Matthew D. Zimmerman, Ph.D.

By now you’ve probably heard of Terry Jones, the preacher in Florida who put the Koran on trial, found it guilty, and “executed” it by burning a copy of the book. Subsequently, riots broke out in Afghanistan in which 16 people have been killed, including 7 U.N. employees. Now Americans, including Sen. Lindsey Graham, are starting to suggest that perhaps Mr. Jones should be prosecuted for his actions.

First things first: the preacher is an idiot. To protest the actions of radical, fundamentalist Muslims, he did something considered to be blasphemous to all Muslims. That’s like protesting the KKK by burning Bibles. He and his congregation are world-class twits for having done what they did.

But how can anybody be considering taking legal action against him? Seriously? How does this not fall squarely into the First Amendment? Freedom of speech extends to people who say things that we–perhaps vehemently–disagree with. Frankly that’s the very point of it.

Some have compared it to shouting “Fire!” in a crowded movie theater. I don’t see the comparison. The panic induced in a theater would result in harm even though the people involved would act (more or less) rationally: trying to get away from the perceived fire. In this case, 16 innocent people were killed because somebody burned a book thousands of miles away. I don’t care how blasphemous it is; that is not rational. To somehow suggest that Mr. Jones should be prosecuted because of what he said, no matter how stupid, is completely contrary to the principles this nation was founded on.

I have never been more enraged by punditry than all of the criticism that has been leveled at the President about our intervention in Libya. It feels like pundits have produced  thousands of column inches and countless hours of television and radio coverage has been devoted to criticizing the President’s plan (in many cases by the  people who pressured the White House to set up a no fly zone  in the first place!). And yet none of the criticisms I have read or watched have provided a single practical, workable alternative.

Guess what? Every possible plan can be criticized one way or another. We do nothing– an abdication of our moral responsibility to prevent the slaughter of innocent civilians. We do a full-scale invasion to depose Gaddafi– a slap in the face to our overtaxed armed forces already fighting two foreign wars. We wait for UN approval– we’re subservient to the whims of the United Nations. We act unilaterally– we’re an out-of-control superpower wanting to impose our colonial ambitions on the world.

So rather than having the courage to advocate and defend an unpleasant plan of action, the pundit-verse is cowardly sniping at the adminstration’s plan. So to all the pundits out there– do us a favor, would you? Tell us YOUR plan, or else shut the &@#$ up!!

One thing has been bothering me about the debate over the new health care bill is that every discussion between lawmakers I’ve heard in the media goes something like this:

Opponent: “Forcing people to buy health insurance is unprecedented and violates the commerce clause of the Constitution.”

Supporter: “It will cover 30 million new people and make health care cheaper and all of my constituents want it.”

Am I missing something? I am really hopeful that the healthcare bill they’ve will result in better and cheaper access to health care, but shouldn’t somebody, y’know, make some sort of cogent argument that it is constitutional? And then tell me what it is?

Here’s the thing: 18 state attorneys general are filing a federal lawsuit challenging the bill. Somebody please tell me the defense in the case has a better argument than “Hooray Obamacare.”

A whole comprises its parts:

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

while the parts constitute the whole:

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

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.”

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

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:

http://www.learnyourdamnhomophones.com/

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>

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.

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”

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.

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.