1、训练成为独立思考的科学家- 共识与“偏见”Why do give such a talk?- As an over-achiever, I appreciate more about the good training I have received. - Getting old, and on the down slope in the career, I am more interested in talking. -A class at Fudan Medical School训练自己尽早成为一个全面的科学家- 读研究生时做学问的方法决定了你将来科学生涯的基调- 正确的训练将帮助你在竞争
2、好的博士后或者其他职位时优势更加明显- 只有以正确的方式进行研究才能感到科学的乐趣训练的目标是什么？- 正确的科学道德- 思考科学问题和解决方法的能力- 合理利用时间高效完成各种任务的能力- 阅读和分析文献的能力- 口头表达和确立观点的能力- 撰写研究论文和综述的能力- 与他人交流合作的能力- 和同事愉快相处的能力如何评价学生- 推荐信和电话交谈- 发表的论文- 对科研兴趣的自我表述面试How do NIH panels evaluate postdoctoral fellowship applicants? Confidential letters by the advisor and ot
3、her professorsRanking following aspects (1-5): - Research Ability and Potential- Write and Verbal Communications- Perseverance in Pursuing Goals- Self-reliance and Independence- Laboratory Skills and techniques- Originality- Accuracy- Scientific Background- Familiarity with Research Literature- Abil
4、ity to Organize Scientific DataExample of the evaluation of a good studentExample of the evaluation of a weaker studentWhat are the pre-requisites to be a successful graduate student? High GPA? Great GRE score? Wealth of your family? Type of undergraduate college? Fudan vs others? Rao Yis argumentMo
5、re about your college grades Good grades in high school and college are far from sufficient. In fact, they are not even necessary. There are other important traits.Tom Cech: 1989 Noble Prize in ChemistryPresident of Howard Hughes Medical Inst Professor at the University of ColoradoIt isnt always tru
6、e that the people who are the brilliant high school students, who get the highest grades on the exam, are the ones who do well as practicing, experimental scientists. There are a lot of skills in doing experimental science that cant be tested on standardized exams Cech says. B students often are the
7、 ones who end up doing the really great work in research. Example: Graig Hunter- Professor at HarvardUndergraduateGPA Oregon State University (80-81): 3.3University of Oregon (81-84):3.1Graduate Student University of Coloradosuper starPostdoctoral trainingUCSFsuper starProfessorshipHarvard (main cam
8、pus)One of the best young guysWhat besides the grades for him?Recommendation letters from the advisor: Craig has had complete freedom in designing his own experiments and deciding overall strategy in the research he has conducted in my lab. His understanding and mastery of the techniques of molecula
9、r biology and his sound scientific judgment compares very favorably with that of some of our best graduate students. I have the utmost confidence that Craig Hunter would be extremely successful as a graduate student in any.More about grades-Difference between US and China- Changes in US high schoolW
10、hat are the pre-requisites to have the potential to be trained into a good scientist ?2. Being hard-working is essential, but not sufficient3. Loving what you do is important. - Motivated, but for the right reason - Good scientists often sacrifice other aspects of life.1. Need to be smart. Yes. But
11、.5. Ethical4. Having the potential to be initiative and independentGraduate school is not for everyone How to make sure that is what your want? Have some research experience first.Learn to address good scientific questionsThis is a major objective of your training in graduate school.- Easy to say, h
12、ard to do. - Many researchers are not good at it. “small science” often demands more on this. - This is THE most important thing I learned from my thesis advisor. Learn to address good scientific questionsBig question 1: leading the field# of papers/yeartimeABCDA: ground breakerB: leading the trendC
13、: working in a hot fieldD: catching the tailWhat is your work?Level of the fieldsA major fielde.g. Developmental geneticsA specific areae.g. Wnt signaling in developmentA very focused fielde.g. function of wnt receptorsWhat can we learn from its tradition? The “MRC”The Medical Research CouncilIn 194
14、7 the Medical Research Council set up a Unit for “Research on the Molecular Structure of Biological Systems” to enable Max Perutz and John Kendrew to develop their work using X-ray diffraction to study proteins. The “Laboratory of Molecular Biology” became known simply as the“LMB”. The independence
15、of the researchersFrancis Crick2nd studentJim Watson1st PostdocMax PerutzJohn Kendrew1st studentAll four won the Noble Prize Max Perutz John Kendrew Francis Crick James Watson Fred Sanger Cesar Milstein Sydney Brenner John Sulston Many others were trained there: Sydney Altman, Bob Horvitz, Andy Fire
16、 .The “Culture” created by Perutz at MRC- Students and Postdocs were independent. PIs did not take credit for their work. - They addressed big time questions.- The funding mechanism encouraged risk taking. - It was an extremely stimulating environment: - Eating, drinking, and talking- Many very smar
17、t and devoted people around Brenner & Benzers “ridiculous” exploratory visionSydney BrennerSeymour BenzerPhage geneticistsC. elegansDrosophilaMRCCaltechWhat was Brenners thought?In a letter to Max Perutz, June 1963“ .It is now widely realized that nearly all the “classical” problems of molecular bio
18、logy have either been solved or will be solved in the next decadebecause of this, I have long felt that the future of molecular biology lies in the extension of research to other fields”“The new major problem in molecular biology is the genetics and biochemistry of control mechanisms in cellular dev
19、elopment”“.The great difficulty of these fields is that the nature of the problem has not been clearly defined, and hence the right experimental approach is not known” (= very risky)What did Brenner do?In 1965, Sydney Brenner chose a nematode Caenorhabditis elegans, as a promising model animal He pu
20、blished his first paper in Genetics in 1974.Since then, knowledge has accumulated to the extent that C. elegans is now probably the most completely understood metazoan in terms of anatomy, genetics, development, and behavior. Sydney Brenner Bob Horvitz John SulstonBig Question Example 2Apply technol
21、ogy to study important problemsUsing temperature sensitive mutations to study how a phage is assembled step by stepFunctional map of T4 assembly genesBob Edgar addressed the question and isolated temperature sensitive mutants that disrupt each step of the assembly process in 1960s. Bob Edgar and Bil
22、l Wood collaborated on the project at Caltech, early 1970sLee Hartwell was a student at Caltech He heard about Bob Edgar Ts mutants. Harwell asked another big question: How is the cell division cycle regulated? He isolated TS mutants that disrupt various steps of the cell division cycle. Cdc mutants
23、 (1970s UC Irvine and UW)2001 Noble prize. A great genetic tool was used to attack a big time question.Common “ unattractive” projects- Wanting to do gene knockout, but does not address a good scientific problem.- Doing two-hybrid screen on a protein of which function is unknown and there is no visi
24、on about what is going to happen.- Repeating studies on proteins that have been well-characterized in another organism and do not have a good idea about what are the new things to be learned. - Applying an advanced technique to something for the sake of applying the technique. - Making interesting o
25、bservations, but not sure how to study the mechanism or develop the story. Practice: - When reading research papers, question the questions addressed by the papers.- When listening the seminars, question the questions addressed by the speakers. - Write a proposal on your research plan. “BIG” or “sma
26、ll”, the questions should besignificant, interesting, and solvable重要的， 你喜欢的， 实际的Writing a research proposalC. Experimental designsDescribe in detail how you would experimentally address the questions. You often need to justify what you would do. You need to consider possible problems and alternative
27、 methods. A.Specific Aims1. A short paragraph to summarize the goal of the proposal2. List 2-3 specific aims. Clearly address the specific questions and state the approaches used to attack the problems.B.Background and SignificanceWhere the questions come from, why the questions are important, and t
28、he rationale of the approach suggested. Science 1987 Oct 23;238(4826):542-5A cytoplasmic protein stimulates normal N-ras p21 GTPase, but does not affect oncogenic mutants.Trahey M, McCormick F.The role of guanine nucleotides in ras p21 function was determined by using the ability of p21 protein to i
29、nduce maturation of Xenopus oocytes as a quantitative assay for biological activity. Two oncogenic mutant human N-ras p21 proteins, Asp12 and Val12, actively induced maturation, whereas normal Gly12 p21 was relatively inactive in this assay. Both mutant proteins were found to be associated with guan
30、osine triphosphate (GTP) in vivo. In contrast, Gly12 p21 was predominantly guanosine diphosphate (GDP)-bound because of a dramatic stimulation of Gly12 p21-associated guanosine triphosphatase (GTPase) activity. A cytoplasmic protein was shown to be responsible for this increase in activity. This pro
31、tein stimulated GTP hydrolysis by purified Gly12 p21 more than 200-fold in vitro, but had no effect on Asp12 or Val12 mutants. A similar factor could be detected in extracts from mammalian cells. It thus appears that, in Xenopus oocytes, this protein maintains normal p21 in a biologically inactive,
32、GDP-bound state through its effect on GTPase activity. Furthermore, it appears that the major effect of position 12 mutations is to prevent this protein from stimulating p21 GTPase activity, thereby allowing these mutants to remain in the active GTP-bound state.Cited 1000 timesExample 3, A more spec
33、ific questionRASGDPRASGTPPiGTPGDPtargetActiveInactiveDiscovery of GTPase activating protein (GAP)Observing or reading the literatureGTPase of Ras体外weakt 1/2 30 min体内strongt 1/2 3 hours, 1000XQuestion: What is it in cells that stimulates the GTPase activity?RASGDPRASGTPPiGTPGDPtargetActiveInactiveXon
34、cogeneGAP was discoveredGAP- Read a lot about the subjects to gain good sense-Have good discussion with your advisor - make him think hard. Do not always trust your bosss initial thoughts. - Talk to other senior students (or postdocs) in the lab.Picture this: If all the experiments worked without an
35、y problems, would a paper resulting from the work be good enough to be published in a significant journal? In reality, only a limited percent of projects will get the most desirable results. However, if you know from the very beginning that the best results of your work would have no chance, dont ev
36、en start!Learn to judge the significance of a problemYour major work should be published in a journal with a rigorous review process that warrants respect -Do not take the impact factor too seriously.-Great papers are not always published in the big journals.- Not all papers in big journals are good
37、 ones. At the same time:Great papers in non-top journals - S. Brenners first worm genetics paper: Genetics (1974, 2500X) Nobel Prize 2002-Sulstons worm lineage papers: -Dev. Biol. (1983, 1200X; 1977, 1100X)-Nobel prize 2002-Jack Dixon: PTEN is a lipid phosphatase: JBC (1998, 500X)About secondary cit
38、ations. Question yourselfWhy are we working so hard in the lab? 1. We will contribute to the science of China and world2. We are getting the training for our future.Without addressing good questions, you will accomplish neither.And you might have .Push your advisor?PIs need to constantly learn (read
39、, listen, discuss, etc) to improve themselves so that they can address important questions in their current research programs. Three factors in choosing a lab/advisor- Advisor: fame, reputation, personality, training philosophy - Laboratory: other people in the laboratory, funding- Projects: questio
40、ns addressed, potential project for you At your university, how do students choose their labs?In US: a decision is made by both students and PIs after rotationsHow did I select my thesis laboratoryChoices:Michael Grunstein: genetics on histone functionsNice guy but unpopular labHistones were conside
41、red extremely boringSteve Clark: Protein methylation- Super nice and smart- Pure biochemistry- Significance of the work was not clear then.Arnold Berk: Mechanism of transcription regulation- the most popular professor at UCLA- Super nice and brilliant - All three invited me to join their labs. I was
42、 the first Chinese student that ever worked in these labs.Went with the questions on histones Michael Grunstein had good questions but was still in the stage to find effective genetic approaches1. What are the fundamental cellular functions of histones and nucleosomes?2. Are histones and their modif
43、ications relevant to transcription regulation?Why should we do genetics on histones? - Biochemical roles already well known- Giants in the transcription field did not believe that histones or nucleosomes have anything to do with transcription regulationSpecific Question: What are the cellular conseq
44、uences if you conditionally shut down the production of a histone gene and disrupt nucleosome formation? Gal10 promoterHistone H2B or H4Galactose: promoter onGlucose: promoter off 1000 xSimple ResultsG2 arrest, chromosome segregation disrupted. Dramatic transcription de-repression even without the e
45、nhancerUASGal GluPublicationsYoshinaga, S., Dean, N., Han, M. and Berk, A. J. (1986). Adenovirus stimulation of transcription by RNA polymerase III: evidence for an E1A-dependent increase in transcription factor IIC concentration. EMBO J. 5, 343-353.Schuster, T., Han, M. and Grunstein M. (1986) Yeas
46、t histone H2A and H2B amino termini have interchangeable functions. Cell 45: 445-451.Han, M. Chang, M. Kim, U. and Grunstein M. (1987). Histone H2B repression causes cell cycle specific arrest in yeast: effects on chromosomal segregation, replication and transcription. Cell 48, 589-597.Han, M., Kim,
47、 U., Kayne, P. and Grunstein, M. (1988). Depletion of histone H4 and nucleosomes activates the PHO5 gene in S. cerevisiae. EMBO J., 7, 2221-2228.Kim, U., Han, M., Kayne, P. and Grunstein, M. (1988). Effects of H4 depletion on the cell cycle and transcription of Saccharomyces cerevisiae. EMBO, J. 7,
48、2211-2219.Kayne, P., Kim, U., Han, M. and Grunstein, M. (1988). Extremely conserved histone H4 N-terminus in dispensable for growth but essential for repressing silent mating type genes in yeast. Cell 55, 27-39.Han, M. and Grunstein, M. (1988). Nucleosome loss activates yeast downstream promoters in
49、 vivo in the absence of UAS elements. Cell 55, 1137-1145.Grunstein, M., Han, M., Kim, U., Schuster, T. and Kayne, P. (1989). Histone and nucleosome function in yeast. In Molecular Biology of Chromosome Function. Ed. K.W. Adolph. Springer-Verlag, New York.Role of histones and chromatin in transcripti
50、on# of people /$/ papers/yeartimeAbout taking riskMax Perutz On Seeking an interesting scientific problem“Look for the important problem and dont be detoured if it turns out to be difficult because the important ones always are difficult. And young people now are under great pressure to produce publ
