April 2004 Archives

Since I live in the area, you’d think I’d have heard about this before now: Virginia Passes Anti-Gay Civil Unions Bill. The extent of the hatred in this legislation is breathtaking. Not only does the bill outlaw civil unions in Virginia, it contains “no benefits of marriage” language, much like the proposed federal Constitutional amendment. So, not only no civil unions, but gay couples that have been able to assemble some of the benefits of marriage by piecing together powers of attorney and other kludges, will no longer be allowed to. No more “second parent” adoptions. No more power of attorney to grant your significant other the right to make medical decisions when you’re incapacitated. No more leaving money or property to your significant other in your will. No more “domestic partner” coverage in health care.

The Democratic governor tried to send the bill back, with amendments to remove some of the worst provisions. The amendments were defeated, and the bill is on its way to becoming law. If you live in Virginia, this would be a good time to contact your elected representative to let them know how you feel about this bill.

I saw a story this morning about the flap caused by Washington Rep. Jim McDermott, who lead the House in the Pledge of Allegiance the other day. The flap is because he neglected to say “under God” at the appropriate point. Now, that in itself is no big deal — lots of people don’t say that part, because they don’t agree with it, or more often, because they learned the Pledge well before 1953, when that phrase was inserted. So, a good excuse for the right-wing Godbotherers to get up in arms, but nothing else.

But then I read this part of the article:

The House’s presiding officer Tuesday, Rep. Mike Simpson, R-Idaho, said the words “under God” would appear in the Congressional Record of Tuesday’s proceedings, regardless of how McDermott had recited the pledge.

That’s the part that bothers me: the need of the Godbotherers to rewrite history — literally! — because somebody did something that they didn’t like. I suspect some readers are nodding their heads, and some are confused, and I’d like to hope that the breakdown isn’t along strict partisan lines (but I suspect that it might be). For the benefit of the confused, my issue isn’t whether saying “under God” as part of the Pledge is or isn’t correct, legal, and/or moral. My issue is that if you’re going to have an official recording of the proceedings of one of our top legislative bodies (and I think we’ll all agree that such a record is a Good Thing), then you want that record to reflect what actually happened, not what you wish had happened.

So, the ACLU is suing the government over certain provisions of the Patriot Act — only, because of provisions of the Patriot Act, they weren’t allowed to tell anybody about the lawsuit. Feel safe yet?

In related creepy-Orwellian-vibe news, Loyalty Day still sounds like something out of a bad dystopian novel — only it’s actually happening, this Saturday. Whee.

Openpark.net is an NPO that’s working on rolling out free wireless Internet access on the National Mall in DC. They just fired up the first hot spot in the project, near the Supreme Court building.

down and out

Cory Doctorow made a pretty big splash with this book (well, at least in some of the circles I travel in), because he released the content for free on his website, craphound.com, at the same time the bound version (the “dead tree” version, as the cool kids say) came out. It also probably didn’t hurt that he works for the EFF and is a frequent contributor to Boing Boing, a popular blog.

There was a lot of hype about this book that really didn’t have anything to do with the subject matter or the writing, is what I guess I’m trying to say. And because of that hype, I sort of shied away from reading it — thinking that it would probably be underwhelming, relative to the hype. Doctorow has a second novel out now, _Eastern Standard Tribe_, and it’s getting some of the same hype, because he’s still using the “free online or buy the book” model — but it’s also getting good reviews because of the content. So, when I was in $BIG_CHAIN_BOOKSTORE recently, and saw _Down and Out_ in a trade paperback version, I said, “what the hell”, and grabbed a copy. I figured that even if the book wasn’t that great, supporting the business model was a good thing (because I like the idea of lots of freely available web content).

That’s a long-winded way of saying that finding out that the book was really quite good was a bit of a happy surprise. The story Doctorow weaves is of the “Bitchun society” — what Western capitalism turns into when scarcity — energy scarcity, material scarcity, even death — is eliminated. The Bitchun society is in many ways on the other side of Vinge’s Singularity from our current world — it’s a bit hard to imagine the motivations of characters when death is about as damaging as pushing the “reset” button while playing a video game — but Doctorow makes the story work, mainly because he’s just applying another coat of paint to a classic story of betrayal, confusion, and loss.

The story is of Jules, who works at Disney World as part of the “ad-hoc” that runs the Hall of Presidents. An “ad-hoc” is a, well, ad-hoc autonomous collective — a group of people, operating by consensus. When Jules’s assassination paves the way for a new ad-hoc to seize control of the running of the Hall of Presidents, he becomes obsessed with convincing people that the leader of the upstart ad-hoc is up to no good. His obsession leads him further and further afield, until finally… Well, no giving up plot points, but I will say that this is one of those books where the “can’t wait to turn the page” factor ratchets up and further up the closer you get to the end.

oreilly book page
Mastering Perl for Bioinformatics is the follow-up to Tisdall’s earlier Beginning Perl for Bioinformatics. Both books are part of O’Reilly’s lauded “animal books” series; Beginning was graced with tadpoles, while Mastering sports a frog.

Naturally, the book picks up where the earlier one left off, diving headfirst into the details of Perl modules. Chapter two is a quick pass over some basic data structures, with discussion of how you’d implement each in Perl. Subsequent chapters cover object-oriented programming in Perl, using Perl with relational databases, using Perl with web services, generating graphics on the fly with Perl, and the use of the Bioperl (http://www.bioperl.org) suite of libraries.

As might be expected, all the coding examples in the book are drawn from reasonably realistic bioinformatics situations. There’s a little bit less hand-holding on the biological side in this book, relative to the earlier volume — which I think is a good idea, as it gives more space to focus on the programming material.

The one weakness of this book is that it covers quite a few topics, which means that it doesn’t really go into great depth on any of them. The “survey” approach is well done, and it’s very nice to have biologically relevant examples and exercises for the breath of material that is addressed, but I think the book might have been stronger if it forewent the “Perl and the Web” and “Perl and Graphics” chapters in favor of more focus on the Bioperl libraries.

If you’re a bioinformatics programmer who enjoyed Beginning Perl for Bioinformatics, and you want to get a better idea of what more advanced Perl programming looks like and what sorts of things you can do with Perl, this book is a nice place to start. However, if you’re looking for more specific information, other more focused books might be a better choice, if you can live without the biologically focused code examples.

I know I’m going to be building a new computer here in a few months. I’m pretty sure it’s going to be a 64bit Opteron box. The main thing that I’m trying to decide at this point is whether it will have one processor or two. Creating Corwin is the story of a guy who decided “two”.

Two is sounding better and better to me as well…

Seven habits of effective text editing, by Bram Moolenaar (aka “that guy that wrote Vim”).

Finished Learing the bash Shell; owe a review of that as well as Mastering Perl for Bioinformatics and Pragmatic Programmer

Some things that might come in handy at some point:

How to be a Programmer: A Short, Comprehensive, and Personal Summary.

Speaking of the class, reading continues apace. Reviews of Mastering Perl for Bioinformatics and The Pragmatic Programmer are forthcoming; I especially enjoyed the latter book.

Al’s having some IT static at the House of Pain. Sounds like it’s either based in budgetary issues, or in incompetent IT staffers (which is also potentially a budgetary problem, I guess…)

Thinking about how you’d set up the enterprise for a hospital is a fun intellectual exercise. I’m thinking dual live systems (in an active/passive setup) for everything in the “core”, with an on-the-shelf (i.e., racked, cabled, but powered off) spare system for emergency use. Individual workstations being down shouldn’t be that big of a deal, but you want the core stuff to be big and beefy and 24/7/365. The active/passive setup for the live systems means you could do any upgrades or maintenance on the passive half first, test it out and make sure you didn’t have any regressions, then swap the active/passive status and work on the other half — so your downtime would be reduced to sub-minute “blips” during the cutovers, instead of the hours-long outages Al is seening.

The opposite approach would be to radically decentralize everything, push it all out to the edges, and then have a lot of logic for locating bits and pulling them to other places on request — a Google-ish sort of setup. This is an initially appealing idea, but the more I think about it, the more potential downsides I see — and that’s without even thinking about HIPPA.

This topic feeds into another thing I’ve been bumping my nose on recently: the generally poor regard most people have for their IT support. At one point, I think I would have been inclined to attribute that more to the users, but I’m more and more realizing that the problem probably lies more on the IT side. The bright side of that, of course, is that I shouldn’t have any troubles staying gainfully employed; the downside is the frequent wincing and muttering when I hear people talk about the IT situation at their workplaces…

Seems there won’t be a US Postal team after this year’s Tour. I’m sure Armstrong’s team won’t have too much trouble picking up another sponsor, but it’s still sort of a shame. [via flutterby]


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Was in Vegas for a goodly part of last week; am still digging out of crater that dug in personal and work “things to do” efforts. One of the high points of the trip was meeting up with Hal “blivet” Rager for lunch. As soon as I get more dug out, I’ll write up a brief trip report, toss some pictures in it, and put it up.

I watched the Presidental news conference last night. Actually, since I was working away on the laptop for most of it, it’s probably more accurate to say I listened to the news conference — which was just as well, given the way Bush’s tie was pulsating.

Overall, I thought it was a poor performance, but there was one bit, towards the end of his opening statement that was okay — a stump speech-ish riff on bring freedom to the Iraqi people. Not great, by any means, but if you closed your eyes and forgot about most of the last couple of years, it was decent.

There was one thing he is absolutely right about: if we don’t get Iraq right, the whole Middle East is going to be worse than it was before, and the long-term safety of America is seriously imperiled. I don’t think you’ll find a lot of disagreement with that position in any segment of the political spectrum.

That said, the fact that Bush and his administration are aware of this problem isn’t particularly comforting, because they don’t seem to have any sort of plan about how to resolve the mess that Iraq has recently devolved into. They’re still planning on turning over authority to somebody in about 2.5 months, but they don’t have any idea of who might be the lucky recipient of that authority. This does not bode well, given the whole “it’s critical that we get this right” aspect of the problem.

There were a cavalcade of other cringe-worthy moments — the “I can’t think of any mistakes I’ve made” moment, the “you’re going off script!” moment, the “I really can’t explain why I have to appear with Cheney before the 9.11 Commission” moment, and the crowning cringe of the eveving: the ironically incoherent response to Don Ganyea’s “do you think you have trouble communicating?” question — but really the most depressing, dis-heartening moment of the night was the one bit that the President got correct: not screwing up Iraq is vital.

The on-going culling of the Wired back issues continues to yield interesting bits:

Death To Newsgroups
by Andrew C. Bulhak

Usenet is in trouble. Newcomers must choose an appropriate newsgroup — if one exists — from some 8,000. In addition, the system is easily abused; an unscrupulous advertiser can flood thousands of newsgroups, wasting bandwidth and disk space.

The solution? Get rid of newsgroups. Articles can be kept in one large pool and called up with word searches. To post an article, just throw it into the ocean — the reader’s software will fish it out. If you desire a speciality forum, you can create a virtual newsgroup by naming it, as with IRC channels; it will last as long as people use it. Since all posts are kept in one pool, spamming is eliminated.

Sounds far-fetched? The technology exists, and DEC’s Alta Vista search engine provides a preview.

Wired, June 1996, p. 124

It seems like Google+blogosphere is damn near what the author was talking about. Good job it’s done in all the spamming, eh?

(The author appears (unsurprisingly) to have a weblog. Whee.)

My father, like many men “of a certain age”, has a scrollsaw in his shop. He’s also got a decent eye and a talent for various types of art. (He went through pen-and-ink and charcoal phases while I was growing up.) Lately, he’s been exploiting the intersection of those talents and making wood puzzles — these are the most recent three we’ve been gifted with.

mouse over images…


The Marvin the Martian one is a right pain to get back together again!

Because the great mass of people appear to be mainly, um, jackholes, I finally gave in and implemented some hotlink blocking for the images on sites in the Mighty Genehack Web Empire. On the off-chance that you’re not a jackhole but have nonetheless engaged in jackhole-ish behavior by linking directly to an image on one of my sites, you might want to reconsider. You’re now sending a very different message, courtesy of everybody’s good friend Goatse.

(I just realized that the title of this entry could be interpreted as a rather unfortunate pun. Not intended, I assure you. (No pun on the “ass”ure, either. Okay, stopping now.))

I’ve got this huge stack of Wired magazines, which I’ve been carting around for the last two or three moves (one cross-contiental). I can’t bring myself to just pitch the whole stack in the trash, but I can’t imagine ever actually needing these magazines in any way.

I recently figured out that a good way for me to deal with this sort of issue is to make it a daily goal to do a little bit of work on it. So, one of my daily tasks recently has been “cull two issues of Wired”. I’ve added several pieces to the massive collage that’s going to end up covering the closet door in my office, I’ve had several times the LD50 of tech nostalgia (hey, look, print ads for modems! and “screaming fast 6X” CD-ROM drives!), and I’ve found some long lost gems. Here’s one:

Why I Hate the Web
by Tim Bray

The Web sucks. It is lightweight, shallow, trivial, and disposable. It is simple enough that any idiot can use it, and this, weirdly enough, is considered good. Properly considered, the Web is similar to television. Both are fragmented: TV into schedule slots, intercommercial breaks, ever quicker cuts; the Web into servers, pages, gifs. Smaller is better because — just like a laugh track — faster is better.

The Net, on the other hand, offers much more. On the Net, as in life, you put some in and you get some back. You send mail, you post news, you share your work. The Web is a 500,000-channel TV; you sit back and let it flow over your passive brain cells, with only your forearm and mouse finger moving.

The Net, it’s been said, is too difficult. so are great novels. Nobody ever said the Web was hard. But of all the Web pages you’ve ever hit, how many did you read to the end? The same proportion of the TV programs that you watched until the next commercial break? After all, clicking on hypertext requires about the same effort as changing the channel.

Wired, October 1995, p. 122

More to come, I’m sure.

Keep in mind what day it is, y’all.

Oh, and happy Mailman list reminder day. Man, I’m on way too many mailing lists…

In other news, your humble correspondant is now going to go curl up in a ball and mutter “I can’t believe the year is 25% gone, I can’t believe the year is 25% gone” for a few hours.