There’s a fairly interesting case developing around some hackers who developed some software that decrypts the blacklists of a couple of popular web “filtering” programs. There’s an interesting item in the latest RISKS about the whole deal, which notes that the two filtering programs have begun to quietly blacklist — under all available categories — any web pages that either contain the code or are critical of the programs. (Wired News also has a story.) It leaves out some recent interesting developments that have been reported on SlashDot: First, the two authors (facing lawsuits) have sold all rights to the code to Mattel, the corporate owner of one of the filtering programs — despite having the legal support of the ACLU. The authors’ motivation for the sale remains unclear; insert your favorite conspiracy theory here. However, things might get really, really interesting, as the code had been released under the GNU Public License — which means that anyone who wants to repost it should have the legal authority to tell Mattel to go blow. The moral of this story: Be careful about the blinders you put onto Barbie’s horse, or something like that…

Salon covers marijuana distribution in Maine, where the state government is preparing to do an end-run around the Feds, and distribute confiscated marijuana to medical patients with prescriptions for it. (Maine is one of the states that has passed a medical marijuana law.) The Feds are, of course, not terribly happy about this. It’s also interesting fodder in the continuing (or is that renewed?) States Rights discussions I think we’re likely to see as the US presidential race heats up.

There were quite a few interesting bioinformatic type links I found yesterday. First, an interview with Matt Ridley, who has a new book about the various genome sequencing projects, their effects on biology, and long term effects on society in general. The first 2/3s of the interview is personal fluff, which I found rather boring, but towards the end, it begins to pick up a bit:

**Regarding the possibility of a chimp-human hybrid**<br> "It
would be unethical to do such an experiment. You would bring into
the world a new individual. And this new individual would
presumably have rudimentary language, a low IQ by human standards,
but a high IQ by chimp standards. I think it's unethical because
it's very hard to see how you could treat such an individual
kindly, however hard you tried. It would be a very social
creature, a creature that very much wanted society, but it
wouldn't find a chimp colony in a zoo very interesting, and on the
other hand, it would find Wall Street rather daunting. It would
end up having a very lonely life. And that's the only reason it
would be unethical, because it would be cruel to the individual
you would create."

What if we made a whole colony then? Would that make it acceptable? (Insert David Brin’s Uplift series here.)

There were a couple of articles about the protests of the BIO2000 conference in Boston that I found interesting: [ABC News (AP)] [Wired News]. I’m still not sure where I fall in this debate — once you start to consider some of the larger issues, like the requirements for feeding our rapidly growing planetary population, it stops being quite so simple — but I do think that having two sides shouting at one another might not be the best way to accomplish anything. There have to be some scientists that have publicly questioned gengineered foodstuffs, that are (at least somewhat) trusted by the anti-GMO movement(s) — why not send them to the conference, let them actually talk to people, try to reach some sort of compromise? Or am I being entirely too rational here? I guess I’ve already accepted (and perhaps the protesters haven’t) that gengineering food organisms is going to happen — that is, unless we start taking the advice of the mysterious “anarchists” (apparently the only sensible group there) and Stop Breeding Now.

The SF Gate had a puff piece on Craig Venter, head of Celera. Venter attempts to defend Celera’s business model by pointing out that they’re not as bad as some of the other biotech companies working the gene/drug target discovery space — but doesn’t mention that for many people, patenting one human gene is just as bad as patenting all of them.

Finally, some preliminary results (ohh — actual research! how novel…) seems to indicate that one of the prime fears associated with gengineering might not be an issue. The concern is over antibiotic resistance genes — required for the first steps of assembling a recombinant gene for insertion into another organism — and whether they could leave the gengineered critter and get into bacteria, which could lead to the spread of even more resistant pathogens. The work is ongoing, and even when complete probably won’t be able to say that gene transfer won’t happen, but it seems that it’s going to be a fairly rare event.

Salon analyzes the business models of online bookmarking sites, which allow you to save bookmarks on a remote server, so that you can access them independently of your meatspace location. I use one such service, Blink, to bookmark sites that I see at work so I can ‘blog them later.

There’s an online course in XML for scientists in bioinformatics — something for me to look at more closely once I get to the NCBI.

Ask Doktor Komputor:

Greetinks, vebfolk. Velcome to Ask Doktor Komputor, ze first HTML
guide on ze Vorld Vide Veb written in ze amusinkly overblown
German accent. In zis guide, you vill learn how to make veb pages
zat vork every time, on every browser. Forget all zose other HTML
guides vith zeir difficult instructions. Doktor Komputor vill show
you ze vay.

A couple more LaTeX-type links: first, TeXmacs, which is just what it sounds like. Second, Pybliographer, which is a Gnome-ish bibliography manager that can interface with Lyx.

While we’re on article management type links, BioMail looks pretty useful — it’s an app that will periodically run a Medline search and notify you when new articles matching your criteria are found. They’ve even got a public server running the software, so you can use it or evaluate it without having to set it up on a server of your own. Sweet!

A couple of other software links that I mean to check out later: I’ve been interested in The Brain — which lets you record thoughts or ideas and link them in a non-linear way — for a while, but it doesn’t play nice with my favored OS. ThoughtTracker might be the solution.

Whew! I really ran off at the mouth today, eh? This is probably the last sizeable update for the next week or so — I leave on Thursday for the drive to D.C., and after I arrive (hopefully Sunday), the first couple of days (at least!) I’ll be occupied with unloading the moving truck and getting things unpacked. If there are any D.C. area people out there reading this, I’ve love to hear about reputable DSL providers or good local ISPs. Additionally, we’re trying to decide between the NIH employee credit union and Crestar for our bank — any input on the service/user friendly-ness of those two institutions would be welcome. Mail jacobs@genehack.org with any thoughts.

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