heywaitaminute

This just in: notice that my paper has been successfully submitted to the Journal of Biomedical Informatics.

Not that I wrote it. My colleague F wrote it; I'm just a co-author.

I'm a coauthor who has not been allowed to get too close to this manuscript, because F knows only too well that if he lets me see it, I will disagree with half of what it says, and even the other half still needs to say what it says differently. And if he gives me the manuscript for revision, it will be a long time in revision.

Yeah, I know. I'm slow getting his papers back to him. My official excuse is that this paper is item #63 on my priority list. Which is not a lie! But I admit: it's the writing. The text is disorganized. The language is approximative and vague, full of annoying circumlocutions and jargon. Little difference is made between key points and interesting but inconsequential details. If I say to streamline, he leaves in the details and cuts the essentials. Althogether, it's incomprehensible.

This particular paper was submitted a few months ago to a nice computing journal, without my having read it. Last week it came back with the commentary 

- incomprehensible algorithm

- poorly written text

- not adapted to their journal

It was never even sent for review, but rejected directly by the editor.

We agreed to address these concerns before submitting elsewhere, but F was adamant about not wasting a lot of time revising. Now it has been resubmitted, in record time, and I have still not seen it. So the quickness goal was achieved. But what is the value of that, if the new editor just sends it right to the dustbin?

And now back to your regularly scheduled tour of Italy...

what would you do?

So, say you're writing a book chapter, and you have a colleague with whom you sometimes write these chapters with, and you're not writing it in your native language. Say furthermore that your writing style tends toward literary flourishes and parentheses within whole parenthetical paragraphs, not really the clear and direct scientific ideal.
Your colleague is, however, a native speaker and something of a grammarnazi, and for a few chocolates you can count on her to put the text into shape. And to rein in your wilder speculations.
Do you:
A) plan out the chapter with her and keep her informed both of your progress and of the looming deadlines
or
B) don't bother the colleague with boring information, wait until the reminders start coming from the editor before starting, and then the day before it's "really" due, ask your colleague if she might have a few spare minutes to look over a couple of pages?
Hmm?
What would you pick?
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Trials and tribulations of a manuscript

First review:
Who cares? A piddling paper on a piddling family. The authors have this one unusual family, and from there are suggesting the whole world change the way people with mutations in this particular gene are treated. One family is an anecdote. Just because they escaped getting stomach cancer* doesn’t mean that the next family that comes around shouldn’t be recommended to have prophylactic gastrectomy. Get outta here!

Alright, that’s a pretty crude paraphrase, but you get the idea. Our paper was very forcefully struck down. While naturally depressed at the failure, I was secretly satisfied that the complaints were exactly the points I thought my coauthors insisted too heavily on. But such are the squabbles between coauthors. I have something of a reputation with my boss for setting my sights too low in submitting papers. I don’t set them too low: I really try to send a manuscript where it has a decent chance of getting in.

Admittedly, if you don’t shoot for the stars, you’ll never bag one. But I hate the multiple rounds of rejection this entails, plus the precious time lost at it. If my performance review says my goal is to publish 3 papers this year, should I really mess around with fanciful submissions that will never succeed? And I play a certain counterweight role against my boss, who is thinking Nature or Science every time we have the least result.
So we (I) revised, and added a second, smaller family with the same story that we’d found in the meantime, and submitted to a very good, though not quite so lofty journal.

Second review:
Nice paper, but not big enough news for us. Get a dozen such families and we'll consider it.

Finally the senior author was convinced that the top journals weren’t interested in our story. They have bigger fish to fry. So we resubmitted to a good, middle-level journal.

Third review:
Nice paper, very important for the medical community. Will be one of the milestone papers in the changing evaluation of the effects of mutations in this gene. A few minor modifications, and we’ll be happy to publish it.

Certainly, this wasn’t exactly the same manuscript as the first submission; we rewrote in view of the first batch of criticism. But it’s essentially the same message, based on the same family. And it's the level of journal I wanted to target in the first place. I'm just very pleased to get to the end of the story!

*this is usually fatal, and terribly hard to catch early. Prophylactic gastrectomy (removing the stomach from healthy people at risk) in young adults is the only reliable way to avoid it. But just imagine living the rest of your life with the dietary restrictions that involves!

Out of the Mines at last

Grammar Mines, part the last

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My coauthor on this chapter tells me his writing style is a holdover from a certain style of teaching, where the teacher provides the students with all the tools but never provides the final step linking things together. That step is for the students to make on their own. And when they make it on their own, they ‘get it’ much better than they would if it were spoon-fed.
It’s the ‘coitus interruptus’ style of teaching, where the professor will get right up to the concluding word, and pause, and the student is meant to fill the word in himself. It works for some people, but Man, I hated that kind of lecture in college! It's nice to know there's a reason for all the missing information, though.

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I’ve been going on excessively about the form and content of this book chapter I'm working on. Yes, I assure you, those of you who were becoming worried about my progressively deranged state of mind, that the form is being kicked into shape.
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But what of the substance??

Aye, that be tha heart of tha matter.
I’m no expert on the role and efficiency of hypnosis in cancer care. I didn’t look up more than a handful of the papers cited. (For shame!) But all the same, there are a certain number of conclusions that can be made.
First off, nobody ever found that hypnosis was harmful. I think everybody can agree on that.

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Whether it does any good should be cut into two parts, which I have taken care to separate:
Does it help slow down, or cure, cancer?
Does it make the patient feel better?

The first answer is, right now there’s no evidence that hypnosis makes anybody live longer. My colleague thinks that’s only because it hasn’t been studied enough. I think that if there were a real effect, big enough to pop out of the uncertainty of never knowing how long a given person ‘should’ live anyway, in all the studies that have been done, we’d have seen it. So there might be a small effect, but it’s not curing anyone. If there is an effect, it probably works by making you feel better, which in turn can boost your immune system just enough to get a handle on things. Plus the whole will-to-live thing.

For the second answer, YES! Yes, we can control nausea. We can alleviate pain. We can lessen anxiety. We can lessen fear.
We can do this using hypnosis with a therapist, with self-hypnosis, with guided imagery, with relaxation techniques, meditation, yoga... A dozen different routes are available. Some work better than others. Which works better for a particular person is up to that person.

So the thing is out the door, and I can get on with my regular life.

Which will now turn toward bitching and moaning about teaching. No - just kidding!
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Grammar Mines, page 23

I've been assured that it's good to rant. Within reason, of course. You can't just fill your life with ranting. But opening the steam-valve a bit when necessary does a world of good in getting the garbage and gunk out of your mind, leaving you fresh to work. So I'm feeling free. And I'm not promising to be any more coherent than the text I'm working on. But here I don't have to be!

Sometimes I think I'll never be done with this thing.

One of my problems is with the style of the manuscript. Style, you'd think, shouldn't be such a big deal. But it is.

When a scientist sets out to explain how something works, he describes how it works. References are added as support, but it isn't necessary to go into the gory details of what's in those references. If the reader wants to know more, he can go look it up. You just go ahead and make a statement, and at the end of the sentence you add [Smith, 2007; Jones et al., 2008b] to show where the data is that allows you to say what you're saying.

If as in my present case you're describing a field of knowledge, you can group together information from diverse sources into one whole. If they don't overlap perfectly, it's fine to say what's common, and what's unique to different studies.

What you don't do is use the references as the text. In 1998 Albertsen said... Then in 2002 Harris noted... Lastly Wickwood used the same technique but added a widget to get...

That's an annotated bibliography.

And it can actually impede the formation of a global idea of what's going on.

Putting the author and year up front makes that appear to be the prime information to be gleaned from each entry, when these things are in fact utterly dispensable to our understanding of the topic. Second, we're drowning in details about how each study was done, how many people involved, what exact disease, what exact measures. These details are not essential to the big picture. When a detail really is essential, okay. But you can't make everything top priority because then nothing is. Finally, the looked-for synthesis is never provided. We have a catalog.

Yes, the reader can ponder the gathered information and create a synthesis, but that's what the author should be doing. I'm not suggesting that reading a review should replace coming up with your own ideas, or that everything must be pre-digested, pre-thought. But we do in fact read reviews to have much of that groundwork done for us. So that we can continue on from there. Plus, as a chapter in a textbook, our readers usually have minimal prior experience with the subject. They're lost in the woods here, and describing yet another tree does little to advance their understanding the forest.

But maybe it's me who's getting lost in the woods. There's so much to mess with that I only just now identified my biggest style problem: there's not a single Topic Sentence in the whole 33 pages. Not a one.

I'm not such a Paragraph Structure Nazi that an odd paragraph now and then bothers me. You get them all the time in creative texts like blogs and novels and blatherings. There, not even sentences have to be complete, even words can get chopped or scrambled, and that's fine. But that's why I've had such a teeth-grinding time of trying to figure out what the point is. Aha. Mrs Kirby was right. Much as we hated having our metaphorical knuckles rapped with a ruler in high school English, there just might be something to it after all.

Topic Sentence. Who'd'a Strunk it?
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I can't believe I'm not even halfway through

arrrrrrr. still in the grammar mines. working my way slowly toward the midpoint.
I'm going to let off some steam here, just to stay sane.
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this is a textbook chapter where we have something to say, supported by the data in the medical literature.
But. Question of style. My colleague writes Smith et al did a study, gives a sentence about the study design, gives a sentence covering the major results. Goes to the next paper, same thing. Some sections are more of an annotated bibliography than a synthesis with something global to say. It takes some rearranging, but I can smooth that out. Conjugating verbs and choosing prepositions is the easy part.
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And then, what keeps me flipping over to facebook or Free Cell or Blogspot instead of staying the course, there's the bias. My friend is an enthousiast. He wants hypnosis to work. He thinks it does work; it just hasn't been studied well enough to prove it. Usually, he's a good enough author to keep most of his personal perspective out of it, and just tell us what's known, what worked, what didn't, where the grey zones are. But not always. And since I don't share his belief but am rather waiting to be convinced by the evidence, this drives me nuts.
to wit:
'Somehow, a recent study of Classen et al (2008) attempting to determine ..... ' found no effect.
Alright, using 'somehow', which conjures an image of shaking one's head and wondering how on earth they came up with this, it must surely be wrong, might just be a language thing.
A little further on, there's a study that found a small and not statistically significant decrease in measures of depression in patients undergoing therapy using hypnosis. It was a 5 to 8% difference, and only one study, but the next sentence waves that aside and hails the therapy as a 'strong alternative to conventional psychotherapy'. Let's slide a may be in there, and cut the strong.
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I will get through it, and we will meet in the middle and get a good, balanced, chapter out of it. But it's slow going, frustrating, and I'm very, very glad this is not my real job.
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Deep in the Grammar Mines

In fixing English, the hardest part is a text which is only slightly wrong.

Combine that with a significant and growing familiarity with certain kinds of mistakes, and the mistakes start looking not so wrong. Nobody will really misunderstand the sentence, but still, it's just not right. It's not the way a real anglophone would write.

OMG, does that mean I'm not a real anglophone any more?

A study on...

A study of...

It's like taking a wrong turn to go someplace, then the next time taking the same wrong turn, and on further trips the wrong way looks so familiar you keep taking it!

Then of course the content is not exactly my usual domain. It's all fuzzy, and slippery. (fuzzy and slippery at the same time?? that's permitted; that would be algae growing underwater.) It's appropriate in a way that a discussion of relaxation techniques would resort to massaging the data. In one place we're going to group together similar studies in order to get a more meaningful result: we've got two papers on hypnosis that set up a model, which is used by 'a whole set' of other studies, and we permit ourselves to add studies -plural- that use guided imagery. Add that up and it somes to a minimum of six papers, perhaps many more. Mmm. A minimum of five, since technically one is a set even if it would be strange here to mean it that way. But whatever. The actual total is four.

It's hard to build a field of study with just four bricks.

And they're kind of squishy bricks.

I do exaggerate. It's fun to exaggerate in blogland. Or is it nitpicking? Yes, nitpicking. Four is not an exaggeration; it's four.

Besides, the point is to show that there is in fact a crying dearth of data, that more work needs to be done. I guess. And from that angle, well, four is good for the cause.

Yes, I admit, another rant.

Being a co-author on a book chapter is not supposed to make one cringe.

Wellllll.......

A colleague has given me this chapter to correct the english before sending it in, and it's quite a job. I'm accustomed to all sorts of levels of mastery of the Bard's tongue, and I've seen far worse.

(I think the very worst was a case where a student wrote their paper in french with no idea of how to write a paper; she just tossed out a long disorganized mishmash of speculation, irrelevant details, hollow generalizations and unsupported conclusions, then used a cheapo computer program to translate. The computer picked words out of a dictionary based on their frequency of use, with no account of context. It couldn't tell a noun from a verb sometimes. The result was a treat, I assure you. I didn't wail and moan at the student - it's perfectly normal for a student's first manuscript to be utterly naive in the ways of writing science, but this had been passed to me by her boss, who apparently had not read it but considered it ready for submission.)

Grammar is grammar; you just fix it. Don't you? Let me think about that comma. Scientific texts are clear. Nuanced, yes, but english is a very precise language and we get where we're going. There's a reason English has far more words than other languages. With two or three or four duplicates, you can really split some hairs.

Normally, the content is not my business. The author wants to say what? No skin off my nose. I just try to make the saying of it correct and readable. This time I have to care about content. It would help to have some context, too. Is the whole book about hypnotism? cancer? alternative medicine in general? Who will be reading it?

This text is all about the role of hypnosis in cancer patient care and the application of 'hard science' statistical techniques and measured parameters with nice solid numbers attached to 'psychosocial interventions', and it's requiring a fair amount of belief in the truth of what's being said. Things that don't belong in a scientific paper usually litter the floor when I'm done with a text, and here I'm having such trouble swallowing the legitimacy of what's being said that it's difficult to resist and not write rebuttals every third line or turn the thing into a paper snowflake.

I'm trying. I'm sticking with it. It is, after all, something I'm definitely in favor of, this application of rigorous methods to a traditionally fuzzy subject. And I'm truly interested in the results, too. If you can help somebody live longer and more comfortably by teaching relaxation techniques, by all means! Hypnotism can get your sleep schedule back on track, thus boosting your immune system and making you less crabby to boot? Go for it! Just keep the snake-oil salespeople outside. Well, unless believing in snake oil is what floats your boat, er, boosts your endorphins.

So okay with the subject matter. I'm just going to wail and moan and tear my hair out over diction and syntax and that french way of dancing around the point so long the author just skips it and goes on (the point? it's that hole there in the middle of the paragraph...) for the next week or so. And while I'm at it, since I am an author and not just a correcter, I'll be putting my centimes in two by two and keeping us to the discernable facts.

It's a shame Strunk and White never caught on in France.

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