Good Reading

(Updated May 5, 2000)

This page was originally intended as a way of keeping track of any good papers and articles, mostly computer-related, that I've downloaded from the Internet. However, that got to be more trouble than it's worth - I can always look up a paper using a search engine - so I've mostly been adding links to collections of papers and articles, e.g., magazines with on-line articles, E-zines, etc. There is lots of good stuff out there - enjoy!

Computers
Fiction
Genomics
Literature
Medicine
Periodicals
Religion
Science

Papers

Computers

• DevJournal - articles mostly about Microsoft Windows programming.
• InformIT - articles, book excerpts, etc.
• Ubiquity - "An ACM IT Magazine and Forum".

Fiction

• Anotherealm: A Zine of Short Speculative Fiction
• InterText: The Online Fiction Magazine - an established E-zine with great short stories in a variety of genres: "Present Tense", "Science Fiction", and "The Fantastic", as they say.

Genomics

• "BoulderIO" by Lincoln Stein - is a brief overview of and manual for a PERL-friendly, data interchange format for genome analysis software. The PERL objects? Boulders, stones, and pebbles (nested stones), of course!
• Primer on Molecular Genetics by Denise Casey, for the Department of Energy - an excellent, fairly detailed overview of the Human Genome Project. I see so many links to it, would it be fair to call it a "classic" in the field?
• "An Introduction to Biocomputing" by David Steffen - is the informative introduction to the BioComputing HyperText Coursebook.
• "Doing Sequence Analysis With Your Printer" by D. B. Searls - describes RSVP (Rapid Sequence Visualization in PostScript), a suite of PostScript programs that perform preliminary sequence analysis and generate graphic output. The programs also run on any computer that has a PostScript interpreter, so you're not restricted to a printer! (Since our printer couldn't handle the graphics in the paper, I had to manually delete the figures from the PostScript file in order to print it. An example of the graphic output is found on RSVP's home page.)
• "The Importance of Standards and Componentry in Meeting the Genome Informatics Challenges of the Next Five Years" by Nathan Goodman, Steve Rozen, and Lincoln Stein - discusses the benefits of building tools in a modular fashion with standardized interfaces between the modules and proposes a study of the existing practices and of ways of merging them into some type of cohesive standard. (Also see "The Case for Componentry in Genome Information Systems" by the same authors.)

Literature

• "Shakespeare's Good Book " by Mark Anderson - presents the case for Edward de Vere as the actual author of Shakespeare's works. The article and related links are found on the home page of the Shakespeare Oxford Society, a group which argues that de Vere, the 17th Earl of Oxford, was the real "spear-shaker". Opposing viewpoints and links are found on The Shakespeare Authorship Page.

Medicine

• Emerging Infectious Diseases - "a peer-reviewed journal published by the National Center for Infectious Diseases".
• Perspectives - A Mental Health Magazine - an on-line magazine for the layman, covering various topics in psychology.
• Prevention & Treatment - "a peer-reviewed, rapid publication, electronic journal".
• Psychiatric Times - "a monthly trade publication with news and clinical articles read by psychiatrists, allied mental health professionals and primary care physicians who treat mental disorders".
• ShrinkMagazine.com: Psychotherapy Ethics, Fraud, Legislation, Commentary - a "Consumer's Guide and Review of the Psychotherapy Industry".
• Stitches: The Journal of Medical Humour - great stuff! You'll need to register (for free) with Medscape® in order to access the text of the articles.
• The Write Brain - "a compilation of short stories, poetry, essays and artwork created by consumers, caregivers, [and] mental health professionals".

Periodicals

• The American Prospect: A Journal for the Liberal Imagination
• The Atlantic Monthly is a wonderful source of interesting articles, both past and present. A special treat are the classic book reviews.
• Boston Review: A Political and Literary Forum
• The Early American Review, "A Journal of Fact and Opinion on the People, Issues and Events of 18th Century America".
• London Review of Books and its archives.
• Mother Jones
• The Nation covers political and social issues. It has the full text of selected articles from the current issue and from back issues, including some gems from Paul Newman (the actor)!
• The New Republic and its archives.
• New York Review of Books has the full text of selected articles from current and back issues.
• Perspectives on Science and Christian Faith - a publication of the American Scientific Affiliation.
• Quest of the Unquietmind: A Webjournal of Thoughtful Dissent - thoughtful essays on everything from politics to computers. (archives)
• Salon Magazine is an on-line magazine with articles and columns on a variety of subjects.
• Slate Magazine - free again! Also see Stale, a parody of Slate.
• Utne Reader
• Civilization Magazine
  --- Back Issues --- 1998 Dec 1998 Nov 1998 Aug/Sep 1998 Apr/May 1998 Feb/Mar 1997 Oct/Nov
• Right-on Writing - if you can stomach it!
  • First Things - "A Journal of Religion and Public Life". A wealth of on-line articles, editorials, and book reviews from past issues.
  • The Independent Review, "A Journal of Political Economy".
  • The New Criterion - and its archives.
  • Links to Various Conservative Periodicals

Religion

• Antithesis: A Review of Reformed/Presbyterian Thought and Practice
• Christianity Online - hosts a number of Christian magazines, all of which have on-line articles from current and past issues. Your tastes may differ, but I found the following magazines the most interesting, despite the occasional fundamentalist and/or evangelical slant:
  • Books & Culture: A Christian Review - "An Incisive Review of Culture for Thinking Christians". (Archives)
  • Christianity Today (Archives)
• Contra Mundum: The Journal
• The Ethical Spectacle
• The Lutheran - "general-purpose monthly publication" of the ELCA.
  
  
• "What Is the Koran" by Toby Lester in The Atlantic Monthly, January 1999 - is a brief overview of the history of the Koran and of the current state of research into that history. The subject piqued my interest and a search of the web led me to ...
• "Is the Qur'an the Word of God?" by Jay Smith - a more in-depth overview of the history of the Koran and of the current academic controversies concerning that history.

Science

• American Scientist - "The Magazine of Sigma Xi, The Scientific Research Society".
• Discover - a popular science magazine. Check out the full text of recent issues and the searchable archive of older issues.
• New Scientist (the British counterpart to Science News?) also has the full text of selected articles, both from the current issue and from back issues. The articles are aimed at the interested layman and cover a broad range of scientific subjects.
• Science News - "the weekly newsmagazine of science".
• Scientific American - scientific paradise - for the layman, more or less.
• Skeptical Inquirer - published by the Committee for the Scientific Investigation of Claims of the Paranormal (CISCOP).

• Essays on Science and Society - a collection of monthly essays from Science magazine.

• "The Outer Reaches of Life", excerpted from John Postgate's book of the same name - discusses (with some humor thrown in here and there) the conditions required to sustain life as deduced from the range of life known on earth.

Papers

• "Language Research: Functional Languages and Object-Oriented Programming" by John DiCamillo - a brief overview of functional programming and languages.
• "Object-Oriented Scanning and Parsing" by John DiCamillo - an interesting overview of the design and implementation in C++ of scanners and parsers intended for special purpose languages; e.g., for embedding in tools.
• "Usability and Class Library Design: Guidelines for Simplicity and Power" by Arthur T. Jolin, in Dr. Dobb's Journal, October 1996 - an excellent set of general guidelines for designing class libraries and object frameworks.
• "Building Bug-Free O-O Software: An Introduction to Design by Contract" from ISE, Inc. - sounds like it was written by Bertrand Meyer and, like anything he writes, it was both interesting and worthwhile to read.
• "SWIG: An Easy to Use Tool for Integrating Scripting Languages with C and C++" by David M. Beazley, from the 4th Annual Tcl/Tck Workshop - describes a tool for automatically generating bindings of scripting language commands to user-written C and C++ functions and variables. Of particular interest is the capability of adapting the tool to arbitrary scripting languages; e.g., Tcl, Perl, etc. A generic Language class defines methods for emitting the C++ code that implements the binding of scripting language constructs to C++ constructs: create_function(), link_variable(), declare_const(), etc. To generate bindings for a new scripting language, derive a new class from Language and override the methods to genearte the appropriate C++ "wrappers" for the scripting language.
• C++?? A Critique of C++ by Ian Joyner - hasn't slowed the juggernaut - or should I say, bandwagon.
• "Java and the New Internet Programming Paradigm" adapted from Edward Yourdon's Rise & Resurrection of the American Programmer - a fairly in-depth overview of the capabilities and features of Java, including an interesting look at its potential impact on the software industry.
• Steve McConnell's web site has his "Best Practices" columns from IEEE Software, some articles from Software Development, and excerpts from his Code Complete and Rapid Development books.
• "Eiffel vs. C++: One Language Designer's View" by Bertrand Meyer - a USENET posting from 1989. Back then, multiple inheritance and templates in C++ were just "around the corner" and exception handling was just a gleam in someone's eye. Eiffel, of course, already had all three; see my own "TPOCC and Object-Oriented Programming".
• "Effective STL" by David Harvey - is one among several useful and well-written articles of his on C++ and the Standard Template Library. Also see G. Bowden Wise's well-done "An Overview of the Standard Template Library".
• "Threads: Just Say No" by Michael Spertus - argues against the use of threads. It is one of a number of columns and feature articles available from the on-line magazine, Object Currents; each monthly issue also includes links to on-line articles from its hardcopy sister publications: C++ Report, JOOP, etc. On the subject of threads, also see John Ousterhout's presentation, "Why Threads Are a Bad Idea (For Most Purposes)".
• "Scripting: Higher Level Programming for the 21st Century" by John Ousterhout - appears (to me) to be a subtle attempt to make people realize that Java is not the be-all and end-all of the world. This white paper is vintage Ousterhout: very readable, very interesting, and making very good points. Unfortunately, most of the other documents at his web site are slide presentations in PostScript or PowerPoint form.
• "Unix Talking with PC's" by Andrew Tridgell - is, truthfully, an "entertaining account of the development of the Samba package" and is one of several, equally entertaining articles available on-line from the Linux Journal.
• "libscheme: Scheme as a C Library" by Brent W. Benson, Jr. - describes a well-designed, embeddable Scheme interpreter inspired by the embeddable Tcl interpreter. In the same vein are:
  • Elk, a deluxe, embeddable Scheme interpreter with all the bells and whistles, described in Oliver Laumann's and Carsten Bormann's, "Elk: The Extension Language Kit"
  • MzScheme, another deluxe Scheme interpreter, patterned after libscheme and described in Matthew Flatt's, "Inside MzScheme".
• "Escaping the Event Loop: An Alternative for Multi-Threaded GUIs" by Matthew Fuchs - makes the interesting point that the reactive style of programming with event loops is equivalent to continuation passing style. Fuchs then attempts to show how using continuations as callbacks simplifies the implementation of a multi-threaded program in the context of an event loop, but he loses me at this point.
• "Erlang - A Survey of the Language and Its Industrial Applications" by Joe Armstrong - presents an overview of Erlang, a virtual machine-based, industrial-strength, functional language used to write operational, real-time, telecommunications software. This article made my blood boil - why do we put up with the likes of C++ and Java?
• Revised(4) Report on the Algorithmic Language Scheme edited by William Clinger and Jonathan Rees - is a concise, but very readable specification for the Scheme language, often contrasted with the lengthy and dry specifications of other languages. (This is apparently the official home of R^4RS - the HTML document is correctly formatted and the bibiliography has links to the proper, 2-column PostScript version of the report.)
• "A Distributed Computing Model for Telemetry Data Processing" by Matthew Barry, Kevin Scott, and Steven Weismuller - presents the Information Sharing Protocol (ISP) used to distribute Space Shuttle telemetry and other data to remote computers. In a nutshell, distributed data servers publish data to which clients can subscribe. The paper discussed a number of applications of ISP, but was lacking in implementation details. These can be found, however, in the User's Guide.
• ARIANE 5 Flight 501 Failure - is the report from the Inquiry Board which investigated the failure shortly after launch of the Ariane 5 rocket in June 1996. Briefly, failure in a software module (reused from Ariane 4) which shouldn't have been active post-launch caused CPUs in both the active and backup Inertial Reference Systems (SRI) to halt. As a result, erroneous attitude data was forwarded to the main computer, which then attempted to correct for the extreme "attitude" of the launch vehicle. The report is very readable and well-worth reading, particularly the final conclusions and recommendations. Also see:
  • "Put It in the Contract: The Lessons of Ariane" by Jean-Marc Jiziquel and Bertrand Meyer - suggests that if the reused software from Ariane 4 had been written following the Design by Contract principle, the potential violation of constraints (which in fact caused the actual failure) would have been detected earlier during the Ariane 5 software design, build or test.
  • "Critique of 'Put It in the Contract: The Lessons of Ariane'" by Ken Garlington - is an informed response to Jiziquel's and Meyer's not-totally-convincing thesis.
  • Usenet comments on "Put it in the contract: The lessons of Ariane", compiled by Jean-marc Jiziquel.
• "Experiences Converting a C++ Communication Software Framework to Java" by Prashant Jain and Douglas C. Schmidt, in C++ Report, January 1997 - discusses the conversion of ACE from C++ to Java. (Also see Schmidt's other on-line publications.)
• "Cygwin32: A Free Win32 Porting Layer for UNIX® Applications" by Geoffrey J. Noer. (Also see The Cygwin Project.)
• "Back to the Future: The Story of Squeak, A Practical Smalltalk Written in Itself" by Dan Ingalls, Ted Kaehler, John Maloney, Scott Wallace, and Alan Kay, in OOPSLA '96 (or '97?) - describes the design and implementation of a portable Smalltalk software development environment - very interesting and very impressive! (Also see the Squeak home page for more documentation and ports to Windows 95 and NT, Macintosh, most UNIX platforms, various PDAs, Acorn's RiscOS, OS/2, DOS, BeOS, and NeXT.)