What ever happened to “major and minor revisions?”


Since I started submitting papers (around the turn of the century) editorial practices have evolved. Here’s a quick guide:

What used to be “Reject” is still called a “Reject.”

What used to be “Reject with Option to Resubmit” rarely ever happens anymore.

What used to be called “Major Revisions” is now called “Reject (With Invited Resubmission)” with a multiple-month deadline.

What used to be called “Minor Revisions” is now called “Reject (With Invited Resubmission)” with a shorter timeline.

And Accept is still Accept.

Here’s the explanation.

A flat-out rejection — “Please don’t send us this paper again” — hasn’t changed. (I’ve pointed out before, that it takes some experience to know when a paper is actually rejected.)

If your paper needed some tweaks, but mostly looked in shape, then it was then it was common to get this decision: “Accept With Minor Revisions.”

I can’t even remember the last time I got an Accept With Minor Revision, except when the only required changes were formatting. As far as I can tell, that category no longer exists. What happened to Accept With Minor Revisions? That is sometimes now called just Minor Revisions, or more often, just Revisions.

Editors are not using “accept” in connection with a manuscript, unless the paper is in its absolutely final version. This is a change from prior practice.

Nowadays, authors have less leverage, it is inadvisable to be vociferous about the need to comply with minor revisions about a paper that is not yet “accepted.” This is neither good, nor bad, in my view.

What used to be “minor revisions” is now “Reject With Invited Resubmission.”

There also used to be an “Accept With Major Revision” and that’s also gone the way of the passenger pigeon. It wasn’t a common thing, but it did happen.

Not all “Reject With Invited Resubmission” decisions are the same. Some of them will go back out to reviewers, what used to be called “major revisions.” Some of them won’t go back out, what used to be called “minor revisions.”

How can you tell the difference? How do you know whether it’s going back out to the reviewers? If you’re in luck, the editor will tell you the plan. But they might hold their cards to their chest on this one, because if they say that they’re not planning to send it back to reviewers, then it authors might try to slide through without as much attention to the revisions.

Here’s one clue: How much time do you have to do the revisions? If you have just a month, then it’s not major revisions. Those are unlikely to go back out to reviewers, I would think. But if you’ve got three months or six months to do the revisions, then those are a bigger deal in the mind of the editor and those are likely to be seen by reviewers again.

Back in ye olden days, a “Reject with option to resubmit” used to mean “There are pretty good reasons why we aren’t accepting this paper, but if you can do something big — like extra experiments or reconfiguring the central premise — then we’ll be glad to take a look.”  Nowadays, those papers are usually just rejected.

So why have these changes happened? Why is it that editors don’t say “accept” until the final version arrives in their inbox? I see there are two main factors. The first one is that it’s easier for the editor to make sure that the authors comply with suggested edits. As an editor, as I’ve had authors at the “minor revisions” stage push back against smallish but important changes. This was frustrating for me (and I’m sure it was for the authors too), but it would have been a lot harder to handle the transaction if the authors had already been told the paper was accepted.

The second reason (as far as I can see) we don’t get “accept” decisions at the revision stages is because of changes in scientific publishing and bibliometrics. There are a lot of new and good journals. Authors have options, and people are (often irrationally) focused on rapid turnaround time for their manuscripts. A couple metrics are “time to acceptance after submission” and “time to print after submission.” If a paper is officially rejected with invited resubmission, and a new version is resubmitted with revisions, then this dramatically cuts down on the time-between-submission-and-acceptance metric. If authors get an acceptance with revisions, then they have no reason to rush the edits, and time-to-print would take a lot longer. And the journal looks slower according to the bibliometrics. And journal editors are under pressure to keep those bibliometrics looking good. Am I off base on this? That’s at least what it looks like to me.

In a separate development, journals are more likely to pull the trigger on “desk rejects,” rejecting a paper without sending it out for review. If an editor is pretty sure the reviews wouldn’t end up being positive enough, or if the project can’t be made fit the journal’s scope, this makes sense. Considering how hard it is to land reviewers, you don’t want to waste reviewer effort for a manuscript you’re sure you’d reject anyway. (I’ve gotten a number of raw desk rejects, by the way.)

I don’t think the game itself hasn’t changed that much, it just has different labels. Now it’s harder to tell whether or not the editor is going to send your revisions out to reviewers.

What prompted this post? Well, several months ago I submitted what I thought were minor revisions, and I haven’t heard bupkis back. (I’m in no hurry, though.) And on a different paper, I just got what looks like minor revisions just yesterday, and only a month to do them, and that short time-frame is a bit rough with the field season starting tomorrow morning.

And I got a rejection last week too. At one point those used to bum me out, but, well, I’ve got thick manuscript calluses. My annoyance-after-getting-reviews-back lasts a minute or so. At some point I’ll write about those calluses.

Words can be powerful: encouraging young women in science.


I’m writing this post because I have been thinking about my career goals and how they have changed since my days as an undergraduate. It is only recently that I have seriously thought that becoming a professor is something I want to do and that it might actually be possible for me to do. One really simple thing helped me to come to this realization. It’s not the only thing, but it was a really important thing for me, so I want to share the story here.

I’ve read a lot of things about why there are fewer women than men in academic science, and one idea seems to be that women just aren’t as motivated as men to become professors. Maybe that’s true – but why?

Maybe girls grow up watching TV shows featuring scientist characters that are mostly male, nature documentaries mainly hosted by men, and news stories or interviews with scientists who are usually men. Maybe most of the science books and toys are marketed towards boys. Maybe girls aren’t encouraged to join the math club or Odyssey of the Mind. Maybe most of their science teachers and the scientists in their textbooks are male.

But putting all that aside for a moment, let’s assume a young woman can enter University with an open mind, believing that any career path is potentially open to her. I was such a young woman.

I didn’t really know what I wanted to do at first, but realized during my first year that I loved math, and entered a mathematics degree program. Over the course of this program, male professors taught all but one of my math courses. A female postdoc taught the exceptional course. Many students complained about the quality of the course and her teaching, and at least one wondered aloud about her qualifications. (She was actually an excellent teacher, but she had a quiet voice and a thick accent so her lectures were hard to follow with so many students talking over her. There was a male professor in the department who was also very soft-spoken and had an accent. When he was lecturing, the room was always silent.)

I never seriously considered a career in mathematics despite doing very well in my program. I did think that maybe teaching high school math was something I could end up doing – I learned that I loved teaching as an undergraduate TA for a first year calculus course in my 3rd and 4th year.

Later I went back to school while working part-time, taking some undergraduate courses in biology. Of the 13 biology courses I took, male professors taught 8. Of my 5 female teachers, four were full-time lecturers; only one was a professor. All of these women were amazing and inspiring teachers. My impression was that my one female professor must have been really exceptional to make it the way she has.

It turned out that I loved biology even more than I loved math. When I considered potential careers, I thought that maybe I could become a lecturer in biology – I still loved teaching. It never crossed my mind that becoming a professor was something I could do, until during my work as a summer research assistant, my PhD-student-mentor’s supervisor stopped me to chat in the hall one day. He told me that he hoped I would pursue a graduate degree in his lab, and that he saw me becoming a professor one day.

I was frankly shocked by that conversation, but also really excited. I still have some trouble imagining myself becoming a professor, but not quite so much as I did then. Since my recent MSc defense, when my supervisor* again told me that he believes I can and will become a professor, it’s something I’ve actually started thinking is within the realm of possibility.

My parents always told me I could do anything I set my mind to, and encouraged my interest in science. Maybe I’m just not that ambitious, and that’s why I didn’t aspire to become a professor during my undergraduate work, despite the fact that I knew I wanted to continue in science and enjoyed both research and teaching. I never consciously thought to myself, hmm, looks like professing is for men (and maybe the occasional extraordinary woman) so that’s obviously not open to me. But it’s pretty clear to me that when I was considering potential careers in science, I looked at the people around me (and noticed people’s attitudes towards them) and that influenced my thinking about what I might be able to do.

The number of women in academic science is increasing, and I think things are slowly improving in a lot of ways. Having good role models and mentors (both male and female), and being a role model and mentor, is really important for female students and academics. And whether you’re male or female, you can help by encouraging girls and young women to do science. Just telling them out loud that they can be scientists and professors if they want to might make a difference.


*My inspirational MSc supervisor was Gerhard Gries, who has been fiercely supportive ever since we first met. I am extremely grateful to him for his continued mentorship, and for always believing in me.

What unemployment taught me about dual-career parenting


I’ve made a point to not mention this over the last several months, because I try to keep this site (mostly) professional. But — of course —  personal and professional matters interfere with one another. We are all working on the same 24 hours per day, no matter how it gets sliced up. Continue reading

Dealing with caffeine addiction


large-shirt-you-want-some-coffee-spies-like-us-parodyScientists drink more coffee than anybody else. (At least, according to those dubious pop-culture listicles.)

I didn’t drink coffee until graduate school. But when you’ve been working for too long, and a friend comes by to ask “You want some coffee?” there is only one good answer.

Now, I have a straight-up physiological addition to coffee.

What’s this addiction like? If I have an anomalous day and I don’t get around to enjoying at least one biggish-sized cup of coffee, then I’m in for a heinous headache the next day. A headache that’s substantial enough to keep me from working effectively.

I’m able to deal with withdrawal symptoms and kick the habit. I did that a few years ago, and after a few days of withdrawal, I was fine with lower-caffeine beverages. Irish breakfast tea was my favorite (maybe because it had more caffeine?). I stayed with non-coffee for a few weeks.

But then I went back to coffee. Why? Because it’s just so good.

I knew that I’d be going back to a physiological requirement for daily caffeine, but I decided that it was preferable to not having coffee. I don’t claim enough personal detachment to say that the decision was rational, though it’d be nice to think that it was my choice. I just wanted to drink coffee.

Is there a cost to this addiction, aside from the money you need to spend on the coffee itself? Yes, but it seems minimal compared to some other addictive substances. But it’s an addiction that requires that, at least once a day, I make or buy coffee, even if it’s inconvenient.

Perhaps it’s not so bad to have a physiological dependence that requires you to take a break from work once in a while.

Recommended Reads #52


What the heck do they put in denatured ethanol, and how and why did they start doing this? “The little-told story of how the U.S. government poisoned alcohol during Prohibition with deadly consequences.”

Here’s a really worthwhile new paper from The Journal Formerly Known as Conservation Ecology: “Unstructured socializing time, education for daring exploration, and cooperation with the arts are among the potential elements. Because such activities may be looked upon as procrastination rather than work, deliberate effort is needed to counteract our systematic bias.”

When I first went to Costa Rica as a graduate student in 1995, The National Institute of Biodiversity (INBio) was full of gleaming promise as a privately-supported venture to catalog, explore, share and profit from the country’s biodiversity. In recent years, it’s been slowly shutting down, and now it’s kaput. Here’s a good story of the ascent and atrophy of INBio from, Scientific American. [update: I’ve been informed that there are a number of factual errors and bias issues in this article, that frankly hadn’t occurred to me when I linked to it. Now that they were pointed out, I definitely see them. Caveat emptor.]

Here is one of the most hilarious things I’ve seen in a long time: “Cambridge, we have a problem.” It’s a news story in Boston when Harvard and MIT don’t get a prestigious NASA grant. Even though, as the article points out, that it doesn’t even seem that the institutions even applied for the grant! Yes, that’s right. there’s a whole article in the Boston Herald about how it’s an outrage that MIT didn’t get a grant that it didn’t apply for. 

The NSF Division of Environmental Biology outdoes itself again with a big summary of numbers about per-person success rates. Because some PIs get multiple awards, the awards statistics can be confusing. These data fix that problem. One thing that caught my eye: men are more than 70% of the participants of DEB grants.

Community colleges are great for people who are clearly on a well-paved trajectory for a four-year university. For those who aren’t, though, not so much. “Enrolling in a four-year college brings large benefits to marginal students.”

What is the relationship between student performance and their evaluations of the professors who taught their prerequisite courses? The more students dislike your course, the better they do in future semester. At least according to this paper (actually I didn’t read it, but according to the blog post that cites the NPR report of this paper, that’s the take-home.)

Student effort declines as the average grade increases.

Open peer review: a randomised controlled trial. Signed reviews are, very very slightly, better in quality.

Ecologists far too often use causal language for relationships that clearly are not known to be causal.

Two scientists die while conducting Arctic fieldwork, because of the thin ice that they were out there to document.

Here’s an interesting conversation between developmental biologist Sean B Carroll and EO Wilson.

How to become a(n) ________ologist. The post says “arachnologist,” but it just as easily be any any other organism. Next time a parent asks you, “my kid wants to study X, and what should I do?” – this link can help that conversation.

Even more from Arthropod Ecology: Do students who complete an exam more quickly (or more slowly) do better on the exam? Chris Buddle’s answer is “no.” (I actually did the the same thing several years ago for a few exams, and in contrast, I consistently found an overt negative relationship between the completion sequence and exam score. In that course, the time allotted for the final exam was rather long, and I found that students who were unprepared would just spend a lot of quality time with the exam with the hope that enlightening might strike before they handed it in. Those who prepared were just, “bam – bam – bam – I’m done.” If you’re curious, my exams were about 4-5 pages of short-answer responses, and some problem-solving sections. Unlike Chris, I don’t have the data to share with you.)

Mythbuster Adam Savage has a great prescription of for STEM education: Bring back shop.

Planning your field work? Have you thought about safety?

The New York Times is still pretty good. But man, they don’t just understand California. Exhibit A and Exhibit B. Does LA suck or does it rock? Make up your mind, folks. (Anyhoo, the NY Times still does a good job with other stuff. Like this gorgeously illustrated piece about Messenger’s mission to, and collision with, Mercury.)

Instead of the NY Times, learn more about Los Angeles from filmmaker Werner Herzog and why he chose LA as his home. And also about how and why he chose to end Grizzly Man as he did. And about how nonchalantly he took getting shot while getting filmed for an interview with the BBC.

While we’re talking about LA — it turns out that >80% of nail technicians here are Vietnamese. That’s not a surprise, but is it really true that this is the case because of Tippi Hedren? And just for current context, there are ethical misgivings about nail salons.

Here’s a nice story from BBC about how one species of ant excavates really well, with some good video. (But you can ignore the pitch about how successful digging is part of the success of an invasive species. That’s just a dumb part of the sales pitch. For all we know, non-invaders dig just as well.)

From last year, here’s a great backstory about Maryam Mirzakhani, who was awarded the Fields Medal in 2014. If you know a girl who loves math but doesn’t feel good at it (does anybody feel they know enough math?), this could serve as some inspiration.

Here’s an important post about Gender Issues in Taxonomy – more than just Latin. If science has a gender problem, then systematics has a big big gender problem.

If you’re reading this site, then you also probably have heard elsewhere about the outrageously sexist review that one scientist got from the editors of PLOS ONE. It’s summarized here in a story from Science. Considering how bias in reviews like this isn’t an extreme rarity, it’s interesting how this one picked up so much steam. I’m guessing it’s because one specific argument of the reviewer (about how women are less vigorous than men) are so absurd and offensive and bizarre. An additional negative consequence of this affair is that PLOS ONE might be requiring reviewers to be non-anonymous. That would just require the sexist reviewers to hide their bias more effectively, meanwhile making the environment more difficult for junior scientists. Ugh. But as people point out, if you’re asked to do a review non-anonymously, then you don’t have to say yes. Then again, that’s not a good way to win the favor of influential editors, either :(

As for the outrageous PNAS paper that erroneously declared a bias in favor of women in STEM hiring decisions, this is the wittiest and most-spot on response. Meanwhile the authors of the original piece have chosen to respond to the great number of critical replies, the majority of whom are women. However, the authors somehow only chose to respond to the male critics. Huh? That irony itself speaks volumes.

Here is a summary of a good conversation about informal science education.

The anticlimax of finishing your dissertation.

Ta-Nehisi Coates on the Baltimore uprising. (This event resonates on my campus. We were essentially created as a university fifty years ago, in the aftermath of the Watts Rebellion. The campus was put in a huge patch of undeveloped land, just two blocks from Compton, to provide higher education for a community that has historically been denied access. We — as an institution — are a tangible example of a positive community response to uprisings that manifest from systemic violence and murder by police. Creating our university obviously didn’t fix the problem of police violence against black men — the LA uprising in 1992 was a response to the acquittal of the police who assaulted Rodney King. By remembering that we were united with the charge of rectifying a diffuse systemic illness, we are able to have higher expectations of ourselves and our broader community.)

Faculty mentoring faculty: Relationships that work (and those that don’t.): “If mentoring between colleagues happens in the context of relationships, then that explains why structured mentoring programs are only intermittently successful.”

Macroecology is not like particle physics


There are different kinds of mystery. Subatomic particles are almost illogically tiny, so we can only figure out what’s happening with big machines, long-term data, ingenious experiments, and a bunch of logical inferences. Because science is hard, then there are some simple facts about the world that we don’t know. For instance, the cause of gravity. It’s a mystery, but we have a specific question that we’re trying to answer, even if we don’t know the direction from which the answer will emerge.

We are missing fundamental facts at the foundation of physics. As Donald Rumsfeld would say, there are known unknowns. We know that there are certain things that we don’t know about physics, and are working to know them.

Ecology has a different kind of mystery. Continue reading