Miscommunication between my professor and me


When I received feedback on the 3rd chapter of my thesis from Dr. Kimmelman, there were three really specific criticisms that didn’t make much sense to me. I went in to his office to ask about them, and he mentioned casually a paper that he had published in Science. (For people outside of academia, Science is one of the most prestigious academic journals in which to have an article published.)

“You had an article published in Science?” I asked.

“Yeah, a lot of your thesis is supposed to be based on it. Are you sure it wasn’t in that package of papers I gave you in September?”

“Pretty sure.”

“Wow. You would have had to do a lot of re-inventing of the wheel, huh?”

I have now read his paper in Science, and everything is so much clearer now. Over the weekend, I was able to write 5 pages on my thesis as a result of reading it. And it was easy writing those pages.

I feel like I’m actually getting some work done now, and like this project is manageable now. Also, I finally understand why my supervisor was so often confused by my confusion over the course of the year.

Endnote X4 and Microsoft Word for Mac


I found a solution to my reference manager problem.

Step one: (Re-)Install Endnote

I had an older version—Endnote X2 installed on my computer from last year when I went to a seminar on reference management at the McGill library. When I installed it the first time, I did not have a copy of Word on my computer. It turns out that if you install Endnote before you install Word, it doesn’t work at all. This caused me some confusion. After upgrading to Endnote X4, it automatically configured itself to work with Word automatically.

Step two: Convert BibTeX reference library to Endnote

I was really afraid that this step would take a long time. And indeed, if I were to do it all manually, it would have taken a long time. That’s why I’m glad I found this: A BibTeX to Endnote converter. It worked really well. Suspiciously well. I’m half-afraid that something is going to go terribly, terribly wrong.

Step three: Insert references into Word document

View > Toolbars > Endnote X4

Then, click on the fourth icon in the toolbar. Away you go.

Step four: Making page numbers show up in in-text citations

This one took me a while to figure out, and if you do a Google search for help on this, you’ll only end up at this unhelpful FAQ.

Here is how I tried to do it: I’d right-click my in-text citation, click Edit Citation(s) > More …, then I’d try adding the page number there, and it wouldn’t show up in my citation. I’d try a million different ways of doing this, and none worked.

Then I tried right-clicking and then choosing “Toggle Field Codes.” This showed me that the page numbers were actually being inserted correctly, but because of the citation formatting choice, it wasn’t being displayed. All I had to do was go back to “Format Bibliography,” then choose a bibliography style that displayed page numbers in in-text citations. APA, for example, works wonderfully.

Things that make me worry about EndNote X4

Maybe this is shallow of me, but for a $300 piece of software, I’d expect the programme’s icon to look a little less ugly. (Don’t worry, I didn’t pay $300 for it. McGill students can download EndNote X4 for free from the Library website.) I mean, it’s an eyesore in my Dock.

Also, the paperclip in the “attachments” column has jagged edges and is not centred correctly.

This sort of thing worries me. It makes me think things like, If they couldn’t even be bothered to fix the paperclip, what else have they let slip through the cracks?

I mean, BibDesk had a nice-looking user interface by comparison. BibDesk’s icon, while it was not beautiful, wasn’t an eyesore. And it was free. The really expensive software looks terrible, and makes me wonder if there’s other things wrong with it.

That said, I’m willing to give it a solid try. It seems to do all the things I want it to, and it has a long list of bibliography formats, including the journal to which my prof wants to submit my 3rd chapter.

A review of Microsoft Office 2011 for Mac


A wizard has turned you into a whale

A wizard has turned you into a whale

Bright and early yesterday morning I went to the bookstore at McGill to buy a copy of Microsoft Office. If you are a student, at certain places, you can get a cheaper “education version” of Microsoft Office. When I left the store, I was the reluctant owner of a copy of Microsoft Office 2011 for Mac. This happened because my supervisor felt that for editing a paper for publishing, he would be more comfortable using the collaborative tools that are a part of Word. More on that later.

When I got to the bookstore, I was greeted by a young man wearing a red hoodie over a t-shirt with the design featured in the image attached to this post.

“Can I help you?” he inquired.

“Do you work here?” I asked.

When that was settled, he took my credit card and then gave me a receipt and told me to go to the basement, where there would be someone at the pick-up window where I could redeem my receipt for the install CD’s. I got down to the basement and there was a sign on the door of the pickup window, “Be back in 5 mins.”

I rang the doorbell anyway, and after a few minutes, the very same man who had been working upstairs in the computer section had rushed downstairs to meet me. He joked about how he should wear a fake moustache when he works both upstairs and downstairs. I agreed that this was a good idea.

When I took it home and had it installed on my computer and registered, I actually involuntarily shuddered. I usually don’t have such a visceral reaction to computer software, but then it’s actually been a full ten years since I used Microsoft Office. I was in grade 11 then, and it was the first edition of Office for Mac OS X, which was a big thing. I only got the 30-day free trial download version, but I remember thinking that there was something clunky and un-Mac-like about it.

It’s not half as bad as I remember, but there are a few things that I’m still not too happy about.

Initial Review of Microsoft Office 2011 for Mac

In this review I will mainly be focussing on Microsoft Word. Perhaps in the future I will use Excel or the other parts of Office enough to have strong feelings on them.

I’m gonna come clean about my prejudices: I am used to using LaTeX and BibTeX for pretty much all of my word processing. I have used them exclusively for essays and other school projects since 2004 or so. I really appreciate the separation of content and form and the exacting control of all the details of the typesetting that I have when I’m using LaTeX. I can just write, and not worry about where my words are on the page, since LaTeX will take care of that.

I could also separate chapters of my thesis into separate files, which somehow made my work more manageable. Maybe it’s that the scroll bar at the right of the document gets so tiny when your file is huge or something. It would feel unwieldy to have my thesis in a single file, and so I separated the main body text it into four files: I had Thesis.tex, Ch1.tex, Ch2.tex and Ch3.tex. Then, I’d just include each of the chapters inside the Thesis.tex file and have all the formatting and style information in that file, so the other files could just be bare text files with no formatting distractions at all. It was wonderful.

I also really liked the way BibTeX took care of my references. If I needed to change a reference that I make a number of times throughout my thesis, I could change a single file, Sources.bib, then the next time it re-typeset the document for me, all the changes would be made to all the references throughout the document, including the Works Cited. Not only that, but I found a way to have it automatically change repeated references into “ibid.” so that it didn’t look so cluttered. Not having to think about things like this is actually fairly important to me.

Things I dislike about Microsoft Word 2011 for Mac

The most frustrating thing for me right now in using Word is that I can’t turn off the WYSIWYG editor. I feel like I should be able to edit the underlying code that is generating the document, but there’s really no way to do that. This is unsettling for me. I feel like I’m not in control. Word is. I just shuddered again.

Also, it does some things that are very un-Mac-like. For example, if I push command-up, I expect to be taken to the beginning of the document. In every other Mac application, that’s what that combination of keys does. In Word, it moves you to the top of the paragraph. This is a bug. There is already a key combination on the Mac for moving to the top of a paragraph. It’s option-up. (Same thing, mutatis mutandis for command- and option-down.)

Linking Word files together

On the upside: I can still separate the chapters of my thesis into separate files, and then link them together into a single document for formatting. It’s not that hard. I just type up chapter one in one file, save it, then click Insert > File …

The tricky part is that you have to remember to check off the box that says “Link to File” when you insert your Chapter One.docx file into your Thesis.docx file. This way it automatically updates the Thesis with the contents of Chapter One. Unfortunately, it doesn’t do this automatically automatically. Whenever you make a change to Chapter One, you have to go back to Thesis and click Edit > Links … and then update it. This isn’t too bad, except every time I do this, I have to fix the numbering of chapters manually for each chapter, even if I set each individual chapter file’s chapter heading to start numbering at the appropriate chapter number. This is silly.

Another thing that I like about this is that if you use the Styles at the top of the ribbon instead of formatting everything manually (for example, when formatting a book’s title, choosing the Book Title style rather than just hitting the italicise button), then when you link your Chapter files into your Thesis file, the formatting that you chose in your Thesis file is applied even to the content that is automatically pulled from the Chapter files. This is nice. If I accidentally change the formatting on one of my chapters at some point, it will all be consistent in the final Thesis file.

Microsoft Word’s citation manager

I have found Microsoft Word’s built-in citation manager, which isn’t pure evil, either.

Here’s a couple things I’d like to know how to do: insert a citation without parentheses, and how to have it automatically put “ibid.” when appropriate. Also, I’m not sure that it will automatically update the citations in the body text if I change something in the citation manager, but I have a bad feeling it won’t and this will cause me endless grief later.

Can anyone suggest a good solution for citation management that’s compatible with Microsoft Word for Mac? I don’t trust the built-in one.



My entire thesis so far could fit on a single 3.5″ floppy diskette.

That includes the final PDF, all the .tex files used to generate it, my bibliography, my style files, and a few PDFs of important articles that I make reference to.

I’m kind of tempted now to try to find a floppy diskette and an old computer and see if I can write my thesis onto it, just for the retro appeal.

LaTeX, BibTeX and ibidem


Apparently, having been trained in the philosophical tradition, I’m unused to citing sources. My supervisor says that a typical attitude for a philosopher to take toward sources is that if your bibliography has 6 citations, that’s 5 too many. So, on the advice of my supervisor, I have been trying to include more references to published sources in my thesis. As he puts it, “think less; read more.”

Having done that for the last chapter or so (I’m going back later to add lots and lots of citations to the other chapters), I realised that the citations were taking up way too much space on the paper. So, I put them all in footnotes. They still took up a lot of space, and they were hard to read down there.

So, I decided that I should change my citation style, so that when I have multiple citations from the same source, the second, third, etc. citations after the first one would just be “ibid.” (From Latin ibidem, meaning “the same place.”) This would have been a time-consuming and mind-numbing task, going through my entire thesis and picking out all the citations where there’s two or more in a row and replacing all but the first one with “ibid.

Fortunately, I use LaTeX and BibTeX (and OS X front-ends called TeXShop and BibDesk) for writing my thesis and citation management.

I found a great package, called inlinebib that does just that. It actually took a bit of digging to find a bibliography style package for LaTeX that worked the way I wanted it to, with ibidem and all. But once I found it, all I had to do was put inlinebib.bst and inlinebib.sty in my project folder, then write \usepackage{inlinebib} in my document preamble, and it worked just fine!

Backing up, backing up, backing up, backing up


What do you use for backing up your computer files? I’ve had a number of close calls in my academic career, and so I compulsively back everything up. Here’s how I do it:

First, I keep multiple revisions of my thesis in folders on my own personal computer. So I have the first revision of my thesis in a folder marked with the date I started it, and then when I make changes to it, I just copy the whole thesis folder and change the date. That way, if I really mess it up somehow and then push “save” by accident, the previous version is there, at least.

The next level of backing up is my periodic Time Machine backups. At the risk of sounding like an Apple commercial, I do actually like the way that my computer backs up my files. I just plug in the hard disc, and click on the little clock in my menu, and then it backs up all the files on my computer. This particular piece of software has saved me a number of times that I can think of. It is, in fact, one of the top five reasons why I would be reluctant to switch to Linux as my main computer of choice—there just isn’t any really comparable backup software that I could find.

That said, if someone wants to enlighten me as to some software for Ubuntu that does what Time Machine does—backs up the computer’s entire hard disc onto an external hard disc, and gives a nice interface for restoring old files, only backs up files that have been modified and doesn’t do anything weird—then please leave a comment!

What’s nice about using the Time Machine backup is knowing that even if someone were to steal my computer while I’m at the library or something like that, I would still have a copy of it in my backup at home.

The highest level of paranoia that I reach is that every once in a while, when I remember, I compress the most recent revision of my thesis into a .zip file, and then upload that to my Google Documents account.

This way, even if my apartment were to burn down and both my computer and external hard disc were destroyed in the blaze, my thesis would be alive and well, in the cloud.

Do you back up your files? How? Four points for anyone who has a more elaborate backup scheme than me!

A non-paternalistic justification for human research subject protections


Just this morning I had a great meeting with my prof regarding my thesis. I showed him the outline for my thesis and we put together a schedule for completing it. He even gave me a few references to go on in terms of researching the topic. I’m starting to feel good about it.

I’ve had a number of people asking me what my thesis is about, so here it is in brief:

There are restrictions that institutions place on the sorts of human research that can be done, and the justification for such restrictions are usually given in terms of subject harm or benefit. Unfortunately, such justifications are paternalistic. By that, I mean there is a sense in which, if someone wants to engage in a very risky research protocol as the subject, what right does the institution’s ethics board have to stand in her way?

That said, there is also a sense in which we do not want human research to just be a free-for-all house of horrors, where anything goes. My thesis is that we should rather justify human research subject protections in terms of protecting the integrity of the human research project as a whole.

So, in colloquial terms, I’m suggesting that rather than saying, “We won’t let you do that risky research because we know better than you what ends you should be pursuing,” rather we should say something more like, “We won’t allow such risky research because allowing such research to go on would make the human research enterprise look sketchy.”

An interesting application of this thesis is in the area of phase IV human research studies. A phase IV study is one that occurs after the drug is already approved for use, and it is essentially a marketing study. The drug company wants to see how to best market the drug to doctors and patients. Often it is even the marketing division of the drug company that applies for the phase IV study.

Ethicists have generally been trying to criticise phase IV studies on the basis of some sort of risk that it may pose to the research subjects. This position is difficult to hold because really, the drug has already been approved for use on humans. I will argue that it is much more defensible to say that such studies are unethical because they do violence to the integrity of human research.

Et voilà. My thesis. All I have to do now is write 80 pages on that, and I’m golden.

The Bioethics Unit party


My classmates at Vendome station after the Bioethics Unit party

My classmates at Vendome station after the Bioethics Unit party

Today was the Bioethics Unit party, held at the beautiful home of the director of the Bioethics Unit. I finally got a bunch of long-awaited details on exactly how the programme works.

We discussed supervisors, length of thesis (no more than 100 pages – darn :P) and details regarding the practicum that will be happening in the Winter term. The majority of the evening was spent getting to know my classmates and other members of the Unit.

It was both a “Welcome to the Bioethics Unit” party and a “Happy Retirement” party for one of the profs who will be stepping down as the Unit director.

Pictured to the right are two of my four classmates at Vendome station. They were headed in the opposite direction from where I was going, so I took the opportunity to photograph them from the opposite platform.


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