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Unformatted text preview: 1/9/2008 Announcements NYT articles on Carmen appear on right side of web page Only need to read articles we discuss in class Announcements Newspaper articles to be read for quiz: "In Greenland, Ice and Instability A vast frozen dome erodes. What will happen to the seas? NYT, 8 Jan 08 D1 D4 NYT 08, D1, "Virus linked to vanishing birds" first lecture notes "Get religion out of science education" blog assignment ??? Check here after lecture for complete list Also need to read articles from other newspapers (e.g., Columbus Dispatch) that are discussed in class e.g., West Nile Virus article in Lecture 1 All articles will be posted on Carmen Final versions of lectures will be posted to Carmen Quiz format Multiple choice 15 questions, 30 points, ~ 20-25 min. What will we be tested on? Emphasize general concepts presented in lecture Application of general concepts Main ideas of newspaper articles and application of lecture concepts to newspaper articles What's news? "In Greenland, Ice and Instability A vast frozen dome erodes. What will happen to the seas? NYT, 8 Jan 08 D1 D4 NYT 08, D1, In Greenland, Ice and Instability Researchers studying how Greenland glaciers are melting Ice cap is getting smaller and melting appears to be accelerating pp g Lakes and rivulets form, darkening the ice cap and absorbing up to 4 times as much energy as white snow Moulins carry melt water to the bedrock In Greenland, Ice and Instability Water at bedrock may lubricate the movement of glaciers May cause release of water backed up behind ice dams Most i ti t M t scientists agree sea level will rise, th l l ill i the question are "How much?" and "How fast?" Some say feet to yards Some say the ice cap will remain relatively stable so sea level may rise only inches Seas rose <1 foot in 20th century 1 1/9/2008 In Greenland, Ice and Instability No significant debate any more if greenhouse gas emissions follow "business as usual", significant melting of Greenland and Antarctic ice sheet will occur "...hope that the public and policy makers did not interpret uncertainty in the 21st century forecast as a reason for complacency on the need to limit risks by cutting emissions" What do we know about: Four perspectives: Spontaneous Generation Panspermia Special Creation/Intelligent Design Biogenesis "Origin of life is not a simple issue" Scott 2004 What is life? Is this an issue that pits science and religion in direct conflict? Or does it? Universe made up of matter and energy, a material universe Goal of science: to describe the world in terms of matter and energy Most people believe there is more but that is outside the realm of science Difference between science and religion Science seeks answers to the question "how?" and not "why?" Religion seeks answers to the question "why?" Scientific method Observation Question Hypothesis Test does not Prediction support t hypothesis: Conduct Test: additional tests; Experiment revise or pose or additional new hypothesis observation Hypothesis must be testable against the natural world Test supports hypothesis: Make additional predictions 2 1/9/2008 Four perspectives: Spontaneous Generation Panspermia Special Creation/Intelligent Design Biogenesis Spontaneous Generation It happens every day! Mosquitos From Mud! Mice From Old Mi F Shirts and Barley Grains! Disease From Marsh Gas! Flies From Meat! Fireflies From Morning Dew! Four perspectives: Spontaneous Generation Panspermia Special Creation/Intelligent Design Biogenesis Panspermia Life is common in the universe and was brought to Earth by: or? Four perspectives: Spontaneous Generation Panspermia Special Creation/Intelligent Design Biogenesis Special Creation Iroquois view - Skywoman (~1400 AD) Babylonian view (~2000 BC) 3 1/9/2008 Special Creation Yahwist text: Genesis ( (850-750 BC) ) Intelligent Design: Life is too complex to have evolved, so it must have been designed by an intelligent designer
Special Creation Interpretations of events, religious theories, anecdotal evidence, beliefs, beliefs but NOT science and the application of the scientific method Scientific method cannot be used to test these ideas since they invoke supernatural events Four perspectives: Spontaneous Generation Panspermia Special Creation/Intelligent Design Biogenesis Biogenesis Basic Premise: Life evolved on earth from pre-existing life...but how did pre-existing come about? Four Stages: 1) 2) 3) 4) Abiotic Synthesis of Organics Abiotic Synthesis of Polymers Origin of Self-replicating Molecules Formation of Pre-cells Origin-of-life (biogenesis) research has focused on: 1) Abiotic Synthesis of Organic Chemicals how Evolutionary History of Earth (Astronomical, chemical) were simple organic chemicals produced? 2) Abiotic Synthesis of Polymers how were proteins produced? 3) Origin of Self-replicating Molecules formation of "hereditary" organic molecules 4) Formation of Pre-cells how did cell membranes form? Big Bang 10-12 billion years ago Explosion of extremely dense mass 4-5 4 5 billion years ago: Earth solidifies 4.2 billion years ago: Oceans and atmosphere stable Atmosphere thought to be reducing in nature 4 1/9/2008 Today's Atmosphere The Early Atmosphere NH3 HCN H2S H2 N2 O2 CO2 H2O An Oxidizing Atmosphere: Things Combine with Oxygen A Reducing Atmosphere: Things Combine with Hydrogen SO2 NO2 CH4 H2O Evolutionary History of Earth (Chemical, biological) Evolutionary History of Earth (Chemical, biological) 4.1 billion years ago: oldest sedimentary rocks 3.8 billion years ago: earliest "chemical" fossils 3.5 billion years ago: earliest unequivocal fossils 3.2 billion years ago: earliest photosynthetic fossils ( yg (oxygen as a waste p product) ) 3.2 2.5 billion years ago: atmosphere begins to shift from reducing to oxidizing Evolutionary History of Earth (Chemical, biological) Stage 1: Abiotic Synthesis of Organic Compounds The experiments of Stanley Miller in the 1950s 1.5 billion years ago: earliest multicellular fossils 1.1 billion years ago: atmosphere substantially like that of today 5 1/9/2008 Other Researchers Showed: Miller's Experiments Showed: Abiotic Synthesis of Small Organic Molecules, e.g. Amino Acids Molecules that have been produced abiotically in the laboratory All 20 amino acids Several sugars Lipids Li id Nucleotides ATP Organic molecules could be produced under conditions assumed to exist in ancient atmosphere and sea Stage 2: Abiotic Synthesis of Polymers (Chain Compounds) Stage 3: Origin of Self-Replicating Compounds (like DNA and RNA) Laboratory experiments - short RNA molecules can assemble spontaneously Concentration of building blocks: Dripping onto hot sand Evaporation in tide pools Adsorption onto clay particles Around deep sea thermal vents G-guanine, C-cytosine, A-adenine, U-uracil Stage 3: Origin of Self-Replicating Compounds (like DNA and RNA) 1980s RNA in cells has catalytic activity Catalytic RNA called ribozyme Protein (enzymes) not needed for reactions Ribozymes catalyze their own replication; template for protein formation Complementary Base Pairing provides mechanism for: Replication of RNA, DNA; transfer of information from one "generation" to the next Transfer of information from DNA, RNA to p proteins Some attributes of life as we know it passing of "hereditary" information 6 1/9/2008 Stage 4: Formation of pre-cells Self-replication of RNA Self-replicating RNA acts as template on which polypeptide forms Polypeptide Polypeptide acts as primitive enzyme that aids RNA replication RNA Stage 4: Formation of Pre-cells Liposomes - (fatty, little globules) Coacervate droplets (protein-based spheres) are common today Some properties of life emerge from interaction of molecules organized into higher levels of order Membrane Formed during lab experiments Polypeptide Stage 4: Formation of Pre-cells Membranes are made of amphiphiles - molecules with parts that are hydrophilic (water loving) and parts that are lipophilic (fat loving) Hydrophilic head that interacts with water soluble things on inside & outside of cell Hydrophobic (or lipophilic) tail that is double layered Stage 4: Formation of Pre-cells Membranes also contain proteins and other molecules that allow physiological functions to be p performed e.g., ion channels, chemical transport Important points from this lecture: Four views on the origin of life on earth: Special creation, spontaneous generation, panspermia, biogenesis Basic premise of biogenesis: life evolved on earth th Four stages of biogenesis: 1) Abiotic Synthesis of Organics 2) Abiotic Synthesis of Polymers 3) Origin of Self-replicating Molecules 4) Formation of Pre-cells All four of these stages have been formed in laboratory tests 7 1/9/2008 Additional HOT issues: So...it's all solved...right? Laboratory experiments and simulations show that the types of chemical reactions needed to produce life COULD HAVE occurred under the conditions of early earth They do not prove it DID happen that way! Where did it happen? Shallow, warm seas or The moons of Jupiter? Additional HOT Issues When does a membraneenclosed globule with lots of proteins and other stuff in it actually become a living thing? Where's the border between living and non-living? What's life, anyway? Characteristics of Living Things: 1) Have a complex organized structure 2) Contain a heritable code (e.g., genetic information) 3) Use energy to convert materials from their environment into various macromolecules 4) Actively maintain their complex structures 5) They grow 6) Respond to stimuli 7) Reproduce 8) They mutate and evolve Additional HOT issues: What's news? "Creating first synthetic life form" Toronto Globe & Mail, 12/19/05 Scientist trying to create the first bacterium from "scratch" New fi ld of " N field f "synthetic bi l th ti biology" uses " computers to assemble nucleotides to make specific sequences of DNA Craig Venter, of human genome sequencing fame, says "we're going from reading to writing genetic code" If we know all the steps so well, when will we actually make life? 8 1/9/2008 What's news? "Creating first synthetic life form" Toronto Globe & Mail, 12/19/05 Starting with Mycoplasm genitalium 1 chromosome with 517 genes g Think that only 250 to 400 genes are needed to survive and live Hope to determine the number of genes needed to "breathe life" into the bacterium and create genes that don't exist in nature What's news? "Creating first synthetic life form" Toronto Globe & Mail, 12/19/05 Objective is to synthesize useful biochemicals vaccines hormones vitamins for human vaccines, hormones, uses Governments worried about potential applications to bioterrorism Concerns about humans altering the "nature of nature" What's news? "Tiny Specks of Misery, Both Vile and Useful" NYT, 8 Jan 08, D1, D6 How a virus works Glycoproteins on virus envelope bind to specific receptors on host cell membrane Virus enters cell, viral genome duplicates d directs host ll d li t and di t h t cell protein synthesis machinery to synthesize virus components Many viruses repackaged, bud from host cell, infect other cells These viruses do not always kill the host cell Viruses Noroviruses (stomach) Rhino and corona virusus (common cold) Herpes (cold sore) Infectious parasitic agents pass through microfilters that would trap bacteria Contain RNA or DNA with instructions for making more viruses What's news? "Tiny Specks of Misery, Both Vile and Useful" NYT, 8 Jan 08, D1, D6 What's news? "Tiny Specks of Misery, Both Vile and Useful" NYT, 8 Jan 08, D1, D6 Encased in protein capsids with correct structure to bind to specific cells Thought to have evolved with living cells Found everywhere but very short-lived shortoutside of host Straddle border of life and non-life nonViral elements are a large part of our genetic material Comparing human genetic code to viruses, base for base humans are over 50% viral Viral elements initially dismissed as "junk junk DNA" However, some scientists suggest that viral DNA is critical for our immune system to adapt so rapidly to viral infections "Viral infections have shaped the nature of the human immune system" 9 1/9/2008 This Tuesday: Quiz 1 Covers lectures, video (Prisoners of Silence), Silence) and newspaper articles (from Carmen) from 1/3 through 1/10 10 ...
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- Winter '08