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Introducing Mark Johnson's Weblog

3 replies on 1 page. Most recent reply: Jul 8, 2003 7:48 AM by Sankarasubramanian

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Mark Johnson

Posts: 15
Nickname: mj
Registered: Mar, 2003

Introducing Mark Johnson's Weblog (View in Weblogs)
Posted: Mar 24, 2003 12:10 PM
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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!



Posts: 1
Nickname: vrl
Registered: Jan, 2003

Re: Introduction Posted: Mar 26, 2003 6:34 AM
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Nice introduction. Since you have already done transition
from computer-software domain into bio-inofrmatics, could
you shed some light on:

o For a software engineer, what's the best way to transition
into bio-informatics? Is the transition as easy as
changing the job or are there pre-requisites one needs to
do before the transition - what are the pre-requisites?
o How about a traditional SQA (software quality assurance)
folks looking to get into bio-informatics ? I am sure
there is a whole lot of testing required in drug
o What are the core technology/tools used in bio-informatics
these days ? For example in a traditional networking-sw
jobs, one need to know protocols and C/C++/Java - What
is the equivalent in bio-info ?

Thanks for starting this blog..


Mark Johnson

Posts: 15
Nickname: mj
Registered: Mar, 2003

Re: Introduction Posted: Apr 17, 2003 11:12 AM
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Thanks for your great questions. I've been trying to write a long answer to all your questions, and have written several pages. So I'm going to answer your questions one at a time as separate posts. Each topic is interesting! Also, that way, other interested people can focus on what they want to discuss.


Posts: 1
Nickname: abirami
Registered: Jul, 2003

Re: Introducing Mark Johnson's Weblog Posted: Jul 8, 2003 7:48 AM
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I am a Software Developer working in Singapore. I am also interested in Bio-Informatics. I just wanted to give my support and appreciation for your future articles in this area.

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