Format, then delete

I don't want to polish text that's just going to get deleted.

That was my attitude about early drafts of papers that became my thesis. I wanted my advisors to read my work when it was relatively immature so that I could get reassurance that I was on the right track. I wanted to know the content was ok before I really got my hands dirty with the presentation.

But, as much as I wanted to do things that way, my advisors were unable to read early drafts for content without getting distracted by style. They would comment on all sorts of relatively minor things that were low on my priority list (although I'm sure they would say the problems were not minor). For example, tables with the gridlines showing, text that wasn't super well crafted. I would think, I'm not going to spend the time to format that table if you're going to tell me I should cut it. But it just couldn't work that way.

I had to learn to suck it up and make my drafts better before I handed them over for comments. My advisors sometimes wouldn't really get into the challenges of improving content if there were easier problems to fix. And they are so slow at reading my stuff that I realized I needed to make it as painless as possible for them. Further, their slowness means I want them to have to read fewer drafts, so making the first one as good as possible means less time waiting for feedback. Now I do everything I possibly can before I hand over a draft: journal-specific formatting, contact info, keywords, figures, whatever. I want them to know I'm serious about the draft so that they're serious with their feedback.

Interestingly, my postdoc advisor is great at reading early drafts. He has no problem ignoring presentation problems and commenting on the direction of a document. I'm not sure if it's because I'm so much better at the presentation now, making my drafts better and him feel like he doesn't have as much to teach me about writing, or if it's because he's not the perfectionist that my old advisor is. Probably both.

One dot

I'm trying to switch from using two periods between sentences to just one. I prefer the look of two, but I know the world is switching, and I know my OCD boss uses one (although I haven't noticed him deleting periods from my documents, which wouldn't necessarily be out of character).

To facilitate this change and to help with other issues, I've starting writing with the formatting showing in Word. Research Advisor does that, and I always thought it was super distracting. Now I'm not only turning into my mother, but also my advisor.

Can you tell I'm in writing jail?

Another one down

I can't believe I didn't tell you guys: I submitted a paper last week!  From one of my thesis chapters.  It was the one for the special issue and I managed to get it in by the deadline. 

One of the coauthors gave me very important comments very quickly.  One didn't have any comments, but that was fine given the circumstances.  Another gave me feedback on Friday night, and the last suggested relatively substantial changes on Saturday night.  The paper was due COB Monday.  I really, really appreciated that the last two read the paper, thought critically about it, and gave me feedback.  But some of those comments didn't get addressed because I just didn't have enough time.  That sucks for two reasons: 1) they spent their valuable time making comments that were ignored, and 2) my confidence was undermined because I knew there were problems that I couldn't fix before I had to submit.

I'll have a chance to incorporate more of their suggestions after review, either to go back to this journal or to try somewhere else, so ultimately those comments will get used.  And I guess it's good for my own perfectionism/impostor syndrome to just have to move forward even though I felt a little out of control.  I think the experience was positive on the whole, especially because the paper never would have gotten out so fast if there hadn't been a deadline.  I think I'll be able to say that more emphatically if the paper is accepted.   

Keywords

Does anyone have a good strategy for choosing keywords for papers?  I can never decide on the best 4-6 words that are informative but not already in the title or abstract.  Sometimes I'm perplexed at the keywords on papers I read, so I think other people also find it challenging to pick good keywords.

Writing highs and frustrations

The paper we submitted to the GlamorMag is going out for review!  We're ecstatic.  Everyone cross your fingers for the next six weeks or so.  kthnx.

On the other hand, all the other papers are such a struggle.  And you know, getting feedback, or even a rejection, doesn't bum me out in a defensive way.  I rarely feel like the reviewers are stupid or assholes or whatever and the comments almost always make the paper much stronger.  But frankly, I'm over it.  I'm tired of most of the papers I'm working on.  My reaction to substantive comments is can't it just be done? Can't I just not have to look at this fucker anymore?

I'm making it sound worse than it is, of course.  I'm venting my frustrations because what's a blog for, after all?  In addition to finding out about our paper's progress at the GlamorMag, there has been movement on a couple of other publications this week.  I submitted the meeting report on Monday, and we already heard back that they don't want it as is, but they invited us to try again with a change in focus (requiring major revision).  That's fantastic and the paper will be much more interesting, but can't I just be done with it?  I also tweaked a draft of a manuscript from my thesis work and resent it to the coauthors today, but I'm expecting requests for big annoying changes.  Can't it just be pretty much fine?

I say, it's a hard knock life being a scientist with stuff to publish.

Welcome 2011

I love New Year's resolutions (NYRs), but I'm having trouble coming up with good ones this year.  I've had really good success with NYRs in years past, notably the year I paid off a bit of stubborn credit card debt thanks to the motivation from a NYR.  Last year I made a few that I really liked, but I abandoned them almost immediately. This year, rather than setting super-specific rules for my behavior, I need an over-arching theme. 

This year needs to be about getting my shit together.

On paper, 2010 was a really good year for me.  After defending late in 2009, I finished my thesis revisions and deposited in January.  I went on a fantastic cruise vacation with my BFF.  I started my postdoc.  I'm making way more money with better health insurance.  We moved to a great new apartment, which improved my quality of life dramatically (I should write a post about that improvement).  We got engaged.  I had a success with a big responsibility at work.

But I felt kind of off all year.  No, not off.  Just not quite on top of it.  We didn't visit my family frequently enough, which has made me feel kind of out of touch with them and my BFF.  Although some things at work have gone very well, I still haven't collected any new data.  We have a venue for our wedding, but no other plans.  I haven't gotten any more of my thesis papers published since I defended, although I submitted one that got rejected.  Nothing went badly at all, but I feel like I could be doing better.

My work-related goals are twofold.  First, I will publish the rest of my thesis, damn it.  My thesis should generate four papers: One is published; Two is going in a special issue related to a conference and is due January 31; Three has been rejected once and is almost ready to resubmit; and Four might go to another special issue and in that case would probably be due in March.  If Ecogeoman and I want to have any hope of finding decent jobs together, this just absolutely must happen soon.  Second, I need to be a bit more aggressive with my lab work.  I've got some cool things started, but now it's time to make data happen. 

I have a longer list of personal goals. The highest priority is to not let wedding plans fall though the cracks.  I don't want to feel like decisions and preparation for this wedding are a big ball of guilty blah because I waited too long.  I'll probably have to make more trips to my hometown to make arrangements, but that will will also address the issue of not seeing my fam enough.  I'd also like to entertain more.  Our social life, frankly, is pretty good.  However, I think we're kind of passive socializers, so having friends over more often should help me feel more in control of our plans.  And it should go a long way toward another goal: keeping the house in order.  We're messy.  I have to just accept that.  But just a tiny bit of effort could go a long way. 

All of this is about being assertive and proactive.  Time to take responsibility for how I want my life to be and make it happen.  Happy New Year!

December slump

Last week I posted my ambitious list of goals for the month.  Since I claimed that post was meant to provide accountability, I will now give an update on my progress.

1. Submit a commentary piece based on the meeting we hosted.  It's written, but I'm waiting for feedback from two coauthors.  I expect them to make few comments, so with any luck this will go out early next week.

2. Turn around the manuscript that was rejected over the summer.  Working on it.  I did all the easy changes, but I'm having trouble getting my A into G to tackle the harder ones (e.g. rearranging the discussion).

3. Draft manuscript for special issue paper.  Started today.  I put the text from my thesis chapter into a new document, formatted it to meet the journal requirements, and generally refamiliarized myself with the work.  I also made a first pass over the new data.

4. Work with PI to revise big manuscript.  Done!  He's waiting on feedback from a couple of people but intends to submit (to a GlamorMag) on Monday.  Unfortunately, I think we'll start pretty much straight away on reformatting/revising for a more attainable journal.  Good practice, of course, but I'm so sick of this paper right now!

5. Establish protocol for sample processing.  Part 1 is done.  Part 2 is drafted, and PI and I have discussed it but a few kinks remain.  I think one more (focused) discussion and one practice session ought to take care of it.

6. Finalize protocol for lab experiment.  All I've done so far is gather up all the stuff I had spread in multiple labs and move it to a new lab space I'll be using for this project.  I hereby downgrade my goal for this item to get shit organized and make a plan for developing protocol in January.

I could have done more in the past week, but my predictable December slump is in full swing.  When I feel all blah like this, I'm happy to get anything done at all even if I'm not functioning in high gear. Like, I'll suddenly realize I've been sitting at my desk for an hour just spacing out/making sure the Internet doesn't disappear/looking at colleagues' publishing records/whatever. Thus, although I intended to finished and submit the first manuscript before I started on the second, the edits on the first seemed too hard and I figured I should get something done even if the order of tasks didn't make the best sense.  I know that if I just chip away at things and leave work each day a little further ahead than when I arrived, it will all get done. 

End-of-year ambition

It's December tomorrow, which means there is just one month left to meet my 2010 goals.  I failed miserably on whatever New Year's resolutions I made, but I do have some goals for the next month that are attainable, if a bit lofty.

1. Submit a commentary piece based on the meeting we hosted in October.  Today I finished a draft and sent it to the coauthors.  This has to get done quickly no matter what, since timely publication is vital.

2. Submit the paper that got rejected this summer to a different journal.  I revised it and got comments back from my coauthors over break, so now it's time to dive back into it.  There's more work to do than I expected, but it's not insurmountable.

3. Write a manuscript for a special issue associated with the meeting I attended in September.  I have a decent draft from my thesis, but right before Thanksgiving I got new data to incorporate into it.   I want to have a complete draft to give to the coauthors before winter break so I can deal with their comments before the January 31 submission deadline.

4. Continue helping PI revise a major paper that needs to be submitted -- when else? -- before winter break.  The data were collected before I started in this lab, but the manuscript was a total mess.  We've been working on it together for several weeks and it's looking a whole lot better, but there's still plenty of work left to do.

5. We completed a major field sampling a couple of weeks ago.  I need to get the protocol in place so that technicians can get sample processing underway.  It's unclear how involved I'll be with the processing, so I might need to make time for that, too.

6. Finalize the protocol for the lab experiment that was giving me grief earlier this year.  It kind of went by the wayside between late summer travel, the meeting we hosted, and the field work.  I know PI is very anxious for me to make progress on that project now.

So that's what's on my plate for the next few weeks.  I'm hoping that sharing here will give me some accountability, and I intend to post updates throughout the month.  I really want to accomplish all of this before January, so I think I'll be able to do it!

Tired with a side of disappointed

Today I found out that a paper I submitted a few weeks ago has been rejected.  It was the weakest of my thesis chapters, but we aimed low journal-wise so I'm surprised the reviews were as bad as they were and the rejection was as solid as it was.  So far I have only skimmed the review comments and they struck me as comprehensively negative but polite.  Research Advisor thinks they were mostly constructive--some complaints were refutable, some were founded and can help us revise, and some were flaws were knew were there--and that we can reframe the story for another journal.  I'm less disappointed about the rejection itself than I am bummed that it's going to take that much longer to shore up my weak publishing record.

In other news, today I learned a lab technique that is very new to me.  The technician who trained me is just as fantastic as Awesome Technician so it was a pleasant enough experience, and I am thrilled to be learning new skills.  Furthermore, this is the first lab work I've done as a postdoc and it felt great to be away from my desk for a spell.  However, I was awkward and uncertain about the choreography of the protocol and it is always exhausting to learn brand new stuff.  On top of that, by the end of the day I was so frustrated with the scale of everything.  I had to stand on a step stool to do several different tasks, and some critical tools didn't fit in my hands very well which contributed to my lack of coordination.  So irritating. 

To avoid going home and wallowing, I went shopping after work.  On the bright side, I found bargains. I got some low-heeled, moderately dressy shoes that I've been looking for for a while ($13), socks to wear with them ($5 for 6 pairs), jeans ($33 for two pairs), and a big splurge, perfume ($25).  I'm disappointed with the jeans though and bought them because they were on clearance and I was pissed off; I had tried on some cool designer ones at another store and there were comically long, reinforcing my disdain of being a short person in a tall-person world.  Phooey. 

Working without a net

I think we can all agree that writing grants mostly sucks.  But: would you feel comfortable starting a new project without having first formally proposed it?  Would you feel ok about carrying on with an idea without spending time on a comprehensive literature review?  without crystallizing your ideas in a structured document? without the approval of peer review?

I'm in a position to do some new experiments without having to get funding for them.  That's very, very cool for so many reasons, so trust me when I say I'm not complaining.  I'm just observing that writing a proposal has its merits.

On waiting

How much time should a coauthor be allowed for reviewing a manuscript before it is submitted?  How long is too long? At what point do you feel it is appropriate to start complaining?  Or making ultimatums?

What if that coauthor is your advisor?

What if that coauthor is your student?

Personally, I think things are going pretty well if all coauthors respond to a request for feedback within a month. Gentle reminders are appropriate beginning about three weeks after the coauthors receive the manuscript, and can increase in frequency and sternness of tone after that.  I think three months is too long, unless there are extenuating circumstances, and is the point at which serious complaining may start.  I can't imagine making an ultimatum to an advisor or coauthor who made a major contribution, but I can imagine engaging in hard-core whining.

Am I off base?


In other news,  we successfully added a second computer to our wireless network with absolutely no drama.  The new router is teh awesome.

The Endnote thing

So I've mentioned that I don't use Endnote, or any other reference manager. Before you all go apeshit on me, I will say that I recognize that it's the 21st century and that I am missing out on a real convenience by not using reference-managing software. But here's why I don't: I'm lazy.

I keep pdf copies of all my papers in one giant folder. They are labeled by author and year with a few keywords, and despite the fact that this folder now has hundreds of papers, I seem to be able to manage it.

I finally got a copy of Endnote several years into grad school. For a while, I made an effort to build a library with all the papers I had. I was pretty excited about it, but I soon decided it was a pain in the ass to transfer my makeshift pdf system to Endnote. And then I lost interest. And then I got a new-to-me computer that didn't have Endnote. I didn't think to ask for it, and that meant that I couldn't throw my dissertation references into it at the last minute.

Perhaps more importantly, I get a lovely sense of satisfaction from manually building the reference list for each paper. The gradually accruing list is like a progress meter for the paper. Look at how much I've written! Look at how many papers I've read! Look at how thorough I am! Ha-ha!

Admitedly, the big pdf file is starting to get a little out of hand now. I will probably spend some time sorting something out before I get hot and heavy into a post-doc. I downloaded Zotero a few months ago, but I didn't take the time to figure out how to use it. Since it seems I'm not committed to anything, so I'm open to suggestions!

They came through

All five chapters have now be read at least once by at least one of my advisors.

I planned to distribute the complete document next week. Research Advisor suggests I ask the other committee members if they plan to read it that far in advance in hopes of getting a little more time to polish. That would be great. Even if I get the extra time, I'm glad I planned to finish it this soon so I can maybe have time to "polish" rather than "frantically finish".

Reminding the Passengers that I'm not a special snowflake

The last two days didn't go so well. I got stuff done, but not as much as I wanted. My normal emotional stability vanished, and I was a bit of a mess. The passengers on my bus were screaming at me, and it really distracted me from my work. They were saying things like your dissertation is going to be a mess; your defense is going to be awful because Difficult Committee Member isn't going to understand this train wreck of a dissertation; you'll be wasting Out-of-State Committee Member's time with your shitty diss.; and so on.

But then today I was venting to Awesome Technician, as usual, and she reminded me that I'm not the first person to feel this way, which of course I know, and that I'm not the first person to have a diss. that's not perfectly polished, which I also know. But somehow her reminder kicked me out of my self-pitying state so I could work again. There's a reason I call her Awesome.

Another helpful thing happened today as well. Academic Advisor had indicated he wanted to review the main introduction to my diss., so I sent him a rough draft of it on Saturday. I ran into him yesterday morning when he was on his way out the door. He he said he had been reading it, had found some issues, and would finish with it and send me comments in the afternoon. Then I never heard anything else. So late this morning I sent him an email saying, basically, that it was shitty to tell me he had problems with my intro but to not tell me what they were. I got comments within an hour. They were super helpful, and really pushed me through the remaining work on that part.

So, ladies and gentlemen, I now have a finished introduction.

Final lap

Okay, I'm starting to spaz. I have a week, maybe a week and a half to finish my diss. I have a lot left to do. That means I'm in dissertation jail this week. Here's the status.

• Introduction: written, in the last 2.5 days. Still pretty rough, but I think everything's in there. Except most of the references. Emailed to Advisors today, because one of them expressed interest in providing guidance/feedback. Any bets on if it will actually get read before I have to distribute the diss to my committee?
  
• Chapter 1: written, needs revision. This is the Poopsicle, which was meant to be Chapter 2 but we decided to put it the first position to deal with the data issues (the conclusion will be: this method sucks, other methods are way better, I used the better methods in the rest of the chapters - see?). Thus, I had to revamp the intro to the chapter, which I did today. I also redid some of the stats, and I still have to incorporate those results in the results and discussion sections. Plus fill in some more references and some general editing for style.
• Chapter 2: totally done. This is the one that is already accepted for publication, so it won't change other than formatting.
  
• Chapter 3: written. First draft went to Advisors in July. One never read it. One gave me really general comments in September. I revised it and sent it back. No reply. I do, however, have comments from a friend to help me polish it.
• Chapter 4: written. Emailed to Advisors on Saturday afternoon. Hopefully at least one of them will at least skim it before I have to distribute the diss. Still need to fill in a few last references.
  
• Conclusions: not started. But this part will be short.
• Formatting: not done. Started last night, then Word crashed and took my formatted chapter with it. Gah! I will have lots of time after my defense to get it just right for the Graduate College, so for now it just has to be formatted well enough for my committee to navigate it.
  
• Abstract, acknowledgments, table of contents, references: not done. Although each chapter has it's own reference list that I will have to fold into one. Did I mention that I'm a jackass who doesn't use reference managing software? I will be doing this manually.
  

On top of that, there is some distracting post-doc drama going on, and I got the proofs for the in-press paper. It's going to be an intense week. I best stop blogging!

Something is better than nothing

Yesterday I stayed home and failed to work, so today I went to my office. I was there for about 6 hours, and I got maybe 2 hours of real work done. It's tempting to feel really shitty about that, but I'm trying to have the mindset that something is better than nothing.

I remember the Dissertation Coach commenting that she has clients who avoid work all week, and then finally get motivated by her impending phone call (she has weekly phone meetings with her clients, who report their progress and then work with her to make a new plan for the next week). So they work for only a few hours in total all week, but still they get more done than they otherwise would without the accountability of the scheduled phone calls. Today when I sensed I was straying too much, I called EGM and we agreed to write for 30 minutes and then call back. It worked. Then we did it again. I still ended up reading a bunch of crap on wikipedia, but at the end of the day I had the introduction to my last chapter fleshed out, made the realization that I needed to report some addition results, calculated said results, and made a table to display them. So I could have done a lot more, but it was better than nothing.

Countdown relief

So, things have gotten better for me lately, stress-wise. The change happened as soon as I got my defense lined up. This strikes me as a little paradoxical, since you'd think that once the clock was officially ticking, I'd be freaking out about finishing. I think the crux on my anxiety was that grad school was starting to feel interminable.

I had a committee meeting in May 2008, and at that point we all thought I'd finish in about a year. Actually, I thought I might be able to defend in March 2009. When it became clear that wouldn't happen, I thought I could do it in June. Then October. Finally I put my foot down with December.

I had sort of a low point mid-summer. The proximate reason was my frustration with the slow pace of paper revisions. The ultimate reason, however, was that I just could not see the light at the end of the tunnel. It seemed like I should be wrapping up, but there was so much left to do and no one seemed to be thinking I should be nearing completion except me.

I was adamant that my defense had to be done this year. There's not a good reason for that, though, except for the psychological cost of waiting longer -- I've completely missed the graduation deadline for fall semester. I simply could not handle pushing it off any more.

Fortunately, I feel like the tension broke over the last few weeks/months for several reasons: 1) I got my advisors' blessings to schedule the defense in December; 2) my out-of-state committee member agreed to come and scheduled his travel; 3) I finished a draft of the pile-o-shit paper (aka poopsicle); and 4) I have all my data in hand.

Now all I have to do is finish the mother fucker.

Not so fast

On Monday, I emailed a draft of another diss chapter to Awesome Technician (AT) and my advisors. AT sent me comments on Tuesday, but I didn't look at them right away. Today when I came in, there was a book on my chair with an unsigned note marking a page saying something like "this might be a good reference for [statement X]" (I had some sentences in the discussion that still needed references). I thought the handwriting was Research Advisor's, and I got super excited that she had read my draft already. There was a problem with my email server this morning, so I couldn't sign in right away to see if she had emailed full comments, but the fact that she had left this book indicated that she had read the draft. I wanted to thank her straight away, but she was in a meeting.

I stopped my AT's office a little later to talk about some lab things, and I mentioned how happy I was that Research Advisor had already read my draft and that I couldn't wait to thank her. AT made this odd face and said, "well, I left a book on your chair. Were there two books?" uuuooooooohh. It wasn't my advisor after all. But AT did make a bunch of really helpful comments, so that's good.

I'm glad that Advisor was in that meeting, because I would have felt like a total jackass if I had barged into her office with a big grin, thanking her for her prompt feedback, and put her in the position of saying that she hadn't done it. That would have been awkward.

Accepted!1!!Eleventy!!11!!!

This morning there was an email waiting for me to tell me that my paper is accepted! You know, the one I've been fretting about here basically since this blog's inception. Yay!

There are a few minor revisions to make, but basically the reviews were, dare I say, glowing. One of the reviewers who read the first version of the manuscript reviewed it again. This person didn't like it at that point because it wasn't novel enough, but now s/he says I addressed all of his/her concerns, so the paper is okay. The other reviewer, who is different from last time, said things like the paper is "well organized" and "very concise" and "illustrate some great evidence [for phenomenon we were trying to measure]". Woot.

Ecogeoman took me out for a very nice dinner tonight to celebrate. Our tradition, which we established long before either of us had anything ready to publish, is that we go out for beers when one of us submits a paper, out to a nice dinner when a paper gets accepted (on the other's dime, of course), and then a smaller dinner like pizza when the paper finally comes out. Tonight we went all out with a bottle of wine and dessert, but this was partially justified by it being our official five-year anniversary tomorrow. :)


You know how sometimes when you are waiting to hear the result of something, you say negative things but deep down you expect a positive outcome? On the contrary, I really expected this paper to get rejected from this journal, but to get accepted elsewhere. Since the 2008 data have been integrated, this journal is one of highest ranked in my field. I'm obviously super pleased with this, but that's in part because I think this is the only piece of my Ph.D. work that is broad enough in scope to be suitable for anything but a specialists' journal.

Honestly, this feels even better than I thought it might. How rare.

Don't give me shit and call it ice cream.

A friend of Eastern European origin once shared this phrase with me, and I love it.

I'm currently trying to turn shit into ice cream in the form of my next chapter/paper. It's the least interesting part of my of my Ph.D. work. The data were collected mainly to provide baseline information for another study, but it took so much effort that I wanted to get something more from it (remember the counter I had going on my sidebar a while back? it's that project). Unfortunately, some of the findings contradict one of the main conclusions from the first chapter/paper, and I think it's because the design of this second study kind of sucks. However, I can't just say that, nor can I present explicitly contradictory data. For one thing, I don't want to completely undermine the ongoing study before I even collect the data from it.

So, what to do? The design has specific weaknesses that are quite common in my field. But honestly, I think that the natural phenomenon I am trying to describe interacts with those weaknesses in a way that enhances them. When others have tried to address the same question, they sometimes find result A, occasionally find result B, and sometimes find no difference between A and B. I think I need to take a look at the experimental design that generated each result to see if there are trends. Perhaps result A is only possible to detect if you have the proper design? Maybe all the studies that find B or no difference use this common, yet crappy design? I suppose that would be sort of interesting.