Archive for the 'publishing papers' category

My year in numbers and books

Some years are characterized by all sorts of spectacular numbers, like having 3 different jobs and living on 2 different continents, like 2014 was for me. This was not one of those years. This year was mostly characterized by me learning that a marriage is something you should never take for granted and always put work, effort and love into in appropriate amounts. Having little kids and a busy job, I seemed to have forgotten this and I sincerely hope the wake-up call I got this year came soon enough. I haven't written about this on the blog and will not write about it more than the two sentences I just wrote because this is clearly not just about me.

Otherwise, this was 2018 in numbers for me:

1: the number of manuscripts submitted with my name on it. I might actually publish something again in 2019 after 4 years of no new Pubmed entries.

3: the number of countries I visited. All with family, none for work this year sadly. Although now that I think about it we drove though more countries on our way to these, but I guess those don't really count.

5: the number of jobs I applied for.

Also 5: the number of jobs I didn't get. Which was a blessing in itself because halfway through the year I realized the cool things I can do in my own job that I had lost sight of earlier in the year.

6ish: the number of things I crocheted. The 6th item is by no means finished yet, because it's going to be a pretty large blanket for on the couch and I've been working on it for over a year. It's almost a meditation of enjoying the process instead of being focussed on the end product, probably something I should learn how to do better.

16: the number of books I finished, highlights being:

  • Ellen de Bruin: Onder het ijs --> such a good book, when will it be translated in English so most of you can read it too?! It's about academia, #MeTooSTEM and I just could not put it down!
  • Angela Saini: Inferior --> about how science and society have told women that they are inferior to men and all the reasons why this is not the case. Highly recommend!

All the books I read this year

750: the number of kilometers I ran this year, thanks to many people on twitter cheering me on!

All the kilometers I ran this year

10,000: the number of views this post received back in February when it went a little viral.

Happy New Year's Eve (if that is something you care about) and see you in 2019!

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On finishing papers after leaving the lab

Yesterday Michael Eisen tweeted this. I replied that I had actually finished 2 papers from grad school during my post-doc and 2 post-doc papers in my next job. In all honesty, I also still have an unfinished paper from grad school. So how did I do this and what factors are important in determining whether you'll be able to finish that paper after leaving the lab?

I think what helped me most is to make it non-negotiable with yourself whether those papers are going to be finished. They just have to get finished. Think of it as brushing your teeth: you don't ask yourself each day whether or not to do it, you just to it and that makes it take much less effort than to continuously negotiate with yourself whether to do it or not. And especially during the transition between grad school and post-doc, I just HAD to finish those papers because I knew that getting them published would make me more competitive to obtain a fellowship (my long-time readers may know that I never actually got a fellowship or grant, but still). After transitioning into industry it was a bit different, but in my current job I can still use published papers as a sign that I was productive, collaborative, etc during my post-doc.

What worked best in my experience to finish papers while in another job, was to allocate an hour in the morning to work on the paper and then switch back to my actual job. I would probably do this 1 or 2 days a week so progress was generally slow. Every now and then I took a whole day of, for example to write the discussion, which is really not something I can do in an hour here and there but requires a longer stretch of attention. With the generous amount of vacation days where I am now, this was something I could afford every now and then to get the paper finished. Also, sometimes I would work evenings or weekends on an unfinished paper, but I'd like to keep that to a minimum.

A big determinant in whether or not you are able to finish papers after leaving the lab is whether your co-authors are cooperative and also want this paper published. If they need to play a big part in getting it finished and for some reason don't do their part, this is clearly outside your circle of influence and will make it hard to get it done. So before you start taking days off to finish a paper, it is wise to make sure that everyone is on board and agrees on who does what.

And I want to finish by saying that while I believe it is do-able to finish a paper after leaving the lab, if you are the grad-student or post-doc that leaves, I think it is also okay if you decide not to finish a paper. If getting the paper published is not going to bring you much, and the costs of putting in the effort outweigh the benefits, then just don't. But in that case, I would be clear about that because there are few things I dislike as much as revisiting decisions and keeping half-finished things in the back of my mind and/or harddrive.

What about you? How do you deal with unfinished papers after leaving the lab?

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On the time given for a resubmission

A discussion I've been having recently: If an editor gives you x amount of time for the resubmission of a manuscript, but the reviewers suggest additional experiments that take longer than x amount of time do you:

A. assume you don't need to do those experiments to get your manuscript accepted

B. ask for additional time to do the experiments?

I suggested to do B by the way.

4 responses so far

Guest post: Baby vs. work - why choose?

This is a guest post from a friend who would like to remain anonymous. She is a bioinformatics post-doc and a single mom by choice, and this is her story about combining work as a post-doc with being a parent.


I am incredibly lucky.

Let’s put that first, because I’m very aware that this is the case: not only do I get paid for doing what I love, but every day I get to bring my infant son with me, too. My boss is OK with it, the department is happy to tolerate my son’s occasional shrieks echoing through the hallway, and my office mate is completely in love with him. (I totally understand that last one, by the way.) Also, I’m not working in the lab at the moment, so there is no risk of spilling acid on my brand new baby. All of this means that I don’t have to choose between work and family: I get to do both, and whichever part insists the loudest gets most of the attention at any given time. I know that not everyone has this option; I am thankful that I do.

Here’s how the logistics work out: I have a playpen in my office, where he spends most of the time gurgling and attacking his mobile while I do low-level work; assembling figures, processing images. When he nurses, I read. In fact, I feel I get a lot more mileage out of my reading time now, as there is very little incentive to multi-task. And when he naps, I get to focus properly, and code or write. (He won’t nap in the playpen, only on me — but it turns out I am perfectly able to code with a three-month-old on my chest, drooling on my shoulder and snoring in my ear.)

That’s not to say that our arrangement does not lead to the occasional conflict. When I am trying to figure out something difficult, and he’s fussy or crying — or simply wanting my attention. Fortunately there is almost always a colleague who doesn’t mind taking a baby for 10 minutes (I never realized how much work could be accomplished in 10 minutes of baby-free time! Take note, ye childless!) while I finish whatever needs doing, so I can then focus on my child.

Also surprisingly doable, I found, are meetings and seminars — provided people are aware that I am there with a baby, and OK with it (or at least not too vocal in their disapproval). Carrying him in a sling usually means he falls asleep, and if he gets fussy I can walk around a bit to calm him down. He’ll never be completely quiet, but really he’s no more disruptive than a random audience member with a cough.

In fact, the biggest barrier to success in that case is me: I once snuck in a seminar after it had already started, with my son sleeping in the sling. Sleeping babies, I found out at that moment, are actually quite noisy, and his occasional squeals made some people turn around to check the source of the sound. That — not the noise itself — made me so self-conscious I spent all my time worrying about being disruptive and trying to shush a sleeping baby.

(Yeah. That makes no sense to me, either.)

Then a few weeks later, I joined a seminar at a university I was briefly visiting. My host quickly pointed out to their colleagues that “we have a very young scientist in the audience!”, everyone smiled, and the speaker started. This time, no one was annoyed at the intermittent baby noises — they already knew he was there, and I knew they knew, so I could relax, too. My host had opened the door so I could walk in and out in case he started to cry. This worked well for me (I could actually focus on the talk!), and while I didn’t poll the audience afterwards, I would guess it worked for them, too.

No, I am not as productive as I used to be and as I would be without him. But low-level productivity is productivity still. For example, when he was 10 days old, I submitted a paper. It took me two days, assembling all the documents and filling out forms in between feeds, diaper changes, and many, many cuddles. I typed the cover letter with one hand (which was not that bad, as my brain was about as slow as my typing at that stage). Nevertheless, at the end of these two days I could tick it off my list. Point here: there is a lot of downtime in taking care of an infant, and you might as well use it. That is not to say you shouldn’t use it for Netflix or naps — I did a lot of that, too — but think of it as an IKEA workday: some assembly required.

I know his is not going to go on forever: in a few short months he’ll be mobile (I both dread and look forward to that time), which will most likely throw a wrench in the works. But I’ll worry about that later: this is precious time in a baby’s life, so every day I get to spend and bond with him is valuable. For now, this is what works for us. And I feel very lucky indeed that it does.

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How I should have handled the thing

The other day I wrote about how the following thing happened. As many people have pointed out: a. it is hard to distinguish exactly who the idea-owner was, and if so, this is not that important, and b. I should have said something earlier. Looking back, I clearly see what I should have done differently:

First, while we were brainstorming about what I could write my fellowship about, I should have asked if our stuff would be different enough. Perhaps I should have even asked if they were okay with me proposing this, as they may have felt it was close to their research-niche. I guess being open about this, rather than assuming someone would speak up about this could have avoided this situation.

Next, when they told me after I had just joined the lab that they were performing these experiments, I should have said something other than "Oh. Okay", which is what I said because I was so surprised. I should have expressed my surprise and have a conversation about how to move forward. Instead, I never said anything because I was afraid I would get upset and cry about it. And the longer I waited with saying something, the more upset I got about it.

So the biggest lesson here was that it is important to immediately have a conversation about things like this, instead of just whine about it on the internet.

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The following thing happened

A couple years ago I was applying for personal fellowships to return to the homecountry and work in a PI's lab in order to set up my own group within their bigger lab (which is how things usually go in the homecountry). I talked to a junior groupleader (JG) in this lab and we brainstormed about what I would write in my fellowship. I wrote the fellowship and asked JG for feedback because they had experience with said fellowship. I submitted the fellowship and it got rejected. Twice. Then I moved back to the homecountry and JG told me they were doing one of the experiments that I had proposed in my fellowship. And recently I saw that they had published the results. Aim 1 of my fellowship is done. But not by me. If this doesn't make you a disgruntledpostdoc, I don't know what does.


What is the worst academic backstabbing you have experienced?

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How many of your co-authors have you never met?

Looking at a large list of co-authors on a paper I came across, I wondered what it would look like if all of those people were ever in a room together discussing who would be first author and why. Would every author have met the others? Then I realized that I have published with a couple of people that I have never met in person for a variety of reasons. In fact, of the 12 papers I published, I counted 11 names of people that I have never met in person. I may have corresponded with them via email but I've never actually met them. That may be because I was only briefly involved to do one experiment for somebody else's paper, because there was a collaborator on my paper who figured that their department head also needed to be a co-author or because collaborators were on the other side of the world and my role in the project was never big enough to warrant going there.

What about you? How many of you co-authors have you never met in person and why?

15 responses so far

On receiving feedback

When I just started as a grad student I got annoyed and upset when receiving feedback. For example, when I wrote the first draft of my first abstract for a conference, my advisor rewrote it almost entirely. There were maybe a couple words there that were still mine and they were probably "the" and "rats". Otherwise, the abstract was completely different. And with different I mean better of course, but then I found it hard to admit that back then.

Now, when I write something and I receive hardly any feedback or none at all, I get annoyed and upset. Over the years, I have learned that feedback means that people care and they want you to help improve the thing you wrote. No feedback means they either don't care, or don't have enough time to look at it.

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Is it necessary to have a high impact factor paper for a job outside academia?

Recently, when discussing how to make the transition from academia to industry, someone asked me if you need high impact factor papers to get a job in industry. I started the answer by saying that I am no expert on this. I am just one person who got one job in industry, so I do not pretend at all to know how things work. But, after talking to people involved in hiring other people, I gave the following answer:
Just like having a PhD shows that you can bring a multi-year research project to a successful end, having a first author high impact factor paper also implicitly shows some things – even to recruiters or hiring managers who do not necessarily know much about academia. It shows that you have worked on an important scientific topic, usually with other people from other disciplines, and that you have been very persistent in getting your work written in a persuasive way and fought the battle to get it published.*But at the same time, we all know that there’s a whole bunch of luck involved in getting a high impact factor paper. There are plenty of people who work just as hard, but happen to not show that hypothesis hold true. Or that p-values are lower than 0.05. Or have the ability to do all the experiments that reviewer 3 asks for. Those people may have worked just as hard and have exactly the same experience that is valued outside academia- if not more.

So in that sense, getting to a high impact factor papers is like climbing a mountain, where the getting the paper accepted in that high journal is like the picture taken at the summit. If you show the picture to people, it is immediately clear what you have done to get to the top. But some people were less lucky and they climb the mountain when it is so cloudy that on the picture you can’t even see that they are on top of the mountain. They climbed the same route and may even have had a harder time due to the clouds, but it’s not as easy for them to prove it.

My answer to the person who asked this, was that it you do not have high impact factor papers, you may have to work a bit harder in your CV to point out all the things that you have done in academia. To compare it to the mountain, you may add a map of the trail you took to the top, or you have to explain more about who you climbed the mountain with.

*Alternatively, it shows that you were at the right place at the right time and the grad student who was working on the project decided to leave so you only had to pick up the pieces, massage the data to get to put some stars on your graphs, give them to your BSD advisor who writes a persuasive cover letter and gets the paper right into Nature. That shit happens too, I hear.

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What the nature series on post-docs forgets to mention

Naturejobs has a whole series about post-docs which is quite interesting. Today's post is about finding the right lab and PI.

“If you chose the wrong lab, a lab that isn’t publishing heavily or is not pushing you, you’re not going to be able to get the papers you need to get into that lectureship or fellowship position that you’re looking for.”

They list a bunch of important things to consider and most of them have to do with strategically planning your career as a post-doc. What they forget to mention is that it is very helpful when your PI is flexible and open to change. As a post-doc, you can change from someone who is single and in the lab 80 hrs a week to someone with a family who needs to leave at 5 to pick up their kid. Or you can change from someone who wants to become tenure track faculty at a fancy-named university to someone who would rather pursue a career as a science writer. Then, it is no longer the most important thing to that your PI is an important scientist who cranks out high impact factor papers, but it is nice if she is supportive of your choices. (luckily the nature piece acknowledges this in their last paragraph, that loving what you do is very important too). But when looking for a post-doc position, knowing that I would maybe want to have a baby in the time I was there, that was the hardest thing: figuring out if a PI would be supportive. I've seen instances where the support of a PI greatly diminished when post-docs started their family or looked for jobs outside academia and it doesn't seem like something to bring up at your interview. So, how do you find out if that supportive mentor is willing to support you through periods of change from the initial plan?

And then just before posting this I saw this post from the new PI about the questions to ask when interviewing for a post-doc position.


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