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2015 March 14

Not been blogging much

Those who have been following my blog for a while may have noticed that my blogging frequency has dropped quite a bit for the past few months.  I had planned to blog after every class meeting of the freshman design seminar, as I did last year, but I’ve simply been too busy. In addition to teach the freshman design seminar, I was also teaching the senior thesis writing course. Although both of these are 2-unit courses with small numbers of students (so the department gets essentially no additional resources as a result of my teaching them), they are both somewhat time-consuming, though the senior thesis writing much more so than the freshman design.

This weekend is the first weekend that I did not have a stack of thesis drafts to provide detailed feedback on (I’ve been averaging over 6 drafts a week to comment on all quarter).  In addition to the thesis drafts, I also arranged to have a 20-minute individual meeting weekly with each of the 19 seniors writing theses this year.  Because the meetings often ran over, I spent about 7 hours a week on those meetings.  I started each meeting with the student giving me a 2-minute elevator talk (after telling me what audience they were addressing the talk to and with what purpose). This served two purposes: to get the students to practice concise descriptions of their projects and to remind me which of the 19 projects we were talking about. (Several pairs of students were doing closely related projects in the same lab, so it was really easy for me to mix up the projects—and I have almost no memory for faces and names, so I needed the prompts!)

Next weekend I’ll pay for this weekend off—I’ll have all 19 theses to grade between Thursday night and Tuesday morning.  I won’t be doing as detailed feedback on this round—first, because there aren’t enough hours to do 2–3 hours a thesis; second, because I suspect that half the students won’t come by my office to pick up the graded theses (even those who still have a quarter to go before their theses are complete).

I hope to have the freshman design course all graded before the senior theses come in—they have their last lab on Monday and their design reports are due Tuesday.  The freshman reports are much shorter than the senior theses, so I can probably get them all graded on Wednesday.  If I get them done in a timely manner, I may take the time to try to do an end-of-quarter summary of the freshman design project course, which I think ran more smoothly this year, though not quite in the direction I had originally thought we would go.

This weekend, I’m getting back to work on my book, since I want to release a draft for the applied electronics course that starts in 2 weeks. I at least want the chapters and labs for the first two weeks to be finished, with no major overhauls planned for the remainder. I spent about 4 hours on the book today (after goofing around for a while with some phototransistor circuits that aren’t really relevant to the course—I’ll probably blog about that when I have more time, but it will take about 8 hours to do a good blog post on it, and I don’t have that much spare time this week). I hope to have the schedule for all the labs finished this weekend also—I made a good start on that in December, when I last had time to work on the book.

Next quarter will not give me much writing or blogging time—instead of the 12 contact hours (plus office hours and grading) that I had this quarter, I have 19 contact hours (3.5 hours of electronics lecture, 12 hours of electronics lab, 3.5 hours of banana slug genomics) plus grading 15 prelab assignments and 15 design reports a week for the electronics course. I’m hoping I can convince my co-instructor to do what grading we’ll need for the banana slug genomics, or that we won’t assign much that needs grading.

Also Spring quarter is when most students declare their majors, so I’ll probably have to increase my office hours from 2 hours a week to 3 or 4 to handle the advising load.  Two hours a week was just about right this quarter, especially since I allowed students to reserve a place in line by email.  I only had an empty office once or twice, and only ran an hour over once or twice.

On the administrative side, at least I’ve gotten the 20-page bioengineering self-study  and my 3-page contribution to the bioinformatics self-study done, so I won’t have too much to do on those next quarter.  The Curriculum Leave Plan is done for next year, and I hope it won’t need further modification. I’m reducing my teaching load next year to merely heavy (from insane this year), and some of the buyouts we had counted on for paying lecturers are not coming through, so the department has a structural deficit of about $30k, and only enough reserves to cover that for a couple of years (with no way to replenish the reserves).  I don’t know what we’re going to do long term, as we need to add more offerings of some of our more popular courses, at a cost of about $20k each.

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 26

More senior thesis pet peeves

Filed under: Uncategorized — gasstationwithoutpumps @ 22:17
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I previously posted some Senior thesis pet peeves. Here is another list, triggered by another group of first drafts (in no particular order):

  • An abstract is not an introduction. Technically, an abstract isn’t really a part of a document, but a separate piece of writing that summarizes everything important in the document. Usually the abstract is written last, after everything in the thesis has been written, so that the most important stuff can be determined. Most readers will never read anything of a document but the abstract.
  • Every paragraph (in technical writing) should start with a topic sentence, and the remaining sentences in the paragraph should support and expand that topic sentence. If you drift away from the topic, start a new paragraph! The lack of coherent paragraphs is probably the most common writing problem I see in senior theses.
  • I don’t mark every error I see in student writing. It is the student’s responsibility to learn to recognize problems that I point out and to hunt down other instances themselves. Students need to learn to do their own copy editing (or copy edit each other’s work)—I’m not interested in grading my own copy editing on subsequent drafts of the thesis.
  • Every draft of every document that is turned in for a class or to a boss should have a title, author, and date as part of the documents.  Including this meta-information should be a habitual action of every engineer and every engineering student—I shouldn’t be seeing last-minute hand-scrawled names and titles on senior thesis drafts.
  • Page numbers!  Every technical document over a page long should have page numbers. If you don’t know how to get automatic page numbers with your document processor, either stop using it or learn how!
  • Earlier this quarter I said that I did not care what reference and citation style you used, as long as it was one of the many standard ones. I’ve decided to change my mind on that—I do care somewhat what style you use for the reference list. Use a reference style that contains as much information as possible: full author names, full journal name, dates, locations of conferences, URLs, DOIs, … .  You may format it in any consistent manner, but provide all the information.
  • Use kernel density estimates instead of histograms when showing empirical probability distributions. My previous post explains the reasons.
  • Avoid using red-green distinctions in graphics. About 6% of the male population is red-green colorblind. There are color-blindness simulators on the web (such as http://www.color-blindness.com/coblis-color-blindness-simulator/) that you can use to check whether your color images will work.  Modern gene-expression heat maps use red for overexpression, blue for underexpression, and fade to white in the middle.  This scheme has the advantage of having the strong signals in saturated colors and the weak ones in white or pastels, blending into the white background.
  • Comma usage continues to be a problem for many students. I discussed three common comma situations in English:
    • Comma splices. Two sentences cannot be stuck together with just a comma—one needs a conjunction to join them. If a conjunction is not desired, an em-dash can be used (as in the previous sentence). Sometimes a semicolon can be used, but never a bare comma.
    • Serial comma. There are two different conventions in English about the use of commas before the conjunction in a list of three or more items. In American English, the comma is always required, but in British English the comma is often omitted. I strongly favor the American convention (also known as the serial comma or the Oxford comma), and I will insist on it for the senior theses—even for those students raised in the British punctuation tradition.
    • When using “which” to introduce a relative clause, the clause should be non-restrictive. That is, omitting the clause beginning with “which” should not change the meaning of the noun phrase that is being modified by the relative clause. Non-restrictive relative clauses should be separated from the noun phrase they modify with a comma. If you have “which” without a comma starting a relative clause, then check to see whether you need a comma, or whether you need to change “which” to “that”, because the clause is really restrictive. Note: “which” is gradually taking over the role of “that” in spoken English, but this language change is still not accepted in formal writing, which is more conservative than speech.
  • The noun “however” is a sentence adjective, but it is not a conjunction. You can’t join two sentences with “however”. You can, however, use it to modify a separate sentence that contrasts with the previous one.
  • Colons are not list-introducers. Colons are used to separate a noun phrase from its restatement, and the restatement is often a list. The mistaken notion that colons are list-introducers comes from the following construction: the use of “the following” before a list. The colon is there because the list is a restatement of “the following”, not because it is a list. Note that two sentence back, I used a colon where the restatement was not a list. Similarly, I don’t use a colon when the list is
    • the object of a verb,
    • the object of a prepositional phrase,
    • or any other grammatical construct that is not a restatement or amplification of what came before the colon.
  • Most students in the class use “i.e.” and “e.g.” without knowing the Latin phrases that they are abbreviations for. I suggested that they not use the abbreviations if they wouldn’t use the Latin, but use the plain English phrases that they would normally use: “that is” and “for example”. If they must use the Latin abbreviations, they should at least punctuate them correctly—commas are needed to separate the “i.e.” and “e.g.” from what follows, just as a comma would be used with “that is” or “for example”.
  • Some students use the colloquial phrase “X is where …”, when what they mean is “X is …”. The “where” creeps in in some dialects of English to serve as a way of holding the floor while you think how to finish the sentence—it doesn’t really belong in formal technical writing.
  • “First”, “second”, and “last” are already adverbs.  They don’t need (and can’t really take) an “-ly” suffix. It grates on me the way same way that “nextly” does. “Next” has exactly the same dual status as an adjective and an adverb, but for some reason does not often suffer the indignity of being draped with a superfluous “-ly”.
  • I recommend that students not use the verb “comprise”, as few use it correctly. You can say that “x, y, and z compose A”, “A is composed of x, y, and z”, or “A comprises x, y, and z”. The construction “is comprised of” is strongly frowned on by most grammarists—avoid it completely, and avoid “comprise”, unless its usage comes naturally to you.  “Compose” and “is composed of” are less likely to get you in trouble.
  • “Thus” does not mean “therefore”—”thus” means “in this manner”. Note that “thus” is an adverb, so there is no “thusly”.
  • “Amount” is used for uncountable nouns (like “information”), while “number” is used for countable nouns (like “cells”). There are many distinctions in English that depend on whether a noun is countable or not (the use of articles, the use of plural, “many” vs. “much”), but “number” vs. “amount” seems to be the one that causes senior thesis writers the most difficulty.

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.

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