The iLab generation – Fast Counter

Time for a new app recommendation today ! A while ago, it was suggested to me in a comment on this very blog, and when I saw the description in the iTunes Store, I was immediately enthusiast. It’s called the Fast Counter.

It’s basically the app that does the annoying job of colonies on petri dishes. Look at that :

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I had time to try it out a bit , by taking a classic LB plate with bacteria after transformation (about 200) and tried to count. You can set the threshold, and the color of the background; and once this is done, it is pretty effective. It does capture -LIVE- your colony number (is it the future already, right ?), but you can also take a snapshot, and count “manually” by tapping on them.

My point is, if you need a good estimate, and not a super-super-precise count (which is generally not required anyway), you should definitely try it out.

Also, the company developing that tool also made some other apps, if you like all nerdy apps for the lab like me, check it out on their website ! It’s called Shazino. 

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PI Quotes 8 – “Laziness is a great quality for a scientist”

Hi all,

After christmas break I dragged myself back to the lab (ok, I was happy to return) and though of  this professor who once told during a master course :

“Laziness is a great quality for a scientist” 

That was a bit unsettling at first, my overall felling being that scientist are in the great majority hard workers (but is it really work ? ;-)). For example, injecting 1400 adult Drosophila‘s today is not an act of laziness !

Actually, his reasoning was slightly more twisted: 

The more lazy the scientist = the less experiment he does

The less experiments he does = the better his choose the good ones to do

And he focuses on succeeding immediately to avoid unnecessary extra replicates or troubleshooting work due to inattention.

Beyond the witticism, there is some truth in the fact that good scientists are always the ones who can choose well the key experiments, and make them look perfect.

So, should we all just be a bit more lazy ? 

Food for thoughts … 

gaston-paresse2

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 ? 

You know you’ve worked too long in a lab when …

I’m not taking credit for the content of this post. This has been on the internet forever, and was initiated by a facebook group. I found a categorized summary here, and since it’s really an effort of all the nerdy white coat out there, it’s probably okay to paste it here.

Fill free to comment and add your own. An more importantly, get ready for a great laugh.

So, You know you’ve worked in the lab too long when…

Linguistics:

  1. You say “mills” and “migs”.
  2. You say “orders of magnitude” in regular sentences.
  3. You say “conjugation” instead of “sex”, and “pili” sounds dirty.
  4. You can no longer spell normal words but have no trouble with spelling things like immunohistochemistry or deoxyribonucleic acid.
  5. You refer to your children as the F1.
  6. You think the following is a quality insult: “I’ve seen cells more competent than you!”
  7. You use acronyms for everything and never stop to elaborate.
  8. You use the word “aliquot” in regular sentences, especially with reference to tea, coffee or curry.
  9. You flinch when you hear the word “significant”.
  10. For you, media is something which increases your culture.
  11. When you hear tween, you think of the surfactant not the age group.
  12. You are fed up of people saying alcohol, when they mean ethanol.
  13. SOB is not an insult; it’s what you grow your bugs in.
  14. You actually threaten your cells whilst waving a bottle of virkon or some other disinfectant.
  15. You give the lab equipment motivational pep talks: “Work for me today or I’ll reprogram you with a fire axe” is my favorite.

Entertainment:

  1. You’ve seen how far away you can hit a target with a squirty water bottle or seeing how far away from the bin you can fire pipette tips.
  2. You still get amusement out of “freezing” things in liquid nitrogen.
  3. You rejoice when grabbing a handful of eppendorfs/bijous/anything and it turns outs to be the exact number you needed.
  4. You decide the courses and conference you want to go on by the quality of the food served.
  5. When you start making patterns in your pipette tip box as you take the tips out.
  6. You’ve played Battleship using tip boxes.
  7. You’ve used, “I’d like to get into your genes” as a pickup line.
  8. You have made some kind of puppet out of a nitrile glove and kept it as a pet.
  9. The scent of latex reminds you of work, not play.

Couture:

  1. Safety equipment is optional unless it makes you look cool.
  2. A timer clipped to the hip is not only practical, but dead sexy.
  3. People wearing shorts under a lab coat disturb you slightly as they look as though they might be naked underneath.
  4. You can tell what cheap and expensive white coats look like.
  5. You hate having to change your lab coat to a new one because ‘it just won’t fit right’ and because the wrist bits are way too tight.
  6. You’ve never worn a clean lab coat.
  7. You have an irresistible urge to rip your shirt off superman style because it has press stud fasteners just like your lab coat… Most often occurring as you walk through a door just like exiting the lab… (I prefer to apply the Hulk style to disposable PPE)
  8. You’ve left the lab wearing a piece of PPE (personal protective equipment) because you forgot you had it on.
  9. You consider a green laser pointer to be science bling.
  10. You own Invitrogen t-shirts and actually wear them.

Kitchen and home skillz:

  1. No matter what the timings in the experiment protocol, there is always time for lunch in the middle.
  2. When you organize your kitchen cupboard contents the way you would your chemicals… all labeled in alphabetical order.
  3. Although all cooking is a glorified chemistry experiment you just still can’t seem to get it right.
  4. You’re also very good at transferring small amounts of liquid between containers.
  5. You’re very good at diluting things.
  6. When your fruits go bad and you get fruit flies, you can’t help but check their eye color.
  7. You open the toothpaste with one hand.
  8. You want to have parafilm at home too.
  9. You wonder what absolute alcohol tastes like with orange juice.

Professional:

  1. Showing up at 10AM and having a coffee is a productive day.
  2. You’ve worked out that a trained chimp could probably do 90% of your job.
  3. You always seem to use the microscope after the person with the impossibly close-set eyes.
  4. When you say goodnight to your microscope on a Friday night and tearfully hug it goodbye as you won’t see it all weekend.
  5. You can identify organs on roadkills.
  6. You can’t wait for lab clean-up because you get to do random pointless “experiments” to figure out what’s in all the dodgy unlabeled bottles.

Accidents & discomfort:

  1. Accident reports are a badge of honor.
  2. Warning labels invoke curiosity rather than caution.
  3. Blinking real fast has saved your eyesight on more than one occasion.
  4. Burning eyes, nose and throat indicate that you haven’t actually turned on the fumehood/ downdraft bench.
  5. Liquid nitrogen is only about a 1/3 as dangerous as you thought.
  6. You bitch about not being able to pipette by mouth any more.
  7. When you wonder: how much will it hurt if I pour just a smidgen of this phenol/chloroform/ trichloroacetic acid/ any random chemical on myself?
  8. The fire alarm ceases to bug you. You only evacuate when you see the fire. (Hand on the floor to check for heat is a good indicator.)

C’est la vie:

  1. No one in your family has any idea what you do.
  2. Sometime you momentarily vanish from social activities because of a time-point.
  3. The front page of Science is your light reading.
  4. You realize that almost anything can be classed as background reading.
  5. When a non-scientist asks you what you do for a living, you roll your eyes and talk science at them until they’ve lost the will to live.
  6. When you rejoice when grabbing a handful of eppendorfs/bijous/anything and it turns outs to be the exact number you needed.
  7. When you’ve got that callus on the side of your thumb from opening PCRtubes (0.5ml and 1.5ml eppendorf tubes for me).
  8. You are strangely proud of the collection of junk you’ve stolen from vendors at trade shows.

Technology:

  1. You can make a short film in Powerpoint.
  2. You can’t watch CSI without cursing at least one scientific inaccuracy.
  3. You don’t fear rodents, rodents fear you.
  4. You have to check the web to find out what the weather is outside.
  5. You’ve bent down to pick something up off the floor only to scatter the contents of your top pocket under the largest machine in the lab.

Health and Hygiene:

  1. You wash your hands before and after using the washroom.
  2. You’ve suffered carpal tunnel from the pipetman.
  3. You’ve used Kimwipes as Kleenex.
  4. You’ve wondered why you can’t drink distilled water in the lab- shouldn’t it be clean?
  5. Your nose invariably itches when you’re doing mucky stuff with your hands so you develop the habit of scratching it on your upper arm. Unfortunately, you sometimes carry this habit over to real life, where it looks like you’re sniffing your armpits.
  6. You are slightly too fond of the smell of (pick one or many) Xylene/ Agar/ Ethanol/ Undergraduates/ Alcoholic hand-wash.
  7. You’ve removed your gloves to find a small hole which has left you with either – wrinkly old person hands, a brightly colored finger (histologists especially) or a burning sensation and dermatitis at some point.

I’ll add: 

-You try opening your door at home with the badge of the lab. (Yes, I did it)

-You wish you add  10%bleach / 70%EtOH to clean your home

-Cooking is basically following a protocol

-Thursday means Nature, and Friday means Science.

-…

PI Quotes 7 – “Drosophila, these are the kind of things you fall in love with …”

This is good stuff. Since a few weeks, I am the supervisor of an undergrad. When she came to the lab; my supervisor introduced her to our work, and told her: “Drosophila …, these are the kind of things you fall in love with …” with this semi-serious/semi amused look.

I found it terribly funny and terribly true. I know quite a few people who are in love with their flies. I am in love with them also. And I have pictures of them hanging over my bench.

The most recent one if have it here :

It can be found here, and is designed by the fly jedi and brilliant scientist Pavel (Tomancak), and made by his colleague Radek . (Both can be congratulated for the beautiful picture on twitter, btw)

In the book “Fly pushing: the theory and practice of Drosophila”, by Ralph Greenspan, it is written that you cannot decently work with an animal model without connecting with it in some way. You have to love your model. And sure enough, after a few weeks, I can see that my student is totally falling for them also 🙂 They must have some kind of super-power.

Famous Scientists Quotes -2- : “They will fool you every time”

I’m still a little bit in my Drosophila’s-are-the-best phase, and I remembered today one of the many witty quotes from Alfred Sturtevant, one of the father’s of Drosophila genetics, who worked with Thomas Hunt Morgan himself. (More on his life and achievements here) 

This man had a lot of wisdom to say: “They [the flies] will fool you every time”.      Every person who ever worked in a fly lab knows it’s true. I think about it every time my experiments turn out weird. And it makes me smile again.

Indeed, if there is a way for them to escape the tube or the room, they will find it. If your crossing scheme is dodgy or risky, they will fail you. Even if it’s not, they will still try. Sometimes, it just feels like they resent us for keeping them in the lab, and messing with their genes 🙂 I swear that I once felt one bite me (still not kidding).

So, new drosophilists in the making, now you cannot say you didn’t know 🙂

Book review 1 : Mastering your PhD

Here come a new “series” of posts … books ! Not nerdy science articles, but real books that you can buy in hardcover for the old-fashioned ones (;-)) or download on your tablet for the geeks !  I wish I would take more time to read books instead of surfing the internet for hours, but somehow it’s a difficult take that step …

Anyway, there is a book that I read back to back about 6 months after I started my PhD, and surprise surprise, it’s about doing a PhD !

Mastering your PhD: Survival and Success in the doctoral years and beyond is a book written by Patricia Gosling and Lambertus Noordam, edited by Springer. (Amazon link over here)

What is is about ? 

It’s about all the not-directly-related-to-science aspects of the PhD, and the chapters come in the natural order all these subjects arise  : How to design good experiments, dealing with setbacks, how to deal with your lab mates and mentor, mastering presentations, first international conference, from data to manuscript, the final year, and what comes after … (and many more)

What did I think ? 

Thumbs up …  

-The book looks very serious and “academic”, but it’s actually very fun, and nice to read ! The description on the different types of research groups, from the “young ambitious investigator” to the “empire, lead by an old scientist and senior post-docs” was so good ! Also, the analysis of the different characters of the lab, like “Golden boy”, is very close to the reality …

-The advices given are realistic and totally applicable. Some of them seem actually very natural.

-It goes through the entire PhD path, so you can basically make usage of the book anytime.

Thumbs down … 

– The book consists mainly of  “theoretical” chapters, but offers here and there some “side stories” about a fictional research team. It sounds nice like that, but I did not like these parts that much, and skipped them towards the end.

– I cannot find anything else …

Well, I am not doing any “promoting” or publicity here, just giving my opinion about the book I read, you can judge by yourself if you want to read it or not sometime !