Essential Biology - Topic 1 Study of Life PDF

ESSENTIAL BIOLOGY TOPIC 1 STUDY OF LIFE Set book: Raven P., Johnson G., Mason K., Losos J., and Singer S. (2022). Biology (14th Edition). New York: McGraw-Hill Week 1 2 1.1 Definition of life What is life?? Definition of Life 3   What is life? How to differentiate an inanimate object and a living...

ESSENTIAL BIOLOGY TOPIC 1 STUDY OF LIFE Set book: Raven P., Johnson G., Mason K., Losos J., and Singer S. (2022). Biology (14th Edition). New York: McGraw-Hill Week 1 2 1.1 Definition of life What is life?? Definition of Life 3   What is life? How to differentiate an inanimate object and a living organism? Definition of Life 4  Cellular organisation – made of cell  Ordered complexity – complex and with level  Sensitivity – respond to stimuli  Growth, development, reproduction  Energy utilisation - use energy to perform work  Homeostasis – maintain stable internal condition which different from external environment  Evolutionary adaption 5 1.2 Biology Organization Different level of study Biology organization – different level of study 6 Cell Tissue Organ Organ System Organism The basic building block of life When similar cells aggregate Collection of tissues and similar structures that all function as one. Association of different organs and other anatomical structures that perform a certain physiological process. Living thing that is composed of various organ systems that function altogether. Population Community Ecosystem Biome Biosphere When such individuals reside a common environmental at a given time The interactions of different populations with each other The interaction of community to the abiotic or non-living environment Huge geographic area where various ecosystems exist and different organisms adapt to it. Global system where life exist and the abiotic environments they reside in, all blending with each other. Cellular Level 7 Cellular Level – Biomolecule, organelle, cell  Major molecules found in cells is called biomolecules  Biomolecules form organelles and cells  Cell is the basic unit of all life forms  Biochemistry, cell biology, microbiology, molecular biology, molecular genetics, Organism level 8 Organism level - tissue, organ, system, organism  Same type of cells form tissue  Many different tissue work together to form organ  Many organ work together to form system & organism  Histology, anatomy, physiology, zoology, botany Population level 9  Population level – Population, community, ecosystem, biosphere  Same organism (species) form population  Different population live/interact together form community  Interaction between organisms, communities and the abiotic environment (habitat) is ecosystem  Biosphere is the global system comprise of everything where life exists and their abiotic environment  Population genetics, ecology, community ecology, conservation biology Did we miss anything? 10  We have something in between living and non-living  Virus – by itself it cannot fulfil the definition of life  Prion – it can “reproduce” Seven unifying concepts /Themes in biology 11  Living systems are organized into cell – Cell theory  The molecular basis of inheritance explains the continuity of life  The relationship between structure and function underlies living systems  The diversity of life arises by evolutionary change  Evolutionary conservation explains the unity of living systems  Cells are information-processing system  Living systems exist in a non-equilibrium state 12 1.3 Scientific Methods of studying biology How do we study and understand the living world? What is Science? 13  Science is the way or a set of method to understand the natural world (nature)  So physics, chemistry, biology, geology, geography, astronomy are all science  So, is ”Fung Shui” or the part about God’s creation in Bible ‘Genesis’ a science? What is science? 14  They are not science because these practice or saying does not use the set of methods used in science.  ‘Fung Shui’ and ‘Genesis’ are either superstitious or a believe / faith / religion So what is the method science use? 15  Observations (descriptive)  Objective  Verified by others  Reasoning (logic)  Deduction  Induction Guess > Compute > Observation 16    We start with a question of “why”? But before we can ask ”why”, you have to see something we don’t know first i.e. observations and description https://www.youtube.com/watch?time_continue=64&v=EYPapE-3FRw Guess > Compute > Observation 17  After we understand the question before us clear enough, then  We guess the possible reasons of why something is like that  i.e. we make hypothesis (hypotheses [p])  After we make hypothesis, we need to predict what will happen if the hypothesis is correct https://www.youtube.com/watch?time_continue=64&v=EYPapE-3FRw Guess > Compute > Observation 18  Finally, we test the hypothesis by doing experiments to see if the nature behaves as we predicted  If yes, then the hypothesis may be correct  If no, then the hypothesis is wrong  i.e. we observe again > new question Our process is easy 19 1. Observe and describe the question 2. Setting hypothesis and predict what will happen 3. Testing the hypothesis by experiments Hypothesis-driven science makes and tests predictions 20 Raven P. et. al. (2017). Biology (11ed). NY: McGraw-Hill. p5 Guess > Compute > Observation 21  That’s why  People think biology is about facts only because of a lot of description of observations  Answers often lead to more questions  Biology is an experimental science How to compute and predict 22  We predict by deductive Reasoning (演繹法) For example:  All mammals have hair  You find an animal that does not have hair  You may conclude this animal is not a mammal  A biologist uses deductive reasoning to infer the species of a specimen from its characteristics How to Test Hypothesis 23    We test by Inductive Reasoning / Scientific Method (歸納法) We assume “we can’t know what is right, but can only know what is wrong” Why? Deductive Reasoning 24  Eg. For the statement of “Human is mortal”  Why we think that it is true?  Because all human that we have seen so far are all mortal  Because we can’t observe all human beings, so we take a leap of faith and assume human are mortal (generalise) Deductive Reasoning 25    But when one day we find one individual human is immortal Then the statement of “Human is mortal” will be rejected/disproven, i.e. wrong Science is developed around this concept This is why… 26    Science is about how to handle uncertainty Why in statistics, we have the measure of ”confidence interval” and “p-value” (how much leap of faith we are taking”) We design our experiment not to prove an hypothesis is correct but to disprove an hypothesis 27 1.4 Basic Technique and Tools Techniques and Tools for Observations and Measurements 28  Observations and description are crucial to science  Have to be precise and accurate  Measurement is to describe something very precisely   Except in ecology, many of the experiments take place in laboratory Many of the experimental techniques used are for liquid handling and visualisation Liquid Handling 29   Pipetting (taking), mixing, aliquoting (distribute evenly), diluting, concentrating Tools for pipetting, mixing, aliquoting, diluting liquid  Pipette – precise pipetting (0.1ｕL – 1mL)  Pipet tip  Pipet aid – rough pipetting of large volume (5mL – 25mL)  Serological pipet Auto-pipette 30 p10 (0.5 – 10 uL) P2 (0.2 – 2 uL) p100 (10 – 100 uL) p200 (20 – 200 uL) p1000 (100 – 1000 uL) Liquid Handling 31   Tools for holding liquid  Microcentrifuge tube (0.2 mL – 2mL)  Centrifuge tube (5 mL, 15 mL, 50mL)  Conical flasks (50 mL– 250 mL) Tools for separating solid from liquid  Microcentrifuge for microcentrifuge tube  Centrifuge  Filter Tubes (0.5ml, 1.5ml, 2ml) 32 0.5mL tube 1.5mL tube 2mL tube Tubes (15ml, 50ml) 33 Corning™ 50 mL tube / falcon 15 mL tube Centrifuges 34 Mini-Centrifuge No specific speed control For spin down splashed liquid in tubes For 0.2mL to 2mL tubes Bench-top centrifuge Specific speed control Some with cooler For precipitation or separation of solid from liquid 1.5mL – 2mL tubes Centrifuges 35 Bench-top centrifuge Specific speed control Some with cooler For precipitation or separation of solid from liquid 15mL – 50mL tubes 96-well plate Techniques in Liquid Handling 36    Pipetting – transfer of liquid Aliquot – distribute a same vol. of liquid to different tubes. Eg. Transfer 10mL of sample to 10 tubes, 1mL @ Serial Dilution – dilute a sample at a fixed ratio Serial Dilution 37  E.g. Concentration of a sample is 10,000X  We dilute 10X each time for 5 times  10,000X; 1000X; 100X; 10X; 1X; 0.1X  Assume each tube need 1mL Usually 10x 38 Adjust the inconsistencies of our eyesight in one or both eyes Primary lens. Usually 4x, 10x, 20x, and 100x Collect and focus the light from the illuminator on to the specimen Focus the microscope by moving the stage up and down Controls the amount of light reaching the specimen Support the microscope and house the illuminator/light source https://www.timvandevall.com/microscope-diagram-parts-of-a-microscope/ Microscope imaging 39 https://www.keyence.com/ss/products/microscope/bz-x700/study/principle/003/index.jsp Magnification 40 End of Topic 1 If you have questions, please send email / phone me to make an appointment for asking questions. 41