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:


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 ?




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.


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 ?

Book review 3: Sydney Brenner – A Biography

I’m reading more and more often now, and continuously buy book from amazon, on hardcover or kindle version. One of the latest is this one:


“Sydney Brenner : A biography” by Errol Friedberg. (Amazon link here)

What did I think about it ? 

LOVED IT !  Sydner Brenner is one of these scientists that enters in the “living legends” category. If you wouldn’t know he still lives on the same planet then us (and gives conferences), you would bet this book describes a fictional and slightly unreal character.

I read it more like a historic novel about molecular biology then a biography; and was totally hooked to the story. For the biologists of my age (25), DNA, RNA, PCR, molecular cloning, sequencing genomes, are stuff we learned from text books as undergrads, without realizing it was such recent history. I still have a hard time wrapping my head around the fact that 40-50 years ago, people where trying to figure the very basics of DNA, genes, genetic code, mutations, etc … 

When reading the book, you are not even tempted to think  “come onnnn, how was that not obvious to you, geniuses ?” or be bored, because it’s written so well that you forget about your own knowledge, and “live” the discoveries with Brenner, Watson, Crick, Nirenberg, and so on. Seriously they could make a nerdy TV Show out of this. 

And you realize (because you tend to forget) that it’s easy for no one in science, not even “geniuses”. The chapter describing Brenner and Jacob doing the “Tape experiment” in California was an eye opener. For a month, they did not get any results and where completly depressed about it. But they did this “extra-mile”; taking a deep breath (at the beach); and going to the lab one more time. And make it work. Good to remember it when stuff fails.

Aside of the anecdote, the book is literally a journey trough Brenner’s scientific, from school in South Africa to Singapour & beyond. From the birth or molecular biology to next-generation sequencing. 

I learned so many things reading it, but also laughed a lot; because Brenner seems to be one quirky and funny fellow. One anecdote I can remember is this fake “personal communication” they put as a reference in a 70 pages long article as being from “Leonardo de Vinci” ! An one of the reviewers picked it up saying “Who is this italian guy ?” There are so may of these little jewels in the book, I will probably read it all over and bookmark them ! 

That last sentence probably tells you everything that actually needs to be said … 

And you, could you give up your bench work ?

There are so many different kinds of scientists out there. And lately, I’ve been talking to post-docs. The kind of post-docs stuck at the bottleneck of the academic world. They are good scientists, enjoy doing science, and have been doing it very well for quite some time already. But they would not like to become PI’s.

Why ?

They like the work in the wet lab, at the bench. Doing experiments, smelling, tasting ?, troubleshooting, optimizing, supervising, etc …Occasionally they write grants or teach, but most of the time they work in the lab like us, PhD students.  They do not want to give that up, but there is very little space for these experienced and qualified people in academia. At some point, they know they have to get their own group or get “a real job”. (I don’t like how that sounds either, but that’s what they said.)

I’m always a bit surprised to hear people who like so much working at the bench. For me, working on the bench compares to driving a car. It is absolutely necessary, and I have no problem doing it, but I don’t love it. If I had to, I could give it up.

I like reading literature, doing computer work (getting started in bioinformatics), doodling stuff, listening to podcasts, writing, tweeting, etc … I do not necessarily need to work with smelly bacteria, under noisy hoods, sweating under plastic gloves, or having crappy 12-hour time points. (OK, exaggerating a bit, when things work, I really like it of course)

One big exception tough, I would not like to give up my flies.  I like the fly work to much I guess. There, you got me.

So, I’m asking you readers ? Could you give up working on the bench ? 

About being at the right place, at the right time


Although I don’t like the idea that much, I do believe that part of the success of a scientific career relies greatly on the people who trained you, the labs where the training took place, and the field you “fell” into.

On that subject, I’d like to share a link to an article written by Ronald Dale in the latest issue of Nature Medicine, in the “Lasker Award” special edition. Is is entitled: “How lucky can one be? A perspective from a young scientist at the right place at the right time” 

The article in not open access, but I hope you’re part of an institution paying for the access; because it is a nice read.

Basically, this person has been lucky and hard working at the same time, which is the perfect combination for success in the tough world of academic science 🙂

He started his own lab at 27; after publishing shitloads of Cell papers, and doing some ground breaking research. And he basically gives advices to us, the young scientists. Among them are the importance of having great mentors, and squeezing down your laundry time (yep) ! I will not spoil it more, but just give the proper reference for it !

Enjoy !

Vale, R. D. (2012). How lucky can one be? A perspective from a young scientist at the right place at the right time. Nature Medicine, 18(10), 1486–1488. doi:10.1038/nm.2925

Student Quotes -1- “They don’t hire technicians anymore, they hire PhD students”

We have quite a lot of students around in the lab these days. They are either at the level of bachelors, technician school, masters, etc … and it’s quite funny to hear them talk about our world sometimes. Somehow, they are still “outsiders” and incredibly naive about things. But they can also be unbiased observers.

A few weeks ago, one of them said : “You know, they don’t hire technicians anymore, they hire PhD students”. Hummmmm ….. that kinda felt like a SLAP in the face. Although is was not meant like that. And I might be over-thinking it a little bit.

Somehow, it still felt like the secondary meaning of that remark had some truth. Sometimes, you do feel like a technician, with just some more theoretical knowledge. But you have to do the pipetting and the thinking/reading/writing; and the pressure of getting good data makes it difficult to keep these two activities balanced.

With my bench mate, we decided to tackle this problem by buying a big white board for our desk where we doodle ideas, sketches, etc … Standing in front of it, we talk about our weird observations and far-fetched theories. These moments of pure speculations going wild and wilder are among the best moments in our PhD’s.

So no, we are not technicians, but sometimes you have to actively work on it. 

PI Quotes – 5 “Grad students don’t stay at the lab on week-end if their salary is too high”

I realized that until now, all my PI Quotes were either funny, either truly positive.  Nevertheless, we all know that some PI’s go from being a little offensive here and there to complete jerks. You can judge by yourself where on this ladder this one stands …

Let’s give some context: I’m on a conference, around a table, talking with other PhD’s, Post-Doc’s, and PI’s about our salary. We note that a swiss PhD student earns probably more then a french PI … (true story)

Then, this  PI says : “Grad students don’t stay at the lab on week-end if their salary is too high. They rather book a flight for a week-end in Barcelona ! That’s not good.”

That literally knocked my socks off because : 1 – He/She was not drinking, and 2 – It was not meant as a joke … 1% of me knew that there was so truth there, but 99% of me also shouted at him “sorry whhaaattttt ?” , noting that this person really thought that “grad student = dumb research robot that is meant to stay in the lab 24/7” …

At the end, beyond revolting, disrespectful, and contemptuous, it’s just really sad …