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.

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.

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:

• EditCSS Mozilla plugin: dynamically modify stylesheets
• Strace kernel test tool: “the most aggressive general purpose kernel tester available. Strace Test generally crashes my system within 5 minutes (2.6.1-rc2).”

Metascene surfaces.