The art of good science writing

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The art of good science writing

  1. 1. flickr.com/photos/srsphoto The art of good science writing Keith Bradnam This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. Copyright Keith Bradnam 2013
  2. 2. Overview I end up reading a lot of: reports; paper manuscripts; applications for grants, scholarships, and grad school; resumes and other job enquiries; and of course lots of emails. A lot of these are written by young scientists in our lab (http://korflab.ucdavis.edu) and I spot a lot of similarities in how these written scientific texts are often rough around the edges. Often bursting with potential, but needing some polish.
  3. 3. Why do you need good science writing skills?
  4. 4. Why do you need good science writing skills? Grants Papers Presentations Posters QEs Resumes Blogging Scholarships Emails I think some people forget that science communication is a key part of being a scientist. Written communication takes many forms, and increasingly the scientists that actively blog/ tweet about their work are the ones at a comparative advantage to those who don't (all other thigns being equal).
  5. 5. Three things to always keep in mind...
  6. 6. EVERY SENTENCE SHOULD BE THERE FOR A REASON! Your text — be it a resume, grant, or grad school application — should have sort of goal. I.e. you should be writing to secure a job interview, or get successfully funded. So every sentence that you should write should be working towards that goal. If it isn't, then maybe it is not really needed.
  7. 7. EVERY WORD SHOULD BE THERE FOR A REASON! Sometimes there is a tendency to use two words when one would suffice. Sometimes we don't think about whether that noun or adjective is the best possible one that helps build the story that you want to tell.
  8. 8. EVERY PIECE OF PUNCTUATION SHOULD BE THERE FOR A REASON! Punctuation can assist your text, or it can get in the way and be obstructive. Don't use punctuation characters if you don't really know what they are for.
  9. 9. flickr.com/photos/wrote The River Cam in Cambridge. Calm water being rowed upon. A good rower will be smooth and consistent, building up a good flow. A bad rower catches the surface of the water, causing disruption and losing their rhythm. This is how I regard good and bad writing. There is nothing more frustrating than having to stop and re-read a sentence because it confused you or even it had just contained one jarring word.
  10. 10. Keith's red-ink-machine I am always happy to proof-read material for students in the lab. But I don't hold back. I am honest and detailed with my feedback because I want the students to succeed and if I think that rewriting half of their text will help them succeed, then I will tell them so.
  11. 11. An example of one page of feedback I gave to one student.
  12. 12. And another.
  13. 13. And another.
  14. 14. Some specific examples Hopefully the students, who will remain anonymous, won't mind be taking some examples from some of the material I have proof-read. The examples will highlight different categories of writing where there are clearly things that could be improved.
  15. 15. Titles Does the title reflect the most important aspects of your work? Can you better sell your work (without lying)? The title of your work, or even the subject line of your email, should get to the point and focus on what is most important.
  16. 16. A bioinformatic approach to determining the effect of DNA duplication on the brain genome and epigenome. This was the title of a research proposal for a Grad School Qualifying Exam (QE). There is nothing terribly wrong about it. But...
  17. 17. A bioinformatic approach to determining the effect of DNA duplication on the brain genome and epigenome. It leads with the focus of the techniques. Bioinformatics is becoming more and more common, so should we really draw attention to it?
  18. 18. A wet-lab approach to determining the effect of DNA duplication on the brain genome and epigenome. We would never do this for instance. But if bioinformatics is a crucial aspect of the project, then maybe the title should allude to this.
  19. 19. A bioinformatic approach to determining the effect of DNA duplication on the brain genome and epigenome. This could mean running a single Perl script Another issue with this title is that refers to a singular approach. If you are doing more than one thing...
  20. 20. Bioinformatic approaches to determining the effect of DNA duplication on the brain genome and epigenome. ...then maybe you should say so.
  21. 21. Novel bioinformatic approaches to determining the effect of DNA duplication on the brain genome and epigenome. Novel, high-throughput, large-scale etc... We can often better describe our work with adjectives that reveal more details about the scope of the work. Don't do this if is not true, but if you have truly invented a novel method (as opposed to just using someone else's software) then maybe the title can reflect this?
  22. 22. Utilizing novel bioinformatic techniques to determine the effect of DNA duplication on the brain genome and epigenome. A suggested rewording of the first part of the title.
  23. 23. A bioinformatic approach to determining the effect of DNA duplication on the brain genome and epigenome. Back to the original title. Anything else to improve on?
  24. 24. A bioinformatic approach to determining the effect of DNA duplication on the brain genome and epigenome. 'Effect' is singular. One approach that reveals one effect?
  25. 25. A bioinformatic approach to determining the effect of DNA duplication on the brain genome and epigenome. 'DNA duplication' could refer to a single base or the entire genome. The title gives no sense of scale.
  26. 26. A bioinformatic approach to determining the effect of chromosome abnormalities on the brain genome and epigenome. The student in question is also looking into chromosome rearrangements as well as regional duplications. Therefore I suggested the title could encompass both parts as 'chromosome abnormalities'. This reveals that the project is a) broader in scope and b) on a larger scale than indicated before.
  27. 27. Overly long sentences Assume that the reader can only take a breath when you reach a period (or semi-colon) Assume that the reader will pause at commas Long sentences can be tough to read.
  28. 28. Aim 2C: Determine changes in chromatin interactions using Circularized Chromosome Conformation Capture (4C) with a targeted focus on 15q domains demethylated in chromosome 15 duplicated cell line (SH-SY5Y-15M) compared with the non-duplicated parental cell line (SH-SY5Y). Like this one. Consider semi-colons or just breaking it into multiple sentences.
  29. 29. Avoid too much repetition E.g. if you establish that you are studying the human genome, don't need to keep on mentioning 'human'. Don't start a sentence with the same word that ends the preceding sentence.
  30. 30. Chromosome pairing is a necessary requirement for recombination and chromosome segregation, which is particularly important in forming gametes that have the correct number of chromosomes. Chromosomes missegregating accounts for 30% of spontaneous miscarriages in humans, and in the few instances that missegregation is not lethal, detrimental genetic disorders, such as Down syndrome (trisomy 21) or Turner syndrome (monosomic for X) can occur. This is just two sentences. Spot the repetitions?
  31. 31. Chromosome pairing is a necessary requirement for recombination and chromosome segregation, which is particularly important in forming gametes that have the correct number of chromosomes. Chromosomes missegregating accounts for 30% of spontaneous miscarriages in humans, and in the few instances that missegregation is not lethal, detrimental genetic disorders, such as Down syndrome (trisomy 21) or Turner syndrome (monosomic for X) can occur. This can be hard to skim read Don't assume that your reader/reviewer will be reading *every word* you write. If they skim reading (because they have 30 other similar reports to read), then lots of repetitive text makes it much harder to understand what you are writing about.
  32. 32. One cutting-edge application of this technology is DNase-seq. In DNase-seq, the DNaseI enzyme cuts DNaseI hypersensitivity sites (DHS) and then uses high- throughput sequencing to sequence these sites More repetition.
  33. 33. One cutting-edge application of this technology is DNase-seq. In DNase-seq, the DNaseI enzyme cuts DNaseI hypersensitivity sites (DHS) and then uses high- throughput sequencing to sequence these sites Sometimes we might be able to assume that something is common knowledge (e.g. that DNaseI is an enzyme). We also can implicitly refer to things without having to name them over and over again.
  34. 34. One cutting-edge application of this technology is DNase-seq, where DNaseI hypersensitivity sites (DHS) are cut and the resulting fragments are sequenced. This is my suggested rewording.
  35. 35. Try to make sense It may make sense, but only in your head Remember, that others will not be so familiar with the work you are writing about The grammar should make sense as well as the scientific content This sounds so obvious, but it needs to be stated because a lot of what we write doesn't make sense when inspected closely.
  36. 36. Chromosome pairing is a necessary requirement for recombination and chromosome segregation, which is particularly important in forming gametes that have the correct number of chromosomes. This all looks okay, but consider two words in the middle...
  37. 37. Chromosome pairing is a necessary requirement for recombination and chromosome segregation, which is particularly important in forming gametes that have the correct number of chromosomes If we simplify the first part of the sentence, you'll see why I find this unclear.
  38. 38. A is needed for B and C, which is particularly important for D What is important for D? Is it B, C, or B *and* C?
  39. 39. The HMM will search four different states based on conditional probabilities for each state, starting with background, increasing DNaseI digestion state, decreasing DNaseI digestion state, and a footprint DNAseI digestion state The repetition here makes it unclear...
  40. 40. The HMM will search to four different states based on conditional probabilities for each state, starting with background, increasing DNaseI digestion state, decreasing DNaseI digestion state, and a footprint DNAseI digestion state Could be written as a bullet point list, or split into multiple sentences ("Two of the four states related to increasing or decreasing levels of DNaseI digestion. The third state...").
  41. 41. Milk has been previously investigated as it relates to human health and infant nutrition, but there are many factors that show it to be a useful tool to investigate the evolutionary relationship with ancestral species. At first glance this may read okay.
  42. 42. Milk has been previously investigated as it relates to human health and infant nutrition, but there are many factors that show it to be a useful tool to investigate the evolutionary relationship with ancestral species. The price of milk? The global trade of milk? The color? But 'Milk' on its own is very vague.
  43. 43. Milk has been previously investigated as it relates to human health and infant nutrition, but there are many factors that show it to be a useful tool to investigate the evolutionary relationship with ancestral species. Can 'milk' be a useful tool? If so, any biological molecule/tissue could be thought of as being a useful too. Can you use 'milk' itself to investigate evolutionary relationships? Or are you really talking about a comparative analysis of the nucleotide or protein sequences in milk (or in milk-producing genes)???
  44. 44. Don't be too dumb (or smart) Don't use words if you don't fully understand their meaning Don't use long words or phrases just to impress Be clear and concise if possible.
  45. 45. Currently, a comprehensive proteome of milk has not been sufficiently developed, and there are numerous barriers to its dissemination. One of these words doesn't really fit.
  46. 46. Currently, a comprehensive proteome of milk has not been sufficiently developed, and there are numerous barriers to its dissemination.
  47. 47. Don't be vague Be as specific as possible Use correct scientific terminology when possible Don't use colloquialisms
  48. 48. ATHB8 expression in procambium tissue (provascular tissue arising from undifferentiated ground tissue) is considered a point of no return for vascular development. Spot the non-scientific phrase?
  49. 49. ATHB8 expression in procambium tissue (provascular tissue arising from undifferentiated ground tissue) is considered a point of no return for vascular development. The big problem with colloquial phrases is that can be highly subjective.
  50. 50. The complexities of milk can be solved using comparative proteomics, and the extent of its importance in primate evolution will demonstrate one facet of species divergence. Again, this might read okay at first glance. But maybe some words are catching in your brain?
  51. 51. The complexities of milk can be solved using comparative proteomics, and the extent of its importance in primate evolution will demonstrate one facet of species divergence. Can you solve a complexity?
  52. 52. Furthermore, the methods developed will be applicable to many other research questions and can be most advantageous when working with genomes that are less annotated as in the case of non-human model organisms. Something is a bit vague here...
  53. 53. Furthermore, the methods developed will be applicable to many other research questions and can be most advantageous when working with genomes that are less annotated as in the case of non-human model organisms. Can't you specify or give at least one example?
  54. 54. Advances in sequencing, computer, and mass spectrometry technologies have revolutionized biology, and we can now ask questions that would have been considered unattainable a decade ago. This whole sentence is potentially redundant. Because?
  55. 55. Advances in sequencing, computer, and mass spectrometry technologies have revolutionized biology, and we can now ask questions that would have been considered unattainable a decade ago. This was also true a decade ago! Science always improves and gives us new opportunities. Maybe there was a specific question that we can now ask (related to these techniques), but it wasn't stated here.
  56. 56. Don't sell yourself short Don't dwell on negative aspects of project Avoid negative sounding words Don't be too narrow in your focus
  57. 57. • I have familiarity with Microsoft Word. • I currently have no programming experience, but am keen to learn. A fictional example from a resume or CV. As a side-note, you really don't *ever* need to list Microsoft Word as a skill. But what about that second point? Do you want to draw attention to a complete lack of experience? You could start learning something *today* and then you could honestly say...
  58. 58. • I have recently started learning Perl and hope to take a free online course on basic Unix skills in the near future Better. But still a bit weak sounding in places.
  59. 59. • I have recently started learning Perl and hope to take a free online course on basic Unix skills in the near future You 'hope' doesn't sound all that positive. Why mention that the course is 'free'? Why use words like 'basic' that have negative connotations. Why be vague about 'the near future'???
  60. 60. • I have recently started learning Perl and will be taking an online course on essential Unix skills More direct and has more impact. 'Essential' sounds better than 'basic' but means the same thing.
  61. 61. If we fail to achieve aim 3 we will consider our lives to be a miserable failure. A fictional example.
  62. 62. If we fail to achieve aim 3 we will consider our lives to be a miserable failure. Words like 'fail' almost always leave negative impressions in the mind of the reader (even if only at a subliminal level).
  63. 63. We will focus our efforts on the first two aims. Rather than dwell on what might happen if you don't complete aim 3, you could instead make a strength of only doing two things.
  64. 64. Summary
  65. 65. Your 1st draft will never be the best version It's okay to admit this.
  66. 66. Your 2nd draft will never be the best version It's okay to admit this too.
  67. 67. Your 3rd draft will never be the best version Though it might be tolerable Slow but steady improvements are the name of the game.
  68. 68. Your last draft will never be the best version But that's okay. Life goes on. Whatever you write can almost always be improved with time. We don't have the luxury of infinite time, but we can accept that several rounds of revision will improve things. Especially if we can sleep on it between revisions.
  69. 69. Suggestions
  70. 70. Get someone else to read it Someone in your field, and... someone outside of your field People outside your field can often bring some very fresh perspectives on your work.
  71. 71. Start writing as soon as possible Give yourself the most time possible to revise your text Expect that there will be multiple revisions
  72. 72. Write to please people Write something that you would want to read if it wasn't your own research If there are review criteria (e.g. grants), write something that satisfies those criteria Make life easier for your reviewers There are often checklists that you can work to when writing (especially for grants).
  73. 73. Review criteria: 1) address significance of this research This work is significant because... Grant reviewers don't want to hunt to see if you did mention the criteria somewhere. Make it obvious!
  74. 74. Make it clear Use whitespace Use subheadings Use figures If you have a one-page proposal to write, don't assume that you should use every inch of that page. Also, don't keep on reducing font size to fit more text in. Adding subheadings can break up a page and make it easier for the reader to see where you are going with the text. Figures don't have to be a whole-page affair. Embed small figures where you would otherwise need a thousand words to explain what is happening.
  75. 75. Think of who will read it They will probably be reading lots of other resumes/grants/emails etc. They will be pushed for time Do not assume they will read everything! Most reviewers are going to be extremely busy. They may, with the best will in the world, *want* to read every word you wrote, but may simply not have enough hours in the day to do so.
  76. 76. Learn the tricks of your trade Colons vs semi-colons Hyphens vs en-dashes vs em-dashes Avoid double spaces! Learn about hard (non-breaking) spaces You should understand the differences of these things and when to use them.
  77. 77. Genome studies of the budding yeast Saccharomyces Cerevisae have led to many insights concerning fungal genome evolution. The genome was sequenced between 1993-1995 - though corrections continue to be made to the underlying sequence - and the original sequencing revealed the presence of ~6,000 genes. Other high- throughput methodologies have continued to shed light on the S. cerevisiae genome, and it remains a useful model organism. Some example fictional text with numerous problems.
  78. 78. Genome studies of the budding yeast Saccharomyces Cerevisae have led to many insights concerning fungal genome evolution. The genome was sequenced between 1993-1995 - though corrections continue to be made to the underlying sequence - and the original sequencing revealed the presence of ~6,000 genes. Other high- throughput methodologies have continued to shed light on the S. cerevisiae genome, and it remains a useful model organism. Species names should be italicized and only have the genus capitalized. Don't put double spaces after periods. This is a hang-up from the days of mechanical typewriters. Use en- dashes to separate numerical ranges. Use em-dashes for when you want to indicate a break in thought. Use non-breaking spaces (hard spaces) to keep species names on the same line.
  79. 79. Genome studies of the budding yeast Saccharomyces cerevisae has led to many insights concerning fungal genome evolution. The genome was sequenced between 1993–1995 — though corrections continue to be made to the underlying sequence — and the original sequencing revealed the presence of ~6,000 genes. Other high- throughput methodologies have continued to shed light on the S. cerevisiae genome, and it remains a useful model organism. En-dashes and em-dashes have various keyboard shortcuts that will produce them. Non- breaking spaces can sometimes be done with option-space (on a Mac) in programs like Microsoft Word.
  80. 80. The end Hope you found this useful.

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