A note on tense

Use what was done (past), what is still true of the data (present) and don’t mess around with others - i.e. be consistent.

In this work the extent of residue-residue interaction was assessed by calculating the number of contacts that every residue makes with all other residues in each of the available structures. Two residues were assumed to be in contact if any two heavy atoms of these residues are closer than 5.0Å.

Published data are normally described in the present tense (i.e. as a fact) while your data are normally past tense e.g.

‘Loop12 is highly flexible in the absence of ligand (Jones et al.)’ but ‘the the results presented here show that Loop12 is stabilized by both ligand and effector binding’

Accuracy and precision

Try to be concise, unambiguous and impersonal. Clarity of style and consistency of format are essential. The greatest failings of the inexperienced are to meander in a disorganized pattern, to use far to many words and to write in a way which may be aesthetically pleasing but is open to misinterpretation.

‘Jones et al determined the effect of X on Y and showed an increase in the growth rate of Y in response to X’

Should read

‘X increased the growth rate of Y (Jones et al.)

Less is best, do not be repetitive let the data speak for themselves - do not labor the point.

Be quantitative and precise

Avoid terms such as ‘most, many sometimes, occasionally’ unless you give a value to it e.g.

‘most (%70) of cells responded’

These data not this data

Data are plural ‘these data’

Common mistakes by students

Here are some common mistakes I see in student drafts (not including the common mistakes covered in The Elements of Style):

  • Incorrect punctuation of et al. (it is short for et alia, which is Latin for “and others,” so there is a period after “al.” but not after “et”).
  • In common U.S. usage, commas and periods often go before closing quotation marks. (Note that this is different from British English punctuation, and probably most other languages.)
  • Single quotes should only be used to quote something within double quotes, e.g. “Bob said, `Me too!’ “ (Again, this is U.S. usage.) If you want to draw attention to or define a non-standard word usage, double quotes should be used.
  • Capitalized Names. The word Boolean should always be capitalized (in honor of George Boole). Same with Brownian, Eigen etc.
  • Citations at the end of a sentence should be placed before the period McMains, 2005.
  • Incorrectly using “which” instead of “that” as the relative pronoun for a restrictive clause.

Here is a summary of the correct usage adapted partly from “Side by Side Spanish and English Grammar” by Farrell and Farrell:

Relative pronouns begin relative clauses. If the relative clause is a “restrictive clause” defining the noun that precedes it, the clause is not set off by commas and “that” is used: “The one that you want is over there” (in this example, “that you want” is the relative clause). Restrictive clauses are essential definitions; often if you were to omit the relative clause the sentence would make no sense. Sometimes you can cross out a restrictive clause and still end up with a reasonable sounding sentence (as for “The book that you want is over there”), but the meaning is not clear without the definition provided by the restrictive clause.

A non-restrictive relative clause, on the other hand, is not essential to the meaning of the sentence. It gives additional information, but the meaning of the rest of the sentence wouldn’t change if it were to be omitted. It is typically set off from the rest of the sentence by commas: “My favorite book, which I re-read regularly, is Strunk’s `Elements of Style.’” If you can put the relative clause in parentheses without changing the basic meaning of the sentence, it is a non-restrictive clause. Non-restrictive clauses begin with “which” (when they refer to things, that is – if the relative clause refers to people, there are different relative pronouns to worry about, but I won’t get into that). Note that a comma should precede the use of “which.”

Personally I think that when to use which is the most subtle rule of English grammar, and as such I may not always catch a misused “which” when I check your papers. But for readers who have internalized the rule, misuse diminishes the clarity of your writing. So if you haven’t internalized the rule, make a special effort to consciously double-check that every “which” in your paper is really introducing a non-essential description, not an essential definition.

Spelling out numbers

Dave Patterson also has great advice on not spelling out numbers less than ten if the reader will be doing arithmetic with them, as well as other useful tips on his page on common errors in grad student writing.

“The general rule of thumb is to spell out one to ten and use numbers for numbers for 11 and up. However, I find its much better to consistently use numbers when the reader might naturally compare or do arithmetic with the numbers with a sentence or a paragraph. For example, “ The 8-processor case (model 370) needs only 4 computers to hold 32 processors. “ Blindly following the rule of thumb would change the sentence to “ The eight-processor case (model 370) needs only four computers to hold 32 processors. “ Its easier to read and understand we use numbers (84=32) instead of words (eightfour=32)”.

Confusing Words (Affect vs Effect)

Affect means to produce a change in something Effect is defined as a result of something or the ability to bring about a result


These compounds affect microtubule stimulated ADP release Multiple simulations were used determine the allosteric effect of inhibitor binding

In summary:

  • affect - to influence, to pretend (verbs); feeling (noun)
  • effect - a result; being in operation (nouns); to make happen (verb)

More examples:
Self-concept affects learning. She affected intellectualism by wearing glasses and using long words Her affect is always sour in the morning. One effect of lunar gravity is tides. The new state income tax was in effect last fall. The president effected a new policy on international trade.

Note: Most often affect is used as a verb and effect is used as a noun. Something that affects you will have an effect on you.

If in doubt use effect!

However, to make these words even more confusing than they already are, both can be used as either a noun or a verb.

Let’s start with the verbs. Affect means to influence something or someone; effect means to accomplish something.

“Your job was affected by the organizational restructuring” but “These changes will be effected on Monday.”

As a noun, an effect is the result of something: “The sunny weather had a huge effect on sales.” It’s almost always the right choice because the noun affect refers to an emotional state and is rarely used outside of psychological circles: “The patient’s affect was flat.”

Summery: When using as a noun, if in doubt use effect!

Also for commonly [miss-spelled]](http://www.yourdictionary.com/index.php/pdf/articles/52.commonlymisspelledmisusedwords.pdf) and miss-used words see http://www.confusingwords.com/.