Objectives

1. Objectives Be able to research a scientific topic from primary sources Be able to synthesize a coherent and instructive story based on these findings Communicate this story in written prose, paying attention to correct referencing

2. Assessment 20% - literature web, Fri 22nd Feb 10% - first paragraph, Fri 1st March 70% - final report, Fri 22nd March 2500 words maximum

3. Lecture Schedule * class-led discussion

4. Guides to the Chemical Literature • These guides provide further information to the above-mentioned sources, suggest strategies for chemical research, and suggest ways of keeping current with the literature: • Bottle. Information Sources in Chemistry Ref Z5521 B67 1979 (LC) KSL • Maizell. How to Find Chemical Information QD8.5 M34 (LC) CHEM and Ref QD8.5 M34 1979 KSL and Ref QD8.5 M34 ENGN • Mellon. Chemical Publications Z5521 M52 1965 KSL • Wiggins. Chemical Information Sources Ref QD8.5 W54 1991 KSL, ENGN

5. Web Resources • NIST Chemistry WebBook: • http://webbook.nist.gov/ • The 1997 release is the third edition of the NIST Chemistry WebBook which contains thermodynamic data for over 5000 organic and small inorganic compounds and ion-energetics data for over 14,000 compounds. A number of new classes of data have been added including vapor pressure data for over 5000 compounds, Antoine coefficient data for over 1200 compounds, heats of reaction for over 1300 compounds, mass spectra for over 8000 compounds, and IR spectra for over 5000 compounds. There are many avenues for searching the database. Structures are given for most species, as well as common and commercial names

6. Web Resources • DGRweb ACS' Directory of Graduate Research http://dgr.rints.com/ • Conversion factors http://www.wsdot.wa.gov/Metrics/factors.htm • WebElements periodic table http://www.webelements.com/ • Measure 4 Measure (estimate, calculate, translate) http://www.wolinskyweb.net/measure.htm#science • ASU Index to Property Data http://www.asu.edu/lib/noble/chem/property.htm

7. Web Resources • ThermoDex - An Index of Selected Thermodynamic and Physical Property Resources http://thermodex.lib.utexas.edu/ • Chmoogle - finds chemical structures by substructure or SMILES http://www.chmoogle.com/ • Flash animation of The Elements by Tom Lehrer http://www.privatehand.com/flash/elements.html

8. The Role of a Literature Review • Exposes main gaps in knowledge [and] identifies principal areas of dispute and uncertainty. • Helps identifygeneral patterns to findings from multiple examples of research in the same area. • Juxtaposing studies with apparently conflicting findings helps explore explanations for discrepancies. • Helps define your terminology or identify variations in definitions used by researchers or practitioners. • Helps to identify appropriate research methodologies. • You can also identify validated scales and instruments.

9. From Usyd Library • WHAT IS A LITERATURE REVIEW • A literature review is a critical evaluation of literature published on a particular topic. Literature reviews are different to other types of writing you may have done at University. • LITERATURE REVIEWS VERSUS ESSAYS • While literature reviews and essays require many of the same skills – for instance, critical thinking skills, academic writing skills and referencing skills – they have different purposes. Whereas essays require you to support your own arguments, literature reviews require you to critique the arguments of others.

10. From Usyd Library • LITERATURE REVIEWS VERSUS ANNOTATED BIBLIOGRAPHIES • While literature reviews and annotated bibliographies both require you to summarise sources, literature reviews involve much more than this. Annotated bibliographies are primarily descriptive, whereas literature reviews are primarily analytical. • Literature reviews and annotated bibliographies are also structured differently. Annotated bibliographies are presented in an alphabetical list format, and each reference is treated separately. In contrast, literature reviews synthesise the ideas contained in each reference, and are structured around a central concept divided by subheadings.

11. From Usyd Library • WHAT ARE THE PURPOSES OF A LITERATURE REVIEW? • Literature reviews serve many purposes. They: • Provide useful background information to your topic, which enables readers to better understand your topic. • Demonstrate your knowledge of the subject area. • Make clear your perspectives on the topic • Justify your choice of research design. For instance, your choice of qualitative over quantitative approaches, or your method of data analysis. • Explain how your work will fill in a gap in the scholarly literature.

12. From Usyd Library • WHAT ARE THE KEY FEATURES OF A LITERATURE REVIEW? • Literature reviews require you to critically evaluate the literature. To ‘critically evaluate’ a source is to scrutinise it to determine its strengths and weaknesses. The following REVIEW criteria will assist you in critically evaluating sources: • R is for Relevance • Does the reference completely cover your topic, or only one aspect of it? Have you read widely to determine how relevant it is in relation to other sources? • E is for Expertise of author • What is the educational background of the author? What are their qualifications? Are they writing in their area of expertise? Are they regularly cited by other authors in the field? • V is for Viewpoint of author/organisation • Does the author have any personal or professional affiliations that may bias their work? Has the research been sponsored by an organisation with a vested interest in the topic? What is the purpose of the source – to inform, persuade or entertain?

13. From Usyd Library • WHAT ARE THE KEY FEATURES OF A LITERATURE REVIEW? • Literature reviews require you to critically evaluate the literature. To ‘critically evaluate’ a source is to scrutinise it to determine its strengths and weaknesses. The following REVIEW criteria will assist you in critically evaluating sources: • I is for Intended audience • Is the reference aimed at the general public or a scholarly audience? Is it intended for professionals in the field or a community of researchers? Is it intended for a large or small readership? • E is for Evidence • Are opinions supported by scholarly evidence? Is a particular referencing style used properly and consistently? Has the reference been subjected to peer review? • W is for When published • Was the reference published recently? Have significant developments been made in the subject area since the reference was published?

14. First Sentence/Paragraph • Perspectives Instructions: • You should begin with an introductory paragraph that captures the reader's interest and immediately gets to the point. • If you are discussing a specific scientific paper, be sure to refer to the paper somewhere in the first paragraph. • Your introduction should be general enough to orient the reader not familiar with the specifics of your field. • Here, and throughout the text, you should avoid jargon and the special terms of your field. • If the language of specialists is necessary, please briefly define it for the general reader. • Please keep the use of acronyms to a minimum.

15. First Sentence/Paragraph • PERSPECTIVE • GEOPHYSICS • Caught Offside • Tim Elliott • Eighty percent of global volcanism occurs out of sight, at submarine volcanoes along the 56,000 km of mid-ocean spreading centers that straddle Earth. This volcanic activity is confined to very narrow (~1 km) zones between two separating tectonic plates. This concentration of volcanic activity is particularly remarkable when the volume of the rock producing the magmatism is considered: a triangular melting region, with a base at least 60 km deep, extends 60 km on either side of the ridge axis (see the first figure).

16. First Sentence/Paragraph • PERSPECTIVE • GEOPHYSICS • Caught Offside • Tim Elliott • Eighty percent of global volcanism occurs out of sight, at submarine volcanoes along the 56,000 km of mid-ocean spreading centers that straddle Earth. You should begin with an introductory paragraph that captures the reader's interest and immediately gets to the point.

17. First Sentence • What makes a good first sentence?

22. First Sentence • What makes a good first sentence? • SHORT • Single idea • Not too technical • Words with a deeper underlying meaning (tantalising?) • Familiar terms or ideas used in an unexpected way • Posing a question • Strong verbs • Active • Present/Future tense • “Epic” • Title, can tie in with first sentence • Gets to the point quickly/relevant • Inherently interesting subject • Telling you something new and surprising • Sex! • Uses an apparent contradiction to engage the reader • Uses imagery/analogy to make the science more accessible • Clarity

23. First Sentence • What makes a bad first sentence? • The Bulwer-Lytton Fiction Contest is an annual contest sponsored by the English Department of San Jose State University. • Entrants are invited "to compose the opening sentence to the worst of all possible novels" – that is, deliberately bad. • It is named for English novelist and playwright Edward George Bulwer-Lytton, author of the much-quoted first line "It was a dark and stormy night”: • It was a dark and stormy night; the rain fell in torrents, except at occasional intervals, when it was checked by a violent gust of wind which swept up the streets (for it is in London that our scene lies), rattling along the housetops, and fiercely agitating the scanty flame of the lamps that struggled against the darkness. • Paul Clifford 1830

24. First Sentence • It was a dark and stormy night; the rain fell in torrents, except at occasional intervals, when it was checked by a violent gust of wind which swept up the streets (for it is in London that our scene lies), rattling along the housetops, and fiercely agitating the scanty flame of the lamps that struggled against the darkness. • Why is this sentence so bad?

25. First Sentence • It was a dark and stormy night; the rain fell in torrents, except at occasional intervals, when it was checked by a violent gust of wind which swept up the streets (for it is in London that our scene lies), rattling along the housetops, and fiercely agitating the scanty flame of the lamps that struggled against the darkness. • Why is this sentence so bad? • Subject and object too far away • Too many qualifiers (adjectives) • Redundancies • Irrelevant information • Parentheses don’t work • Too many prepositions • Ostentatious erudition (“Epic”?) • LONG (B-L Prize guidelines recommend 50-60 words) • very detailed and descriptive to an unnecessary point (ie florid) • Convoluted, too many clauses, ideas (ie commas, pauses, parentheses) • Contradictions • Clichés

26. First Sentence • “Lyttle Litton prize (limited to 25 words) • The red hot sun rose in the cold blue sky. • Judy Dean (2011 winner) • Why is this sentence so bad?

27. First Sentence • “Lyttle Litton prize (limited to 25 words) • The red hot sun rose in the cold blue sky. • Judy Dean (2011 winner) • Why is this sentence so bad? • “First, you've got the eyeroll that comes from the ham-handed contrast between "red hot" and "cold blue" — and then a second later you realize that "red hot" actually means a temperature of about 1000 kelvin, and is therefore hilariously inadequate as a descriptor of the sun, a gigantic nuclear furnace with a core temperature of roughly ten million kelvin. Intentionally writing a sentence that seems unintentionally bad is hard; writing one that suggests an author going for hyperbole and accidentally winding up with woeful understatement is masterful. Thus, we have our winner.” • http://adamcadre.ac/lyttle.html

28. First Paragraph • From article on the website: • The smallest of the URF's (URFA6L), a 207-nucleotide (nt) reading frame overlapping out of phase the NH2 terminal portion of the adenosinetriphosphatase (ATPase) subunit 6 gene has been identified as the animal equivalent of the recently discovered yeast H+ ATPase subunit 8 gene. The functional significance of the other URF's has been, on the contrary, elusive. Recently, however, immunoprecipitation experiments with antibodies to purified, rotenone-sensitive NADH ubiquinone oxido-reductase [hereafter referred to as respiratory chain NADH dehydrogenase or complex I] from bovine heart, as well as enzyme fractionation studies, have indicated that six human URF's (that is, URF1, URF2, URF3, URF4, URF4L, and URF5, hereafter referred to as ND1, ND2, ND3, ND4, ND4L, and ND5) encode subunits of complex I. This is a large complex that also contains many subunits synthesized in the cytoplasm. • Why is this hard to read?

29. First Paragraph • Technical vocabulary; it requires specialized background knowledge. • Remove the technical words: • The smallest of the URF's, an [A], has been identified as a [B] subunit 8 gene. The functional significance of the other URFs has been, on the contrary, elusive. Recently, however, [C] experiments, as well as [D] studies, have indicated that six human URF's [1-6] encode subunits of Complex I. This is a large complex that also contains many subunits synthesized in the cytoplasm. • The passage is still difficult! Why?

30. First Paragraph • What has the first sentence of the passage to do with the last sentence? • Does the third sentence contradict what we have been told in the second? • Is the functional significance of URF's still "elusive"? • Will this passage lead us to further discussion about URF's, or about Complex I, or both? • The intended audience of this passage would probably possess at least two items of essential technical information: • "URF" stands for "Uninterrupted Reading Frame," which describes a segment of DNA organized in such a way that it could encode a prtein, although no such protein product has yet been identified; • both ATPase and NADH oxido-reductase are enzyme complexes central to energy metabolism. • Although this information may provide some sense of comfort, it does little to answer the interpretive questions that need answering. It seems the reader is hindered by more than just the scientific jargon.

31. First Sentence • The smallest of the URF's (URFA6L), a 207-nucleotide (nt) reading frame overlapping out of phase the NH2 terminal portion of the adenosinetriphosphatase (ATPase) subunit 6 gene has been identified as the animal equivalent of the recently discovered yeast H+ ATPase subunit 8 gene. • Subject-Verb Separation • It is relatively long, 42 words; but that turns out not to be the main cause of its burdensome complexity. Long sentences need not be difficult to read; they are only difficult to write! • Sentence structure needs to present information to readers in the order the readers need and expect it. • This first sentence does the opposite: it burdens and obstructs the reader, because of an all-too-common structural defect. Note that the grammatical subject ("the smallest") is separated from its verb ("has been identified") by 23 words, more than half the sentence! • Readers expect a grammatical subject to be followed immediately by the verb.

32. First Sentence • Revisions: • The smallest of the URF's is URFA6L, a 207-nucleotide (nt) reading frame overlapping out of phase the NH2-terminal portion of the adenosinetriphosphatase (ATPase) subunit 6 gene; it has been identified as the animal equivalent of the recently discovered yeast H+ ATPase subunit 8 gene. • The smallest of the URF's (URFA6L) has been identified as the animal equivalent of the recently discovered yeast H+-ATPase subunit 8 gene. • The smallest of the URF's is URFA6L, a 207-nucleotide (nt) reading frame overlapping out of phase the NH2-terminal portion of the adenosinetriphosphatase (ATPase) subunit 6 gene; it has been identified as the animal equivalent of the recently discovered yeast H+ ATPase subunit 8 gene.

33. Structural Principles • Follow a grammatical subject as soon as possible with its verb. • Place in the stress position the "new information" you want the reader to emphasize. • Place the person or thing whose "story" a sentence is telling at the beginning of the sentence, in the topic position. • Place appropriate "old information" (material already stated in the discourse) in the topic position for linkage backward and contextualization forward. • Articulate the action of every clause or sentence in its verb. • In general, provide context for your reader before asking that reader to consider anything new. • In general, try to ensure that the relative emphases of the substance coincide with the relative expectations for emphasis raised by the structure.

34. Your First Paragraph: • You should begin with an introductory paragraph that captures the reader's interest and immediately gets to the point. • If you are discussing a specific scientific paper, be sure to refer to the paper somewhere in the first paragraph. • Your introduction should be general enough to orient the reader not familiar with the specifics of your field. • Here, and throughout the text, you should avoid jargon and the special terms of your field. • If the language of specialists is necessary, please briefly define it for the general reader. • Please keep the use of acronyms to a minimum. • Provide a link to the second paragraph.

35. Writing Style • Goal in academic writing is not to sound intelligent, but to get your intelligent point across • Don’t be too “wordy” ie using more words than you absolutely need to say something, especially words that don't actually have anything to add to the meaning of our sentences. Wordiness often derives from uncertainty about your topic, lack of a developed argument, or lack of evidence. If you're not sure what you want or have to say, you may have trouble saying it. • Don’t do the reverse and make the style too chatty/informal in the wrong context. • Example: • Especially when we talk, we use a lot of little "filler" words that don't actually have anything to add to the meaning of our sentences. • How many words can you remove from this sentence without altering its meaning? (http://writingcenter.unc.edu/resources/handouts-demos/citation/style)

36. Writing Style • Clichés • Example: France bit off more than it could chew in Vietnam, and America's intervention was too little, too late. • How to correct it: Clichés stand in for more precise descriptions of something. Slow down and write exactly, precisely what you mean. If you get stuck, ask yourself "why? or "how?” • Better example: As the French faltered in Vietnam, even American intervention could not save the collapsing regime. • Qualifiers (very, often, hopefully, practically, basically, really, mostly) • Example: Most people usually think that many puppies are generally pretty cute. • How to correct it: Eliminate some of these qualifiers and you will have a stronger, more direct point. Some qualifiers are necessary, but you should use them very carefully and thoughtfully. • Better example: Most people think that puppies are cute. (http://writingcenter.unc.edu/resources/handouts-demos/citation/style)

37. Writing Style • Redundancy (Using two words that mean the same thing) • Example: Adrienne fulfilled all our hopes and dreams when she saved the whole entire planet. • How to correct it: Choose the most precise term and delete the extra one. • Better example: Adrienne fulfilled all our hopes when she saved the planet. • Some "wordy" constructions take a little more practice locating and correcting (http://writingcenter.unc.edu/resources/handouts-demos/citation/style)

38. Writing Style • Overuse of prepositional phrases (words such as in, over, of, for, at, etc.) • Example: The reason for the failure of the economic system of the island was the inability of Gilligan in finding adequate resources without incurring expenses at the hands of the headhunters on the other side of the island. • How to locate and correct this problem: Locate this problem by circling all of the prepositional phrases in your paper. A few are okay, but several in a sentence (as demonstrated here) make the reader struggle to find and follow your subject and point. Correct this problem by reading the sentence, looking away from it, and writing or saying out loud what you meant when you wrote the sentence. Try asking yourself "Who did what to whom?" Replace the first sentence with your new sentence. • Better example: Gilligan hurt the economic system of the island because he couldn't find adequate resources without angering the headhunters. (http://writingcenter.unc.edu/resources/handouts-demos/citation/style)

39. Writing Style • Stock phrases you can replace with one or two words. • Examples: The fact that I did not like the aliens affected our working relationship.The aliens must be addressed in a professional manner. • How to locate and correct this problem: Locate this problem as you do clichés. Is this just something people say? What do the words actually mean? Correct this problem by looking for a single word that expresses your meaning. • Better examples:
My dislike of the aliens affected our working relationship.The aliens must be addressed professionally. (http://writingcenter.unc.edu/resources/handouts-demos/citation/style)

40. Writing Style • Common stock phrases to replace with one or two words. • The reason for • For the reason that • Due to the fact that • Owing to the face that • In light of the fact that • Considering the fact that • On the grounds that because, since, why (http://writingcenter.unc.edu/resources/handouts-demos/citation/style)

41. Writing Style • In the event that • If it should happen that • Under circumstances in which • On the occasion of • In a situation in which • Under circumstances in which • As regards about • In reference to • With regard to • Concerning the matter of • Where ___ is concerned if when about (http://writingcenter.unc.edu/resources/handouts-demos/citation/style)

42. Writing Style • It is crucial that • It is necessary that • There is a need/necessity for • It is important that • Is able to • Is in a position to • Has the opportunity to • Has the capacity for • Has the ability to • It is possible that • There is a chance that • It could happen that • The possibility exists for must, should can may, might, can, could (http://writingcenter.unc.edu/resources/handouts-demos/citation/style)

43. Writing Style • Prior to • In anticipation of • Subsequent to • Following on • At the same time as • Simultaneously with • It is possible that • There is a chance that • It could happen that • The possibility exists for before, when, as, after may, might, can, could (http://writingcenter.unc.edu/resources/handouts-demos/citation/style)

44. Writing Style • In the same spirit: • Not different similar • Not many few • Not have lack • Not include omit • Not consider ignore • Not the same different • Not often rarely • Not allow prevent • Not admit deny • Not accept reject (http://writingcenter.unc.edu/resources/handouts-demos/citation/style)

45. Verbs • Nouns (person, place, thing, or concept) and verbs (words that describe an action or state of being) are the hearts and souls of all sentences. They become the essential elements—the "subject" and the "predicate" or the "actor" and "action" of every sentence. • The reader should be able to clearly locate the main subject and verb of your sentences and, ideally, the subject and verb should be close together in the sentence. • Some style "crimes" are varied symptoms of one problem: the subjects and verbs or the actor and action of your sentence are hiding from the reader. The reader has trouble following who is doing what to whom. • Using a "passive voice" or "weak verbs”, although grammatically correct, can make the reader work too hard to decipher your meaning. Use passive voice and weak verbs strategically once you get the hang of them. If you're still struggling to figure out what they are, aim for "active voice" and "strong verbs”. (http://writingcenter.unc.edu/resources/handouts-demos/citation/style)

46. Verbs • Problem: Passive voice. When you hide the actor by putting it somewhere after the action (not in the usual subject part of the sentence) and add a "to be" verb, you are using passive voice. For more detailed coverage, see our handout on the passive voice. • Examples: Here's a passive sentence with the actor at the end of the sentence: • The alien remains were lost by the government. • Some passive sentences omit actor entirely: • The alien remains were lost. • The car was wrecked. • Better (active) examples: • The government lost the alien remains. • I wrecked the car. (http://writingcenter.unc.edu/resources/handouts-demos/citation/style)

47. Verbs • Problem: Passive voice. When you hide the actor by putting it somewhere after the action (not in the usual subject part of the sentence) and add a "to be" verb, you are using passive voice. • How to locate and correct this problem: Locate passive voice by circling every "to be" verb (am, is, are, was, were, be, been, being ). Not all of these verbs will indicate a passive construction or one you want to change, but if the "to be" verb is sitting next to another verb, especially one that ends in "ed," ("was lost", "was wrecked") then you may be using passive voice. If you have trouble finding "to be" verbs, try finding the subject, verb, and object in each sentence. Can the reader tell who or what is doing the action in your sentence? Correct passive constructions by putting that actor back in the subject of the sentence and getting rid of the "to be" verb. Note that you may have to add information in the sentence; you have to specify who in your sentence and thereby keep the reader from guessing. (http://writingcenter.unc.edu/resources/handouts-demos/citation/style)

48. Verbs • Problem: Nominalization—making verbs and adjectives into nouns. Again, sometimes you want to use nominalization and may do so purposefully. But too much nominalization can sound abstract and make the reader work to decipher your meaning. (Professional academic writing often has a lot of (too much?) nominalization—that's one reason why you may struggle with it!) • Examples:The discovery of the aliens was made by the government. • The car wreck was a result of a lack of visual focus. • How to locate and correct the problem: Locate nominalization in your papers by circling all of the nouns. Do you have several in a single sentence? You might be hiding the action (the verb) of your sentence inside of a noun. Correct nominalization by returning the abstract noun to its function as verb or adjective. This will take practice—focus on making the sentence simpler in structure (actor and action). • Better Examples: The government discovered the aliens. • My sister wrecked the car when she forgot to wear her glasses. (http://writingcenter.unc.edu/resources/handouts-demos/citation/style)

49. Verbs • Problem: Nominalization – also, look for sentences that begin with the following phrases: there is, there are, this is, that is, it is. Sometimes you need these phrases to refer to an immediately preceding sentence without repeating yourself, but they may be hiding nominalizations. • Example: There is a need for further study of aliens. • How to locate and correct this problem: Circle these phrases and try omitting them from the sentence. Who is doing what to whom? • Better example: We need to study aliens further. (http://writingcenter.unc.edu/resources/handouts-demos/citation/style)

50. Verbs • Problem: Weak verbs. If you have located and corrected passive voice and nominalization problems but your sentences still seem to lack meaning or directness, look for "weak" verbs. Verbs such as "to be" verbs and "have" verbs can often be replaced by "strong" verbs, ie verbs that carry specific meaning. Concentrate on what the subject of your sentence does and make that the verb in the sentence. • Example: The aliens have a positive effect on our ecosystem. • How to locate and correct this problem: Locate weak verbs by circling all of the "to be" and "have" verbs. Correct weak verbs by omitting them and replacing them with a more meaningful verb. Notice that you will need to add information as you specify the nature of the action. Answer the question: "What does the subject really do?" • Better example: The aliens improve our ecosystem. (http://writingcenter.unc.edu/resources/handouts-demos/citation/style)