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Biotechnology and Bioinformatics Open Source Software
Introducing Mark Johnson's Weblog
by Mark Johnson
March 24, 2003
Introducing Mark Johnson's weblog on Biotechnology, Bioinformatics, and Open Source Software.


Welcome to the Artima Weblog on Biotechnology, Bioinformatics, and Open Source Software. My name's Mark Johnson. My nickname, here as is elsewhere, is mj, because I'm a geek, and when I went to school in the early 80's, two-letter logins were all the rage. I'm a computer engineer (Purdue 1986) and long-time software guy. Last year I published a book on enterprise software, and am now a full-time college student, studying molecular biology, biochemistry, and cell biology in preparation for a career shift to bioinformatics.

Biology is absolutely the coolest thing in the world. The way biological systems works puts to shame even the most intelligent and sophisticated attempts at human design. And biological systems were designed (if you can call it designed) in ways that are very different from how people think about design.

In this weblog, I plan to post on the following topics:

Bioinformatics. information technology for the biotechnology revolution. A hundred years from now, historians will say, "There used to be these things called 'digital computers'. We still use them today to run elevators and radios and so on. We only mention them because they made possible the earliest forms of biotech." The so-called "computer revolution" will be a footnote to the biotech revolution.

Biotechnology. Everything from GMOs to new clinical interventions to in-vitro systems for research. What's cool, what's new, what may be coming.

Open-source Software. some of the best bioinformatics software around is free, open-source, and public domain. Such software is usually cross-platform. It also often has only command-line interfaces. I'd like to discuss how to make publicly-available OSS bioinformatics software more usable by researchers, both public and private.

Risks of biotechnology. As interested as I am in biotech, I'm also scared to death of it. The history of technology is littered with "oopses": unintended consequences. Remember Thalidomide? (Thalidomide is actually still useful--just not for pregnancy-related nausea.) Even conventional microbiological techniques could produce nightmare bioweapons. And what about GMO food? Particpate in discussions on the risks of biotech, how they can be ameliorated, and where maybe we just shouldn't go.

Biomimetic design. Kevlar is non-biodegradable and is fabricated in an environment of boiling H2SO4 (sulfuric acid) under high pressure. Spiders make a biodegradable fiber stronger and more resilient than Kevlar at room temperature in aqueous solution. As I said above, compared with the "designs" that life has come up with, human designs are pitiful. (Of course, life has had upwards of 3 Gy to solve problems, wherereas humans have had 10-100 ky.) But we can learn from nature if we're willing to listen. I'll be posting about designs and design approaches that come from nature. Biocompatible technology, natural capitalism, genetic programming. [Interested in the spider silk thing? See "AN AIRBUS COULD TIPTOE ON SPIDER SILK" at

More on spider silk (and other biomimetic designs) later. By the way, I consider the open source paradigm in software a form of biomimicry. Check in later to hear why.

Welcome to the Blog!


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About the Blogger

Mark Johnson is a software developer, trainer, writer, and speaker living in Silver Spring, MD. He works at the National Center for Biotechnology Information, writing documentation and tools for open-source bioinformatics software. He is also president of Elucify Technical Communications ( He has published dozens of articles on Java component technology, enterprise software development, and XML, and is co-author of the book "Designing Enterprise Applications for the J2EE Platform, Second Edition" (Addison-Wesley 2002). He is currently the author of the monthly Enterprise Java Tech Tips newsletter for Sun Microsystems. Mark has been interviewed on CNN,, and, and is a member of the National Association of Science Writers.

This weblog entry is Copyright © 2003 Mark Johnson. All rights reserved.

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