living things require energy? Self-Assessment Exercises 3 1. How does the process of reproduction in single celled organisms begins? 2. How does organisms respond to environmental changes? 1.6 Summary You have learned about the concept of Biology as the study of living things. You have studied about the characteristics of living things such as order, sensitivity or response to stimuli, reproduction, adaptation, growth and development, regulation, homeostasis, and energy processing and the organization of life itself into hierarchy that includes atoms, molecules, organelles, cells, tissues, organs, and organ systems. Organisms, in turn, are grouped as populations, communities, ecosystems, and the biosphere. 1.7 References/Further Readings/Web Sources Mader, S. (2017). Essentials of Biology. Published by McGraw-Hill Education. ISBN 10: 1259660265 ISBN 13: 9781259660269 Putman, R.J. and S.D. Wratten (1984). Principles of Ecology, Publisher Springer Dordrecht, eBook PackagesSpringer Book Archive, DOIhttps://doi.org/10.1007, /978-94-011- 6948-6, eBook ISBN978-94- 011-6948-6. 388pp https://opentextbc.ca/biology/chapter/1-1-themes-and-concepts-of-biology/ https://bio.libretexts.org/Bookshelves/Introductory_and_General_Biology/Book%3A_General_B iology_(Boundless)/04%3A_Cell_Structure/4.03%3A_Studying_Cells_-_Cell_Theory#title https://www.youtube.com/watch?v=cQPVXrV0GNA https://www.youtube.com/watch?v=juxLuo-sH6M https://www.youtube.com/watch?v=juxLuo-sH6M https://www.youtube.com/watch?v=ltRApt0IpCE 1.8 Possible Answers to Self-Assessment Exercises Answers to SAE 1 1. The first forms of life that appeared on Earth are thought to have been microorganisms 2. Humans have inhabited this planet for only the last 2.5 million years Answers to SAE 2 1. Several theories attempts to offer explanation on the possible mechanism of origin of life and prominent of these are: 1. Theory of Special Creation 2.Theory of Catastrophism 3. Cosmozoic Theory 12 4. Theory of Chemical Evolution 2. According this theory, Origin of life on earth is the result of a slow and gradual process of chemical evolution that probably occurred about 3.8 billion years ago. Answers to SAE 3 1. 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 2. As an environment change, natural selection causes the characteristics of the individuals in a population to track those changes. Unit 2: The Diversity of life and its organization Unit Structure 2.1 Introduction 2.2 Intended Learning Outcomes (ILOs) 2.3 The Diversity of Life 2.4 Levels of Organization of Living Things 2.5 Evolutionary Relationships of Life Forms 2.6 Summary 2.7 References/Further Readings/Web Sources 2.8 Possible Answers to Self-Assessment Exercises 2.1 Introduction You will learn about the diversity of life on planet earth today. You will study about evolutionary relationships of life forms and the levels of organization of living things 2.2 Intended Learning Outcomes (ILOs) By the end of this unit, you should be able to: Explain the diversity of life on planet earth. Describe the levels of organization of living things and Explain the evolutionary relationships of life forms 2.3 The Diversity of Life Biology is a science with a relatively broad field of study because there is a wide variety of life on Earth. Evolution, the process of progressive change in which new species develop from more established ones is the cause of this diversity. The development of living beings in all spheres of existence, from the microscopic to ecosystems, is studied by evolutionary Biologists. The idea of classifying all known species of creatures into a hierarchical taxonomy was first put forth in the 18th century by a Scientist by name Carl Linnaeus. In this concept, a genus is a collection of the species that are most similar to one another. Additionally, within a family, comparable genera (plural of genus) are grouped together. The level at which all creatures are gathered together into groups is reached at the end of this grouping. From lowest to highest, the eight levels of the present taxonomic hierarchy are: species, genus, family, order, class, phylum, kingdom, and domain. As a 13 result, species are grouped inside genera, families and orders are grouped within classes, and so on. The system's highest level, domain, has only recently been added since the 1990s. There are currently three recognised domains of life: Eukarya, Archaea, and Bacteria. Eukaryotic creatures are those that have cells with nuclei. It comprises various protist kingdoms as well as the kingdoms of fungi, plants, and animals. Numerous extremophiles, single-celled organisms without nuclei that can survive in extreme conditions like hot springs, are members of the Archaea. Another distinct category of single-celled organisms without nuclei is the bacteria. Bacteria and Archaea are both prokaryotes, a colloquial term for cells devoid of nuclei. The suggestion to categorise life into three domains was inspired by the 1990s realisation that some "bacteria," now known as the Archaea, were different genetically and biochemically from other bacterial cells as they were from eukaryotes. This abrupt shift in our understanding of the tree of life shows that classifications are subject to change when new data becomes available. Linnaeus was the first to name creatures using two distinct names, commonly known as the binomial naming system, in addition to the hierarchical taxonomic system. Because there were regional variations in these popular names prior to Linnaeus, using them to refer to species caused confusion. The capitalised genus name and the species name make up binomial names (all lower- case). When printed, both names are put in italics. Every species is given a distinct binomial that is known around the world, allowing any Scientist to identify the species being discussed. As an illustration, the North American blue jay has its own scientific name, Cyanocitta cristata. Homo sapiens is our own species. Who was the first to come up with the idea of classifying all known species of creatures into a hierarchical taxonomy in the 18th century? Self-Assessment Exercises 2 1. What is the source of biological diversity? 2. Who was the first scientist to name organisms using two unique names, now called the binomial naming system. 2.4 Levels of Organization of Living Things Living things follow a hierarchy from little to large and are highly structured and organised. The atom is the lowest and most basic unit of matter that yet has elemental characteristics. It consists of an electron-surrounded nucleus. Moles are made of atoms. A molecule is an organic compound made up of at least two atoms joined by a chemical bond. Numerous biologically significant molecules are macromolecules, which are huge molecules created typically by joining monomers, or smaller building blocks. Deoxyribonucleic acid (DNA), which carries the blueprints for an organism's operation, is an illustration of a macromolecule. Organelles are collections of macromolecules seen in some cells that are encased in membranes, and they carry out specific tasks within cells. The smallest essential unit of structure and function in living beings, the cell, makes up all living things. Some organisms only have one cell, whereas others have several cells. There are two types of cells; eukaryotic or prokaryotic cells. Prokaryotes are single-celled organisms that lack nuclei and organelles that are encased in nuclear membranes. In contrast, eukaryotic cells do include nuclei and organelles that are encased in membranes. The majority of multicellular organisms combine cells to form tissues, which are collections of comparable cells performing the same function. Organs are assemblages of tissues arranged 14 according to a shared purpose. Organs can be found in both plants and animals. An organ system is a more advanced level of organisation made up of organs with similar functions. Vertebrate animals, for instance, have a variety of organ systems, such as the circulatory system, which carries blood to and from the lungs as well as throughout the body. This system is made up of the heart and blood arteries. Organisms are unique forms of life. For instance, every tree in a forest is a living thing. Even though they are commonly referred to as microbes, single-celled prokaryotes and eukaryotes are also regarded as organisms. A population is the aggregate term for all members of a species that are present in a given location. For instance, a forest can have a lot of white pine trees. The population of white pine trees in this woodland is represented by all of these trees. Various populations may coexist in the same region. For instance, there are communities of flowering plants, insects, and microbiological colonies in the forest of pine trees. A community is made up of all the people who live in a certain location. For instance, the community of a forest is made up of all the populations of trees, flowers, insects, and other living things. An ecology exists in the forest itself. Abiotic, or non-living, elements of the environment, such as nitrogen in the soil or precipitation, coexist with all the living things in a certain area to form an ecosystem. 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. 15 Figure 2.1. Biological Levels of Organization: The biological levels of organization of living things follow a hierarchy, from a single organelle to the entire biosphere, living organisms are part of a highly structured hierarchy, such as the one shown above. What does the biosphere represent at the highest level of organization of living things? 16 Self-Assessment Exercises 1 Explain the meaning of each of the following 1. molecule 2. macromolecule 3. polymerization 2.5 Evolutionary Relationships of Life Forms A phylogenetic tree can summarise the relationships between different types of life on Earth in terms of evolution. A phylogenetic tree is a diagram that depicts the relationships between biological species in terms of their shared and unique genetic, physical, or both features. A phylogenetic tree is made up of branches and branch points, or nodes. The internal nodes indicate ancestors and are instances in evolution when two new species are believed to have sprung from a common ancestor, according to scientific data. Each branch's length can be viewed as a relative time estimate. Animals, plants, fungus, protists, and bacteria were the five kingdoms that Biologists previously divided living things into. However, the groundbreaking research of American microbiologist Carl Woese in the early 1970s has demonstrated that the three lineages of life on Earth—Bacteria, Archaea, and Eukarya—have developed over time. To represent the new evolutionary tree, Woese proposed the domain as a new taxonomic level and Archaea as a new domain. Extremophiles are creatures from the Archaea domain that thrive in harsh environments. Woese built his tree using genetic linkages rather than morphological similarities (shape). In phylogenetic analyses, various genes were employed. Woese's tree was created using comparative sequencing of genes that are widely distributed, conserved (meaning that they have undergone only minor changes during evolution), of an appropriate length, and can be found in some form in every organism. 17 Figure 2.2. The Phylogenetic tree of life How was Woese's tree built using genetic linkages? Self-Assessment Exercises 3 1. List the past grouping of living organisms into the five kingdoms 2. Who is the 18th century scientists that first proposed the grouping of organisms into a hierarchical taxonomy? 2.6 Summary You have studied about evolution as the source of biological diversity on Earth. A diagram called a phylogenetic tree was also used to show evolutionary relationships among organisms. You have also learned about the many branches and sub disciplines of Biology such as molecular biology, microbiology, neurobiology, zoology, and botany, among others. 2.7 References/Further Readings/Web Sources Miller, G. Tyler Jr. and Scott E. Spoolman (2009). Essentials of Ecology, 5e, Brooks/Cole, Cengage Learning, 10 Davis Drive Belmont, CA 94002-3098 USA, ISBN-13: 978-0- 495-55795-1, 383pp Putman, R.J. and S.D. Wratten (1984). Principles of Ecology, Publisher Springer Dordrecht, eBook PackagesSpringer Book Archive, DOIhttps://doi.org/10.1007, /978-94-011- 6948-6, eBook ISBN978-94- 011-6948-6. 388pp https://opentextbc.ca/biology/chapter/1-1-themes-and-concepts-of-biology/ https://www.youtube.com/watch?v=xSIrobQxuzI 18 https://www.youtube.com/watch?v=wxjSx9wluAQ https://www.youtube.com/watch?v=fV2aaV-Hp2U https://www.youtube.com/watch?v=P3lsApPq-OQ 2.8 Possible Answers to Self-Assessment Exercises Answers to SAEs 1 1. The source of the diversity is evolution, the process of gradual change during which new species arise from older species. 2. Carl Linnaeus Answers to SAEs 2 The meaning of the following terms: 1. molecule: The smallest particle of a specific compound that retains the chemical properties of that compound; two or more atoms held together by chemical bonds. 2. macromolecule: a very large molecule, especially used in reference to large biological polymers (e.g. nucleic acids and proteins) 3. polymerization: The chemical process, normally with the aid of a catalyst, to form a polymer by bonding together multiple identical units (monomers). Answers to SAEs 3 1. In the past, biologists grouped living organisms into five kingdoms: animals, plants, fungi, protists, and bacteria. 2. In the 18th century, a scientist named Carl Linnaeus first proposed organizing the known species of organisms into a hierarchical taxonomy. Unit 3: Introduction to Biological Inquiry Unit Structure 3.1 Introduction 3.2 Intended Learning Outcomes (ILOs) 3.3 Scope of Biology 3.4 The Study of Life 3.5 The Nature of Science 3.6 Summary 3.7 References/Further Readings/Web Sources 3.8 Possible Answers to Self-Assessment Exercises 3.1 Introduction You will learn that the scope of biology is broad and therefore contains many branches and sub disciplines. You will study about the shared characteristics of the natural sciences and understand the process of scientific inquiry. You will also be able understand the application of forensic science in law and describe the basic scientific ethics in research. Science is knowing. Scientists search for knowledge through inquiry, which is a way of questioning and explaining phenomena that occur in nature. Let's begin by exploring how biologists and researchers use the scientific method in the scientific inquiry of life 19 3.2 Intended Learning Outcomes (ILOs) By the end of this unit, you will be able to: Appreciate the various branches of biology Identify the shared characteristics of the natural sciences Describe the application of forensic Scientist to answer law matters Understand the basic Scientific ethics in research 3.3 The Scope of Biology Since biology has a wide range of applications, there are numerous branches and subfields within it. It is possible for biologists to specialise in one of such subdisciplines. For instance, the study of biological processes at the molecular level, including interactions between molecules like DNA, RNA, and proteins as well as how they are controlled, is known as molecular biology. The study of the composition and operation of microbes is known as microbiology. It is a somewhat diverse field in and of itself, with additional specialists including geneticists, ecologists, and microbial physiologists depending on the area of research. Neurobiology is a different area of biological study that focuses on the biology of the nervous system. It is acknowledged as a branch of biology as well as an interdisciplinary subject of study. This sub- discipline, which is interdisciplinary in nature, uses molecular, cellular, developmental, medicinal, and computational approaches to study many aspects of the nervous system. Another area of biology called palaeontology examines the evolution of life using fossils. The study of animals and plants is known as zoology and botany, respectively. Biotechnologists, ecologists, and physiologists are just a few of the areas in which biologists can specialise. Biotechnologists employ their understanding of biology to develop practical products. Ecologists investigate how creatures interact with their surroundings. Physiologists research how cells, tissues, and organs function. These are just a few of the numerous careers that biologists might choose from. Biology-related discoveries can have a very significant and immediate impact on us, on everything from our bodies to the environment we live in. We rely on these findings for our food security, our health, and the advantages our ecosystem offers. Because of this, having a basic understanding of biology might help us make better judgments in our daily lives. Biology has been altered by the technological advancements of the 20th century, notably those related to the description and manipulation of DNA. This change will make it possible for scientists to continue learning more about the evolution of life, the human body, our ancestry, and how we can continue to exist as a species on this planet despite the pressures brought on by our expanding population. The fact that biologists are still solving complex questions concerning life suggests that we are only at the beginning of our understanding of the planet's history, the origins of life, and our place within it. For these and other reasons, the biology information you acquire from this textbook and other printed and electronic materials should be useful in whichever line of work you choose. Which area of biology examines the evolution of life using fossils? Self-Assessment Exercises 1 1. What is the scope of molecular biology? 2. What is the interest of Forensic Science? 3.4 Forensic Science and Scientific Ethics 20 Forensic science is the application of science to answer questions related to the law. Forensic scientists can be biologists, chemists, or biochemists. The work of forensic scientists involves looking at evidence linked to crimes and providing scientific testimony for use in court. In recent years, interest in forensic science has grown, probably as a result of well-liked television programmes that showcase forensic scientists in action. Additionally, the types of work that forensic scientists can perform have been updated thanks to the advancement of molecular techniques and the creation of DNA databases. The majority of their work is focused on crimes against humans like murder, rape, and assault. Their work entails processing DNA from a variety of locations and materials in addition to evaluating samples including hair, blood, and other bodily fluids. Other biological evidence, such bug fragments or pollen grains, that has been left at crime sites is also examined by forensic specialists. Most likely, students who want to major in forensic science will need to complete chemistry, biology, and some challenging math courses. Scientists have a responsibility to protect people, animals, and the environment from unwarranted harm. Additionally, they must make sure that their research and communications are impartial and that all relevant factors—including financial, legal, safety, and replicability—are correctly balanced. In the significant and ever-evolving discipline of bioethics, scholars cooperate with other organisations and individuals. They try to establish standards for current practise and are constantly thinking about new innovations and upcoming technology to come up with solutions for the coming years and decades. Unfortunately, a number of patently unethical activities, where biologists failed to treat research subjects with dignity and, in some cases, actually harmed them, preceded the development of the area of bioethics. 399 African American men were diagnosed with syphilis in the Tuskegee Syphilis Study of 1932, but they were never told they had the infection, so they continued to live with it and spread it to others. Because the aim of the study was to comprehend the effects of untreated syphilis on Black males, doctors even withheld proven medicines. While the choices made in the Tuskegee research cannot be justified, certain choices are really challenging. Bioethicists, for instance, may investigate the ethical implications of gene editing technologies, such as the potential for creating species that could supplant others in the ecosystem and the potential for "designing" human beings. Ethicists will probably attempt to strike a balance between the positive and negative effects of their work, such as bettering medicines or preventing specific diseases. Because bioethics is seldom straightforward, scientists frequently must weigh benefits and risks. You will learn about medical advancements that, at their root, have what many people view as an ethical failing in this literature and course. Henrietta Lacks, an African American woman in her 30s, received a cervical cancer diagnosis at Johns Hopkins Hospital in 1951. Her illness-specific traits allowed her cells to divide continuously, effectively rendering them "immortal." Researchers obtained samples of her cells without her knowledge or consent and used them to make the immortal HeLa cell line. Major medical advancements made possible by these cells include the development of the polio vaccine, as well as studies into cancer, AIDS, cell ageing, and, most recently, COVID-19. Lacks' contributions to those discoveries have largely gone unrecognised, and neither she nor her family have reaped the millions of dollars in pharmaceutical revenues made possible in part by the use of her cells. Even if it could save the lives of other patients, taking tissue or organs without the patient's permission nowadays is not just regarded as unethical but also unlawful. Examining related concerns before, during, and after research or practise is conducted, adhering to accepted professional standards, and taking into account the 21 safety and dignity of all organisms participating or impacted by the work are all part of the function of ethics in scientific research. What is forensic science? Self-Assessment Exercises 1 1. What is the scope of molecular biology? 2. What is the interest of Forensic Science? 3.5 The Nature of Science However, what exactly is science? Biology is a science. What connections exist between the study of biology and other scientific fields? The definition of science is "knowledge of the natural world" (from the Latin scientia, "knowledge"). A particularly precise method of learning about or knowing the world is science. The previous 500 years have shown that science is a highly potent way of understanding about the world, and that it has played a significant role in the technological revolutions that have occurred during this time. The tools of science, however, cannot be used to study all fields of knowledge and human experience. These include things like providing answers to only moral questions, questions about aesthetics, or questions that can be broadly characterised as spiritual concerns. These topics are not within the purview of material phenomena, the phenomena of matter and energy, and hence cannot be witnessed or quantified. The scientific method is a structured approach to research that includes meticulous observation and experimentation. The testing of hypotheses is one of the most crucial parts of this strategy. A testable hypothesis is a theory put out to explain an occurrence. Typically, tentative explanations, or hypotheses, are developed within the framework of a scientific theory. A widely accepted, rigorously investigated, and verified explanation for a collection of observations or a phenomenon is what is known as a scientific theory. The basis of all scientific knowledge is scientific theory. Additionally, there are scientific laws that describe how parts of nature will act under specific circumstances in many scientific disciplines (less so in biology). These laws are succinct descriptions of areas of the world that can be expressed using formulas or mathematics. There is no progression from hypotheses to theories to laws, as though these concepts signified a rise in worldly certainty. The value of various branches of science has been a topic of discussion within the scientific community for the last few decades. Is it worthwhile to pursue science for the sake of merely learning something, or does scientific information only have value if we can use it to solve a particular issue or improve our quality of life? The distinctions between basic science and applied science are the main subject of this query. Basic science or Regardless of how such knowledge might be used in the near future, "pure" science aims to further knowledge. It is not concentrated on creating something with immediate commercial or public benefit. Although knowing for knowledge's sake is the immediate aim of basic research, this does not preclude the possibility of an application in the long run. In contrast, The goal of applied science, sometimes known as "technology," is to apply scientific knowledge to solve practical issues. For instance, it could be possible to identify a treatment for a specific disease, increase crop yields, or save animals in danger from a natural disaster. In applied science, the researcher typically has the problem defined for them. Some people could view basic science as "useless" while viewing applied science as "helpful." These people might ask, "What for?" to a scientist who promotes knowledge acquisition. However, 22 a close examination of the history of science indicates that many outstanding applications of enormous value have been made possible by fundamental knowledge. Since many scientists believe that a fundamental understanding of science is required before an application can be produced, applied science is dependent on the findings of basic science. Others believe it is time to move beyond fundamental research and focus on developing answers for real-world issues. Both strategies are appropriate. 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. The understanding of the molecular mechanisms driving DNA replication that resulted from the discovery of DNA structure is one instance of how basic and applied science can cooperate to solve practical challenges. Our cells contain DNA strands that are particular to each individual and which carry the instructions for life. Before a cell divides to create new cells, DNA replication creates new copies of the DNA. In order to identify genetic illnesses, locate people who were present at a crime scene, and establish paternity, scientists had to first understand the principles of DNA replication. It seems doubtful that applied science would exist without foundational science. The Human Genome Project, a study in which each human chromosome was examined and mapped to ascertain the specific sequence of DNA subunits and the precise position of each gene, serves as another illustration of the relationship between basic and applied research. (The genome is a person's entire collection of genes; the gene is the fundamental unit of heredity.) As part of this project, research on other organisms has also been done in order to better understand human chromosomes. Basic research using non-human organisms and later the human genome was crucial to the Human Genome Project. Utilizing the data for applied research to find treatments for genetically based diseases eventually became a significant end goal. It is crucial to remember that while research projects in both basic and applied science are typically meticulously planned, some discoveries are made by serendipity, that is, by way of a fortunate accident or a happy surprise. When biologist Alexander Fleming unintentionally left a petri dish of Staphylococcus bacteria uncovered, penicillin was accidently discovered. The microorganisms were killed by an unwelcome mould growth. Penicillium was found to be the mould, and a new antibiotic was found. Even in the highly structured field of science, serendipity can produce surprising discoveries when combined with an attentive, inquisitive mind. What is a genome? Self-Assessment Exercises 3 1. What is the scientific method? 2. Which is the one of the most important aspects of the scientific method? 3.6 Summary You must have learned about the scope of biology as containing many branches and sub disciplines. You have also studied the shared characteristics of the natural sciences and the process of scientific inquiry. The nature of science as a critical component of scientific literacy that enhances students' understandings of science concepts and enables them to make informed decisions about scientifically-based personal and societal issues have been highlighted in the unit. 3.7 References/Further Readings/Web Sources Miller, G. Tyler Jr. and Scott E. Spoolman (2009). Essentials of Ecology, 5e, Brooks/Cole, Cengage Learning, 10 Davis Drive Belmont, CA 94002-3098 USA, ISBN-13: 978-0- 495-55795-1, 383pp 23 Putman, R.J. and S.D. Wratten (1984). Principles of Ecology, Publisher Springer Dordrecht, eBook PackagesSpringer Book Archive, DOIhttps://doi.org/10.1007, /978-94-011- 6948-6, eBook ISBN978-94- 011-6948-6. 388pp https://www.cambridge.org/core/books/nature-of-life/what-is-the-meaning-of- life/77B3F144E9C039AEB1CC06FCE39D470A https://study.com/academy/lesson/the-basic-nature-of-life.html https://pubmed.ncbi.nlm.nih.gov/6679625/ https://people.reed.edu/~mab/papers/life.OXFORD.html https://www.youtube.com/watch?v=IadAzzx7EHc https://www.youtube.com/watch?v=HaVmHJzBrMg https://www.youtube.com/watch?v=hBBEOgD_bwY https://www.youtube.com/watch?v=oIMUPPIoqPY 3.8 Possible Answers to Self-Assessment Exercises Answers to SAE 1 1. Life of the body (physical), life of the mind and life of the spirit. 2. The methods of science include careful observation, record keeping, logical and mathematical reasoning, experimentation, and submitting conclusions to the scrutiny of others. Answers to SAE 2 1. Molecular biology studies biological processes at the molecular level, including interactions among molecules such as DNA, RNA, and proteins, as well as the way they are regulated. 2. 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 material associated with crimes. Answers to SAE 3 1. The scientific method is a method of research with defined steps that include experiments and careful observation. 2. One of the most important aspects of this method is the testing of hypotheses Unit 4: Scientific Inquiry method Unit Structure 4.1 Introduction 4.2 Intended Learning Outcomes (ILOs) 4.3 Scientific Inquiry 4.4 Hypothesis in Science 4.5 Basic and Applied Science 4.6 Summary 4.7 References/Further Readings/Web Sources 4.8 Possible Answers to Self-Assessment Exercises 4.1 Introduction 24 You will learn the meaning and method of the scientific inquiry in this unit. You will study the meaning of hypothesis and how to test and apply it in science research. You will also learn about basic and applied research in science. 4.2 Intended Learning Outcomes (ILOs) By the end of this unit, you should be able to: Understand the meaning and method of the scientific inquiry. Explain the meaning of hypothesis Describe how to test and apply hypothesis in science research. Explain the meaning of basic and applied research in science. 4.3 Scientific Inquiry All branches of science share the same ultimate objective, which is "to know." The advancement of science is fueled by curiosity and enquiry. The goal of science is to comprehend the world and how it works. Inductive reasoning and deductive reasoning are the two types of logical thinking that are employed. Inductive reasoning is a type of logical reasoning that draws a generalisation from a set of related observations. In descriptive science, this kind of thinking is typical. A biologist or other life scientist will make observations and note them. These data may be quantitative (containing of statistics) or qualitative (descriptive), and the raw data may be supplemented with illustrations, photographs, films, or other visual media. The scientist can draw conclusions (inductions) based on evidence from several observations. Formulating generalisations via inductive reasoning requires close observation and in-depth data investigation. This is how many brain studies operate. While people are performing a task, several brains are being watched. It is then shown that the area of the brain controlling the reaction to that task is the part that lights up, signifying activity. Science that is hypothesis-based employs a sort of logic known as deductive reasoning or deduction. In contrast to inductive reasoning, deductive reasoning follows a different pattern of thought. Deductive reasoning is a type of logical reasoning where specific outcomes are predicted using a general principle or law. A scientist can infer and forecast specific conclusions from those broad principles, provided that the general principles are true. For instance, it is expected that as a region's climate warms, the distribution of plants and animals will alter. Distributions in the past and the present have been compared, and numerous alterations have been discovered that are compatible with a warming climate. The discovery of the distributional change serves as support for the validity of the climate change conclusion. The two primary avenues of scientific inquiry, descriptive science and hypothesis-based research, are connected to both types of logical thinking. While hypothesis-based science begins with a specific issue or problem and a potential response or solution that can be investigated, descriptive (or discovery) science attempts to observe, explore, and discover. Because most scientific activities use both methodologies, the line separating these two fields of study is frequently blurred. Observations spark questions, those questions prompt the creation of a hypothesis as a potential response, and finally the hypothesis is put to the test. As a result, descriptive science and science based on hypotheses are constantly conversing. What are the two primary avenues of scientific inquiry? Self-Assessment Exercises 1 1. What are the two methods of logical reasoning in science? 2. What are the two main pathways of scientific study? 25 4.4 Hypothesis in Science By asking questions about the living world and looking for logical answers, biologists investigate it. Other sciences also use this process, which is frequently referred to as the scientific method. Although Sir Francis Bacon (1561–1626), an Englishman, established inductive methods for scientific investigation, the scientific method was employed already in antiquity. The scientific method can be used to solve practically any logical problem; hence it is not just used by biologists. The scientific method often begins with an observation that prompts a query (often a problem to be solved). Let's consider a straightforward issue that begins with an observation and use the scientific process to find a solution. A student walks into class on a Monday morning and immediately notices that the room is too warm. The classroom is excessively warm, which is an observation that also indicates a problem. The youngster then inquires as to why the classroom is so warm. Remember that a hypothesis is an explanation that has been proposed and may be tested. There may be various hypotheses put out to address a problem. One possible explanation, for instance, could be that "No one switched on the air conditioner, thus the classroom is heated." However, there might be other answers to the query, and as a result, different hypotheses might be put out. Another possibility is that the air conditioner isn't working because there is a power outage, which is why the classroom is heated. A prediction can be made after a hypothesis has been chosen. Similar to a hypothesis, a prediction usually follows the structure "If... then..." For instance, if the student turns on the air conditioning, the classroom won't be overly warm any longer, according to the prediction for the first hypothesis. For a theory to be proven correct, it must be testable. A hypothesis that depends on what a bear thinks, for instance, cannot be tested because it is impossible to know what a bear thinks. Additionally, it must be able to be refuted by the outcomes of experiments, or be falsifiable. The statement "Botticelli's Birth of Venus is beautiful" is an example of an unprovable hypothesis. There is no experiment that might disprove this claim. A researcher will carry out one or more experiments meant to rule out one or more of the hypotheses in order to test a hypothesis. This is crucial. Although a theory can be refuted or rejected, it can never be proven. Like mathematics, science does not deal with proofs. We find evidence in favour of an explanation when an experiment fails to refute a hypothesis, but this does not preclude the discovery of a more convincing explanation or the use of a more meticulously planned experiment in the future. There will be one or more controls and one or more variables in every experiment. Any element of the experiment that is subject to modification or variation is referred to as a variable. A control is a variable that stays the same throughout the experiment. The next example asks you to look for the variables and controls. As a straightforward illustration, a test may be done to see whether phosphorus limits the growth of algae in freshwater ponds. Half of a series of man- made ponds that contain water are treated each week by adding phosphate, while the other half are treated by adding a salt that is known not to be consumed by algae. The phosphate (or lack thereof) is the variable in this situation; the experimental or treatment instances are the ponds with added phosphate, while the control ponds are those with inert additives like salt added. Another safeguard against the likelihood that adding more matter to the pond has an impact is to just add something. If the treated ponds exhibit decreased algal growth, then our hypothesis is supported. If they don't, we'll have to abandon our hypothesis. Be mindful that rejecting one hypothesis merely eliminates the one that is invalid, not whether the other hypotheses can be accepted or not. The scientific method is used to disprove assumptions that don't match up with the results of experiments. Due to the exponential growth of data deposited in various databases in recent years, a new method of 26 testing hypotheses has emerged. A new discipline known as "data research" (also known as "in silico" research) offers new techniques for data analysis and its interpretation using computer algorithms and statistical analyses of data in databases. The demand for experts in both biology and computer science will rise as a result, creating an exciting employment opportunity. What does "in silico" research step to offer? Self-Assessment Exercises 2 1. What is the new approach of testing hypotheses? 2. What happens to the hypotheses that are inconsistent with experimental data using the scientific method? 4.5 Basic and Applied Science The value of various branches of science has been a topic of discussion within the scientific community for the last few decades. Is it worthwhile to pursue science for the sake of merely learning something, or does scientific information only have value if we can use it to solve a particular issue or improve our quality of life? The distinctions between basic science and applied science are the main subject of this query. Regardless of how such knowledge might be used in the near future, basic or "pure" science aims to advance understanding. It is not concentrated on creating something with immediate commercial or public value. Although knowing for knowledge's sake is the immediate aim of basic research, this does not preclude the possibility of an application in the long run. In contrast, applied science, also known as "technology," tries to apply research to solve real-world issues. For instance, it may be able to increase crop yields, discover a treatment for a specific illness, or save animals in danger from a natural disaster. In applied science, the researcher typically has the problem defined for them. Some people could view basic science as "useless" while viewing applied science as "helpful." These people might ask, "What for?" to a scientist who promotes knowledge acquisition. However, a close examination of the history of science indicates that many amazing applications of fundamental knowledge have been made. Since many scientists believe that a fundamental understanding of science is required before an application can be produced, applied science is dependent on the findings of basic science. Others believe it is time to move beyond fundamental research and focus on developing answers for real-world issues. Both strategies are appropriate. While it is true that some issues require immediate attention, few would be resolved without the aid of the information produced by basic research. The understanding of the molecular mechanisms driving DNA replication that resulted from the discovery of DNA structure is one instance of how basic and applied science can cooperate to solve practical challenges. Our cells contain DNA strands that are particular to each individual and which carry the instructions for life. Before a cell divides to create new cells, DNA replication creates new copies of the DNA. In order to identify genetic illnesses, locate people who were present at a crime scene, and establish paternity, scientists had to first understand the principles of DNA replication. Applied science is unlikely to exist without foundational science. The Human Genome Project, a study in which each human chromosome was examined and mapped to ascertain the specific sequence of DNA subunits and the precise position of each gene, serves as another illustration of the relationship between basic and applied research. (The gene is the basic unit of heredity represented by a specific DNA segment that codes for a functional molecule.) As part of this 27 initiative, research on other organisms has also been done in order to better understand human chromosomes. Basic research with non-human species and later the human genome was crucial to the Human Genome Project. Utilizing the data for applied research to find treatments for genetically based disorders subsequently became a significant end aim. It is crucial to remember that while research projects in both basic and applied science are typically meticulously planned, some discoveries are made by serendipity, that is, by way of a fortunate accident or a happy surprise. When biologist Alexander Fleming unintentionally left a petri dish of Staphylococcus bacteria uncovered, penicillin was accidently discovered. The microorganisms were killed by an unwelcome mould growth. Penicillium was identified as the mould, and a brand-new, very important antibiotic was found. Similar to this, Percy Lavon Julian was a renowned medicinal chemist who was working on a method to mass synthesise chemicals used in the production of significant medications. It wasn't until water inadvertently leaked into a sizable soybean oil storage tank that he discovered his strategy for using soybean oil to produce progesterone, a hormone crucial to the menstrual cycle and pregnancy. He started the process of reproducing and industrialising the procedure after immediately identifying the produced molecule as stigmasterol, a key component in progesterone and comparable medications. This has benefitted millions of individuals. Even in the highly organized world of science, luck—when combined with an observant, curious mind focused on the types of reasoning discussed above—can lead to unexpected breakthroughs. What is the main aim of applied science research? Self-Assessment Exercises 3 1. What value of different types of science was the scientific community debating for the last few decades? 2. What can lead to unexpected breakthroughs even in the highly organized world of science? 4.6 Summary You must have learned about the meaning and method of the scientific inquiry in this unit. You have studied about the meaning of hypothesis and how to test and apply it in science research. You must have also learned about basic and applied research in science. 4.7 References/Further Readings/Web Sources Allchin, D., H.M. Andersen and K. Nielsen, (2014). “Complementary Approaches to Teaching Nature of Science: Integrating Student Inquiry, Historical Cases, and Contemporary Cases in Classroom Practice”, Science Education, 98: 461–486. Anderson, C. (2008). “The end of theory: The data deluge makes the scientific method obsolete”, Wired magazine, 16(7): 16–07 Fox, K., E. (2003). “Models, Simulation, and ‘computer experiments’”, in The Philosophy of Scientific Experimentation, H. Radder (ed.), Pittsburgh: Pittsburgh University Press, 198–215. Gimbel, S. ( 2011). Exploring the Scientific Method, Chicago: University of Chicago Press. https://plato.stanford.edu/entries/scientific-method/ https://thescienceteacher.co.uk/the-scientific-method/ https://www.teachstarter.com/au/teaching-resource-collection/scientific-method/ https://openbooks.lib.msu.edu/isb202/chapter/nature-of-science-draft/ https://www.youtube.com/watch?v=16Q6NMCsLq8 28 https://www.youtube.com/watch?v=lN7yd23hCbE https://www.youtube.com/watch?v=Fu2TS0DjBxE 4.8 Possible Answers to Self-Assessment Exercises Answers to SAE 1 1. The two methods of logical thinking are inductive reasoning and deductive reasoning. 2. The two main pathways of scientific study are descriptive science and hypothesis-based science Answers to SAE 2 1. In recent years a new approach of testing hypotheses has developed using computer algorithms and statistical analyses of data in databases, known as "data research" which provides new methods of data analyses and their interpretation. 2. Using the scientific method, the hypotheses that are inconsistent with experimental data are rejected. Answers to SAE 3 1. The scientific community has been debating for the last few decades about whether it is valuable to pursue science for the sake of simply gaining knowledge, or does scientific knowledge only have worth if we can apply it to solving a specific problem or bettering our lives? 2. Luck—when combined with an observant, curious mind focused on the types of reasoning discussed above— can lead to unexpected breakthroughs even in the highly organized world of science Unit 5: Microscopy and the Cell Theory Unit Structure 5.1 Introduction 5.2 Intended Learning Outcomes (ILOs) 5.3 The Cell and Cell Theory 5.4 How Cells Are Studied 5.5 Role of Cell Technologist in the Study of the Cell 5.6 Summary 5.7 References/Further Readings/Web Sources 5.8 Possible Answers to Self-Assessment Exercises 5.1 Introduction You will study the meaning of cell, structure, and functioning in this unit. The various essential characteristics of cells will also be highlighted. You will also learn about the different types of cells. You will study the differences between Prokaryotic and Eukaryotic Cells. You will also learn how cells are being studied with the use of microscopes. Electron microscopes provide higher magnification, higher resolution, and more detail than light microscopes. 5.2 Intended Learning Outcomes (ILOs) By the end of this unit, you will be able to: Justify that cell is the basic structural and functional unit of all organisms 29 List the components of the cell and state cell theory Differentiate between prokaryotic and eukaryotic cells Describe the roles of cells in organisms Compare and contrast light microscopy and electron microscopy 5.3 The Cell and Cell Theory In biology, the cell is the fundamental building block of all living things. It is the smallest structural unit of living matter capable of functioning on its own. A cell is a collection of cytoplasm that is held together on the outside by a cell membrane. Cells are the smallest structural units of living matter and make up all living things. They are typically tiny in size. Numerous organelles, including one or more nuclei, are present in most cells and perform a range of functions. Like a bacterium or yeast, some single cells are entire organisms. Others serve as specialised components of multicellular organisms like plants and animals. As in the case of bacteria and protozoans, a single cell can be an entire organism in and of itself. In multicellular organisms like higher plants and animals, specialised cell groups are arranged into tissues and organs. Prokaryotic cells and eukaryotic cells are two different types of cells.Eukaryotic cells include those found in animals, plants, fungi, and protists, whereas prokaryotic cells include those found in bacteria and archaea. Prokaryotic and eukaryotic cells have different shapes, yet they have a lot of similarities in their molecular make-up and functions. Proteins, polysaccharides, and nucleic acids make up the majority of the molecules in cells. A membrane that surrounds a cell allows it to exchange specific materials with its environment. This membrane is contained within the rigid cell wall of plant cells. By the late 1830s, zoologist Theodor Schwann and botanist Matthias Schleiden were researching tissues and putting forth the unified cell hypothesis. According to the unified cell theory, each living entity is made up of one or more cells, each cell is the building block of life, and new cells develop from existing cells. Later, this idea benefited greatly from the contributions of Rudolf Virchow. Schleiden and Schwann advocated spontaneous generation (also known as abiogenesis) as the mechanism for cell origination, but spontaneous generation was later demonstrated to be false. "Omnis cellula e cellula"—"All cells only come from pre-existing cells"—was a famous phrase used by Rudolf Virchow. "However, the portions of the hypothesis that did not concern the genesis of cells withstood scientific investigation and are now generally accepted by the scientific community. The following are the elements of contemporary cell theory that are commonly acknowledged: 1. The basic unit of structure and functionality in living things is the cell. 2. One or more cells make up every living thing. 3. Cellular division creates new cells from existing ones. The cell theory can be broadened to cover the following as well: 1). All cells have roughly the same chemical makeup; 2). All cells carry genetic material that is passed on to daughter cells during cellular division. and 3). Energy flow (metabolism and biochemistry) takes place inside of cells. The following are the essential characteristics of cells: Cells provide structure and support to the body of an organism. The cell interior is organised into different individual organelles surrounded by a separate membrane. The nucleus (major organelle) holds genetic information necessary for reproduction and cell growth. Every cell has one nucleus and membrane-bound organelles in the cytoplasm. 30 Mitochondria, a double membrane-bound organelle is mainly responsible for the energy transactions vital for the survival of the cell. Lysosomes digest unwanted materials in the cell. Endoplasmic reticulum plays a significant role in the internal organisation of the cell by synthesising selective molecules and processing, directing and sorting them to their appropriate locations. What does specialized cells in multicellular creatures like higher plants and animals, come to form as the next level of organization of life? Self-Assessment Exercises 1 1. How is the unified cell theory stated? 2. What are the components of the expanded version of the cell theory? 5.4 How Cells Are Studied The majority of cells are too tiny to be seen with the human eye, therefore, in order to study cells, scientists must utilise microscopes. Electron microscopes offer greater magnification, resolution, and details compared to optical microscopes. All organisms are made up of one or more cells. In multicellular organisms, a number of cells of the same kind interact with one another and carry out shared functions to form tissues (eg. muscle tissue, connective tissue, and nervous tissue), a number of tissues come together to form an organ (eg. stomach, heart, or brain), and a number of organs make up an organ system (such as the digestive system, circulatory system, or nervous system). Together, various systems compose an organism (such as an elephant, for example). Now let's examine how biologists study cells. Light Microscopes Sizes of cells differ. Individual cells are typically too small to be observed with the human eye, therefore researchers employ microscopes to investigate them. An instrument that magnifies a thing is a microscope. Micrographs are photographs of individual cells that are typically taken under a microscope. A typical human red blood cell measures eight millionths of a metre, or eight micrometres (abbreviated as m), in diameter. In comparison, the head of a pin measures approximately two thousandths of a metre (millimetres, or mm). Thus, 250 red blood cells or so may fit on the head of a pin. A light microscope's optics adjust how the lenses are oriented. When examined using a microscope, a specimen that is upside-down and facing right on the microscope slide will seem upside-down and facing left, and vice versa. Similar to how the slide would appear to move right and left when viewed through a microscope, moving the slide down will make it appear to move up. This happens as a result of the two sets of lenses that microscopes use to enlarge the image. The way light passes through the lenses in this lens system causes an inverted image to be created (binoculars and a dissecting microscope work in a similar manner, but include an additional magnification system that makes the final image appear to be upright). Light microscopes are the most common type of student microscope. The lens mechanism allows the user to see the specimen by allowing visible light to flow through while also deflecting it. Light microscopes are useful for observing live things, but since individual cells are typically transparent, it is difficult to tell which parts of an organism are which without the use of specific stains. However, staining typically results in cell death. Light microscopes, which are frequently 31 used in lab settings in undergraduate colleges, may magnify up to 400 times. Magnification and resolving power are two factors that are significant in microscopy. The degree of an object's enlargement is known as its magnification. The ability of a microscope to differentiate two nearby structures as separate is known as its resolving power; the greater the resolution, the closer those two items can be and the clearer and more detailed the image would be. Magnification is typically increased to 1,000 times when oil immersion lenses are used to investigate smaller cells, such as the majority of prokaryotic cells. Light microscopy can be used to view a specimen because light entering a specimen from below is directed into the observer's eye. For this reason, a sample must be thin or translucent in order for light to travel through it. The dissecting microscope is a second kind of microscope utilised in labs. These microscopes can give a three-dimensional image of the specimen and have a lesser magnification (20 to 80 times the object size) than light microscopes. Thick objects allow for the simultaneous examination of numerous components in focus. These microscopes are made to provide a clear, enlarged image of both the anatomy of the entire organism and the tissue structure inside it. The majority of contemporary dissecting microscopes are binocular, meaning that they contain two different lens systems, one for each eye, just like light microscopes. As a result of the distance between the lens systems, the subject appears to have depth, which facilitates manual manipulations. Dissecting microscopes also have optics that correct the image so that it appears as if being seen by the naked eye and not as an inverted image. The light illuminating a sample under a dissecting microscope typically comes from above the sample, but may also be directed from below. Electron Microscopes Electron microscopes, as opposed to light microscopes, employ an electron beam as opposed to a light beam. This offers higher resolving power in addition to increased magnification and, thus, more detail. Live cells cannot be examined using an electron microscope since the preparation of a specimen for viewing under one will kill it. Furthermore, because the electron beam moves best in a vacuum, it is not possible to observe live things. A scanning electron microscope reveals the specifics of a cell's surface properties by reflection when an electron beam travels back and forth across it. The typical coating on cells and other structures is made of a metal like gold. In a transmission electron microscope, the electron beam is transmitted through the cell and provides details of a cell’s internal structures. As you might imagine, electron microscopes are significantly more bulky and expensive than are light microscopes. How is the electron beam transmitted in a transmission electron microscope? Self-Assessment Exercises 2 1. What is a microscope? 2. What is the contrasting feature between the light and an electron microscope? 5.5 Role of Cell Technologist in the Study of the Cell Cytotechnologists (cyto- = cell) are professionals who study cells through microscopic examinations and other laboratory tests. They are trained to determine which cellular changes are within normal limits or are abnormal. Their focus is not limited to cervical cells; they study cellular specimens that come from all organs. When they notice abnormalities, they consult a pathologist, 32 who is a medical doctor who can make a clinical diagnosis. Cytotechnologists play vital roles in saving people’s lives. When abnormalities are discovered early, a patient’s treatment can begin on time, thus increasing the chances of survival. Have you ever heard of a medical test called a Pap smear? In this test, a doctor takes a small sample of cells from the uterine cervix of a patient and sends it to a medical lab where a cytotechnologist stains the cells and examines them for any changes that could indicate cervical cancer or a microbial infection. The microscopes we use today are far more complex than those used in the 1600s by Antony van Leeuwenhoek, a Dutch shopkeeper who had great skill in crafting lenses. Despite the limitations of his now-ancient lenses, van Leeuwenhoek observed the movements of protists (a type of single-celled organism) and sperm, which he collectively termed “animalcules.” In a 1665, a scientist Robert Hooke coined the term “cell” (from the Latin cella, meaning “small room”) for the box-like structures he observed when viewing cork tissue through a lens. In the 1670s, Van Leeuwenhoek discovered bacteria and protozoa. Later advances in lenses and microscope construction enabled other scientists to see different components inside cells. By the late 1830s, botanist Matthias Schleiden and zoologist Theodor Schwann were studying tissues and proposed the unified cell theory, which states that all living things are composed of one or more cells, that the cell is the basic unit of life, and that all new cells arise from existing cells. These principles still stand today. Who is a Cytotechnologist? Self-Assessment Exercises 3 1. Who is a Cytotechnologist? 2. When did van Leeuwenhoek discovered bacteria and protozoa? 5.6 Summary You have studied about the smallest unit that can live on its own and that makes up all living organisms and the tissues of the body. You have also learned about the different types of cell and the three main parts of the cell: the cell membrane, the nucleus, and the cytoplasm. The cell membrane surrounds the cell and controls the substances that go into and out of the cell. 5.7 References/Further Readings/Web Sources Anderson, C., (2008). “The end of theory: The data deluge makes the scientific method obsolete”, Wired magazine, 16(7): 16–07 https://www.britannica.com/science/cell-biology/Secretory-vesicles https://nios.ac.in/media/documents/SrSec314NewE/Lesson-04.pdf https://ncert.nic.in/pdf/publication/exemplarproblem/classVIII/science/heep108.pdf https://med.libretexts.org/Bookshelves/Anatomy_and_Physiology/Book%3A_Human_Anatomy _and_Physiology_Preparatory_Course_(Liachovitzky)/04%3A_Smallest_Level_of_Complexity_ Alive-_Cells_Their_Structures_and_Functions/4.01%3A_Cell_Structure_and_Function https://www.youtube.com/watch?v=URUJD5NEXC8 https://encrypted- vtbn0.gstatic.com/video?q=tbn:ANd9GcRvB4Sn3kiummaGCLdnWMbpRu8faf_dNOAMzQ https://www.youtube.com/watch?v=kcG1F88KQA0 33 https://www.youtube.com/watch?v=V6s0xOTNmT4 5.8 Possible Answers to Self-Assessment Exercises Answers to SAE 1 1. The unified cell theory states that: all living things are composed of one or more cells; the cell is the basic unit of life; and new cells arise from existing cells. 2. The expanded version of the cell theory is made up of: Cells carry genetic material passed to daughter cells during cellular division All cells are essentially the same in chemical composition Energy flow (metabolism and biochemistry) occurs within cells Answers to SAE 2 1. A microscope is an instrument that magnifies an object 2. In contrast to light microscopes, electron microscopes use a beam of electrons instead of a beam of light. Answers to SAE 3 1. Cytotechnologist (cyto- = cell) is a professionals who study cells through microscopic examinations and other laboratory tests. 2. 1670s Glossary Applied science: a form of science that solves real-world problems Basic science: science that seeks to expand knowledge regardless of the short-term application of that knowledge Control: a part of an experiment that does not change during the experiment Deductive reasoning: a form of logical thinking that uses a general statement to forecast specific results Descriptive science: a form of science that aims to observe, explore, and find things out Falsifiable: able to be disproven by experimental results Hypothesis: a suggested explanation for an event, which can be tested Inductive reasoning: a form of logical thinking that uses related observations to arrive at a general conclusion Life science: a field of science, such as biology, that studies living things Natural science: a field of science that studies the physical world, its phenomena, and processes Physical science: a field of science, such as astronomy, physics, and chemistry, that studies nonliving matter Science: knowledge that covers general truths or the operation of general laws, especially when acquired and tested by the scientific method Scientific law: a description, often in the form of a mathematical formula, for the behavior of some aspect of nature under certain specific conditions Scientific method: a method of research with defined steps that include experiments and careful observation Scientific theory: a thoroughly tested and confirmed explanation for observations or phenomena 34 End of the module Questions 1. What process causes the diversity of life? 2. How do we organize diversity of life? 3. How does evolution lead to both the diversity and unity of life? 4. Why is organization of life important? 5. List the levels of organization, ranging from simplest to most complex. 6. Describe what it means to "Construct a Hypothesis." 7. What does a scientist do if the hypothesis is not supported? 8. Outline the steps of a scientific investigation. 9. Give an example of a scientific question that could be investigated with an experiment. Module 2: Structure and Functions of the Cell Module Structure In this module we will discuss about the cellular organization, structure and functions Unit 1: Cell and Cell Components Unit 2: Cells Communication Unit 3: Tissues, Organs and Organ Systems Unit 4: Characteristics and Classification of Living Things Unit 5: The Study of Genes and Chromosomes Unit 6: Reproduction Process and Life cycles Glossary End of note questions Unit 1: Cell and Cell Components Unit Structure 1.1 Introduction 1.2 Intended Learning Outcomes (ILOs) 1.3 Cellular Organization 1.3.1 Prokaryotic Cell 1.3.2 Eukaryotic Cell 1.4 Cell Organelles 1.5 Other Organelles 35 1.6 Summary 1.7 References/Further Readings/Web Sources 1.8 Possible Answers to Self-Assessment Exercises 1.1 Introduction You will learn in this unit that the cell falls into one of two broad categories: prokaryotic and eukaryotic. You will study that the predominantly single-celled organisms of the domains Bacteria and Archaea are classified as prokaryotes (pro- = before; -karyon- = nucleus), and all other animal cells, plant cells, fungi, and protists are eukaryotes (eu- = true). You will also learn how to draw and describe the structure of the various cell organelles 1.2 Intended Learning Outcomes (ILOs) By the end of this unit, you will be able to: Illustrate the structure of a prokaryote and eukaryote cells Describe the structure of plant and animal cells by drawing labelled diagrams; Differentiate between a Unicellular and Multicellular organisms describe the structure and function of the various cell organelles 1.3 The Cell and its Components Although all cells share certain features (for example, every cell has a plasma membrane), biologists recognize two fundamentally different categories of cells: prokaryotic and eukaryotic. We compartmentalize cells into several structures, organelles with specific functions. Organelles are subunits in the anatomy of the cell. The compartmentalization inside the cell allows many different functions to be localized in specific places. This brings about a high level of organization and efficiency in the cell. In this unit we will discuss the structures and functions of the different parts of the cell. 36 Figure 1. An image illustrating the difference between Prokaryotic and Eukaryotic Cells. Note that the prokaryotic cell is a complete individual organism. Source: www.byjus.com Advancements in science and technology shed more light into the cell, with new findings and discoveries about its structure and cellular components. In 1950s, scientists postulated the concept of prokaryotic and eukaryotic cells, with earlier groundwork laid by Edouard Chatton, a French biologist in 1925. Anatomically, cells vary in respect to their classification, thus, prokaryotic cells and eukaryotic cells differ from each other drastically. Read on to explore how they differ from each other. 1.3.1 Prokaryotic Cell The term “prokaryote” is derived from the Greek word “pro” (meaning: before) and “karyon” (meaning: kernel). It translates to “before nuclei”. Prokaryotes are one of the most ancient groups of living organisms on earth, with fossil records dating back to almost 3.5 billion years ago. These prokaryotes thrived in the earth’s ancient environment, some using up chemical energy and others using the sun’s energy. These extremophiles thrived for millions of years, evolving and adapting. Scientists speculated that these organisms gave rise to the eukaryotes. Prokaryotic cells are comparatively smaller and much simpler than eukaryotic cells. The other defining characteristic of prokaryotic cells is that they do not possess membrane-bound cell organelles such as a nucleus, and reproduction is by binary fission. 37 Structurally, each prokaryote has a capsule enveloping its entire body which functions as a protective coat. This is crucial for preventing the process of phagocytosis (where the bacteria gets engulfed by other eukaryotic cells, such as macrophages). A hair-like appendage found on the external surface of most prokaryotes is called pilus, and it helps the organism to attach itself to various environments. The pilus is commonly observed in bacteria and essentially resists being flushed, hence, it is also called attachment pili. Right below the protective coating lies the cell wall, which provides strength and rigidity to the cell. Further down lies the cytoplasm that helps in cellular growth, and is contained within the plasma membrane. This separates the inner contents of the cell from the outside environment. Ribosomes exist within the cytoplasm; it is also one of the smallest components within the cell and plays an important role in protein synthesis. Some prokaryotic cells contain special structures called mesosomes which assist in cellular respiration. Most prokaryotes also contain plasmids, which contain small, circular pieces of DNA. To help with locomotion, flagella are present, though, pilus can also serve as an aid for locomotion. Common examples of Prokaryotic organisms are bacteria, archaea and all members of Kingdom Monera. 1.3.2 Eukaryotic Cell The term “Eukaryotes” is derived from the Greek word “eu“, (meaning: good) and “karyon” (meaning: kernel), being translated to “good or true nuclei.” Eukaryotes are more complex and much larger than prokaryotes. They include almost all the major kingdoms except kingdom monera. Structurally, eukaryotes possess a cell wall, which supports and protects the plasma membrane. The cell is surrounded by the plasma membrane which controls the entry and exit of some substances. The nucleus is surrounded by the nuclear membrane and contains DNA, which is responsible for storing all genetic information. Within the nucleus is the nucleolus, and it plays a crucial role in proteins synthesis. Eukaryotic cells also contain mitochondria, which are responsible for the production of energy utilized by the cell. Chloroplasts are the subcellular sites of photosynthesis present in only plant cells. The endoplasmic reticulum helps in the transportation of materials. Besides these, there are also other cell organelles that perform various other functions, these include ribosomes, lysosomes, Golgi bodies, cytoplasm, chromosomes, vacuoles and centrosomes. Examples of eukaryotes include almost every unicellular organism with a nucleus and all multicellular organisms. 1.3.3 Difference between Prokaryotic and Eukaryotic Cells Though these two classes of cells are quite different, they do possess some common characteristics. For example, both possess cell membranes and ribosomes. The complete list of differences between prokaryotic and eukaryotic cells is summarized as follows: Feature Prokaryotes Eukaryotes Organisms Bacteria Protists, fungi, plants and animals Cell size Average diameter 0.5 - 10µm Diameter commonly 1000 – 10000 times the volume of prokaryotes Form Mainly unicellular Mainly multicellular Evolution origin 3.5 thousand million years ago 1.2 thousand million years ago, evolve from prokaryotes 38 Cell division Mostly binary fission, no spindle Mitosis, meiosis or both, spindle formed Genetic material DNA is circular and lies freely in the DNA linear and contained in a cytoplasm (no true nucleus). DNA is nucleus. DNA is also associated also naked; not associated with with RNA to form chromosomes RNA to form chromosomes. Protein synthesis 70s ribosomes, no endoplasmic 80s ribosomes, and may be attached reticulum to endoplasmic reticulum Organelles Few organelles, none surrounded by Many organelles and envelope- envelope (two membranes) bound organelles present eg. nucleus, mitochondria, chloroplast. There are also some organelles bounded by single membrane eg. golgi apparatus, lysosomes, endoplasmic reticulum. Cell wall Rigid and contain polysaccharides Cell walls of green plants and fungi with amino acids; murein are rigid and contain strengthening compounds. polysaccharides; cellulose is the main strengthening compounds of plant cell walls. Chitin for fungal cell wall while there is no cell wall in animal cells. Flagella Simple, lacking microtubules; Complex

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