watching the detectives

Update to an earlier post; title cribbed from Verities, who has (have?) been on Fact Check’s case about the latter’s Bush AWOL coverage (with an update here). I’ve sent the FactCheck editor a note, so we’ll see whether they take notice of an upstart blogger (that’s you, Verities, in case you’re reading this!).
While I’m at it, here are two more potential occupants of the no spin zone:
Media For Democracy 2004 calls itself “a non-partisan citizens’ initiative to monitor mainstream news coverage of the 2004 elections and advocate standards of reporting that are more democratic and issues-oriented”. It’s email-only; what’s so special about these “alerts” that they can’t publish them to the web? There’s not much on the about page; if this is “a grassroots citizens initiative” (they keep saying it, so it must be true), why will no one put their name to it? The executive director of (who are also pretty evasive about who they are) doesn’t count.
Project Vote Smart, on the other hand, looks good. A 501(c)(3) non-profit that doesn’t accept donations from “lobbyists, governmental organizations, corporations, businesses or special interests” and is funded “exclusively through private donations by over 45,000 members, and grants from private philanthropic foundations, including the Carnegie, Ford, Pew and Revson Foundations”, they do not “lobby for, support or oppose any candidate, position or issue”.

Project Vote Smart, a citizen’s organization, has developed a Voter’s Self-Defense system to provide you with the necessary tools to self-govern effectively: abundant, accurate, unbiased and relevant information. As a national library of factual information, Project Vote Smart covers your candidates and elected officials in five basic categories: biographical information, issue positions, voting records, campaign finances and interest group ratings.

There’s that “citizen’s organization” again, but this group means it. The site has an enormous amount of information available; I’ll be making use of the introduction to US government in particular.

dean ain’t done yet

For the record, and for what it’s worth, I disagree with my net buddy Stavros, and agree with the spousal unit on this one.
Update: Doc Searls has a useful roundup of opinions on the Dean thing. Read ’em all. I’ll just point out that at the time of writing Dean is in fact winning the primary race as I understand it1. Stavros has responded in fine style to my remarks, so you can play along over there if you’re interested.
1For those watching in bewilderment from across various seas: brief explanations of the primary system can be found here and here, and more than you ever wanted to know is available here.

ooh, shiny

sunflowers by van Gogh How rich art is; if one can only remember what one has seen, one is never without food for thought or truly lonely, never alone.    — Vincent to Theo, 1878
The Vincent van Gogh Gallery is the site for van Gogh online. It’s endorsed by the van Gogh Museum (<brag> I’ve been there! </brag>) and features, well, everything: 2200 images and 874 letters, every surviving thing that Vincent ever painted, sketched or wrote. Chronological and subject matter indices, a canonical works gallery, commentary and analysis, biography, an online forum and more, available in thirteen languages on a clean, well designed site. Bravo, Mr Brooks.

small pendant by artist Sandra Marchewaart-o-mat vending machine The Art*o*mat is just plain cool. In 1997, Clark Whittington converted a recently-banned cigarette vending machine to sell his black&white photos for $1 each. Today, his company Artists in Cellophane operates 60 art vending machines in 18 states, featuring the work of over 300 artists from 10 different countries. I note that there are no artomats in Oregon yet; I wonder what it costs to sponsor one?
Way cool update: the artist whose pendant is shown here, Sandra Marchewa, showed up in comments. You can see more of her art here. While I’m updating, it appears there’s now an Art*o*mat in Oregon, at Lane Community College — but still none in Portland…

a reliable source of good news

One of the best things about being a research scientist is that there is always good news to be had from somewhere in my own field or one close by. It always cheers me up to be reminded that the knowledge base is growing every day.

electron micrograph of SIV electron micrograph of SIV Closest look yet at HIV surface: a Florida State University team has used electron tomography to put together the most detailed images ever seen of the surface of HIV and SIV (S = “simian”) particles. The pictures on the right show engineered SIV expressing high levels of the surface protein gp120 (indicated by arrows), from above (right) and from the side (far right). The propeller-like shape of the gp120 trimer can be clearly seen in the top-down view and again in the close-up below (also from above). electron micrograph of gp120 trimer electron micrograph of HIV1 The final picture shows a wild type HIV particle, showing the much lower density of gp120 (which came as a surprise; most researchers thought it would look like the SIV pictures). The white bar in the HIV picture is 100 nm, about 1/500th the thickness of a human hair; the same scale applies to the SIV pictures.

This is neat, but it isn’t new: FRET (fluorescence resonance energy transfer) has been around for a while. The basic idea is to take two fluorescent molecules whose excitation and emission spectra overlap in such a way as to make it possible to excite one using the emission of the other. If you put energy in to the system at the lower excitation frequency and get back light at the higher emission frequency, it proves that the two molecules are in close contact. If you’ve attached one to protein A and one to protein B, wherever you see the higher frequency emission proteins A and B must be very close together (interacting); you can do this in a living cell to see when and where A and B interact. What’s new in this study is that the two fluorophores have been attached to opposite ends of a single molecule which happens to fold differently in its active and inactive states. That’s neat, because it allows you to monitor the activation state of the protein by monitoring the emission from the fluorophores. It’s true that this is “the first probe of its kind that allows us to actually see in a living system where, when and how proteins are activated”, but only because that’s very narrowly defined, and the authors do not claim (as the article does) that it’s an entirely new kind of probe. Bad reporter, no vodka.

Classic science; first, some background. Listeria monocytogenes is a most unpleasant organism, one of the most common causes of bacterial meningitis. Most bacteria, when taken up by specialized immune cells — professional eaters-of-foreign-bodies called macrophages — find themselves trapped in a small bubble of membrane called a phagosome, in which they are rapidly killed by acidification and digestive enzymes. Listeria, though, has found a way to break out of the phagosome, using a phospholipase called listeriolysin O. Macrophages are also professional antigen-presenting cells, meaning that they present foreign proteins to other cells of the immune system, enabling those cells to mount a specific response. Macrophages typically present proteins taken up from outside themselves (like bacterial proteins) to T-helper cells, which act to drive humoral (antibody-based) immunity. When what you want is to drive cellular immunity, macrophages can do that too, but usually the protein of interest has to be synthesized within the macrophage (like a viral protein). One of the long-standing problems in vaccinology has been how to get a foreign protein which is taken up from outside the cell (your vaccine) to be presented like a viral protein, as though it came from within the cell, so as to get a cellular immune response to back up the antibody response, which is often insufficient on its own.
So, what Lee’s team has done is to make a vaccine formulation containing their vaccine target protein together with listeriolysin O. When liposomes containing both proteins are taken up by cells, the listeriolysin acts to release the vaccine protein into the cytosol of the cell, at which point it can enter the presentation pathway normally reserved for proteins made within the cell. In other words, Lee and co. have taken the method that Listeria uses to get safely out of the phagosome, and used it to get a vaccine protein out of the phagosome and into a cellular pathway that has until now been very difficult to access. Beautiful, elegant work. They showed, using a mouse viral meningitis model, that liposomes containing listeriolysin plus viral protein elicited a stronger cellular immune response than liposomes containing viral protein alone without antagonising the antibody response, and that this dual response was sufficient to provide sterile immunity against a challenge that killed half of the viral-protein-only group and 100% of unvaccinated controls. Inclusion of listeriolysin in vaccine formulations may provide a way to boost the levels of protection that can be obtained against agents that attack from within a cell, notably viral infections (SARS, HIV, Ebola, ‘flu…) and cancer.
(You can read the whole paper for this one; because the study was reported in the first issue of a new journal (Molecular Pharmaceuticals) it’s available online as a free sample).

colorless green ideas syndicate furiously

Have I mentioned how much I love Bloglines? I just sent them this via the contact form:

Dear Bloglines,
I would like to be able to see the public subscriptions of people whose blogs I like. Currently, this requires knowing whether they have a bloglines account and, if so, what name they signed up with. Would it be possible to annotate each blog’s entry in the directory with a link to the owner’s bloglines account, if they have one?
Also, when the ads start, please please please make the paid service ad-free. I’ll happily pay a reasonable fee for bloglines, which I think is the best thing since sliced bread, but not if I can’t get rid of ads.

I’ll update this post when I get a reply.
One other issue, not under Bloglines’ control: too many people have crappy feeds that show only the first few words, or just a headline. When I am trying to keep up with 126 sites, I want to be able to skim, and headlines-only feeds make that difficult. That’s what the new “full text feeds please” folder in my bloglines account is for: I’ll be quarantining those sites for now, and probably only checking them “by hand” once a week or so.
(The post title? “Full text feeds please” reminded me of Chomsky’s famous phrase. Perhaps you had to be there me.)
Update: it’s been pointed out to me that there are bandwidth issues with providing full feeds (although I think those are minimal if you only feed text), and, more importantly, that presentation is stripped bare in an RDF format. Full-text feeds are nice, but I am also happy with enough of an excerpt to give me a good sense of the post. I didn’t mean to demand that other people’s designs should be subordinate to my convenience, so I’ve changed the folder title to “longer excerpts please”, but I’ve let the post stand to remind me what happens when I post without sufficient thought. (I generally won’t delete anything, and I’ll always make original versions available.)
Update the second: Bloglines’ reply to my email:

We’ll be adding a directory of public feeds soon. And we currently are planning on having a no-ads version available when we do start running ads.

grab bag

I have pretty much given up on keeping my bookmarks organised on a day-to-day basis; I keep a few handy reference links that I use regularly (like Merriam-Webster online) and just use Google to find anything else I want from time to time (say, a currency or temperature scale converter). Other than that, I keep a toolbar folder into which I dump all the interesting links that come my way, and every now and then I sort those links into an organised set of folders. It’s cleanup time again, so here are a couple of web goodies:
Winning greater influence for science. Daniel Yankelovich argues that there is an unspoken agreement between science and society which provides science with a “separation from involvement with goals, values, and institutions other than its own”, and that

This “social contract” has allowed science to pursue long-term fundamental questions and to build slowly on the basis of its new knowledge. Science has been able to do this even in the context of a society such as ours, which in most domains is impatient, excessively pragmatic, and thinks only in the short term. But this same social contract is responsible for the widening disparity between the sophistication of our science and the relatively primitive state of our social and political relationships.

Most scientists of my acquaintance (and I am guilty of this too) treat the gulf between the public and our “ivory towers” the same way as everyone treats the weather: we complain, but we do nothing. Yankelovich at least suggests a model for dealing with the problem.
On a related note, Eugene Goodheart’s essay Imperial Science takes on the “two cultures” view of CP Snow and his inheritors EO Wilson, Jared Diamond and Richard Dawkins. I’m probably a little more sympathetic to Wilson’s side of things than Goodheart is, but the essay is a welcome thorn in the side of “sociobiology”, that misbegotten offshoot of evolutionary biology which attempts to reduce human lives to formulae and ape-behaviours.

TANSTAAFL; or, in which his drowning is mercifully quick

Iain J Coleman has a good post up on Fistful of Euros highlighting this paper by UCDavis economist Peter Lindert (that Carlos mentioned in this Electrolite comment thread about this NYT article about the working poor in America). See what I mean about conversations? Anyway, the paper describes why a high-spending welfare state doesn’t depress GDP (viz., “looks like a free lunch” but isn’t). Here’s Iain’s summary, emphasis mine:

… social spending is good for personal productivity, and democracy is effective in ensuring that real-world governments avoid the costly mistakes that anti-welfare theorists assume. Apart from illustrating the dangers of hand-waving economic arguments, this tells us that the choice between a European-style high-welfare state, and a US-style low-welfare state, has nothing to do with promoting economic growth and is simply a matter of which kind of society we find more pleasant to live in.

I’d better confess that I haven’t read the paper yet and will likely be out of my depth if I do, the dismal science being mostly Martian (or worse, mathematics) to me; but that’s why I read blogs, and the excerpt makes intuitive sense to me. I certainly know which kind of society I prefer; besides, “growth for the sake of growth is the ideology of the cancer cell”1. I keep hearing that modern economic theory is predicated on infinite growth, but that can’t be right: it’s too crazy. Nonetheless, Economic Growth does seem to have become some kind of modern deity, Mammon’s offsider, and it’s not obvious to me that economic growth is intrinsically good, or that the opposite of growth is shrinkage (or stagnation). Why is it bad if we don’t make more, build more, spend more, own more crap this year than we did last year? What has happened to the concept of “enough”, as in, “I have enough, I don’t need more possessions or security, I can afford to pay into a pool of common good from which those in need can draw”? For what kind of person is a bigger television more important than that the hungry should have food?
But as I said, I’m probably just out of my depth.
1Edward Abbey
Update: fixed the link to the Electrolite thread.

i read everything on the web so you don’t have to

Happy second birthday (for yesterday) to creatures in my head.
Eliot Gelwan is right on the money again, this time about the anti-SSRI backlash. If you have reason to know what SSRI stands for (and even if you don’t), you should be reading Eliot regularly.
Mark Liberman plays interesting sociolinguistic search engine games (see also this earlier post) at Language Log. Personally, I dislike the use of “refute” to mean “deny”, and I strongly dislike the “”refute/refutes/refuted that” construct, but (as Mark points out) those are side issues. (Don’t take me for one of those barbaric descriptivists though!) What’s really interesting is the kind of analyses that a huge body of searchable text makes possible.
Filtering is a life-raft on the sea of information, and taste tribes are emerging as one of the best filtering mechanisms available (link-fu props to Jerry Kindall). I’m a bit surprised that Joshua Ellis didn’t mention by name (and that he did mention the dismal Blogshares) but it’s a good essay. As I’ve mentioned before, I think that trackback and syndication and metablogging tools are turning blogs into a conversational medium of sorts, out of which it is easy to build your own taste tribes. I note that Ellis’ sense of the term seems to be more interactive than mine — superspecialrock versus Bloglines — so maybe I need a different term for solitary geeks assembling a virtual panel of cultural taste-testers. Whichever way you look at it, I think it’s safe to ignore Xeni’s so-hip-it-hurts whining about “that post-Friendster/Tribe/LinkedIn/SixDegrees oh-god-not-again feeling” on the otherwise excellent Boing Boing. Taste tribes, and applications that pander to them, are here to stay.
Skippy at The American Street points out that CBS, which wouldn’t take‘s “Bush in 30 seconds” ad because they don’t run “issue-oriented” ads, is planning to run anti-Mary Jane ads during the Superbowl. He has some addresses if you want to let the rat bastards know that their hypocrisy has not gone unnoticed.
Speaking of rat bastard hypocrites, I am all tingly with Schadenfreude as I note that the American Family Association has had to abandon its “gay marriage” poll because the position they liked lost out by nearly two-to-one. Hat tip to Atrios, whose “go torture X” memelet probably helped. “Pro-family” my arse.
(via Doc Searls) First the Great Old Ones, now pathogenic microorganisms. When they made a plush Cthulhu, I did not speak up because I was not an Elder God of unspeakable evil…
Via Body and Soul, Obsidian Wings has truly outstanding coverage of the Maher Arar travesty. Arar is a Canadian citizen whom the US gummint deported to Syria so that they could have him tortured. I kid you not. Go read about it; this shit could happen to you next.
If you’re part of the choir and you like being preached to (I am and I do), go read this from Rep. Bernie Sanders (I, VT) (via Dave):

The middle class is collapsing, and we need a fundamental alternative to trickle down economics and unfettered free trade.
We’ve got to raise the minimum wage to a living wage.
We’ve got to renegotiate our disastrous trade policies that have cost us millions of decent paying jobs.
We’ve got to change labor law so that workers can join unions when they want to.
We’ve got to protect the overtime pay that workers have earned.
We’ve got to put people to work building affordable housing, schools, mass transportation, and a sustainable energy system.
Our health care system is disintegrating… we can guarantee health care to all Americans through a single-payer national health care system. […]
Our national priorities are backwards. Instead of giving huge tax breaks to the rich and large corporations, we should provide for the middle class and working families of this country. […]
Environmental degradation is threatening the wellbeing of our planet. We must move to sustainable and nonpolluting forms of energy as well as energy conservation. […]
We must work for world peace, and not U.S. imperial power. […]

This, via Boing Boing and Atrios, is no surprise to me, but I hope it gets tremendous coverage:

Republican staff members of the US Senate Judiciary Commitee infiltrated opposition computer files for a year, monitoring secret strategy memos and periodically passing on copies to the media…

It’s not clear that the thieving bastards in question can be prosecuted, but then the law is an ass.
“You just wrong, and I be tryin’ to right you.” Via pretty much everyone, Margaret Cho is a class act, yo.

das glasperlenspiel

micrograph of 5-micron silica beadsThis could move biology forward in the same way (that is, to the same extent) that PCR did. Chemists at UC Berkely and Lawrence Berkeley National Laboratory have devised a novel method of measuring protein-protein interactions at cell membranes. Microscopic glass beads are coated with artificial membranes in which functional receptor molecules are embedded, and the behaviour of the beads in response to the presence of various binding partners in the surrounding solution is monitored. From the Nature article (vol 427, pp. 139 – 141):

The behaviour of a colloidal system is driven by the pair interaction potential between particles. In the case of membrane-derivatized silica beads, the pair potential is dominated by membrane