ESWTOTD: “Comprise” vs. “constitute”

A whole comprises its parts:

  • “12 different enzymes comprise the system.” WRONG
  • “The system comprises 12 different enzymes.” RIGHT

while the parts constitute the whole:

  • “The system constitutes 12 different enzymes.” WRONG
  • “12 different enzymes constitute the system.” RIGHT

The word compose is often used in place of comprise, though like constitute, the parts compose the whole, not visa versa. But by using the “is composed of” construction, the roles of the subject and object are reversed:

  • “The system is composed of 12 different enzymes.” RIGHT

In my experience, this idiom is more common, especially in spoken English; probably due to the confusion about the proper use of comprise.

[Edit: due to broken CSS, wrong sentences were not properly marked wrong. Fixed.]

ESWTOTD: Learning homophones (albeit not for the easily offended)

Here’s a little levity for a Monday morning: the authors of “Learn Your Damn Homophones” are a little angry about the misuse of homophones (words that are pronounced identically but spelled differently). Okay, incredibly angry. But the advice they give is good, and it’s a good and funny read, provided you don’t mind abundant cuss words and barely controlled rage:

ESWTOTD: Abbreviations, acronyms and initialisms, oh my!

An abbreviation is any shortened form of a word or phrase: “HEPES,” “Ph.D.,” “etc.,” etc.

Initialisms comprise a subset of abbreviations where the first letter of each word (more or less) of a phrase are combined. Some examples include the “Food and Drug Administration” = “FDA,” “adenosine di-phosphate” = “ADP”, and “4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid” = “HEPES.”

In physical science manuscripts, nearly all initialisms should be written in all capital letters without spaces or periods. (There are some exceptions, such as “a.m.,” “r.m.s.d.,” etc.) This is certainly the case if you introduce new initialisms for brevity or clarity. When introducing an initialism, write it out first, followed by the abbrevation in parentheses: e.g. “structural genomics (SG).” Don’t underline or otherwise highlight the letters used in the initialism.* Don’t introduce new or uncommon initialisms unless you will be using the term several times.

Technically, not all initialisms are acronyms, even though in common spoken English the terms are largely used interchangeably. Acronyms comprise the subset of initialisms that are pronounced as a word rather than a spelled list of letters. For example, “AIDS” and “laser” are acronyms, while “ADP” and “NIH” are initialisms.

* Yes, I know I did that in the prior paragraph. Hey! What’s that over there! <runs away>

ESWTOTD: “Bioinformatics”

The field of bioinformatics, namely the use of computing to collect and analyze biological and biochemical information, is exploding in popularity. The word itself, however, is new. The noun “bioinformatics” was coined by researchers Paulien Hogeweg and Ben Hesper in 1978. According to the Merriam Webster dictionary, it is a special kind of collective noun that is plural but singular in construction. This means that it refers to a group of computational techniques, the group itself is treated as a singular subject:

  • “Bioinformatics are the study of…” WRONG
  • “Bioinformatics is the study of…” RIGHT

There is some debate as to how “bioinformatics” should be used as an adjective. In English, some nouns may be used to modify other nouns in the same way as an adjective:

  • “I studied biology in school.” (noun)
  • “I used a biology textbook in my classes.” (noun modifier)

However, many nouns also have adjective forms, which are preferred in most contexts. For example, the adjective form of “biology” is “biological":

  • “I did a biology analysis.” (noun modifier)
  • “I did a biological analysis.” (adjective)

While the former is grammatically correct, to my ear the latter sounds more natural and idiomatic. For the noun “bioinformatics,” the Merriam Webster dictionary identifies “bioinformatic” as the adjective form:

  • “I did a bioinformatics analysis.” (noun modifier)
  • “I did a bioinformatic analysis.” (adjective)

Like the previous example, while I can’t definitively say that the former (noun modifier) form is grammatically incorrect, I prefer the adjective form “bioinformatic” when an adjective is called for.

ESWTOTD: An article about articles

By far the most difficult issue for speakers of several languages—such as Polish or Japanese—is the use of indefinite articles like  “a” and “an,” or the definite article “the.” Those languages do not have articles, which is a problem, as they are the most common words in the English language.

Articles are a subset of the group of words that modify nouns called determiners. The use of determiners is sophisticated and complex, and there are many rules that describe when they should be used, which should be used, and what nuances of meaning they convey. I meant to write a whole series of tips about their proper use, but then I came across an excellent page that beat me to it:

The English Word “The”

ESWTOTD: Should there be a space between a number and its unit?

Should there be a space between a number and its unit? This is a matter of style, and when in doubt, you should follow the style of whatever publication or organization you are preparing for. Having said that, I think there is some consensus for the style given in the Chicago Manual of Style, which is used by many publications in the biological and other physical sciences. Namely, the Manual recommends that there should be a space between the numeral and the unit:

  • 250mM imidazole” WRONG
  • 250 mM imidazole” RIGHT

The only exception to this rule is the use of degree, minutes, and seconds for angles and longitude:

  • 12 ° 45 ´ 54 ´´ WRONG
  • 12°45´54´´ RIGHT

Note that other uses of the degree symbol do not fall under this exception. In particular, when specifying degrees Celsius, put the degree symbol next to the “C”, not the numeral:

  • “37° C” WRONG
  • “37 ° C” WRONG
  • “37 °C” RIGHT

See also here and here.

ESWTOTD: Where may adverbs go? OR the use and misuse of “also”

Adverbs are remarkably flexible words, and may be placed in several places in a sentence. Specifically, there are three general places they may go:

  • Rule #1: At the beginning of the sentence, before the subject
    • <adverb> <subject> <verb> <direct object>
  • Rule #2: Before the verb
    • <subject> <adverb> <verb> <direct object>
  • Rule #3: After the direct object
    • <subject> <verb> <direct object> <adverb>

Some examples, using the adverb also:

  • Also, I processed the data.”
  • “I also processed the data.”
  • “I processed the data also.”

(There is one extension to rule #2: if there is a modifier on the verb, the adverb goes between the modifier and the verb (underlined): “I have also processed the data.”)

These are all grammatically correct (though they do convey subtly different meanings). In contrast, there is one place where adverbs cannot go, and that is between the verb and the direct object:

  • “I have processed also the data.” WRONG

In general, adverbs are never after the verb, save only in cases of intransitive verbs:

  • “My computer exploded also.”

Here we are following rule #3, placing the adverb after the (nonexistent) direct object.

Today’s tip is dedicated to Maks, who was its inspiration.

ESWTOTD: “Lead” versus “led”

This one I see quite commonly: the present tense of the verb to lead is “lead”. The past tense is “led”:

  • “Our work lead to several results.” WRONG
  • “Our work led to several results.” RIGHT

Why is this so confusing? It is probably due to the similarity of “to lead” to the verb to read:  namely, both the present tenses and the past tenses of the two verbos rhyme when spoken aloud. However, while the present tense “read” and “lead” are spoken (with a long “ee” vowel) and spelled similarly, the past tense “read” and “led” sound alike (with a short “eh” vowel) but are spelled differently.

This, I am sad to say, is one of the many examples of the very complex relationship between the way English words are spelled and spoken. However, the good news is that this behavior, at least for verbs, is limited to irregular verbs like “read” and “lead.”

ESWTOTD: Where to put adverbs of frequency

Adverbs of frequency include words like “always,” “usually,” “sometimes,” “often,” “never,” etc. They are often misplaced with respect to the verbs that they modify. These adverbs come before the main verb:

  • “The enzyme cleaves usually the bond when…” WRONG
  • “The enzyme usually cleaves the bond when…” RIGHT

However, if the verb contains a derivative of to be, the adverb comes after the to be (and before the main verb):

  • “The sulfonyl usually is deprotonated…” WRONG
  • “The sulfonyl is usually deprotonated…” RIGHT

ESWTOTD: Restrain versus restraint

Restraints and constraints are often used in crystallography, but there is some confusion as to the verb and noun forms of these words. Namely, when using the terms as nouns, the “t” at the end of the word is necessary:

  • The restrains applied were…” WRONG
  • “The restraints applied were…” RIGHT

However, the verb forms of the terms do not have an ending “t”:

  • “The program does not constrain the data…”
  • “We restrained the collected reflections…”

In which contexts does one use constraint vs. restraint ? Some scientists maintain that the two terms differ in meaning: namely, that a constraint  fixes a term in a refinement process to an absolute value, while a restraint maintains a term around a correct value via some sort of energy or weighting function (as used for example by AMBER). However, if you’re not (say) the developer of a refinement program, the terms can be used more or less interchangeably.