Did your student write the paper, or did you?

Hmmm. Not sure I’m happy with that title, my students probably could have done better.

I was talking with a colleague about paper writing the other day. In comparing mental notes, we had completely different experiences of how our papers got written as graduate students. I wrote mine. Well, that is a lie.  I wrote the complete first draft. That first draft came back to me absolutely bathed in red pen. Yeah- that’s right PEN. These were the days before you could just hit ‘accept all’ on the track changes function and have a nicely edited draft with the touch of a few buttons. I alternately hated (not really, only figuratively of course), and loved, and hated (only figuratively), and loved my mentor as rounds of drafts were turned in and handed back sometimes with words edited back to read exactly as they had been written in some earlier version. In the end I admired my mentor’s technique with this whole thing- because he/she made paper writing a very valuable learning experience for me, the trainee.

I try to torture teach my students this way now, and I see both the strengths and weaknesses of this approach. The biggest strength I have already mentioned- the learning experience of becoming a better writer and learning the thought process of putting a data, a paper, a story really- together. To build a case, make an argument on paper. The weakness- of this approach is that it can take what feels like forever and a day- as green students cobble together their idea of what constitutes something publishable (with anxious advisers prodding them along). The difficulty, the time and the effort involved for the adviser depends on the language, writing ability, and background knowledge of the student. When English is the second language- having the student write the first draft can mean that the mentor re-writes practically every.single.word. Re-writing at this scale can be incredibly labor intensive for the mentor.

My colleague, on the other hand, never had the experience of putting a paper together and doing the crazy amounts of editing during their graduate training. Oh they may have lightly edited some draft- but the bulk of the text was written at the outset by the mentor themselves. I’m sure that this approach ultimately brings the paper to submission status faster, and students may still learn what pieces of data are needed to put a paper together- but I bet a lot of the learning of scientific writing is lost when papers are written this way. There are clear benefits to the mentor, the student, the lab and the project in being able to publish quickly. What happens though- when the student has to put together a thesis? What happens when they move on to their postdoc and haven’t yet written a whole manuscript from start to finish?

And finally- I wonder how career stage of the PI plays into this… are more seasoned PIs more secure ($s, papers) and not as needy of quick pubs… thus able to let newbie paper writers flounder a little? Does the necessity of as many pubs as quickly as possible that early career stage PIs make them more prone to do the paper writing for their trainees? Or are these factors irrelevant… are we bound to repeat what our mentors trained us to do- do it like they did it. That seems to be how I do it… then again – I think I had a stellar mentor in this respect.

General thoughts on writing useful reviews

I wrote a lot of grants in my first 3 years as faculty. A LOT. Nearly 30. And so I’ve read a few reviews, and a few summaries of review panel discussions that took place over my grants. I take reviewing grants incredibly seriously because I know that more often than not, someone’s career is on the line. If I agreed to do the review then the applicant absolutely deserves the most careful review that I can possibly deliver. These reviews can be very instructive if correctly written.  They can also be totally useless if not carefully done. I have gotten a totally useless review or two, and that meant waiting out a year to re-submit a proposal and not knowing what to change on it in the resubmission.

From the perspective of the reviewee, the most important thing to remember when you are writing a grant review is to let the applicants know the specific strengths and weaknesses of their proposal (I feel like the new NIH format is well set up for this BTW, but it still depends what you put into it). Feedback like ‘aim 2 is weak’ is not particularly helpful. If you are going to make a general statement about a weak section in the proposal, buttress that with the specific points about WHAT exactly in those experiments is weak. Are the experiments unjustified? Is the technique inappropriate? Have the applicants not considered the range of experimental results that they might get and proposed alternatives for each case? No preliminary data? This takes considerable thought on the part of the reviewer to put such reviews together, but this is someone’s career you have in your hands. Wouldn’t you want the same kind of thoughtful consideration?

Feel free to comment on the positives (if there are any). I think sometimes we get in this mode that we have to be ‘critical’ when we are reviewing something. But being critical doesn’t mean being negative, and it sure doesn’t mean never pointing out a positive.  And shoot- while C PP would say that science isn’t a care bears tea party- some positive reinforcement where applicable goes a long way to keeping morale up in what right now, quite frankly, is a pretty shitty dismal funding atmosphere.

Once you have a huge laundry list(s) of strengths and weaknesses- find a way to prioritize so you can give the applicants a feel for which weaknesses (or strengths) were key in determining the score that they got, and/or what the deal-breakers were. If you feel that the proposal has a major flaw, feel free to say ‘this is a major flaw’.  I always appreciated (HA! After a couple of nights drinking maybe) it when reviewers let me know exactly what needed fixing, when something was unfixable, and when I shouldn’t bother sending something back.

And one final note. Us applicants appreciate it when reviewers use professional (and positive when possible) language and stick to the facts.  Snarky or inflammatory language is pointless in a review. Data or lack thereof is not ‘disturbing’- moral failings are ‘disturbing’.  Saying that a certain element ‘would be nice’ is unhelpful. More important to outline WHY a certain element would strengthen the proposal. Saying the PI… who may be  junior faculty … is young and naïve doesn’t accomplish anything except making that person feel small. This kind of stuff in a review is unnecessary.

(And actually, although I wrote this about grant reviews- all of this applies to manuscript reviews as well)

Cranky Reviewers

It is always that third reviewer (well, actually in my case it was the second reviewer). That one that can just kill ya.

You know the one I mean. The one that said that you did the assay ALL wrong, the assay you’ve been doing for 20 years and can produce at least 15 references from top labs in your field that support the method that you used as perfectly correct. Uh huh. Or the one that uses clearly condescending language- like… THANK GOD they decided to do XYZ  (implies… at least one of the authors over there knows what they are doing!). Or how about the … you didn’t cite my work… disguised as ‘the authors should correct an egregious omission of the work referencing bla bla bla by famous scientist X. These references  should be cited on in the relevant section’. Ok sometimes that one is for real. Or better yet- you didn’t cite the biology I work on, even though it is only peripheral to the biology that you put in this paper. Or how about the reviewer that seems to have trouble integrating panel A with the controls in panel B, and keeps claiming that your image is an artifact of your technique, even though your experimental sample and your control sample use the same technique and the results have been quantified and are clearly statistically significantly different. Finally… there is the reviewer that complains endlessly about the poor grammar and spelling … in a review that is filled with spelling and grammatical errors. (and just so you know, I may have made any or all of these points at one time or another…. although I hope that I did not).

Name your favorite cranky reviewer stock review points.

Red pen, or track changes?

Because it is, you know, Sunday morning, and I have a nice cup of tea in front of me, and the kids are playing quietly in the back of the house, and DrMrA is watching soccer, I think I’ll blog. The New York Times sitting next to me can wait.

I know I’ve not been writing a lot here- and this is because I’ve been writing my little fingers off for my real job in the last month or so. Some of the text has been student written drafts edited by me, some has been my drafts edited by others, some has been all mine. All of this has led me to think a little about the process of editing, and about juggling a manuscript back and forth between multiple individuals.

When I was in graduate school, my thesis adviser edited everything on the printed page, and it was good (for those of you youngsters remember that the internet was hardly invented at that time). You were expected to write the first draft of your manuscript, then would get whole deal returned to you bathed in red pen. I am sure that it took him/her hours to do this- because the level of detail that he considered a manuscript in was truly exquisite. You would spend hours trying to interpret the chicken scratch handwriting in the margins and over the printed text. Now and then you would have to ask for a translation of what he had written in there because his/her handwriting was so unintelligible (not to insult the handwriting- but who knows if he/she was juggling a kid in one arm while writing with the other). In the end though, you really had to read the text extremely carefully to figure out what he/she wanted in the text, and then you had to type it in.  For me, this was an important part of the process of learning to write.

The ‘track changes’ function was totally foreign to me in grad school, for all I know it didn’t exist then, so I can only assume that it became popular while I was out of the lab. For those of you that don’t know- track changes is a function in Word where you can edit a document and your edits appear a different color in the electronic document, then the person that you hand the manuscript off to can go through each change one by one and accept or reject them in the electronic document, or you can just accept or reject all the changes in one step.

Fast forward to my postdoc. Postdoc adviser did everything with track changes, and nothing on the printed page. I confess it took me a while to get used to looking at manuscripts like this, being wedded to looking at the print copy and all, but I can’t deny the efficiency of being able to pass things back and forth electronically.

Now I’m fairly reliant on being able to write and edit like this, but I’m not a total convert. I frequently write with colleagues located in different physical locations than me, and for that it is critical to be able to pass text back and forth quickly- so electronic editing methods are a must. However, I still like to read the last versions of a manuscript on the printed copy and write notes in the margin. Why? I don’t know- I purposely go somewhere quiet and without a computer when I do this, so suppose it allows me to block out every other distraction, especially those on my computer. But I wonder, which is a better way for students to learn the process of writing, the red pen or track changes? By using track changes on manuscripts that my students write, am I doing what is easiest or most convenient for me- and not what is necessarily best for them to learn the process of writing? Do they really have to read as carefully as they would if I put it all down in pen- are they just selecting ‘accept all’ and not processing what I wrote to any significant extent?

Or does it depend on the student?

Research program first, teaching second?

Ok, well I’m back. Not that I was holidaying it up or anything. I feel like I’ve spent the whole of December lying on my back in bed. First that little GI thing I got from my daughter and then the nasty sinus head cold that I’ve had for the last 5 days. Imagine cooking Christmas dinner for a houseful of guests, and walking 3 households worth of dogs like that. I’m better today, thanks.

Now I’m starting to think about January and February, and all of the competing responsibilities I have for the next few months.  See, I think I’ve taken on a lot….rather, I KNOW I’ve taken on a lot. Writing and teaching are going to be especially heavy in the next couple of months, and I’m always asking myself how much I can logically take on in any given time period, and of those tasks- where my efforts need to be focused most and what can get less attention, at least in the short term. There is triage going on in my head, and the triage is based first on what needs to be done to get grants goals accomplished and get grants renewed, and second on everything else.

Anyway, as far as getting grant goals going and grants renewed. I know that in order to get these things to happen I have to get the new people that I have hired up to speed and working, and I have to push out papers. I have 3 papers that I want to turn out relatively quickly, for one I have a nearly complete manuscript, for a second I have to motivate my postdoc to give me some text, and for the third I need to put my head together with my collaborators and we have to turn out a manuscript quickly or we are going to get scooped on the story. I’m DELIGHTED to have all this writing to do, writing about actual data, that is. It is this, and getting the lab moving now that I have filled up the group, that I really want to be doing. The fact that I want to be doing the writing makes it easy to have this as my top priority.

There are also lots of tasks that are less fun, or let’s say that I get less personal satisfaction from, that also need to be done.  I’m teaching here and there in various courses in the spring, and for two of these courses it will be the first time I am delivering the material. For one of the courses, taught out of my home department, I am taking over some established course material and I am charged with updating the content. I don’t find this fun (I’m not sure anyone does), but I know it needs to be done. For the second course there was a bit of a crisis and I decided to be a good citizen and help out. Now, I know what you are all saying… (you… VOLUNTEERED?…WTF)… but I think these things need to be done from time to time, and this teaching is in a department where I have a joint appointment- so it is a bit of calculated pay-it-forward.

This all seems pretty straightforward when you look at it from the research intensive faculty perspective. Individual research program first, teaching second. Right? But the problem with this is that this is not how the institution seems these responsibilities- or it is, at least, not how they talk about them. I hear about a bazillion hours of stuff in meetings on curricular redesign, how and where lecture hours are to be delivered, and the needs of the professional/undergraduate students, and absolutely zero on developing a strong research program and managing and running a productive group. I spend countless hours fighting for small amounts of resources, mainly facilities type resources, that are necessary for me to get research done- it just doesn’t seem to be a priority of the institution. Sometimes it feels like their triage is the exact opposite of my triage… theirs is teaching first research second… and mine is research first… teaching second.

For lack of a better topic…. (UPDATED)

I’M ALIVE!! Ok, I don’t really have any deep post topic today. I’m feeling constrained by that medium right now- so I’m just going to riff and we will see where that goes. Feel free to stop paying attention at any time.

I can’t believe it is 7 pm and I am only just now getting started with the things I want to do today. I told DrMrA just last night if I could get this blasted book chapter and a second piece of writing that I’m working on off my plate this week, I’d be a happy camper over the holiday. I could relax and polish up a manuscript- and maybe even submit it between the holiday and the new year…. We carefully went through the weeks negotiation about who would be home early on which nights this week, and who was taking care of what responsibilities with which kids… and when. The handoffs with the babysitter were carefully choreographed. Yeah, well, THAT was last night.

This morning the shit hit the proverbial fan. What’s that they say about the best laid plans?? Ours were bloody beautiful. But a couple of unexpected crises at my job are going to suck some of the little time that there is out of Monday, Tuesday, and probably Wednesday. Leaving Thursday (not my night to work late), and Friday (which, as it happens is an important family birthday for which we have dinner reservations, and the day I pick littleA up from school at 3 pm)…. for writing.

#$!!@

Ok, I’m calm. I can do this, NO SWEAT.

BUT- I’m not doing another book chapter until …say….2015. Don’t EVEN ask me. (I’m still learning about how to set boundaries)

I expect you all to remind me I said that when I pop out some chirpy sentence in the middle of a blog post somewhere about how delighted I was to be asked to do another.freaking.book.chapter.

Yikes. 7:22 now, better get cracking!

**UPDATE** And it just keeps getting better every time I turn around. Last night when called home at 9:22 pm- the kids were still up. The three of them (the kids and their dad) got a tongue lashing about bedtime being at 8:15, and about I don’t want to hear ANY whining about how tired everyone is this morning. Sheesh.

THEN, when I arrived home at 9:45 pm…. DrMrA announced that I am now also taking care of the neighbors dog for two days (WEDS, WAS my night to work late, and THURS)…. cause a relative passed away and they have to travel. (Seriously though-I don’t mind. Really.)

Just keep piling it on. I KNOW I’m being tested.

On Writing: Part V… Step 1, .. It’s all about the figures.

A while ago I started a series on writing that I’ve been meaning to come back to. I’d been on sort of an extended hiatus from reviewing papers, just because I had a bunch of grant deadlines in the spring- but the few papers I’ve reviewed recently have made me think about paper writing organization of data and figures, how to decide when you are ready to write, the content of the different sections, what order I write things in, and so on… and so on. An endless topic for blog posts.

Anyway. The process of writing a paper begins long before you actually sit down to type the words into the document itself, at least for me.

Team Paper Writing

I’m working on putting the finishing touches on a paper. A really lovely paper. The project and the writing itself have been a lot of fun, but coming to the end of the writing process has been a little more taxing. Did I mention that I really love this paper??

Here’s the deal. There are lots (>5) authors on this paper that are all involved in the editing of the text. Very hands on, all of us are. While I think that’s awesome, I also see problems with the complete democratic approach to editing a manuscript- especially when you can’t all physically be in the same room talking about issues that need to be resolved, and especially in the final stages prior to submission. When I’ve looked at the manuscript in the last couple of days  I felt like there are parts of the text that I was reading for the first time…. and that shouldn’t be happening one or two days prior to submission!! Yesterday someone decided to remake one of the figures in a new way… but looking essentially exactly the same as the original version. I’m asking myself WHY??? We should be at the dotting the i(s) and crossing the t(s) stage, not the re-inventing the wheel stage.

Why is this happening? Who knows. Maybe I didn’t read the manuscript very well on previous runs, maybe my memory is shot, maybe I’m cranky?, Maybe we have too many cooks in the kitchen. Actually, I think the answer is in that last option (although I freely admit I probably am a little cranky)- there are too many of us pulling in too many different directions, or writing with slightly different emphasis. Normally I wouldn’t mind this- all good intellectual exchange and bla bla bla, make the manuscript better bla bla bla,  but we are NOT at the early manuscript stage anymore here-we are the T-1 ready to submit revised manuscript stage. I think its time to start cutting back on the number of cooks, and have someone be the ‘decider’ (or maybe the two senior authors) on when we’ve reached the appropriate level of awesomeness in the manuscript to stop worrying about absolute perfection and push this thing out the door.

Otherwise, the manuscript will languish here for too much longer with too many cooks each adding their own secret sauce.

Contradicting Yourself

I’m re-writing my A1….. to be an A2.  So- I’ve been holed up writing the response to previous review. I’m grumpy… and I just thought I’d show you an example of what I’m irritated by.

Reviewer #1 sez:

Moreover, there is little support for the contention that in fact any truly novel new factors will be identified.

Ya, ok, you can disagree with me…but here’s the maddening thing.. In the same pink sheets- the following statement appears:

In addition, the applicant has already identified some novel factors (>20). What approach will be used to understand what these do?

Yup. You guessed it. The same reviewer that wrote that first statement, wrote that second statement. And- in the summary statement they appeared together like this:

Moreover, there is little support for the contention that in fact any truly novel new factors will be identified. In addition, the applicant has already identified some novel factors (>20). What approach will be used to understand what these do?

Just shoot me now.

Unsolicited Advice: Writing Part IV… A Proper Paragraph

So, let’s see, we’ve covered sentences and passive vs. active voice… I’m doing things a little out of order. I’m going to try to build on the sentence, and take you all to the paragraph in this one.

I somehow feel that this is high school stuff, or maybe even elementary school stuff.  I’ve seen BigA write some quality 4th grade paragraphs that put the writing of undergraduate college students to shame. However, I recognize that she is extraordinary and that public education in this country might not be what it used to be (Sniff,… sob!), that my dad may have been only dad holding the red pen to a kid’s writing in high school, and that I was a prolific letter writer in the snail-mail era.

Good Education+Tough Critic+Lots of Practice = Ability to write killer reasonable paragraph.

The paragraph is a unit used to convey a unified thought,