Writing Academic Papers

Jonathan Bennett has another post up in his Year of Emacs series. This one is about writing academic papers. Bennett is in the humanities but still uses Emacs and Org-mode to write his papers. I’m always interested in posts like this because writers in the humanities have special conventions they need to follow so seeing how they adjust the Org workflow to meet them is instructive. You shouldn’t think, however, that his post is useful only to those working in the humanities. The same setup will work for any discipline.

Bennett’s tool chain is mainly

  • Zotero for library management
  • Org-mode and LaTeX to produce PDFs
  • org-ref to manage his citations
  • PDF tools for reading and marking up papers
  • Magit/Git for version control

Zotero is a nice tool and open source so there’s no reason to avoid it but as shown in Kitchin’s video on org-ref you probably don’t need it. Org-ref can download papers in several ways and using it means there’s one less tool to learn and worry about.

One very nice thing about Bennett’s post for beginners is that he doesn’t assume you know how to configure things for a workflow like his and he show’s everything that’s necessary.

This is a nice post and well worth reading if you’re involved in writing papers either professionally or as a student. Bennett explains why he prefers not to use Word or one of its evil progeny but, of course, Irreal readers are already familiar with reasons to avoid them. Really, it’s hard to envision a nicer writing environment than one involving Org and org-ref.

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Notion

Ali Abdaal is a Junior Doctor (sort of like a Resident in the US) practicing in Cambridge, UK. He’s also a YouTuber producing videos on productivity, efficient study habits, tech reviews, and life as a Junior Doctor. I’ve been following him since his medical school days after I saw his excellent video on how (and why) he uses an iPad and Notability to take notes in medical school. If you’re still in school you must watch this video.

One of his favorite topics is productivity apps and how he uses them to organize his life and manage his many activities. His latest favorite is Notion, a notetaking app with many features and ways to display your data. Normally, I wouldn’t pay any attention to something like this because I have the power of Emacs and Org-mode to do everything that Notion does and much more but when Abdaal gives such a positive review of an application, it’s worth taking a further look.

My quick take is that it’s a nice application that has much of the Org-mode note taking capabilities all wrapped up in a pretty GUI. It is, of course, mouse-centric so if you aren’t a point and clicker you might not like it. If you’re not an Emacser—or more generally, don’t live in your editor—you may find it a useful way to organize your notes and data. It will probably appeal to the same sort of person who likes and uses Evernote. There are mobile as well as desktop versions so you can have access to your data on the go and make notes when you’re out and about without a laptop.

All-in-all it seems to be a pretty nice application if you don’t mind the point and click aspects. Or it would be except for one fatal flaw: Your data lives on someone else’s server1. If you want more than the free version, you have to buy a subscription to the service. That would be Okay—after all, you’re renting space on someone else’s computer—but what Notion really is is software as a service and that’s inherently dangerous as Eric Raymond had occasion to point out just the other day.

Of course, a huge number of people aren’t bothered by this—until they are—and happily commit their irreplaceable work to Google apps despite Google’s record of freezing accounts if they detect what they suspect might be BadThink. I don’t know anything about the people running Notion and what their thoughts are on this sort of thing but I’m not willing to risk my data and workflow to someone else’s whim. Especially not when Org-mode gives me the same or better functionality and I can keep control of my data.

Footnotes:

1

I can’t tell for sure that the client apps don’t keep a local copy of your data but their Web page suggests not. If I’m wrong, perhaps some Notion user will let me know and I can update this post.

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How to Limit Google Tracking You

It turns out that there are some steps you can take to limit the type and amount of data that Google collects on you. This is especially relevant if you live in the Android ecosystem but even for those of us, like me, who prefer to live in the Apple world, some of these steps are useful to stop some of the collection.

Via John D. Cook’s excellent Data Privacy twitter feed, I found a pointer to a Wired article entitled All The Ways Google Tracks You—And How To Stop It. The article tells you how to find the Google pages concerned with managing your data and how to turn the collection off. If you’re signed into your Google account (such as Gmail) you can simply follow a link in the article and it will take you to the page. Once there, you can turn off the collection of various sorts of data and delete what they have.

I’ve made a point of not being signed into Google for some time now. About once a month I check my Gmail account and then delete cookies so that I’m signed out again. If you’re like me, simply sign in to your Gmail account or whatever you have, follow the link, and set things the way you want them. When you’re done, delete your cookies and everything should be fine.

This is, I know, like bailing out the sea with a teaspoon but every bit helps.

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Cell Phones and the Crime Rate

The New Luddites current favorite hobby horse is the evils of smart phones and all the myriad ways they are destroying civilization as we know it. These people are exceptionally tiresome but they never seem to tire of badgering us with their end-of-the-world warnings.

Rather than repent, I offer the following: according to a study by Lena Edlund and Cecilia Machado, cell phones may be responsible for the dramatic decrease in crime from 1990 to 2000. Well, at least there is a negative correlation between cell phone usage and the homicide rate. Mathematical grownups know that correlation doesn’t imply causation but the paper is suggestive and the reason Edlund and Machado give for correlation appears reasonable.

You might think that that reason is obvious: cell phones make it easier to quickly report crime as it’s happening. But that’s not the reason Edlund and Machado give. They say that cell phones changed the illegal drug trade making it less important for gangs to hold and defend territory. They attribute the fall in homicide rate to a decrease in gang violence.

The paper has received some push back—mainly from people with their own theories of what caused the decline—but its explanation seems more sensible than some of the competing theories such as the rise in abortions.

The cautious reader should always treat studies like these with suspicion. Most of them boil down to “Hey! Look at this correlation.” Still, it’s a pleasant change from the New Luddites’ incessant doom saying.

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Hidden Gems #4: TODOs

Cheong Yiufung has another great post up in his Org-mode Hidden Gems series. The latest post takes a look at Org-mode TODO functionality. As usual, I learned some new things proving again that the “hidden gems” tag is appropriate, at least for me.

Most Org users know that you can specify your own TOTO tags and make them anything you want. Yiufung shows how you can use that fact to implement a sort of lightweight task assignment system. I’d probably implement this with check boxes under a project heading but you may like Yiufung’s system better: take a look and see.

Next, he discusses TODO statistics. Those are the cookies that tell you how much of a task has been completed. Normally, the statistics cover the entire subtree so that even subtasks are counted. It’s possible, though, to specify that you want them to act in a hierarchical manner. Then, each (sub)subtree is treated as a unit and can have it’s own counter. Yiufung has a video that shows this and makes it clear how the two modes differ.

Finally, he looks at the Org habits functionality. This is useful for repetitive tasks such as exercising when you want to track your progress. Org gives you a nice graphical summary of how well you’re doing. Again, take a look Yiufung’s video to see what it looks like.

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The Story of VisiCalc

Via Karl Voit I found this video of Dan Bricklin telling the story of how VisiCalc came to be. Many younger Irreal readers probably don’t remember Lotus 1-2-3 let alone VisiCalc so it’s worth mentioning that VisiCalc was the first electronic spreadsheet.

It’s a typical hacker story of writing some code to scratch an itch. Bricklin was getting his MBA at Harvard where the curriculum was based on case studies and involved, among other things, making manual spreadsheet calculations. Bricklin found that it was easy to make a calculation error and of course that error would propagate to other rows and columns. Since grading was based in large part on class participation, it was important to have the calculations correct in order to contribute in an intelligent way.

Bricklin had an undergraduate degree in Computer Science from MIT so automating the calculations on a computer seemed a natural solution. Along with his classmate Bob Frankston, Bricklin starting working on VisiCalc. This was in 1979 when the only reasonable small computer available was the Apple II. Although it ran on the Apple II, VisiCalc was developed on a Multics system that Bricklin and Frankston had access to.

An interesting part of Bricklin’s talk is how he struggled to find the right interface for the program. These days the grid paradigm with numbered rows and lettered columns is so well established that it’s hard to imagine any other way of doing it but Bricklin tried several schemes before settling on the now familiar pattern.

It’s an enjoyable talk and well worth the 12 minutes it takes to watch it. Steve Jobs said that VisiCalc was largely responsible for the early success of Apple so it’s more important than you might think.

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A Year of Emacs

Jonathan Bennett has an interesting project underway. He’s a longtime Vim user whose evolving needs led him to Emacs. At first, he used Spacemacs but he had problems with its speed and had difficulties configuring it. So he moved on to vanilla Emacs and used it to write his Masters thesis.

Now he’s planning on writing a blog post every week for a year that considers a single Emacs package or use case. His first post, Introduction to a Year of Emacs, recounts his journey from Vim to Emacs and his plans for his “Year of Emacs.”

I’m looking forward to his posts. I like that they’ll be appearing regularly and will consider a single subject in depth. He has an RSS feed so it should be easy to keep up with the series.

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Taking It Very Seriously

The other day I wrote about the costs Equifax is finally having to bear for its 2017 breach of 150 million consumer records. Apparently, First American Financial Corporation upon learning of the Equifax breach said, “Hold my beer.”

Over the Memorial Day weekend Brian Krebs tweeted about a “Truly massive—possibly superlative—sensitive data exposure.” That turned out to be First American’s leak of hundreds of millions of mortgage deal documents from 2003 to present. Those documents included tax returns, bank account numbers and statements, social security numbers, driver’s license images, and other sensitive information. You can read Krebs’ full article here.

Who were the master crackers behind this exploit? Well, no one. First American simply put them unsecured on the Internet. Anyone with a Web browser who knew just one URL could get access to all the records. First American is, of course, taking the breach “Very Seriously.”

Vicki Boykis has a wonderful post on the event in which she rightly ridicules the “taking it very seriously” line. It is, she says, what companies who have never given a second thought to security or safeguarding consumers’ sensitive information always say when they get caught playing fast and lose with other people’s data. She goes on to say that the real problem is that companies have no incentive to do better.

She notes that Equifax, which is only now beginning to suffer for their negligence, is still in business and none of their executives have gone to jail. There is some hope, however. She notes that the GDPR in Europe and California’s CCPA (California Consumer Privacy Act) have started to worry these companies. As I said in my previous post, until it is crystal clear that collecting and storing people’s information entails an unconditional obligation to keep that information secure and that violating that obligation carries substantial financial and criminal penalties, companies will calculate that the typical penny-ante fines meted out by the government are simply a cost of doing business and nothing will change.

I think Boykis is right. Until the consequences of slipshod handling of consumers’ information is draconian and certain, nothing will change. As for First American, if their executives had any honor they would resign and join a monastery.

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More on Multics Emacs

Back in January, I wrote about Bernard Greenberg’s history of Emacs on the Multics system. I just found a set of contemporaneous notes on the first 110 days of Multics Emacs’ development.

What’s amazing is how quickly they were able to get a basic editor framework up and working. As I mentioned in my first post, the Multics system presented some formidable challenges for a full screen editor. Chief among these was that there was no way to do character I/O so the OS itself had to be patched just to get in the game. Achieving a working Emacs was much more complicated than just writing an editor.

After only 110 days, they had an Emacs that was usable as a working editor. Read Greenberg’s notes to get a feel for what a remarkable feat this was. Multics no longer exists—except as a hobbyist project running on a simulator1—so in a way Multics Emacs no longer matters but its enduring legacy is being the first Emacs to be written in Lisp.

If after reading these (fairly short) notes you’d like more information, see Greenberg’s longer history of Multics Emacs. It adds context and details to many of the points in the short notes.

UPDATE [2019-05-29 Wed 11:12]: Lars Brinkhoff comments and also wrote to me out-of-band that, in fact, EINE was the first Emacs to be written in Lisp. Brinkhoff, whom I’ve written about before, maintains a really great repository of old Emacs code. It’s worth taking a look at if you haven’t already.

Footnotes:

1

See the Multicians.org website for more details.

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The Past Comes Due for Equifax

For those who have forgotten, 2 years ago Equifax—one of the top three credit reporting services in the world—suffered a catastrophic breach that resulted in the loss of data on 150 million people. The details are drearily familiar: Equifax had an outdated system and had failed to apply patches that had been available for months. Congress and others have accused the corporation of negligence and stupidity.

Now the cost of their negligence is becoming clear. Moody’s, a Wall Street bond rating service, has downgraded Equifax to a negative outlook. Lawsuits and investigations have already cost Equifax 690 million dollars in 2019 and the company is expected to pay out another billion dollars through 2021 to deal with the breach.

Equifax, and companies like it, vacuum up every bit of information that they can about people. Much of it, I’m sure, is only peripherally, if at all, concerned with credit worthiness. That’s bad enough but what’s really bad is that Equifax couldn’t keep that information secure. The data was exposed not from an “act of God” but from negligence and a “who cares” attitude about security.

I doubt their problems are existential but I wouldn’t be sorry to see them sued into oblivion. Until society makes it clear that if you gather people’s information, you’re unconditionally responsible for keeping it secure, we’ll continue to see this sort of thing. Regular readers know that Irreal is invariably suspicious of government attempts to insert themselves into our lives but this seems a case where the government could benefit us all by making the penalties—both financial and criminal—for mistreating citizen’s confidential information explicit.

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