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 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 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

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….

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