January 2001 Archives

net storm forecast
Is the recent BIND hole going to cause net.havoc? My ISPs DNS is acting a bit wonky on a site or two, but I’m not seeing anything widespread — yet.

death by data drowning
Scientific American has a layperson-level overview of molecular biology’s current Hot Thing: microarrays. The article also touches on the current Big Problem: how to manage and analyze the massive amounts of data generated by microarray experiments.

because it is broken!
I’m still slogging through a C++ book with a group of people at work, hating most every moment of it and cursing the book’s authors at every opportunity. Sounds like some of the conclusions I’m drawing aren’t that far off base…

mixmaster genome
Scientists have recently discovered that a well-known pathogenic E. coli strain has over 1000 extra genes when compared to base-line E. coli, as well as a high degree of genome polymorphism. Viruses specific to bacteria are thought to be responsible for the shuffling ‘round of all these extra genes. I’ve been saying for a while now that horizontal gene transfer is going to be one of the next breaking areas in genomics; looks like I might be right on this one.

Link via Robot Wisdom

no, really, it’s good not bad for you!
The AMA has released a report saying that genetically modified foods aren’t more dangerous than ‘regular’ food. I haven’t read the original report, but from the summary it doesn’t sound as if any new ground was broken — there are potential problems, they’re not all the likely to occur, stay the course, etc., etc.

kick ‘em while they’re down
Some good news out of Davos: the CEOs are worried about the net disrupting their power.

“The Internet is a kind of power shift,” said Nobuyuki Idei, chief executive of Sony, which has extensive music copyright holdings. “Now the consumer has more power than the company.”

And Bill Gates isn’t all bad, apparently; he slammed on Big Pharma for the amount of R&D money they’re spending. Big Pharma, however, wasn’t buying it:

Henry McKinnell, president of the world’s largest drug company, Pfizer, said the pharmaceutical company wanted to help solve the problems, but there had to be an incentive to develop new drugs.
When work first began to treat AIDS, only one drug was available. Now there are 50, with another 100 under development, he said.

I wonder how many of those are based on work initially funded by the FedGov or HHMI?

language advocacy
Interesting thread on Nodalpoint about the prefered language for bioinformatics development. My answer’s over there…

it’s everywhere!
Turns out that the ocean (or at least the part a group of scientists recently surveyed) is teeming with archae. Every little bit we learn shows us how much further we have to go…

my kennedy assassination
Fifteen years ago Sunday, I was in the gym at my high school. I had gym right after lunch, and after I got done eating, I’d dress out early and shoot around while waiting for class to start. I know where I was, because Danny Fulton, my principal, came on the intercom and told us the Challenger had exploded. I stopped for a moment on Sunday to remember not only those who gave their lives to the Dream, but also those that continue to risk their lives for it. We’re messing up this planet pretty fast; I hope we get off while we can.

these aren’t the ones to worry about
So, for a while now, I’ve been saying that the question wasn’t “should we clone humans?” but “when will humans be cloned?”. (Maybe I should start a pool…) The competition is heating up, as a third group shoots its pipet tip into the ring.

I’m more concerned about the ones who aren’t talking. Face it, if you were seriously going to try to do this, why would you make any sort of advance announcement? Better to do it on the QT, and then make the announcement once you’ve got a nice mediagenic baby to stick in front of the cameras. The win for this approach is it keeps the cameras away from the less appetizing early failures that will occur while the bugs are being shaken out of the technique. (For those of you wondering, yes, I do scare myself sometimes…)

there doesn’t need to be only one
Peter Duesberg is back. Some of you may recognize the name; Duesberg was possibly the loudest voice in the “HIV doesn’t cause AIDS” camp. He’s apparently decided to switch tacks a bit and tackle cancer for a while. Some recent results from his group seem to back his theory that a cascade of point mutations doesn’t cause cancer. Duesberg instead hypothesizes that aneuploidy — distortions in the number of chromosomes per cell — is the root cause of cancer. The main problem I see with this hypothesis is that it doesn’t really explain what causes the aneuploidy in the first place; the most likely cause I can think of would be a point mutation or two in the genes that control chromosome segregation during cell division — in which case, we’re right back to the “cascade of point mutations” model. Any cancer and/or cell biologists out there want to comment?

captain, we’re a bit off course…
Plane transiting Sol. (big version) Cool.

what time is it?
It’s Howdy Doody time! (“Howdy Doody” is the nickname a cow-orker has bestowed on GWB.) And since it’s been a day or two since we’ve poked fun at Our Leader, I’ll offer up the Presidential Palm helper. Here’s my favorite. Or maybe this one. Actually, all of them are pretty good…

meeting roundup
So I’ll remember to tell people at ork about them:

that’s all, folks
I’m really behind on email, but I think I’m going to just head to bed. If you sent me something recently, I’m on it, ‘kay?

personal infodump
So much for that ‘more frequent updates’ resolution, eh? Let’s see, what’s happened this past week… Lor and I went down to the inauguration — actually, to one of the protest marches. The plan was to meet up with Fred, but we missed him during our hunt for restroom facilities. The march itself was uneventful; we got to the police barricade, watched a crush of people build up (I’m still not sure if they were checking people through where we were or not) for about a half-hour, and then headed home. Apparently there was a fracas after we left, as the Sunday Post had a picture of a protester with a bloody scalp captioned “at 14th and K”, which was where we were.

On the way home, we stopped in Bethesda for lunch and a bookstore run. I emerged with copies of Steven Levy’s new Crypto and Zinn’s People’s History of the United States. Finished the former later that night — it was pretty good. Not much that I hadn’t read before in other places, but it’s nice to have it all together, and to get a bit more background on Diffie. Recommended if you liked Cryptonomicon, or if you’re into the whole “crypto to preserve privacy and freedom” thing. The Zinn is proving to be much slower going; it’s hard to read big chunks of, because his writing is very dense. Oh, and I keep getting pissed off at various historical events. 8^/=

Hmm, that’s basically it — other details at the Advogato diary, or appearing there shortly.

good times
The very next person that mails me a warning about viruses is going to get a copy of this in return. Maybe several copies, depending on how pissy a mood I’m in.

when copying is outlawed…
Anybody with a copy will be a criminal. John Gilmore (who turns up, not oddly at all, in Crypto) has a rant about “What’s Wrong With Content Protection”. All I can say is that if and when this comes to pass, I won’t be taking part. I’ll be the one holed up in the book-lined bunker, third from the left…

local colour
Kevin hits the nail on the head with his observation about the changing DC fashion scene:

It appears the stereotype about Republican chic is true. I’ve seen more fur and fedoras on the Metro in the past three days than I have in the preceding three years. The worst of it was on the way home yesterday, when I was stuck at the L’Enfant Plaza station with a group of loud, abrasive, middle-aged (presumably) Texans, the men in huge cowboy hats and the women wearing most of the Scandinavian GDP across their shoulders. For fifteen minutes, I had to hear these people go on and on about the same topic - “Is this a safe part of town? I’ve heard Washington is a big ghetto. Is this a safe part of town?” I wanted to scream at them, NO part of town is a safe part of town when you’re running around dressed like Yosemite Sam. Everybody knows you’re rich, not from here, probably lost, and more than likely an asshole. I have half a mind to hold you up myself just so you’ll put a sock in it. But, instead I immersed myself in PalmChess and Dopewars as usual.

It hasn’t gotten that bad out here in the Maryland suburbs (yet…), yet I have the pheer…

stem cell sources
Not too long after the House of Lords made a momentous decision to allow certain limited forms of research using human embryos as stem cell sources, a British researcher has claimed to have discovered a method to produce stem cells from fully differentiated adult cells. It the method proves to work (and the jury is definitely still out at this point), this is pretty huge. Stem cell based therapies are expected to yield cures for a wide variety of fairly nasty problems. That said, this is “science by press conference” at its worst, and I, for one, smell a rat, given the close timing of the announcements.

Second link via nodalpoint.org

for later…
Tutorials on Perl Object Environment and Perl-GTK.

big brother
1984 is going to need some updating, it seems. The British Home Secretary (at some point I’m going to have to buttonhole one of the Brits at work and find out what the deal is with the various positions in their government, and how they map onto ours) has introduced a bill that would allow police to retain fingerprint and DNA samples of everyone detained by the police — even if the detainee isn’t ever charged with a crime. Civil liberty groups are, to put it mildly, concerned about the consequences of the law, should it be enacted. Jack Straw, Home Secretary, tries to downplay fears with this comparison:

[Straw] said the introduction of closed circuit television in streets and shopping centres had been seen at the time as an attack on civil liberties but was now welcomed by the public.

Watch your step, folks, Slippery slope ahead…

no broadband for you!
And at this point, after hearing countless horror stories about DSL installs from hell, as well as subsequent bad service, I’m not too sure I’m missing out on anything. It’s gotten so bad that Verizon is getting sued. (There’s also a story at the Reg.) Gosh, I guess changing the name of the company didn’t help with the perception that they’re a bunch of clueless lusers, did it?

why it’s good to be a woman
Or at least one reason. (Note: horribly sexist (or is it sex-positive?) humor behind that link…)

Blog rolling
First, the final vote form for the Bloggies is up. I voted in the first round; I’m a bit annoyed that more of my picks didn’t make it into the finals, but whadya gonna do?

Second, a bit of feedback on Lyn’s latest journal entry: I’m exactly the opposite. I fear and hate the dentist, but going to the eye doctor doesn’t faze me at all. I think Lyn might have had a mixture of good and bad fortune: she got one of the few bad eye doctors as a child, but one of the few good dentists. My childhood eye doctor, in contrast, was wonderful — actually, every eye doctor I’ve ever seen has been wonderful; my childhood dentist, I suspect, had a sideline in strangling puppies, or something. The man was evil. I’ve never been to a dentist that bad since, but whenever I go to see a new one, I approach him or her with the picture of that first dentist in the back of my mind…urg, must stop typing now, starting to get upset…

site meta
The minor tweaks to the design are due to a bit of prodding by Paul Nagai; thanks for the feedback, Paul, and for getting me off my butt to fix the problems. New logo is my attempt to produce a picture of what a “genehack” actually looks like; please feel free to laugh.

slagging off biochemists
Heh. Check out this Nodalpoint article. 8^)=

Well, I thought it was funny.

Oh, $DEITY. DA prosecutes mom who gave 13-year-old son condoms. I don’t even know where to start with this one — I just hope that District Attorney is an elected position in that county.

(Link via Al.)

be prepared
The always-useful Reg has some guidelines covering Federal search and seizure of computer equipment. Nothing too startling — don’t consent to warrent-less searches, encrypt everything (especially if you share a computer with other people), and remove any naughty bits (or bits that might look naughty) before you send it out to the repair shop.

think different
Nice article on thinking creatively. I need to work on developing some of those habits…

they hadda pick the worm
O’Reilly is has a bioinformatics book coming out soon. I’m not thrilled with the cover animal choice 8^)=, but I am pretty excited about getting my hands on this one. If anybody from ORA happens to be reading this, I’d be happy to provide technical proofing or peer review for this volume.

minor meta
As I discussed yesterday, I started updating my Advogato diary. First entry is pretty lame; hopefully they’ll get better. One of these days, I’ll put up a more permanent link around here, but I thought I’d mention it in case anybody out there has an obsessive need to read my meta stuff.

rip factory

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Busy, busy, busy. I can already tell that I’ve got a chock-full few months ahead. I give group meeting next week, so I need to get the stuff I’m working on to the next level, so I’ll have something interesting to talk about. I’m supposed to give a little talk Tuesday in our journal club on the FASTA and BLAST sequence alignment algorithms. In about a week, it’s my turn to lead the discussion in my C++ study group. I’m leading a Perl study group, which will be working through the Llama over the next couple of months. I’m teaching a couple of classes in my boss’s bioinformatics course. Oh yah, and I’ve got a couple of research projects that I’m supposed to be thinking about and working on.

And that’s just the work stuff in my life — I really want to kick the BOP project into gear. I might be doing some volunteer stuff for bioinformatics.org. I’m going to be at the DCLUG booth for at least one day during a local computer show. I’m going to be in a book club that’s starting up. I started working out semi-regularly. And I’d like to be updating here more than once a week.


disease in context
Review of a promising looking book that advances the theory that germs may have a lot more to do with human disease than we think. The real problem is that bio-scientists are generally trained to think reductionistically, to isolate things down to the smallest possible system that displays a behavior of interest. That means we miss a lot of interesting stuff happening at the interface between different organisms.

Rash prediction of the day: Just as the web and peer-to-peer interactions are making people realize that (to steal a phrase) the network is the computer, one of the themes of biology over the next few decades is going to be interactions, between organisms, between genomes, and between proteins. You heard it here first.

do what you love
The most inspiring people (for me) are those doing something that they love to do, because they love to do it. Salon has an interview with one of those people, Ian Mackaye.

Link via snowdeal.org/ex machina

more gmo noise
The anti-GMO-foodstuff backlash is starting. Example 1: an editorial from the (apparently neo-conservative) Competitive Enterprise Institute. Makes a good point or two, but also says some stuff I’m going to quibble with. First, this statement:

GM is merely an extension, or refinement, of less precise and predictable techniques for genetically improved products with which consumers and government regulators have long been both familiar and comfortable.

This is a slightly modified version of the “genetic engineering doesn’t do anything that plant breeders haven’t been doing for centuries — it just does it in a more precise and faster way” argument. That might have been true at one point, but it’s currently not the case. For example, plant breeders would have been hard pressed to come up with a way to cross corn and bacteria in order to produce the StarLink variety that’s caused so much recent controversy.

Second point, from the article’s conclusion:

Rather than punishing those who develop and market insect-resistant, chemical pesticide-replacing, low-fungal-toxin, potentially more healthful corn, we need to regulate as science and common sense dictate.

Exactly what isn’t common sensical or scientifically dictated in the way the GMO foodstuff issue has been handled? I’m all for using all the technology at hand to attempt to solve the food problems we’re facing (which aren’t just pesticide-related, by the way, but also include things like food supply, period, in many parts of the world), but we’re not yet at the point where we need to rush anything — especially when all the calls for faster testing and less oversight come from the groups wanting to sell the stuff, rather than those who want to buy it.

referrer log gazing
Meta-blogging proceeds to the next level with borrowed blogs. Of course, I think I’m meta-meta-blogging, just by posting this. Whee.

more stuff i wish i had time to help with
Reefknot looks cool (and it’s a Skud-ly project, so it’s got cred out the wazoo). Maybe I’ll just lurk the mailing list for awhile — that can’t hurt, can it?

Oh, and there are draft versions of a bioperl tutorial in the project’s CVS server. Maybe once I get the newbies at work through the Llama, we can do a week or two on bioperl stuff…that might be the motivation I need to get my ass into gear and learn this stuff.

eat beef?
Absolutely stunning review of the recently finalized British government inquiry into the BSE crisis.

(Major Genehack points, and tons of valuable weblog cred to the first person to email me with an explanation of the review’s title, and how it relates to my next point.)

Given the recent spread of BSE onto the Continent, it might be time to start thinking about whether this is the next HIV/AIDS. Long incubation times, devastating disease end-point, complete lack of treatment options. (Boy, I bet the vegans in the audience are having a good laugh right now.)

Idea for the biotechies reading this: prion-protein knock-out cows (and chickens, and pigs, and sheep…) Cow cloning is old hat at this point. Finding the prion protein in bovines (assuming that’s not already done) should be trivial. Knocking it out will be the tough point, but it parallelizes nicely, and it might be possible to automate large portions of it. Evidence from mouse suggests that whatever the protein does, it’s not essential for a relatively normal lifespan — and we don’t really care if our cows are more stupid or not. Bonus: the end product is highly patentable under current US law, and if you angle it right, you can get a total market lock on prion-protein-minus livestock. Hop to it; it’s free for the taking, although I wouldn’t turn down a beer or something once you get to market.

Guess I have to mention that a genetically modified primate was unveiled last week. Fairly bogus, if you ask me, in a “the operation was a success but the patient died” kind of way. The inserted gene isn’t being expressed (and the point of putting genes into critters, generally, is to express them in those critters), and the technique that was used to do the insertion (retroviral vectors) is recognized as having problems that make it highly unsuitable for “serious” work (i.e., gene therapy).

doubleplus ungood
NIH Negotiating with Celera for Access to Celera’s Database. Never mind that we (in the taxpayer sense) would be paying for access to stuff that’s already mostly available for free. Never mind that the money that will be spent on the database subscription could be plowed back into improving those already-available free resources, and educating researchers how to use them, probably producing more long-lasting benefits to the public. We’re going to pay for access, because that’s the way the system works:

Some scientists at the NIH are uncomfortable with this arrangement, but many NIH officials don’t see any problem in it, according to Science . ” We do it all the time” with scientific journals, Steven Hyman, director of the National Institute of Mental Health, told Science . ” We pay for the research, we pay for publication costs, and then we pay for the journal subscription for our scientists. We do it without complaining…”

Maybe the right solution, Dr. Hyman, is not to roll over everytime the school bully asks for your lunch money, but instead to start fighting back…

speaking of fighting back
Here’s a short guide on copyrighting your own DNA. This is almost certainly not going to hold up in court, but it’s kind of a neat idea, and I imagine it’s a pretty potent educational exercise. It also sounds like a good reason to have a theme party. 8^)=

Guide to GNU Privacy Guard (GPG) over at UnixReview.com.

actions and consequences
Some good words over at Lilo’s Advogato diary:

We are rapidly reaching a fork in the road. If we go in one direction, human beings will either have more freedom to communicate than they’ve ever had; if we go in the other, they’ll have less freedom of all sorts than any of them have now. Open communication is a powerful protection for human freedom, and has been utterly necessary to the scientific and technical progress the human species has made so far. The Internet depends on open communication. But such communication is more and more clearly inconsistent with the rights of a small number of extremely large organizations to make money from the sale and resale of copyrighted material.

I really should start using the diary part of my Advogato account….

playing hooky
Oh, the things I have to do — but first a little procrastination blog update…

the gene is dead?
Interesting review of Evelyn Fox Keller’s The Century of the Gene. Great — like I really needed more stuff to read!

Say, if someone reading this is thinking about organizing a book club, this might make a good selection at some point. Wink, wink.

somebody needs a whack with the clue stick
Caleb Carr, who you might remember as the author of The Alienist and The Angel of Darkness, is the subject of a Salon interview. It starts out okay; some of his points actually resemble those made by geek-god Neal Stephenson in In the Beginning Was the Command Line — but then he veers wildly off course. He starts with the implicit, wildly erroneous, and yet all too common assumption that the Internet equals the Web, and moreover, that the United States government is going to (somehow) be able to control all the content on the ‘Net. Hey, Caleb, where the hell do you think all those servers whose names end in ‘.cn’ are, anyway? (Hint for Caleb: it’s not Connecticut.) Carr then proceeds to build a house of cards on this false foundation, in which he envisions schemes like licensing ‘Net users (to stop the pedophiles, and presumably, to protect the chiiiildrrrruuuunnn) and having the FedGov harass Matt Drudge into shutting down his web site — for the good of the intellectual health of the country. (No, really, I’m serious — see page 4, paragraph 3. I can’t make shit like this up.)

And why would we want to do this? Because this is the better of the two alternatives that Carr can envision — the other one has corporations controlling everything. How this would be different than government controlling everything isn’t really made clear, although he mentions that government control is preferable because the government is (at least technically) responsible to the voters. Of course, corporations are (at least technically) responsible to the states that issued their articles of incorporation, i.e., the people; that hasn’t seemed to slow them down too much.

Anyway, read the interview, spot the crap spots, laugh, poke fun, etc. Kill this meme, please.

speaking of memes
Here’s another that I’m trying to start: If the 1990s were supposed to make the 1960s look like the 1950s, I’m predicting that the 2000s are going to make the 1950s look like the 1960s.

Pass that one along, won’tcha?

okay, time to do a bit of real work…
…before I stagger off to bed. See you kids later on in the week!

yah, more frequent updates, that’s the ticket…
Gonna be a long one today, I think. I really need to work on doing this every night, instead of storing it all up and then exploding…

New design, too, as you might have noticed. 8^)= Let me know about any issues.

just not getting it
I figured we were going to see some crazy ideas as the advertising-funded model broke down, but I didn’t see this coming: pay to link schemes. Here’s hoping this one dies a quick, painful death.

speaking of crazy ideas
Sounds like the Blogger kids have gotten enough scratch from their IPB (Initial Public Begging) to upgrade a server or two. Wouldn’t it be ironic if the most successful funding model on the web turns out to be the donation-driven one that public television and radio have been using for years?

I might be inclined to rant about some of the bitching I’ve seen about Pyra’s request for donations, but Al said it better.

I haven’t made a donation yet, cuz I don’t use PayPal, but I am going to mail a check tomorrow. I don’t use Blogger myself, but I read and enjoy the sites of people that do, so I’m going to contribute.

Oh, and a note to Blogger users — it might be in your best interest to let the world know what tools you’re using, just so people realize how important the continued availability of Blogger is.

also not getting it
It the “continued struggle to control what you do” department, the Register offers up Everything you ever wanted to know about CPRM. If CPRM doesn’t mean anything to you, you should definitely have a look at that link.

link graveyard
This probably won’t surprise anybody who has tried to get links of weblog archives, but link rot is becoming a serious issue in academic bibliographies. Yet another reason why a central repository for “published” scientific information, like PubMedCentral, is critical for the future of research and academic inquiry.

more porn
Last week I got a thoughtful email from Seth Golub about my Am I Porn or Not? scheme. I finally got around to replying to him today, and about two minutes later, I got an email from him saying that he had posted his email on his site. So, here’s my reply (edited somewhat from the form I sent to him:

Seth> It's not that simple, unfortunately.  Humans are able to spot porn,
Seth> but it's not just because of rules we know.  We also have systems for
Seth> extracting complex high level information from images.  We can look at
Seth> a picture and know whether it contains people or people-like things
Seth> and can easily recognize their poses, expressions, and situations.
Yah, I realize that it's not that simple. The idea was (at least
partially) intended to be a bit tongue-in-cheek. Alternatively, you
could argue by the time that enough data has been collected, there
might be some sort of conceptual break-through in computer vision
and/or expert systems design, so that it _will_ be possible to process
high-level rules out of the data.
On the gripping hand, the one thing that I consider the biggest
problem (which nobody has mentioned yet) is that you're relying on
humans to build the initial dataset -- and there are people out there
who would intentionally (for a variety of reasons) input erroneous
data. In fact, since 'porn' is at least partially a social construct,
different people with different backgrounds are going to have
different ideas of what 'porn' constitutes. To do this right, you'll
need to track demographic info about participants, and correlate that
with their choices about what is 'porn' and what isn't. 
Seth> David Forsyth, an associate professor at Berkeley, has published
Seth> several papers on his research into automatically detecting naked
Seth> people in images.
This sort of thing makes me somewhat nervous (not nervous that the
research is being done, but because it's all too easy to see it being
mis-applied). Naked people != porn; sometimes naked people == art, and
sometimes people in porn are completely clothed. As I said above, what
you consider porn is very much a function of your socialization and
your individual sexuality, and I think extracting abstract rules out
of that mess is going to be very, very difficult. 
What I was sort of talking about trying to do would involve the
development of some sort of heuristic; it wouldn't be right all the
time, but it might be better than what we've currently got.

Seth did send me a reply to the above, but I’m not comfortable posting it here without explicit permission; I’m pretty sure it’ll appear on aigeek soon.

linux newbies, heads up!
Helped a friend get some stuff set up on his Linux box this weekend. He’d done most of the hard stuff, but was having an issue or two with X and PPP, which I was able to solve. He might find these 10 tips useful, and you might too, if you’re just getting started out.

distributed itch scratching
Ian Clarke has a word or two for people bitching about Freenet’s ease of use. I think this sort of “piss off or pitch in” message is going to become increasingly more common as use of Open Source software spreads. People need to understand that being given a gift doesn’t place the giver under any obligation to the recipient; unfortunately, most people have to be publicly spanked before this sinks in.

dsl deadbeats
Looks like the telco strategy of providing crap service to DSL resellers is starting to yield fruit: two DSL resellers are shutting down. This indirectly hurts Covad, because they’re not getting paid for the service they provided, and it directly benefits the telcos, who would like nothing better if all the third-party providers would just go away. Boy, nothing like market forces at work, eh?

right/wrong blindness
A company has purchased a patent on the human genes for red-green color blindness. Aside from my often-stated opposition to gene patenting in general, there’s one glaring problem: the title of the press release: “Medical College of Wisconsin Awards ColorMax Patent for Human Color Genes”. News flash: the US Patent Office awards patents. What actually happened here was that the Medical College of Wisconsin sold the patent to this company.

your biological future
Red Herring has an interview with Leroy Hood, one of the pioneers of modern biology. He says some interesting stuff, but the interviewer didn’t ask any of the tough questions. I would have liked to hear Hood’s viewpoints on gene patents and data release. For example, Hood lists four major impacts of the human genome project, but he doesn’t mention that all of these impacts were dependent on the open release of data from the project, a practice at odds with the way most biotechs do business.

(Link via the always top-notch snowdeal.org {bio,medical} informatics.)

Breaching the Web has submerged. Thanks for the links, Kris, and hurry back.

site meta
Far more than you probably wanted to know on the 2000 Genehack stats and search terms wrap-up.

back up to speed >>> Welcome to the real new millennium. Hope you had a good time ringing it in; I certainly did.

Since my last update, I’ve spent basically no time web surfing (hence the lack of links in this update). Dave, my gradual school buddy, was in town for a couple of days, so I did spend a lot of time hanging out with him. We saw Crouching Tiger, Hidden Dragon, we did the New Year’s Eve thing, we went to Ikea (and ran into a ratbastard). It was good.

year end thoughts >>> This was a good year. I finally finished gradual school, and I think getting my Ph.D. has to be good for several hundred points in the ‘win’ column. Getting a kick-ass post-doc and moving to a great city hasn’t hurt a bit, either. I’ve met a lot of new people, made some new friends, and in general have come out of the asocial shell I was in for the past couple of years. I’m a lot less angry than I have been, and I think that’s a good thing.

My marriage, even after seven and a half years, continues to get better. Lor continues to complete me, and I think I’m starting to complete her more and more as well. I can’t imagine where I’d be without her, or how much poorer my life would be if she wasn’t in it.

I’m not usually a resolution type of guy, but there are a few things I’d like to try to improve on in 2001. I figure if I list them here, maybe I’ll have a better chance of following through on some of them.

Exercise more/lose weight: I like to drink beer. I’m not into any activities that require lots of running or jumping around. I have a job where I sit on my ass all day (don’t get me wrong, I love what I do, but coding just doesn’t burn all that many calories, eh?). All of these things together mean I’m carrying around a bit more weight than is good for me. Add in a genetic predisposition to hypertension (controlled via meds, but…), and you get a situation where I need to be doing something.

Strive for balance: I have a tendency to get into one thing to the exclusion of others, realize I’m way behind on everything aside from the one thing I’ve been concentrating on, then panic and thrash about wildly trying to catch up. Or, I get really into something then burn out when I’m 75% of the way done with the project. This needs to stop; I need to work on staying caught up with everything equally, all the time. I need to realize when I’m getting to into something and letting other things fall behind. Mostly, I need to maintain focus on projects, and see them through to the end.

Keep learning: One of the reasons I got my current job was because I’d managed to develop some coding skills while picking up a biology doctorate. Not the most common thing to do, but not all that uncommon either. I need to keep looking around for new interesting skills, and keep picking them up — not just computer-related things, either, but biology, math, etc.

Keep blogging: Blogging has been one of the best things I ever started doing. It played a part in me becoming more social, in picking up those new skills, and keeping me informed and opinionated. Sometimes, however, that lack of balance I talked about has caused me to let the blogging slide a bit. Genehack was not as good this year as it was last year; I let myself get into a rut, I started second guessing the content I put up, and I started to care a bit too much about whether people would like the things I wanted to say. In the coming year, I want to update more frequently, and I don’t want to worry as much about the content I’m putting up.

Be a more active presence in the blog world: Once upon a time, I was all over various weblogging fora, I commented on discussion boards, and I dropped people email when I liked something they said, or even when I disagreed with what they said. Due to that lack of balance thing, I’ve let a lot of that stuff slide. I need to find my voice again, and in order to do that, I need to exercise that voice.

Figure out what I want to be when I grow up: I still don’t know what I want to do with the rest of my life. I like my current job, a lot, but it’s definitely a temporary deal. By this time next year, I need to have a very clear idea of where I want to go, and what I want to do — stay in the DC/Balto area, or move again; stay in science (either industry or government — academia is out, I’m sure about that) or jump ship and try my hand at coding or PFYing.

Anyway, that’s what I’m looking to do in the days ahead; we’ll see how it actually goes. I’ll catch up with you kids later this week.

(PS: If you’ve got any ideas on how I could accomplish some of these goals, or if you just want to jeer at the likelihood of me actually following through on them, drop me a line at jacobs@genehack.org.)