Showing posts with label coursera. Show all posts
Showing posts with label coursera. Show all posts

Coursera - Writing in the Sciences - Week 8

Continue with week 8, the final unit of this course.

8.1: Talking with the media
The main objective if you've published your paper which caught the attention of the media or journalists? Basically the media needs something for them to write a clickbait title (or newshook) to drive readership. You, as a researcher should focus on what is the take home newsworthy message and how that message will affect people.

When giving number, use whole number instead of percentage or fractions. For example, instead of "20% increased risk" (sounds alarming), it's better to write it as "eleven cases in ten thousands per year may be affected".

8.2: Panel Interview
Discussion with her three ex-students, Dr. Kit DelgadoDr. Crystal Smith-Spangler, and Dr. Eran Bendavid.

Each university has their own media relation person who are in charge of press release. Practice the interview with them if possible and go through the list of documents needed for the interview. Also, good to do background check on journalists who are interviewing you. On the safe, you can ask for the questions ahead of interview session.

Don't let the journalist mislead you to speculate on something. Refocus back to the original topic.

8.3: Writing for general audiences
There is a career in science writing. When writing for general audience, be concise, clear, and engaging (telling a story). Focus on the take home message (this has been stressed repeatedly over the course).

8.4: Writing a science news story
There is a format for this type of writing according to this structure.
(1) Lead. First paragraph (1 - 2 sentences) that is catchy and short.
(2) Nut Graf. 5 W's (who, what, where, why, and when) and 1 H (how).
(3) First quote (3 - 6 paragraphs) and bring in the human element (evidence or opinion).
Use noun-verb for attribution. For example,
Do this. "Blah blah blah...," Professor X said.
Don't do this. "Blah blah blah...," said Professor X.

(4) Body which includes what was done before, what was done in this study as in key experiments or key findings, and last implication or caveats.
(5) Kicker. Create parting thoughts for ending. Use quote if necessary.

8.5: Interviewing a scientist
Lecture given by Amy Adams, Directory of Science Communication at Standford.

How to interview and write for general public. For a start, no jargon.

What kind of questions that elicit good quotes? Here are a few.
(1) What is the significant of this work?
(2) Who will benefits from this work?
(3) What do you think when you got the result?
(4) What made you look into this question?

Use the quote as it. Don't modify the quote.

Anatomy of a interview. The steps as follows:
(1) Can you describe the key finding?
(2) Why is this important?
(3) How does that work?
(4) Is there anything you want to add?

8.6: Social media
Why we need to engage in social media? Promoting yourself, cause, brand, or institution. It also connect with other like minded person.

Effective of social media depends on what you want to measure. Focus on this before that using social media.

Engage but don't teach. In other words, create awareness.

8.7: Concluding Remarks
Effective writing and communication is essential to fence off an increase number of science

Learning Objectives
(1) Recognize the importance of communicating science with broader audiences.
(2) Be prepared to be interviewed by a journalist.
(3) Recognize the difference between writing for scientific audiences and writing for lay audiences.
(4) Understand the structure of a science news story.
(5) Learn tips for how to interview a scientist.

Coursera - Writing in the Sciences - Week 7

Continue with week 7.

7.1 Writing a review article
Why you need to write a narrative review article or literature review? It lets you understand the current primary literature in your field of study. And by doing so, learn to read, organize, and summarize papers, and lastly write it out. By doing so, you will get an overview of the field of study. Furthermore, the review paper is a good resource for anyone to quickly dive into the the are of study.

There are three types of review articles.
(1) Non-systematic review. Also known as "narrative" review, not comprehensive, and is also a qualitative review.
(2) Systematic review. To summarize all relevant studies in a systematic way following pre-defined criteria. This is also a quantitative review.
(3) Meta-analysis. Basically a systematic review but using statistical techniques to pool data. This is something that I've never heard before.

What is the structure of a review articles?
(1) Abstract. Write this last as discussed in the previous week.
(2) Introduction. Define the aim.
(3) Method. Search strategy.
(4) Body. Main content of the review. Group it by methodology or theme. Upon this, analyze, interpret, critique, and synthesize these studies.
(5) Conclusion and future directions. Discuss recommendation and gaps. What's next for this field of study you've identified?

7.2 Grant I
Why you need to write research proposal? You're applying for grant for your research. Certain research need significant fund to proceed ahead. There are committee that review and approve this, learn the application and review process.

For successful application, you will need to identify the gap or niche in the area of research. Some questions to ask yourself.
(1) Is the question important?
(2) What is the overall goal?
(3) What specifically can be done?
(4) What is the expected payoff?

Note you're not a sole research. Research grant will be used and allocated for a whole research team. Build your team.

Plan your research. Ask yourself.
(1) Is there a need.
(2) How will be the specific aims be accomplished?
(3) How long will the project take?
(4) What is next?

Read the editorial post, "Ten Simple Rules for Writing a Postdoctoral Fellowship".

7.3 Grant II
Whole section focus on tips and strategies on writing Specific Aims document. Again, write the document follows these four key questions.
(1) Is the question important?
- Attention grabbing first sentence.
- Bring reviewers up to speed.
- Frame the knowledge gap/need.

(2) What is the overall goal?
- Big-picture goals.
- Objective of this proposal.
- Best bet / hypothesis.
- Supportive preliminary data.

(3) What specifically can be done?
- Aims.
- Working hypothesis.
- Methods.

(4) What is the expected payoff?
- Return on investment.
- Related to goals of the funding announcement.

7.4 Grant III
Further investigation and key questions to ask yourself before proceed ahead.
(1) Is there a need?
(2) How will the project be accomplished?
(3) How long will the project take?
(4) What is the payoff and what is next?

The outline of the research plan.
(1) Background/Significance.
(2) Aims.
(3) Timeline.
(4) Conclusion and future directions.

7.5 Writing letters of recommendation
When a student ask you to write a letter of recommendation, request below information from him/her.
(1) CV / resume.
(2) Information about the position / award.
(3) The dateline.
(4) Specific information on how to submit the information.

Note this is academic type recommendation letter, so the format of the letter should be following old-fashioned letter.

One interesting note. When you're asking for recommendation letter, you should avoid recommenders who ask your to draft your own letter. I wonder why?

7.6: Writing personal statements
Why we need this? Scholarship (usually), internship, or jobs.

Some tips.
(1) Make is personal (duh).
(2) Give specific examples and stories.
(3) Don't read your CV line by line.
(4) Avoid big words or cliches.
(5) Show interest in / flatter your readers. Do your homework!
(6) Explain gaps and failures.

Learning Objectives
(1) Understand how to write review articles.
Nothing much into the details of how to write review articles. The meta-analysis review article was quite new to me.

(2) Become familiar with the grant-writing process.
Always a long winding process. Lots of red tape.

(3) Understand how to write a strong letter of recommendation.
Both sides should prepare well. Rejection is understandable.

(4) Understand how to write a strong personal essay.

Coursera - Writing in the Sciences - Week 6

Continue from week 5.

6.1 Plagiarism
How do we write something original like your ideas or thoughts? You can to different materials on the said topic and understand it before you can form your opinions on it. From there you then convey your ideas in written words. In short, read a lot and differently, copy and quote the materials, and write from memory. Why? plagiarism is not really just word for word copy, we can subconsciously copy the author's sentence structure or word choices.

Self-plagiarism is also not acceptable. No need to republish something old as new. If the manuscript have been published in other journal, it's illegal to republish in other journals due to copyright rules.

There are tools that detect plagiarism like CrossCheck, Turnitin, PlagScan, or iThenticate. I've personally used Turnitin before and quite accurate to a point.

Be careful with miscitation and inaccurate citation as well. The issue with primary and secondary source, especially when we did literature review.

To be safe, just quote your writing in you are not sure.

6.2 Authorship
If you're collaborating a paper with multiple authors. Discuss this upfront.

Don't put your name in any papers as co-author if you don't want to take full public responsibility or fully responsible for the paper. You can put those who help in acknowledgement section.

What sequence of names should be placed in the paper.  First name is the primary author. Last name is the senior author or team lead like your advisor. But the sequence order may be different from one journal to another journal.

Ghost or honourary author is actual writer that draft the paper but no authorship in the paper. Guest author someone that lend his name to boost the paper, usually research done or sponsored by an organization, especially the medical literature. Example is the incident of Merck's Vioxx medicine scandal.

6.3 The Submission Process
(1) Pick the journal you want to publish.
(2) Follow the write style and convention.
(3) Get all copyrights sign off and submit your paper.
(4) Feedback from the publishing journal. Rejected but still able to resubmit. In other words, you should revise based on the reviewers feedback and resubmit again.
(5) Resubmit and comment on the reviewer's feedback.
(6) Final proof reading on the final print.

How to handle criticism will determine your success in publishing your paper. Separate your ego from the review.

According to the book Guidebook to Better Medical Writing Revised Edition by Robert L. Iles, good writing and good presentation (tables or figures) are essential for getting your paper published.

6.4 Interview with Dr. Bradley Efron
According to Wikipedia, he is an American statistician. So his opinions is based on statistics papers. Some of his key points.

(1) Statistics papers have both philosophical and technical side.
(2) Paper is written not only for publishing but also for reading as it's an essay for communication. Follow the writing style of journalist. Good heading that piqued the interests of the reader to continue reading the story.
(3) Send your paper to the right journal.
(4) Treat journal like a magazine (which is true) and it should be fun to read.
(5) Focus on the abstract or introduction (the beginning) and add in good figures and styling. Make it easy (dumbing down) and fun to read your paper.
(6) Go read papers published by good writer in your field.
(7) If you're publishing for the first, let editors know so they will be more understanding.
(8) Even himself have his papers rejected.
(9) Less papers is better. Quality over quantity.
(10) Rejection is common. Don't take it personally.

6.5 Interview with Dr. George Lundberg
According to Wikipedia, he is a pathologist, writer, and editor. He will share his opinions on publication process and getting your paper published.

(1) Journal wants papers that make it looks good. Hence, quality and ground breaking papers are well sought.
(2) Pick the journal that fits your goal. Want to improve your CV or get funding, go for high impact journal. Want to influence the industry, something else instead.
(3) Use the publication process to improve your research and writing.
(4) Don't write too long. Short and clear. Following the instructions for journal.
(5) Don't draw conclusion beyond the data.
(6) Edit your writing, be as mean as possible and ask for reviewers to review before submitting.
(7) No one like rejection. Everyone experience it.
(8) Eugene Garfield created the impact factor. He disagree with the usage of impact factor on journals on readership and citation counts. To him, impact means does it change the field.
(9) Don't resubmit the same paper to different journals, it maybe be sent to the same reviewer.
(10) If the research were funded using public fund, then the paper should be released to the public and not locked behind a publisher payment gateway.

6.6 Interview with Dr. Gary Friedman
Can't find much any information on him

(1) Don't submit repeating finding research paper.
(2) "Salami problem". Splitting your research into multiple papers.
(3) Don't over-evaluation your research or paper.
(4) Don't write a publication paper like a thesis.

6.7 Doing a peer review.
Peer review is good for your learning and understand the whole publication process.

Young peer review is a better reviewer because they are more up-to-date in the current field and more careful in reviewing.

Watch your tone in your review. Be tactful. Instead of identifying problems and criticizing the author(s), suggest a better way of doing it.

Reviewing is not lecturer. It may be condescending.

Reviewing types:
(1) Single-blind review where the reviewer knows who is the author are but not the opposite.
(2) Double-blind review. Both parties don't know each other.
(3) Open review. Both parties are aware of each other.
(4) Post-publication reviews. Done after the publication of the paper in the form of blogs or online comments.

What or how to review?
(1) Write one paragraph on the key finding and importance of the paper.
(2) What are the positive of the paper? Be specific.
(3) What are the limitation of the paper? Be specific.
(4) Don't focus on grammar or spelling issue. Focus on the research or the content itself.

6.8 Predatory journals
Bogus open access journal that was created to make money through scam. This was exposed by John Bohannon in this article, Who's Afraid of Peer Review?

Learning Objectives
(1) Identify and avoid plagiarism.
Be careful of accidentally copy the writing structure.

(2) Understand the peer review process.
Read the publication process and talk to your peer.

(3) Understand criteria for authorship.
Find the right co-author and use acknowledgement when necessary.

(4) Recognize common pitfalls for new authors.
Follow the publication rules and processes. Follow up with the feedback. You are not your research or paper. Differentiate between these two separate things.

(5) Recognize predatory journals.
Seek your advisor or peer advise on these fraud journals.

Coursera - Writing in the Sciences - Week 5

Continue with Week 5.

Way more delay like a year and two months ago. Good I've keep a todo-list and revisit it from time to time. One good lesson when come to learning, the key thing here is not the distraction but the recovery from interference. One bite at a time. One step at a time. One paragraph at a time. You will not feel the task daunting. Otherwise you will procrastinate and won't be able to get started.

5.1: Tables and Figures
Did I wrote my thesis in the wrong sequence? Dr. Dr. Kristin recommended that you should write in such order:

(1) Tables and Figures. No shell table but actual collected data. These are the core idea or story of your paper.
(2) Results. Basically high-level summary of each table and figure.
(3) Methods. What you have done to achieve the results.
(4) Introduction. Background story of your research topic.
(5) Discussion. Probably the longest part of your thesis. If you've done (1) till (4), then this part should come naturally to you. You should already know what to say.
(6) Abstract. "Abstract means to pull out". Yes, that sounds a bit weird. Pull, in the context here means to extract summarized details from other sections.

In the past, my sequence is reverse from (6) to (1). No wonder I spent so much time rewriting the (4), (5), and (6). In other words, focus on the results first and write the other parts later. What about reading a manuscript, the sequence should be (6), (4), (5), (3), (2), and (1).

Some additional reading.
(1) Clinical Chemistry Guide to Scientific Writing.
(2) Essentials of Writing Biomedical Research Papers. Second Edition by Mimi Zeiger

Why tables and figures are important? Because these are the foundation of your manuscript. The two items should be self-explanatory without looking around the elaborated section like method and discussion.

Between tables and figures, which one should you choose? If you need to visually show trends, patterns, or distribution, pick figures. Otherwise, use table when you need to show precision (like number of decimal points), many values, or multiple variables. However, a table or figure may not be need, sometimes a single sentence is sufficient enough.

It's crucial to understand the anatomy of a table which includes title, legend, data, and footer. Likewise for the anatomy of a figure which contains title, legend, picture (primary evidence), diagram, graph, and label. Best to follow the journal guidelines on layout and styling. One trivial rule in styling, remove grid lines from a table (doesn't look professional), just three horizontal lines. Also, add unit of measurements to your variables, for example, Age (years) or Age (months) for toddler. Lastly, don't add unnecessary columns which clutters the table.

Next, graph. There are may types of graphs.
(1) Line graph shows trends over unit of measurement (time, age, or others).
(2) Bar graphs compares group of data at a time point.
(3) Scatter plots shows relationship between two variables or linear correlation (does A causes B?). This graph shows all the data.

If you graph is too complex or cluttered, maybe you should use a table.

When should you use diagram or drawings? If you need to illustrate an experimental set up, workflow (causal diagram), or anatomy of a human or an animal.

5.2: Results
The main focus in this section is to summarize the data by showing relationships and trends through citing data from tables or figures. Do not repeat the raw data from tables or figures data by data. Just focus on the high level summary or take home messages. Pay attention on complementing (not repeating but may highlight) the data in the tables or figures. In summary, result section tells the reader of what you've discover with the supporting data from tables or figures.

Additionally, one key point is result section is what your data shows and discussion section is that your data means.

What verb tense should you use in this section?
(1) Use past tense for completed action like experiment result. Example is "We found that ......"
(2) Use present tense for what is still to be true like showing the table data. Example is "Table 1 shows ......"

You can mix both in the same paragraph. For example, "We found that ...... as Table 1 shows ......".

5.3: Practice writing results
Revise and edit those part where the author is just reading the table, repeating the result line by line in writing. Only pick and highlight important and interesting statistics.

5.4: Methods
Overview of what have been done and instructions for someone else to replicate the study like recipe. Use who, what, when, where, how, and why checklist to guide you to draft the content. These questions should tell in details of material, participant/subject, experimental protocol / study design, measurements of the research, and analyses.

To make your life easy, reference to other papers if the approach is a general well-known method. Also, use flow-diagram to simply your approach, like participant flow again.

What about verb tense?
(1) Use past tense to report method. For example, "We measured ......".
(2) Use present tense to described how data is presented in the paper. For example, "Data are summarized ......". Why? When you read the paper, the data are still being summarized to you.

Is okay to use passive voice or mix of passive and active voice in this section. A lot of emphasis is on the method or the variables.

Read the BMJ Christmas issue or archive for some humourous and light reading.

5.5: Introduction
Some general rules, typically 3 or 2 to 5 paragraphs, don't focus on general ideas but hypothesis or aim of the paper. Read the details rules recommended by Thomas M. Annesley in his paper, "It was a cold and rainy night" : Set the Scene with a Good Introduction. Following this top-down structure to plan the content.

(1) Background, known information.
(2) Knowledge gap, unknown information.
(3) Hypothesis, question, purpose statement.
(4) Approach, plan of attack, proposed solution.

Or a similar structure.

(1) What's known or background. (paragraph 1)
(2) What's unknown or limitations and gaps in previous studies. (paragraph 2)
(3) Your burning question, hypothesis, or aim. (paragraph 3)
Example of phrases are "We asked whether ......", "Our hypothesis was ......", "Our aim/s were ......".
(4) Your experimental approach. (paragraph 3)
(5) Why your approach is new, different, and important to fill in the gaps. (paragraph 3)

5.6: Introduction practice
Find any papers that interests you and mark these three sections from the introduction section.
(1) What's known or background.
(2) What's unknown or gaps or limitations.
(3) The aims of approach of this specific study.

5.7: Discussion
Start this section by following these four rules.
(1) Answer the question asked.
(2) Support your conclusion (your data, others' data).
(3) Defend your conclusion (anticipate criticisms)
(4) Give the "big-picture" take-home message.

In the discussion section, your writing should answer the question that why should anyone cares?

For further breakdown of the structure of this section as shown below.
(1) Key findings that answers the question(s) asked in the Introduction section.
(2) Key secondary findings.
(3) Context.
(4) Strengths and limitations.
(5) What's next.
(6) The "so what": implicate, speculate, and recommend.
(7) Strong conclusion.

And what verb tense to use? Past tense for any discussion of the result of completed experiment (we found that ......) and present tense for the suggestion of the data (the result suggests ......).

5.8: Abstract
Abstract is the combination of "ab" (out) and "trahere" (pull). This means to "pull out" key point from each sections. Length wise, the paragraph should be around 300 to 500 words. The structure as follows:

(1) Background or context.
(2) Question / aim / hypothesis.
(3) Experiment(s) details on materials and methods.
(4) Key results.
(5) Conclusion or the answer to the question. The take home message.
(6) Implications, speculation, or recommendation. Why should reader cares?

Learning Objectives
(1) Understand how to write the sections of an original scientific manuscript.
The key take here is to understand the anatomy of the manuscript (more on this in future post), tables, and figures. Understanding each part and the visual styling will lead to professional looking and readable paper.

(2) Critique poorly formatted tables and figures.
Use the standard good practices.

(3) Practice writing strong Results and Introduction sections.
You will need to read good papers on these two sections.

(4) Summarize the elements of a Discussion section.
Following the steps in the structure.

Coursera - Writing in the Sciences - Week 4

Continue with week 4. I've been quite behind the schedule and needs to stick back the schedule. Managed to finally sit down and went through all the week 4 modules in one session straight which took me around 3 hours. For the coming weeks, I should be able to get back on track.

4.1 More paragraph practice
The key take away from this module is emphasis on paragraph. Two important things:

(1) What's the paragraph about?
(2) What's the main idea or important points?

Good exercise to learn this is to summarize the main idea of the blog posts, papers, or other published literature. Webshit Daily is a good example of such writing with humour and sarcasm.

When you've a paragraph with complex idea, we can represent the concept as table or diagrams. As they said, a picture is worth a thousand words. If there are repetitive words or ideas, shorten it to take away the repetition. Wordiness may also leads to ambiguity, rewrite it to become more specific.

When to use passive voice? When it doesn't matter who did it.

Use "However" when you want to contrast something in the previous sentence.

One paragraph should contains one main idea. If you have two ideas within a paragraph, rewrite it into two paragraphs instead.

A paragraph can contains 1 - 3 sentences. Yes, there a paragraph with one sentence. I always think that a paragraph should at least have four sentences. One topic sentence, two supportive sentences, and one final concluding sentence.

4.2 Overview of the writing process
The main point is how do you approach writing? There are three major steps:

(1) Pre-writing.
A process of collecting, synthesizing, and organizing your data and ideas of your writing.

(2) Writing the first draft.
Turn the ideas into complete sentences. Writing should be fast and quick. Fsck grammar!

(3) Revision.
Revise to make it sounds better.

As a writer, you should follow the three steps in a sequential manner. Don't do two steps in one time. Multi-tasking is always bad! For example, start writing without much research is a typical approach by most people but this is not recommended. Not only this will stress you out, you are also prone to distraction as you're busy googling and doing something else. As you all know, googling for information will often leads to other unproductive online activities like reading news, checking social media status, and others. Also, when you're focus on the details of writing, you will lost focus on the big picture. Therefore, invest more time in pre-writing step.

Similarly, do not carry out writing the first draft and revision at the same time. Fsck grammar! Just make sure you have written down the ideas in complete sentences. Is okay you've wrong grammar, spelling, or the sentences do not sound good. That is for the last step -- revision!

The next question is how much effort or time we should spend on each step? The recommended breakdown are as follows:

- Pre-writing (70%)
- Writing the draft (10%)
- Revision (20%)

See how important the pre-writing process is. While going through this module, I've realized that my approach to writing, especially writing for learning should follow in this sequence!

4.3 The pre-writing step
Again, remove the bad habit of writing and gathering information simultaneously. Focus on gathering information. Don't starting writing unless you've gather and organize the information. If you have a sense of overall structure of your writing, then you can proceed to the next step.

To have an overview, use several available organization system. For example, mind map or road map so that you've an outline of the overall document. By organizing the ideas, you will know what are the missing pieces and what to search next. This process will take a while. If you're stuck, do something else. Subconsciously, the missing pieces will come to you, eventually in one way or another. Always carry a recorder, a pen, or any capturing ideas tools. You can even put a water proof whiteboard in your bathroom.

When come to organizing ideas with different viewpoints, group the arguments. For example, you can group the ideas by those who support it, the counter arguments, and the rebuttals.

4.4 The writing step
Just write. Fsck grammar or spelling or what ever style. Convey your organized ideas into complete sentences. Focus on the logical organization of your ideas. Best to set a timer on this so that your priority is to finish the writing instead of doing any revision or editing.

Do not edit your writing. Just write it down!

4.5: Revision
Six important steps which will improve the revision process. These are:

(1) Read your writing out loud.
The main purpose is to identify awkwardness in your writing. When the writing sounds good, then the reader will appreciate the natural flow of the writing.

(2) Do a verb check.
To make sure your writing is expressed in a direct way, underline all the main verb in each sentence. There are three issues with verb:

(a) Lackluster verb. For example, "are".
(b) Passive verb. For example, "was".
(c) Burried verb. For example, the main verb is too far from the subject. We have discussed this in previous week.

(3) Don't be afraid to cut.
Identify these issues to improve your writing. Those marked in bold are my bad writing habit.

(a) Dead weight words or phrases.
(b) Empty words or phrases.
(c) Long words or phrases.
(d) Unnecessary jargons and acronyms.
(e) Repetitive words or phrases. 
(f) Adverbs. (very, really, quite, or basically)

(4) Organizational review.
Tag the paragraph of your writing. Each tag is a summed up main point of the paragraph.

(5) Get outside feedback.
As the reader with or without the domain knowledge for feedback. The reader should be able to identify the main point, the take-home message, or the significance of your writing. If they are unable to do so, ask them to identify the part which are hard to grasp. Their feedback is the focus of your revision.

(6) Find a good editor.
Someone know have the domain knowledge and good in writing.

4.6: Checklist for the final draft
Finally, before sending out the writing to the editor or journal, go through these check list below to ensure consistency and accuracy.

(a) Check for consistency.
You writing style and so forth.

(b) Check for numerical consistency. 
For example, is the writing match the result in the table? Sometimes, sloppy copy and paste can cause inconsistency between the numerical data and the writing.

(c) Check your references.
One main issue is citation propagation where the writer back his/her statements based on a secondary source instead of the main source. Always do fact checking and reference to the main source.

Learning Objectives
(1) Practice writing clear and concise paragraphs.
Some common tips.

(2) Describe the steps in the writing process.
Most important lesson learned here. Pre-writing is so crucial that we also neglect it and do it together with writing. There will be no writing until you have completed the pre-writing step.

(3) Recognize the importance of spending sufficient time pre-writing.
This learning note was done in such way where I jot down the ideas which took me 3 hours. The writing was fast and it took around 1 hour.

(4) Recognize that good writing requires extensive revision.
Read, review, revise, and repeat.

Coursera - Writing in the Sciences - Week 3

Last week, I've learned two important things, using strong verbs and cut unnecessary words. However, due to schedule conflicts, I'm way, way behind the schedule with week 3.

On a side note, interestingly, I've managed to organize the note in a more visually pleasant way. My future blog posts will follow such visual style.

3.1: Experiment with punctuation
Why use different punctuation? To vary your sentence structure so it won't become boring and monotonous. However, the examples and discussions in this module are quite limited. I've googled around for better one.

Different punctuation marks have different separation power. Below are the list starting from the lowest to the highest separate power. Read aloud when you use these punctuation marks, it will help to focus and stress on which part of the sentence.

This module will focus on the middle four (emphasis in bold). Dash and parentheses are less formal, use when necessary.
- Comma (shortest pause)
- Colon (bigger pause than comma)
- Dash (bigger and more abrupt pause)
- Parentheses (slip something extra into a sentence)
- Semicolon (near complete stop because it separate two related sentences)
- Period (complete stop)

(1) Dash
I seldom or never use this punctuation mark. Two purposes: to add emphasis or abruptly insert a definition. We can use dash to replace either commas or parentheses. Good example to compare three different usages.
"The food, which was delicious, reminded me of home."
"The food—which was delicious—reminded me of home."
"The food (which was delicious) reminded me of home."
(2) Colon
To main purpose is to introduce a list, quote, explanation, conclusion, or amplification.

(a) To introduce a list.
"I have three sisters: Daphne, Rose, and Suzanne."
Another example I love using number in the list.
This research follows four distinct phases: (1) establishing measurement instruments, (2) measuring patterns, (3) developing interventions and (4) disseminating successful interventions to other settings and institutions.
(b) To amplify and extend independent clauses where the second explains the first.
"He made three points: First, the company was losing over a million dollars each month. Second, the stock price was lower than it had ever been. Third, no banks were willing to loan the company any more money."
(c) To explain and amplify.
"After three weeks of deliberation, the jury finally reached a verdict: guilty."
(3) Semicolon
Something that I never use in my writing. I still can't seems remember or use this properly. Surprisingly, you can interchange period and semicolon! Use semicolon in these two situations:

(a) To connect two independent clauses (an independent sentence which contains a subject and a predicate), typically between the transition words (emphasis in bold).
"Mushrooms grow very quickly; in fact, after a good rain, it takes only a few hours and you start picking them."

(b) To separate series of items where items in the list contains internal punctuation. For this case, a comma.
"Science fiction includes Star Trek, with Mr. Spock; Battlestar Galactica, with its Cylons; and Star Wars, with Luke Skywalker and Darth Vader."
As a visual cue to group items in a list. I always have problems when describing a list of items with adjectives.
"I bought shiny, ripe apples; small, sweet, juicy grapes; and firm pears."
(4) Parenthesis
Use this when you want to put optional sentence fragment in your sentences or don't want to break the flow of your sentences, an afterthought. I'm referring to my own typical writing.

(a) To specify date in the sentence where you have extra comma which will break the flow of the sentence.
"We will schedule our appointment on this coming Sunday (24th September, 2017)." 

(b) To write informally or as an interjection, a style I commonly used.
"Anyone can afford (ahem, cheap!) the amplifier."
3.2: Practice, colon and dash
Still needs more practices to nail this down and it's quite hard to remember all the rules.

3.3: Parallelism
Also known as Parallel Structure. Definitely something you may encounter before but never know its actual name. Some good examples found in proverb:
"Easy come, easy go."
"No pain, no gain."
"Sometimes you win, sometimes you lose."
"One man's trash is another man's treasure."
"A bird in the hand is worth two in the bush." 
Two common types of Parallel Structure:

(a) With the -ing form (gerund) of words.
"Mary likes hiking, swimming, and bicycling."
(b) With infinitive phrases.
"Mary likes to hike, to swim, and to ride a bicycle."

3.4: Paragraphs
The key concept here is "1 paragraph = 1 idea". To elaborate, good paragraph is short (3 to 5 sentences) which encourages more white spaces (good for readability).

Apply the inverted pyramid style (see image below), similar to newspaper writing style where you put most important information at the beginning of the paragraph or writing. In the web, this is known as clickbait title.

Good paragraphs can consists of three things:

(1) Logical flow of ideas.
Three types as well, sequential in time, general to specific, and logical arguments.

(2) Parallel sentences structures.
We have discussed this earlier.

(3) Transition words (use with cautious and as simple as possible)
We use transition words in a sentence to indicate "changing gear". Popular transition words is "but", simpler than over exotic one like "on the other hand" or "nevertheless". But I'm surprised that she recommended to use two transition words ONLY:

(a) But, to signal a change of discussion.
(b) And, to further discuss some additional information.

Do not start every sentence with transition word within a paragraph. You can write beautiful flowing paragraph without using much transition words.

Focus on the first and last sentence in a paragraph. These are the only two things a reader will remember.

3.5: Paragraph Editing I
Some general advice from this module.

(1) Don't overuse transition words.
(2) Identify the main idea of the paragraphs.
(3) Identify the supporting ideas of the main idea.

One good example from the editing which illustrates brevity and reduce wordiness.

"Although the methodological approaches are similar, the questions posed in classic epidemiology and clinical epidemiology are different."
"Despite methodologies similarities, classic epidemiology and clinical epidemiology differ in aim."

3.6: Paragraph Editing II
When editing, outline the existing paragraph into several main points or sentences. Reconstruct these main points to replace the existing paragraph. The editing is shown below. It dawned to me that reviewing and editing other published literature is also crucial step to become a better writer.

Another example but shorter. However, if you pay attention to the editing, the main reason for wordiness is because the author wants to vary its writing and sounds intelligent (we discussed this is earlier post) and this impacts understanding.

3.7: A few more tips
In this module, Dr. Kristin raised an important question that I've encountered in most of my writing- repetition. To fulfill the number of pages in your writing assignment, you will inadvertently rewriting the same idea in different ways or using different words. How do you know? If you need to use thesaurus to find synonyms to avoid repeating a word in a sentence or paragraph, then you have the wordiness issue. For example, within the same sentence or paragraph, you find the words "illustrates" or "demonstrates". Another example, is "banana" or "the elongated yellow fruit". The second example is known as Elegant Variation. I have mixed feeling on this second example because for normal writing, it does add variety to writing.

If you are aware of such writing behaviour, ask yourself these two questions:
(1) Is the second instance of the word needed?
(2) Is the synonym of the word is better than repeating the word?

There are exceptions. Keywords in scientific writing can and should be repeated as those are the key concept of the writing. For example, anything in abbreviation list should be use consistently.

Learning Objectives
(1) Practice using colons, dashes, parentheses, and semi-colons.
Read it aloud and identify the duration of the pause. Then, pick the right mark punctuation.

(2) Recognize the importance of varying sentence structure.
Look into varying your transition words.

(3) Practice writing focused, organized paragraphs.
Look into Inverted Pyramid Style.

(4) Recognize that it is OK to repeat key words in scientific writing.
Look into the issue of Elegant Variation.

(5) Fix sentence parallelism.
Consistency is the key here. Follow the same sentence structure within a paragraph thus increase the cohesion.

Coursera - Writing in the Sciences - Week 2

Continue with week 2 study. Notes as follows.

2.1: Use the active voice
An active voice is a type of sentence that follows a format of subject-verb-object. Or it's the way we normally talk. Example as shown below.
She (agent) throws (verb) the ball (the recipient).

For passive voice, is the reverse which follows a format of object-verb-subject. Rewriting the above sentence as passive voice.
The ball (recipient) was thrown (verb) by her (agent).

Alternatively, we also can remove the agent. The sentence below does not tell us who throw the ball.
The ball (recipient) was thrown (verb).

Passive voice is useful when we're want to exclude the recipient. Good example is shown below where to evade any admission or person responsible.
Mistake was made.

How do we recognize a passive voice? Identify "to be" verbs in the sentence. "To be" verbs are weak and wordy and you can replace them with stronger verbs. List below shows the step-by-step guide to eliminate "to be" verbs.

(1) Identify
(2) Substitude
(3) Convert
(4) Change
(5) Combine

The restaurant’s parking lot (is) narrow.
(There are) not very many parking spaces and those (that are) available (are) too cramped.

The restaurant (suffers) from a narrow parking lot with only a few cramped spaces.

To convert a passive voice to active voice, ask yourself this question. "Who does what to whom?"

Active voice have several advantages as listed below.

(1) Emphasis author responsibility.
Why passive voice is prevalent in scientific papers? Because first-person pronouns (I/We) usages should be kept to a minimum. In method section of your paper, you're encourage to use passive voice as what have been done is far more important that who done it. APA (The American Psychology Association) have different opinions on this. More on this in next module.

(2) Improves readability.
I like the example below because it shows we can skip first-person pronouns.

A strong correlation (was found) between use of the passive voice and other sins of writing.

(We found) a strong correlation between use of the passive voice and other sins of writing.

(Use of the passive voice) strongly correlated with other sins of writing.

(3) Reduces ambiguity.

2.2: Is it really OK to use "We" and "I"
Is using personal pronouns like I/We in scientific writing acceptable? Based on her explanation, it's okay to do so although some said not using personal pronouns make your writing more objective.

However, different journal have different opinions on using personal pronouns. Check the publication style guides you are submitting to and follow its guidelines. For example, the style guide of Science Magazine recommends:

Use active voice when suitable, particularly when necessary for correct syntax 
(e.g., "To address this possibility, we constructed a λZap library . . .," 
not "To address this possibility, a λZap library was constructed . . .").

Note to self. Do search and read up these style guides. Start with the The Element of Style that you've bought few months back.

2.3: Active voice practice
Some practices on converting paragraphs from passive voice to active voice. Pretty much quite straight forward. One of the key or first step is to recognize passive voice is to find these keywords : be, is, are, a, was, were, has been, have been, will be, and being.

2.4: Write with verbs

We must follow three rules.

(1) Use strong verbs.
When you have limited vocabulary, your writing is boring. One way is to expand your vocabulary. But how? Read a lot, really a lot. I like this approach of treating every read is a write to expand your vocabulary. The example shown in the lecture exemplified this point. Pay attention to the verb. Compare the verbs. See how using strong verbs change the tone of the sentence.

Note to self: Expand your vocabulary. Read and write more.

"Loud music (came) from speakers embedded in the walls, and 
the entire arena (moved) as the hungry crowd (got) to its feet."


"Loud music (exploded) from speakers embedded in the walls, and 
the entire arena (shook) as the hungry crowd (leaped) to its feet."

One good way is to identify and underline all the "to be" verbs like is, are, was, were, has, been, am, and others and replace with with stronger and more vivid verbs. Example of boring usage of "to be" verbs as shown.
"She is an excellent scientist. Her research is top notch. Her experimental
technique is also beyond compare."

(2) Avoid turning verbs into nouns.
Again, another example where I always use in my writing. Using nouns instead of verbs. Why using now is not recommended? It lack the impact of using a verb and may lead to ambiguity.

Let's start with the example given.

"During DNA damage, (recognition) of protein one by protein two results in (recruitment) 
of protein three and (repression) of cell proliferation genes."

"During DNA damage, protein one (recruits) protein two and protein three, which together 
(repress) cell proliferation genes."

(3) Don't bury the main verb.
Another good example here where the subject and the main verb (predicate) close together.

"(One study of 930 adults with multiple sclerosis (MS) receiving care and one of two 
managed care settings or in a fee-for-service setting) (subject) (found that) (predicate) only 
two-thirds of those needing to contact a neurologist for an MS-related problem in the prior 6 
months had done so."

"One study (found that), of 930 adults with multiple sclerosis (MS) who were receiving 
care in one of two managed care settings or in a fee for service setting, only two-thirds of those 
needing to contact a neurologist for an MS-related problem in the prior six months had done so."

2.5: Practice examples
A few rules while going through these examples.

(1) Don't use long subject
(2) Don't use buried, boring predicate and passive verb.
(3) Don't turn verb into noun.
(4) Don't use negatives words
(5) Don't use "hedge" words.
(6) Don't use "fluff" words. For example, very, important, and others.

(The (fear)(3) expressed by some teachers that students would (not learn)(4) statistics 
well if they were permitted to use canned computer programs)(1) (has (not been)(4) realized)(2). 
(A careful (monitoring)(3) of achievement levels before and after the introduction of computers 
in the teaching of our course)(1) (revealed)(2) no (appreciable)(5) change in students' performances"

"Many teachers feared that the use of canned computer programs would prevent 
students from learning statistics. We monitored student achievement levels before and 
after the introduction of computers in our course and found no detriments in performance."

The whole exercise makes me want to pick any scientific papers out there and identify and issues and rewrite it. As I love to read papers, this should be quite an interesting writing exercise.

2.6: A few grammar tips
And I thought I was aware of these grammar rules.

(1) Data is plural.

(2) Affect and effect.
Yes, the RAVEN (Remember Affect Verb Effect Noun) rule is not entirely correct. We can use the word affect as a noun and the word effect as a verb.

(3) Compare to and compare with.
Compare to is used to compare similarities with different things.
Compare with is used to compare differences with similar things.

The bike that is broken is in the garage. (one bike out of many bikes)
The bike, which is broken, is in the garage. (regarding one particular bike)

(4) That and which.
That is a restrictive pronoun.
Which is a nonrestrictive pronoun. Meaning that the word is optional and if you remove it, does not change the meaning of the sentence. Also, there is a comma, before the word.

Learning Objectives
(1) Distinguish between active and passive verbs.
When to use passive voice? When you're asking a questions!

(2) Practice writing with strong, active verbs.
As I was going through the week 2 course, I tends to write more in active voice rather than passive voice these days. Surprising to find that I use more passive voice than ever in my writing. While changes is inevitable, I still struggle to adapt to the new writing and constantly needs to remind myself to write in active voice.

(3) Fix sentences where the subject and predicate are too far apart.
Definitely something new for me and I don't even realize that.

(4) Correct specific grammar mistakes.
I can't remember what I've learned here.

Coursera - Writing in the Sciences - Week 1

Writing is always hard for me. I always feel this invisible gap of what you want to say and how it's conveyed down in writing. Six years ago, around 2011, frustrated with this gap, I've started writing through blogging. Even since, writing have become a way for me to express my understanding in my learning as well as a medium for me to unwind (mindless ramblings). These days, while writing becomes more natural but still crappy, I still exploring numerous ways to improve my writing.

Last Thursday, I received an email from Coursera that the course Writing in the Sciences, taught by Dr. Kristin Sainani is currently opened for registration. Since I have a long holidays ahead, might as well make good use of the free time and pick up something useful along the way.

Below are some of the key points and additional notes of each module in week 1.

1.1: Introduction; principles of effective writing
What is good writing? Effective communication between the writer and the reader. And how do we achieve effective communication? Simple writing. While we want to sound smart, elegant, and stylish through our writing, the priority should be on getting your message across in a clear and effective manner. If the reader cannot understand what you're trying to say, then the writing does not serve its purpose.

Good writer have something to say, something they passionate about. In other words, good story teller. When come to scientific writing, you will need logical and clear thinking. Read anything. Read what professional wrote. Study, learn, and imitate their writing. Superhuman by Habit is the first book I can think of which have simple and clear writing. Contrary to popular opinion, I can't say much about William Zinsser's On Writing Well.

If we write like how we talk, then the writing will be in more simple and conversational tone. Academic writing is totally opposite of that, more formal and wordiness. However, talk about something before writing it down is also a good approach. As you can treat your conversation as your first draft.

Reevaluate and rethink your approach to writing as well as the writing process. Elegant and stylish writing have to go through numerous edits and revisions. You just can't get it done in one shot. Don't worry about getting your writing done right the first time. You can't. Nobody can. Even professional writer. There is no such thing as get it done right the first time when comes to writing!

Focus on revision instead of the initial draft. Get your first draft done as soon as possible. Forget grammatical rules or spelling errors. Just churn it out. Next, start the revision process. Be ruthless and cut all unnecessary words. Repeat this process until there is nothing else to remove.

1.2: Examples of what not to do
How to evaluate good writing? Ask yourself these questions. Is the writing easy to to understand? Is the writing enjoyable and interesting to read? If not, you reader will not care.

Grammatical Normalization, a fancy word where a verb, an adjective or an adverb is turned into a noun. The side effect of writing in such way are wordiness and can irritate the reader. For examples,

Unnecessary nouns:
Bad : We have a discussion on that particular incident.
Good : We discussed on that particular incident.

To-be verbs:
Bad: There is this restaurant that attracts all the tourists.
Good: This restaurant attracts all the tourists.

The lesson learned here is don't start a sentence with "There is ......", "There are ......", or "It is ......". Be aware of this during revision.

1.3: Overview, principles of effective writing
The preference to use verbs instead of nouns in writing may sounds formal but hard to read. Clear writing prefers verbs over nouns. During revision, identify those nouns in a sentence. Look for any words that end with -ion, -ment or -al.

Be specific. Be careful with your word choices that leads vagueness. In scientific writing, if you are experimenting on a particular type of fish, name the fish directly.

Don't use acronyms unless it's necessary and generally known.

What are the principles of effective writing? 

(1) Reduce wordiness. Cut unnecessary words or phrases.
(2) Use active voice (subject + verb + object).
(3) Writing and using strong verbs instead of nouns.

1.4: Cut the clutter
These two examples illustrate how we going to cut the clutter. Read aloud yourself.

Several issues were found with these examples.

(1) Verb turned into noun.
(2) Vague amorphous words.
(3) Repetition or repeated words with the same meaning.
(4) Stylistic or better word choice.

Example 1:
"This paper (provides a review)(1) (of the basic tenants of)(2) cancer biology study design, using as (examples studies)(3) that illustrate the ((methodologic)(3) challenges)(2) or that (demonstrates)(3) (successful solutions)(3) (to the difficulties (inherent in biological research.)(3))(3)"

So after revision, the rewrite looks like this.
"This paper reviews cancer biology study design, using examples that illustrate specific challenges and solutions."

"successful solution". Do we need the adjective here? Dr. Kristin raised the question whether there exists an unsuccessful solution? Because solution implies successful.

One key point that relates to my writing is that I always use different words to explain the same things but in different way. For example, to buy or to acquire. Pay attention to the grammatical conjunction of and/or. Something you may not even need it. Most of the time, I just want to make the sentence longer, thus causing wordiness. As Dr. Kristin said, just use the important words to get the idea across.

Example 2:
"(As it is well known)(3), increased athletic activity (has been related)(4) to a (profile of)(2) lower cardiovascular risk, lower blood pressure (levels)(3), and improved (muscular and cardio-respiratory performance.)(4)"

The phrase "As it is well known" is known as Throat Clearing Phrases, which is a long and unnecessary introductory phrases at the beginning of the paragraph. According to Dr. Kristin, just put a citation at the end of the sentence if you want to indicates that certain idea is well known. Some examples of these dead weight words and phrases:

(1) As it is well known ......
(2) As is has been shown ......
(3) It can be regarded that ......
(4) It should be emphasized that ......

After the rewrite.
"Increased athletic activity is associated with lower cardiovascular risk, lower blood pressure, and improved fitness."

Another more aggressive rewrites using strong verb. Notice the two "and"s. (emphasis in bold)
"Increased athletic activity lowers cardiovascular risk and blood pressure, and improves fitness."

Example 3.
"The (experimental demonstration)(3) is the ((first of its kind)(3). And is (a proof of principle)(3))(4) (for the concept)(3) of laser driven particle acceleration in a structure loaded vacuum."

"is" is a boring verb. You can replace dull verbs with vivid verbs.

After the rewrite.
"The experiment provides the first proof of principle of laser-driven particle acceleration in a structre-loaded vacuum."

The main point of this module is to cut unnecessary words. Sometimes, it's good to take a break from working on your draft. Take a break and review back a few days later. We have invested so much time in writing and may hard to part with what we have written.

Also, take note of adverbs, for example, very, really, quite, basically, generally, and etc. If you write like the way you talk, you will subconsciously add those adverbs in your writing. Adverbs is not suitable for scientific writing which needs precision.

1.5: Cut the clutter, more tricks
Several more tricks have been added in this module. These are:

(1) Eliminate negatives
If you see a sentence like "He did not win the match". We can rewrite this in positive manner like "He lost the match". The first sentence is a negative sentence where the reader have to identify the key first (win) and then negate it (did not). The second sentence is more affirmative and concise. Some more examples:

Negative            Affirmative
Not honest         Dishonest
Not harmful       Safe
Does not have    Lacks

In other words, if you found any "did not" or "not" words in your sentence, consider rewrite it to be more affirmative.

(2) Eliminate superfluous uses of "there are/there is".
Most of the time, "there are/there is/there was ...... that" is unnecessary. For example,

Before: There are many ways in which we can arrange the pulleys.
After: We can arrange the pulleys in many ways.

(3) Omit needless prepositions.
Use "that", "on" or other prepositions with care. Overuse of these prepositions leads to wordy sentence.

Before: They agreed that it was true.
After: They agreed it was true.

1.6: Practicing cutting clutter
This example below illustrates one of my common mistake when writing papers.

Before: As we can see from Figure 2, if the return kinetic energy is less than 3.2 Up, there will be two electron trajectories associated with this kinetic energy.

After: Figure 2 shows that a return kinetic energy less than 3.2 Up yields two electron trajectories.

Review Learning Objectives
Review back the learning objectives with my current understanding of the notes and writing approach.

(1) Recognize that writing is hard for everyone.
I've written about this in previous paragraph and all my previous notes.

(2) Recognize that writing is a skill that you learn through practice.
My approach is always quantity over quality. Since I've already built up a weekly habit of writing about stuff I've learned for the past week, maybe it's time to adapt my approach by focusing more towards quality over quantity. Not just random rambling writing, just deliberate writing practices.

(3) Practice removing clutter from writing.
Revision, a crucial step missing from my writing process. I always publish the draft copy as soon I've finished writing. Furthermore, wordiness indicates a false sense of importance. Also, sometimes we need to write to a certain number of pages or words. Hence, to meet the requirements, you have to pad your writing causing wordiness and leads to bad writing habit. However, Enjoy and appreciate the elegance of brevity.

(4) Practice writing clearly and concisely.
Word choice. I need to work on this.