Slide 1Slide 2Slide 3First Theme: Building a CellOrder of Magnitude Biology: Why the Numbers?Living Organisms are Made of CellsSlide 7A Tension: General Ideas or Embracing the DiversitySlide 9Biology’s Greatest IdeaSlide 11Slide 12Slide 13Slide 14Slide 15Slide 16Slide 17Slide 18Slide 19Slide 20Slide 21Slide 22Slide 23Slide 24Slide 25Slide 26Slide 27Slide 28Slide 29Slide 30Slide 31Slide 32Slide 33Slide 34Slide 35Slide 36Slide 37Slide 38Slide 39Slide 40Slide 41Slide 42Slide 43Slide 44Slide 45Slide 46Slide 47Slide 48Light and Life: Building a Cell Part 1APh/BE161: Physical Biology of the CellWinter 2009“Lecture # 1” – will take several daysRob Phillips(Behrenfeld, Falkowski et al., Science, 1998)“Who am I? Why am I here?” Who are you? Why are you here? - the diversity question.A few words on what this course is? Style and approach (graduate course in spirit and all that implies – “I don’t know”, all learning together, open-ended homeworks, trying to find the right questions to ask) – thinking, estimating and calculating biological phenomena. Often start with a) data from some experiment to change your life for and b) show and tell. This is followed by model building and analysis.Photosynthesis: show and tell - drinking from a powerpoint firehose. Course logistics: when, grades, TAs, expectations, website, etc.162?????????????????????????????????Logic of LectureDoes Quantitative Insight Lead to Biological Discovery? Not Just Crossing “t”s and Dotting “i”sPhotosynthesis: carbon and oxygen stoichiometryPhotosynthesis: photons,light collection and electrontransferGenetics and counting The first map of a chromosome“… no one has concentrated on the number of different forms that appear among the offspring of hybrids... No one has counted them. But doing all this counting and sorting appears to be the only way by which we can finally solve a question whose importance cannot be overestimated.” – Gregor MendelFirst Theme: Building a CellOrder of Magnitude Biology: Why the Numbers?(Smith et al.)The approach: simple order of magnitude estimates followed by description of how numbers are measured and what their significance is.Estimating and measuring the numbers serve complementary purposes. (Wu and Pollard, Science, 2005) The plan: figure out the number of molecular actors of various kinds in the drama of a cell.Reasons why: stoichiometrically correct descriptions of biosynthetic pathways, understanding of binding, regulation and cooperativity, dissection of mechanism, etc.Living Organisms are Made of CellsWhy bother? One of the great insights in the history of biology. Cells as the minimal living unit bring us to the heart of some of the great biological mysteries.``If in some cataclysm, all of scientific knowledge were to be destroyed, and only one sentence passed on to the next generation of creatures, what statement would contain the most information in the fewest words? I believe it is the atomic hypothesis.. that all things are made of atoms’’ - Richard FeynmanCells are the fundamental units of living organisms.“Omnis cellula e cellula” - every cell from a pre-existing cell. Rudolf Virchow.Cells are extremely diverse!Every time I show you a picture of a cell, ask yourself how the architecture works.For cyanobacteria, we are going to examine several remarkable specializations related to their ability to perform photosynthesis.Architecture of Cyanobacteria(Cannon et al.)A Tension: General Ideas or Embracing the DiversityThere is a great charm in both finding the unity of things and in celebrating their differences.The diversity of living organisms is thrilling and astonishing.Darwin’s notebook shows him with the realization of the single biggest unifying idea in biology: descent with modification from a common ancestor.Diversity of life gives us a gold mine of beautiful puzzles.“Nothing in Biology Makes Sense Except in the Light of Evolution”And that so includes the study of: a) how to build a cell, b) photosynthesis – our first two big themes.Biology’s Greatest IdeaLagrange on Newton: he was "the most fortunate, for we cannot find more than once a system of the world to establish.” The same can be said of Darwinand Wallace.It is a great moment to reflect on evolution: 200th birthday of Darwin, 150th anniversary of his great work “On the Origin of Species”Fascinating essay of T. Dhobzhansky entitled: ``Nothing in biology makes sense except in the light of evolution.’’ - the phrase has become hackneyed, but the idea has not.Darwin found data led to inescapable conclusion, ``it was like confessing a murder’’ he wrote.Darwin’s “species question” already helps us think about the photosynthetic process.The theory of evolution is built up on many different threads of evidence and one of the most important of those threads is the frequent extinctions revealed in the fossil record. Species have typical lifetimes measured in millions of years.Darwin’s one and only drawing in “On the Origin of Species” highlights extinctions.Darwin’s Only Figure: Extinctions and EvolutionThe Great ExtinctionsThe history of life on Earth has been punctuated by massive extinction events, some of which are famous (i.e. end of dinosaurs), but some of which are much more impressive (i.e. end Permian).For the famous dinosaur-ending extinction, a leading hypothesis argues for damage to the ability of photosynthetic organisms to collect sufficient light, with this effect propagating viciously through ecosystems.See “Extinction: Bad Genes or Bad Luck” by David Raup or “Extinction” by Doug ErwinLosing Light and LifeThe leading hypothesis on the K-T extinction event is an asteroid impact in Central America though others argue for increased volcanism.One common feature in these different scenarios is a change in the light reaching Earth with a concomitant impact on photosynthetic organisms.I bring this up here as an attempt to drive home the importance of photosynthesis to life on Earth.For those with an interest in the history of Earth, photosynthesis is also a huge player in the composition of the atmosphere.http://science.nasa.gov/headlines/y2002/images/exo-atmospheres/ATM_Time_Earths.jpgOur Pale Blue Dot: Eating the Sun“Look again at that dot. That's here. That's home. That's us. On it everyone you love, everyone you know, everyone you ever heard of, every human being who ever was, lived out their lives. The
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