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?

Long sentence

Joseph Mitchell created a marvelous long sentence (found in A City of Many Pasts in The New Yorker):

And I should also say that when I say the past I mean a number of pasts, a hodgepodge of pasts, a spider’s web of pasts, a jungle of pasts: my own past; my father’s past; my mother’s past; the pasts of my brothers and sisters; the past of a small farming town geographically misnamed Fairmont down in the cypress swamps and black gum bottoms and wild magnolia bays of southeastern North Carolina, a town in which I grew up and from which I fled as soon as I could but which I go back to as often as I can and have for years and for which even at this late date I am now and then all of a sudden and for no conscious reason at all heart-wrenchingly homesick; the pasts of several furnished-room houses and side-street hotels in New York City in which I lived during the early years of the Depression, when I was first discovering the city, and that disappeared one by one without a trace a long time ago but that evidently made a deep impression on me, for every once in a while the parlor or the lobby of one of them or my old room in one of them turns up eerily recognizable in a dream; the pasts of a number of speakeasies, diners, greasy spoons, and drugstore lunch counters scattered all over the city that I knew very well in the same period and that also have disappeared and that also turn up in dreams; the pasts of a score or so of strange men and women—bohemians, visionaries, obsessives, impostors, fanatics, lost souls, gypsy kings and gypsy queens, and out-and-out freak-show freaks—whom I got to know and kept in touch with for years while working as a newspaper reporter and whom I thought of back then as being uniquely strange, only-one-of-a-kind-in-the-whole-world strange, but whom, since almost everybody has come to seem strange to me, including myself, I now think of, without taking a thing away from them, as being strange all right, no doubt about that, but also as being stereotypes—as being stereotypically strange, so to speak, or perhaps prototypically strange would be more exact or archetypically strange or even ur-strange or maybe old-fashioned pre-Freudian-insight strange would be about right, three good examples of whom are (1) a bearded lady who was billed as Lady Olga and who spent summers out on the road in circus sideshows and winters in a basement sideshow on Forty-second Street called Hubert’s Museum, and who used to be introduced to audiences by sideshow professors as having been born in a castle in Potsdam, Germany, and being the half sister of a French duke but who I learned to my astonishment when I first talked with her actually came from a farm in a county in North Carolina six counties west of the county I come from and who loved this farm and started longing to go back to it almost from the moment she left it at the age of twenty-one to work in a circus but who made her relatives uncomfortable when she went back for a visit (“ ‘How long are you going to stay’ was always the first question they asked me,” she once said) and who finally quit going back and from then on thought of herself as an exile and spoke of herself as an exile (“Some people are exiled by the government,” she would say, “and some are exiled by the po-lice or the F.B.I. or the head of some old labor union or the Mafia or the Black Hand or the K.K.K., but I was exiled by my own flesh and blood”), and who became a legend in the sideshow world because of her imaginatively sarcastic and sometimes imaginatively obscene and sometimes imaginatively brutal remarks about people in sideshow audiences delivered deadpan and sotto voce to her fellow-freaks grouped around her on the platform, and (2) a street preacher named James Jefferson Davis Hall, who also came up here from the South and who lived in what he called sackcloth-and-ashes poverty in a tenement off Ninth Avenue in the Forties and who believed that God had given him the ability to read between the lines in the Bible and who also believed that while doing so he had discovered that the end of the world was soon to take place and who also believed that he had been guided by God to make this discovery and who furthermore believed that God had chosen him to go forth and let the people of the world know what he had discovered or else supposing he kept this dreadful knowledge to himself God would turn his back on him and in time to come he would be judged as having committed the unforgivable sin and would burn in Hell forever and who consequently trudged up and down the principal streets and avenues of the city for a generation desperately crying out his message until he wore himself out and who is dead and gone now and long dead and gone but whose message remembered in the middle of the night (“It’s coming! Oh, it’s coming!” he would cry out. “The end of the world is coming! Oh, yes! Any day now! Any night now! Any hour now! Any minute now! Any second now!”) doesn’t seem as improbable as it used to, and (3) an old Serbian gypsy woman named Mary Miller—she called herself Madame Miller—whom I got to know with the help of an old-enemy-become-old-friend of hers, a retired detective in the Pickpocket and Confidence Squad, and whom I visited a number of times over a period of ten years in a succession of her ofisas, or fortune-telling parlors, and who was fascinating to me because she was always smiling and gentle and serene, an unusually sweet-natured old woman, a good mother, a good grandmother, a good great-grandmother, but who nevertheless had a reputation among detectives in con-game squads in police departments in big cities all over the country for the uncanny perceptiveness with which she could pick out women of a narrowly specific kind—middle-aged, depressed, unstable, and suggestible, and with access to a bank account, almost always a good-sized savings bank account—from the general run of those who came to her to have their fortunes told and for the mercilessness with which she could gradually get hold of their money by performing a cruel old gypsy swindle on them, the hokkano baro, or the big trick; and, finally, not to mention a good many other pasts, the past of New York City insofar as it is connected directly or indirectly with my own past, and particularly the past of the part of New York City that is known as lower Manhattan, the part that runs from the Battery to the Brooklyn Bridge and that encompasses the Fulton Fish Market and its environs, and which is part of the city that I look upon, if you will forgive me for sounding so high-flown, as my spiritual home.

Although this sort of long sentence may be amusing as a tour de force in literary writing, marvelous mainly for its ability to remain grammatical, despite the length, I hope never to see such a long sentence in technical writing.

Still more senior thesis pet peeves

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.

More senior thesis pet peeves

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.

Senior thesis pet peeves

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.