Writing science notes

My co-advisor Dr. Bodong Chen recommended me this book last year: Writing science – how to write papers that get cited and proposal that get funded, by Joshua Schimel. I got it and put in my shelf for several months. Everytime I opened this book, I could find something else to do instead. Recently, facing a big dissertation fellowship proposal, I am eager to improve my change to get funded. So I opened this book again. I really hoped I could read it before I submitted all my manuscripts so far. Sorry editors and reviewers. I will get them better very soon. What a learning and unlearning process.

chapter 1 scientist is a professional writer: core writing principle is: it is the author’s job to make the reader’s job easy.

chapter 2 science writing as storytelling: draw simple story out of your data, let the story grow from data, don’t impose story on data; overinterpret your data widely, explore all possibilities, then find the simple core, don’t be afraid to abandon your first story.

chapter 3 making a story sticky: SUCCES principle (simple, unexpected, concrete, credible, emotional, story). Simple: find the core of the problem, propose a simple idea; unexpected: find knowledge gap not matter how small it is, make it clear, highlight the novel and new element; concrete: use specific examples and languages; credible: avoid buzzy words, make them concrete; emotional: ask a novel question, engage readers, trigger their curiosity; story: think about internal structure, make small units into a coherence.

chapter 4 story structure: four kinds of structures: OCAR, ABDCE, LD, LDR. OCAR: open with setting the stage, no argument or leading point -> frame questions -> what you did -> what are results, conclusions; ABDCE: open with a challenge -> introduce background -> develop climax (what you did, what is the result) -> ending resolution/ conclusion; LD: open with opening, challenge and resolution (strong at opening) -> develop; LDR: open with argument and challenge -> develop -> end with resolution/synthesis (strong at both opening and ending).

chapter 5 opening (O): three goals: identify problems, introduce characters, target audiences. most you can use OCAR or ABDCE/LDR. using OCAR: two-step strategy (engage audience with a broader topic/question -> transition to a specific question; using ABDCE/LDR, open with challenge and problem, or action.

chapter 6 funnel, connecting O and C: opening a large problem – tunnel – challenge (a specific question). define a specific/concrete problem, identify a small knowledge gap, don’t dump info (don’t tell everything you know), make logic connection between info and knowledge, don’t sell a solution before you identify a problem.

chapter 7 challenge (C): to do X, we did Y, do not reverse the two. (1) explicitly state knowledge gap you want to gain, clearly pose the question, must come first, must be clear, clean and straightforward; (2) tell us how you approach it, what data you collected, what method you use

chapter 8 action (A): method, result, discussion. Let the story guide you, don’t just present data/info, your goal is to present knowledge/understanding. every section (method, result, discussion) is a mini-story, choose one structure for each section. method: LD; result: LD; discussion: LDR or OCAR.

chapter 9 resolution (R): can use a step-backward structure of OCAR. overall conclusion/accomplishment -> results -> expanding/widening to a big picture, general application -> close the circle or pose a new question. ending is a powerful position, end strong and positive, don’t tell us what you don’t achieve at the end, don’t introduce new info, show how the starting point moved, how you explicitly answer/widen the questions.

chapter 10 internal structure: create flow and arc, arcless writings 1) lack thematic coherence, 2) story is unclear, 3) put down every thoughts, no logics. how to fix them? go over paragraph by paragraph and section by section and ask these questions: 1) does each unit make a single clear point? 2) when several paragraphs together form a section, are the linkage among them clear? 3) has every extraneous thought that breaks the serial arc structure been removed? 4) when you introduce a topic, do you resolve that discussion before introducing a new topic? 5) is every major unit of the work defined by either a subhead or clear opening text?

chapter 11 paragraphs: a paragraph is a unit of composition when it tells a complete story with a coherent structure, a story that fits into and contributes to the larger work; paragraphs usually use topic sentence-development (TS-D) structure (like LD structure; point-first structure); or you can use point-last structure, that is LDR or OCAR. a paper usually has 70% point-first paragraphs and 30% point-last paragraphs. short is better than long. three-step strategy to fix long and rambling paragraphs: 1) identify the real story, 2) decide whether this needs a point-first or point-last structure, 3) pull apart different threads of the story to clarify their relationships.

chapter 12 sentences: a sentence = a subject (opening: “topic”) + verb (challenge/action) + object (resolution: “stress”);weighting of words in a sentence follows an order: the stress carries the greatest emphasis, the topic is the next, the middle carries the least (2-3-1 principle). it follows OCAR structure, open with subject topic, action should immediately follow the subject, key message comes at the end as stress, add nuance if needed. if it is a long sentence, use sub-clauses, the ending of each clause is a minor stress position.  how to fix bad sentences: 1) find the topic, make it the subject, move it toward the beginning, 2) find the action verb and connect it closely to the subject, 3)find the stress and move it to the end of the main clause. if you have additional material to add, move it to the right so that it modifies rather than intrudes in the main story

chapter 13 flow: make a relay: sentence 2’s topic is sentence 1’s stress, don’t introduce new info/topic and break the arc; this principle is the same for flow between two paragraphs. so core is to identify topic and stress. by linking stress and topic, resolution and opening, you can tie together sentences and paragraphs and make the sweep of your arguments compelling.

chapter 14 energizing writing: principles: 1) most of the time, use active voice over passive voice, 2) find the action and use clear and concrete action verb, show what happened not just something happened, put verb early in the sentence, 3) don’t transfer concrete verb or adj into noun. why nominalizations are not good? 1) lose the power of using verbs, 2) a nomialization can easily become a jargon. when to use passive voice: 1) make the acted-on the subject of the sentence, 2) avoid mentioning the actor’s names

chapter 15 words: three principles: 1) avoid jargon (undefined terms, nouns), if you can use a plain and simple language equivalent, use it, don’t use the jargon! you can use 2-3-1 rule here: open with something people are familiar with + technical terms + explain of the technical terms in more details 2) use common words, instead of unnecessary technical words, this can increase clear understanding and engage a stronger schema 3) pay attention to prepositional phrases, don’t use noun train!

chapter 16 condensing: avoid 1) redundancies: use several words where one does all the work that needs doing, 2) obvious: obvious ideas are well known or implied and so don’t need to be said anywhere, e.g., “there is evidence that …” 3) modifiers: don’t use unnecessary adj, and adv when you can use clear and concrete noun and verb 4) metadiscourse e.g., “we found, we argue, the data may indicate, to conclude..” 5) verbosity: show authors’ mental processes from the story they are trying to tell

chapter 17 putting it all together: 1) structure: get the structure of the story into shape, 2) clarity: ensure that your idea are clear and concrete 3) flow: make the idea flow, linking one thought to the next, 4) language: make it sound good

chapter 18 dealing with limitations: principle: but, yes. open about limits and highlight strength/resolution/conclusion. 1) introduction: many problems arise not from inherent limitation but from a mismatch between the question and methods. go back to introduction, find the knowledge gap and what is your research question? what the story is? 2) methods: discuss limitation of analytical methods immediately to lay any concerns to rest, you are much better off if you can address readers’ concerns as soon as they arise, if you avoid mentioning the negatives, readers will find them and criticize you for them 3) discussion: limitations affect how you interpret data, you should avoid the power positions of the discussion’s opening and resolution, early in the body of the discussion to discuss the work’s limitation and constraint.

chapter 19 writing global science, data-info-knowledge-understanding-applicaiton, we are offering knowledge/understanding/application, not just present data and info

chapter 20 writing for the public: A and B: issue and audience -> problem? -> so what? -> solution -? benefits

chapter 21 resolution: I prefer to focus on success strategies instead of survival strategies; you don’t succeed by getting papers published but by getting them cited; quality ultimately trumps quantity and it will stand out in a crowded scientific universe; simply remember who your real peers are;


No Boundary

No boundary was written by one of my favorite philosopher Ken Wilber, it is an amazing book to understand different levels of human consciousness. I made a concept map to capture the core ideas of chapter 7 8 9 in this book.

Screen Shot 2016-12-02 at 1.56.40 PM.png

Here is the spectrum of consciousness proposed by Wilber in this book. It is interesting to think about how we see ourselves and human beings from different levels, and what could be changed as we move from the top level to the bottom level (from narrower to wider spectrum, as shown in this figure)


Wilber, K. (2001). No boundary: Eastern and Western approaches to personal growth. Shambhala Publications.

rules for critical conversation

Notes from book becoming a critically reflective teacher, S. D. Brookfield

we tend to be trapped in the framework that determine what we have experienced and how we view them. we tend to be trapped in a self-confirming cycle. we tend to use our uncritically-accepted assumptions to shape our actions, and then serve to confirm the truth of those assumptions. we find it difficult to stand outside ourselves and see how some of our most deeply held values and beliefs lead us into distorted and constrained ways of being.

group peer conversation can be a new possibility for analyzing and responding to problems. but conversation is not necessarily critical. it is truly critical and self-aware only when participants have tolerance, patience, respect for differences, a willingness to listen, the inclination to admit that one may be mistaken, the ability to reinterpret or translate one’s own concerns in a way that makes them comprehensible to others, the disposition to express oneself honestly and sincerely.

the first step in setting up this critical conversation group is to create group rules for our participation.

  1. thinking of the best group conversation you have ever been involved in. what things happened that made it satisfying?
  2. thinking of the worst group conversation you have ever been involved. what things happened that made it unsatisfying?
  3. take turns in talking about what made conversation groups work so well for you. listen for common themes, shared experiences, and features of conversation that a majority of you would like to see present in this group.
  4. take turns in talking about what made conversation groups work so badly for you. listen for common themes, shared experiences, and features of conversation that a majority of you would like to see avoided in this group.
  5. for each the characteristics of good conversation you agree on, try to suggest three things the group could do to ensure, as far as possible, that these characteristics are present.
  6. for each the characteristics of bad conversation you agree on, try to suggest three things the group could do to ensure, as far as possible, that these characteristics are avoided.
  7. try to draft a charter for critical conversation incorporating the specific ground rules that you agree on

facilitate an effective discussion

I found his helpful to think about when we facilitate a discussion:

Strategies for encouraging equal participation in discourse from Cranton’s Understanding and Promoting Transformative Learning: A Guide for Educators of Adults, second edition.

1. Find proactive ways to stimulate dialogue from different perspectives – controversial statements, readings from contradictory points of view, or structured group activities that lead people to see alternatives
2. Develop discourse procedure within the group. In order to meet its goal of validity testing, discourse needs to stay focused. Group members can be encouraged to take on the roles of checking and controlling the direction of the discourse, ensuring equal participation, and watching out for coercion and persuasion
3. Avoid making dismissive statements or definitive summaries. To minimize the role of disciplinary power and self-surveillance, the educator must be careful not to shape the discussion through implicit regulatory functions
4. Be conscious of nonverbal communication such as smiles, nods, and eye contact that can give clues as to what the educator is approving
5. Encourage quiet time for reflection within any exchange

community creatures

We know the rules of community; we know the healing effect of community in terms of individual lives. If we could somehow find a way across the bridge of our knowledge, would not these same rules have a healing effect upon our world? We human beings have often been referred to as social animals. But we are not yet community creatures. We are impelled to relate with each other for our survival. But we do not yet relate with the inclusivity, realism, self-awareness, vulnerability, commitment, openness, freedom, equality, and love of genuine community. It is clearly no longer enough to be simply social animals, babbling together at cocktail parties and brawling with each other in business and over boundaries. It is our task–our essential, central, crucial task – to transform ourselves from mere social creatures into community creatures. It is the only way that human evolution will be able to proceed.

refer to The different drum: Community making and peace. by M. Scott Peck

Peck is such a truth teller. Love him.

A community is a dynamic whole that emerges when a group of people share common practices, are interdependent, make decisions jointly, identify themselves with something larger than the sum of their individual relationships, and make a long-term commitment to well-being (their own, one another’s, and the group’s). It’s our human’s yearning for a sense of belonging, kinship, and connection to a greater purpose. The need for connectedness does not necessarily mean giving up autonomy or submitting to authority in order to become part of a group. Instead, creating a community is a mutual empowering act – a means by which people share with each other, work, and live collaboratively.

refer to Creating commuinty anywhere, by Carolyn Shaffer, Kristin Anundsen

Even though I don’t see myself a very sociable person, after reading these, I agree that a healthy community is the place where human gets improved and developed. Not easy to build, of course.


Contents come from: Palloff, R. M., & Pratt, K. (2007). Building online learning communities: Effective strategies for the virtual classroom. John Wiley & Sons.

The conquest of happiness, Bertrand Russell

Ch01 – What makes people unhappy? The typical unhappy man is one who, having been deprived in youth of some normal satisfaction, has come to value this one kind of satisfaction more than any other, and has therefore given to his life a one-sided direction, together with a quite undue emphasis upon the achievement as opposed to the activities connected with it. p22

A man may feel so completely thwarted that he seeks no form of satisfaction, but only distraction and oblivion. He then becomes a devotee of “pleasure.” That is to say, he seeks to make life bearable by becoming less alive. p22

Ch02 – Byronic unhappiness I am persuaded that those who quite sincerely attribute their sorrows to their views about the universe are putting the cart before the horse: the truth is they are unhappy for some reasons of which they are not aware, and this unhappiness leads them to dwell upon the less agreeable characteristics of the world in which they live. p25

The habit of looking to the future and thinking that the whole meaning of the present lies in what it will bring forth is a pernicious one. There can be no value in the whole unless there is value in the parts. p29

I do not deny that the feeling of success makes it easier to enjoy life…. Nor do I deny that money, up to a certain point, is very capable of increasing happiness. What I do maintain is that success can only be one ingredient in happiness, and is too dearly purchased if all the other ingredients have been sacrificed to obtain it. p43

Ch03 – Competition What people mean, therefore, by the struggle for life is really the struggle for success. What people fear when they engage in the struggle is not that they will fail to get the breakfast next morning, but that they will fail to outshine their neighbors. p40

The root of trouble springs from too much emphasis upon competitive success as the main source of happiness. I do not deny that the feeling of success makes it easier to enjoy life. Nor do I deny that money, up to a certain point, is very capable of interesting happiness; beyond that point, I do not think it does. What I do maintain is that success can only be one ingredient in happiness, and is too dearly purchased if all the other ingredients have been sacrificed to obtain it. p43

Men and women appear to have become incapable of enjoying the more intellectual pleasure. p45

The trouble arises from the generally received philosophy of life, according to which life is a contest, a competition, in which respect is to be accorded to the victor. This view leads to an undue cultivation of the will at the expense of the senses and the intellect. p46

Competition considered as the main thing in life is too grim, too tenacious, too much a matter of taut muscles and intent will, to make a possible basis of life for more than one or to generation at most. After that length of time it must produce nervous fatigue, various phenomena of escape, a pursuit of pleasures as tense and as difficult as work (since relaxing has become impossible), and in the end a disappearance of the stock through sterility. It is not only work that is poisoned by the philosophy of competition; leisure is poisoned just as much. The cure for this lies in admitting the part of sane and quiet enjoyment in a balanced ideal of life. p47

Ch04 – Boredom and excitement One of the essential of boredom consists in the contrast between present circumstances and some other more agreeable circumstances which force themselves irresistibly upon the imagination. It is also one of the essentials of boredom that one’s faculties must not be fully occupied. p48

Boredom is essentially a thwarted desire for events, not necessarily pleasant ones, but just occurrences such as will enable the victim of ennui to know one day from another. The opposite of boredom, in a word, is not pleasure, but excitement. p49

A life too full of excitement is an exhausting life, in which continually stronger stimuli are needed to give the thrill that has come to be thought an essential part of pleasure. A certain amount of excitement is wholesome but like almost everything else, the matter is the quantitative. Too little may produce morbid cravings; too much will produce exhaustion. A certain power of enduring boredom is therefore essential to a happy life, and is one of the things that ought to be taught to the young. p52

Altogether it will be found that a quiet life is characteristic of great men, and that their pleasures have not been of the sort that would look exciting to the outward eye. No great achievement is possible without persistent work, so absorbing and so difficult that little energy is left over for the more strenuous kinds of amusement, except such as serve to recuperate physical energy during holidays. p53

A boy or a young man who has some serious constructive purpose will endure voluntarily a great deal of boredom if he finds that it is necessary by the way. But constructive purposes do not easily form  themselves in a boy’s mind if he is living a life of distractions and dissipations, for in that case his thoughts will always be directed towards the next pleasure rather than towards the distant achievement. p54

Ch05 – Fatigue To a great extent fatigue is due to worry, and worry could be prevented by a better philosophy of life and a little  more mental discipline. Most men and women are very deficient in control over their thoughts. I mean by this that they cannot cease to think about worrying topics at times when no action can be taken in regard to them. p59

Our doings are not so important as we naturally suppose; our successes and failures do not after all matter very much. Even great sorrows can be survived; troubles which seem as if they must put an end to happiness for life, fade with the lapse of time until it becomes almost impossible to remember their poignancy. p60

Over and above these self-centered considerations is the fact that one’s ego is no very large part of the world. The man who can center his thoughts and hopes upon something transcending self can find a certain peace in the ordinary troubles of life which is impossible to the pure egoist. p61

The mental discipline is the habit of thinking of things at the right time. This has its importance, first because it makes it possible to get through the day’s work with less expenditure of thought, secondly because it affords a cure of insomnia, and thirdly because it promotes efficiency and wisdom in decisions. p62

Worry is a form of fear, and all forms of fear produce fatigue. A man who has learned not to feel fear will find the fatigue of daily life enormously diminished. Fear, in its most harmful form, arises where there is some danger which we are unwilling to face. p63

Probably all these people employ the wrong technique for dealing with their fear; whenever it comes into their mind, they try to think of something else; they distract their thoughts with amusement or work, or what not. Now every kind of fear grows worse by not being looked at. The effort of turning away one’s thoughts is a tribute to the horribleness of the specter from which one is averting one’s gaze; the proper course with every kind of fear is to think about it rationally and calmly, but with great concentration, until it has been completely familiar. p64

One of the worst features of nervous fatigue is that it acts as a sort of screen between a man and the outside world. Impressions reach him, as it were, muffled and muted; he no longer notices people except to be irritated by small tricks or mannerisms; he derives no pleasure from his meals or from the sunshine, but tends to become tensely concentrated upon a few objects and indifferent to all the rest. p66

CH09- Fear of public opinion 

Very few people can be happy unless on the whole their way of life and their outlook on the world is approved by those with whom they have social relations, and more especially by those with whom they live. page 100

Whenever possible … young people who find themselves out of harmony with their surroundings should endeavor in the choice of a profession to select some career which will give them a chance of congenial companionship, even if this should entail a considerable loss of income. page 105

One should respect public opinion in so far as is necessary to avoid starvation and to keep out of prison, but anything that goes beyond this is voluntary submission to an unnecessary tyranny, and is likely to interfere with happiness in all kinds of ways. page 107

Fear of public opinion, like any other kind of fear, is oppressive and stunts growth. It is difficult to achieve any kind of greatness while a fear of this kind remains strong, and it is impossible to acquire that freedom of spirit in which true happiness consists, for it is essential to happiness that our way of living should spring from our own deep impulses and not from the accidental tastes and desires of those who happen to be our neighbors, or even our relations. page 109

CH10- Is happiness still possible

Fundamental happiness depends more than anything else upon what may be called a friendly interest in persons and things. … The kind [of interest in persons] that makes for happiness is the kind that likes to observe people and finds pleasure in their individual traits, that wishes to afford scope for the interests and pleasures of those with whom it is brought into contact without desiring to acquire power over them or to secure their enthusiastic admiration. The person whose attitude towards others is genuinely of this kind will be a source of happiness and a recipient of reciprocal kindness. … To like many people spontaneously and without effort is perhaps the greatest of all sources of personal happiness. pages 121-122

The secret of happiness is this: let your interests be as wide as possible, and let your reactions to the things and persons that interest you be as far as possible friendly rather than hostile. p123

Ch13- Family

Of all the institutions that have come down to us from the past none is in the present day so disorganized and derailed as the family. Affection of parents for children and of children for parents is capable of being one of the greatest sources of happiness, but in fact at the present day the relations of parents and children are, in nine cases out of ten, a source of unhappiness to both parties, and in ninety-nine cases out of a hundred a source of unhappiness to at least one of the two parties. This failure of the family to provide the fundamental satisfactions which in principle it is capable of yielding is one of the most deep-seated causes of the discontent which is prevalent in our age. page 145

Ch15 – Impersonal Interests

The man who can forget his work when it is over and not remember it until it begins again next day is likely to do his work far better than the man who worries about it throughout the intervening hours. And it is very much easier to forget work at the times when it ought to be forgotten if a man has many interests other than his work than it is if he has not. p171

To bear misfortune well when it comes, it is wise to have cultivated in happier times a certain width of interests, so that the mind may find prepared for it some undistrubed place suggesting other associations and other emotions than those which are making the present difficult to bear. p177

Ch17 – The happy man

It should be our endeavor, both in education and in attempts to adjust ourselves to the world, to aim at avoiding self-centered passions and at acquiring those affections and those interests which will prevent our thoughts from dwelling perpetually upon ourselves. p187

Fear is the principal reason why men are so unwilling to admit facts and so anxious to wrap themselves round in a warm garment of myth. But the thorns tear the warm garment and the cold blasts penetrate through the rents, and the man who has become accustomed to its warmth suffers far more from these blasts than a man who has hardened himself to them from the first. p187

The happy man is the man who lives objectively, who has free affections and wide interests, who secures his happiness through these interests and affections and through the fact that they, in turn, make him an object of interest and affection to others. To be the recipient of affection is a potent cause of happiness, but the man who demands affection is not the man upon whom it is bestowed. The man who receives affection is, speaking broadly, the man who gives it. p188

Admit to yourself every day at least one painful truth,… teach yourself to feel that life would still be worth living even if you were not, as of course you are, immeasurably superior to all your friends in virtue and in intelligence. Exercises of this sort prolonged through several years will at least enable you to admit facts without flinching, and will, in so doing, free you from the empire of fear over a large field. p189

The happy man is the man who does not suffer from either of these failures of unity, whose personality is neither divided against itself nor pitted against the world. Such a man feels himself a citizen of the universe, enjoying freely the spectacle that it offers the the joys that it affords, untroubled by the thought of death because he feels himself not really separate from those who will come after him. It is in such profound instinctive union will the stream of life that the greatest joy is to be found. p191

Notes from The conquest of happiness, Bertrand Russell

more notes can be found from http://www.gurus.org/dougdeb/Courses/Happy/Conquest/

Randy Pausch, The Last Lecture

The brick walls are there for a reason. The brick walls are not there to keep us out. The brick walls are there to give us a chance to show how badly we want something. Because the brick walls are there to stop the people who don’t want it badly enough. They’re there to stop the other people.

Experience is what you get when you didn’t get what you wanted. And experience is often the most valuable thing you have to offer.

The key question to keep asking is, Are you spending your time on the right things? Because time is all you have.

It’s not about how to achieve your dreams, it’s about how to lead your life, … If you lead your life the right way, the karma will take care of itself, the dreams will come to you.

Look, I’m going to find a way to be happy, and I’d really love to be happy with you, but if I can’t be happy with you, then I’ll find a way to be happy without you.

Showing gratitude is one of the simplest yet most powerful things humans can do for each other.

Luck is where preparation meets opportunity.

Time is all you have and you may find one day that you have less than you think.

If I only had three words of advice, they would be, Tell the Truth. If got three more words, I’d add, all the time. (my favorite)

A lot of people want a shortcut. I find the best shortcut is the long way, which is basically two words: work hard.

Find the best in everybody. Just keep waiting no matter how long it takes. No one is all evil. Everybody has a good side, just keep waiting, it will come out.

When we’re connected to others, we become better people.

Follow your passions, believe in karma, and you won’t have to chase your dreams, they will come to you.

Another way to be prepared is to think negatively. Yes, I’m a great optimist. but, when trying to make a decision, I often think of the worst case scenario. I call it ‘the eaten by wolves factor.’ If I do something, what’s the most terrible thing that could happen? Would I be eaten by wolves? One thing that makes it possible to be an optimist, is if you have a contingency plan for when all hell breaks loose. There are a lot of things I don’t worry about, because I have a plan in place if they do.

The questions are always more important than the answers.

Its important to have specific dreams. Dream Big. Dream without fear.

Notes from The Last Lecture by Randy Pausch, video on Achieving your childhood dreams.