The Art of Writing Scientific Papers

1. The Art of Writing Scientific Papers Dan Hawkes Editor Earth Sciences Division Lawrence Berkeley National Laboratory

2. The Art of Writing Scientific Papers • I. Starting the Process—Getting the Paper Outside Yourself 1. Download your knowledge. 2. Make it conversational—Creating an (imaginary?) friendly, interested listener. 3. Identify your high concept. 4. Write your intro. • II. Writing from the Outside 1. Keep It conversational. • III. Editing for Your Listener 1. Individual sentences (building complexity) 2. Sentences in context (paragraphs, coherence, emphasis) • IV. Quick Editing Checks (voice, punctuation, grammar)

3. A Creative Writing Paradigm • “When I speak of writing, the image that comes first to my mind is not a novel, a poem, or a literary tradition; it is the person who shuts himself up in a room, sits down at a table, and alone, turns inward.” • Orhan Pamuk, The Nobel Lecture, 2006. • Translated, from the Turkish, by Maureen Freely

4. A Science Writing Paradigm • “Scientists as writers must offer objective knowledge to their readers in plain language. Scientifically plain writing is objective, simple, precise, concrete, direct, and above all readable….Fundamentally, the concept of readability places readers at the center of communication.” • Robert Goldbort, Writing for Science, • Yale University Press, 2006

5. Five Distinct Obligations Shared by Scientists in Their Professional Communication(adapted from Goldbort) • 1. Publishing their methods and findings truthfully, clearly, and fully, so that they can be verified and extended by fellow researchers • 2. Writing critical reviews that synthesize current knowledge in their field • 3. Seeking financial resources • 4. Sharing their knowledge and its practical implications with the public • 5. Teaching what they know to future generations of scientists • WE’LL BE CONCENTRATING HERE ON THE FIRST ONE.

6. Dan Law 1 • Reading about science is difficult, even for other scientists. • So when writing about science, you must avoid adding to the already inherent difficulty of the subject matter, by writing as clearly as possible. • (COROLLARY TO FIRST PHYSICIAN’S LAW: DO NO HARM)

7. Knowledge Download • As a one-hour exercise, put down on paper: • all you know about, what you want to write about. • Let it all hang out! (1960s slang) • BUT • Write in complete sentences!

8. Outline from the Outer World • As a 1–2 hour exercise, ask yourself: • What Is Your Smart Beer-Drinking Scientist Friend (SBDSF) Liable to Ask You in Conversation over Drinks? • Your SBDSF would likely want to know the following: • (adapted from Judith Swan, Science of Style, Princeton University Press, 2003): • What’s the general problem being studied? • Why is this important? • How is this problem connected to other work in the field? • What is the specific system or approach used to study the problem? • What is unique or new about the experiment/modeling? • What is the basic experiment/model? • (“Gee, I think I see the beginnings of an introduction here!”)

9. Now You’re on a Roll! Your SBDSF is getting interested. • How would I repeat this experiment (or go about constructing this model)? • Where would I purchase materials? • How long would I do X (a certain experimental action or process)? • How many times do I do X to obtain a result? • (“Golly gee, I think I see the beginnings of a materials/methods section here!”)

10. The Roll Continues! • What was the experiment or simulation performed? • What were the critical conditions? • What were the critical controls? • How did the experiment or simulation turn out (give details!) • (“Holy mackerel, I think I see the beginnings of a results/discussion section here!”)

11. Now You’re Beyond a Roll(But don’t have that imaginary second beer yet!) • What is the significance of the results? • How is it connected to other results? • How might it be wrong? • Why is it likely (or unlikely) to be correct? • Do you have problems (related to this project!)? • How would you handle them? • How does this result address the questions and problems posed when we started talking? (this is why you can’t have that imaginary second beer yet) • What other experiments or information might be needed to better understand these results? • Now what? What next? • (“Wow, I think I see the beginnings of a discussion/conclusions here!”) • THE OUTLINE GENERATED FROM YOUR 1-3 SENTENCE ANSWERS TO THESE QUESTIONS, AND ULTIMATELY YOUR PAPER, IS YOUR SIDE OF THIS CONVERSATION.

12. The High Concept • The “high concept” (a term borrowed from the film industry) is a one-sentence encapsulation of what your paper is about. • It doesn’t have to be a simple statement. It does have to be an understandable and readable statement—whether or not it is simple, it has to be clear! • It is useful in organizing and unifying your writing. • It guarantees you more social success (the “wow factor” so indispensable at cocktail parties).

13. Write an Introduction That Ends the Suspense • Point your introduction toward your high concept • Orientation—(First sentence) Start with orienting the reader—what is the general subject that you’re talking about? • 2. Statement of the Problem/Issue—1-X paragraphs (depending on length)— • What is the problem confronting you? This part might typically include a description of the problem, or a literature review to convey the state of science in relation to the problem—for example, potential leakage at CO2 sequestration sites. • 3. Statement of the Agenda and the High Concept—In the last introductory paragraph, present your agenda in the paper (how you will address the problem in the paper), but don’t stop there! Either directly afterwards (at the end of the sentence in which you introduce your agenda, or in the next sentence) or at the end of this last introductory paragraph, state your high concept—for example, “After thorough investigation, we find that the DNA molecule has a double helix structure.” • In your introduction, tell your whole story in a broad, simple way.

14. Dan Law 2 • The First Sentence Must Be Readable. • Keep the first sentence of your paper short and sweet. The first sentence should quickly orient your reader, informing him or her in one or (at most) two lines, 25 words or less, what your general subject matter is. And then it should end!

15. Dan Law 3 • The high concept should be part of the introduction because: • The earlier the reader gets a sense of the whole, the easier it is for the reader to assimilate the parts, as these parts accrue in the process of reading.

16. A Sample Last Introductory Paragraph • In this study, we present numerical simulations of the injection of CO2-H2S and CO2-SO2 mixtures into an arkose with similar hydrogeologic properties and mineral composition to that used in the preceding two studies. Our objectives are (1) to analyze changes in aqueous chemical composition, mineral alteration, acid-gas immobilization through precipitation, and changes in porosity induced by the injection, and (2) to compare modeling results with prior investigations and with limited field observations of analogous natural systems as a basis for validation. We use a fully coupled model of multiphase CO2 fluid flow into a saline aqueous (H2O + NaCl) phase, transport of aqueous species, and geochemical reactions. Reactive geochemical transport simulations are performed over a period of 10,000 years. The sensitivity of the model to differing dissolution rates and kinetic schemes on the evolution of the chemical system and on CO2 sequestration are also addressed.

17. A Sample Introduction • On CO2 Fluid Flow and Heat Transfer Behavior in the Subsurface, Following Leakage from a Geologic Storage Reservoir • The amounts of CO2 that would need to be injected into geologic storage reservoirs to achieve a significant reduction of atmospheric emissions are very large. A 1000 MWe coal-fired power plant emits approximately 30,000 tonnes of CO2 per day, 10 Mt per year (Hitchon, 1996). When injected underground over a typical lifetime of 30 years of such a plant, the CO2 plume may occupy a large area of order 100 km2 or more, and fluid pressure increase in excess of 1 bar (corresponding to 10 m water head) may extend over an area of more than 2,500 km2 (Pruess et al., 2003). The large areal extent expected for CO2 plumes makes it likely that caprock imperfections will be encountered, such as fault zones or fractures, which may allow some CO2 to escape from the primary storage reservoir. Under most subsurface conditions of temperature and pressure, CO2 is buoyant relative to groundwaters. If (sub-)vertical pathways are available, CO2 will tend to flow upward and, depending on geologic conditions, may eventually reach potable groundwater aquifers or even the land surface. Leakage of CO2 could also occur along wellbores, including pre-existing and improperly abandoned wells, or wells drilled in connection with the CO2 storage operations. • Escape of CO2 from a primary geologic storage reservoir and potential hazards associated with its discharge at the land surface raise a number of concerns, including [(1) … (2) … (3) … (4) ….] • In order to gain public acceptance for geologic storage as a viable technology for reducing atmospheric emissions of CO2, we must address concerns related to leakage from the primary storage reservoir and demonstrate that CO2 can be injected and stored safely in geologic formations. This requires an understanding of the risks and hazards associated with geologic storage, and a demonstration that the risks are acceptably small or can be mitigated. General probabilistic and systems-analysis approaches based on identifying features, events, and processes (FEP) scenarios are being used to evaluate risks associated with geologic storage of CO2 (Maul et al., 2004, Espie, 2004; Wildenborg et al., 2004). These approaches are similar to what has been used for nuclear waste repositories.

18. II. Write the Dang Thing! • As Karsten put it in his talk, write before you feel ready! • If you’re like me, you’ll be editing a bit as you go, correcting spelling, punctuation, and so forth. But the less you do that at this stage, the better! (So don’t be like me!) • Explain, support, illustrate, using both the knowledge download and the “conversation” with your SBDSF (and the outline developed from that conversation) for supportive material. • ABOVE ALL, KEEP IT CONVERSATIONAL!

19. III. Editing • Individual Sentences • (Building Complexity) • 2. Sentences in Context • (Paragraphs, Coherence, Emphasis)

20. Individual Sentences • (Gee, why is clarity so complicated?) • Dan loved his old, beat-up car. • But how about • Because Dan loved his old, beat-up car. • ?

21. Complex Sentences • Because Dan loved his old, beat-up car he could never consider selling it. • If Dan truly loved his old, beat-up car he would never consider selling it. • Although Dan loved his old, beat-up car he would be willing to part with it for the right price.

22. Sentences in Context—ParagraphsTopic Sentence • Most paragraphs contain a topic sentence that comes at the beginning of the paragraph (first or second sentence). • This topic sentence announces the central idea of the paragraph, and limits what follows in the paragraph to that central idea. • It should be thematically related to the high concept or to the topic of the previous paragraph (you could even call it a deputy high concept or a subdivision of the high concept). • Topic sentences of your paragraphs are derived, as much as possible, from your responses to your SBDSF questions and the outline generated from those responses.

23. A Sample Main Body Paragraph • Limiting CO2 injection pressure so as not to exceed the capillary entry threshold of the caprock may not be sufficient to ensure containment. In some subsurface environments, microbially mediated conversion of CO2 to methane may be possible (Hoth et al., 2005). Such conversion may occur on an equimolar basis (generating one mole of methane for each mole of CO2 consumed) and therefore would be accompanied by large pressure and/or volume increases. This is because the real gas compressibility factor Z is approximately twice as large for methane as for CO2 at typical temperature and pressure conditions of interest for geologic storage of CO2 (Lemmon et al., 2005). A complete conversion of CO2 to CH4 would therefore be accompanied by a doubling of the pressure/volume product. This possibility of microbially mediated pressure/volume increases in a storage reservoir of CO2 appears not to have been previously recognized as an issue for storage integrity. • HC: “Wemust address concerns related to leakage”

24. Identity and Transition • A paragraph should make a single impression of developing thought. Its sentences should not only be related, they should also sound related. • A sentence within a paragraph should contain signals of identity or transition that refer back to the previous sentence, so that the reader can easily see the kind of relation that’s implied between one statement and the next one.

25. Signals of Identity • Terms of identity assert that something already treated is still under discussion. • These signals are usually pronouns, repeated words and phrases, demonstrative adjectives (this, these, that, those), and omissions that are understood in the light of a previous sentence. • Pronouns • In the third round, Tiger Woods sustained his precarious one-stroke lead. He teed off on Sunday knowing that eleven endorsement contracts hung in the balance. • Repeated Words or Phrases • Mayor Newsom’s foremost concern is with keeping his career alive. It is a concern bound to be shared by all other city mayors with an overly cooperative staff. • Demonstrative Adjectives • The entire football team showed a significant improvement in reading and math scores. This result came as a surprise to everyone but the coach, who had volunteered to do the grading. • Omissions • The treaty placing a limiting ban on greenhouse gas emissions has now been signed by 119 nations. More than a hundred [nations], including Togo and Burundi, have also signed a nuclear nonproliferation treaty.

26. Signals of TransitionTerms of transition indicate how a statement will build on the previous one. • Time or Place: afterward, later, earlier, formerly, elsewhere, here, there, subsequently, at the same time, simultaneously, above, below farther on, so far, until now • Consequence:therefore, then, thus, hence, accordingly, as a result • Likeness:likewise, similarly • Contrast/reversal:but, however, nevertheless, on the contrary, on the other hand, yet • Continuation/Amplification: again, in addition, furthermore, moreover, also, too • Example: for instance, for example • Insistence:in fact, indeed, anyway • Sequence:first, second, third…, finally • Restatement: that is, in other words, in simpler terms, to put it differently • Recapitulation: in conclusion, to summarize, in summary • Concession: of course, to be sure, granted, it is true • Such signals needn’t appear in every sentence, but they become useful whenever the relation between two sentences wouldn’t be immediately clear without them—as is the case fairly often in science writing! • TRANSITIONS ARE AN INDISPENSIBLE PART OF GOOD SCIENTIFIC WRITING. THEY’RE ALSO SOMETHING YOU DO NATURALLY IN CONVERSATION!

27. Continuity (Identity and Transition)Within a Paragraph • This extensive body of work on discharging of CO2 in volcanic areas …can help to define conceptual models for CO2 leakage systems ….The ultimate source of these discharges is deep-seated magma that contains dissolved noncondensible gases and volatiles. Eruptive discharges are primarily powered by thermal energy, which makes them of limited relevance in connection with potential leakage from man-made geologic storage reservoirs of CO2. In the volcanological literature, the possibility of “pneumatic eruptions” has been suggested…. Whereas hydrothermal (or "phreatic") eruptions are powered by the thermal energy of hot liquid water that is flashing into steam, pneumatic eruptions are presumed to be primarily driven by the mechanical energy contained in accumulations of compressed gas, chiefly CO2 …. Noncondensible gases, chiefly CO2, are known to have played an ancillary role in many hydrothermal eruptions… and it is rather obvious that the presence of CO2 can contribute to and enhance a hydrothermal eruption process. Indeed, when CO2 is present, less pressure reduction is needed for a gas phase to evolve, and large volume expansion and gas saturations with increased fluid mobility can be more easily attained. No direct evidence exists, however, either from field observations or numerical simulation, that an eruptive release from a subsurface storage reservoir can be powered solely by the mechanical energy stored in an accumulation of compressed gas, without substantial contributions from thermal energy.

28. Emphasis: Transitions and Natural Reader Expectations • Readers expect the material at the beginning of a sentence to provide a connection backwards to already established material. • The guiding principle is that rather than rushing to present new information at the beginning of a sentence, begin with old information that connects backward to provide a context for the new information to come later in the sentence. • Thus, the information at the beginning of a sentence should provide a launching pad for the new and important material to be presented toward the end of the sentence.

29. Dan Law 5 • End strong. • As a general rule within a sentence, express the information or idea that you most want to emphasize at the end of the sentence. • Also as a general rule, place your independent clause in that position of emphasis. • The paragraph will echo, and develop from, what you emphasize in your topic sentence. • Dan is a nice guy. Dan beats his dog. • Combining these ideas/sentences, imagine what the sentences following them within a paragraph would be like. • Dan is a nice guy, although he beats his dog. • Although he beats his dog, Dan is a nice guy.

30. Your Conclusion • Except perhaps in a really long paper, avoid repeating exactly what you’ve said in your results or discussion sections (avoid repetitiveness). • Just as at the very beginning of your introduction, where you orient your reader (telling your reader what you’ll be talking about), you want in your conclusion to reorient your reader, indicating how things have changed (or could change) in light of what you’re saying in this paper. • Check conclusions against your high concept. They should support it!

31. Our CO2 Paper Conclusion • CO2 leakage from man-made storage reservoirs is possible through a variety of mechanisms. A credible analysis of the associated risks must be based on a sound understanding of the underlying physical and chemical processes, and on an adequate characterization of potential leakage pathways. Naturally leaky CO2 reservoirs provide ideal settings for studying the behavior of CO2 in the subsurface over the large space and time scales required for CO2 storage. Studies of natural CO2 discharges in the Colorado Plateau region have documented extensive mineral deposition, yet many CO2 vents and springs do not self-seal, and persist for thousands of years …. These observations are consistent with recent findings from reactive-chemical-transport modeling …. • Popular news media have made reference to the lethal CO2 bursts at Lake Monoun … and Lake Nyos …to suggest that geologic storage of CO2 may be dangerous …. Even though the mechanisms that released major CO2 accumulations at these lakes cannot be replicated in subsurface storage reservoirs; concerns raised by these eruptions may seriously impede public acceptance of CO2 geologic storage. Focused research efforts are thus needed to provide a rational basis for assessing risks associated with geologic storage of CO2, to identify favorable as well as unfavorable geologic conditions, and to gain assurance that a high-energy, eruptive discharge is not possible.

32. Abstracts • An Abstract? • “A Study of the Abstract” • “A partial biography is given. The abstract is discussed. What should be covered by the abstract is considered. The importance of the abstract is described. Dictionary definitions of ‘abstract’ are quoted. At the conclusion, a slightly revised abstract is presented.”

33. The Abstract: Worth Your Tender, Loving Care • In terms of market reached, the abstract is the most important part of the paper—for every person who reads your entire paper, from 10 to 500 will read the abstract. • An abstract is an abbreviated, accurate representation of the paper containing in itself the essential information of that paper. It should state the purpose, methods, results, and conclusions presented in the document, if possible with special emphasis on results and conclusions. • Not quite a summary, in that a summary is typically a restatement within a document of its salient (its most important) results and conclusions, and is designed to complete the orientation or a reader who has studied the preceding text.

34. CO2 Paper Abstract • Geologic storage of CO2 is expected to produce plumes of large areal extent, and some leakage may occur along fractures, fault zones, or improperly plugged pre-existing wellbores. A review of physical and chemical processes accompanying leakage suggests a potential for self-enhancement. Numerical simulations that account for these processes confirm this expectation, but reveal self-limiting features as well. It seems highly unlikely that CO2 leakage could trigger a high-energy run-away discharge, a so-called “pneumatic eruption,” but present understanding is insufficient to rule out this possibility. The most promising avenue for increasing understanding of CO2 leakage behavior is the study of natural analogues. • WHAT WOULD YOUR SBDSF SAY ABOUT THIS?

35. IV. Quick Editing Checks(Individual Sentences) • Prefer Active over Passive Voice. • Passive Voice • The warning was displayed by the browser. • Two parties were connected by telephones. • Barometric pressure was measured. • Active Voice • The browser displayed the warning. • Telephones connected the two parties. • The team measured barometric pressure. • VERBS IN THE ACTIVE VOICE ARE STRONG, • DIRECT, FORCEFUL, AND ECONOMICAL. • AND THEY ARE NATURAL TO YOUR CONVERSATIONAL VOICE.

36. Prefer Active over Passive Voice(continued): Scrutinize Nominalizations • (adapted from Swan) • As much as possible, express the crucial action as a verb. • As much as possible, use verbs only for expressing action. • The dean made a decision to conduct a review of the matter. • The dean decided to review the matter. • There was a modification of the program by the director. • The director modified the program. • “Decision” and “modification” are examples of nominalizations, nouns made from verbs. • When editing, you should note your nominalizations and look to see if you can turn them back into verbs that express key action within a sentence. • This will add clarity and grace to your writing.

37. Using “which” or “that”(commas or no commas) • Grammatically, • thatintroduces a restrictive clause (providing identifying information about its antecedent). No comma before that or at the end of the clause it introduces; • whichintroduces a nonrestrictive clause (providing information but not identifying information about its antecedent). Place a comma beforewhichand at the end of the clause it introduces.

38. More That/Which • The software communication problems that had resulted from the merger of the two companies were suddenly solved. • The software communication problems, which had resulted from the merger of the two companies, were suddenly solved. • The rats that were fed a high-calorie diet were all dead by the month’s end. • The rats, which were fed a high-calorie diet, were all dead by the end of the month. • Mice of the DBA strain that metabolize acetaldehyde slowly drink significantly less ethanol than other mice. • Mice of the DBA strain, which metabolize acetaldehyde slowly, drink significantly less ethanol than other mice.

39. Serial Comma(Commas Separating Elements of a Series) • “He rose up from his chair, took a key out of his pocket, opened a locked cupboard, and brought forth a sack, a crowbar of convenient size and shape, a rope, a chain and other fishing implements.” (from Charles Dickens, A Tale of Two Cities)” • Sentence structure: He a, b, c, and d 1, 2, 3, 4, 5(?) • The returning knight had countless tales to tell of adventure, conquest of hideous monsters and helpless damsels in distress.

40. Semicolon • TO SEPARATE TWO INDEPENDENT CLAUSES THAT YOU WANT THE READER TO SEE AS CLOSELY CONNECTED • The first of the hikers began to arrive not long thereafter; a light breakfast of coffee and freshly baked rolls was laid out in the small dining room.” • TO SEPARATE ELEMENTS IN A SERIES THAT ARE ALREADY DIVIDED BY COMMAS • Conferences were held in Arlington, Texas, on May 1, 1989; in Golden, Colorado, on April 14, 1990; and in San Jose, California, on July 25, 1991.

41. Colon • TO INTRODUCE A LIST • We will discuss three editing problems today: misplaced modifiers, unclear antecedents, and redundancy. • (Note that you don’t introduce a list/series with a semicolon! Semicolons can divide elements in the list if the elements are lengthy or have commas within them, but they can’t introduce a list or series. • TO INTRODUCE THE ANSWER TO AN IMPLIED QUESTION RAISED IN THE FIRST PART OF A SENTENCE • One idea emerges, above all others: almost anything is possible.

42. Hyphens • The main use of hyphens is in compound modifiers occurring before the word they modify: But if the compound modifier occurs after the word (thus losing its role as a modifier), omit the hyphen: • mass-balance equations, but equations pertaining to mass balance • Many compound words (originally separate words) are now spelled as one word (no hyphen) in common usage. • henhouse, typesetting, makeup, notebook, byproduct

43. Hyphens, cont. • Some prefixes require following hyphens, but most (the most common ones) don’t— • self-sufficient, quasi-realistic, but semisweet, nonqualified, underinflated, overexcited, interstate, intramural, postoperative • Sometimes hyphens are helpful (and thus allowable) when they clarify a word that otherwise might not be: • pre-test, post-test; pre-emptive, post-trauma • There’s a gray area in using hyphenation, and there are plenty of cases that are “up for grabs.” The writer needs in those cases to choose what would be the clearest form (in his/her judgment) and be consistent with it throughout the document.

44. “The Dash Between Numbers” • Whenever you’re indicating a number range, you want to use the en dash (–), which in width size is between the hyphen (-) and the dash (—). En dashes can often be found in reference lists, indicating the page number range of a paper within a journal. • Wood, W., 1973, A technique using porous cups for water sampling at any depth in the unsaturated zone. Water Resour. Res., R 9 (2), 486–488.

45. Dashes • Known as em dashes in typesetting to distinguish them from the aforementioned en dashes, dashes can be used in much the same way as colons, to introduce and emphasize what comes later in a sentence. You can also use dashes to indicate a summing up of what you’ve said in the first part of a sentence, to indicate that you’re moving on to the last part of the sentence. • We will discuss three editing problems today—misplaced modifiers, unclear antecedents, and redundancy. • Misplaced modifiers, unclear antecedents, redundancy—whatever your problem, call Dr. Phil (not Dr. Dan).

46. Dashes, cont. • Much as with parentheses, you can resume a sentence that the first dash interrupted, after a second dash. Thus, dashes are often an effective way of “shortening” a sentence (as are parenthesis), helping the reader get through a long, fully packed sentence with other kinds of punctuation. • Note that with respect to the reader, the psychological impact of the information enclosed in dashes is somewhat different from information similarly enclosed in parentheses. Whereas parentheses subordinate or “diminish” the information they contain, making it seem more tangential, information enclosed in dashes tends to stand out, drawing attention to itself. • No direct evidence exists, however—either from field observations or numerical simulation—that an eruptive release from a subsurface storage reservoir can be powered solely by the mechanical energy stored in an accumulation of compressed gas, without substantial contributions from thermal energy.

47. Empathy