A paper. A day

a aper

I am now, very officially, in the last year of my PhD. In about a year, a big chunk of results will be published, and I’ll be defending my thesis in front of a committee. One of the things I don’t do enough, in preparation of this, is to read. It’s difficult to find time for it -especially during busy days-, but I decided I just have to take it, anyway.

I ambitiously decided to read 1 paper each day, until the day I defend. With a few exceptions authorized, I am not a robot. Hey.

I’m not very good at keeping resolutions, but that one, I’d really like to. I also see it as a bit of a challenge. So, to keep track,and also share it, I decided to create a Tumblr. account especially for this: https://www.tumblr.com/blog/drosophilista

Basically, I’ll post each day the paper I’ve read. Not sure I will have time to incorporate notes. But I’ll tag is at open/closed access. Good way to estimate how many papers I would miss if my university didn’t have a suscription to all main journals.

I started already last monday, and have been quite diligent since, so let’s hope it continues like that. How much do you read ? How do you do it ? I’m interested to hear your experience, so please leave a comment !

Let’s not give up just yet. Change might be ahead.

After last month’s rough patch, things have -fortunately- improved a bit. Just at the time I was jaded about the wonderful world of academia, a few little things happened. And they have the merit to put me back  in a more combative and optimistic state of mind.

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Everyone I’ve been talking about the worst sides of academia actually agreed with me on the system’s unsustainability. It’s bad, because it reflects how weary people are this days. It was also irritating, because most people would just say things like “It’s the system, it won’t change, you have to play the game …”. I deeply think my french education clashes with this. I simply can’t understand this attitude. Not doing anything against this consumes my energy bits by bits. Petitions, strikes, but more importantly, constructive changes and improvements are incredibly important to me.

A few events  -small or more consequent-, the past week proved me, once more, that I’m not the only one to think like that.  And it seems things could change for the best in the future.

First, let’s start with the smallest thing. Lego is starting to commercialize women scientist toys. It’s a very small step, but it deserves to be highlighted. And probably does a better promotion of women in science then that awful spot EU had managed to come up with a few years ago.

Second, I made a pact. With a friend of mine, a senior post-doc, and aspiring future PI. If we ever get in these positions, we will take action to improve the system. Not that we cannot start now. For example, I decided that my thesis committee will be approx. 50/50 men and woman. Because sometimes you have to force things before they seem normal. And I don’t want to defend in from of a committee with only 55+ men; even tough it’s almost a tradition at my university.

Third, the cherry on the cake. We received an email from our department’s administration, asking for a report on the research output from each PI. A report they want every 3 MONTHS. MONTHS. I will not even take the pain to explain how crazy that is. Anyway, one of the PI’s  send an email back (cc-ing everyone) saying that this was simply demotivating, un-inspired, and useless. I was so happy someone actually stood up and dared to say no. No to this non-sens. No to administrators who have no idea that a good research paper necessitates years of work. No to evaluating research on a simple count of papers. Whatever they contain. I, and a few more PhD’s were so happy about this that we decided to buy a bottle of excellent scotch as a sign of support to that PI.

So yes, I think it will be possible to change things, as long as enough people are willing to simply say no to non-sense. And I hope our generation will have that strength.

5000 words, 3.5 years, and …

and now it really starts. La merde. The past week has probably been one of the most hellish week of my PhD.

See, the last 3 years, a.k.a., phase 1, I’ve been happily working on a research project. Starting almost from scratch, developing hypotheses, performing lots fo experiments, and slowly building up enough data for a good research paper, making the final figures, and writing (summarizing) it in 5000 words. That was the good, innocent and enjoyable part of being a PhD student.

Then came phase 2. Submission. And rejection. And submission. And rejection. And submission. And rejection. And submission. I don’t know when it will end.

Nooooo, I wasn’t cranky. No, I wasn’t sad. No, I did not feel like my main job had become formatting stuff in Word. And counting character numbers. And converting PDF’s. And all of this meaningless s*****, just to be done for one or two days, before it came back, again, without explanations. Or standard letters. No, I did not half-joke with my supervisor I would open a bakery after my PhD and be done with all this non-sense. No, we did not have that depressing debate at university, about non-existant career perspectives, burn-outs, and universities being ruthless and terrible employers.

So let me make it clear: I know that no paper ever gets accepted just like this. It’s normal that it gets rejected, and reviewed, and edited. Nevertheless, it’s hard, because this is my work. My project for the last 3 years. Week-ends and late evenings. Overall, very hard work. And I find it impossible to stay calm, neutral, unaffected, placid, and objective in that case. We are people, not emotionless humanoids.

Yes, this is all normal. And it will eventually go away, because, yeah, experiments need to be done. The classic 4 phases I described previously. (I’m almost in phase 4, by the way).

 It is a bit less normal that subjective (or do I want to say, profit and hype-driven) editorial decisions control your scientific career. And by this I mean, it is even less normal that an impact factor, which is nothing more then a stupid number, is almost the only, yes, only, indicator, on paper, of the quality of your science.

And you know the part that revolts and disgusts me deeply ? It’s that we, scientists, do nothing about this. Or let’s say, almost nothing. “It’s the system, you have to play the game, it’s a phase we all go trough, you’ll never change it, bla bla bla …” .Yes, we are scared people, collaborating with an unfair and stupid system that ultimately drives good scientists in an other direction. Or should I say, kicks them out as soon as they are not productive enough. But why should it matter when you have tenure, or publish enough, or get grants … everything’s fine, right ? And why should it matter when you know the expiration date of your career already ? Haha.

Now, the question that I haven’t figured out yet is, can I comply to these unwritten rules ? Can I accept and play that game ? When do you stop looking at yourself in the mirror ? Frankly, I have no idea. I’ve written on this blog mostly positive things about science (1,2,3,4, and many more). They remain true, and I do still enjoy all these things. This hasn’t changed.  But is the price to pay really worth it ? That’s the million dollar question. Bah. Future me will figure it out. For now, I have to get back to the paper factory sometimes called university.

And, if I ever make my way in there (less then 10% chances, yes), dear bloody system, I am coming for you. I’m not alone. And you don’t know who you’re messing with. Like all revolutions, this one will start when the last straw breaks the camel’s back.

 

–Sorry for slight excessive dramaturgy, I really needed to rant write this down and get it out of my head.

Can you … Count flies with your iPhone ?

… The answer is YES !

I got this question from a reader of this blog a few month ago on a previous post. I thought I would share the answer I had given him over here as well. Just in case a poor student, somewhere, spends time counting manually and googles something like “isn’t there a better way to do this ?” …

If you recall, I wrote about this app called Fast Counter, developed by Shazino, and available on the App Store. It does a very decent job counting bacteria on petri dishes, as long as there are not too small and dense.

For a drosophilist, the connection from counting colonies on a plate to counting flies on a pad is not too difficult to make. So I tried it by myself (because, really this was a high priority ;)) and it worked very well.

Of course, flies should not be too dense, and not sticking to each other. By setting the detection threshold in the app, you will actually get an extremely decent accurate number.

Here is an example of the read-out you get:

Experience_#16

Pretty good stuff, huh ?

Maximal number of flies you can count would be around 200-300, accuracy of course is better if you put less.

Have you eve tried it ? If so, what are your impressions ?

 

 

 

A new year, the last year

It’s been long since I have not written about anything here. As the title of this blog says it, this new year 2014 is officially the last one of my 4-year PhD track. It feels weird and right at the same time.

Weird because time goes by so fast, because I’m starting to seriously think about what I want to do next, and because I can actually see my PhD ending in a still-blurry but imaginable future.

Right because the 4th-year PhD student I am is so different from the 1st-year PhD student I was. I enjoy being in the lab so much more, I feel like I belong there. Right because I look forward to be a post-doc. It’s scary, but I guess the right kind of scary. The same I had before I started the PhD. Right because although I love the place I’m currently living in (The Netherlands), I can also see myself moving somewhere else. Some place more sunny, and maybe a bit of a bigger city.

I’m blogging not-so-regularly (to say the least) anymore because everything got busier, denser, intenser the last months. Paper writing, experiments of course, but also conferences, abstracts, student supervision, and having a life besides of this. And it works well right now. I generally enjoy this business, and somehow work more efficiently and productively in this context.

But I wanna try posting stuff here regularly in the coming year. For the few people out there it could be interesting for. And for myself, because I like this idea of holding a “mood board”, or “journal” of my PhD times.

So I’ll come back soon, hopefully with something more substantial then New year’s Resolutions.

Always on our minds ?

We had an interesting discussion today around coffee break … a colleague asked me if I had been thinking about my research during my week off. I immediately said yes, but it was not everybody’s answer.

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I have to admit I find it difficult to “disconnect” just over a week of holiday. It is easy to quickly check e-mails, and even to think of your projects just by looking around you. I see insects, I think fruit flies. I see sick people, I think immunity. I think I made my point. Now, if I am on holiday far away for a month, I could imagine not thinking about it every single day. But otherwise probably not.

Now, what is the good attitude (if one can do anything about it) ?

  • Is it good to be able to forget, take a few steps back, and start up with a fresh mind ?
  • Or is it just normal that people very much into their subjects like us cannot completely exclude it form their lives ?

I don’t have a clear opinion about it, since people in research can be quite different in the way they approach research, and in the way they pursue this demanding career. I will ask a few more people around me and update this post if I have more comments !

Please share you opinion in the comments and fill in the poll ! 

10 ways to insult a scientist

Although the scientific world is relatively civilized, people developed subtle ways of insulting each other without really saying it. Here is my top 10.

fighting1

1- Does mainly applied research. The rivalry, despise, and even haste between “fundamental” and “applied” researchers is just as legendary then the one between New York and New Jersey, France and England, Mac and PC’s. Somebody coming from the “fundamental” side will use the sentence “does mainly applied research” if they want to say “Basically, does no research at all“. Baaam.

2- Is a good teacher. Can be the correlate of ” … but, is bad at science”.

3- Has been tenured since a long time. Sounds positive at first, but actually means this person has been like a mussel on the rock. Inactive, boring, and aggregating foam on the back. Motivation to do novel and innovative research is close to zero.

4- Publishes in specialized journals. Sneaky one. Although publishing sounds like a good thing, the “specialized” part of this sentence actually means low-impact, low-interest or low-quality.

5- Is often gone on conference. Generally said of big wigs. Actually means they spend all their time attending meetings and doing PR, rather then taking care of their lab and research.

6- Research is mainly based on correlations/descriptions. That’s an other way of saying that the research lacks depth, or mechanistic details. Ouch.

7- Is good at bench work. Implies that this person is basically a technician, and is not interested/capable of sitting down to read, write, or think. You never want to hear this about yourself.

8- Is present during work hours. Again, seems like a nice comment at first, but this is actually a hidden way of saying “is present only during work hours”. Means this person is never in the lab late or during week-ends. Possibly implies low motivation level, or low output.

9- Is a nice person. Hum, like in other relationships, the adjective “nice” is generally used when nothing else is applicable. Smart, pretty, funny, etc … In science, the “nice person” is the one people like to hang out during lab outings; and chat with, but not about science. So it basically means not-very-good-at-science-but-nice-person, again.

10- Is too busy to attend seminars. Missing a seminar here and there, because a crucial experiment is going on is understandable. But some people might always claim being too busy. This means, uninterested in anything else then there own little subfield, and lazy to walk up a few floors to the seminar room.

 

So, do you recognize some of these ? Isn’t science a cruel world to live in, after all ?