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2015 February 25

Freshman design seminar writing notes

Along with the senior-thesis writing course this quarter, I’m also teaching a freshman design seminar. Many of the problems in their first design reports are similar to the problems I see in senior theses (Senior thesis pet peeves, More senior thesis pet peeves, and Still more senior thesis pet peeves). I hope that by catching them early, I can squelch the problems.

Here are some things I saw in the first design report turned in by the freshmen:

  • Every design document should have a title, author, and date. If the document is more than one page log, it should have page numbers.
  • Passive voice should be used very sparingly—use it to turn sentences around to pull the object into the first position, when that is needed to get a smooth old-info-to-new-info flow.  Sometimes you can use it to hide the actor, when you really don’t know who did something, but that should be very rare.
  • Errors in schematics, programs, block diagrams, and other low-redundancy representations are very serious.  In the circuits class, any error in a schematic triggers an automatic REDO for the assignment.  I’m not as harsh in the freshman design class, but there is no notion of “just a little mistake” in a schematic.
  • The battery symbol is not the right way to show a voltage source that is not a battery.  Use the power-port symbol, to indicate connect to a power supply that is not included in the schematic, or include the Arduino board from which you are getting power as a component in the schematic.
  • Bar charts are not appropriate for all that many data representations in the physical and biological sciences.   If you have 2-D data, use a scatter diagram.  A bar should only be used when the area of the bar communicates the quantity of something that is labeled in discrete classes.  (And even then a single point is often clearer.)
  • Captions on figures should be about a paragraph long.  Remember that people generally flip through a paper looking at the pictures before deciding whether to read it.  If the figures and captions are mysterious, they’ll give up without ever reading the paper.  A lot of academic authors, when writing a paper for publication, start by choosing the figures and writing the captions.  Those figures and captions then form the backbone of the paper, which is written to explain and amplify that backbone.
  • In academic writing, figures are treated as floating insertions, not fixed with respect to the text.  Therefore, it is correct to refer to the figures by name, “Figure 1”, but not by location (“above” or “below”). Every figure in a paper should be referred to explicitly by name in the main body of the text, and the floating insertion put near where the first reference to the figure occurs.
  • Citations in modern scholarly works are not done as footnotes—those went out of style 50 or 60 years ago, and only high school teachers still use that style.  Modern papers put all the citations at the end (in any of several different styles, usually specific to a particular journal).  I have a slight preference for reference lists that are sorted by author, rather than by order cited in the paper, and I have a preference towards high-redundancy reference list formats rather than minimalist ones, but I don’t have a particular style that I recommend.
  • There is no point to saying “web” in a citation—if something comes from the web, then give me the URL (or DOI). For material that is only on the web (not citable as a journal article), you must give the URL or DOI.
  • When typing numbers, never start them with a decimal point—use a leading zero to prevent the easily missed leading decimal point. Even better is to follow the engineering convention of using numbers between 1 and 1000 with exponents of 10 that are multiples of three.  That is, instead of saying .01, or even 0.01, say 10E-3.  The advantage is that the powers of 1000 have prefix names, so that .01A becomes 10mA.  Don’t worry about significant figure meanings, because engineers express significance explicitly, not through imprecise sig-fig conventions.  That is, and engineer would say 10mA±2mA, not 1.E-2A (which a physicist would interpret as 10mA±5mA) or 1.0E-2A (which a physicist would interpret as 10mA±0.5mA).
  • In describing where components are in a schematic diagram, “before” and “after” don’t make much sense.  I have no idea what you mean if you say that a resistor is before an LED. When engineers use “before” or “after” it is generally in an information-flow sense.  For example, you may filter before amplifying or amplify before filtering, but if a resistor and capacitor are in series, neither is “before” the other.
  • Students use “would” in many different ways, but mostly incorrectly, as if it were some formal form of “was” or “will be”, while it is actually a past subjunctive form of the modal auxiliary “will”.  There are many correct uses of “would” in general English, but in technical writing, it is usually reserved for “contrary to fact” statements. When a student writes “I would grow bacteria for 2 days”, I immediately want to know why they don’t.
  • The pronoun “this” is very confusing, as the reader has to work out what antecedent is meant. A lot of effort can be saved if “this” and “these” are not used as pronouns but only as demonstrative adjectives modifying a noun. This usage is much easier for people to follow, as the noun helps enormously in figuring out the antecedent.  If you can’t figure out what noun to use, then your reader has no hope of understanding what you meant by “this”.
  • “First” is already an adverb and needs no -ly. The same is true of “second”, “third”, and “last”.  For some reason, no one makes the mistake with “next”, which follows the same pattern of being both an adjective and an adverb.  I wonder why that is?

2015 February 11

Still more senior thesis pet peeves

Filed under: Uncategorized — gasstationwithoutpumps @ 21:33
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I previously posted some Senior thesis pet peeves and More senior thesis pet peeves. Here is another list, triggered by a couple of groups of second drafts (in no particular order, though some are repeats of earlier ones—the students hadn’t gotten the message):

  • Passive voice is not to be used. When passive voice is used, the reader has a hard time figuring out who actually did anything. A thesis is written toestablish that someone is competent to do research and write about it. If the entire thesis is written in passive voice, with no first-person singular, the implication is that all the work was done by person or persons unknown.If you did the work, claim it! If you didn’t do the work, tell me who did!
  • “however”≠”but”: “However” is a sentence adjective, but it is not a conjunction. “However” is best used in the middle of a sentence—it can, however, be moved to the beginning, if necessary for readability. However, there is some danger when it is at the beginning of a sentence of merging the sentence with the previous one, and treating it like a conjunction. If you make that mistake, replace “however” and the following comma with “but”.
  • A number of students are using dangling modifiers: starting sentences with modifiers that would apply to the subject of the sentence, then changing their mind and putting a different subject in the main part of the sentence.  (I won’t embarrass students by quoting their work here—there are a number of examples at http://examples.yourdictionary.com/examples-of-dangling-modifiers.html.)
  • Lists need to consist of parallel items.  The items need to be grammatically parallel as well as semantically parallel. If one is a noun phrase, then all need to be noun phrases.  If one is a verb clause, they all need to be verb clauses.  The semantic parallelism is a little subtler—don’t mix properties of an object with instructions for using the object, for example.  The bulleted lists of visual aids for talks are a particularly important place to apply the rules of parallelism.
  • I recommended that students start each chapter on a new page. Not only is this conventional book and thesis formatting, but starting each chapter on a new page makes it easier for the reader to distinguish between chapter breaks, section breaks, and subsection breaks.  Anything that makes it easier for a reader to stay oriented in a large document is useful. (I also recommended numbering sections and subsections with the chapter.section.subsection style used in most computer-science documents.
  • Figures and tables should be sequentially numbered, and the name of the figure is the word “Figure” followed by an unbreakable space, followed by the number. Because this is the name of the figure, it is capitalized like other proper nouns: Figure 1, Table 3, … . All figures should be referred to in the text, and the figures should appear near where the first reference to them is (unless there are a group of figures relegated to an appendix, with their existence mentioned in the main body, but not discussed there). If you need to insert a new figure, you need to renumber everything after that point—so make all your figure numbering be handled by automatic cross references by the program, as manual renumbering is highly error-prone. If you have a name like Figure 2b, it means a subfigure of Figure 2, not a figure you added late between the old Figures 2 and 3.  (Incidentally, I hate how WordPress throws away unbreakable spaces when converting back and forth between “Visual” and “Text” editing.  No matter how carefully I put them in, WordPress manages to mess them up and turn them back into ordinary spaces.)
  • “parse”≠”scan”: Every year I get a number of students who have picked up the word “parse” from a computer science class, and misunderstood it to be a synonym for “scan”. That’s not what it means. To parse something is to determine its structure—to break it into parts and analyze the relationship among the parts (generally in terms of some grammar). The verb “parse” is transitive—it takes an object, not a prepositional phrase, that holds the thing being analyzed.
  • Students are still having trouble with countable and uncountable nouns. For some students, this is understandable, as their native languages do not make the countable/uncountable distinction that English does.  I pointed students to the Oxford Student Dictionary of American English, edited by Hornby, which is now out of print, as being a dictionary that actually tells you whether a noun is countable or not.  The Oxford Advanced American Dictionary for learners of English is not as nicely formatted, but also has the [C] and [U] markings and is still in print.I used two examples of nouns that changed meaning depending on whether they were countable:  “grub” and “time”.  “Grub” is food, but “a grub” is the larval form of an insect, which may or may not be food. “Time”, when uncountable, is a duration, but “times”, when countable, are separate events.

    Even native speakers of English sometimes mess up the countable/uncountable distinction (though usually not with articles). The contexts where native speakers mess up are “amount of”/”number of”, “less”/”fewer”, and “much”/”many”—in all of which the first form should be used with uncountable nouns and the second with plural forms of countable nouns.

2015 January 18

Senior thesis pet peeves

Filed under: Uncategorized — gasstationwithoutpumps @ 19:47
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Every week in my senior thesis writing class, I go over some of the things I saw in student writing that I think need to be fixed.  I’ve decided to try to collect some of the notes here, though I doubt that I’ll ever get a full set, since a lot of the talk is extemporaneous or prompted by questions.  They are not in any particular order.

  • One of the first things I tell students about the structure of a thesis, is that it must start with a clear statement of the research question or design goal of the thesis. (This is traditionally called the “thesis statement,” but I don’t use that term.)  Without explicit demands to put the statement in the first paragraph, and (if possible) the first sentence, students tend to write pages of background material before getting to the point of their thesis. In journalism, this mistake is called “burying the lede”, and it is just as serious a problem in a thesis or thesis proposal as it is in a newspaper article.

    Even after getting this instruction, a lot of students want to write about the overall goals of the lab they are working in, rather than giving the specific goal of their thesis. It sometimes takes two or three iterations before students get a clear, correct statement of the research question or engineering design goal that they are addressing in their thesis.

  • One pervasive problem (often encouraged by the students’ research mentors) is to write the entire thesis in the passive voice. Writing journal articles in passive voice is fairly common, and some people have gotten the mistaken notion that passive is somehow more formal and correct than active voice. But passive is wholly inappropriate for a thesis.The point of a thesis is to establish the research skills of the person writing the thesis. So most of the thesis should be written in first-person singular: I developed a new protocol … ; I transfected the cells … ; I analyzed the data … ; I hypothesize that …  Plural is strongly discouraged—”we” should only be used where other people are explicitly called out by name. Passive voice, which amounts to an assertion that the actor is unknown or unimportant should be avoided.

    I don’t want to prohibit passive voice, though, as there is an important use for it in technical writing, even in theses. That use is inverting sentences, to put the object before the subject: “X did Y” ➜ “Y was done by X”. This reordering can be very useful for improving flow, which relies on putting the old information at the beginning of a sentence and the new information at the end of the sentence.

  • Students often borrow figures from lab mates or from published papers to put in their theses, particularly in the background section. I’d like students to create their own figures as much as possible, but there are plenty of times when copying a figure is the right thing to do. What students usually miss, however, is the need to put an explicit figure credit at the end of the figure caption—something of the form “Figure copied from Smith and Ng [Smith and Ng, 1999]”. A simple citation is not enough, just as a citation is not sufficient defense against plagiarism for copied text, unless there are explicit markings indicating a direct quotation.  When a figure is redrawn or modified, the figure credit should have the form “Figure adapted from …”, rather than “Figure copied from …”, but the explicit credit is still needed.

    One reason I object to copied figures is that students usually do a very bad job of it, copying a low-resolution image off the internet, often with screen-capture tools, so that the image in their thesis is blurry or jagged. Going to the original articles and extracting the PDF images would eliminate at least a little of the awfulness of the copies.

  • Speaking of citations, students often ask what citation format they need to use for their theses. There aren’t any standards for senior theses at our campus, but there are for PhD theses, so I suggest using that style. The PhD thesis citation style on our campus calls for parenthesized author and year format: (Smith and Ng, 1999). That style, though rather long-winded, has the advantage of not requiring the reader to keep flipping to the reference list to see what the citation refers to (a huge advantage in the days of microfilm, but slightly less important now).

    The citation list itself can be in any standard format—I prefer to have the list sorted alphabetically be author and using the full author names, article titles, full journal names, and URLs and DOIs when available. Many journals use a much terser style to save space, but having the full information is useful to scholars, as it provides some redundancy to help correct for typos in the citation.

  • I have to tell a number of students about the concepts of paragraphs and making the first sentence of each paragraph be a topic sentence. Many of the students otherwise start stream-of-consciousness dumps of ideas that go on for pages with no internal structure. Stream of consciousness may have worked for James Joyce (I wouldn’t know, as I could never read more than a page or two of his stuff), but it doesn’t work for scientific writing. Every sentence of a paragraph should be supporting or amplifying the topic sentence.
  • Students often have trouble with vague antecedents for their pronouns—particularly when they use “this” as a pronoun. I strongly suggest that they check every “this” and “that” in their writing, and if it is used as a pronoun, replace it with a noun phrase: “this technique”, “this method”, “this protein”, … Where they can’t find the appropriate noun to use, their readers certainly won’t be able to figure out the intended antecedent. Incidentally, this usage of “this” is referred to as a demonstrative adjective, though it might be more useful to refer to it as an article (like “the” or “an”), since that is the position in the noun phrase that it occupies.
  • A lot of what I tell students has to do with typography and copy editing, rather than with writing per se. For example, I tell them about the 4 types of dashes:
    hyphen –
    a very short mark used inside compound words, to turn a noun phrase into a modifier of another noun, or to mark the end of a line where the word continues onto the next line.
    en-dash –
    a somewhat wider mark (about the width of a lower-case “n”) that is used to represent ranges, such as 1–10 or Jan–Jul.
    em-dash —
    a much wider mark, used for sentence-level punctuation—somewhat like a semicolon or parentheses
    a minus sign –
    used only in mathematics, the minus sign is usually the same size as the en-dash, but has different spacing rules. The text marks (hyphen, en-dash, and em-dash) have no space around them (though some typographers will put thin spaces around em-dashes), but the minus sign has the same spacing rules as the plus sign (with different rules depending whether it represents a unary or binary operator). Basically, if you are not an expert in math typography, you should use LaTeX to typeset your math and trust it to do a better job than you can.

    While I’m on the subject of hyphens, I usually tell students that when they use a noun phrase to modify another noun, they should hyphenate the whole modifying noun phrase. For example, the process of synthesizing amino acids is called amino-acid synthesis, and the pathway that does it is the amino-acid-synthesis pathway.

  • A lot of biology acronyms and gene names are case-sensitive and start with lower-case letters (like tRNA, siRNA, dsDNA, p53, … ). Sentences should not be started with uncapitalizable symbols. If you need to start a sentence with “p53”, try “Tumor suppressor p53” instead. Sometimes just adding an article helps: “tRNA genes” ➜ “The tRNA genes”.
  • Biology papers have two major uses for italics: for new jargon terms in the context where they are first defined and for genus-species names (like Escherichia coli or C. elegans). The genus-species typesetting rules are a bit complicated —genus is capitalized, but species is not; genus can be abbreviated to a single letter with a period, if unambiguous; subspecies or strain names are not italicized. Italicizing words when they are first defined is a simpler concept, one which can be applied to almost any academic writing.
  • There a few words that I object to also. Perhaps the most common problem is the ugly neologism “utilize”, which is used far too often by students, when what they mean is “use”. (The older meaning of “utilize”—to make useful—has disappeared.

2013 May 10

Avoid passive voice

Filed under: Uncategorized — gasstationwithoutpumps @ 20:45
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I’ve been reading 13 different senior theses this quarter (5 drafts of each—we’re currently on the 3rd drafts).  One of the biggest writing problems that I’ve been trying to fix is the gross overuse of passive voice. Passive voice is often overused in scientific writing, partly out of a misguided attempt to sound formal and partly to remove the people who did the experiment from the description of the experiment.  The result often sounds like the authors are trying very hard to disassociate themselves from the project.

Nick Falkner describes this use of passive well in The Blame Game: Things were done, mistakes were made:

The error is regretted? By whom? This is a delightful example of the passive voice, frequently used because people wish to avoid associating the problem with themselves.

But the whole point of a senior thesis is to show what a particular individual knows and has done (and presumably can do again).  The author must attribute every concept and action in the thesis to the right person: those ideas that come from the literature need to be properly cited, work done by others in the lab needs to be properly credited, and work done by the author of the thesis needs to be explicitly claimed.  (I’m aware of all the passive in the last sentence—see below for explanations of some acceptable uses of passive voice.)

Along with passive voice, students misuse the first-person plural, which has little role in a single-author work like a thesis. Almost the only time that “we” should appear in a thesis is shortly after a listing of who “we” are. It is ok to say, for example, “Alpha Beta and I ran alternating shifts for the 48-hour data collection period.  We collected samples every hour …”, but it is not ok to say “We collected samples every hour … “, if you did it alone, or (worse) if someone else in the lab did it and not you.  Saying “Samples were collected every hour …” sounds like you don’t know or are not willing to say who collected the samples (perhaps because it was done illegally?).

I am not going to prohibit students all use of the passive (as some writing instructors do, or used to do)—passive voice is sometimes useful. For example, passive can be used for improving the flow of a paragraph, since it allows flipping a sentence, which can strengthen the old infonew info flow heuristic.  This flipping of sentences is best shown with some schematic sentences: we start with

A creates B. C modifies B. D controls C.

and we can improve the flow by modifying to

A creates B. B is then modified by C, which is controlled by D.

Note that the second sentence of the above paragraph uses passive (“passive can be used …”) in order to connect better to the topic sentence.

Aside: The “we” in the middle of the paragraph above is not the multi-author “we”, which is as wrong for this single-author blog post as it would be in a thesis, but the “you-and-I” version of “we”, which is also acceptable in theses.

Students worry that if they avoid passive, then they’ll end up starting every sentence with “I”.  Certainly, starting every sentence identically would be a problem, but avoiding that problem is fairly easy, particularly if students talk about the goals and purposes of experiments, rather than just giving technician-level protocol dumps of what they did. Note that I did not use passive at all in this paragraph, and only this last sentence has “I” as a subject—forming gerunds is one good way to create alternative subjects for sentences.

Although my writing instructor’s despair about overuse of passive voice has been the theme of this post, that was not the point of Nick’s blog post—it was a plea to students (and others!) to take responsibility for their actions.  He wants people to be aware that actions have actors:

Responsibility doesn’t have to be a burden but it does give you a reason to exercise your agency, your capacity to act and to make change in the world. If all of your problems are in the passive voice, then “assignments are handed in late”, “the money ran out”, “mistakes were made” rather than “I didn’t start early enough or put enough time in or I was horribly ill and thought I could just push through”, “I spent all of my money too quickly” and “I made a mistake”.

His point is a good one (go read the whole article), but his equating passive voice with refusal of responsibility is the message I want to get to the thesis writers.  The whole goal of a thesis is to establish agency—that the writer of the thesis knows and has done certain things, so the writer should avoid using passive voice.  (I initially had written “passive voice should be avoided as much as possible”, but I didn’t trust that all my readers would get the joke—my apologies to those who would have.)

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