PLOS Biology, 19 Oct 2017; 15(10): e2003026
Ethoscopes: An Open Platform For High-Throughput Ethomics
Quentin Geissmann, Luis Garcia Rodriguez, Esteban J. Beckwith, Alice S. French, Arian R Jamasb, and Giorgio F Gilestro
We present ethoscopes, machines for high-throughput analysis of behaviour in Drosophila and other animals. Ethoscopes provide a software and hardware solution that is reproducible and easily scalable. They perform, in real-time, tracking and profiling of behaviour using a supervised machine learning algorithm; can deliver behaviourally-triggered stimuli to flies in a feedback-loop mode; are highly customisable and open source. Ethoscopes can be built easily using 3D printing technology and rely on Raspberry Pi microcomputers and Arduino boards to provide affordable and flexible hardware. All software and construction specifications are available at http://lab.gilest.ro/ethoscope.
Supplementary material 1 – webGL model of the ethoscope.
Supplementary material 2 – instruction booklet for the LEGOscope.
Supplementary material 3 – instruction booklet for the PAPERscope.
Supplementary Video 1 – Introduction to the ethoscope platform.
Supplementary Video 2 – The optogenetics component of the optomotor in action.
What is teaching? In general terms, I believe there are two possible answers to this question. In its simplest – yet admittedly not trivial – form, teaching is the organised transfer of information from a teacher to a student. Finding the best strategy to act on this process may seem like a novel problem to a newly starting university lecturer but, conceptually, it is a problem that mankind has in fact solved about 5000 years ago, during the bronze age, with the advent of writing. Information, especially when factual, does not require the physical co-presence of teacher and student, for it can almost always be conveyed using written words and diagrams. Especially in the Biological Sciences, a textbook is a sufficient instrument of information transfer more often than not. What we teach is factual, usually not conceptually challenging and only partly mnemonic. In general, all the factual contents we offer to first and second-year undergraduate students can be easily found on a plethora of textbooks; third years’ and postgraduate contents should be found in textbooks and in academic literature. If all the information we aim to transfer can be conveniently and efficiently read on paper, why do we even bother? Why are the students investing time and resources to pursue an activity that could be easily be replaced by accessing a library? The answer to this latter question is what I refer to as “the added value” of university teaching and it describes the second, less obvious, and most challenging definition of what teaching really means.
My teaching philosophy has evolved around this concept of added value. What is my role as teacher and how can my work and presence enrich the learning experience of the student? What can I offer than a very well written book cannot? I came to the conclusion that my added value breaks down into 4 parts:
Being able to recognise quality in information is a fundamental translational skill. University libraries are normally maintained by scholars to feature only reliable sources and therefore students learn to see the University library as a knowledge sanctuary where any source can safely be considered as “trusted”. This indubitably helps them in selecting material, but will not develop their critical sense. Being able to find and recognise trusted sources and reliable material should be a key translational skill of their degree, which they will value in their careers and also as responsible citizens. To help with this goal, I encourage them – read: I force them – to go out of their literature comfort zone. In the classroom, I focus lectures on topics that are new and developing so that they will be driven to explore primary literature and not rely on textbooks when studying and revising. Another advantage of selecting developing topics is that these are often genuinely controversial. Research that is still developing is usually prone to multiple, often contrasting, interpretations by scholars. I present students with the current views on the topic and ask them to dissect arguments in one or another direction. This develops their critical sharpness. Literature dissertations and “problem-based learning” (PBL) are also an excellent exercise for them to browse and pick literature. I dedicate half spring-term to literature dissertation in the MSc course I am currently co-directing, and I supervise PBL tutorials for the 2Yr Genes and Genomic course. Both activities are very successful.
Obviously, not all our students will become scientists but I believe they should all be trained to be. Thinking and acting according to the Galilean method is an undervalued translational skill of modern society. Also, not many other Universities in the world have a research environment as vibrant and successful as Imperial College London, and being exposed to real cutting-edge Science is certainly an important potential added value for our students. I try to bring scientific ethos in the classroom by presenting the actual experimental work behind a given discovery. In a second year module on RNA interference, I present one by one the milestone papers that created and shaped the field and I elucidate the key experiments that have led, eventually, to a Nobel prize. In the same course, I also teach about CRISPR-Cas9, presenting the controversy between the two research groups that are still fighting for the associated patent (and, most likely, for another upcoming Nobel prize). I present experiments in the way they are naturally laid out, from hypothesis to theory. I also try my best to instil a sense of criticality and a sense of “disrespect towards Aristotelian authority”. Ultimately, my goal is for students not to be afraid to contradict their teacher – as long as they can back up their claims with factual information, that is. Admittedly, this exercise does not achieve the same result with all students as it requires a particular mindset of self-confidence that not all students possess. It does, however, greatly benefit the most independent and intellectually acute ones, who show great appreciation informally and formally on SOLE.
Being able to intellectually capture the students’ curiosity is possibly the most powerful skill of a teacher. My ultimate goal is to “seed” information into my lecture and let the students develop it on their own. If they develop wonder and curiosity towards an argument, they will be more likely to master it and enjoy it. There is no secret recipe for doing this – as passion must be genuine and cannot be mimicked – but I found there are four steps that definitely help.
a) and b) are factors that largely depend on the course convenors. For instance, convenors can organise lecturers so that they are asked to lecture on topics that are close to their own research area. This is a very easy way to generate transmissible enthusiasm. For developing b), it is normally preferable to have longer contact with the same cohort of students: I would very much rather do 8 hours in the same course than 8 hours spread to a different cohort of students. c) can be achieved by intercalating the lecture with historical anecdotes, for instance about the biography of scientists behind a certain discovery or even about personal events that I lived or witnessed in my research activity, throughout my career. This teaching style will make the lecture conversational, it will generate curiosity and set a more natural discursive pace of interpersonal communication. d) is an underestimated, very powerful exercise. In fact, I think the EDU office should actually consider a new course devoted to teaching without the use of powerpoint slides. Not relying on anything but our own theatricality is the best way to gather the undivided students’ attention.
I am quite satisfied with the progress I made so far on points 1-3, and this last fourth step represents my next challenge as a teacher. When facing a cohort of 150 students, as we do with our 1st and 2nd year UG courses, we clearly deal with students of different academic abilities. For whom should we teach? What pace should we follow? Where shall we set the intellectual bar? I found that creating a right mix of “facts and passion” is a good strategy: the average student will receive all the facts; the more intellectually gifted one will then expand on those inspired by the newly found passion. However, I also believe that delivering different contents to different parallel streams is the one aspect where modern technology can really come to help. My plan for the future is to develop a series of “reverse classroom” lectures, presenting all students with prerecorded material and – possibly – with lecture notes too. The goal is to keep classroom time for passion and discussion and stream the basic factual information through video and notes.
I found my experience as a teacher so far together with the introductory courses of the EDU team gave me enough background material on the educational science. However, my goal for the future is to tackle the theoretical aspects of teaching in the same way and to the same extent as I do my research. In particular, I want to deepen my knowledge of andragogy and venture in the current literature of instructional theory.
This is something I actually had to produce for my educational training at the College. I thought it may be useful to share with the world. Apologies for the akward writing style.
eLife 2017 Sep 12;6;e27445
Regulation of sleep homeostasis by sexual arousal
Esteban J. Beckwith, Quentin Geissmann, Alice S. French, and Giorgio F. Gilestro
In all animals, sleep pressure is under continuous tight regulation. It is universally accepted that this regulation arises from a two-process model, integrating both a circadian and a homeostatic controller. Here we explore the role of environmental social signals as a third, parallel controller of sleep homeostasis and sleep pressure. We show that, in Drosophila melanogaster males, sleep pressure after sleep deprivation can be counteracted by raising their sexual arousal, either by engaging the flies with prolonged courtship activity or merely by exposing them to female pheromones.
eLife insight: Sleep: To rebound or not to rebound — Stahl BA, Keene AC
Why we sleep remains an unresolved mystery of biology. Why do humans have to spend one-third of their lifetime in a status of profound unconsciousness which leaves them vulnerable and endangered? What do we gain from it? We still do not possess an answer to this question but we assume that it must be something tremendously important, also considered that sleep appears to be a necessity not just in humans but in all animals – including fruit flies. A particularly intriguing evolutionary conserved feature of sleep is what we call “sleep homeostasis”, that is: the innate modulation of sleep pressure based on previous sleep amount. If we have a good long nap, we may have a harder time falling asleep at night; conversely, if we pull an all-nighter partying on Sunday night, we are going to have a hard time at the office on the following morning. That is sleep homeostasis.
Is sleep homeostasis an unmodifiable, sovereign need in the animal or can it somehow be suppressed? Previous studies showed that migratory birds may be able to resist the temptation to sleep while flying above the ocean. Similarly, male pectoral sandpipers, a type of Arctic bird, can forego sleep in favour of courtship during the three weeks time window of female fertility. Could we find a similar behaviour in a genetically amenable animal model, like fruit flies?
In a “blind date” experiment, we forced interaction in a restricted space between socially naive, young, male fruit flies and receptive females. The interaction between the two led to an uninterrupted passionate courtship lasting the entire 24 hour period (and to one – and, in some case, more – events of copulations). Surprisingly, not only did male flies forego sleep when prompted with a receptive female counterpart, they also suppressed their natural sleep homeostasis and never recovered for the sleep lost courting. In a second set of experiments, we forcefully kept flies awake by employing robots that would automatically disturb the flies whenever they would fall asleep. At the end of the sleep deprivation treatment, flies would normally recover the lost sleep by having an extra nap. However, raising the sexual arousal of male flies by simply exposing them to the female pheromone, abolished their homeostatic need.
Ours is a study on the fundamental biological underpinnings of sleep. Our goal is to show that sleep is not a disconnected, uncontrollable phenomenon but a biological drive that can, in some conditions, be overcome. The study is particularly directed at other researchers and provides an important caveat not to be forgotten when conducting sleep experiments: it possible to create an internal state in the animal that will heavily affect sleep regulation, without interfering with sleep regulatory circuits. A researcher may be artificially activating neurons that make an animal stressed, anxious, angered, or in love and all of these neurons will ultimately have an effect on sleep. Yet, they shall not be classified directly as “sleep neurons” or we will end up with a false map of where sleep neurons really are.
Randy Sheckman’s recent decision to boycott the so called glam-mag Cell Nature & Science (CNS) made me realize that I never expressed on this blog my view on the problems with scientific publishing. Here it comes. First, one consideration: there are two distinct problems that have nothing to do with each other. One is the #OA issue, the other is the procedural issue. My solution addresses both but for sake of reasoning let’s start with the latter:
Ok, so let’s assume tomorrow morning CNS cease to exist. They close down. How does this solve the issue? It doesn’t.
CNS are not damaging Science. They are simply sitting on the very top of the ladder of scientific publishing and they receive more attention than any other journal. Remove them from the top and we have just moved the problem a bit down the ladder, next to whatever journal is following. Some people criticise CNS for being great pusher of the IF system; “to start”, they say, “CNS could help by making public the citation data of the single papers and not just the IF as journal aggregate”. This would be an interesting move (scientists love all kind of data) but meaningless to solve the problem. Papers’ quality would still be skewed and knowing the citation number of a single paper will not be necessarily representative of its value because bad papers, fake papers & sexy papers can end up being extremely cited anyway. Also, it takes time for papers to be cited anyway.
So what is the solution? The solution is to abolish pre publication peer review as we know it. Just publish anything and get an optional peer-review as service (PRaaS) if you think your colleagues may help you get a better paper out. This can create peer reviewing companies on the free market and scientists would get paid for professional peer review. When you are ready to submit, you send the paper to a public repository. The repository has no editing service and no printing fees. It’s free and Open Access because costs are anyway minimal. What happens to journals in this model? They still exist but their role is now different. Nature, Cell and Science now don’t deal with the editorial process any longer. Instead, the constantly look through the pool of papers published on the repository and they pick and highlight the ones they think are the best ones, similarly to how a music or a videogame magazine would pick and review for you the latest CD on the markets. They still do their video abstracts, their podcasts, their interviews to the authors, their news and views. They still sell copies but ONLY if they factually add value.
This system solves so many problems:
Now, this is my solution. Comments are welcome.
The alternative is: I can publish 46 papers on CNS, win the Nobel prize using those papers, become editor of a Journal (elife) that does the very same thing that CNS do and then go out on the Guardian and do my j’accuse.
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, continous 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 intersting 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 clothings 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)? Yupe, 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 consumism. 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. Below, 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.
Nat Protoc. 2012 Apr 26;7(5):995-1007.
Video tracking and analysis of sleep in Drosophila melanogaster.
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.
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.
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.
Data analysis, computer vision, machine learning, component.
Techniques used: mathematics and statistics applied to data analysis and computer science
Building and testing the hardware component.
Techniques used: principle of electronics, basic physics of lasers
Additional material and links.
This project is funded by a Royal Society research grant.
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, and the same is true for sleep: what is the biological relevance of this observation.
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