September 1999 Archives

Yesterday was one of those days

A report on the status of E-biomed, the on-line publishing initiative for the life sciences. It’s difficult to peer through the legalese, but it looks like somebody wussed out. The rules for screening organizations may be a small loop hole, however. We shall see.

Cheap chips! Wired also had a report. Might be time to consider unloading that Affymetrix stock…

Another Wired piece from earlier this week: There are 140,000 genes in the human genome, according to researchers at Incyte. Of course, the technique they’re using will err on the high side, as noted by Francis Collins:

“The trick here is how do you count genes using this strategy?” he asked. “You are going to encounter this same gene over and over again if you don’t recognize the sequence. These are not complete copies — they are usually pretty fragmented.” … “If you have a piece from one end and one piece from the far end and one piece from the middle, you might not recognize that they are from the same gene — you might count them as three genes,” Collins said.

Is there some rule that biotech web sites have to be ugly? Just asking. (Incyte’s isn’t that bad, actually.)

From /., and going in the ‘At leisure’ section: The Programmers’ Stone

Wow! I’m actually caught up on my bookmarked stuff; time to start the hardcore surfing again, I guess.

mini-me

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dan gillmor on coming issues raised by computers. the interesting thing for me (and a point which isn’t addressed) is how many of the issues inter-relate: crypto touches privacy, surveillance, and anonymity; surveillance and anonymity touch on the issue of age-appropriate content; and so on. no solutions here, either.

drivers beware! spike the bike is out there… (also added to the ‘at leisure’ list).

this book could be interesting, especially as i was just diagnossed with borderline hypertension. the good news is i can know say i’m under doctor’s orders to finish graduate school as soon as possible…

Harry Noller’s group at UCSC crystallizes ribosomes to new higher levels of resolution. pretty cool, and i’m sure that the science articles will have many pretty pictures, if you’re into that sort of thing.

There’s a thread over at molbio.org about some goof-ups with celera and the drosophila sequencing project. interesting parallels with corel and open source software are left as an exercise for the reader.

I also started the thread over there that I threatened to start last week.

minus minutes

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real life intrudes; must read 40 page draft review for colleague, and hack on xemacs.org (21.1.7 released this weekend…), and write job search cover letters and do miscellaneous house things. back tomorrow? (i hope!)

oy! both jason and wes (no, the other one) updated! …and there was much enjoying throughout the land…

vanity.com

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genehack.org

on friday i was browsing around mood swings, and found a link to www.mydomain.com. i followed it, and as i was playing around i ended up registering genehack.org. so, we’ll see how the finances are when the bill gets here, but i think i’m gonna keep it 8^)=. hopefully it’s propagated across the net by now, so clicking that link will take you right back here. i’m using the domain redirection from www.mydomain.com, but eventually i’ll find a real hosting service. if you link to me, please get in the habit of using the genehack form; it will be more stable in the long run. (you can mail me at jacobs@genehack.org now too…)

[plate from www.acme.com/licensemaker/]

my isp has started using brightmail.com for spam trapping. anybody have any positive or negative stories to share?

linuxppc.com has started posting security updates for the 1999 release.

resampling statistics play a large part in my current research project; it’s odd that there’s a whole web site about them…

buried in this month’s rolling stone was a blurb noting a plan by universal music group (apparently one of the largest record companies in the world) to raise prices on perennial cd favorites such as bob marley’s legend — to US$18.98. and they wonder about the popularity of mp3s…

wired has another bio-biz story, this one about micropayments for sequences. this business model makes no sense to me, which probably means it will be a great success.

another dna computer. i’m not too fond of science daily; the repackaged press releases often make it hard to figure out why something should be exciting.

perl.com put up another issue last week.

this news will cause either joy or great fear and confusion: sawmill is a new window manager that uses lisp as it’s config language. it’s nice and speedy, but a little too bare bones for my everyday use. if i had a bit more time to play, however, i think i could get it set up nicely. (it plays ok with gnome, in case you were wondering.)

Linux Journal’s 1999 Readers’ Choice Awards

poll: What is the best piece of software ever written?. [results] current winner: photoshop.

guess how i first parsed this entry from telsa cox’s diary:

September 20st : Goodness. Where does all this gunk inside mice come from?

hurmmm. must update more often, if only because skipping days results in more time trying to cull the mass of bookmarks. and the damn start page didn’t get re-done! grrrr.

i was going to take the night off, but…

salon on the coolness of start ups. i have no personal experience (yet!), but it seems coupland nailed this part of the zeitgeist in microserfs:

    “That’s not the point, Abe.”
    “What *is* the point, then?”
    “One-Point-Oh,” I said.
    “What?” replied Abe.
    “Being One-Point-*Oh*. The first to do something cool or new.”

the dot-coms meet the bio-info geeks. the story has a bit of detail about pangaea and celera, and also this tidbit:

Such are the capabilities of the computational biology that underlies bioinformatics — a field that Francis Collins, director of the Human Genome Project for the National Institutes of Health, says he now often counsels promising graduate students to look to for career opportunities. “I just think it is going to hit us like a freight train and we really have too small a supply of expertise in that area,” he said.

yah baby! show me the money…or the 1.0 opening. either one will do. now i just need to graduate…

here’s a question for the bio-geeks in the audience; i know you’re out there, i parse my logs regularly. (yes, lanl.gov, i’m talking to you 8^>=.) when you see a bioinfo paper without the source code, or a bioinformatics service provider, like i linked to last week, that doesn’t provide source, how do you evaluate the results they present? it seems to me like you can’t, but i’m curious as to the opinion of the field. i was surprised (but not really) today to find out that the software that affymatrix provides to interpret the data from their expression profiling chips is closed. if (when?) a bug gets found, what happens with all the papers based on data from those chips? maybe i should take this over to molbio.org… thoughts, comments, flames to jacobs@azstarnet.com

much work to be done on the start page. suggestions welcome, of course.

good weird

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Wired News picks up the giant gengineered salmon story.

some person reviews many ‘blogs. or is it just an exercise to see how many ‘blogistas will point to the page? time will tell. i also disagree with many of the reviews…

actually, after a bit of thought, i disagree with the whole idea. one of the points of ‘blogs (IMNSHO,OC) is to supplement your browsing, to extend your reach, and to leverage collective filtering to cut out the cruft. a big part of that is shopping around to find the right ‘blogs for you, not listening to some self-appointed reviewer’s opinion. the preceding has been a deeply ironic statement, especially considering the rest of today’s entries. i’d quote you some whitman, but you most likely already know it..

i love how reading lemonyellow.com is like a slow slide down a smoothly greased track, surrounded by surreal scenery. i also love how abada abada is like sitting very still while solidified dreams slide slowly by you. the question is, who’s the external observer that lets you tell the difference? suggestions welcome.

dan has already been drumming, without really realizing it. he is about to change his beat, however, and i think (i hope!) the new cadence will be a powerful one. good luck!

ugh; monday

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Event Horizon has some interesting chat transcripts, including ones with Vernor Vinge, John Shirley, and everybody’s favorite of late, Neal Stephenson.

ScriptCentral - Freely available perl code for the life sciences

About 4/5’s of the way down this photo page is a shot of one of the coolest piercings I’ve seen lately. (Not that I’ve been out looking all that hard, mind ya.) It looks just like the eyelet for a sneaker, only embedded in an ear.

crabby

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it’s the lab-on-a-chip from hp, and it’s damned expensive (us$19000). they also are fairly vague as to what it’s actually good for, but it does appear to be buzzword complient.

the “ROBOKONEKO” (Kitten Robot)

The main aim of the CAM-Brain Project is to build/grow/evolve an artificial brain by 2001 with a billion artificial neurons.

why do we need an artificial cam-brain when we have a real one?

the third voice thread over at userland has had some high points. i don’t have access to a box that is able to run third voice; if there are any scribbles up on geneHack, could someone send a screenshot? thanks.

wanna ‘blog? start here. remember, the first hit’s free.

hope everybody has a good weekend; see you on monday

crazy years

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if it looks like a ‘blog and quacks like a ‘blog, it’s a ‘blog.

i want!

plans to use data from multiple sequencing projects to identity the minimal set of genes needed to make a bacterium. oh yah, they’re also going to actually make it. even more amazing, the catholic church is on-board (or at least one spokesperson is):

But yesterday, Dr Helen Watt, a philosopher and bio-ethicist working for the Catholic Church in London, said that “provided the motivation is right”, then creating a bacterium is acceptable.

“God creates human beings with intelligence and if they can use this intelligence to create a bacterium then that’s fine,” she said.

the cause of chronic sinitis?

i think i’ve mentioned this before, but it bears repeating: anyone who wants to discuss any of my links or posts in a public forum is welcome to bring up anything on jorn’s weblogs egroup. (you’re also more than welcome to mail me directly, of course.)

the cryptonomicon review mentioned yesterday is up. (i agree with most of it, fwiw.) one addition: i heard somewhere (/.?) that the manuscript stephenson gave the publisher was much longer and that for some combination of economic and book binding reasons, it had to be split up. i hope that explains the somewhat abrupt ending.

still looking for that perfect counter…

today was a crappy, crappy day. however, there is recovery in the ‘blog…

settled in

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whew! all the old genehack pages on treefort have been replaced with pointers to the appropriate new pages. hopefully this will make search engine users happy, ‘cuz they won’t hit a dead link.

paranoia or prediction? ‘blogs would be hard hit by this kind of regulation. scary stuff…

Medley gets a slight face-lift, with more apparently on the way (i’ve a soft spot for Medley; we share a birthday.) and i’m looking forward to that cryptonomicon review…

compelling floyd journal, via fresh hell.

bionavigator looks as if it would be an interesting place to work. doesn’t appear as if they’re hiring, though.

anybody out there using gtml?

breeding pigs to be more lean (to fulfill market demand) lead to ‘thin sow’ syndrome, a condition that appears to mimic anorexia.

boggle um, maybe you should just browse on your own, then. it’s the net equivalent of ‘change the channel’.

an interesting tactic in the battle to keep a large home depot out of central tucson.

the ecology howto. probably not exactly what you’re thinking.

site cruft: i’m looking for a good reliable web counter service. i’ve tried theCounter.com and sitemeter.com, and haven’t been happy with either. anybody with recommendations? (jacobs@azstarnet.com, but you knew that already, right?

milestone

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i gave my boss a draft of my manuscript today. i feel like progress was made. that should last until i get it back…

everybody’s linking to the geeks and autism article. i saw far too much of myself in the article; it was a bit frightening, really. also got a bit of insight, too…i hope.

all the genehack readers in florida should probably keep their heads down at least for the next little bit.

i got my fabulous clip2.com t-shirt today. swag is good!

s’all for the day, me’thinks. still spending too much time on the old site move plus the re-design…

web monkey

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welcome to the new home of genehack! i got tired of waiting on the server repairs, and the only reason i was using the treefort server was so i could run some cgi scripts i never got around to writing…

a couple other administrivia-type things: first, not everything is in place yet, so you might get some 404’s if you poke around. sorry ‘bout that; should be fixed soon. second, even though i couldn’t upload last week, i did still update. see below. (the problem started on the 8th; the 7th is included for context.)

i could have sworn i book-marked some stuff, but i guess not. well, the old stuff and the new look will have to do for today…

back in black

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still can’t get to the damn server. prepping for the move to a different server, and (finally) making some progress on the redesign. the colophon is done, for example.

The blackout continues….

not going to bother with links today. also in <carpal> mode; deal.

this weekend i found a copy of !%@:: a directory of email addressing & networks, from 1995! it’s an o’reilly (of course) that lists various mail networks and how to connect to them. most of the book is a list of domain name registration info!. it’s in good condition, too — still has the cards in the back and everything. i wonder what it would bring on ebay…

Still can’t FTP; posting anyway. If the much hyped “Nines Day” is a problem (ha!), this will all have been for naught. [insert rant about clueless media and y2k hype and how (obviously, dammit!) 09/09/99 == 090909 not 9999 or 999999.]

Today on Scripting News, Dave said:

And after the writing is “finished” I take the [In Progress] disclaimer off and then people respond. And to my surprise, the writing isn’t finished! I get more ideas. I incorporate other people’s ideas into the piece. Add some links and a screen shot. The writing is tweaked, in real time, it’s a fast process. I have a feeling that I’m using the most advanced editorial system in existence. I love that feeling. (It pays to click on Reload.)

[ quote from piece entitled ‘The Evangelist Is In’, from 08 Sept 1999. Given the above, it may or may not still contain the above quote. Sorry, but that’s the best I can do. ]

Dave’s description of his posting style disturbs me. I realize link rot is a real problem, I realize that expecting things to hang around at the same spots on the web is at best naive, but I do have a certain expectation that if something I point at changes, it will be relatively obvious to the casual observer that it changed. I could point to something Dave said, following which he could change the text, which might remove the reason I pointed at it in the first place. Hell, he could totally invert his position on something, which could make it look as if I didn’t understand what he was saying! Note that I don’t object to changes while the ‘[In Progress]’ disclaimer is present; it’s the changes afterwards that bother me. Maybe I’m too old-fashioned, or not cutting-edge enough, but I don’t think I’ll be pointing at Dave’s stuff anymore, because I can’t be arsed to keep checking that it stays the same (and maybe now the reason for the large pull quote is apparent). In fact, I’m not sure if I’ll even keep reading Scripting News , given that I have to assume an implicit [In Progress] disclaimer on the whole site, given the above description.

This is kinda cool: highschoolalumni.com will track the people you went to high school with. If they’ve got the tiny little school I attended (~100 people in four grades), they’ve probably got yours too. It’s basically like a really dumbed-down version of sixdegrees.com , but probably a bit easier to explain to non-net people.

Speaking of relationships, how come friendfinder.com doesn’t have options for anything other than couples? Suppose you’re looking for a third, fourth, or fifth?

Many many moons ago, I used to see a band called Rex Daisy whenever they played in Iowa City. Apparently they’re still around, after surviving a label screw job. Anybody in that part of the world seen them play lately?

usenet.startshere could be very useful. I’d love to read usenet at work (the faster connection is nice), but the UA news server is seriously lagged. This might be a solution…

You can tell I’ve been posting too much on the weblogs egroup mailing list when GeneHack is at the top of this list. 8^)=

preview

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This is basically the new look; it still needs quite a bit of tweaking. Today’s update is short short short, cuz I’m working on the update, and switching to Dvorak (again), so everything takes longer to type. Oh yah, and my ISP is currently sucking bilge; took 20 minutes to get connected tonight. Grr..

I caught Dan’s rants on Flutterby about spectators and Burning Man and I feel a bit guilty about my plea for picture links yesterday. Anybody want to drop me a line and clue me in on why picture taking is considered verboten? Is it just ‘tourist-y’ style picture taking? If you participate and take pictures, is it okay? Hell, can’t taking pictures be considered a form of participation?

Anyway, that’s it for the day; mail me with comments or criticisms or whatever. thanks.

Greetings. I know some of the people who visit here regularly were at Burning Man; hope you had a good time. Wish I could have been there. When you get around to scanning those pictures, let me know where they get posted at, okay? Anybody else who runs across good pictures sites, drop me a line too.

No links today; I’m slaving away over a hot text editor, working on (yet another) GeneHack redesign. My ambivalence over the current design switched to distaste this weekend, so I’m working to fix that. Updates will probably be a bit sporadic for the next couple of days as I get stuff whipped into shape.

In re-design related news, Bring the Rock underwent a kick-ass make over this weekend, and the Eatonweb weblog portal had quite a face lift also. Good job to Jason and Brig!

Oh, BTW: the little qbullets are going away; they got too annoying.

Thought for the day: Is it at all weird that the anchor person on the ZDTV News would be using paper notes? The anchors on the local newscasts don’t even do that anymore, do they?

Here’s a nice tutorial on setting up SSH. (For those of you not in the know, SSH is somewhat like an encrypted version of telnet. It’s so people can’t sniff your remote site passwords as they go drifting about in clear text on the ‘net.) Maybe I can finally get trusted entry working for my work box!

I think this is the last ‘dusty link’ I’ve got: A Salon review of a book on crypto-zoology, the search for new and undiscovered creatures. Sounds reasonable, until you realize they’re looking for Bigfoot and Nessie. Still might make for an interesting read, I suppose.

Ugh. This has been one of those weeks. I feel like I’ve got a million things to do, none of them are getting done, and I’m not sure where the time is going. Must get organized!