A geat perspective on editing and on bad science writing

Take Out the Trash
by PW, July '06

A spectacular example of bad writing is in a recent issue of Science. Here's the first paragraph (don't read too closely: you'll get a headache):

Although many results from in vitro and in vivo models that express mutant Huntingtin, a-synuclein, tau, superoxide dismutase-1, amyloid-b peptide, or prion proteins are consistent with the proposal that non-native species can form toxic folding intermediates, oligomers, and aggregates, distinct mechanisms for toxicity have been proposed for each. These mechanisms range from specific protein-protein interactions to disruption of various cellular processes, including transcription, protein folding, protein clearance, energy metabolism, activation of apoptotic pathways, and others. This has led us to consider how the expression of a single aggregation-prone protein could have such pleiotropic effects and whether a more general mechanism could explain the many common features of protein conformation diseases. Moreover, because each cell and tissue contains various metastable polymorphic proteins, could the chronic expression of an aggregation-prone protein have global consequences on homeostasis and thus affect folding or stability of proteins that harbor folding defects?
(T. Gidalevitz et al., Progressive Disruption of Cellular Protein Folding in Models of Polyglutamine Diseases, Science, 10 Mar 2006, p. 1474 ff.)

The report describes experiments showing that the presence of one misfolded protein in a cell may provoke misfolding in others. The experiments are ingenious and have implications for diseases like Huntington's and Mad Cow disease. But the paper's impenetrable language not only neutralizes its impact, but even arouses the suspicion that the low quality of its prose might reflect that of the research itself.

The writer gets off on the wrong foot from the first word. The conjunction "Although" is separated from the two statements it connects (non-native proteins promote toxic folding intermediates; there are distinct toxic mechanisms) that do not appear until much later in the long, turgid sentence. The order of the statements themselves is inverted for no good reason. "Although" also implies a dependency or reciprocal relationship between the statements (e.g., "although I am a sinner, I do not despair") that does not actually exist in this instance. Here the two statements are parallel, not reciprocal. "Although" turns the sentence into a non-sequitur.

Other problems: the two complicated noun clauses crowd in so much detail that meaning is hidden rather than revealed; they would be better off in their own sentences. "Mechanism" occurs three times in a row, each with a somewhat different meaning (specific cause; general causes; systematic explanation). "Distinct" is another wrong word. It emphasizes the separateness of the toxic pathways. But in biology overlap between pathways is always possible, if not likely. "Different" would be better word: it allows some blurring. The imprecision gets worse with the appearance of the passive voice in the second half of the sentence, heightening the impression of the writer's confusion. The final offense is the dangling pronoun "each" at the end of the sentence, which is so far away from its antecedent that it's not easy to know if it refers to "species" or "intermediates ...".  This is just the first sentence, but the abuse continues as the reader is obliged to slog on through the paragraph, parsing it in order to get at its meaning.

Here's how this dreadful paragraph might have been written:

Proteins that form toxic folding intermediates, oligomers and aggregates cause different kinds of cellular damage. The proteins include mutant Huntingtin, a-synuclein, tau, superoxide dismutase-1, amyloid-b peptide, and prions. The damage may be to specific protein-protein interactions or to general processes including transcription, protein folding and clearance, metabolism and apoptosis. Why do proteins with toxic folding defects give rise to so many different kinds of damage? Do they exert a global effect by destabilizing other proteins in the cells and tissues they reside in? A general mechanism would go a long way toward explaining the etiology of misfolding diseases.

Writing clear expository prose is not so difficult, but it does take time and patience. Lots of iterations may be needed to get a passage right. You look at the topic from several angles, like a judge considering a case. If you get fatigued you have to take time off from the task, then come back and resume work when you're refreshed. A few simple principles guide the process: whenever possible get rid of jargon, replace big words with small ones, use simple sentences unless the idea contains component statements so closely connected that a compound sentence is positively justified. Rewrite repeatedly. Keep asking yourself, what am I really trying to say? What's the point of the passage? Not infrequently some internal contradiction will reveal itself during the interrogation, demanding further rewriting and reorganization. Gauge progress by counting the words. As long as there's no loss of meaning, fewer words are better.

Watson and Crick knew these principles:

We wish to suggest a structure for the salt of deoxyribose nucleic acid (D.N.A.). This structure has novel features which are of considerable biological interest ... This structure has two helical chains each coiled round the same axis (see diagram). We have made the usual chemical assumptions, namely, that each chain consists of phosphate diester groups joining beta-D-deoxyribofuranose residues with 3',5' linkages. The two chains (but not their bases) are related by a dyad perpendicular to the fibre axis. Both chains follow right-handed helices, but owing to the dyad the sequences of the atoms in the two chains run in opposite directions. ...
(JD Watson, FHC Crick, A structure for deoxyribose nucleic acid, Nature, Apr 25, 1953 p 737)

Even omitting the diagram their meaning is clear. Sentence structure is clean and uncomplicated, and when the uncommon usage "dyad" is encountered it's obvious from context that what's referred to is a hydrogen bond. The compound sentence is used judiciously to unite two closely related ideas (there are two right-handed helices; they run in opposite directions). A single reading of the paper suffices, and one emerges at the end with a feeling of uplifted understanding.

In this lovely passage by Darwin a positive, sympathetic connection is easily established between author and reader:

... I watched a group of plants on two or three occasions for an hour; each day I saw numerous specimens of two small Hymenopterous insects, namely, a Hæmiteles and a Cryptus, flying about the plants and licking up the nectar; most of the flowers, which were visited over and over again, had already had their pollinia removed, but at last I saw both these insect-species crawl into younger flowers, and suddenly retreat with a pair of bright yellow pollinia sticking to their foreheads; I caught them, and found the point of attachment was to the inner edge of the eye; on the other eye of one specimen there was a ball of the hardened viscid matter, showing that it had previously removed another pair of pollinia, and had subsequently in all probability left them on the stigma of one of the flowers.

As I caught these insects, I did not witness the act of fertilisation; but C. K. Sprengel actually saw a Hymenopterous insect leave its pollen-mass on the stigma. My son watched another bed of this Orchid at some miles' distance, and brought me home the same Hymenopterous insects with attached pollinia, and he saw Diptera also visiting the flowers. He was struck with the number of spider-webs spread over these plants, as if the spiders were aware how attractive the Listera was to insects, and how necessary they were to its fertilisation.
(Charles Darwin, "On the Various Contrivances by which British and Foreign Orchids are Fertilised by Insects, and on the Good Effects of Intercrossing," 1862, p 146-7)

Why does the author of the Science paper fail so dismally at communicating his findings? And why have the editors of one of the world's premier scientific journals tolerated the appearance of such graceless and confusing prose in their pages? Fatigue, disorganization, deadline pressure – perhaps even the narrow education of the writer – may explain, but do not excuse, what has been done.

Professional science today is a production industry. Labs are factories and the research productivity on which funding and careers depend is measured by papers. Up to a point, the research can be speeded up with reagent kits, software, high throughput machinery, and by laying on more low-cost grad student labor. In communicating the results, even certain elements of the writing may yield to engineering efficiencies: the References can be automated with End Note software, and perfunctory treatment may be adequate for the Materials & Methods, and perhaps in some cases even the Results.

But the heart of the job – the Introduction, Discussion and Abstract – remains a solo, green eyeshade, midnight oil kind of business, a process not much different from the one that Linnaeus, Darwin or Haeckel sat down to do, demanding of time, patience and a respectful consideration for the reader who will later share the work. Communication of results is crucial to the scientific enterprise, but poorly written prose is likely to be misunderstood or ignored, and to prejudice the reader with feelings of alienation and mistrust. Writers and editors of scientific prose should insist on a level of clarity, grace and economy that is all too often not attained in the scientific literature today.

A piece of writing is an invitation to the reader. Gidalevitz's invitation is like one to an unruly house where you arrive to find the light in the entryway burned out, a bicycle negligently left on the threshold, the front hall dark, narrow and unwelcoming.  As you make your way through the disorder, you say, I wish they had cleaned this place up. They should have taken out the trash.

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