March 2000 Archives

Anybody get a word count on Neale’s short-is-beautiful-too rant the other day? (Sorry, I’m a sucker for cheap irony.)

Reading Dear Sally (see Brig’s 3.29 entry for the whole backstory) made me wonder where GeneHack fits into the ‘blog timeline. Whenever someone mentions “The Old Guard”, they throw out names that I was reading before I really started ‘blogging, but whenever “The Youngbloods” are mentioned, the names that come up are people that I know started after I was already seriously going at it. Where, I wonder, do I fit in? (It’s the same thing chronologically, BTW — I’m not really a GenX’er, but I’m definately younger than… than… whatever came before GenX’ers. Anyway, sorry for the blatent navel gaze, but it’s something that I’ve been wondering about.

(BTW, I think I ‘get’ Bloat a whole lot better after reading Sally’s response.)
I’m sure Sally’s going to give a rat’s ass…

Free idea for the taking — there’s a (potentially great) West Side Story-based satire just begging to be done, given the above “Old Guard” vs. “Youngbloods” split mentioned above. Hmm — this would probably be right up Brad’s alley…

Okay, the rest of this is probably going to be somewhat of an atypical GeneHack entry, because I haven’t really had time to do any surfing for links (as opposed to just reading other ‘blogs), but I’ve got a whole load of personal crap that I feel like unloading, so I’m going to do it here.

It was my last day at work today; I handed in my keys, and I walked around and said ‘Bye’ to a bunch of people (those that I could find). I was more sad than I thought I’d be; I’ve been anticipating this for so long, wanting it, working towards it, planning it, dreaming about it, and now that it’s here I’m finding that part of me doesn’t really want to go — the part that prefers stability and stasis over change is actually quite scared of the whole moving and new job thing. A much bigger part is excited of course, and I think that the move, and the NCBI position are really the best thing for me right now, but that’s not doing a lot for the scared part.

I also killed my work box. The network people didn’t want a Linux box just sitting there without someone looking after it, so I backed up my stuff to CD-R, unplugged the network connection, and ‘rm -rf /‘d the filesystem. It’ll be back as a ‘doze box, but it won’t be *mine anymore. It was the first Intel-based computer that I used on a regular basis, and it was a good box, and I’m sorry to see it go. Just one more milepost on the road out of Tucson, I guess.

Lor gets back into town tonight, after being gone for almost a week. We’ll have a couple hours together, but I have to get up tomorrow morning and start driving, so it’s almost like we won’t have time to catch up at all. As Brig noted the other day, being without your partner really does suck rocks. Brig, it’s not any better when you have to do it from a house that’s mostly empty, because you’ve given your worldly possesions into the hands of strangers, whom you’re trusting to deliver them to the right place, at the right time, in mostly the same condition they were when you last saw them.

Today was a fairly unique specimen of a day — a Day of Lasts. Last time I’ll be in the building I worked in for seven years, last time I’ll eat at my favorite Tucson lunch spot, last time I’ll have to fight for a parking space in the crowded university lots, last time (probably) that I’ll see some people I’ve spent a lot of time with. Minor Last Days are pretty common — the end of conferences, the end of vacations — but this is only the third Major Last Day of my life — high school and college graduations being the other two.

If my life were a book, this would be the end of Chapter Three, and the beginning of Chapter Four — I wonder what the title of Chapter Four is going to be?

I’ll be back sometime next week, probably in the Wednesday to Friday time frame. Hopefully this time I’ll be able to stay around for more than a couple of days…

There’s a fairly interesting case developing around some hackers who developed some software that decrypts the blacklists of a couple of popular web “filtering” programs. There’s an interesting item in the latest RISKS about the whole deal, which notes that the two filtering programs have begun to quietly blacklist — under all available categories — any web pages that either contain the code or are critical of the programs. (Wired News also has a story.) It leaves out some recent interesting developments that have been reported on SlashDot: First, the two authors (facing lawsuits) have sold all rights to the code to Mattel, the corporate owner of one of the filtering programs — despite having the legal support of the ACLU. The authors’ motivation for the sale remains unclear; insert your favorite conspiracy theory here. However, things might get really, really interesting, as the code had been released under the GNU Public License — which means that anyone who wants to repost it should have the legal authority to tell Mattel to go blow. The moral of this story: Be careful about the blinders you put onto Barbie’s horse, or something like that…

Salon covers marijuana distribution in Maine, where the state government is preparing to do an end-run around the Feds, and distribute confiscated marijuana to medical patients with prescriptions for it. (Maine is one of the states that has passed a medical marijuana law.) The Feds are, of course, not terribly happy about this. It’s also interesting fodder in the continuing (or is that renewed?) States Rights discussions I think we’re likely to see as the US presidential race heats up.

There were quite a few interesting bioinformatic type links I found yesterday. First, an interview with Matt Ridley, who has a new book about the various genome sequencing projects, their effects on biology, and long term effects on society in general. The first 2/3s of the interview is personal fluff, which I found rather boring, but towards the end, it begins to pick up a bit:

**Regarding the possibility of a chimp-human hybrid**<br> "It
would be unethical to do such an experiment. You would bring into
the world a new individual. And this new individual would
presumably have rudimentary language, a low IQ by human standards,
but a high IQ by chimp standards. I think it's unethical because
it's very hard to see how you could treat such an individual
kindly, however hard you tried. It would be a very social
creature, a creature that very much wanted society, but it
wouldn't find a chimp colony in a zoo very interesting, and on the
other hand, it would find Wall Street rather daunting. It would
end up having a very lonely life. And that's the only reason it
would be unethical, because it would be cruel to the individual
you would create."

What if we made a whole colony then? Would that make it acceptable? (Insert David Brin’s Uplift series here.)

There were a couple of articles about the protests of the BIO2000 conference in Boston that I found interesting: [ABC News (AP)] [Wired News]. I’m still not sure where I fall in this debate — once you start to consider some of the larger issues, like the requirements for feeding our rapidly growing planetary population, it stops being quite so simple — but I do think that having two sides shouting at one another might not be the best way to accomplish anything. There have to be some scientists that have publicly questioned gengineered foodstuffs, that are (at least somewhat) trusted by the anti-GMO movement(s) — why not send them to the conference, let them actually talk to people, try to reach some sort of compromise? Or am I being entirely too rational here? I guess I’ve already accepted (and perhaps the protesters haven’t) that gengineering food organisms is going to happen — that is, unless we start taking the advice of the mysterious “anarchists” (apparently the only sensible group there) and Stop Breeding Now.

The SF Gate had a puff piece on Craig Venter, head of Celera. Venter attempts to defend Celera’s business model by pointing out that they’re not as bad as some of the other biotech companies working the gene/drug target discovery space — but doesn’t mention that for many people, patenting one human gene is just as bad as patenting all of them.

Finally, some preliminary results (ohh — actual research! how novel…) seems to indicate that one of the prime fears associated with gengineering might not be an issue. The concern is over antibiotic resistance genes — required for the first steps of assembling a recombinant gene for insertion into another organism — and whether they could leave the gengineered critter and get into bacteria, which could lead to the spread of even more resistant pathogens. The work is ongoing, and even when complete probably won’t be able to say that gene transfer won’t happen, but it seems that it’s going to be a fairly rare event.

Salon analyzes the business models of online bookmarking sites, which allow you to save bookmarks on a remote server, so that you can access them independently of your meatspace location. I use one such service, Blink, to bookmark sites that I see at work so I can ‘blog them later.

There’s an online course in XML for scientists in bioinformatics — something for me to look at more closely once I get to the NCBI.

Ask Doktor Komputor:

Greetinks, vebfolk. Velcome to Ask Doktor Komputor, ze first HTML
guide on ze Vorld Vide Veb written in ze amusinkly overblown
German accent. In zis guide, you vill learn how to make veb pages
zat vork every time, on every browser. Forget all zose other HTML
guides vith zeir difficult instructions. Doktor Komputor vill show
you ze vay.

A couple more LaTeX-type links: first, TeXmacs, which is just what it sounds like. Second, Pybliographer, which is a Gnome-ish bibliography manager that can interface with Lyx.

While we’re on article management type links, BioMail looks pretty useful — it’s an app that will periodically run a Medline search and notify you when new articles matching your criteria are found. They’ve even got a public server running the software, so you can use it or evaluate it without having to set it up on a server of your own. Sweet!

A couple of other software links that I mean to check out later: I’ve been interested in The Brain — which lets you record thoughts or ideas and link them in a non-linear way — for a while, but it doesn’t play nice with my favored OS. ThoughtTracker might be the solution.

Whew! I really ran off at the mouth today, eh? This is probably the last sizeable update for the next week or so — I leave on Thursday for the drive to D.C., and after I arrive (hopefully Sunday), the first couple of days (at least!) I’ll be occupied with unloading the moving truck and getting things unpacked. If there are any D.C. area people out there reading this, I’ve love to hear about reputable DSL providers or good local ISPs. Additionally, we’re trying to decide between the NIH employee credit union and Crestar for our bank — any input on the service/user friendly-ness of those two institutions would be welcome. Mail jacobs@genehack.org with any thoughts.

Okay, I know I said that I’d be back with a real update today, but I can’t seem to get into gear. Post-thesis-defense burnout, maybe. We (I, Lor, a friend, and my parents) did get the truck loaded up with all our stuff, and it left Thursday. Lor left Thursday too, for job training in Chicago. It’s her birthday today — the first one I haven’t spent with her since we’ve been together — Happy Birthday Laura!

I’m bouncing around our mostly empty house, killing time until next week, when I’ll climb into the car and drive it to DC. Lor and the friend who helped us pack will be flying into Baltimore with the cats. Once I get there, we’ll unload the truck (into the fourth floor apartment — ouch!), and then life should get back to normal.

The Bill of No Rights. I think I can get with several of these:

   You do not have the right to happiness. Being an American means
   that you have the right to pursue happiness -- which, by the
   way, is a lot easier if you are unencumbered by an
   overabundance of idiotic laws created by those around you who
   were confused by the Bill of Rights.

The Antique Vibrator Museum has some interesting pictures of early ‘massaging’ devices, and might make interesting reading for people looking for a return to the Good Old days, before all this smut crept into our lives.

Want some free ‘net access, but can’t find it because you don’t use ‘doze or the MacOS? Check out TCI: FreeWWWeb for Linux. No annoying ads to look at; all they want you to do is use their site for your browser home page. Seems to work okay, especially given the price, but the news server is shite, and the SMTP server was running pretty slow the other day. I’m hoping to get by with this when I first get out to DC, until I can get some type of broadband connection.

Back in high school, I spent far too much time playing a computer game called Elite. There’s a project out there to reverse engineer the source; hopefully this will lead to a version that will run on a computer I currently own.

I spent a little bit of time trying to do my thesis in LaTeX, before giving up and cranking it out in Word. One of the things I was going to try to do was use BiBTeX to format the references; gBiB would have probably been useful.

Well, not the best update I’ve ever done, but considering my current computer set up (I’ll spare the gory details, but milk crates play an important role, and using it for longer than about an hour leads to some decent back pain), it’s going to have to do. I’ll prolly be back for more tomorrow.

yay!!!

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Okay, just a quick little update to let y’all know that I successfully defended my thesis yesterday, so (once I take care of the remaining paper work) I’m now a Piled Higher and Deeper. The moving schedule has moved around a bit, however, so the next couple of days are still pretty busy. Look for a real update sometime around the beginning of next week.

hiatus

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Okay, I had thought that I’d be able to handle all the other things going on right now such that I’d still be able to get a little ‘blogging done. Unfortunately, that’s not turning out to be the case. It’s time for me to bite the bullet, so I’m going to go ahead and officially put GeneHack on hiatus, until after I get to DC — which should be some time in the first week of April. If you want mail when updates resume, subscribe to the notification list.

For those that care, here’s my (planned) schedule for that time period:

  • now - March 20: prepare for thesis defense (format thesis and practice defense talk).
  • March 21: defend thesis
  • March 22: submit thesis to Grad. College; general drunkenness.
  • March 23 - March 25: pack madly.
  • March 25: going away party; more general drunkenness.
  • March 26 - March 27: continue packing madly.
  • March 28: load u-pack-it truck.
  • March 31: leave current apt; take Lor and cats to airport.
  • April 1 - April 4: drive car from Tucson to DC.
  • April 5 - April 9: unload truck; move in to new apt.
  • April 10: first day at NCBI.

Just so y’all don’t think I’m slacking off…

Anyway, I hope to see all of you back in a couple of weeks; email is still welcome, and may even be responded to. 8^)=

busy bee

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I’m back in town, but things are still going to be pretty quiet ‘round here — hopefully I’ll get some ‘blogging done next week, but don’t hold your breath — I’ve got to format my thesis and practice my defense talk, and Lor and I have to figure out how we’re moving kit and kitties and then actually go about doing carrying out that plan.

The trip to DC was great; we got an apartment, which was the major goal. We also got to have lunch with my new boss and several other people I’ll be working with, which was nice. The high point of the trip was definitely the dinner we had with Fred “Metascene” Pyen, and the excellent driving tour of DC that Fred treated us to afterwards. All in all, I’m even more excited about getting out of Tucson, and getting to DC — just a few hoops left to jump through.

See ya Monday, or maybe Tuesday (or maybe Wednesday…)