What is Life? How is it Organized? How do we Classify it? What is Knowledge? How do we obtain it?

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Within the electron cloud Scale: meters = 1 pm = 1 picometer The inner electron cloud Scale: meters = 10 pm = 10 picometers Carbon's outer electron shell Scale: meters = 100 pm = 100 picometers The molecules of DNA Scale: meters = 1 nm = 1 nanometer DNA within a virus Scale: meters = 10 nm = 10 nanometers A virus Scale: meters = 100 nm = 100 nanometers Virus on a bacterium Scale: meters = 1 m = 1 micrometer Bacteria Scale: meters = 10 m = 10 micrometers Pollen Scale: meters = 100 m = 100 micrometers A bee's eye Scale: meters = 1 mm = 1 millimeter A bee's head Scale: meters = 1 cm = 1 centimeter A lily and a bee Scale: meters = 10 cm = 10 centimeters The one-meter square Scale: 1 00 meters = 1 meter A pond with lily pads Scale: 1 01 meter = 10 meters Japanese Tea Garden Scale: 1 02 meters = 100 meters Golden Gate Park Scale: 1 03 meters = 1 km = 1 kilometer San Francisco Scale: 1 04 meters = 10 km = 10 kilometers The San Francisco Bay Area Scale: 1 05 meters = 100 km = 100 kilometers California Scale: 1 06 meters = 1 Mm = 1 megameter North and Central America Scale: 1 07 meters = 10 Mm = 10 megameters Earth Scale: 1 08 meters = 100 Mm = 100 megameters Earth and Moon Scale: 1 09 meters = 1 Gm = 1 gigameter Four days in July Scale: meters = 10 Gm = 10 gigameters Venus, Earth, and Mars Scale: meters = 100 Gm = 100 gigameters The orbit of Jupiter Scale: meters = 1 Tm = 1 terameter The Solar System Scale: meters = 10 Tm = 10 terameters: Sol Scale: meters = 100 Tm = 100 terameters Sol Scale: meters = 1 Pm = 1 petameter Sol Scale: meters = 10 Pm = 10 petameters (1ly) Stars within 50 light years Scale: meters = 1 Em = 1 exameter (~100 light years) The nearest stars Scale: meters = 10 Pm = 100 petameters (~10 light years) Quarks Scale: meters = 100 am = 100 attometers Within the protonScale: meters = 1 fm = 1 femtometer The carbon nucleus Scale: meters = 10 fm = 10 femtometers The nucleus Scale: meters = 100 fm = 100 femtometers Scale: meters = 10 Em = 10 exameters (~1 000 light years)The stars within the arm Scale: meters = 100 Em = 100 exameters (~ light years)Our spiral arm Scale: meters = 1 Zm = 1 zettameter (~ light years)The Milky Way Scale: meters = 10 Zm = 10 zettameters (~1 million light years)The local group Scale: meters = 100 Zm = 100 zettameters (~10 million light years)The Virgo Cluster Scale: meters = 1 Ym = 1 yottameter (~100 million light years)Galactic Clusters Scale: meters = 10 Ym = 10 yottameters (~1 thousand million light years)The limit of our knowledge

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What is Life? How is it Organized? How do we Classify it? What is Knowledge? How do we obtain it? Get out a piece of paper and a pen. Watch this video Write down anything that you recognize, or any thoughts that come to your mind as you watch. Within the electron cloud Scale: meters = 1 pm = 1 picometer The inner electron cloud Scale: meters = 10 pm = 10 picometers Carbon's outer electron shell Scale: meters = 100 pm = 100 picometers The molecules of DNA Scale: meters = 1 nm = 1 nanometer DNA within a virus Scale: meters = 10 nm = 10 nanometers A virus Scale: meters = 100 nm = 100 nanometers Virus on a bacterium Scale: meters = 1 m = 1 micrometer Bacteria Scale: meters = 10 m = 10 micrometers Pollen Scale: meters = 100 m = 100 micrometers A bee's eye Scale: meters = 1 mm = 1 millimeter A bee's head Scale: meters = 1 cm = 1 centimeter A lily and a bee Scale: meters = 10 cm = 10 centimeters The one-meter square Scale: 1 00 meters = 1 meter A pond with lily pads Scale: 1 01 meter = 10 meters Japanese Tea Garden Scale: 1 02 meters = 100 meters Golden Gate Park Scale: 1 03 meters = 1 km = 1 kilometer San Francisco Scale: 1 04 meters = 10 km = 10 kilometers The San Francisco Bay Area Scale: 1 05 meters = 100 km = 100 kilometers California Scale: 1 06 meters = 1 Mm = 1 megameter North and Central America Scale: 1 07 meters = 10 Mm = 10 megameters Earth Scale: 1 08 meters = 100 Mm = 100 megameters Earth and Moon Scale: 1 09 meters = 1 Gm = 1 gigameter Four days in July Scale: meters = 10 Gm = 10 gigameters Venus, Earth, and Mars Scale: meters = 100 Gm = 100 gigameters The orbit of Jupiter Scale: meters = 1 Tm = 1 terameter The Solar System Scale: meters = 10 Tm = 10 terameters: Sol Scale: meters = 100 Tm = 100 terameters Sol Scale: meters = 1 Pm = 1 petameter Sol Scale: meters = 10 Pm = 10 petameters (1ly) Stars within 50 light years Scale: meters = 1 Em = 1 exameter (~100 light years) The nearest stars Scale: meters = 10 Pm = 100 petameters (~10 light years) Quarks Scale: meters = 100 am = 100 attometers Within the protonScale: meters = 1 fm = 1 femtometer The carbon nucleus Scale: meters = 10 fm = 10 femtometers The nucleus Scale: meters = 100 fm = 100 femtometers Scale: meters = 10 Em = 10 exameters (~1 000 light years)The stars within the arm Scale: meters = 100 Em = 100 exameters (~ light years)Our spiral arm Scale: meters = 1 Zm = 1 zettameter (~ light years)The Milky Way Scale: meters = 10 Zm = 10 zettameters (~1 million light years)The local group Scale: meters = 100 Zm = 100 zettameters (~10 million light years)The Virgo Cluster Scale: meters = 1 Ym = 1 yottameter (~100 million light years)Galactic Clusters Scale: meters = 10 Ym = 10 yottameters (~1 thousand million light years)The limit of our knowledge Nature appears to have order. There is an underlying organization to it. How do we know this? It is a basic human instinct to seek order in things. There is an, underlying premise to the way in which we examine things. How we learn: Authority (Look both ways before crossing the street!) Experience (I should have looked both ways before crossing the street) Intuition (If Ive seen cars driving by fast, then when I get to the corner, I should probably look both ways before crossing the street) Science (90% of people that cross the street but do not look both ways before moving cost upwards of 1.2 million dollars a year in public health costs. According to these statistics, we strongly recommend those crossing streets to look both ways)* *I made that up. AB The Dumbbell NebulaA Cancer Cell Nucleus AB Cateye NebualActin Filaments & PML Bodies Our mind comprehends reality by categorizing and dividing things up into chunks Science is the methodological way in which we go about this. While it is of course prone to error (were only human), when attempted faithfully, it removes our emotions and subjectiveness, yielding the most accurate information to the best of our ability. General Idea Specific Knowledge My back is killing me Sitting for long periods of time Can hurt my back Induces you to think Inductive Reasoning Deductive Reasoning General Idea Specific Knowledge Old Milk CurdlesMy milk might taste bad. You deduce that Definitions Inductive Reasoning: Bottom-Up; moving from something specific to something general. (induce brings something from nothing induce change, etc. It brings something new into being.) Deductive Reasoning: Top-Down; moving from the general to the more specific. (Deduce is subtracting deduct a sum of money from an account, etc. Take away the layers and uncover whats underneath. In the case of the science, you dig through the data and uncover a conclusion. Scientific Method - Summary Experiment Controls Phenomenon Something Interesting Hypothesis Inductive Reasoning Data Analysis Observation Senses / Instruments Prediction Falsifiable Conclusion Does it fit the hypothesis? Principle / Law A theory that has been around long enough without being refuted. Theory A hypothesis that is continually supported by experimental data over time, with no direct contradictions Cell Theory Atomic Theory Evolution Theory Gravitational Theory Etc. Gather into groups of 3-4. Designate a group leader. As a group, write a list of 5-10 biological objects. They can be anything (reasonable). Keep It clean! As a group, discuss and pick two. Link them together in a creative way to describe some kind of phenomenon, from which you will form a hypothesis using inductive reasoning. Raise your hand for help. Group leaders make final decisions if there are any disagreements. Each group will read their hypothesis out loud. Each group will then come up with a Prediction for that hypothesis by deductive reasoning. From that prediction, each group will design a simple experiment to test the prediction, and include appropriate controls. Each group will briefly describe their experiment and controls. We will try to go over each experiments strengths and weaknesses. 1. Organized 2.Acquires material & energy 3.Respond to its environment 4. Reproduce & Develop 5. Adapt to its environment Atoms make up molecules which make up macromolecules which make up cellular structures which make up cells which make up cell systems which make up organs which make up organ systems which make up organisms which make up populations which make up communities, which, together with the environment, make up ecosystems which make up the biosphere. 1 Emergence Each new level of organization leads to new properties of the system that the individual components do not have (e.g. cells cant see, but as a system, the eye can) Therefore, new properties emerge from the system as it becomes more complicated. These new traits are called emergent properties. Can you think of other emergent properties? 1 Emergence Elementary particles (electrons, proteins, neutrons) do not have color. But together, they form particle systems (atoms), which can absorb specific wavelengths of electromagnetic radiation. Therefore, Color is an emergent property of elementary particles Surface tension of water emerges as a result of the hydrogen bonding of water molecules Emergent structures of groups of organisms: flocks of birds, ant colonies, schools of fish. 1 Things that are alive can extract energy from their environment, and use it to perform work. This work includes a vast amount of different processes maintaining homeostasis (pH, salts, etc.) Constantly repairing DNA against external insults every cell in your body has about 20,000 DNA damage events a DAY and you have ~3 trillion cells 2 Homeostasis Homos, same, stasis, standing still. Maintaining a stable, constant set of parameters. You sweat when youre hot, shiver when youre cold, hunger when youre low on energy, and thirsty when fluids get low. You breath heavily when you run so you can maintain the same level of oxygen in your system as it uses it faster. Theres a zone for each characteristic. Think of a standard blood test there is a range in which things can fall. The farther you move out of the zone, the more uncomfortable you feel pain and discomfort are necessary survival traits. 2 Metabolism Metabole, change The total sum of all chemical reactions taking place inside an organism responsible for breaking down the raw materials (from food usually) and building what they need to make their parts (e.g. fix a damaged gene, patch a hole in the membrane, etc.) and products (e.g. hormones) 2 Ensures survival. Running away from a bear, fire, or gun-wielding crazy person; Getting closer to the fire on a cold night Moths to a flame so its not always a good thing. Plants bend towards light. This is an example of tropism, in this case, phototropism. What other kinds of tropisms are there? 3 Modern Life only comes from other modern life. Question: What came first, the chicken or the egg? Answer: There is no beginning or end to a circle Development: What decides that an embryo develops into a human or a mouse? Our Genes. Were 85% genetically identical to mice and 99.98% (or so) identical to chimps. It is important to understand that offspring are NOT identical to parents. There are many processes at work that cause a continual variation between generations. 4 If you cant beat it, join it. Brown Fat: instead of making ATP, the cells simply give off extra heat. Webbed feet of a duck Natural Selection: The principle that organisms with beneficial traits with respect to the environment, will, over time, produce more offspring. Descent with modification: All living being share the same basic characteristics (particularly at the molecular level); this suggests there was a single common ancestor (LUCA) We will discuss this at more length when we cover the Principles of Evolution. 5 Invented for our Own understanding Existing relationships we uncover through research Binomial Nomenclature Taxonomy Phylogenetics We work to name all living things. We work to categorize all living things based on their similarity to each other. We discover each living things evolutionary connections with each other Taxonomy: From greek taxis or tasso, meaning arrangement Nomia, method, usage, law The swedish natural philosopher, Charles Linnus, is considered the father of modern scientific classification. A human contrivance that attempts to pigeonhole every living thing on earth, both extinct and extant, into a single category. Problems: Things dont always fit within the system (Platypus, anyone?) There is still MUCH to learn and discover. There are still huge realms of undiscovered country in the realm of life science, and new surprises are happening on a regular basis. Recently: Largest virus discovered, found to be on par with bacteria and possess much but not all of what a cell is thought to have. How do we classify it?? Plasma in outer space is shown to actually develop organized structure. This clearly does not fit within the paradigm of carbon-based life. Are there other paradigms of life? Concept: Life as an emergent property of complex systems. Bottom Line: Were still working on it. Also a work in progress There is a distinction between naming an organism or group of organisms, and grouping them. Whether I group you according to where your ancestors came from, or whether I group by your hair color, you are still homo sapiens and dont change your name. This is important, because while we can readily identify two different species (and therefore give them unique names with confidence), because we are still trying to understand the deepest complexities of biology at the molecular level, our classifications schemes remain imperfect. This is where Phylogenetics comes into play. This is the study of how related species are based on their evolutionary relationships (particularly how their DNA sequences fit together, forming branched lineages. This type of A taxon (plural taxa) is just a group of organisms or sometimes, just a species. The current system underwent its last major revision in 1990, when the most inclusive taxon level (the kindgom) was replaced by an even MORE inclusive taxon called a Domain. Have you ever played 20 questions and wondered why we start by saying is it an animal, vegetable, or mineral? Those were the original Three Kingdoms set up by Charles Linnaeus in his Systema Naturae ( , 10 editions overall) We used to classify things by morphology (how things looks), shared characteristics (bony fishes vs. cartilaginous fishes; warm-blooded vs. cold- blooded), etc. This is the field of taxonomy. With the advent of genetic research, things have changed. We are now beginning to shuffle around the way in which things are classified depending upon their evolutionary relationship to one another. Ultimate goal: The Tree of Life, where every organism is linked to every other through a continuous chain of lineages. Domain Kingdom Class Family Order Genus Species Phylum Currently Accepted Taxons Taxons vary in Botany Zoology Virology BacteriaEukaryaArchae Domain 3 ProtistaPlantaeFungiAnimalia Domain Kingdom BacteriaEukaryaArchae Kingdoms in progress. 4 Protists are the pot-luck kingdom. There are: Plant-Like Protists Animal-Like Protists Fungus-Like Protists 38 animal11 plant6 fungi16 bacteria 2-3 Archae Domain Kingdom Phylum Over 70 ProtistaPlantaeFungiAnimalia BacteriaEukaryaArchae Kingdoms in progress. From the greek Phyle, tribe or clan and phylon, race or stock. Generally speaking, phylum (also known as divisions sometimes, mostly by botanists) are arranged based on shared evolutionary traits and physical appearance (up until only a the last 2 decades have we been able to more accurately classify life based on gene sequences) Domain Kingdom Phylum Chordates: Have notocords. Includes both Vertebrates and Invertebrates. (in higher vertrebrates the notocord is only present during development, and is eventually replaced by the spinal cord) A sub phylum includes the vertebrates. Here is an example in which the current taxonomy isnt very orderly. Domain Kingdom Class Family Order Genus Species Phylum Mammals Domain Kingdom Class Family Order Genus Species Phylum Carnivores. Domain Kingdom Class Family Order Genus Species Phylum Generally named for a type of genus. Canidae (dogs, wolves, foxes, coyotes, dingoes, jackals, etc.) Domain Kingdom Class Family Order Genus Species Phylum Also named for a type of genus. Canidae (dogs, wolves, foxes, coyotes, dingoes, jackals, etc.) Domain Kingdom Class Family Order Genus Species Phylum Domestic Dogs are Canis Lupus. However, some classify them as a sub-species of Grey Wolf, Canis Lupus Familiaris. So genetically speaking, there is VERY little difference between that little fluffy pocketbook dog and the huge mastiff. Classical Taxonomy (organizing life by similar characteristics) is still distinct from Phylogenetics (connecting organisms by their evolutionary relationships, mostly through biochemical and genetic links) It is still unclear how these two will merge.