It's a small and seemingly innocent word, but “with” is increasingly used in some rather annoyingly unnecessary ways. Here's a typical example that I've generated to make the point:
“These animals possess heterozygous sex chromosomes, with recombination at sites close to the pseudoautosomal boundary suppressed.”
This is quite an unfortunate construction, because it leads to a hiatus in reading: a reader thinks that the sex chromosomes manifest recombination until reading the “suppressed” at the end of the sentence.
Worse still is the following example, which I have created with inspiration from a real sentence from a completely different field:
“Such populations form cooperative structures with the aggressive individuals living at their periphery.”
Now the missing comma before “with” compounds the problem of meaning: do the animals use the aggressive individuals living at their periphery to form a cooperative population structure, e.g. they might be advantageous in defending the rest of the population? Or is the peripheral location of aggressive individuals a result of the cooperative population structure?
The solution to both of these problems is not to use the word “with”. It has no place in such constructions, and because it is unwelcome, insisting on its use can create ambiguity – QED. Even if it doesn't create an additional possible meaning, it's simply unnecessary. Here are the two sentences corrected:
“These animals possess heterozygous sex chromosomes in which recombination at sites close to the pseudoautosomal boundary is suppressed.”
“Such populations form cooperative structures, the aggressive individuals living at their periphery.”
The offending “with” often results from an effort to create some kind of connexion between two parts of a sentence. But as in the example above, placement of a comma and use of the gerund of the verb – i.e. “- ing” – is quite enough. Similarly, simply omitting “with” and using, or keeping, “being” later in the sentence, makes for smoother reading, e.g.:
Before: “Purines are heterocyclic aromatic compounds, with adenine being a well-known example.”
After: “Purines are heterocyclic aromatic compounds, adenine being a well-known example.”
And if all else fails, there's nothing wrong with simply starting a new sentence, or separating clauses with a semicolon:
“Purines are heterocyclic aromatic compounds; adenine is a well-known example.”
My next unwelcome guests are the words “begs the question”, which I have rarely seen used correctly, though they have a useful logical, and hence scientific, meaning. I most often see them as an overdressed guest at the wrong occasion: rather like a conductor in bow tie and tails – baton in hand – turning up to run the DJ's mixing desk at a rave night. Clearly no place for such an august classical personage: Latin, but originally from Greek, to be precise, given variously as “petitio principia” or “circulus in probando”. However, the context of use is almost always wrong, because these Latin phrases don't mean “[this] raises the question” – the usual intention of the writer – but “assuming the very point (or truth) that one is seeking to prove”, i.e. asserting a case of circular reasoning.
And the more I read them, the more I wonder at the widespread use of the words “crucial” and “critical”. These too have, at least in science, a meaning that is defined by a logical concept: that of necessity. It's probably no coincidence that “begs the question” and “crucial” are favourites for misuse, because they have a rather attractive “ring”. After all, “raises the question” and “important” don't carry nearly as much heart-wrenching power. But weren't we taught to write science using dispassionate, unambiguous language and consistent logical devices?…