Posts By Giorgio
The Japanese Taxis
Someone says I have a peculiar tendency to dissect all of my experiences and place them in labelled boxes for sake of understanding. It’s possibly true and it is with the same spirit that I found myself dissecting Japan during my recent visit over there. I was invited to teach at a Summer School for Master students in Biology and Computing at the Tokyo Institute of Technology and I decided to spend a few more days sightseeing. So for those who ask what I found most striking about Japan, my answer is going to be “Taxis”.
Taxis like this are everywhere. Why are they special? Look at the car. Not sure what model may be, but one can easily bet this car was produced and sold sometime in the 80’s and then somehow time stopped and it never got old. It is perfectly polished, no tear and wear, not a single sign of ageing internally or externally. The car is fitted with improbable technological wonders, coming out from an improbable sci-fi movie from the 80’s: absolutely emblematic is a spring operated mechanism that open and closes the rear door. This taxi represents Japan for me. This is a country that has lived a huge economic boom from after the war all the way to late 80’s, with annual growth that surpassed any historical record. Then, suddenly, in 1991, met an equally dramatic economic crisis with the explosion of a giant bubble and everything stopped. Economists call the following years The Lost Decade because not much moved after the burst and let me tell you: it’s perfectly visible. To this date, Japan still didn’t really recover from the bubble.
Reaction of the Japanese bank to the 91 bubble was somehow similar to what observed nowadays in the rest of the world after the 2008 crisis: quantitative easing, continuous bailout and a rush to save banks. Bail out was so common that Japan in the 90’s was said to be “A loser heaven”. And yet, society responded very differently: unemployment rate did not really sky rocket as it is happening now pretty much everywhere else. Instead, unemployment in Japan remains one of the lowest world wide and a huge deflation took place instead. My naive gut feeling cannot help but putting these two things together but I don’t know enough to claim with certainty that these two are really consequence of each other so go look for an answer somewhere else, and let me know if I was right, please. Anyhow, what is interesting is that the fact that people maintained their job – yet with decreasing salaries – and that meant society didn’t really collapse but simply froze. And that is why travelling in Japan is like travelling back in time to the early 90’s: everything, from furniture in hotel room to cars and even clothing and fashion, stopped in 1991. Granted, it’s a technological advanced 1991, filled with wonders of the time. Remember the dash of Delorean from the Back to the Future (1985)? Yes, that is what Japan looks like. Why did thing did not get any old? Why does the Taxi above still looks mint new? A Japanese friend gave me the answer: Japan has a tradition of conservatism as opposite as consumerism. In Japan a tool that is important for your life or job, is a tool to which you must dedicate extreme care. Thus, taxi drivers polish and clean and care and caresse their cars as the Samurai took care of their swords. Paraphrasing the first shogun Tokugawa Ieyasu: “the taxi is the soul of the taxi driver”1. Here, some pictures from the trip.
1. Well, the original citation would be The Sword is the soul of the Samurai. This goes a a bit off topic but during one of my jetlegged night I found this video on the history of Samurai swords quite interesting.
Video tracking and analysis of sleep in Drosophila melanogaster
Nat Protoc. 2012 Apr 26;7(5):995-1007.
Video tracking and analysis of sleep in Drosophila melanogaster.
Gilestro GF.In the past decade, Drosophila has emerged as an ideal model organism for studying the genetic components of sleep as well as its regulation and functions. In fruit flies, sleep can be conveniently estimated by measuring the locomotor activity of the flies using techniques and instruments adapted from the field of circadian behavior. However, proper analysis of sleep requires degrees of spatial and temporal resolution higher than is needed by circadian scientists, as well as different algorithms and software for data analysis. Here I describe how to perform sleep experiments in flies using techniques and software (pySolo and pySolo-Video) previously developed in my laboratory. I focus on computer-assisted video tracking to monitor fly activity. I explain how to plan a sleep analysis experiment that covers the basic aspects of sleep, how to prepare the necessary equipment and how to analyze the data. By using this protocol, a typical sleep analysis experiment can be completed in 5-7 d.
Can your lab book do this?
When I was a student I used to be a disaster at keeping lab books. Possibly because they weren’t terribly useful to me since back then I had an encyclopedic memory for experimental details or possibly because I never was much of a paper guy. As I grew older my memory started to shrink (oh god, did it shrink!), I started transforming data into manuscripts and as a consequence I began to appreciate the convenience of going back 6 months in time and recover raw data. Being a computer freak, I decided to give up with the paper lab book (I was truly hopeless) and turned to digital archiving instead. As they say, to each their own!. Digital archiving really did it for me and changed enormously my productivity. One of the key factors, to be honest, was the very early adoption of sync tools like Dropbox that would let me work on my stuff from home or the office without any hassle.
As soon as I started having students, though, I realized that I needed a different system to share data and results with the lab. After a bit of experimentation that led nowhere, I can now finally say I found the perfect sharing tool within the lab: a blog content manager promoted to shared lab book (here). This is what it looks like:
This required some tweaking but I can say now it works just perfectly. If you think about it, a blog is nothing less than a b(ook) log and so what better instrument to keep a lab book log? Each student gets their own account as soon as they join they lab and day after day they write down successes and frustrations, attaching raw data, figures, spreadsheets, tables and links. Here some of the rules and guidance they need to follow. Not only can I go there daily and read about their results on my way home or after dinner, but I can quickly recall things with a click of the mouse. Also, as bonus, all data are backup’d daily on the Amazon cloud and each single page can be printed as PDF or paper if needed. As you can see in the red squares in the above picture, I can browse data by student, by day, by project name or by experiment. That means that if I click on the name of the project I get all the experiments associated to it, no matter who did them. If I click on a experimental tag (for instance PCR) I get all the PCRs run by all the people in the lab.
Except for the protocols, all contents are set to be seen only by members of the lab. However, inspired by this paper, I decided that the project will be then flagged as public as soon as the results will be published.
Automatic detection and analysis of animal behaviour
Description
Even simple animals, like fruitflies or worms, can make complex decisions, for instance when they interact with predators, possible sex mates or explore food sources. Ethomics is a new discipline of neuroscience, attempting automatic and high-throughput analysis of animal behaviour, and investigating correlations and links to explore how genes drive behaviour. The purpose of this project is to create state of the art techniques of computer vision and machine learning to track animals activity and link them to stereotypical behaviours. Ultimately, we aim at building a system that can recognize animals status or intention and interfere with them using for instance laser or mechanical stimulations.
In particular, an initial application of the machine will be to create a new paradigm to study the links between sleep and learning in Drosophila. This new tool will be used for automatized sleep deprivation and learning conditioning. In the past, we created a software to track Drosophila locomotor activity and analyse sleep. The system, released as open source, is highly scalable, offers high resolution, it is affordable and easy to use (www.pysolo.net). With this project, we aim at expanding the existing system so that it would no longer be limited to passive detection of flies activity, but could actively interact with a group of animals, shining a heat-transducing infrared laser beam onto single flies whenever specific conditions are satisfied.
Project timeline.
Data analysis, computer vision, machine learning, component.
Techniques used: mathematics and statistics applied to data analysis and computer science
- The existing software is already able to track the animals position in real time and it would need to use this information to direct one or more IR laser diodes connected to motors. However, it will be necessary to modify the video tracking to recognize multiple interacting flies with higher precision and target only those that satisfy predefined conditions . This part will be done in collaboration with Dr. Stefanos Zafeiriou of the computing department at Imperial College.
- In particular, the software will be modified so that “conditions for shooting” will easily be programmed by the researcher. Also, the software should be able to recognize and output a complete data frame regarding the previous, current and predicted conditions of each flies. This will achieved using machine learning algorithms to identify stereotypic behaviours and act accordingly.
Building and testing the hardware component.
Techniques used: principle of electronics, basic physics of lasers
- Once flies are successfully tracked and conditions established, the software will interact with a motor controller to aim and shoot one or more laser diodes onto single flies
- Laser pulses will have to be theoretically selected and empirically calibrated for wavelength, power and duration, to use them as sleep deprivators or for learning conditioning
- Final protocols will be established for the different possible uses of the machine that will combine part 1 and part 2 of the project
Additional material and links.
- Perona’s and Dickinson’s software for automated fly behaviour is found at this address and described in this paper.
- Another software, again from Perona, is described here.
- A software for ant tracking can be found here, and here are some samples of how it performs.
- A sample of my flies moving in a vial (~15 minutes video at VGA resolution) can be found here
- Other sample movies from the ctrax project can be found here and here
Funding.
This project is funded by a Royal Society research grant.
Ethanol and sleep
Background
Ethanol is an evolutionary conserved neuromodulating agent, effective in mammals as it is in invertebrates. The fruitfly Drosophila melanogaster responds to ethanol with all the stereotypical signs that are also observed in humans: including euphoria, sedation, habituation and addiction (for a review see 1). Genetic predisposition in humans is accounted to be responsible for about 50% of the risk of developing addiction to ethanol, a major medical and social problem in modern society. For all these reasons, Drosophila has successfully been used in the past decades to investigate the genetic and molecular components of ethanol effects in the brain.
Hypothesis Student will Investigate
The student will investigate how ethanol affects the sleep / wake cycle of Drosophila and, conversely, how the sleep / wake cycle affects the behavioural and molecular responses to ethanol. Some questions that the student will address are: is the sedation induced by high concentrations of ethanol similar to sleep, with all the restorative effects associated to it? What are the effects on the sleep / wake cycle of chronic consumption of ethanol? In flies, Response to ethanol has been shown to be under partial control of the genes regulating the circadian clock and regulating synaptic output in the brain[2], and the same is true for sleep[3]: what is the biological relevance of this observation.
Effects of ethanol on Drosophila locomotion (a) Representation of the locomotor velocity of wild-type flies during an exposure to a moderate dose of ethanol (ethanol exposure period is shown by the grey horizontal bar). (b) Computer-generated traces of the locomotor behavior of a group of 20 flies before and during exposure to ethanol vapor. Each panel corresponds to a 10-s time period recorded at the times indicated in (a). Reproduced from (1)
Techniques Student will Use
The student will perform behavioural experiments to investigate the physiological responses to ethanol sub ministration: this will include assaying sleep, anesthesia, sedation, motility as well as learning and memory by mean of Drosophila learning paradigms. The student will also perform anatomical dissections and molecular analysis exploring how gene expression changes in the brain upon ethanol administration.
References and recommended readings
- Drugs, flies and videotape: the effects of ethanol and cocaine on Drosophila locomotion.
Curr Opin Neurobiol. 2002 Dec;12(6):639-45. (pdf) - arouser reveals a role for synapse number in the regulation of ethanol sensitivity.
Neuron. 2011 Jun 9;70(5):979-90. (pdf) - Widespread changes in synaptic markers as a function of sleep and wakefulness in Drosophila.
Science. 2009 Apr 3;324(5923):109-12. (pdf)
Sleep and learning: a genetic approach. The allnighter gene.
Background
Sleep is a vital activity, whose function still remain mysterious despite centuries of scientific research. All animals that have been tested so far, from nematodes to humans, possess and require the fundamental characteristics of sleep. In Drosophila, like in humans, sleep deprivation leads to a remarkable decrease in intellectual performance, learning and memory; chronic sleep restrictions also shows widespread metabolic changes and eventually leads to unexplained death.
My laboratory investigates the many functions of sleep using mainly the fruit fly Drosophila melanogaster as model organism. In particular, current research is aimed at elucidating the connections between sleep and synaptic plasticity, learning and neuronal homoeostasis. In previous work we provided evidence of how sleep may function as a mechanism to maintain a proper homoeostasis for synaptic strength and connections in Drosophila (see [1] for a recent review). We are now extending that line of work and we employ a rich selection of multidisciplinary techniques ranging from genetic manipulation of Drosophila (with transgenes and RNAi) to computer assisted analysis of behaviour to measure intellectual performance, including odours recognition and ability to court and mate.
The project
Following a genome wide screening for short sleeping mutant flies, we identified a novel gene that we called allnighter. allnighter mutant flies are viable but sleep considerably less than wild type controls and show general symptoms (such as tense “eagle” wings) that strongly suggest an underlying problem with neuronal excitability.
The project aims at extending the characterization of this gene, and other belonging to the same family. Some of the questions that you will try to answer are: “where is the gene express and at what stages of development? Does expression change with sleep or experience? Is the enzymatic activity of allnighter required for its function? How do allnighter flies perform when challenged with task measuring their learning and memory capabilities”
Techniques. Working with Drosophila
An MRes rotation in Drosophila allows the unique opportunity to investigate a biological problem in vivo and yet follow the development of a relatively complicated project from the beginning (e.g.:genetic manipulation of a new animal) to the end (e.g.: behavioural testing of the new phenotype). Your daily work will most likely encompass basic techniques of molecular biology (DNA cloning, PCR etc), genetics (crossing flies and follow up progeny) and behavioural neuroscience (analysis of sleep, sleep deprivation, analysis of learning and memory performance).
Drosophila and neurobiology.
For decades, Drosophila has been the most powerful animal models for genetic dissection and manipulation, and the outstanding contributions that flies gave to developmental biology and genetics were celebrated twice with Nobel Prizes(1933, 1995), and countless time in our text books. Recently, more and more laboratories started pairing the incredible genetic tools that we have been building in the past century with new and exciting neuronal techniques, leading to a Drosophila neuronal renaissance. From circuit formation to their function, Drosophila offers the complexity of an animal that can learn, memorize, socialize and yet the accessibility of a 250 thousand neurons brain. Here, I link a few entertaining and informative videos with the aim to communicate the excitement this field is living right now.
- Gero Miesenboeck (Oxford). Engineering the brain (18 minutes TED talk)
- Michael Dickinson (Caltech). Towards an integrated view of brain function (28 minutes video)
- Bjoern Brembs (Berlin). The Drosophila Flight Simulator (3 minutes video)
- Charalambos Kyriacou (Leicester). An interview on the use of Drosophila for studying circadian biology and behaviour (14 minutes video)
Getting in touch.
My office is in room 743 of the Huxley Building, in the South Kensington Campus.
Email and phone number are listed here. I’ll be happy to meet you and show you the lab, just drop me an email.
References and sample readings
- Synaptic plasticity in sleep: learning, homeostasis and disease.
Trends Neurosci. 2011 Sep;34(9):452-63. (pdf) - Waking experience affects sleep need in Drosophila.
Science. 2006 Sep 22;313(5794):1775-81. (pdf) - Widespread changes in synaptic markers as a function of sleep and wakefulness in Drosophila.
Science. 2009 Apr 3;324(5923):109-12. (pdf)
Patches for Nautilus “move to trash” bug
Warning, this post contains a geek rant.
If you use the nautilus or nautilus-elementary filemanager (the default file manager in any gnome-based linux distro, including Ubuntu), you are probably aware of the annoying bug with file deletion.
Like any other file manager, nautilus allows you to delete your files using keyboard shortcuts: permanently (hit <Shift-Delete>) or temporarily by moving them to the trashbin (hit <Delete> on your keyboard). Removing files is always a critical action so any other file manager will make sure that you don’t do it accidentally: the file manager in MacOS, finder, will require you to hit the key combination <AppleKey+Delete>, difficult to perform by mistake. Microsoft Explorer, Konqueror, Thunar and many others will ask you to confirm that you really want to trash files with a dialog box.
Unfortunately nautilus lacks this ability: if you, your toddler or your cat accidentally hit the Delete key on the keyboard while a file or folder is selected, they go into the trashbin without warning. If you are not looking at the screen while this happens, the item is well gone. Obviously, this flaw was pointed out already long time ago. Users started asking for a fix already in 2004 (that is seven years ago!) and lots of people wanted to get that fixed: see for instance here, here, here, here, here, here…
Surprisingly, reactions of the gnome developers to this problem were of two kinds: “I don’t think this is a real problem”[¹] or “I don’t think you are proposing the perfect solution”[²]. Back in 2009, I accidentaly lost some file and wrote a patch to fix this bug. The patch simply gave the user the option to activate a warning dialog if they wanted to. I figured “people who want the dialog will enable it and be happy, people who don’t will leave it alone and keep discussing about what is really truly the best solution for the next 7 years“. Believe it or not, the problem still exists, so I thought of raising the issue once again (this time, I also proposed a patch to change Delete in Control-Delete).
Guess what: even after 7 years and hundred of people begging for a fix, we are sitting on the same attitude:
This is a real problem, but I don’t think the solution is a windows-like alert dialog. […] An animation with the file becoming red and/or flying to the trash would be a nice addition.
Or maybe a small cluebar with an embedded undo button would already be enough. I like how Google does it in its webapps.
What if deleted files were visible as some ghost-like-icon in the directory they used to be? And it could be possible to turn on/off the visibility of deleted files? And you can have your animation then as well; of an icon that dies.
I think your use case is a real concern, and something we should fix indeed, but as others said in this thread, I don’t think a confirmation dialog is how we want this to be implemented, especially when it carries a new preference with it.
Personality i like my delete and it would felt awkward if the delete didn’t delete anything.
We will rather keep the hole than having a solution we don’t like. Little does it matter if any other browser is actually using that solution or if lots of people want to see the thing fixed.
This attitude is amazingly complicated to understand for my simple brain. For me, getting things done means finding the meeting point between the optimal solution and the best outcome. If my car gets a flat tire on the way, I will accept any new tire a rescuer would give me and I won’t be sitting 7 years waiting for one that really matches the other three. And I like to think this is not Linux true philosophy either.
Anyway, here you can download the patches to fix this issue.
- Fix à la Microsoft/Konqueror/Thunar, will ask for a confirmation upon deleting a file (Nautilus – Nautilus Elementary).
- Fix à la Finder/MacOS, changes Delete to Control+Delete (Nautilus – Nautilus Elementary).
I am using the second one on nautilus-elementary (which also sports a very convenient Undo feature).
Edit 1 April 2011. To much of my pleasure, the patch has now been accepted and from next version on, Control<Delete> will be the shortcut to send stuff to trash. No more accidental deletions! Open Source wins again.
Edit June 2011. If you arrive to this page because you freaked out finding the new nautilus behaviour, this is how to get back to the old key combo
Notes:
1. You are all familiar with the “how many people it takes to change a light-bulb?” jokes.
The one about software developers goes like this:
Q: How many developers does it take to change a lightbulb?
A: The lightbulb works fine on the system in my office. NOT REPRO.
2. The one about C++ programmers goes like this:
Q: How many C++ programmers does it take to change a lightbulb?
A: You’re still thinking procedurally. A properly-designed lightbulb object would inherit a change method from a generic lightbulb class, so all you’d have to do is send it a bulb.change message.
Postdoc, love or hate? A survey.
Following last week’s discussions about the tough life of a postdoc, I’ve realized more data is needed before making general assumptions on what postdocs want and need. Jennifer Rohn’s post had an overwhelming response of sympathizing postdocs who would love to have a “postdoc for life position” and I didn’t find this surprising. What came a bit unexpected to me, though, is that the other voice was hardly heard.
I think the problem has deeper issues that will have to be solved by completely changing the way we define a laboratory.
For sake of smart discussions, I am setting up a survey aimed at all postdocs out there. You’ll find it here: http://thepostdoctrap.gilest.ro
I am not doing this just because I care about the issue: I have been invited to a meeting organized by the postdocs of the MPI-CBG in late May and I’d love to give those guys some numbers about the issue. So, please, take that survey and come back in couple of months for the results.
I am a postdoc and I think I just realized I have been screwed for years
It seems in the past two weeks someone has started going around lifting big stones in the luxurious and exotic garden of science, finding the obvious gross underneath. To be more precise, the topic being discussed here is: “I am a postdoc and I think I just realized I have been screwed for years“.
A couple of weeks ago, a friend of mine blogged about his decision to leave academia after yet another nervous breakdown. I leave it to his words to describe what it means to realize in your early thirties that your childhood dream won’t become a reality because the job market is broken and you can’t cope with that stress. To be honest, while I sympathize with him, I find his rant extreme, but what is more important than discussing anecdotal experiences is actually the huge number of comments that post had, not only on the blog but also on social discussion websites. Literally hundreds of comments from people who went through similar experiences, culminating with the epiphany that finding a job in academia is freaking difficult.
This discussion is not new, of course. Occasionally people from academia feel the urge to let postdocs and PhD student know that this is a very risky road. See Jonathan Katz’s opinion from back in 2005, for instance.
Why am I (a tenured professor of physics) trying to discourage you from following a career path which was successful for me? Because times have changed (I received my Ph.D. in 1973, and tenure in 1976). […] American universities train roughly twice as many Ph.D.s as there are jobs for them. When something, or someone, is a glut on the market, the price drops. In the case of Ph.D. scientists, the reduction in price takes the form of many years spent in “holding pattern” postdoctoral jobs. Permanent jobs don’t pay much less than they used to, but instead of obtaining a real job two years after the Ph.D. (as was typical 25 years ago) most young scientists spend five, ten, or more years as postdocs. They have no prospect of permanent employment and often must obtain a new postdoctoral position and move every two years.
Pretty actual, isn’t it? Although these arguments do emerge now and then, they do it way less than they should¹. Why? The main reason is that PIs have really nothing to gain from changing the current situation: as it is now, they find the field overcrowded with postdocs who cannot do anything else but staying in the lab, hoping to get more papers than their competitors; waiting for the unlucky ones to drop out to reduce competition. That means it’s easy for the PIs to get postdocs for cheap and keep them in the lab as long as possible.
Of course there could be an even better scenario for PIs: postdocs who never leave the lab! Let’s face it: having so many postdocs to choose from is nice, but many of them aren’t actually that good and also it takes time for them to acquire certain skills. So why don’t give them the chance to stay for 20 years in the same lab? This is exactly what Jennifer Rohn was advocating on Nature last week. I think in her editorial Jennifer actually rightly identifies the problem:
The system needs only one replacement per lab-head position, but over the course of a 30–40-year career, a typical biologist will train dozens of suitable candidates for the position. The academic opportunities for a mature postdoc some ten years after completing his or her PhD are few and far between.
But she fails to provide the right solution:
An alternative career structure within science that professionalizes mature postdocs would be better. Permanent research staff positions could be generated and filled with talented and experienced postdocs who do not want to, or cannot, lead a research team — a job that, after all, requires a different skill set. Every academic lab could employ a few of these staff along with a reduced number of trainees. Although the permanent staff would cost more, there would be fewer needed: a researcher with 10–20 years experience is probably at least twice as efficient as a green trainee.
I cannot even start saying how full of rage this attitude makes me. This position is so despicable to me! Postdoc positions exist, on the first place, because they provide a buffer for all those who would like to get a professor job but cannot, due to the limited market. Any economist would tell you that the solution is not to transform this market into something even more static but to increase mobility, for Newton’s sake! Sure, some postdocs may realize too late they don’t really want to be independent and they would gladly keep doing what they are doing for some more time: this is what positions in industry are for², and this is what a lab tech position is for. No need to invent new names for those jobs.
So, here I propose an alternative solution: what about giving postdocs the chance of being independent, without necessarily being bound to running a 4 people lab to start with, or without the need to hold a tenure position? What about redistributing resources so that current PIs will have a smaller lab so that 1 or 2 more people somewhere else could have the chance to start their own career? Isn’t this more fair?
I wrote about this before, so I won’t repeat myself: in short, the big lab model is not sustainable anymore and it is not fair!
The problem, Jennifer, is not that postdoc want to stay longer in the lab: the problem is that they want out!
Notes
1: a recurrent question in the new Open Science society is “should scientists be blogging?“. My answer is yes, definitely (in fact, that’s what I am doing) but I don’t expect them to blog about their opinion on the last paper in their field. I don’t think that is so useful, actually. I’d rather have them talk about their daily life as scientists and speak freely and loudly about controversial issue.
2: My wife is one of them: she realized she didn’t want to have anything to do with academia anymore and she moved to industry where she actually got a salary that was more than twice the one she was getting in the University doing pretty much the same job, without worrying about fellowships and competition. She has never been so happy at work, too.