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I went on a little bit of a mini-rant a while ago (http://news.ycombinator.com/item?id=4680626), which, while not so eloquently worded, attempted to share my frustrations about scientific writing that this article makes much clearer.

I think it's easy for technical people to write something and think "well, this is clear to me", so they don't put much additional thought into thinking about how their writing will come across to others. Someone that writes journals or articles for a living realizes how important clear communication of ideas is, and it would be nice to see this carry over into more technical domains.

The original article suggests ways of writing that will aid reading, and they give reasons why the texts they quote are poorly expressed. The article is useful because of that.

Observation: In the child comments in the post you link to is a comment from xanmas. This user points out the space constraints on much academic publishing. I remember papers in experimental physics where the list of authors took up more space than the text of the paper - however some re-writing always helps.

It might be that my standards are too high - I'm accustomed to reading how-to-write books written by the likes of Orson Scott Card - but I'm a bit worried that the article itself isn't as well-written as it should be. Maybe you need unnecessarily pollysyllabic linguistics for scientists to pay attention to you at all, but it's still a bit worrisome when it comes to my deciding how much to trust the advice.
I regret to announce that I share your sentiments with regard to the circumloquacious fashion of the writing in that article.

I think we've made progress since it was written. Eye-tracking shows how we read and which words or letter combinations trip us up.

By the way, wouldn't that table naturally have time in the left hand column, considering it's probably an independent variable, while temperature is dependent?

As to your final point, the authors were trying to suss out why we want the independent variable first. Their answer: it provides the context to understand the significance of the dependent variable.
Maybe it could be better written, but their advice gels with how I try to approach technical writing. The most common problem I see are authors packing too many concepts or facts into a single sentence. The writing becomes difficult to read for a reason that I was aware of, but could not articulate until I read this piece: readers are searching for syntactic closure. The more stuff - no matter how important - you put inbetween the subject and verb, the harder it is to read. The way I think about it is that until the reader gets that syntactic closure, all new words go into a temporary buffer. If that buffer spills before reaching closure, the reader is lost.

I encounter this in CS papers I read and co-author frequently. My most common editing remark is "split into two sentences."

A reasonable article, however they do not use the term "subject" correctly. The subject of their example is not just "the smallest", but all of the following modifiers (adjectives and relative clauses). From "the smallest" to "subunit 6 gene" is all one noun phrase, albeit a complex one.

The appropriate advice is therefore to have short subject phrases.