Monthly Archives: February 2006

Science and Engineering Talent to be Outsourced

This is what happens when we spend more time fighting off creationists than teaching evolution — we get replaced by people who do things right:

Firms shop overseas, this time for talent – Technology – International Herald Tribune

The American executives who are planning to send work abroad express concern about what they regard as an incipient erosion of scientific prowess in this country, pointing to the lagging math and science proficiency of American high school students and the reluctance of some college graduates to pursue careers in science and engineering.

Of course, our problems aren’t restricted to biology. It’s just a canary of sorts, dying when the air goes foul. We’re still coasting on our former science and engineering prowess, but the party’s over.

First it was assembly. Then it was programming. Next it’s going to be engineers and scientists. I don’t advocate isolation — that’s just a battle against time. I do, however, advocate strengthening math and science education in this country.

Cellular Automata and Tissue Engineering

I’m taking a tissue engineering course right now, (see previous post), and this has rekindled my interest in cellular automata. I was first introduced to them by Stephen Wolfram’s book, A New Kind of Science (freely available online). This is one of the books that helped me to understand how complex life can develop from relatively simple rules.

It’s led me to wonder how much tissue engineering experimentation could be done using 3D cellular automata. Tissue engineering requires all kinds of cell lines and biochemicals, incubation times, and so on, making it somewhat expensive and time consuming. The ability to model, say, mesenchymal stem cells with cellular automata could be used to ‘get a feel’ for tissue development with less time and expense.

I went looking for 3D cellular automata to play with, and came across this one:

Cellumat3D

Cellumat3D is a tool for simulating and exploring cellular automata in 3D space. The application uses OpenGL and is fast enough to give a good impression why cellular automata are regarded as part of artificial life research.

It’s a little obscure, and there’s not really any documentation that I’ve seen for setting up rules. I need to double-check the CVS code for documentation. The author also links to a bountiful resource page on 3D cellular automata. It looks like it hasn’t been updated in a while. At least some of the links work, including one to a java-based 3D simulator of the Game of Life. It’s pretty slick — you can grab and rotate it with the mouse and so on. Here’s another one that’s a little less intuitive but allows editing. Life3D looks interesting, but it’s only available for Windows.

If you know of any other 3D cellular automata for Linux/Unix/OS X please do pass them along in the comments or by email.

ADDENDUM: 2006-02-15 @ 21:04 CST – MathWorld has a page on cellular automata in Mathematica.

Human collagen synthesis achieved

A well-written article on collagen, why it’s important, and how scientists have finally synthesized it in long strands is over on Biosingularity. It’s well worth a read.

Biosingularity » Blog Archive » Scientists find a way to make human collagen

The Wisconsin team discovered a way to make the long, slender collagen molecules, in essence, by having the protein assemble itself. What was required, Raines explains, was a way to give the collagen snippets that scientists could easily make a way to “self assemble” into the long, thin fibers of native collagen. The Wisconsin team was able to modify the ends of the snippets so they could fit together and stick to form long collagen fibers.

Online Biomedical Articles, Reviewed

The author of HubMed (an alternative and nicer interface to PubMed‘s database) recently posted an online journal review on his blog. While he prefers PDFs (as do I, for now), there are various aspects of articles-in-HTML that make them more or less useful and easy to read. All of the major publishers of online biomedical texts are scored. From the post:

HubLog: The state of online biomedical full text articles

I carried out a survey of HTML fulltext pages from the major publishers with the aim of identifying a) problems with usability and b) recurring themes in semantic markup of article elements (which will hopefully lend itself to a microformat recommendation for scientific, or at least biomedical, articles).

This is an issue on which the publishers are way behind. There’s little competition, and therefore little impetus for them to improve.