MCB 140 – GeneticsSlide 2Slide 3Slide 4“Cancer Free at 33, but Weighing a Mastectomy”Slide 6Slide 7Gregor Mendel (1822-1884), and his garden in Brno (Czech Republic)Slide 9Single nucleotide polymorphism (SNP – pronounced “snip”): 1:1,000Slide 11Decode’s claimA few terms from the “detailed scientific background”Two problemsOntology vs. epistemologyMCB140 – an outlineWhat to do so as to do wellObservable phenomena, explainable and notSlide 19Heredity: “blending inheritance”?Slide 21Slide 22Slide 23Slide 24Word of the day: heuristic“Grrrrr”Joseph Kölreuter (1761): plants as a model system1761 - 1900Slide 29Mendel’s most famous wordsNewton, Darwin, Mendel, EinsteinScientific reductionismWhy?Astonishing foresightWords to live byA universally applicable statementWhat plant to pickUseful piece of experimental guidance for a geneticistA litmus test to determine, whether this class is right for youA lesson on how to get on the front page of the New York Timeshh plant and its non-Mendelian offspring“Startling Scientists, Plant Fixes Its Flawed Gene” – NYT 3/23/06Slide 43Slide 44I’m sorry, whose razor?Slide 46They should have listened to MendelSlide 48The garden pea (Pisum sativum) – a powerful “model system” for genetic experimentationAnd now …QuestionsMCB140, 8/27/08 1MCB 140 – GeneticsMCB140, 8/27/08 2MCB140, 8/27/08 3Dr. Thomas Ried, NCI/NIH: spectral karyotype (SKY)MCB140, 8/27/08 4HeLaDr. Thomas Ried, NCIHeLaStay for Prof. Garriga’s and Prof. Brem’s sectionsMCB140, 8/27/08 5“Cancer Free at 33, but Weighing a Mastectomy”The New York Times, Sunday, Sep. 16, 2007Deborah Lindner, 33, did intensive research as she considered having a preventive mastectomy after a DNA test.MCB140, 8/27/08 6The New York Times, Sunday, Sep. 16, 200760-80%MCB140, 8/27/08 7The New York Times, Sunday, Sep. 16, 2007MCB140, 8/27/08 8Gregor Mendel (1822-1884), and his garden in Brno (Czech Republic)MCB140, 8/27/08 9Nov. 17, 2007MCB140, 8/27/08 10Single nucleotide polymorphism (SNP – pronounced “snip”): 1:1,00011.2511.7A SNP that is also a RFLP(rifflip)MCB140, 8/27/08 11MCB140, 8/27/08 12Decode’s claim“Through a variety of sources, including deCODE genetics own pioneering research in population genetics, we have collected and annotated the most accurate and validated information available on genetic variations which have been associated with an average, higher or lower risk of common diseases. We will give you both detailed scientific background and the means to study how this knowledge applies to you. Our current list of diseases includes: Age-related Macular Degeneration, Asthma, Alzheimer's Disease, Atrial Fibrillation, Breast Cancer, Celiac Disease, Colorectal Cancer, Exfoliation Glaucoma XFG, Crohn's Disease, Multiple Sclerosis, Myocardial Infarction, Obesity, Prostate Cancer, Psoriasis, Restless Legs, Rheumatoid Arthritis, Type 1 Diabetes and Type 2 Diabetes. The disease list will be updated continuously as new discoveries are made.”Emphasis mine – fdu. My evaluation of said claim:Disingenuous (a definition from Merriam-Webster): •lacking in candor; •also : giving a false appearance of simple frankness : calculatingMCB140, 8/27/08 13A few terms from the “detailed scientific background”•Haplotype •Linkage disequilibrium•Penetrance•Expressivity•Epistasis •Norm of reaction•Narrow-sense heritability•Odds ratioMCB140, 8/27/08 14Two problems“Most ignorance is willful” (Bill Watterson)Pierre de Beaumarchais:The Barber of Seville (1775), The Marriage of Figaro (1784)“It is not necessary to understand things in order to argue about them”MCB140, 8/27/08 15Ontology vs. epistemology“The way things are vs. the way we go about understanding, how things are.”MCB 140 aims to educate MCB majors in not just key facts about the functioning of the genetic material in processes of heredity, ontogeny, and disease – but also in the power and the limitations of the methods that are used to obtain those facts.MCB140, 8/27/08 16MCB140 – an outlinePart 1: the “classics” – Mendel, Morgan, Beadle-Tatum – the black box of heredity becomes semi-transparentPart 2 (prof. Gian Garriga): the art and craft of genetics – mutations and genetic screens – from a trait to mechanism – putting together a pathwayPart 3 (prof. Rachel Brem): quantitative genetics (“complex traits”).MCB140, 8/27/08 17What to do so as to do well1. Attend class. 1. Note: reliance on the fact that many lectures are on the web, hence can be “crammed” at the last minute is a 100%-guaranteed recipe for failure. 2. Further note: some of the exams will be open-book. This means that information is less important that understanding. Again, postponement of studying to the last minute is a recipe for failure. You have been warned.2. Keep up with the reading.3. Do all problem sets.4. Attend discussion section.5. Study hard and do well on all the quizzes.6. Ask the GSIs questions7. E-mail the faculty: urnov ЭТ berkeley ДОТ eduMCB140, 8/27/08 18Observable phenomena, explainable and not1. Gravity – not understood at all.2. The color of the sky – understood, but highly technical. ~λ-4 (elastic Rayleigh scattering):http://hyperphysics.phy-astr.gsu.edu/Hbase/atmos/blusky.html3. Heredity – understood, and quite simple For millenia, the curse of Yogi Berra – can you observe a lot by “just watching”? – prevented the solution from being foundMCB140, 8/27/08 19 “It’s All in the Genes” New York Times, 5/2/04Children “look like their parents”: … and “act like their parents”:Diana Ross – the SupremesВалерий Люкин Nastia LiukinMCB140, 8/27/08 20Heredity: “blending inheritance”?“The problem was not that thinkers did not look for similarities between the generations, but that they did, and were understandably confused by what they saw. Human families provided striking, highly contradictory and apparently inconsistent evidence — children sometimes looked like one parent, sometimes a mixture of the two, sometimes like neither and sometimes like their grandparents.” Cobb NRG 7: 953.MCB140, 8/27/08 21Surprisingly to the modern eye, no one in the seventeenth century argued that eggs and sperm represented complementary elements that made equivalent contributions to the offspring. Instead, the next 150 years were dominated by either 'ovist' or 'spermist' visions of what
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