Gas station without pumps

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.


  1. FYI: the section on dashes is confusing due to insufficient copy editing… A hyphen is described as “a very mark” (missing word, I presume). In the en-dash section, when describing ranges, you use an em-dash in the range “Jan—Jul”

    Comment by Michael K Johnson — 2015 January 19 @ 03:33 | Reply

    • Thanks. I fixed the problems. The reason for the wrong dash is that I had to edit in WordPress’s “text” mode, because switching back and forth between text and visual mode causes the line breaks to disappear—a very annoying bug in the WordPress editor. In text mode, all the dashes are shown as hyphens, no matter what their length (another annoying bug), so I hadn’t noticed the mistake.

      There are plenty of times when I wish the WordPress editor was a little “dumber” so that I could edit the HTML and expect the edits to remain.

      Comment by gasstationwithoutpumps — 2015 January 19 @ 09:35 | Reply

  2. Ah — a post after my own pedantic heart! Thank you!
    I like the resource, especially in regards to the use of hyphens.

    Comment by xykademiqz — 2015 January 24 @ 11:06 | Reply

  3. […] previously posted some Senior thesis pet peeves. Here is another list, triggered by another group of first drafts (in no particular […]

    Pingback by More senior thesis pet peeves | Gas station without pumps — 2015 January 26 @ 22:17 | Reply

  4. […] 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 […]

    Pingback by Still more senior thesis pet peeves | Gas station without pumps — 2015 February 11 @ 21:33 | Reply

  5. […] 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 […]

    Pingback by Freshman design seminar writing notes | Gas station without pumps — 2015 February 25 @ 19:27 | Reply

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