research publication

TGI December and Reader Questions

‘Tis December!!! Phew. I must admit, posting every day in November has been tough, which was probably obvious from some of the less-than-inspired posts. When you start photographing produce, you know you are scraping the bottom of the blog-fodder barrel.

I think last year’s November blogging was easier, I am not sure why. I don’t remember having quite this many moments like “It’s roughly 11:30 PM, I am completely pooped and I finally got a few minutes to sit down. I want to go sleep, but I haven’t posted today. What the heck am I going to write about?” (Enter squash.) I had more travel but I think I was overall less busy. Or at least I felt less busy. Or I repressed traumatic memories of excessive busyness and insufficient inspiration. Or I just had a higher tolerance for my own vacuous posts. (I was kind of aiming for some serious academic blogging here. I guess that ship has sailed!)

Thanks everyone for reading!


OK, that’s enough meta self-flagellation.  EarthSciProf posted some interesting questions after the 15-Min Improv Blogging post.

1) How long does it usually take you to do a review? I take much less time than I did when I first started but am wondering about how long it takes you since you’re farther along.

It depends a lot on the length of the paper. In my field, there are letters, of 4-page double-column size (like Physical Review Letters) and there are comprehensive articles (like in Physical Review B, for instance), which can be anywhere from 4-5 to 20 pages long. I would say most papers are 6-10 pages of main text, anything over 10 generally means long appendices.

For a well-written letter in PRL, it takes 1-2 focused hours to read and write a good report It may be longer if there’s supplementary material or I have to look at a lot of references. These letter papers also tend to be reviewed for hotness rather than just interest and correctness; a common complaint is “This  is fine technically, but of too narrow a focus, and should be expanded and submitted to a specialized journal instead.”

A comprehensive paper takes longer to go through and write a report. Between 2 and 4 hours, depending on length.  Flying on planes is my favorite time to review papers, as there are no distractions. (Crappy papers take longer to review, because I start reading, get irritated, drop the paper before finishing, then have to still do it later, but then I procrastinate because I have already experienced the pain.)

A few months ago I was a referee for a good review paper, it was probably 60 pages (double column) and it took me all day. It was written by people I respect, so I ended up writing a lot of comments in the margins and scanning the marked-up document into a PDF which became part of the report. There should be some karmic brownie points in it, I hope.

What about you, blogosphere? How long does it take you to review papers? 

2) You posted something about a few months ago here

about only a small percentage of collaborations working out long-term. Any advice/guidelines/rules of thumb that you use to cut things off when a collaboration doesn’t seem to be going anywhere?

Ugh. This is a tough one, but I will give it a shot. All collaborations of mine that have dissolved owing to nonfunctionality were simply abandoned to die by all (dis)interested parties; at some point, no one attempted resuscitation any more. The parties stopped communicating and went on with their lives, never discussing the collaboration. The upside is that technically there was no confrontation, so everyone is still formally on good terms. This is not a bad thing in the long run.

I also have several collaborations that are generally healthy, but are on-again off-again, depending on funding and interests. We work together, then go our separate ways when the grant ends, then rejoin a few years later to do something else. I like this type of collaboration. It’s with people I enjoy working with, who have the same zeal, similar attitude to advising students and publishing, but we don’t have to be joined at the hip. In contrast, I have a colleague who does everything collaboratively, with several long-term collaborators. I find it stifling.

Are you on a grant together? If not, then just cut your losses and part ways. If you are on a grant together, then you need to produce something one way or another for your own sake, even if the collaboration is not working out. Proceed as best you can alone. If you feel appropriate, offer to include the collaborator on papers on your own terms; if they don’t agree or are being difficult, that’s your answer. I have found even very demanding people, when you do all the work and offer to have them as a coauthor on a polished paper, will swallow the pride/whatever other bug they have up their butt and say “Sure, go ahead and submit. Looks good!” I take myself off of papers to which I didn’t contribute enough, but most people don’t.

EartSciProf, if you have a specific situation, I am sure the readers would be happy to offer their insights.

Here are also some thoughts on collaboration from the depths of the Academic Jungle.

Wise academic blogosphere, please help EarthSciProf with the collaboration dissolution tips! 

The Curse of ATTTS

>>   Dear undergrad: You come to class irregularly and don’t come to discussion because you have team meetings for another class seemingly non-stop. You submit homework intermittently. After you had come to inform me how much more important that other class is to you than mine, you asked me to move the time and day when the homework is usually due so that I can even better accommodate your schedule for this other class. My response?



>> I have lost another colleague to the curse of ATTTS (Administrators Taking Themselves Too Seriously).

We are having way too many faculty meetings, one every week. They run for 2 hours each and it’s a waste of time, especially in the midst of the proposal-writing season for most of us. My class somewhat overlaps with the meetings, so I am always late. The other day, I was on my way to the meeting at about 30 min past, when I ran into a colleague who was already leaving the meeting; the colleague informed me the meeting was still in full swing, but that they had to leave. I jokingly pleaded “Take me with you!!!” to which the colleague responded “Oh, it’s not that bad.” The colleague had recently taken up a college-level admin position and the Koolaid has apparently been overflowing their glass. I remember a time not that long ago when the colleague  would have smiled or laughed at the joke, or even commiserated at the thought of yet another meeting. The colleague has since been fully assimilated and, I fear, can never go back to being a real professor. (By the way, the meeting was deathly boring, with the same old characters droning; even though I was late, I left early because I had way too much work to do, and  nothing was getting done. Life is too short anyway to spend listening to people’s verbal onania).

I really hate meetings. That’s probably because too many meetings are poorly run, don’t stay on target, go overtime, and don’t accomplish anything. So I avoid them like a plague. When I am in charge of a committee, I do as much as humanly possible via email and only meet occasionally when the amount of material or the way it needs to be handled is such that it’s more efficient to meet once and knock it all off the list at once. Enjoying daily meetings, which admins do, is completely alien to me. I am now confident that I will NEVER be an administrator, because I would be a really bad one, unable to keep any of the Koolaid down.

There are two types of time I devote to work:

1. Prime time, the large blocks of time when I am at work and fully alert, during the day or early evening. This is the time when I read papers, write manuscripts and proposals, meet individually with my students, essentially do my science. I also prep for classes and teach during this time, create exams, and review other people’s papers and proposals. I am extremely protective of my limited prime time.

2. Not-exactly-prime time, which would be the time when I am tired in the evening, or small amounts of time on the weekend or during the work week, which are insufficient to do a large amount of work that requires creativity or deep focus. This is the time when I grade exams, prepare homework or write solutions, organize upcoming travel, file for travel reimbursement, do the budget or boilerplate for proposal submissions. I might also write letters of recommendation or sometimes finalize reports for manuscript review. If at all possible, I try to schedule most meetings during not-exactly-prime time, since prime time is sacred.

Now that I think of it, my ATTTS-afflicted colleague has always displayed just a little too much tolerance for meetings, while  writing papers or proposals together was just not a very high priority; it seems that a lot of stupid non-research stuff has always cluttered the colleague’s schedule. Perhaps the colleague had been running out of research breath for a while and this might be a natural consequence. I, however, find that I am in better scientific shape than ever, have more and better ideas, am writing better papers and proposals and doing it faster than before, and am feeling bold and confident.

I am not saying admin work is not important. It is, and someone has to do it.
I just don’t understand a scientist who prefers this work to actual science. And who so readily morphs into  a full-fledged Koolaid abuser.

How long does it take to write a proposal?

For my professorial  readers (or otherwise readers with PI status):

How long does it take you to write, from scratch, a single-investigator grant proposal that will undergo peer review?

For physical scientists and many others, I am talking about a standard NSF 15-pager or similar. For biomedical folks, that would be an NIH R01 (however long it is).
I am assuming we are talking about a new proposal (not a resubmission), and I am also assuming that you don’t just drop everything and disappear into a cave to write, but rather continue to tend to other normal academic duties, like teaching or service.



Editorial and Professorial Nuggets

—  I am an associate editor of a specialized disciplinary journal. I try my best to include junior researchers (postdocs, young profs or nonacademic scientists, even some senior graduate students) as reviewers when I know they do good work based on what I have heard or seen them present at conferences. It turns out, a surprisingly high number of people cannot write a review to save their life. Some of them are junior, so they have the excuse of inexperience, but some should really know better.

I get these cryptic two-line reports with a recommendation to reject. WTF? That is not a report. I cannot send that on to authors, it gives me a basis for nothing. Especially if you are going to reject, you better give clear reasons for doing so.  Even if the paper is crap, it usually (although not always) presents a considerable amount of work by the authors. If the paper sucks, tell them precisely why it sucks and how much it sucks, so they would know whether to try and fix it or that there is no hope and they should drop it.

How does one learn to write referee reports? Well, when it comes to my students, I send them samples of my reports to look at (ranging from minor revisions to rejections). But, one first and foremost learns from the reports received of one’s own papers. Which is why I wonder, especially for senior folks, how unobservant and unable to generalize they are,  that they cannot figure out what is to be done based on their own experiences with being on the receiving end of reports.  These are all skills necessary for doing science, how is it possible not to apply them when learning how to write reports?

— There are career editors and then there are editors who are practicing scientists. Either way, the longest part of the review-and-publication process should be the actual peer review. It should not be the time taken by the editorial office staff to check the formatting; it should similarly not be the time the editor takes to make a decision and transmit the referee comments to the authors after the peer review has been completed. I have found myself dreading submission to certain journals, because I know a paper in a certain field will go to a certain editor, and the editor has a habit of just sitting on the paper for days or weeks on end, both when it comes to making referrals and when it comes to making a decision (the time they take doesn’t seem to correlate at all with how hand-wringing the decision-making process might be; hearing about “major revisions” appears to take just as much time as receiving “publish as is”.

For editors who are practicing scientists, why do people take on this role if they are not committed to doing a good job? I know, becoming an editor in a good journal is an honor, but it’s also a job, and an important one. And part of doing it well also means doing it fast. I know some great associate editors who handle dozens of new papers per week very efficiently. But then there are others. And I wish someone gave them a kick in the pants so they’d finally get going.

Yes, I am very impatient. But you can bet that I am very efficient as associate editor.

— In professorial news, once again, the biggest problem of my undergrads is that they don’t know the math that they should know. They don’t have the facility with basic calculus, let alone analytic geometry. While some fairly complicated concepts can be hand-waved down to the levels of calculus or geometry, it’s of little use because these concepts, which should have been internalized long ago, appear only vaguely familiar to students as opposed to being tools wielded with confidence. Part of it, at my university, is the ever-shrinking list of required math courses so students could all get as many free electives as possible (?!); that’s because students feeling warm and fuzzy upon having customized their studies to the point of senselessness  beats actually getting a solid education in the major. The worst thing is the students’ attitude that this insistence on calculating stuff, on — gasp! — using math, is somehow unnecessary and is in the way of actual real knowledge. They want to make it go away and get to the good stuff. They cannot. I am all for pictures and analogies and building one’s intuition. I draw in class more than I write equations. But this is fairly high-level stuff, and the intuition has to be already honed by both math and experience with other similar problems. Students cannot expect everything worth knowing as a senior in a physical science discipline to just be qualitative or requiring no more than arithmetic and high-school algebra. I am really tired of having to apologize for what is really not particularly high-level math that they should be proficient in anyway.

Workaholic Geeky Nonsense

The semester is about to start. Which means that the summer is over. Which means that, in order to fully get into all the fall proposal writing around all the undergrad course teaching and insane service, I have to get these last two papers done and submitted, like, yesterday.


Over the past few days, I worked  12-14 hour every day. Really focused, high-productivity, long days. I fuckin’ loved it. I love working non-stop, and if it were possible to somehow forgo sleep, at least temporarily, without loss of sanity of productivity, I would love to be able to just go-go-go.

Man, I love working.

When I don’t waste my time and energy worrying about whether or not I am appropriately recognized and admired, the bottom line is that I love reading papers, looking at data, analyzing data, coming up with mathematical models and appropriate algorithms for their numerical implementation, troubleshooting, making graphs, writing papers, and talking with graduate student about every single one of these aspects of my job.

I love doing science.

Fortunately, or unfortunately, I am actually a good role model for inspiring people to leave academia. More than one student has said that seeing me and the insane schedule that I keep has convinced them that mine is a job they don’t want.

I read all the time all around the web about there being a surplus of PhDs who all think they will be professors, who are then all surprised when that proves impossible and are also for some reason oblivious to the fact that there are other things they can do. Apparently, I do my part — without even trying! — to discourage young’uns from pursuing an academic career ; the few who were not discouraged have done very well for themselves!

I don’t know what it is that other professors do that (supposedly) makes all of their students and postdocs think they want the professor’s job and there is nothing else. I bet the professors look really cool while doing their job. Luckily, I never look cool, especially not while doing my job.

How do I achieve this elusive goal of discouraging all but a few? You can do it, too!
Look sleep-deprived and incessantly drink coffee, having mild panic  attacks when a coffee cup approaches empty. Send emails before 7 am and after 11 pm. Respond to their emails immediately no matter what time of day or week. Share with them when the deadlines are and name all the things that depend upon certain grants being renewed (their food, shelter, tuition, and health benefits). Work with them closely on every paper and proposal and let them know how much effort goes really, truly into every piece that is meant to be read and understood by others while bearing your signature. Keep track of all the details of all of their many very different projects in your head and be able to give each of their talks at a moment’s notice with no prep whatsoever. Push them to do better and lift them up and don’t let them give up on themselves or their work. Forward them emails from industrial collaborators about job openings. Encourage them to attend all manner of professional workshops to broaden their soft skill set. Sleep less than any of them and take less vacation than any of them.


In life, there are various quantifiable aspects that change over time. More often than not, it’s not the value of the function that we care about, as much as the sign of the first derivative. Sometimes a positive first derivative is good, sometimes a negative one.


If anyone tells you that calculus is stupid or useless, you can print this post, crumble it into a ball, and shove said ball into the mouth of the heretic spouting such nonsense. Calculus is an almost absolute goodness, only surpassed by complex calculus... And calculus on spheres, donuts, and other cool objects, also known as differential geometry… *geekgasmic sigh*


You know how The Oatmeal made me grumpy the other day? It’s all forgiven, as I came across an old classic — The Motherfucking Pterodactyl comic. And there is even a song (below)! It is hilarious,  but view at your own peril.


Lastly, among the comments to the last post emerged the awesomeness that is this guide to acting like a Minnesotan. It has a very Monty Python feel!

What I Do All Summer


I absent-mindedly sketched this with a marker, with the intention of doing a clean version later (pencil first, then ink). But I actually like the rough version; it captures the frenzy.

For nonacademic readers: NSF, DOE, AFOSR, and ONR are federal funding agencies that fund research in the physical sciences (NSF also funds biological and social sciences).  SPO stands for Sponsored Programs Office, the university staff that work on grant administration. The F&A rate is the so-called overhead rate and is anywhere between 40 and 70%, depending on the institution. It means that on top of every dollar  you request for research, you need to request an additional 40 to 70 cents, which go directly to the university in order for it to help you do research (at least in theory). PRL, PRB, APL are reputable journals in the physical sciences (PRL is very prestigious and publishes papers across all physics). Nature is a high-profile magazine that publishes research across all fields of science.


One of the things that annoy me most about collaborating are collaborators who operate on the timescales much different from mine, usually because our priorities aren’t well aligned. I have already written about this particular issue before, but as it periodically resurfaces, I periodically get re-irritated and thus have to periodically re-vent, and reposting old rants just doesn’t seem to have the same therapeutic effect.

I have a  collaborator who doesn’t seem to be encumbered by urgency when it comes to paper submissions. In the past, after a disastrous few papers, where we drove the co-advised (and since graduated) student crazy, I came up with a strategy: the student and I work on each paper until it’s done and ready for submission, I schedule a time with the collaborator in advance for them to look at the essentially polished paper, they suggest touch-ups (which they expect accommodated), I enter those and we submit. Sure, the student and I do all the heavy lifting, but at least the papers get written and edited fast.

This week I have been driven crazy again, and I can tell you it’s a remarkable feat of self-restraint that I didn’t already write about all this days ago.
Early this week, I  emailed the collaborator to tell them that I would be done with the paper later in the week, and then would be off to a conference starting next week, and I asked it they could perhaps look at the paper during my absence. The collaborator wrote back to tell me that they too were leaving town,  but not until around the time when I was to return from my trip. The problem is that they decided they had absolutely no time to look at the paper in the time preceding their departure  (which was almost three weeks from the point at which we were emailing and nearly two weeks after the point at which the final paper was eventually sent to them), but said they they would look at it soon after they came back.

I am really pissed, because, as far as the current student and I are concerned, the paper can be submitted today. It is not a rough draft that requires massive edits, I already took care of all of that. Still, the colleague supposedly does not have the time to look at it in next two weeks, they supposedly have weeks of their time in town fully obligated in the middle of summer (no, they are not writing a proposal), so we now have to wait additional 3+ weeks from the point of completion for the colleague to put on the trivial finishing touches.

This happens every time, with every paper. I do not buy that the colleague is busier than I am, because I am pretty darn busy and their group is not bigger than mine. These joint papers are simply not a priority for the colleague, which is OK, but they *are* a priority for me and the student, and if they cannot help they should at least not hinder!

If submitting a paper were equal to having sex, then the colleague would now be cock-blocking me. I think it’s safe to call the colleague a pub-blocker.

I have been in situations where I was the middle author, cared little and didn’t have the time to go through the paper in detail; in such cases, I either took myself off the paper or found the time to at least quickly skim the paper and said it’s OK to go as is. You either care and find the time to look at the manuscript, or you don’t care and consequently don’t find the time, but then at least you trust your collaborator that they can submit a coherent manuscript. The worst scenario is that you don’t care and don’t find the time, but also want to hold the reigns on submission. That is really, really douchey controlling behavior.

No, I don’t want to wait three weeks or more to submit what is essentially a finished paper. As a courtesy, you have two weeks. The last three days of those two weeks you are away, well boo hoo. There are the other 11 that you are here, find the freakin’ time.

Here’s the deal: papers are important. Papers are VERY important. Papers and graduated students are our products. There is possibly no aspect of our job (our job = professor in a STEM field at a major research university) that is more important than getting papers out. Published papers enable everything else: students graduating and getting jobs, new grants being funded, knowledge advancing.

I have no idea what the collaborator has in the pipeline for nearly two weeks prior to their departure that would prevent them from sitting to read the paper for an hour or two. But whatever it is, unless it’s editing of a whole $hitload of their other papers (and I know for sure that it isn’t) , IT’S NOT AS IMPORTANT!!! Stop pub-blocking. Move stuff around, read the goddamn paper, so we can send it to review ASAP. Then you can get back to whatever leadership or other service BS is so pressing in the middle of the summer. And you are very welcome.


I haven’t been blogging much as I am a) recovering from the semester and b) writing technical stuff 24/7. So I am a little tapped out. As I am thinking about writing, it’s fitting that I write about writing.  Perhaps I should go full-meta and write about writing about writing…  For now, I give you a few technical writing and publishing vignettes.

The wimpy paper

The paper is competently written, correct, and boring as hell. Why? Because there is no story. Each figure is clear, pretty even.  The problem? The text pertinent to each figure is banal — just stating what the figure shows, what each symbol or line means (needlessly duplicating the caption), and trivially reading off trends. For example, all you get is

” For parameter C>C0, A increases slowly with increasing B. For C≤C0, A is independent of B.”

Yeah, I can see that from the figure, so what? Tell me why it’s important! What does it mean about the system at hand? Give me some nontrivial insight that the figure corroborates. For instance, “This dependence has been predicted based on the Orthodox Theory, but it was never experimentally measured before. The measurements presented in Fig. X confirms that Orthodox Theory accurately describes the underlying physics.” Alternatively, “The dependence of A on B presented in Fig. X is in contrast with the Orthodox Theory, which predicts A to be a monotonically decreasing function of B for all values of C.” Then go on to say what you think happens and why, ideally support with a different set of experiments or new theory theory.

I hate the wimpy, non-committal papers where the authors don’t state any conclusions or make any strong statements. Science isn’t stamp collecting, it requires you to understand and interpret data; the understanding and interpretation are what’s included in the body of knowledge.

The “I will make you sweat” paper

In my field (and many others, I am sure), there are comprehensive papers and there are letter papers that are typically 4 pages long. A well-written letter should be readable and understandable with <50% of the focus on the part of the reader. You should nudge me towards what I should think, with figures and text playing off and reinforcing one another. Don’t make me sweat like a constipated buffalo, reading two terse, cryptic paragraphs over and over again, trying to figure out what on earth you are talking about and how any of it has anything to do with the data in the figure (or common sense, for that matter).


This is mainly for professors, but others can play as well, and I know the variation will be drastic among fields.

How many papers can you conceivably write in a year?

I mean, the papers on which you are the lead author or do a significant amount of writing? I work almost exclusively with trainees and each paper is a lot of work: I can’t just sit and write it, we have to do the back-and-forths, the edits and the teaching. It takes a lot of time. I think my upper limit for papers where I am really involved would be 1 paper per month on average (more during the summer, less during academic year); usually, it’s less than that, roughly 1 paper per group member per year (senior ones can do 2, junior ones have 0, but it comes out roughly about 1 per group member per year). Full disclosure, I had 8 papers last year; I suppose if I had more than 12 people in the group we’d run into my own bandwidth limitation.

I see these people with 20+ papers per year from their group and I wonder — how? I suppose it depends on the length of the paper (a 4-page letter versus a 12-page comprehensive paper), how many senior people are on the paper (which can be a blessing, as they hopefully know what they are doing, and a curse, since they can be super busy and make it hard to get the edits done with), if you have good postdocs or research scientists… But still, how do you produce so many papers per unit time? I suppose there are these elevated planes of productivity that are like Mount Olympus: only a select few ever reach them.

Which brings me to a related question: There is definitely a need to edit and revise papers before submission. At some point, the gains from successive edits become insufficient to justify the extra time. This issue is particularly important when attempting to publish in high-profile journals,  as an insane amount of polishing goes on just to get a chance to pass the editorial desk and go out to review. A recent paper of mine with collaborators took years of hard work of several people, and about 2 years of writing and editing, and eventually went into a Glam Offshoot. Unfortunately, it seems we may have missed the wave of interest or whatever, because, after all that time and effort and the battles with reviewers, it doesn’t seem to be attracting much attention. Oh well.

So how do you decide when to pull the trigger? When it’s perfect? (Never.) When you are sick of it? When the student reaches the point of sending you two emails per day, begging you to submit already? When your grants are up for renewal? When you’ve done the three back-and-forths with student, edited the final version for two weeks and it’s as good as it’s going to get in the near future?

Update: This week’s PhD comic