PhD thesis writing: a humility lesson


My thesis abstract, as it currently stands.


This is what I’ve been up to for the last 3 months. My PhD thesis recently grew to have more pages than my Master’s thesis, without having nearly as many figures. I remember writing the Master’s being a tough exercise, but there are several things I forgot.

The thing is, in large collaborations, you don’t get that much experience doing some scientific writing, unless you have the fortunate experience of being an editor on some note. I’m discovering that I’m not only rusty, I’m not that good at having a neutral objective tone. I write things because I have a vague idea in my head that I try to convey, use imprecise wording to do so and end up being completely misinterpreted. And it turns out the vague idea is not really informative or relevant. Those are things I learn by submitting chapters for revision to my supervisor…

After getting over my feelings, I realize that of course, he’s right. He’s a very brilliant guy who knows me very well. If he sees these things in my writing, what are other people going to read? I like to think of myself as someone who has some clarity of thought. Yet, this assertion is promptly destroyed by an honest assessment of the first version of any of my chapters. Academia is full of character-building experiences. Thesis writing is no exception.

You hear stories of people who locked themselves up in a room for 2 weeks and got out of it with a full thesis. I know some of these stories are true, and I have no idea how that’s remotely possible. I’ve been told I’m writing at a very decent pace, yet, it would be impossible for me to do anything like that.

I try not to blame the fact that I’m not a native english speaker, but honestly, I have no idea how much that affects the quality of my writing. I’m not self-aware enough to notice it. I’ve been thinking about particle physics in english for the last 6 years. It’s actually more difficult for me to think or talk about particle physics in french. I have a few french-speaking colleagues, and we always try to discuss in french. Sooner or later however, we revert to english because the conversation is too tedious in french.

I think I’d be fine with getting these comments if I didn’t care about explaining things clearly when I write. Then at least, I wouldn’t be surprised that my first chapter drafts are confusing and sometimes misleading. The worst part is that every time I write a new chapter, I think I’ve applied the lesson I just learned. But it turns out I just crank out new incarnations of the same mistakes.

In the end I take comfort in the fact that the final version will be much better, thanks to these frank comments from my supervisor. I actually think my thesis will turn out to be something I’m very proud of. I’m also hoping that I’m retaining the humility lessons I’m getting right now. Everything, from science to art, from sports to politics, is made better by a fresh outside perspective. It may hurt your feelings, but whatever you are trying to do will be much better for it. Just make sure you get that perspective from the right people. I believe that people who do not want to hurt your feelings, but risk doing so anyway for the sake of honesty are the most important people you can ever have in your life. They are the secret to success.

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A Dream Came True!

I really wasn’t expecting this. My girlfriend got me the most awesome gift ever during the holidays, something I’ve wanted for years. Here it is:
Canon EOS 6DIt’s a Canon EOS 6D. This bad boy is capable of impossible things. I’m probably exaggerating, but I never got my hands on such a potent camera before, so I can’t contain my excitement. Here are a few shots I got today.

Artistic glass patterns on the front window of my parent's house, backlit by the setting sun.

Artistic glass patterns on the front window of my parent’s house, backlit by the setting sun.

Some accumulated snow on the post at the top of the front staircase ramp at my parent's

Some accumulated snow on the post at the top of the front staircase ramp at my parent’s.

The sun setting at the back of our front neighbour's house.

The sun setting at the back of our front neighbour’s house.

A tree on my neighbour's lawn.

A tree on my neighbour’s lawn.

Everything shot by this camera turns into some sort of epic shot. I also started experiencing with astrophotography and time-lapses:

Thanks Emma, this is awesome. This is a tremendous amount of fun!

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My First Recorded Seminar at LBNL

A pictogram of the kind of events we've been hunting for. This shows the particles that we see in the detector when: 1) two quarks from the two colliding protons decide to exchange virtual W or Z bosons, which radiate a Higgs boson; 2) the Higgs boson decays to a pair of tau leptons; 3) one tau lepton decays to a muon and neutrinos; 4) the other tau decays semi-hadronically to neutral and charged pions and a neutrino.

A pictogram of the kind of events we’ve been hunting for. This shows the particles that we see in the detector when: 1) two quarks from the two colliding protons decide to exchange virtual W or Z bosons, which radiate a Higgs boson; 2) the Higgs boson decays to a pair of tau leptons; 3) one tau lepton decays to a muon and neutrinos; 4) the other tau decays semi-hadronically to neutral and charged pions and a neutrino.

I’ve been rather busy in the last few weeks planning my transition from a mere student to a slightly elevated status in the academic world: post-doc researcher. This involves concluding the PhD with the long and laborious writing of a thesis, followed by the defence of said thesis in front of a committee of highly qualified scientists. The transition also involves applying to jobs. I recently applied for a Chamberlain Fellowship at the Berkeley National Lab (LBNL), and I was among 6 candidates to be invited to present a one hour seminar on my research. Some of the Chamberlain committee members based at CERN couldn’t attend the seminar so it was recorded on video for them. They also happened to post the video on their Research Progress Meetings website! I had a total of 13 interviews with various members of the astrophysics/particle physics research group at Berkeley. This was rather intense, but a great life experience to say the least. I will be made aware of the final decision in January. So here I post the link to the abstract, slides and video I presented. It’s quite nice to have something of my own out there!

The seminar is aimed at a technically inclined audience, although I did try to explain as many concepts as I could. A full understanding may require some familiarity with the field, or an extended period of questions with me 🙂 Seriously, I’m fine with answering any questions here on the blog: feel free to ask, go nuts!

Another disclaimer is that I haven’t watched the entire video, so I can’t guarantee any sort of quality of presentation. I did receive a number of good comments though, so I hope it is a decent talk! I’m not very comfortable with a laser pointer, and one of my mistakes was to accept one when it was handed to me. Seriously, if you can cover most of the screen on which your slides are projected with your arms, you don’t need a laser pointer. The laser pointer makes you instinctively point to everything on the slides, which is not necessary. On the other hand, using your arms to point at things on the slides is a great opportunity to use your physical presence during a talk.

A lot of figures in the talk are original, made with Inkscape (free and fantastic vector graphics editor). I’m fine with people borrowing them, but I would appreciate if you could tell me if you plan to do so. I like to keep track of the stuff I do.

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Screen Shot 2013-11-26 at 8.09.22 PM

A reconstruction of an event recorded in the ATLAS detector that has been assessed by our analysis to be extremely likely to be a Higgs boson decaying to two taus. One of the taus has decayed to an electron and the other decayed hadronically, the configuration I have been personally looking for the past two years.

ATLAS now has a new result out there, and it’s the one I’ve been working on for the past 2 years! I still need to assess how much I can talk about the nitty gritty details of our analysis, I can only go with what the ATLAS collaboration has officially approved. Nevertheless, I’m planning a series of posts with my various thoughts on the topic. It’s been a wild ride with lots of juicy stories.

On November 26, there was a special seminar at CERN presenting the result of the search for the Higgs boson decaying to fermions. The presentation was conducted by Dr. Aliaksandr Pranko, someone I had the chance to collaborate with very closely during this analysis. He did a truly excellent job. You may be able to watch the presentation here (under Recent Broadcasts), once it’s been archived on the CERN webcast website. At the very least, you can find the slides here, and the conference note (which serves as a preliminary paper) has just been made public here.

What is this result? Why is it important? Didn’t we already find the Higgs boson? There’s already a Nobel Prize awarded for that thing! What are you talking about?

The Higgs boson was a very precise prediction in particle physics, at least by comparison with the predictions made by current models that attempt to go deeper than the Standard Model. The only thing we couldn’t infer was its mass, but once its mass was determined, we could deduce all of its physical properties. Fundamental particles are pretty simple objects: they only have a few properties. They are:

  • Mass : As far as we can tell, the mass of a fundamental particle is unique. Except maybe for the particles that are massless while still being distinct: photons and gluons.
  • Spin/Polarisation : Spin is one of these esoteric quantum mechanical properties that are very hard to explain in a satisfying manner. The number of spin states a particle can take determines a lot of its behaviour. Among other things, it determines whether the particle is a fermion or a boson. The former would make the particle a constituent of matter while the latter would make the particle a force carrier, responsible of mediating interactions between the constituents of matter.
  • Couplings : Couplings are the buzz word used to talk about which particles one specific particle can interact with. For example, leptons such as electrons will couple to W and Z bosons, the mediators of the weak interaction. On the other hand, they won’t couple to gluons, the mediators of the strong interaction. Couplings determine not only what happen when two particles run into each other, they also determine what an unstable particle will decay to.

The Higgs boson couples to any fundamental particle that has mass. At least, this is what we have been hoping for, because it’s not strictly necessary in the theory of the Standard Model. The Higgs mechanism (note that I distinguish the Higgs mechanism from the Higgs boson) was designed to explain how the electroweak force splits into the electromagnetic force and the weak force in our day-to-day experience. You may ask, why did we think they were a unified force to begin with? This is a very interesting question too, but would take a bit too long to explain for the point I am trying to make here.

In order to break the electroweak interaction in two forces, what you need to do is make some of the bosons responsible for this interaction massive and some others not. As you may guess, the photon, which ends up mediating the electromagnetic interaction ends up massless, but the W and Z bosons end up gaining mass with the Higgs mechanism. That’s all the Higgs boson was intended to do in the first place.

But it was quickly realized that the Higgs boson could give mass to all more fundamental particles, not just to the W and Z bosons. This could be achieved not by the Higgs mechanism itself, but with another type of interaction we like to call Yukawa couplings. The Higgs boson could potentially have Yukawa couplings to quarks and leptons, giving them their masses in the process.

And this is the most exciting part of our new result. ATLAS just showed that the Higgs boson decays to pairs of tau leptons, which means that the Higgs boson does couple to leptons via what appears to be a Yukawa coupling. More precise measurements of the tau leptons coming out of that Higgs boson will reveal if we really have the predicted Yukawa coupling or not. We’ll have to get a lot more di-tau pairs from Higgs bosons in our data to sort this out, but we’re off to a good start with this 4.1 sigma signal.

I’ve been involved from almost beginning to start in this analysis. My most recent contribution being that I was responsible for the final step in the assembly of this plot:


The di-tau invariant mass of the collision events entering our analysis, but with weights applied in a way that the events expected to be the most signal-like are enhanced. When enhancing these events, a clear discrepancy becomes visible between the Standard Model events that we would expect if there was no Higgs and the data. That discrepancy looks eerily like a Higgs boson signal with a mass of 125 GeV, which is compatible with what’s been seen in other Higgs decay modes.

Just to be clear, I didn’t make that plot on my own. It would be terribly unfair to claim something like that. All the work that went behind it is very hard to quantify, and I can tell you that at least 5 other people were directly involved in making it. I just put the pieces together, but I didn’t make the pieces. Esteemed colleagues Noel Dawe, Thomas Schwindt, Damian Alvarez, Stan Lai and Louis helary were instrumental in realizing this plot.

So we’ve essentially shown that the Higgs boson couples to leptons. It’s also the first direct evidence that the Higgs couples to fermions in general, although I don’t like to emphasize that statement as much. The first evidence for the Higgs boson was in the decay to a pair of photons. But the Higgs shouldn’t couple to photons because they are massless! So how does this decay to photons even take place? The answer is this Feynman diagram right here:

Borrowed from the Lancaster University webpage on the Higgs: (click image to go there).

So the Higgs (H) first couples to virtual top quarks (indicated by the t‘s on the diagram), and these virtual top quarks in turn couple to photons (γ’s). The top quarks are called virtual because you would never really see them in the detector from that Higgs event. They exist temporarily to allow the Higgs to decay to a pair of photons. If the Higgs wouldn’t interact with top quarks, which are fermions, this process wouldn’t have been observed. In fact, the Higgs wouldn’t even be produced in the way that is described in this diagram, as you can spot another top quark loop involved in the production of the Higgs boson to the left. This is not the only production mechanism though, but it is the most abundant.

So with the Higgs decaying to two taus, we haven’t shown for the first time that the Higgs decays to fermions. The coupling to fermions can be deduced from the observation of the Higgs going to photons. However, we did show that it couples to leptons for the first time. That I think the biggest reason why our result is notable. There are others, but to be honest I don’t understand them so well yet. There is so much to say about it, I’ll have more to say very soon, as I finally get to writing my thesis 🙂

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Being a graduate student within the ATLAS collaboration

ImageHey! It’s been a while! The analysis I have been working on should be coming to an end at some point this Fall. The last year has been a hell of a ride, but we’re soon going to reap the benefits. The world (well, maybe not the whole world) has been wondering if that Higgs boson thing we discovered also decays into pairs of tau leptons, and my friends in ATLAS and I have been hard at work trying to provide an answer. This partly explains my absenteeism from the blogging plane, and I can’t guarantee that I’ll be back here regularly in the near future. I’m nearing the end of my Ph.D., and I have trying times ahead.

In the meantime, here’s a little something. I have been asked to write a short essay on the life of a graduate student in high energy physics nowadays for Physics in Canada, the journal of the Canadian Association of Physicists. I’m not 100% sure it will appear in the journal, but I thought it was definitely blogging material. So here it is, edited a little by Emma Ideal, someone who now has a lot of experience editing essays (an upcoming post will be dedicated to that awesome book she made called Blazing the Trail: Essays by Leading Women in Science).


Being a graduate student within the ATLAS collaboration has been an incredible ride. I have learned a number of lessons during these last 5 years. Interestingly, the most important ones don’t have anything to do with physics. Physics is the fun part of life in high energy physics. Sure, I learned an astonishing amount about detectors, colliders, collisions, fundamental interactions, and how all these pieces come together when you start looking for new fundamental phenomena, but there are a number of elements that come into this game which someone would be foolish to ignore.

Experimental high energy physics as it’s currently being done on the energy and luminosity frontier involves two things that can be fairly daunting to incoming students: politics and computing. I was lucky enough to be prepared for the computing aspect, but I was little prepared for the political aspect. They try to prepare you in school for teamwork, but it comes short of the reality you face in the ATLAS collaboration. If you choose to pursue the current hot topic (in these days, anything having to do with the Higgs boson), you will find yourself working alongside groups that can be as large as a few hundred people. You will also find yourself competing for attention and recognition with dozens of other smart graduate students. Everyone will seem smarter than you, because nobody shows how much they really struggle to understand what they are trying to do.

Everybody really does struggle, at least in the beginning. There is no exception, no matter how it appears. As you get more experience, you start to have a bigger basis on which to build your understanding of new concepts. The challenges keep coming though. The problems we face in the ATLAS experiment need creative solutions, and there is always something new to understand. I was lucky enough to work alongside very smart people who would answer my “stupid” questions every time I asked. I discovered soon enough that nobody worth worrying about in this collaboration scoffs at a stupid question so I soon started flaunting my stupidity. I discovered fast enough that if I didn’t understand something, odds were that other people weren’t clear on it either.

I spend a lot of time writing and rethinking code as part of the collaboration, but I also spend a lot of time communicating. I sometimes bring new ideas to the table, and these ideas need to be understood by people before they can be adopted. I spend a lot of time thinking about how to represent concepts visually so that they are clear. Sometimes, new worthwhile ideas don’t get across because they are not communicated clearly or because their implications aren’t understood. Don’t be afraid to get creative, but also be prepared to fight for your ideas. It can take a while before that new idea is adopted, but trust that people are reasonable and that they will recognize genuine advantages if there are any. Everyone will be better off, all thanks to your exercising the courage to ask that stupid question that no one ever asks.

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Signs of life

I’m back in Vancouver. I’m about to start writing my PhD thesis soon. The last 4 months have been rather intense, but very rewarding. I can’t tell the whole story just yet, because it hasn’t ended yet. I don’t know how it will end. All I can say is that we have worked very hard to open a new chapter on the Higgs boson, and we are just about to succeed. This required a bit of a paradigm shift in the way we do analysis. It was met with a lot of healthy skepticism, but a relentless stream of proofs of concept and studies eventually convinced the upper management at ATLAS that this was the way to go. We’re in good shape.

I haven’t abandoned the blog. I will come back to writing as soon as things quiet down a bit. I had the itch to write many times, but I couldn’t find the time and energy to write well thought out pieces. The analysis I am working on is superseding everything. It’s a rare thing to be that dedicated to something. I kind of enjoy it.

Being back in Vancouver means that I get back my recording equipment. I felt like dusting off my two condenser mikes and quickly recording something. It’s the first time I record a cover song. It’s the first song I’ve ever learned on the guitar. You may recognize it, even if I took some liberty over the original. Enjoy!

** Edit **: Turns out I still had a bit of motivation to do another recording this week-end. Innocent by Our Lady Peace. Gosh I’m happy to get my recording equipment back!

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Explaining the Higgs boson discovery on the Up-Goer Five Text Editor

The Up-Goer Five Text Editor will check every word you type and make sure it is part of the 10,000 most common words used. It’s fun and frustrating to play with.

I took a crack at explaining the Higgs boson discovery in it. It’s very difficult when you can’t use words like “mass”, “energy”, “particle” or “interaction”. So what do you think? Does it make sense?

We think we found the smallest bits that make the world we live in. Matter can be broken down no further. These bits have four different ways of playing with each other. Let’s call these games. One of these games is not our focus because bits start playing it only when they are in very large numbers. We are interested in the games one bit can play with only a few others bits. We only know of three of those games. It turns out two games out of these three are one and the same, but they don’t appear that way in every day life.

The games are pretty much just the smallest bits of matter throwing other bits at each other. The bits being thrown around are different from the bits doing the throwing. The bits being thrown should all be very easy to push around if the two games we are talking about are to appear the same. But we know they don’t appear to be the same. So what’s going on? Maybe there is a field  that is all over the place that makes it hard for bits to move through. The field would make it harder to throw some kinds of bits around, but only some kinds. There are four kinds of bits that make our two games. Maybe only three of them feel the field. The one bit that wouldn’t feel it would appear to play its own game, while the other three would appear to play a different game.

It is possible to kick a field so hard that bits of it come off. We have been trying to kick the field for years just to know if the field is there at all. Last year, we finally managed to see some bits of it coming off, leading us to believe that the field is really there. This also means that the two games we were talking about really are the same. The field can also make all the kinds of small bits of matter harder to push around. We are checking this right now.

Here’s the text in the actual editor, so that you can check that I haven’t cheated 🙂

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