Switching to left-handed Dvorak

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I’m doing an experiment. A lot of my thesis work consists of me clicking between form elements, spreadsheet cells, or parts of text documents, entering short bits of text and then clicking away to another thing.

I’ve been trying to bring my efficiency up, but running into a wall. The rate-limiting step in my workflow is not my typing speed or how quickly I find information, but rather how fast I can switch from mouse to keyboard.

A few years back, I switched from QWERTY to Dvorak, which was distressing at the time, but turned out to have been an excellent life choice. (Highly recommended!) I’m going to try left-handed Dvorak out for a bit and see how it takes. :)

BibTeX

@online{bgcarlisle2015-4353,
    title = {Switching to left-handed Dvorak},
    journaltitle = {The Grey Literature},
    author = {Benjamin Gregory Carlisle},
    address = {Montreal, Canada},
    date = 2015-01-14,
    url = {https://www.bgcarlisle.com/blog/2015/01/14/switching-to-left-handed-dvorak/}
}

MLA

Carlisle, Benjamin Gregory. "Switching to left-handed Dvorak" Web blog post. The Grey Literature. 14 Jan 2015. Web. 16 Dec 2018. <https://www.bgcarlisle.com/blog/2015/01/14/switching-to-left-handed-dvorak/>

APA

Carlisle, Benjamin Gregory. (2015, Jan 14). Switching to left-handed Dvorak [Web log post]. Retrieved from https://www.bgcarlisle.com/blog/2015/01/14/switching-to-left-handed-dvorak/

Rethinking Research Ethics: The Case of Postmarketing Trials

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Good news!

Toward the end of the year in which I was working on my thesis, my supervisor had me write up a shorter version of my thesis for an attempt at publication. This was no small feat—imagine trying to compress a 90-page master’s thesis into 2 pages!

After my RA-ship ended, my supervisor, Jonathan Kimmelman, and Alex John London took the paper, made some substantial edits, and submitted it to a couple journals. The paper was accepted, and as of this week, it was published in Science.

Needless to say, I’m thrilled. :D

BibTeX

@online{bgcarlisle2012-2878,
    title = {Rethinking Research Ethics: The Case of Postmarketing Trials},
    journaltitle = {The Grey Literature},
    author = {Benjamin Gregory Carlisle},
    address = {Montreal, Canada},
    date = 2012-05-3,
    url = {https://www.bgcarlisle.com/blog/2012/05/03/rethinking-research-ethics-the-case-of-postmarketing-trials/}
}

MLA

Carlisle, Benjamin Gregory. "Rethinking Research Ethics: The Case of Postmarketing Trials" Web blog post. The Grey Literature. 03 May 2012. Web. 16 Dec 2018. <https://www.bgcarlisle.com/blog/2012/05/03/rethinking-research-ethics-the-case-of-postmarketing-trials/>

APA

Carlisle, Benjamin Gregory. (2012, May 03). Rethinking Research Ethics: The Case of Postmarketing Trials [Web log post]. Retrieved from https://www.bgcarlisle.com/blog/2012/05/03/rethinking-research-ethics-the-case-of-postmarketing-trials/

Game theory and medical research

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I recently learned what exactly a Nash equilibrium is, and I’m really excited to start applying the idea in my everyday life. Hence, I will apply what I’ve learned in Game Theory so far to the field of medical research ethics.

First, some definitions: A Nash equilibrium is a set of strategies that the players in a formalised game adopt such that the utility that each player receives for her chosen strategy is the greatest, given the choices of strategies of all the other players in the game.

This could be formalised as follows:

A Nash equilibrium exists when ui (ai, a-i) ≥ ui (ai′, a-i) for all ai′ and all i, where:

  • ui is a function whose range is utility values for player i and whose domain is an ordered n-tuple of strategies taken by all the players in the game
  • ai is the chosen strategy of player i
  • a-i is the set of chosen strategies for all the other players, and
  • ai′ is some alternate strategy that player i might adopt.

What’s interesting about Nash equilibria is that given a particular formalised game, other non-Nash sets of strategies are “unstable”—that is, if a player finds out that given the strategy choices of the other players, she could have made a better decision, she will change her strategy accordingly.

The famous Prisoner’s Dilemma (look it up if you haven’t heard of it) is a great example of a Nash equilibrium where the outcome for each of the players is not optimal, even though they are in equilibrium.

What’s interesting to me about things like this is how it can be applied to medical research, if we make certain simplifying assumptions. Let’s imagine that medical research is like a two-player game. The players are the pharmaceutical industry on the one hand and some other participant in human research on the other.

In the tables below, Big Pharma has two strategies open to it—developing a “seeding” study or developing a “quality” study. The other participant (who could be a research subject or a physician-investigator or a journal that publishes medical research papers) also has two strategies available—participating in the study developed by Big Pharma, or not participating.

If the other stakeholder in the research project doesn’t participate, neither Big Pharma nor the participant receive any benefit. The utility outcomes for Big Pharma and the other stakeholder are 0, 0, respectively.

If the other stakeholder participates and the study is a high-quality study that provides socially valuable medical information, Big Pharma and the other stakeholder receive utilities of 1, 1, respectively.

But, if it turns out that the pharmaceutical company has produced a “seeding” study—one that is designed for narrow ends, namely those of being a marketing tool to get physicians used to prescribing a drug that has already received licensure—the pharmaceutical company receives a utility of 2 and the other stakeholder receives a utility of -1. That is to say, Big Pharma gets a big payout, because hundreds of doctors are now prescribing the drug, but the other stakeholder incurs a net harm in some way. (If she is a study participant, he may feel used or cheated. If she is a doctor, it may be a source of professional embarrassment. If it is a journal that published a “seeding” study, that journal will lose some of its reputation, etc.)

Participate Not
“Seeding” study 2, -1 0, 0 *
“Quality” study 1, 1 0, 0
Table 1. Asterisk (*) indicates Nash equilibrium.

So if we go through each set of strategies that the players in this game can take, we find that the one with the asterisk is the only one that is a Nash equilibrium. This is because if you are Big Pharma in this game, given that the other stakeholder has chosen not to participate, you are indifferent between strategies, and if you are the other stakeholder, given that Big Pharma has chosen to develop a “seeding” study, your best choice is to not participate.

It’s interesting to note that this setup is analogous to markets for financial products and other “confidence goods,” where the buyer has a really hard time telling the difference between high and low quality products.

But what if no one caught on that the study was a “seeding” study? Let’s imagine that Big Pharma got away with running a seeding study and no one ever figured out that that’s what it was. We would end up with a game that can be represented as follows:

Participate Not
“Seeding” study 2, 1 * 0, 0
“Quality” study 1, 1 0, 0
Table 2. Asterisk (*) indicates Nash equilibrium.

Here, the equilibrium has shifted. This explains why pharmaceutical companies try to develop “seeding” studies, and why they try to hide it.

So the question becomes, how can we set up the “rules of the game” of medical research in order to shift the equilibrium such that other stakeholders will participate and the pharmaceutical company will develop quality studies?

Or to put it another way, if we assume that the utility for non-participation for all players is 0, and that both the pharmaceutical company and the other stakeholder should both come away from a quality study having received some utility, what value for x will put the Nash equilibrium where the asterisk is in the table below?

Participate Not
“Seeding” study x, -1 0, 0
“Quality” study 1, 1 * 0, 0
Table 3. Asterisk (*) indicates Nash equilibrium.

The value of x must be less than 1 in order for the Nash equilibrium to fall where the pharmaceutical company develops a “quality” study and the other stakeholder participates. This is because if x = 1, Big Pharma will be indifferent between its strategies, given the choice of the other player, and if x > 1, as we saw in Table 1, the equilibrium will shift to where Big Pharma produces a “seeding” study and the other stakeholder declines to participate.

So in real life, how do we make x to be less than 1? There has to be some sort of sanction or penalty for pharmaceutical companies for producing seeding studies that makes their expected utility less than that of a quality study. This can be done by either putting a tax on seeding studies or by making regulations against seeding studies outright.

BibTeX

@online{bgcarlisle2012-2776,
    title = {Game theory and medical research},
    journaltitle = {The Grey Literature},
    author = {Benjamin Gregory Carlisle},
    address = {Montreal, Canada},
    date = 2012-04-1,
    url = {https://www.bgcarlisle.com/blog/2012/04/01/game-theory-and-medical-research/}
}

MLA

Carlisle, Benjamin Gregory. "Game theory and medical research" Web blog post. The Grey Literature. 01 Apr 2012. Web. 16 Dec 2018. <https://www.bgcarlisle.com/blog/2012/04/01/game-theory-and-medical-research/>

APA

Carlisle, Benjamin Gregory. (2012, Apr 01). Game theory and medical research [Web log post]. Retrieved from https://www.bgcarlisle.com/blog/2012/04/01/game-theory-and-medical-research/

Game theory course

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So the Online Game Theory course that I was talking about started, and it’s just as good as I thought it would be! As of when I’m posting this, you have forty-five minutes left to register, if you want to join me.

I took an actual university course for credit in Decisions Analysis when I was an undergrad, which was one of the best educational experiences of my life. Decisions Analysis is the science of making rational decisions under conditions of uncertainty. The way that the profs for the online Game Theory course describe Game Theory is that it is the science of describing the actions of idealised actors within a particular system, given certain simplifying assumptions. Decision Theory, they say, is like a subset of Game Theory—it is like Game Theory where there’s only one player. This is very exciting to me.

I have already learned how to formalise a number of things that I investigated during the course of my thesis. Further, I now know what the actual definition of a Nash equilibrium is. It’s a concept that I had a sort of fuzzy handle on before, but now I think I could express it formally using proper notation and apply the concept to ideas like the medical research enterprise or smartphone application development systems.

I’ll keep you updated with regard to some of the more interesting results that I find. :)

BibTeX

@online{bgcarlisle2012-2764,
    title = {Game theory course},
    journaltitle = {The Grey Literature},
    author = {Benjamin Gregory Carlisle},
    address = {Montreal, Canada},
    date = 2012-03-25,
    url = {https://www.bgcarlisle.com/blog/2012/03/25/game-theory-course/}
}

MLA

Carlisle, Benjamin Gregory. "Game theory course" Web blog post. The Grey Literature. 25 Mar 2012. Web. 16 Dec 2018. <https://www.bgcarlisle.com/blog/2012/03/25/game-theory-course/>

APA

Carlisle, Benjamin Gregory. (2012, Mar 25). Game theory course [Web log post]. Retrieved from https://www.bgcarlisle.com/blog/2012/03/25/game-theory-course/

Free online game theory course

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So a few months ago I signed up for a free online course in Game Theory, taught by two professors at Stanford. I like Stanford. Ever since I discovered the Stanford Encyclopaedia of Philosophy as an undergrad (the one website that philosophy profs will allow you to cite in your papers), I had a profound respect for this institution’s free online offerings.

The course isn’t for credit at all—there’s just video lectures, and “quizzes” integrated into the videos. I guess I’m sort of interested in it because it relates to my thesis subject. Ever since I wrote my thesis on it, I find the whole idea of collaborative enterprises fascinating, and I would love to be able to more rigorously analyse what regulations would make a complex system with multiple stakeholders work best.

The course was supposed to start in “late February 2012,” so I waited until today—I was going to send the professors an email, since February 29th is about as late in February as you can get. So I opened up the site for the course to find a contact email address, and found the following message:

Regarding the start-date of the Game Theory Online course: The University is still finalizing policies to cover its new online courses, and so there has been some delay in the launching of the courses. We anticipate being able to launch the course soon, and will keep you informed of any news on the starting date. Matt and Yoav

I’ll let you know if anything interesting comes of this. Let me know if you sign up for the course yourself. :)

BibTeX

@online{bgcarlisle2012-2733,
    title = {Free online game theory course},
    journaltitle = {The Grey Literature},
    author = {Benjamin Gregory Carlisle},
    address = {Montreal, Canada},
    date = 2012-02-29,
    url = {https://www.bgcarlisle.com/blog/2012/02/29/free-online-game-theory-course/}
}

MLA

Carlisle, Benjamin Gregory. "Free online game theory course" Web blog post. The Grey Literature. 29 Feb 2012. Web. 16 Dec 2018. <https://www.bgcarlisle.com/blog/2012/02/29/free-online-game-theory-course/>

APA

Carlisle, Benjamin Gregory. (2012, Feb 29). Free online game theory course [Web log post]. Retrieved from https://www.bgcarlisle.com/blog/2012/02/29/free-online-game-theory-course/

A scary email to receive less than a week before the thesis submission deadline

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I bet you thought I was done posting about my thesis. Last Friday (6 days ago), I received this email after I had the pleasure of submitting my thesis electronically.

[Your supervisor] approved your e-thesis on September 23, 2011 at 11:51.

If your thesis has been accepted by all your supervisor(s), it has been sent to GPSO for processing.

If your thesis has been rejected, please make the changes requested by your supervisor(s) to your original document*, and create a new pdf, delete the file on the server, and upload the new file.

You can track the progress of your thesis on Minerva.

Hooray! It was good news to receive this email, and I tweeted about it immediately, of course.

Then, this morning, I received the following email.

Dear Benjamin, … We [at the philosophy department] have been told that you haven’t submitted your thesis electronically, and this is one of the graduation conditions. Can you do this immediately? The conditions have to be met by Tuesday, 4 October. Best wishes.

October 4th is on Tuesday (5 days from now). I’m pretty sure that my thesis has been submitted electronically. Here is my evidence:

  • Minerva lists my thesis as being uploaded and approved
  • I received the aforementioned email from the e-thesis computer

So I really don’t know what this fuss from the philosophy department is all about, but now I’m nervous that something’s messed up.

BibTeX

@online{bgcarlisle2011-2219,
    title = {A scary email to receive less than a week before the thesis submission deadline},
    journaltitle = {The Grey Literature},
    author = {Benjamin Gregory Carlisle},
    address = {Montreal, Canada},
    date = 2011-09-30,
    url = {https://www.bgcarlisle.com/blog/2011/09/30/a-scary-email-to-receive-less-than-a-week-before-the-thesis-submission-deadline/}
}

MLA

Carlisle, Benjamin Gregory. "A scary email to receive less than a week before the thesis submission deadline" Web blog post. The Grey Literature. 30 Sep 2011. Web. 16 Dec 2018. <https://www.bgcarlisle.com/blog/2011/09/30/a-scary-email-to-receive-less-than-a-week-before-the-thesis-submission-deadline/>

APA

Carlisle, Benjamin Gregory. (2011, Sep 30). A scary email to receive less than a week before the thesis submission deadline [Web log post]. Retrieved from https://www.bgcarlisle.com/blog/2011/09/30/a-scary-email-to-receive-less-than-a-week-before-the-thesis-submission-deadline/

E-thesis final submission

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This week, my goal was to make final submission of my thesis. All the actual work on the document was finished. I just needed to figure out how to hand it in. As per instructions on the GPS website, my thesis has to be submitted in PDF/A format.

For those of you who are unaware, a PDF/A is not the same thing as a PDF. What’s the difference? It’s more expensive of course.

The thesis has to be converted to PDF/A using special software to ensure that it can still be opened in the future. So, in order to submit my thesis, Graduate and Postdoctoral Studies recommends that I buy Adobe Acrobat Pro, at a cost of $101.38 with tax—and that’s the reduced student price.

And the most frustrating thing about this? According to the instructions, “Standard PDF files will be rejected unless the thesis was written in LaTeX.” For those of you who are regular readers of my blog, you will recall that up until February, I was using LaTeX to typeset my thesis, and it was a painful and scary transition for me to move to Microsoft Word part-way through.

So ultimately, it came down to a choice between trying to convert my thesis back to LaTeX, or spending $100 to avoid all that hassle.

Laziness won, of course.

On Thursday, I went in to the bookstore and bought the software. When I first installed it and tried to convert my thesis, I got an error. Acrobat couldn’t convert my thesis. This seemed strange, since there wasn’t any strange formatting in it. I fiddled with the settings, tried restarting, but the very expensive software wouldn’t do it. Fortunately after a half hour, it auto-installed an update and after that, the conversion went as planned.

So as of yesterday, I have submitted my thesis to McGill. It’s over! Those are all the requirements for my master’s in bioethics! The only thing that’s left is my supervisor clicking “accept.”

By the way, one of the most satisfying things about making final submission of my thesis is the fact that I can take the ugly EndNote app out of my computer’s dock. It was such an eyesore! :P

BibTeX

@online{bgcarlisle2011-2194,
    title = {E-thesis final submission},
    journaltitle = {The Grey Literature},
    author = {Benjamin Gregory Carlisle},
    address = {Montreal, Canada},
    date = 2011-09-23,
    url = {https://www.bgcarlisle.com/blog/2011/09/23/e-thesis-final-submission/}
}

MLA

Carlisle, Benjamin Gregory. "E-thesis final submission" Web blog post. The Grey Literature. 23 Sep 2011. Web. 16 Dec 2018. <https://www.bgcarlisle.com/blog/2011/09/23/e-thesis-final-submission/>

APA

Carlisle, Benjamin Gregory. (2011, Sep 23). E-thesis final submission [Web log post]. Retrieved from https://www.bgcarlisle.com/blog/2011/09/23/e-thesis-final-submission/

What grad students dream about

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Last night I dreamed that I had to present my thesis to my readers orally—all 87 pages of it. Everything was going well until the end of chapter 2, when I came across a bunch of dummy text and references to tables and figures that I had never heard of. I slowly came to the realisation that in my dream I had incorporated the dummy text into the end of chapter 2 to get an idea of how much I would have to write to reach my desired word count, and forgot to replace it with real text before submitting it. All the professors and classmates who came to hear me speak started laughing as I flipped through the next few pages of my thesis, to see how much lorem ipsum I had padded my thesis with.

Two, three, four … eight pages. When the meaningless padding was removed, my thesis was only 79 pages long—one page short of the minimum required length.

I tried to explain to my readers that the next chapter was where it got interesting, and that I needed to finish with my thesis to start my next academic programme, but by that time, they had already begun walking out.

Apparently this is what grad students dream about. Well, this and dinosaurs. I drew a picture of that dream.

BibTeX

@online{bgcarlisle2011-1921,
    title = {What grad students dream about},
    journaltitle = {The Grey Literature},
    author = {Benjamin Gregory Carlisle},
    address = {Montreal, Canada},
    date = 2011-06-28,
    url = {https://www.bgcarlisle.com/blog/2011/06/28/what-grad-students-dream-about/}
}

MLA

Carlisle, Benjamin Gregory. "What grad students dream about" Web blog post. The Grey Literature. 28 Jun 2011. Web. 16 Dec 2018. <https://www.bgcarlisle.com/blog/2011/06/28/what-grad-students-dream-about/>

APA

Carlisle, Benjamin Gregory. (2011, Jun 28). What grad students dream about [Web log post]. Retrieved from https://www.bgcarlisle.com/blog/2011/06/28/what-grad-students-dream-about/

I submitted my thesis today

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ACCO-Press bound thesis

ACCO-Press bound thesis

When I woke up this morning, I was three steps away from submitting my thesis:

  1. Get French translation of my abstract
  2. Print thesis
  3. Get my supervisor’s signature

Well, it turns out my translator’s computer crashed, and so I didn’t get the French version of my abstract until exactly 12h today.

I printed my thesis—all 87 pages—bound it in ACCO-press binders, applied the necessary stickers, packed everything up and then wondered why I hadn’t heard back from my supervisor. He’s generally very fast at responding to emails, and last night he offered by email to sign my thesis submission form this afternoon, so it was surprising that he hadn’t got back to me.

I called his office. I called his home. I sent another email. I decided to do a stakeout at the Biomedical Ethics Unit and see if I run into him. When I was putting on my shoes, I considered for a moment whether I should put on my running shoes or my regular shoes. I had this nagging feeling like somehow I would end up sprinting to the James Administration Building at the last second, and that I would be happy to be wearing running shoes. Then I dismissed that thought. All I had to do, after all, is get my supervisor’s signature and then walk across the street and submit it. Putting running shoes on would be silly.

I put my regular shoes on and went to the Bioethics Unit to look for my supervisor. I ran into the administrative assistant who informed me that he was having a terrible day. A few seconds later I got a phone call from him.

Apparently my supervisor had a minor car accident and spent the morning in the emergency room. He invited me to his house to have the forms signed. This would not normally have been a problem, but Villa-Maria station (where he lives) is closed until September 6, and so I went to Vendôme station and hired a cab to get me to his place.

I saw the back of his car when I arrived. There were indentations that I’m sure were never intended by the manufacturer to be there. My supervisor and his family are all right, I think, but understandably this has been a bad day for them.

The forms all signed, I sprinted to the nearest Bixi station and decided that it would be fastest to just ride the Bixi all the way to campus. This may or may not have been the case, but I made it back to campus in 25 minutes, which is probably better than what it would have taken to get to a métro, wait, transfer at Lionel-Groulx and then walk from station McGill to the James Administration Building.

On arrival, I was hot, sweaty and breathing heavily, but I still had the presence of mind to turn on the Voice Memo app on my phone, so that I could secretly record it when the person in the Graduate and Postdoctoral Studies office said, “Yes, everything appears to be in order.” (Thank goodness for iPhone headphones that have a built-in mic for clandestine voice recording.)

I guess I’m paranoid because I’ve recently had two separate experiences where I handed in everything on a document checklist only to receive a mystifying message later on, indicating that I failed to submit all the required documents. I don’t plan to use this recording for anything but soothing my own nerves, for the record. It just feels good to hear someone say that I submitted everything.

So after all that, I have now made initial submission of my thesis. Hooray!

BibTeX

@online{bgcarlisle2011-1898,
    title = {I submitted my thesis today},
    journaltitle = {The Grey Literature},
    author = {Benjamin Gregory Carlisle},
    address = {Montreal, Canada},
    date = 2011-06-10,
    url = {https://www.bgcarlisle.com/blog/2011/06/10/i-submitted-my-thesis-today/}
}

MLA

Carlisle, Benjamin Gregory. "I submitted my thesis today" Web blog post. The Grey Literature. 10 Jun 2011. Web. 16 Dec 2018. <https://www.bgcarlisle.com/blog/2011/06/10/i-submitted-my-thesis-today/>

APA

Carlisle, Benjamin Gregory. (2011, Jun 10). I submitted my thesis today [Web log post]. Retrieved from https://www.bgcarlisle.com/blog/2011/06/10/i-submitted-my-thesis-today/

Thesis abstracts in both English and French

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Well what do you know? I have to write a French version of my abstract for my thesis.

This means it’s time to go out and buy some Newcastle beers. I have a friend who’s a translator who enjoys Newcastle beer, and if I’m going to exploit my relationship with her for my personal gain, I might as well make it worth her while.

There’s no way I’m going to risk writing my own thesis abstract in French. In French, I’m most confident in my ability to discuss whether pineapples can talk:

BibTeX

@online{bgcarlisle2011-1872,
    title = {Thesis abstracts in both English and French},
    journaltitle = {The Grey Literature},
    author = {Benjamin Gregory Carlisle},
    address = {Montreal, Canada},
    date = 2011-06-3,
    url = {https://www.bgcarlisle.com/blog/2011/06/03/thesis-abstracts-in-both-english-and-french/}
}

MLA

Carlisle, Benjamin Gregory. "Thesis abstracts in both English and French" Web blog post. The Grey Literature. 03 Jun 2011. Web. 16 Dec 2018. <https://www.bgcarlisle.com/blog/2011/06/03/thesis-abstracts-in-both-english-and-french/>

APA

Carlisle, Benjamin Gregory. (2011, Jun 03). Thesis abstracts in both English and French [Web log post]. Retrieved from https://www.bgcarlisle.com/blog/2011/06/03/thesis-abstracts-in-both-english-and-french/

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