April 1999 Archives

I have to take a friend to the airport this morning, so no updates today…

Head-on collisions with the Belief Engine

The scientific community needs to assemble an interdisciplinary SWAT team of prominent scientists who will be willing on short notice to respond publicly and forcefully to pseudo-scientific claims before they can put down roots.

Biology career development links from the Ward lab.

The ecology of why platform standardization is bad.

I’m getting into reading both peterme.com and jjg.net regularly. I should add them to the Daily Dose page, I guess.

Best New Drug Name: For people with urinary disfunction: FloMax.

JSTOR is a cool idea — taking old copies of academic journals and making them available on the web. This lets libraries reclaim all that shelf space currently devoted to old bound journals.

The Bruce Sterling Online Index: a guide to every Bruce Sterling work on the web

Not-so-stupid space tricks: using common objects to model our solar system.

… there’s more to the exercise, in light of recent discoveries of distant planets. “The solar system is full of open space. In contrast, the giant planets that are being found in orbit around other stars are quite different.”

Stop the dihydrogen monoxide menace NOW! (Okay, it’s actually about the psychology of gullibility, but the first part is amusing in a sad kind of way.)

Sad, just sad.

The gengineered food debate rolls on…

Is sending radioactive iridium by FedEx a Bad Idea, or is it just me?

Washington: The Net Must Pay (from Wired News) Scary quote:

Reed said the First Amendment limited how aggressive the government could be in a crackdown, but another official said he could see a way around it.
I get real antsy when I hear government officials talking about doing an end-run around the First Amendment…

Messy Models

Could bacteria be involved in the genesis of multiple sclerosis? There’s an interesting trend at work here, starting with the H. pylori/ulcer connection a few years ago. I wonder how many other diseases and ‘congenital defects’ have unknown bacterial causes?

Last week, I saw a news item about a Harvard study showing that the antibiotic neomycin inhibits angiogenesis, a key step in cancer metastasis. I can’t find any information (papers, etc.) about this on the web; if you’ve got anything (electrons or atoms) please let me know.

Ursula Goodenough is giving a seminar next week at the UA. Here’s a review of her latest book.

Review of Blaming the Brain: The Real Truth About Drugs and Mental Health from JAMA.

The dopamine theory of schizophrenia and the serotonin-norepinephrine theory of depression are far from conclusively proven, and the pharmacodynamics of the tricyclic compounds, benzodiazepines, Prozac, and lithium remain obscure.

Wow! I’m a Publishers’ Clearing House winner - of a whole dollar. Whee!
For the record, I didn’t buy anything. 8^)=

Michael Moore (of Roger & Me) weighs in on the Kosovo situation

A counter rant to Stephenson’s In the Beginning Was the Command Line…

The Tierra A-life project. Cool pictures, cooler idea.

Columbine shooting incident comment: In all the media deconstruction of the Trenchcoat Mafia, why haven’t we heard anything about City of Angels (or the earlier Wim Wenders work on which it was based), which featured scores of characters wearing black trench coats?

mklinux.org has a nice 3-D dancing penguin, if you’re into that sort of thing.

Something I’m going to have to print out for my wall. (from /.).

Internet Alchemy is a web log I heard about on CamWorld. Also in web-log-ish news, Wes is back up at Hack the Planet.

If you’re into cultural criticism, this book might be worth a go.

People in New Madrid (and St. Louis, too) can breathe a little easier.

XKeyCaps could have made developing my Dvorak keymap a little easier.

I signed up for my.snap.com, after seeing it mentioned on peterme.com. I was attracted by the fact that they actually offer up links to outside, non-co-branded sites. Loads a bit quicker than other personalizable portals, too.

The web site usability test I was in on Friday was non-eventful. The new site, which will go live in August according to the testers, is a lot nicer than the current site.

Fugazi End Hits cover

Old Media Purchases: After my bowling league on Friday night, Laura and I made a Border’s pilgrimage. I picked up the new Perl Cookbook, Darwin Among the Machines, and Fugazi’s End Hits (reviewed at Pillowfight.)

A Fugazi fan site: The official Southern website of Fugazi
(There are lots more out there; try searching Google.)

Whew! I had a good weekend, hacked a lot of Perl, learned a lot of hands-on stuff about using references. I also ended up with a lot of interesting stuff to point at, and some mini-rants that need to come out. Look for the updates to be a bit larger this week and maybe the next, until the backlog gets taken care of.

Shorter update today — in coding mode, learning lots. I think I’ve finally managed to grok Perl references! This is a Good Thing.

I’m participating in a web site usability study for the University of Arizona design team. If anything interesting occurs, I’ll put up some notes later tonight or tomorrow.

Otherwise, it’s a beautiful day (at least in the part of the world where I live), it’s Friday, it’s Spring! Get up and go into the Big Room with the Blue Ceiling…
Geez! Am I channeling Dave today, or what?

Short update today, lots and lots of Perl to be written…

There’s a new version of Window Maker out. Nifty cool workspace name flashy thingies!

A new version of the HMS Beagle came out last week. Do any their ‘designers’ ever visit their site over a modem? The thing’s slower than hell! Maybe that’s why I don’t ever read it much…

The LinuxPPC crowd has a tee shirt available.

The new Linux Gazette is up.

Skeletons in our ancestral closet?

Modeling complexity, simply

There’s a poll on peterme.com concerning Meyers-Briggs personality types. (Results are here.) Swing by and vote — there are links to tests if you don’t know your type. (I’m an INTJ, in case anyone cares.)

There’s a new version of the biff-like WMMail.

Dawkins on memes

A FUD-ish Dallas News article about New Media and the Kosovo war. I say FUD-ish because of this (regarding a list of exterior war-related sites linked to by CNN:

CNN’s list of Web connections is preceded by a parenthetical note stating, “These sites are not endorsed by CNN Interactive.” But for Web users moving from the principal CNN site to the links it offers, there might be no real sense of leaving the news organization’s premises.
.So, the average web user is too stupid to notice the difference between this and this? (Not to mention that the new site opens in a new browser window!)
<sarcasm>Pity the foolish media consumer! Oh please, Old Media, save us from the scary chaos of the Internet!</sarcasm>

www.linuxnewbie.org: Linuxnewbie.org is ‘the place’ for people that are transitioning to Linux from Windows…

In the market for some DNA sequencing equipment?

Gengineered Chlamydomonas turn into heavy metal sponges. (That it’s possible to harvest the cells and then recover the metals is mega-tasty…)

How much of your brain are you using? CSICOP takes on the ten-percent myth:

The myth is not simply a static, misunderstood factoid. It has several forms, and this adaptability gives it a shelf life longer than lacquered Spam.

Geez! I almost forgot! Dave should be back at Scripting News today. YAY!

The FDA approved a new protease inhibitor for HIV therapy: Agenerase (amprenavir). I found a lot of information when I did a Google search. Frighteningly, a lot of it was contradictory. The link above goes to the most complete page I found; if you’re evaluating the drug before taking it, be careful to check out several information sources.

In an un-related Google search, I ran across this link about bioinformatics degrees on a Robot Wisdom page.

New Linux software installs over the weekend: I updated to the recent 2.2.6 kernel release, switched to the Xpmac_mga X server, and built the new postilion mail client.

It looks like there’s some interesting stuff on The Reality Club to wade through, when I get the time.

Hack the Planet is off the air due to ISP problems. Hopefully Wes will be back up and running soon…

I’m still working on the piece about the nature of web logs and the point and future of GeneHack. Initial efforts have shown me that I need to carefully figure out what I want to say; just diving into the writing isn’t going to cut it.

Did some coding last night. It was the first time I’d done that with the Dvorak keymap. It was good, since I still really have to think about what I’m typing — which actually resulted in less buggy code. Now I just need to remap my Emacs keys so that C-q C-o works for C-x C-s.

Building a new LinuxPPC kernel

luigui.org: Linux/UNIX Independent Group for Usability Information — good name, great idea.

Big Bugs. For you Neal Stephenson fans, note the use of the PATEOTS measurement.

Uncontrolled Experiment: America’s dependency on foreign scientists

“American science, in other words, is based on a Ponzi scheme.”

More cool keyboards that I can’t afford on my meager salary (see the above story…)

The bioperl.org gang is going to get together at Bioperl ‘99. Wish I could be there…

Review of the forthcoming MacOS 8.6

More PNAS papers that merit a trip to the library (insert obligatory rant about free Web access to science journals…)

Nice Lego DNA Helix! See more at DNA2Z.

The Awful Truth - Michael Moore’s new Bravo series.
What’s awful is that this is a Flash site, which means that as a LinuxPPC user, I’m screwed. Let me know if it’s any good…

From Mike, some tax-time penis humor.

The Struggle To Decipher the World’s Most Difficult Book.

If you haven’t seen them yet, now is a good time to check out the BOFH series.

The early days of memetics

A report from the chaotic front of the genetically engineered foods debate

A new LinuxPPC site is up at the South Pole

Talking to Non-scientists about your job: This happens to me all the time. I’ve actually gotten to the point where I’ll think about how to explain something to a non-technical person, just so I can keep up with conversation. If I’m successful at getting into bioinformatics, I only expect the problem to get worse.

Today’s update comes to you in Dvorak, which is why it’s so short.

Happy 26th birthday to Cam, and a belated happy 21st to Wes.

OK, that’s all for today. I’m burning brain cells here, and it hurts! More tomorrow.

Hope everyone had a nice weekend and didn’t notice the lack of updates. I decided to ease up on my typing, to see if some of this wrist pain would clear up. It seems to have helped, a little bit.

Lake Superior State Banished Words List. I’d like to propose a ban of my own: on people who use MS Word to edit Web pages and then don’t fix the well-known ’ to ? problem.

A link on peterme.com lead me to the Keirsey Temperament web site. There, an online test told me I was a mastermind, better known as an INTJ.

Creativity, clues about culture could help science: In the lab I work in, we often discuss papers and talks in terms of narrative, of telling a story. I’d also like to point out that many scientists aren’t just bad at communicating with the public, they’re bad at communication period. When people talk about reforming science education, they need to realize that changes need to occur at the post-secondary and graduate school levels too.

Multiple Disciplines, Imagination, and the Big Picture: At last, some of the science fiction authors are starting to pay attention to biology! Maybe this will produce some bio-science fiction I can read with wincing too often. Additionally, as far as Greg Bear’s comments: Some of us are starting to tackle the gene network problem. Just give us a little bit of time, okay?

Where do you want to go tomorrow?

Misc. Cruft: I had intended to use this weekend to do some thinking about GeneHack, why I was maintaining the site, what it had to offer, etc. That only got partially done. Watch later this week if you’re into meta-critique of weblogs and ruminations on the role of the personal web-site.

As promised, I packaged up my Dvorak keymaps. The package also includes dvorak7min, a GPL’d typing tutor. I actually uploaded a LinuxPPC R4 binary in addition to source code, as well as shell scripts to switch keymaps. To load the Dvorak map, type asdf. To remove that and reload the QWERTY map, type aoeu (that’s the same four keys as asdf). To start the tutor program, type htns (Those are the four Dvorak keys under the right hand home position.) More detailed instructions can be found on the Files page.

Dan’s got a rather scary receipt up on Flutterby. I paid about US$13.00 for 10 gallons of gas in Tucson yesterday afternoon.

Scary link relayed from my wife, in the every-damn-thing is on the Net department: Bumper Dumper

Uncle Booger is sending Bumper Dumpers to help with the sanitation problem rapidly growing with the Refugees.

Some of those interesting links from Arts & Letters Daily, now that I’ve had a free moment or two. First, an intriguing,if somewhat one-sided piece about widespread DNA banking. It’s not really an easy question, which means the eventual solution will please no one.

Second, a review of a book that appears to describe the role of serendipity in scientific discoveries. More interesting than the review is the defensive tone of the New England Journal of Medicine reviewer. Sure, our government throws money at researchers to investigate disease. The question is, does this directed approach produce more and/or better results than the pure research approach favored by other, at times less well-funded researchers? I’d like to read a book on that!

PerlSlinger looks interesting, if you’re a Mac Perl person.

Two interesting recent papers that I need to read:
    Correlation between protein and mRNA abundance in yeast.
    TargetFinder: searching annotated sequence databases for target genes of transcription factors.

Site Cruft: In case anyone cares, I added some <META> tags to my page headers. I just got tired of backtracking search engine queries and seeing outdated content show up. Hopefully the change propagates through the search engines quickly. Also, for the browser/OS-heads, I noticed that the 100-plus-hit day earlier this week pushed Windows 95 and Windows NT ahead of Linux. Interestingly, SunOS hits are gaining quickly on the MacOS. Curious mix of viewers I’m attracting here. Much more info available on the Stats page.

I’ve started reading The Right Stuff, and so far it’s been pretty good. I’m intrigued by some parallels between the test pilot sub-culture and the Open Source/hacker sub-culture. (I just re-read Hackers not too long ago.) Might be worth looking into for all you cultural critics out there.

August is a HTML editor for Linux. No syntax coloring, which nixes it for me, but still worth a look. Hopefully, syntax coloring will come (it’s only at version 0.27).

New Cam Rant: Insomnia

If you have to run Windows, why not make it look good?

There were lots of interesting things on Arts & Letters Daily yesterday, but I haven’t had time to look at them yet.

I’ve got a working Dvorak keymap for LinuxPPC. As soon as I get everything wrapped up into a nice tarball, I’ll post it here.

Wow! 107 unique hits yesterday, breaking the 100-in-a-day barrier for the first time. You Simply Porn-seeking kiddies are out of control! (Scroll down for those links if you just got here.)

The Generic Personal Homepage

I’m re-reading Microserfs for about the tenth time. Expect to see some quotes showing up over the next few days. If you haven’t yet read this amazing book by Doug Coupland, drop what you’re doing and go pick it up. Incredible!

I’m experiencing that post-major-push-at-work letdown. Time to go through the pile of crap on my desk, send in those Book-of-the-Month club responses, make an appointment for the car, mail some overdue birthday cards. Life…

EMBL Software Archive

Talk over — went okay, I guess. Self-rated at about 6.5 or 7 out of a possible 10. Updating the site now; lots to talk about…

Apology: I looked at Dan Lyke’s rant about clueless web design. Then, I thought for a minute, changed my Netscape defaults to black background with white text, and reloaded this page. Presto! White background (specified by my <body> tag, with white text (from the prefs). BAD! As penance, I changed all my body tags by hand to specify text="black" in the <body> tag as well. I’m sorry — sorry that I’ve been looking like an idiot for who knows how long…

Got the latest Wired yesterday, and took a little time off from talk prep to power-read it. One of the better issues in a while; the email article was interesting and you can’t beat a Lucas interview. PlanetAll.com looks interesting, as does Arts & Letters Daily

Now’s prolly a good time to mention that in addition to PlanetAll.com, I’m also a member of Six Degrees. If you belong to either and read this site with any regularity, feel free to add me as a contact.

For all you p0rn-hungry kiddies pounding the search engines in search of the (in)famous Simply Porn ad parodies (of the Simply Palm ad campaign), look here. Or maybe look here to go straight to the pictures.
And if you do, karma requires that you keep coming back to this site semi-regularly! Don’t use me and abandon me! 8^)=

Justlinux.com is a cool new Linux ‘portal’ — although that word isn’t entirely accurate. That is, I’m pretty sure that it’s the first portal that offers dynamic DNS services free for the asking…

Mark’s Apology Note Generator

Over on slashdot, Rob has tweaked the moderation scheme again. I think I like it…
For the clueful, my default alignment is +1 — kewl!

On MacCentral the other day, some Mozilla resignation counter-FUD (or anti-spin, depending on your perspective) was posted.

Couple of miscellaneous Dvorak links:
     The Dvorak keyboard
     ABCD - A Basic Course in Dvorak

Big talk today — updates later, assuming I don’t implode from lack of sleep.

It snowed here yesterday. That might not seem that amazing, but I live in southern Arizona — it’s pretty damn odd.

People have been pounding the search engines, looking for information on the new antibiotic Zyvox. Oddly, this is the only site that Altavista returns to such a query. To make those people’s lives easier, here’s the link I ran before:Zyvox article. Also, the generic name for the new rug is linezolid; using that as a query to Metacrawler yielded much better results.

Tomorrow is World Phone In Sick Day ‘99 ( First seen on slashdot )

Yesterday, I gave both lpe and mutt a go. I didn’t really care for either, but you might.

Hack the Planet points to The Mac on Linux project.

QWERTY just as good as Dvorak? (also from slashdot)
Fresh off my User Friendly burn, I’m not sure I buy this one…

The Official Marshmallow Peeps web site

Simply Porn (A parody of the ‘Simply Palm’ ad campaign.)

Light updates today and tomorrow; the weather is clearing up, so I’m off to the Big Room with the Blue Ceiling…

Well, paint me sappy. Like many others, the User Friendly April Fool’s gag sucked me right in.

No Mo Zilla: jwz quits mozilla.org and AOL/Netscape. I’ve already fallen for one April Fool’s joke, but I don’t think this is another.

Ask and you shall receive! Window Maker 0.52 has been released.

Buy LinuxPPC R4.1 now, and get the upcoming R5 release for free. I’m gonna have to look into this deal…

Other product upgrade news: It looks like the MacOS 8.5-compatible version of OneClick is out. This used to be one of my favorite pieces of utility software, but since I’m running Linux as much as possible, it’s probably not worth the US$20 upgrade fee (for me, of course).

Intelligent Systems for Molecular Biology 1999

Of course, since someone is visiting, the weather has taken a turn for the crappy…