Archive for June, 2009

Boosting clarity and reducing reader effort


Here are the slides from the June 18 writing workshop in pdf format.

June 19, 2009 at 1:50 pm Leave a comment

What’s your point?

“It might seem unnecessary to insist that in order to say something well, you must have something to say, but it’s no joke. Much bad writing, mathematical or otherwise, is caused by a violation of that first principle.” (Paul Halmos, How to Write Mathematics)

Question_markWhen you have a mountain of results in front of you, the idea of writing a concise and coherent summary of them and their implications (a.k.a., a manuscript) can be overwhelming. Add even a pinch of uncertainty about where you were going in the first place or the significance of your research question, and the task can seem downright impossible.

But figuring out what you have to say probably isn’t as hard as you think. Many people use outlining to organize their thoughts, and outlines can be useful. However, they can also become so detailed themselves that the big picture of what, why and how (to borrow from news writing) still gets lost. So, my suggestion is to start by answering for yourselves a few simple – but critical – questions. Once you have those answers firmly in mind, you can then begin adding the necessary details.

What types of questions are we talking about? Here’s a set from a 2004 article, “The top 10 reasons why manuscripts are not accepted for publication.” In it, the author, D.J. Pierson, states that writing a manuscript is a matter of answering four questions:

  1. Why did you start? (the introduction, including background and hypothesis)
  2. What did you do? (the methods section)
  3. What did you find? (the results section)
  4. What does it mean? (the discussion section)

Here’s another useful list from the PLoS Biology guidelines for pre-submission inquiries:

  1. What is the scientific question you are addressing?
  2. What is the key finding that answers this question?
  3. What is the nature of the evidence you provide in support of your conclusion?
  4. What are the three most recently published papers that are relevant to this question?
  5. What significance do your results have for the field?
  6. What significance do your results have for the broader community (of biologists and/or the public)?
  7. What other novel findings do you present?

Again, refrain as much as possible from going deeply into specifics as you answer these questions. Instead, step back and try to address each in just a paragraph. Keeping your answers brief will force you to decide what you really want to say. And don’t cheat by listing bullet points either. Challenge yourself to write something that hangs together logically.

Remember, clear writing leads to clear thinking. And vice versa.

June 17, 2009 at 8:45 am Leave a comment

Writing and manuscript acceptance or (gulp) rejection

What role does writing play in the acceptance or rejection of manuscripts? Here’s what some of your favorite journals have to say.

(By the way, It’s worth noting that at journals such as Bioinformatics, PLoS ONE and the Journal of Computational Biology, submitted manuscripts are not copyedited extensively after being accepted. This means that the burden falls almost entirely on you to make your writing as clear and accessible as possible. PLoS Computational Biology also asks its reviewers to assess whether the writing is accessible to non-specialists.)

PLoS ONE (author guidelines):

“PLoS ONE staff do not copyedit the text of accepted manuscripts; it is therefore important for the work, as presented, to be intelligible. Perfect, stylish English is not essential but the language must be clear and unambiguous. If the language of a paper is poor, Academic Editors should recommend that authors seek independent editorial help before submission of a revision. A list of scientific editing services can be found in the PLoS ONE Guide to Authors. Poor presentation and language is a justifiable reason for rejection.”

Nucleic Acids Research (author guidelines):

“Manuscripts must be clearly and concisely written in English. The Editors reserve the right to reject without review those that cannot adequately be assessed because of a poor standard of English. Authors whose first language is not English are encouraged to have their manuscript checked by a native English speaker. If you have difficulty with this you can obtain further help and information at”

The above link also gives insight into what the journal wants by stating that editing will:

  • Correct grammar, spelling, and punctuation
  • Delete redundant words and phrases
  • Replace inappropriate words and generally improve clarity
  • Ensure that the tone of the language is appropriate for an academic journal

PLoS Computational Biology (author guidelines):

“Authors are encouraged to decide how best to present their ideas, results, and conclusions. The writing style should be concise and accessible. Editors may make suggestions for how to achieve this, as well as suggestions for cuts or additions that could be made to the article to strengthen the argument.”

PLoS Computational Biology (reviewer guidelines):

“Is the manuscript well organized and written clearly enough to be accessible to non-specialists? Would you recommend the author seek the services of a professional science writer?”

Bioinformatics (author guidelines):

“Papers must be clearly and concisely written in English and within the recommended length. In the interests of speed, manuscripts are not extensively copyedited and authors are requested to check their texts carefully before submitting them so that proofs will require only correction of typographical errors.”

Journal of Computational Biology (author guidelines):

“Either American or British English is acceptable, but be consistent. Text must be informative without being terse or wordy. Manuscripts will not be extensively copy-edited and it is expected that proofs will require only typographical corrections. There may be an extra charge for extensive changes made in proof.”

June 9, 2009 at 12:23 pm 2 comments

Scientists on scientific writing, part 2

Continuing on from my last post, here is some additional advice from scientists on improving scientific writing.

Use plain language. Many fields of science use more jargon today than ever before, including lots of abbreviations. But jargon alone isn’t to blame for ponderous and inaccessible writing. A larger problem is that scientists tend to shy away from words that are simple and plain, and gravitate toward verbose language that they think sounds smarter.

Consider this rewrite of my first two sentences: “A predominant number of scientific fields utilize a larger quantity of jargon at the present time than in previous eras, including a considerable amount of abbreviation. However, jargon in and of itself cannot shoulder all of the responsibility for writing that is inaccessible and ponderous.”

While the second version is still intelligible, the bloated style makes it harder to digest.

Wordy_resizedCombat wordiness. A related issue is wordiness. As you can see above, using common language should shorten your sentences significantly (i.e., the first version is 26 words; the second, 45). And another way to fight long-windedness is to use verbs instead of nouns as much as possible.

For example: Instead of “This result leads us to the conclusion,” write “From this result, we conclude.” Likewise, “one of the key issues which is the cause of the critical point of the sampling size” can be rewritten as “one of the key issues that causes the critical point of the sampling size…”

Maintain linkage between ideas. “Another mistake often occurs right at the start of a sentence, in the ‘topic position,’” says an article from a May 2003 issue of Nature. “Readers expect to find some sort of bridge between sentences here. If a completely new word or phrase occupies this spot…the reader is momentarily confused.”

In this excerpt from a recent paper, observe how the authors make this common mistake between the second and third sentences:

“DNA breaks arise spontaneously or in response to genotoxic events. Cells respond to double-stranded break (DSB) formation to prevent chromosomal abnormalities. The conserved Mre11-Rad50-Xrs2 (MRX) complex (MRN complex in mammals) is implicated in the DSB response. It binds and holds together the broken extremities, thus preventing chromosome fragmentation and mediates the loading of Tel1/ATM at the break.”

The problem is easily fixed, though, by flipping the third sentence around. Notice how this change also clarifies what “It” refers to at the beginning of the fourth sentence:

“DNA breaks arise spontaneously or in response to genotoxic events. Cells respond to double-stranded break (DSB) formation to prevent chromosomal abnormalities. Implicated in the DSB response is the conserved Mre11-Rad50-Xrs2 (MRX) complex (MRN complex in mammals). It binds and holds together the broken extremities, thus preventing chromosome fragmentation, and mediates the loading of Tel1/ATM at the break.”


The science of scientific writing. G Gopen and J Swan (1990) American Scientist. Read it here.

The infectiousness of pompous prose. MW Gregory (1992) Nature 360: 11-12

Clear as mud. J. Knight (2003) Nature 423: 376-378

June 4, 2009 at 12:18 pm Leave a comment

Science of Scientific Writing

This article describes what readers expect when they read - and how scientific writing often violates those expectations.