Scientific Methods - 論研究方法

上個月參加一場由國科會主辦的研究方法與論文寫作研討會，
主題為『年輕研究者在生物醫學研究之教戰守則 (Survival Skills for Young Biomedical Researchers) 』，
主講人為現任教於 New York University 的孫同天院士 (Tung-Tien Sun)。

這場演講非常的精彩，除了孫院士幽默風趣演講魅力外，
更讓我佩服這位六十幾歲的老教授竟然能連兩天在台南台北長時間主講這課程，
況且獨挑大樑，自早上九點到下午五點連續八小時的演說。( 堪稱老當益壯的阿伯 )

讓人敬佩的除了六十ｎ歲一條活龍外，還有他所帶來豐富精闢的Scientific Methods 論點。
因此在Workshop結束後，我總掛心著想把這些內容分享給大家，
所幸最近順利通過資格考試後，終於有時間把它付諸實行。

不過很抱歉的是，由於事隔近兩個月，以我海馬迴受損的程度勢必已經遺忘不少，
但我會將講義大致放上，並加上我個人補述，但可惜的是由於孫院士即將出版一本Scientific Methods專書，
因此在書商壓力下，他無法提供投影片給大家，不過屆時若書籍出版，
便可在書內或孫院士的個人網站上下載，我相信那會是本值得細讀收藏的好書。

還記得我曾經寫過一篇『打混摸魚研究方法論』，
http://bphouse.spaces.live.com/blog/cns!A1EFBAC5BA991668!251.entry
雖然是當時有感而發，但也深怕誤人子弟:P
這次補上真正的前人經驗，讓我們開始爬上巨人的肩膀吧！

這次的主題雖然主要focus在生物醫學研究， 跟我們Computer Science或許有些許不同，
但好方法放諸四海皆準，大方向一致，只要稍做修改，
不管是哪個領域亦或職場自修，我相信都是會有幫助的。

該課程中主要分為四大主題，分別為：
　Ａ.實驗設計 (Experimental Design)
　Ｂ.文獻分析 與 摘要記錄 (Literature Analysis & Note-taking)
　Ｃ.論文寫作 (Scientific Writing & Scientific Integrity)
　Ｄ.口頭簡報 (Oral Presentation)

Ａ. 實驗設計 (Experimental Design) - How to Get Any Lab Techniques to Work

Puzzles

Risk assessment
　　●.How much can I afford to make (potentially preventable) mistakes?
　　　　○.Time (在computer science (CS) 中可比照演算法執行之耗時)
　　　　○.Expensive or irreplaceable reagents (CS中有如錯誤的儀器採購)
　　　　○.Biological material
　　●.How much can I afford to trust the carious components of this experiment?
　　●.How thoroughly should I plan this experiment?
　　●.Failure is not an option (完整的事前分析有助降低錯誤的發生)

Trust in authorities
　　●.Authorities: an accepted source of expert information or advice
　　●.Blind spots
　　●.How much can you trust an "authority"? Depending on the circumstance
　　●.Frequently perceived "authorities"
　　●.Charles River mice example
　　(BP: 我高中時的啟蒙老師 徐慶堂老師總是告訴我，不要完全相信課本，有能力指正課本的錯誤，這才是真正融會貫通）

When failure is not an option, how to maximize your chance of success
　　●.Attitude　★★★
　　　　○.Detailed planning (養成隨手將idea紀錄並規劃完整也是很重要的)
　　　　○.Thorough understanding of every step
　　　　○.Foresee problems
　　●.Experimental design
　　　　○.Controls
　　　　○.Titration of key components: The N+(N-1) Rule
　　　　○.Good notebook (無論什麼實驗，完整的紀錄過程、心得與討論是非常重要的)
　　●.Notebook
　　　　○.Date
　　　　○.Questions / Hypotheses
　　　　○.Refs and notes
　　　　○.Design (Table)
　　　　○.FLOW CHART (寫下完整流程圖是避免因為時間而遺忘細節，可以不斷修正)
　　　　○.Solutions and reagents
　　　　○.Results
　　　　○.Discussion
　　●."Truth emerges more readily from error than from confusion"

Scientific Attitude
　　●.Long-term habit in decision-making
　　●.Become part of personality
　　●.Consequences: frustration, communication problems, lack of controls
　　●.Scientific attitude can be changed
　　　　○.Graduate course
　　　　○.Round table discussion
　　　　○.Lab culture (一個好的Lab文化可以促進伙伴們的進步，碩班時我們Lab會自發性的舉行Lab meeting，這對研究是有正向的幫助)
　　　　★.Self-reliance :　自己的研究一定要比任何人都瞭解，even是指導教授)

Puzzles
　　●.Diagnosis of the problem
　　●.Constructive suggestions

Further Readings
　　●.Sun, T. T.(2004). Excessive trust in authorities and its influence on experimental design. Nat Rev Mol Cell Biol 5, 577-581.
　　●.Advice for a Young Investigator, by Santiago Ramon Y Cajal, Neely and Larry W. Swanson (Translators), Hardcover - 176 pages (March 1999)
　　●.Advice to a Young Scientist, by Peter Brian Medawar, Paperback (June 1981)
　　●.An Introduction to Scientific Research, by Edgar Bright Wilson, Paperback - 375 pages revised edition (February 1991)
　　●.At the Bench : A Laboratory Navigator, by Kathy Barker, Hardcover Spiral edition (July 1998), Cold Spring Harbor Laboratory
　　●.A Ph.D. Is Not Enough: A Guide to Survival in Science, by Peter J. Feibelman, Paperback - 109 pages (January 1994)
　　●.Advice for New Faculty Members: Nihil Nimus, by Robert Boice, Paperback - 288 pages 1 edition (January 5, 2000), Allyn & Bacon
　　●.Tomorrow's Professor: Preparing for Academic Careers in Science and Engineering, by Richard M. Reis, Paperback - 416 pages (April 1997)
　　●.Jump Start Your Career in BioScience, by Chandra B. Louise, Paperback - 214 pages (March 1998)

Ｂ. 文獻分析 與 摘要記錄 (Literature Analysis & Note-taking)

Literature analysis : Hypothesis -> Active reading -> Note taking

Passive Reading (走馬看花不求甚解是不夠的)

Active reading = with questions in mind
　　●.What are the problems?
　　●.Why are these problems important?
　　●.How Would I approach these problems?
　　●.What kind of data do I need to support their conclusions?
　　●.How would these conclusions fit into "my" thinking?
　　Stop and think - stop and think - after title, ABSTRACT, introduction. Then guess what should be on the next figure - what data would I generate?????
　　(一開始閱讀Abstract時便應該瞭解整個Paper的大綱、輪廓，而不是等讀完整個paper才瞭解Abstract在講什麼！！　讀完Abstract後便可以開始思考上面五個問題。)
　
Note taking
　　●.Three ring binder (將讀過的Paper進行分類，並將該paper論點以自己的想法寫出，並將自己衍生的想法一併寫在筆記中)
　　●.One subject per page
　　●.Alphabetically arranged
　　●."To discover is to bring together two ideas that were previously unlinked"

Pick a research topic

Choosing a research problem:
　　●.Aim High (取法乎上，得乎其中，取法乎中，得乎其下。意思就是做研究眼光要放高放遠)
　　●.Focus! deeper, not broaden
　　●.Realistic
　　●.Steady publications
　　●.Changing projects (急流勇退是種勇氣，並不可恥！)

Ｃ. 論文寫作 (Scientific Writing & Scientific Integrity) - How to Prepare Figures and the First Draft

Two elements of scientific writing:
　　●.Generation of ideas based on a given set of data - more a limiting factor

Writing the first draft: >70% of the battle (這是很重要的，有什麼想法就儘管寫，有寫便有可以修改的地方，若因為覺得不完整而不寫，終究還是空白。)
　　●.Finalize the figures
　　●.Re-read relevant literature
　　●.Taking notes (one idea/key sentence per page, 因為每次Re-read literature後都要寫上與該idea、sentence相關的paper引用)
　　●.Outline 1 (with mentor)
　　●.Re-read some more literature
　　●.Outline 2
　　●.Re-read some more literature
　　●.Convert each key sentence into a paragraph
　　●.Finish first draft in one sitting if possible

Key sentence
　　●.One main idea per paragraph
　　●.Key sentence fully express this idea
　　●.KS preferably as the first sentence of the paragraph
　　The rest of the paragraph support, explain and expand the KS

Converting the KS into a paragraph

Anatomy of a paper
　　●.Title
　　●.Abstract
　　●.Introduction
　　●.Figures
　　　　○.Minimal wording
　　　　○.Maximal utilization of space
　　　　○.Maximal size
　　　　○.First decide one- or two-column width
　　●.Figure legends (要有好的且具吸引力的Title，並且減少technique words)
　　●.Result ( short and sweet, what is the "novel" finding?)
　　●.Discussion　(what's new ，不能僅attack別人而不提出更好的證據)
　　●.Literature citation
　　　　○.Fairly crediting original papers
　　　　○.How we get here
　　　　★.Submit後的paper，copyright在出版的期刊而不是自己，故自己的paper也要refernce)

Further Readings

　　●.The Elements of Style, Fourth Edition, By William Strunk, Jr, E.B.white, and Roger Angell, Price: $7.95
　　●.How To Write & Publish a Scientific Paper: 5th Edition, by Robert A. Day (Editor), Price: $24.50, Paperback - 296 pages 5th edition (June 18, 1998), Oryx Press; ISBN: 1573561657
　　●.Scientific English : A Guide for Scientists and Other Professionals, by Robert A. Day, Price: $19.95, Paperback - 160 pages 2nd edition (August 1, 1995), Oryx Press
　　●.The MIT Guide to Science and Engineering Communication, by James G. Paradis, Muriel L. Zimmerman, Price: $37.95, Hardcover (February 1997), MIT Press

Ｄ. 口頭簡報 (Oral Presentation)

　　●.Psychological build up
　　●.When you are there
　　●.Differences between a Talk and a Paper
　　●.Goal
　　●.Purpose of the slides
　　●.Slide making
　　　　○.Large and simple fonts (32,28 point)
　　　　○.Color (3 colors per slide, consistent color theme)
　　　　○.Margin
　　　　○.Background
　　●.Slide presentation
　　　　○.One point per slide
　　　　○.Short title
　　　　○.Explain Everything (slide上有的就該講清楚)
　　　　○.Explain one element
　　　　○.One min per simple slide
　　　　○.Minimal words
　　●.Strategies
　　　　○.Build up (Data first , conclusions last)
　　　　○.Up front (Begin with conclusions -> Data -> End again with conclusions , 破題法)
　　　　○.Table of content
　　●.Good transition is everything
　　　　○.Curiosity-anticipation-satisfaction
　　●.Summary-conclusions
　　　　○.At the end
　　　　○.Simple
　　●.Stop on time (通常時間愈短愈難控制)
　　★. A key to sucessful presentation : How to "lead" the audience ?

　　Answering Question Do's :
　　　　○.Thank you
　　　　○.Concise and to-the-point
　　　　○.Stall
　　　　　　.I can't hear you.... (當問題不清楚需要時間思考時，這是個好的拖延方法)
　　　　○.Rephrase
　　　　　　.Do you mean.....? (反問對方）
　　　　○.Repeat the question
　　　　○.Talk to the audience
　　　　○.Avoiding entangling
　　　　○.Perhaps you and I can continue later (遇到長舌的發問人可用)
　　　　○.Mr. Chairman (當時間不足又被釘住時，可藉由chairman來解脫，如詢問時間是否足夠等)

　　Answering Question Don's :
　　　　○.Cut off the questioner
　　　　○.Rate the questions (批評別人的問題是很沒禮貌的)
　　　　○.Insult the questioner (應該沒有這麼威猛的人吧?)
　　　　○.I don't know.....I don't know.......(大忌唷！！)
　　　　○.Apologize (多說多錯，承認錯誤也是種美德)
　　　　○.Ramble
　　　　○.Hold your temper

Further Readings
　　●.Dazzle 'Em With Style : The Art of Oral Scientific Presentation, by Robert R. H. Anholt, List Price: $21.77, Paperback - 200 pages (March 1994), W H Freeman & Co
　　●."I Can See You Naked" : A New Revised Edition of the National Bestseller on Making Fearless Presentations, by Ron Hoff, Barrie Maguire (Illustrator), List Price: $12.95, Amazon Price: $10.36, Paperback - 326 pages Revised edition (November 1992), Andrews McMeel Publishing

以上就是孫教授針對Scientific methods的大致分類，
當中有些部分則是我個人補述與註解，若有錯誤請不吝指教！
此外關於Scientific methods的相關補充，亦可至孫院士網站查詢。

NYU School of Medicine - Sun Laboratory : http://www.med.nyu.edu/sun/people/index.html

BP