The Use of Cause-and-Effect Language in the JAMA Network Journals

As a manuscript editor and freelance manuscript editing coordinator for the JAMA specialty journals, I am constantly having to edit out cause-and-effect language from observational studies that are not randomized clinical trials. According to the AMA Manual of Style, the word effect, as a verb, means to bring about a change; as a noun, it means result.

A randomized clinical trial is one of the few types of studies that are designed to assess the efficacy of a treatment or intervention (and thus allowed to use cause-and-effect language) because the participants are treated in controlled, standardized, and highly monitored settings.

Whenever I come across a study in which the authors are trying to determine, for example, whether the use of a certain type of drug will reduce the risk of some complication following a certain type of surgery, I need to verify whether the study is a randomized clinical trial or a report of a controlled laboratory experiment. If it isn’t, and is a report of an observational study (such as a cohort, cross-sectional, case-control, or case series study, or a meta-analysis), then all cause-and-effect language must be replaced. But by what?

Generally, association may be a useful replacement for effect. The AMA Manual of Style defines association as a “statistically significant relationship between 2 variables in which one does not necessarily cause the other. When 2 variables are measured simultaneously, association rather than causation generally is all that can be assessed.” So instead of saying the “effect of this on that,” rephrase as the “association of this with that” or the “association between this and that.”

Sometimes, however, the authors don’t agree and want me to change it back, in which case I calmly let the authors know that it is AMA style to allow cause-and-effect language only for randomized clinical trials and controlled laboratory experiments and that, perhaps in the “Discussion” section of their manuscript, they can try to make arguments to support that the association might be causal. However, to quote from one of our scientific editors, “the expression and ultimate interpretation of the findings can’t be causal.”

The use of cause-and-effect language is quite common in everyday speech, and so it is easy for most people to assume that if one event comes before another, then the first is the cause of the second. In the JAMA Network journals, findings that rely on this type of logic had to have been rigorously tested in a randomized clinical trial.—Paul Ruich

 

Everything Is Relative (Pronouns)

Unless you fell down a Google rabbit hole and ended up here unintentionally, you’re probably already aware just how much information is contained in the AMA Manual of Style. But to put it in perspective, the style guide’s current iteration contains 1010 pages, and that’s not counting the pages at the very beginning that are numbered with Roman numerals (because no one reads those anyway, right? [sorry Cheryl]). Still, despite the borderline-unmanageable amount of information in the AMA Manual of Style, the articles I edit on a day-to-day basis are usually very sound regarding obscure rules found 3 bullet points below a niche subsection of information explaining…you-name-it. I can generally count on authors to italicize gene names and keep corresponding proteins unitalicized or to capitalize virus terms that end in -virales, -viridae, or -virinae, etc.

But the cost of the attention to the more complicated nuances of AMA style seems to be that baseline grammatical rules get overlooked. I’m not saying that the articles that hit my desk are anarchically grammarless, but there are usually at least 1 or 2 hard-and-fast grammatical conventions that get ignored. And the rule that gets violated far and beyond all the others pertains to the usage of the relative pronouns “that” and “which.”

So here’s a quick refresher for everyone (myself included): A restrictive clause directly affects the intended meaning of the subject in the preceding clause, and restrictive clauses are introduced by “that.” Nonrestrictive clauses are not necessary to the intended meaning of the subject in the preceding clause, and nonrestrictive clauses are introduced by “which.”

Example of a restrictive clause: The band The National wrote a song that is my favorite song. Because “that is my favorite song” modifies the subject “song” to a degree essential for the intended meaning, a restrictive clause introduced with “that” is necessary (the subject “song” would not be the particular song in question—my favorite song—if the restrictive clause wasn’t present). The modified subject’s intended meaning hinges on the restrictive clause.

Example of a nonrestrictive clause: The band The National wrote a song called “The Geese of Beverly Road,” which is a perfect example of early-00’s indie-rock songwriting. Because “which is a perfect example…” simply describes the subject “song” and doesn’t change its intended meaning, all that’s required is a nonrestrictive clause introduced with “which.” The modified subject would still be the song in question (“The Geese of Beverly Road”) in this context without the information the nonrestrictive clause provides.

I know, I know, this seems to be a nitpicky issue that no one save the professional manuscript editor would get hung up on, but precision with language hinges on attention to grammatical detail, which is crucial when presenting scholarly research and information.—Sam Wilder

Everybody Tweet Now

Confession time: I have a bit of a Twitter problem. I follow over 1200 different accounts, and probably add another each day. I am not enough of a photographer, or even enough of a visually oriented person, for Instagram. Facebook increasingly annoys me with its endless ads and its “pivot to video.” (WHY.) Twitter is where I’m going to spend (or waste, depending on your point of view) most of my screwing-around-online time.

Sometimes I just let the Twitter timeline wash over me in one big stream, and enjoy the crazy, constantly updated mix of content. But because I follow a lot of accounts, I also make use of lists. I’ve got a list for “breaking news,” a list for Chicago-centric stuff, a “literary” list, with my favorite writers and magazines, and lists for hockey and football. (Go Hawks/Bears!)

(And of course: Make sure you follow the AMA Manual of Style! Follow @AMAManual! Or forever drift, rudderless, through a sea of regret!)

I also follow several novelty accounts, just for the laughs, like the one that tells you every Wednesday that it is Wednesday. With a Budgett’s frog.

Okay, that’s silly (albeit awesome). However, it occurred to me that a few of those novelty accounts are (vaguely) (very vaguely) editing-related. For instance, I follow That’s Not A Word (@nixicon), where a dedicated linguistics scholar laboriously retweets instances of people on Twitter claiming something is not a word.

 

(For an entertaining, conducted-over-Twitter argument about something not being a word, see the Language Log’s summary of the dust-up between linguist Ben Zimmer (@bgzimmer) and The Atlantic about whether “gift” can be a verb. (Spoiler: of course it can.)

And finally, just for the delicious irony: it’s always nice to see @whostheidiotnow pop up in my feed, an account that collects and retweets people who say “your [sic] an idiot” to other people on Twitter. Warning: there are a LOT of idiots out there. Apparently.—Brenda Gregoline, ELS

 

 

Have You Talked to Your Tables About the Dangers of Sex Bias?

The problem of bias is well documented in the biosciences. Even since the Health Revitalization Act of 1993, which laid out guidelines intended to ensure more equitable representation of women and minorities in federally funded scientific research, the problem persists. A 2010 study published in The Journal of Women’s Health found that, among 46 clinical studies enrolling both sexes, women comprised on average 37% of the participants, and among 69 studies, 87% did not conduct analyses by race or ethnicity, and 18% did not report differences in the racial makeup of the study sample at all. Examples of this sort abound and, setting aside the pernicious sociohistorical and nuanced biologic reasons for this phenomenon, the resulting reality is that medicine, as applied to women and minorities, is less evidence based because most research is extrapolated from a homogeneous population—white men.

But even as we attempt to resolve these problems—ensuring that guidelines are in place and that they are followed when conducting new research—there is another, more subtle way that these biases creep into the biomedical literature. Even if the study itself was conducted using a diverse population of participants, sometimes the reporting elides this fact.  As a manuscript editor I have encountered this problem more often than one would expect, and the culprit is usually the table.

In this table, as in many tables that I have encountered, “white” and “male” are the default. Women’s bodies and the bodies of racial and ethnic minorities are implied by the number of white male bodies present.

A good rule when presenting data in tables is to make sure that when you are reporting the sex of participants, if you choose to report only 1 sex, choose the sex that constitutes the majority of the sample. When reporting on racial and ethnic differences, be as specific as possible (even if these comprise a small percentage of participants). Who are the “others?”

The current edition of the AMA Manual of Style does not explicitly lay out these precautions, but in chapter 4, section 1, you will notice that every example shown for presenting data in tables follows these guidelines.

This is not merely a problem of “political correctness” or social equity—it is a question of accurate reporting and just plain good science.—Gabriel Dietz

 

 

 

 

Forest Plots: The Basics

When I was recently asked to give a presentation on forest plots at work, I was less than enthused. Figures are my least favorite part of a manuscript to edit because they usually require a lot of tedious work, and determining how to best visually present statistics makes my brain hurt. Forest plots in particular had become the subject of my nightmares leading up to the time of preparation of my presentation after a few experiences with editing unwieldy ones. However, thanks to being subjected to presenting on forest plots, I’ve gained some basic knowledge that I thought I would share.

There are a few types of forest plots, namely those presenting the results of meta-analyses and those presenting subgroup analyses. Here, I will focus on a forest plot for a meta-analysis. In a meta-analysis, a forest plot acts as a visual representation of the results of the individual studies and the overall result of the analysis. It also shows overall effect estimates and study heterogeneity (ie, variation in results in the individual studies). A forest plot for ratio data should include the following data:

  1. The sources included in the meta-analysis, with citations. If the source author or study name is listed more than once, query the author to ensure that the study samples are unique; overlapping samples would lead to inaccurate estimates. Also, remember to renumber the references if you have renumbered them in the body of the article.
  2. The number of events and total number of participants in each group of the study and in the combined studies.
  3. Risk ratio and 95% CI for each study and overall.
  4. Graphed relative risk and 95% CI, with top labels describing what data markers on either side of the null line mean. The squares represent the results of each study and are centered on the point estimate, with the horizontal line in the center representing the 95% CI. The diamond shows the overall meta-analysis estimate, with the center representing the pooled estimate and the horizontal tips indicating the confidence limits.
  5. Log scale for the x axis with a label indicating the measure.
  6. Percentage of weight given to the study. Weights are given when pooled results are presented. Studies with narrower confidence intervals are weighted more heavily.
  7. Heterogeneity and data on overall effect.

(Open image in a new tab to see more detail.)

The caption should indicate the test and model (fixed or random effects) used in the evaluation and may include an explanation of the meaning of the different marker sizes.

If you follow these basic rules, forest plots are a breeze. If you would like an example of a forest plot for a subgroup analysis, let us know in the Comments.—Sara M. Billings

 

 

 

“NEW YEARS RULIN’S”

As a long-time manuscript editor, it’s not often that I come across things that are full of grammatical errors, but don’t need a lick of editing and are perfect just as they are.

I’ve had Woody Guthrie’s NEW YEARS RULIN’S tacked up in my cube for a while now, and periodically take it down and examine it and marvel at it.

These RULIN’S  are as good as any life advice from any philosopher. What better advice could a person offer than, for instance, to Love Everybody, Learn People Better, Read Lots Good Books, Stay Glad, or Keep Hoping Machine Running—not to mention Dream Good and Change Socks? I love his little sketches and “Middle of Book” note.

I don’t know if Woody was laying on the rustic, ungrammatical charm in his RULIN’S, but I wouldn’t change a thing if asked to edit this advice for a good life.—Karen Boyd

Per Capitalization

Individual words do not usually trigger the same devotion as, say, favorite songs. Yet some people find the time to have a favorite word. A TV host conducts interviews famous for including the question, “What is your favorite word?” His guests know it’s coming, so they are prepared with a word or phrase chosen for either meaning or sound. I have wondered if the favorites are situational. Who can have just one favorite word?

The “sound” choices indicate an appreciation for the particulars of articulation. That is where my instinct points too. No one has asked me lately if I have a favorite word. Then again, I have not been interviewed on Inside the Actor’s Studio. However, there is one phrase I have had to think about so much that it has become a favorite.

“Per capita” occupies a plot of linguistic real estate in my head. Not only is “per capita” a trifecta of plosives (bilabial, lingua-alveolar, and lingua-velar) separating the vowels with a postalveolar “r” thrown in, the phrase also has a pleasing rhythm. It is fun to say and snaps with the summery crispness of the waffle cone holding your scoop of pralines and cream.

Best of all, it presents a hotbed of style issues just waiting for AMA Manual of Style application.

“Per capita” became the contested part of an axis label earlier this year. While not quite an axis of evil, the label was rather vexing. All roads lead to Rome, and all questions lead to the AMA Manual of Style. In Section 4.2.7, “Axis labels in figures are akin to column headings in table, so each word should be capitalized (except minor words such as prepositions of less than 4 letters).” As first presented on the axis label, “per” followed style for a minor word and was thus lowercase. One reviewer suggested initial cap “Per,” which met with the author’s enthusiastic approval. After all, “per capita” is not only a minor preposition with a major noun; it’s so much more! The manual refers to Merriam-Webster’s Collegiate Dictionary as an authority. “Per capita” receives its own dictionary entry, so AMA style considers it a single entity. I went along for the ride, on the right track to make an author happy.

A round later, another reviewer indicated that “per” is never initial cap in JAMA Network journals. I searched “per capita” on The JAMA Network site and the hits from 2010 to the present indicated roughly half with lowercase “per,” roughly half with uppercase “per,” and an outlier with initial cap and hyphen. It appeared that style was up for grabs. I reverted to lowercase, asked for the author’s understanding, and moved on.

Not long after, I mentioned the exchange to an AMA veteran. After a pause, he said, “Well, maybe per capita is considered a foreign phrase like in vitro.”

Wish I had thought of that.

I had lost sight of the origin: Latin for “by the head,” an obvious parallel to Latin for “in glass.” The pesky “per” had sidetracked me. In Section 10.2.1, “In compound terms from languages other than English, capitalize all parts of the expression.” Hence Per Capita. Of course Per Capita reappeared, the next  time in the title of a reference to a book. Now I will be ever alert to “per capita” wherever it may need to be in title case.

The takeaway is that “per capita” in an axis label illustrates several manual of style tenets: follow the latest edition of Merriam-Webster’s, consider word function (stand-alone “per” which is lowercase vs compound term “Per Capita”) in applying the “minor words” rule, and capitalize all parts of a compound term from another language. Not a bad litany of accomplishments for 4 syllables.

Back to favorite words. An article on that topic might not easily fit into one of the network journals, but I would like to see a figure that plots the number of favorite words for each capita in a study population. (The style guide does not rule on whether “capita” can be sold separately from “per” but “for each” seems a good stand-in.). When the day comes that a JAMA Psychiatry article presents a figure depicting Number of Favorite Words Per Capita in Adults Who Edit, I will know this journey has come full circle.—Timothy Gray

Readability

A common assumption about those of us who copy edit science papers is that we have a science background. Some of us do, but by no means all. After [mumble-number] years in the medical publishing field, I might feel like I “practically” went to medical school, but I did not. I could probably take out your gallbladder, though. Want to let me try?

Anyway, as long as you are a good reader, writer, thinker, and editor, and know your way around IMRAD, it is possible to edit a manuscript on a wholly unfamiliar topic. The authors are the content experts; the paper has (probably) been through peer review; and the copy editors have skills, coffee, and Google.

When a paper is excruciatingly hard to edit, it’s not usually because of the science but because of the writing. Some authors pile up jargon like hoarders collect cans of beans, as protection against the deadly apocalypse of someone being able to read their article without feeling squashed by the weight of all those words. Why settle for a teeny nothing word like “use” when “utilize” sounds so much more important? Why give us actual data when you can just talk about “trends” and “robustness”? Make sure you add a lot of “it has been shown that” and “the fact that.” And make sure you start every sentence in the Discussion section with “furthermore” or “moreover”!

Real talk from Nature: “You can always look up jargon, but with a poorly constructed sentence you’re on your own.” The best-case scenario between author and manuscript editor is a partnership—we don’t want to be on our own! We want to help explain complicated things in a simple way, and that often starts with authors picking the most direct words available.—Brenda Gregoline, ELS

Punctuation Gets Famous

 

It’s great to see that copy editors are finally being given the positive attention we deserve. There are now “copyediting stars” like Mary Norris of The New Yorker; John E. McIntyre of the Baltimore Sun; Lynne Truss, author of Eats, Shoots & Leaves; and author and podcast personality Mignon Fogarty, the “Grammar Girl,” who “sparked what you might call a worldwide, syntax-driven fiesta.”

I have to admit that I am surprised as well as pleased by this trend. A while back, when I was taking a break from editing to be a substitute teacher, I wondered if texting-style spelling, the overreliance on spellcheck, and the absence of diagramming sentences in school meant that attention to proper spelling and grammar would become a lost art in the everyday world. Would people outside of scholarly publishing give a darn about, say, the serial comma?

It turns out they do. Witness the case of the Oakhurst Dairy in Maine. The Maine Legislative Drafting Manual does not approve of the serial comma; therefore, there is none in the state law regulating overtime: “The canning, processing, preserving, freezing, drying, marketing, storing, packing for shipment or distribution of: (1) Agricultural produce; (2) Meat and fish products; and (3) Perishable foods.” The ambiguity created by the lack of a comma after “shipment” resulted in Maine truck drivers winning a lawsuit that could cost Oakhurst Dairy $10 million. Some folks may find the serial comma superfluous—but I say that a little symbol that could save a company $10 million is nothing to sneeze at. That fact that so many articles were written about this case show that there is an interest in such topics.—Karen Boyd

Ding Dong: the Death Dagger Is Dead

AMA Manual of Style, section 2.3.2, has an ominous subheading: “Death.” I’ve quoted it below:

Death. If an author of an article has died before the article goes to press or is posted online, a death dagger (†) should follow the author’s name in the byline, and one of the following footnotes should be inserted after the author affiliation footnote.

†Died November 17, 2005.

†Deceased.

Okay. That’s super-goth and all, but…why? Is that useful information for a reader? Does it serve any purpose other than a moment of recognition that life is fleeting, memento mori, etc?

Also, the life of a scholarly article is long—why single out the author who died during a relatively narrow window (from acceptance to publication)? We’re all going to die someday, including every byline author. (Sorry if you came to AMA Style Insider for happy feelings. Here is a picture of a puppy.)

At a recent stylebook committee meeting, we decided to kill the death dagger. (Get it?) If authors want to note that a coauthor is deceased, a note can be put into the acknowledgment section instead.

Interestingly, the dagger symbol is sometimes called an obelus. A variant on this symbol was probably used by Homeric scholar Zenodotus to critically mark lines in manuscripts that were of dubious attribution. The Oxford English Dictionary uses it to note that a word is obsolete. It seems a bit cruel to use the same typographical mark to denote a person as dead and to mark a word as obsolete—-but I suppose I can see the connection.—Brenda Gregoline, ELS