Written by commandline (aka Thomas Gideon) at the request (behest?) of Cory Doctorow, Flahsbake was meant to address the problem of retaining an archival record of the production of digital texts. Cory Doctorow explains:

I was prompted to do this after discussions with several digital archivists who complained that, prior to the computerized era, writers produced a series complete drafts on the way to publications, complete with erasures, annotations, and so on. These are archival gold, since they illuminate the creative process in a way that often reveals the hidden stories behind the books we care about. By contrast, many writers produce only a single (or a few) digital files that are modified right up to publication time, without any real systematic records of the interim states between the first bit of composition and the final draft.

The problem is genuine, I have written about it before. Moreover, I agree that version control has a role to play in its solution. However, I have doubts about the utility of Flashbake. It’s simplicity is its virtue, but it is too simple. No commit messages? A record of ambient information is no real substitute. And Flahsbake’s users are supposed to be geeky enough to use a command line tool, but not geeky enough to master the following simplified workflow?:

$ git init
$ git add mynovel.txt
$ git commit -m "initial commit"
write write write
$ git commit -a -m "new commit message"

I am not sure I get it. Still, any version control is better than none. And maybe Flahsbake will function as a Git gateway technology. If you are interested in a less puzzled reaction to Flashbake see the Lifehacker article. But if you want to be a really nerdy writer, just use Git neat.

For art in printing is not the way
Of wild extravagance, weird display,
But rather the unobtrusive thrall
Of type that gives you no shock at all,
But draws your eye to the page with zest
And holds your mind to the thought expressed;
We must keep ourselves to this simple creed,
Type was made - and is meant - to READ!

Unfortunately, the source provided no citation.

Advanced features of LaTeX are best learned on a need to know basis. The LaTeX Companion can be daunting in its length. If you thought you needed to master all of that material before writing a LaTeX document you would never do so. So start simple, and learn how to do more advanced things as and when you need to.

Learn on a need to know basis, and when you do learn, hack. Don’t feel like you need to know whether the code will work before running it. The worst thing that will happen is that LaTeX will throw an error. LaTeX errors are instructive. Learn to love them.

These reflections arose today when I needed to do something which should have been simple. It was simple—once I learned how to do it. I was preparing a handout for my seminar. On the handout is a summary of the material that I presented on Cook Wilson and the nature of representation and notes on the ensuing discussion. It would be useful if these were visually distinguished.

My first thought was to use the color package. It has a command \colorbox that specifies the background color of a box. However, the results were suboptimal—small strips of white separate the colored lines. Disappointed, I thought, well, perhaps I can just color the relevant text with \textcolor. The discussion however could run for several paragraphs and it turns out that \textcolor chokes when it wraps multiple paragraphs. It was obvious to me, then, that there was no straightforward, out of the box, solution.

I decided to define a new environment, discussion:

\begin{discussion}
    
\end{discussion}

It requires the color package, and you need to define a color that will be used for the background. I used \definecolor{myblue}{rgb}{0.8,0.8,1}. (Readers of the wonderful Tikz Pgf manual will recognize this as the background color of the code blocks.) The strategy was simple—wrap a minipage in a box. The minipage environment defines, well, a small page:

\begin{minipage}[position]{width}
  
\end{minipage}

The minipage is wrapped in a box. Boxes are usually created by commands, but there is a box environment lrbox:

\begin{lrbox}{}
    
\end{lrbox}

The text within this environment is saved in the box <cmd>. Here is the discussion environment with all the bells and whistles.

\makeatletter\newenvironment{discussion}{%
   \noindent\begin{lrbox}{\@tempboxa}\begin{minipage}{\columnwidth}\setlength{\parindent}{1em}}{\end{minipage}\end{lrbox}%
   \colorbox{myblue}{\usebox{\@tempboxa}}
}\makeatother

Here’s the gist:

(Sorry for the duplication, but embedded gists are not showing up in some news readers.)

Two comments. The initial \noindent is required otherwise the entire box will be indented—which would be awkward since the width of the minipage is set to the width of the column. Another issue is that there is no paragraph indentation within the minipage environment. In effect, within that environment, LaTeX sets \parindent to 0. This, however, can be overridden with the \setlength command:

\setlength{\parindent}{1em}

Here is the result:

However, it’s the difference wherein the interest lies. Unlike obsessing about straight versus typographic quotes this is more straightforwardly a “semantic” issue about the significance of embedding material within quotations. But the actual usage of quotation is quite complex as anyone familiar with the recent philosophical literature on quotation will attest. Far more complex than the simple semantics implicit in the charge of rampant use/mention conflation. Personally I abhor the use of quotation marks for emphasis, but the my distaste for it is simply that, distaste. It’s vulgar and largely confined to cheap marketing.

Semantic drift is a reality. Don’t fear change. It will only result in needless rage.

Here is a screenshot illustrating the clean and then dirty state of the development branch.

Legislation that has not kept abreast of changing technology can make the choice difficult.

As a philosopher, I write research papers, drafts of which are distributed on the web as PDFs. Open access to evolving research is important, and I am committed to it. Since I want to give my work the best chance of being understood, I take the time to properly typeset the PDFs with XeLaTeX. There is a problem, however, with distributing PDFs over the web.

PDF files can contain font information in a way that is easily extractable from the file. While the licensing of some type foundries allow embedded fonts in PDFs, many (especially smaller type foundries) do not. Indeed the ones that did probably did so at Adobe’s urging when PDF distribution on the web was relatively small and so not that great of a risk.

I would like to support small type foundries by buying their fonts. There are some brilliant type designers out there, and they should be rewarded. Unfortunately, since the main thing I want these fonts for is for web distributed PDFs, I can’t do that without violating licensing restrictions. And that’s not support.

There are of course open source fonts. Some of them are fine pieces of work. But the choice is limited, and important design decisions should not be so constrained.

DRM is not the answer, as the recent history of music distribution online sadly reveals.

I don’t know how to resolve this problem. It is partly technological, partly, legal. But I thought I would highlight for other academics who distribute their work online.

Upon finishing this post, I came across this essay that has more information about the legal and technological obstacles with some discussion of potential solutions.

To install the GitHub bundle do the following:

$ sudo gem install git
$ cd ~/"Library/Application Support/TextMate/Bundles/"
$ git clone git://github.com/drnic/github-tmbundle.git "GitHub.tmbundle"
$ osascript -e 'tell app "TextMate" to reload bundles'

One of the great features of using TextMate to produce LaTeX documents is the TODO Bundle. The TODO Bundle let’s you to insert TODOs into comments and display these in a nicely formatted HTML window with links to the lines where the TODOs occurred.¹²

There are two limitations with the TODO Bundle, however, which made me look for an alternative (I still use the TODO Bundle, the alternative is merely a supplement):

1. While I try to proof my documents as much as I can onscreen, sometimes I need to proofread the hardcopy. Proofreading hardcopy is easier, and any incremental decrease in distraction is a real boon in proofreading since it requires a lot of attention.
2. Suppose you are collaborating on a LaTeX document and your collaborator isn’t using TextMate. Of course, they can still follow the TODOs in the comments, but it would be great if these could be made more salient.

The Solution

The solution to both of these problems is to use LaTeX to generate the TODO list for you. To do this, I used the index package. The index package reimplements the internal LaTeX index macros adding functionality. Of particular interest is its support for multiple indexes. Add the following to your preamble:

The first line loads the color package (since our TODOs will be colored to make them stand out from the surrounding text). The second line loads the index package. The next two lines:

\newindex{todo}{tod}{tnd}{TODO List} % start todo list
\newindex{fixme}{fix}{fnd}{FIXME List} % start fixme list

define two indexes. The \newindex command takes four arguments. These arguments correspond to the four pieces of information required to generate the index:

1. A short, unique tag that identifies the index.
2. The extension of the output file where the raw index information will be put by LaTeX.
3. The extension of the input file where the processed information created by MakeIndex will be stored to be read in later by LaTeX.
4. The title of the index.

The next two lines:

\newcommand{\todo}[1]{\textcolor{blue}{TODO: #1}\index[todo]{#1}} % macro for todo entries
\newcommand{\fixme}[1]{\textcolor{red}{FIXME: #1}\index[fixme]{#1}} % macro for fixme entries

define two new commands: \todo and fixme. To add a TODO simply add the following at the appropriate place in the text:

\todo{My TODO entry}

Similarly, for FIXMEs.

New commands can be added on a similar pattern. So, for example, suppose you want to add a CHANGE command. To do this, be sure to also define a new index:

\newindex{change}{chg}{cnd}{CHANGE List} % start change list
\newcommand{\change}[1]{\textcolor{green}{CHANGE: #1}\index[change]{#1}} % macro for change entries

Notice, that the commands are color coded, so be sure to change the color. Since the previous two commands were blue and red, I made the CHANGE command green.

If you want to generate a list of the TODOs, FIXMEs, etc, at the end of your document you need to use the \printindex command. This takes as an option the name of the index, so for TODOs and FIXMEs we would use:

\printindex[todo]
\printindex[change]

Before we typeset these indexes, we need to run the makeindex command. Suppose that the name of your LaTeX document is foo.tex. Then, in the terminal we would run:

$ makeindex -o foo.tnd foo.tod
$ makeindex -o foo.fnd foo.fix

The -o option is used to specify the name of the file generated by makeindex that is used, in turn, by LaTeX to typeset the index. Having run makeindex, if we now typeset the document, the indexes will be printed at the end of the document after a pagebreak. And if you are using the hyperref package, these will have links to the pages where the TODOs and FIXMEs are inserted. This step can be automated with a makefile such as Latexmk.pl.

Been working on some scripts to clean up the BibTeX file, to normalize cite keys, to render consistent author and journal names, to strip out local URLs, etc. So look forward to a new development branch and a directory of utilities.

That’s a sharp downturn in spam. I know that this is a little read technical blog by an academic, but there has been no corresponding downturn in traffic that would explain this. Could times be tough, not only for investment bankers, but for spammers as well?

In a recent announcement, GMU reports that they will be dropping their Endnote license:

With litigation pending between Thomson and Mason, we’re letting our campus site license for EndNote expire at the end of November. When it lapses, any copy of EndNote that was downloaded and installed under the terms of that license will have to be uninstalled and removed.

In addition, GMU has provided a helpful website explaining how to migrate from Endnote to Zotero.

This disturbing incident is further evidence, if evidence were needed, of the perils of keeping your data in propriety formats. Keeping your data in formats that comply with open standards is really the only guaranteed way to control and reliably share your data.

To install:

curl http://github.com/defunkt/gist/tree/master%2Fgist.rb?raw=true > gist &&
chmod 755 gist &&
sudo mv gist /usr/local/bin/gist

Some usage examples:

cat file.txt | gist
echo hi | gist
gist 1234 > something.txt

Using gist from within TextMate should now be trivial.

There are two ways to call SyncTeX, from the command line and in source. From the command line simply use the argument -synctex=1, and from source include \synctex=1 in the preamble. The former may be preferable if you want to distribute your LaTeX source—that way it will run without errors even by those whose TeX distributions do not include SyncTeX support.

Here is how synchronization worked with pdfsync. A word in your source is associated with a file name and a line number where it occurs. The file name and line number together constituted the input record. That same word as it occurs in the pdf generated from the source is associated with a page number and a location on that page. Together these constituted the output record. Synchronization was achieved by linking the input record with the output record. Moreover this was done by assigning each of these records with a unique tag. This was necessary since while the TeX engine will place a word in the source on some page in the generated pdf and on some location on that page, by the time it has done this, it has “forgotten” the file name and line number. Unique tags were thus required to preserve this information for synchronization. These tags were stored in special data nodes in every pargraph, math display, etc.

There were three problems, however, with this synchronization solution:

1. The data nodes used by pdfsync could interfere with TeX’s line breaking mechanism and thus affect the layout of the page.
2. pdfsync was incompatible with certain LaTeX packages. While some could be rewritten to accommodate pdfsync, others could not.
3. The mapping from the input record to the output record was not one-one, but one-many. So developers of pdf viewers supporting pdfsync had to choose the right mapping from the input record to the output record, and this was not always easy to do.

Instead of using special data notes, SyncTeX exploits kern nodes and glue nodes that are determined early on in TeX’s processing of the source to track the location of a word in the pdf output.

Another advantage of SyncTeX over pdfsync is that SyncTeX also supports dvi and xdv outputs (not that useful for me, but your situation may differ).

The TeXLive distribution, which MacTeX is built upon, is the first implementation of SyncTeX, and both PdfTeX and XeTeX in TeXLive now have SyncTeX support embedded deep within these TeX engines.

Microblogging can clearly work with fiction, but what about more substantive works, like philosophical treatises? In a moment of intoxication inspiration, I came up with a quick Python one-liner¹ to compute how many lines in an English translation of Ludwig Wittgenstein’s celebrated “Tractatus Logico-Philosophicus” are 140 characters in length or less. I discovered that a bit under half of the lines are short enough to be Twittered (and, as the philosopher would say, what we cannot Twitter, we must pass over in silence).

In my own case, twittering philosophy has so far wholly consisted in mocking philosophers, gossiping about them, and git commit messages, thanks to GitHub’s service hooks. Perhaps others can offer tweets with more substantive philosophical content. After all, aphorism is not unknown to philosophy—the pre-Socratics and Nietzsche come to mind. For now, teh interwebs await a latter day Heraclitus.