A hot topic lately in the US technology media has been the discussion of the right to access the source code forming the basis of the software included in breathalyzers. Citizens accused of drinking while intoxicated have demanded access to the source code for the device in question, the breathalyzers that present the primary evidence against them in the accusation.

The request raises some issues. On one hand, the device - the Intoxilyzer 5000EN - is employed by the police and should as such be subject to scrutiny by the public. On the other hand, the company behind it is a private entity which reserves the right to deny access to the software source on the basis of trade secrets apparent if the code is made public.

Unfortunately, the debate has been somewhat obscured by a sidetrack into an open source versus proprietary software issue. While this is understandable - and more on that later - it is not actually a question of signing over the rights to the code, but simply to allow perusal of the code to ensure that no-one receives an unjust verdict. A commenter on Ars Technica posting under the name xoa suggests that it is unacceptable that this type of device is a “Black box”, an undocumentable analysis engine, and that all such devices should be developed openly and source should be placed in the public domain for inspection.

It is hard to come to an end-all conclusion on this discussion, since it squares a company’s private property against a public demand for - and right to - insight in a technological process which has the potential to influence many lives. But the discussion is important.

Interestingly, as an aside into the open source discussion, Eric Raymond argues in his classic work on the open source development model The Cathedral and the Bazaar that it is in the interest of the company - he mentions as an example producers of graphics cards - to release the driver source code, since this partially outsources the development of the driver and makes little influence on the development cycle, since by the time the competition has been able to reverse engineer the product, the producer will have moved on the next generation of the product. While I am no expert on breathalyzers, I suspect that the breath analysis market is somewhat different from the graphics cards scenario.

But the discussion is relevant, as has also been made clear by the debate around electronic voting machines. The potential for a democratic deficit is a very real and relevant concern, and it should not be dismissed. Contrary to the breathalyzers, the customer base here is clear - and in this case, it is the right (but perhaps not immediately apparent to be in the interest?) of the consumer, the state, to be able to submit the source code for review along with the election results. This is not much different from a right to a recount of votes on paper. In this otherwise technologically advanced country, a pencil mark on a piece of paper remains the method of choice for the citizen’s submission of a vote for referendums and public elections - to avoid the black box, the mystery method, between the voters and the result.

Something similar can be said to apply to medical equipment, but this is the (mine) field of patents, secret methods and methodology, proprietary software and hardware specifications locked down to an extreme extent. Still, one might argue that the source code of the software and the hardware plans of a medical device performing diagnostics or even treatment should be subject to peer review to ascertain that safety protocols have been followed and potential hazards taken into account -  if nothing else, then post mortem in order to examine the cause of the fatality and to avoid further injury. Obviously, only a select few scientists would have the knowledge and abilities to assess this question, a highly specialized combination of medicine and informatics.

I shall finish off with a quote by a representative of the natural sciences, a mathematician to be more exact, who has taken the consequence of scientific accountability and, as the project leader of the free software application TeXmacs, Joris van der Hoeven presented the following conclusions:

As a mathematician, I am deeply convinced that only free programs are acceptable from a scientific point of view. I see two main reasons for this:

• A result computed by a “mathematical” system, whose source code is not public, can not be accepted as part of a mathematical proof.
• Just as a mathematician should be able to build theorems on top of other theorems, it should be possible to freely modify and release algorithms of mathematical software.

However, it is strange, and a shame, that the main mathematical programs which are currently being used are proprietary. The main reason for this is that mathematicians often do not consider programming as a full scientific activity. Consequently, the development of useful software is delegated to “engineers” and the resulting programs are used as black boxes.

Something a bit different today - dipping into the technology pool.
So, why would your favorite scholarly scribe write about Lyx, the document processor? Well, to quote Obi-Wan, it is an elegant weapon for a more civilised age.

A lot of people who have published articles in academic journals will know the LaTeX markup language. This is particularly used in the natural sciences as LaTeX is extremely powerful for creating formulae and reaction diagrams.
Lyx is an attempt to bridge the gap between WYSIWYG - What You See Is What You Get, applications like Openoffice, Abiword, Microsoft Word and the like - and LaTeX, which, while creating some very elegant print-quality documents, is not particularly easy to get into. I have worked with LaTeX from time to time, and it takes quite a while to wrap your head around. LyX is not a text editor - in the sense that it is not just intended for entering text like you would do in an application like Vim, Emacs or the infamous Windows Notepad; the focus of LyX is to create documents ready for printing. Like LaTeX, it makes use of typographical conventions of using no more than a certain number of characters on a line to enhance readability, inserting spacing of a certain size in the text and so on. This makes for beautiful and very readable documents, but it also means that it restricts you to those conventions. For some, that is very challenging; if you are used to formatting freely, it can feel like a restriction.

The screenshots here are using LyX on my Slackware Linux laptop, but LyX is also available for Microsoft Windows, MacOS X and even OS/2. You can get it from the LyX download page. LyX is Free Software published under the GNU General Public License 2.
As a final note before I move into the main review, I should say that I am a linguist and writer, not a mathematician. This means that I will be focusing on what one will be using for document preparation, not the mathemagical features. For those interested in this, there is a brief mathematics intro on the LyX walkthrough. It seems to mostly use LaTeX syntax for that. LyX is quite well-documented for professional linguists, however - there is a dedicated LyX for linguists page.

As you see, the main screen is not much different from a lot of text processors. The interface can be accessed by using a mouse, but one will notice that holding the pointer over a button will show both the function and the keyboard shortcut; so the people behind the application encourage keeping your hands on the keyboard, which makes for less interruption in your work and less strain, which is a constantly increasing problem.

LyX follows the main principle of LaTeX, which means that the first things one does is define which kind of document it is - article, book, letter - and there are certain designs included as pre-defined article types to match the requirements of various journals or institutions.

After having defined the environment, you simply continue to define your text as you write it - as title matter, author, chapters. The system defines the layout as you go along, and it takes full advantage of LaTeX functions like footnotes and cross-references, margin notes for making overview of the text easier - and of course the various lists, such as table of contents, list of figures, list of tables etc. All things which can be har getting into with LaTeX, but is integrated in the LyX interface.

It is possible to insert a bibliography from a BibTeX file. This is the bibliography format associated with LaTeX, but LyX gives you additional options for manipulating the data. The BibTeX article in Wikipedia has a good example.

Actually, the area of bibliography is one of the places where LyX really shines; it is one of the places you can see that the system is intended for the academic community. The whole intention of these systems is to use some fairly simple files, mark them up to indicate what is to go where and then leave the system to output the materials in the format you want.
Lyx will import your bibliography file for reference. Using the citation manager, a citation for the relevant source will be inserted as an endnote. In this way, your bibliographical notes will be kept up to date as you move them around, add or remove. It is quite likely you will not want to use all the books you have been reading underway in your work, and this way the list will be kept correct - and formatted as your article or book style dictates it should be.

What you see here is the basic text editing window. As you see, the text indicates the features inserted there.
Personally, this reminds me of the Reveal Codes feature from WordPerfect. Again, more practical than LaTeX because it still keeps the text readable.

There are some very basic - and I believe this to be intentional - graphical effects. It is possible to insert images (extremely less complicated than with LaTeX), lines and boxes. The program is focused on text and text-derived graphics, which means that the functions for making tables and diagrams are well-equipped.

As I mentioned earlier, LyX has quite a bit of documentation, but this is not limited to the website. As an interesting approach, a lot of documentation is included as LyX files, which means that you can read the documentation as well see it in a final formatted version after processing it. Since LyX creates files for print, it focuses on export to print-oriented format. There are buttons on the toolbars for creating and updating DVI, PDF and PostScript files.
And so, the documentation documents also serve as example files.

If you are working on a thesis or a longer project, try out LyX. The application is quite powerful compared to the system resources it requires, and it scales remarkable well for very heavy documents, also working quite well with pulling in external documents. I have edited a very heavy lab manual for a biomedical conference with a lot of graphs and hi-res images on a fairly low-specification machine.

For an illustration, the first couple of chapters of my BA thesis - in LyX and PDF format.
Note Oct 3rd, 2012: A comment to this article on publishing a book with LyX linked to Holding Broadband Providers to Account: A Consumer Advocacy Manual - a beautiful book said to be done entirely in LyX.