April 2001 Archives

this is genehack, over…
In a couple of hours, I’ll be on a plane bound for the Left Coast, so things are going to be a bit dead ‘round here until sometime next week. Play nice while I’m gone, and the last one out should shut off the lights.

no, it’s real
It looks like somebody went nuts with a marbling filter in the Gimp, but it’s real: Io transiting Jupiter, via Cassini. When I get back, I think the big version is going to be the basis for my new desktop background…

ORA knows bioinformatics
O’Reilly has a book on bioinformatics coming out this month, and the author has a short piece talking about what bioinformatics is. Once again, if anybody at ORA wants to send me a nice review copy, I’d love to have one. 8^)=
Link via snowdeal {bio,medical}informatics

i (heart) my tivo
John Dvorak’s slow slide into senile dementia has apparently accelerated. The evidence? His recent Forbes article about personal video recorders — TiVos, ReplayTVs, etc. He thinks they’re hard to use (they aren’t), don’t work (they do, as I’ll happily attest) and aren’t worth the monthly service fees (they are; additionally, you can pay a one-time fee for lifetime service, or operate the units without the information provided by the service).

Additionally, as evidence of how far we’ve slid in terms of fair use, copyright, and “intellectual property management” in the US, consider his argument about how these devices let you “steal programming”. Dvorak seems unfamiliar with the Betamax case, which established the rights of consumers to “time-shift” programming. It’s not theft, Mr. Dvorak, it’s just that we don’t feel compelled to take the cruft the broadcast networks distribute along with their content. While there was a case that said it’s okay for consumers to time-shift, I don’t recall a case where the courts held that companies had any protection from technological advances that could potentially undermine their business models.

…and out.
Okay, that’s all for me — time to go get packed! Have a good weekend, and I’ll catch you on the flipside.

genehack on the road
Just thought I’d mention that I’m going to be tagging along with Laura as she travels out to Seattle for a meeting. We don’t have any huge plans to do any tourist-y type stuff; we’re just going to hang out and take it easy. I’m there from Friday to early Monday, so if anybody wants to meet up for a coffee or a beer (or a coffee beer), give a holler.

blogrolling
One of the better pieces I saw about Joey Ramone wasn’t at a music site, and it wasn’t over at Salon: it was the April 16th entry at Metascene. Just thought you might like to know that.

the map is not the territory
“A Map to Nowhere” takes on the recent announcements about the human genome and seems to come to the conclusion that the whole thing was a big waste of time, because it’s looking more and more like the real complexity in the genome is combinatorial, arising from different arrangements of exons to create different proteins, which are processed and regulated in different ways.

It’s difficult for me to critique any of the author’s points, because he’s coming at the question from such a completely odd angle — yes, it turns out that the genome might not be as important as we had believed, and some of the hype about medical advances might turn out to be hype, but we had no way of knowing this ahead of time! In order to find out that the genome isn’t the whole story, we had to sequence that genome, and having done that, it will still be a useful tool in figuring out what’s going on inside our bodies, especially in figuring out when something goes wrong inside our bodies. What else would the author have had us do, other than sequence the genome? He doesn’t say, preferring instead to make snarky asides about who said what about whom at the press conference. Phef.

Finally, let me note something that I haven’t seen mentioned anywhere else. There have been several stories recently about the discrepancy in gene numbers — 30,000 from the genome sequence, up to 120,000 if you believe some companies (bearing in mind that the companies think that having more genes increases shareholder value, of course). One of the reasons for this confusion is that the word gene is over-loaded. It means different things in different contexts, or when said by different speakers. In fact, if you ever have a chance to watch two molecular biologists interact, you might see something akin to the handshaking that modems do when they link up. Highly trained people, who work with these concepts day in and day out still have to query each other to establish what somebody means when they say “gene” — are we talking about DNA or cDNA? If cDNA, from normalized libraries? What tissue type? How many isolates before you believe it’s not just a sequencing artifact? PolyA-primed or random primed? Cap-selected or not? The answers to each of these questions, and more, all factor into a complicated internal equation that puts a probability on whether or not you’ve really got two different “genes” or just two isolates of the same “gene”. Moreover, everybody’s internal equation is just a little bit different — some people call things different based on very little evidence; others want strong proof before they’ll concede that more than one “gene” has to be involved.

This semantic confusion and contextual ambiguity is at least partially responsible for the controversy over how many genes there are. Add in a need on the part of the media to simplify these concepts, a need that results in a “gene” being different things to different people, and you’ve got a real mess. Just something to keep in mind the next time you see a number appearing before the phrase “genes in the human genome”.

sheena was a punk rocker
Not shaping up to be a good day — first I’ve got to give the State of Maryland a huge tax payment, then I find out Joey Ramone died. I will be sedating myself in his memory later today.

who let the funk out?
Since it’s getting to be springtime (leastways ‘round here it is), here’s the home page of the Dirty Sole Society, a group of people dedicated to being barefoot. (Hey, everybody has their thing, ya know?)

big bro, watchin’ you watchin’ him
The ACLU has a new ad out spotlighting the US government’s electronic surveillance programs. Too bad they didn’t run the ad in more papers.

when they are out to get you
The Jim Bell “stalking” trial has concluded, unsurprisingly, with a number of guilty verdicts. The trial is summarized here, for those of you who haven’t been following it closely.

#censored#
And while we’re on the subject, Project Censored’s top censored stories for 2000 are out.

quilting with perl
Found via Usenet, a Perl-generated graphic showing all possible triangle-based quilting blocks, and the actual quilt featuring all those blocks.

servicing the customer
Unfortunately, that’s probably going to be the last set of links I get off Usenet for awhile, because Speakeasy, my ISP, cut off Usenet access for its dialup customers on Friday. Yes, dialup customers only; DSL customers still have full access. They did this because “dialup users were slowing the service down” for the DSL users.

I’ve used Speakeasy for about a year. I would have been really happy to get DSL through them and Covad, had it been possible for me to do so. However, I’m stuck behind fibre for the foreseeable future, which means I’m screwed on the DSL tip, and Speakeasy reducing the services I get, with no advance notice, has told me how important my $20/month is to them.

So, I’m looking for a new ISP. Nationwide access would be nice, Usenet access is a must, and they should be at least OS agnostic, if not Linux friendly. Send your suggestions to jacobs@genehack.org.

anatomy of a joke
This was a pretty slow year, April Fool’s joke-wise. One of the better ones I did see was the story about Perl and Python merging to form the new language Parrot. Simon Cozens, the man behind the joke, let’s us in on how it was done.

pretty
In case you missed it, have a look at APOD’s shot of M51, the Whirlpool Galaxy.

it could be worse
While you’re at work on Tax Day (for the USians) or Monday-after-holiday-weekend (if you got time off) or just regular old Monday (if neither of the two apply), and you’re having a bit of a bad day, pause and give thanks that you don’t have any worms in your brain. Probably.

springing forward
Spring has definitely hit the DC area. If it didn’t hit 80 degrees today, it came damn close. I worked from home, with all the windows thrown wide open, and had a wonderfully productive day. I was really looking forward to having a nice wheat beer on our balcony after the sun had gone down, but it started raining about 8:30, which put the kibosh on that idea. Aside from that, it was a spectacular day.

And now I’ve finally got a few spare hours to clean out my link backlog. Some of these are pretty old; you might have seen them elsewhere, but just in case, here they are.

bodies, bodies everywhere!
While I’m doing the personal meta/ramble thing, earlier tonight Lor and I watched “Naked States”, the HBO documentary about photographer Spencer Tunick’s cross-country tour. (No direct link, because it requires Flash, but you can get there from here.) Unless you’ve been under a rock, you’ve likely seen some of Tunick’s work — he does urban scenes featuring nudes, often dozens or hundreds at once. Every shot of his that I’ve seen has been gorgeous, and watching him actually recruiting people to pose (he eventually got people from all 50 states!) was very interesting. Tunick himself came off as a bit of a prima donna (actually, the phrase I used during the show was “whiney bitch”), but he’s a prima donna with a very good eye. The show premiered this past Sunday, but watch for repeats if you’ve got HBO.

gnus
One of the things I did today was upgrade to the CVS version of Gnus, which is a mail/news reader that runs inside XEmacs or Emacs. Every so often, I’ll play around with another MUA or news reader, but I always go back to Gnus, usually within a couple of hours.

If you’re just getting started with Gnus, this tutorial is worth a look.

Once you’ve got the basics down, socha.net has some pointers to more advanced resources that will help you customize Gnus to within an inch of your life.

…and speaking of emacsen
Here’s a couple three more emacsen-specific links:

One of the cool things about editing files in emacsen is that they have the ability to transparently use FTP to access files on remote machines. One of the uncool things is that this brings along all the security issues of FTP. The answer? TRAMP (Transparent Remote (file) Access, Multiple Protocol), which does the same thing, only with secure tools like ssh and scp. I haven’t tried it yet, but it’s on the TODO list.

Clearly, I’m a big fan of using XEmacs, not only for mail and news with Gnus, but for pretty much all the development and systems administration I do. Mark Stosberg sent along a pointer to some tips he has for web and database development in XEmacs. (Mark is the guy who wrote the BBEdit user’s guide to choosing a Unix text editor, which I pointed to back in March.

Finally, if you’re just getting started with Emacs, you might find the new Emacs Beginner’s HOWTO useful.

working to keep speech acceptably free
Like Lyn, I’ve been closely following Declan McCullagh’s updates on the Jim Bell case (most recent story). Seems like the Nuremberg Files decision should make this case mostly moot, but “some animals are more equal than others”, to steal a phrase.

I’m especially disturbed by statements from the prosecution that Bell’s refusal to “renounce his beliefs” is at least part of the reason he’s being prosecuted. “Renounce his beliefs”? Did somebody reconvene the HUPAC and not tell me?

give ‘er more power!
Is the response to the looming electricity crunch going to be more nuclear plants? Watching the interplay between NIMBY-ism, environmentalism, and pragmatism as this gets sorted out is going to be fun — as long as we’re not watching by candle-light, that is.

i will fear no evil
A doctor from Cleveland has transplanted a monkey head onto a second monkey body. First, how perfect is it that this happened in Cleveland?! Second, the feat is actually less impressive than it sounds — there were no nerve connections between the head and body, just vascular and respiratory ones. However, keeping the resulting hybrid alive “for some time” is probably a decent first step.

I can understand the criticism of this work on the grounds that it’s unethical. However, the same researcher who makes that criticism says that the proper way to help “the quadriplegic community” (presumably a big “target market” for such a procedure) is to work on spinal nerve regeneration — if we figure out how to regenerate spinal nerves, what’s to stop head transplanters from using those techniques to attempt to join the nerve networks of the head to the new host body?

that dna looks human!
In the “what’s the date on that story?” file, British scientists think they may have found some Yeti fur. No, really, and the date on the story is April 2nd. Personally, I’m waiting for the Nature article before I commit to a position on this one.

$WEIGHT—
Initially, I thought The Hacker’s Diet was a joke, mostly because of the subtitle: “How to lose weight and hair through stress and poor nutrition”. Poking around a bit, it looks serious:

I’m an engineer by training, a computer programmer by avocation, and an businessman through lack of alternatives. From grade school in the 1950’s until 1988 I was fat—anywhere from 30 to 80 pounds overweight. This is a diet book by somebody who spent most of his life fat.

The absurdity of my situation finally struck home in 1987. “Look,” I said to myself, “you founded one of the five biggest software companies in the world, Autodesk. You wrote large pieces of AutoCAD, the world standard for computer aided design. You’ve made in excess of fifty million dollars without dropping dead, going crazy, or winding up in jail. You’ve succeeded at some pretty difficult things, and you can’t control your flippin’ weight?”

Through all the years of struggling with my weight, the fad diets, the tedious and depressing history most fat people share, I had never, even once, approached controlling my weight the way I’d work on any other problem: a malfunctioning circuit, a buggy program, an ineffective department in my company.

As an engineer, I was trained to solve problems. As a software developer, I designed tools to help others solve their problems. As a businessman I survived and succeeded by managing problems. And yet, all that time, I hadn’t looked at my own health as something to be investigated, managed, and eventually solved in the same way. I decided to do just that.

This book is a compilation of what I learned. Six months after I decided being fat was a problem to be solved, not a burden to be endured, I was no longer overweight. Since then, my weight hasn’t varied by more than a few pounds. I’m hungry less often at 145 pounds than I was at 215. I look better, feel great, and have more energy for the things I enjoy. I spend only a few minutes a day maintaining this happy situation. And I know I’ll be able to control my weight from now on, because I have the tools I need, the will to use them, and the experience to know they work.

I saw a lot of bloggers make New Years resolutions about weight loss; have a look.

mommy, what’s an ‘omics’?
From UCDavis, What is genomics?, which should come in useful the next time I need to explain to a relative what I do for a living.

if this goes on…
Debra Hyde, she of the Pursed Lips, passed along a pointer to a story about a genetic component to early female puberty. I talked this over with a couple of cow-orkers who are more evolutionarily oriented than I am, and it seems like the long-term consequences of this could be pretty big. There are also some nice theoretical complications if it turns out that the version of the gene responsible has opposite effects on male puberty. And that’s not even getting into the societal implications…

yet more stuff to read
Free online geek books that I might have time to read someday:

• GNOME Online Books (GTK+/Gnome Application Development and Writing GNOME Applications)
• Programming Ruby

Ruby has been getting some really good buzz lately; anybody playing with it yet?

don’t tread on my .org
People who own .org domains and other interested parties are invited to sign the petition at www.org-domain-name-owners-lobby-against-icanns-sellout-to-verisign.org protesting any changes in the rules governing the .dot namespace.

blog shoutout
After a hiatus, whim & vinegar is back with a beautiful new design. I think it’s getting to be time to banish the darkness of winter around here, but I’m not sure when I’m going to have the time.

staggering something…
The page title says it all, really: Genius. A brief quote (all spelling and punctuation is as in the original:

GENIUS 147+ I.Q. SEEKING WORK
WOULD YOU LIKE TO I.Q. TEST ME? Thats FINE by me You can have a qualified Psychologist test me, or a qualified Proctor test me, or you can save money and get some I.Q. tests from Book Stores (if they dont have them, they can order them), or you can pull IQ Tests off the Net (search engine). I.Q. Test me, I.Q. Test your staff, Test yourself. But use an IQ TEST, as I.Q. is not a test of knowledge, a Math or English test will not do.

There’s more, much, much more. Just look.

all your muggles are belong to us
JK Rowling, author of the Harry Potter books, is being sued by what appears to be an obvious nut-case. Nevertheless, the case got a bit of media play last week, in what may be the beginning of a larger Potter backlash. There’s a CNN chat transcript, the site of the woman seeking damages (ware the annoying JavaScript there), and a fan site rebuking the claims.

sprung
Wow! I’ve cleaned out the ole link-pouch! Now to just get caught up on the email front. More tomorrow, I hope.

Just wanted to let you all know that I’m still here. I’ve been accumulating pointers to this and that; I’ve got tons of stuff to post, but I have no time to sit down and actually write the stuff up! Anyway, if all goes well, there should be an update in this space tomorrow night, or, failing that, the day after. In the meantime, check out some of the blogs on the Daily Dose, and I’ll catch up with you in a few.