The verifier approach is Gordon Rugg's name for the method he used to investigate the 500-year-old mystery of the Voynich manuscript. Turns out the manuscript is probably a hoax, but that was really just a proof-of-concept for Rugg's method of mapping the work that has been done on a problem and locating the gaps in that map. He now has a host of new collaborators with whom to further test and refine the method; I will be watching with interest. If Rugg is right, he may have fathered a field which will alter the structure of the scientific endeavour and dramatically improve the way we think about and approach complex problems.

Student finds rare whale: I mention this story mainly because of one detail that annoyed me. Paleontology student Maggie Hart found a dead Sowerby's beaked whale on a Georgia beach; she photographed it and "collected its skull", and the article goes on to say

Almost nothing is known about the natural history of the Sowerby's beaked whale. They reach a length of approximately 18 feet long, travel in pods of up to 10 and presumably eat small fish and squid.

Presumably? Well, the first half-dozen google hits indicate that at least some of the stranded specimens from which almost all of our knowledge of this species comes were autopsied, and yes they do eat fish and squid; but any and all additional information is clearly useful. Come on Maggie, you've already cut the damn thing's head off, how much worse could it be to open up its stomach and catalogue the contents? (Well, OK, lots worse; but phenol will get that skin right off, and when it grows back it'll hardly stink at all.)

Nef inhibitors: I didn't think terribly highly of this idea when I was working on HIV and I still don't. A UCI team has used phage display to identify small molecules that can disrupt the interaction of the HIV protein nef with the host proteins p53, actin and p56^lck (read the full article here). Granted this is a valid proof-of-concept for small molecule nef inhibitors (and a means of screening for same), but that leaves a few small issues to be resolved:

• contrary to the press release assertion that it's nef's function, the interaction with these cellular ligands is poorly characterised
  
• disruption of the function of any of the host proteins in question is likely to be lethal (indeed, all the compounds identified were highly toxic)
  
• nef-deleted virus is infectious, can cause AIDS (albeit slowly) and can become more virulent, for instance by mutating coreceptor use (see this paper)
  

I don't want to sound too negative here though: I'm a big fan of antiretroviral drug development, because HIV is proving a tough target for vaccine initiatives and vaccines take a very long time to develop. I don't think the ultimate solution to HIV/AIDS is likely to be chemotherapy (for what it's worth, my money's on a combination of chemo and immunotherapy), but drug development can alleviate a tremendous amount of suffering and strongly curb the spread of the virus. A nef inhibitor could certainly slow down disease progression, adding many years to a patient's life, and would probably also reduce the risk of transmission.

I surprised myself by making it all the way through the first of the presidential synchronous press conferences debates without barfing -- although it helped to have nerf balls to throw at the screen. Kerry did very, very well: he had clear answers with specific data, and he kept to a strong, simple core message. Bush got it wrong, here's how, I'll get it right, here's how. Someone in the Dem camp has been watching the Republican success with the press and taking notes. Kerry pushed home the fact that he has been far more consistent than Bush, despite the "flip-flop" theme, and he pushed hard on Bush's weaknesses: no plan for peace, no credibility with erstwhile allies, no action on bin Laden, insufficient support for the troops, allowing nuclear proliferation to accelerate. Bush looked confused and agitated much of the time, and relied on sound-bite nonsequiturs: it's hard work, the world is safer, you've got to be resolute. No matter the question, Bush kept coming back to the same few tired points without even varying the phrases; compared with Kerry's focused theme, it was unsubtle and ineffective. I am more confident than ever that, come November, Bush is a goner.

I have one specific question: Kerry claimed that Bush has cut funding for nuclear nonproliferation work, whereas Bush claimed he has raised it by 35%. Who's right?

Congratulations to L. and L. on the pitter-patter of little hackerfeets.

Beside the block the butcher stands,
a cleaver in each meaty hand,
who flays away the tender skin,
exposing flesh and blood within,
and with an evil grin, begins
to ply a blood-bespattered trade:
with eager eye and shining blade,
trims off gristle, sinew, fat—
the butcher has no use for that—
plucks the entrails, out they go!
Heedless throws the heart away,
along with liver, spleen and brain,
and then begins to break the bones
with mighty overhanded blows,
to make the limp and lifeless form
closer match the current norm.
For this the butcher hacks and rends,
discards with savage glee, and then—
prepared and packaged, skinned and stripped—
sends me back my manuscript.

If you like poetry and related news-y things, you should read Malcolm Davidson's excellent dumbfoundry, where today he excerpts from A Wodehouse Miscellany that worthy's exposition on the alarming spread of poetry. Let me whet your appetite:

In life I was the village smith,
I worked all day
But
I retained the delicacy of my complexion
Because
I worked in the shade of the chestnut tree
Instead of in the sun
Like Nicholas Blodgett, the expressman.
I was large and strong
Because
I went in for physical culture
And deep breathing
And all those stunts.
I had the biggest biceps in Spoon River.

Two new members of the blogroll today, both of them unusual.

Via Chris Mooney, the weblog of the American Bioethics Journal, blog.bioethics.net:

Why is a scholarly journal sponsoring a blog? We're no ordinary journal. The American Journal of Bioethics has from its inception been an experiment in broadening the reach of bioethics. From the day we first met with MIT Press to discuss their ideas for a new bioethics journal, we have been stretching our imaginations. Why not let writers read each other's commentary before it is published, so that a collection of commentaries on a major article reads like a conversation? Why not publish qualitative and even quantitative studies in a journal about bioethics? Why not use the online page of a journal to collect the core set of information about bioethics? Some of our ideas have been flops. We're betting that an "editors' blog" won't be.

Good points all, and I'm glad of an easy way to keep in touch with news and ideas in bioethics. (It's one of my frequent laments that I have a "doctor of philosophy" degree, and was not required to take even one philosophy of science or ethics class; all my learning in those fields has been self directed since I graduated.)

Via Preposterous Universe, 411blog (the service interface is here): a "mechanism whereby a symbiotic relationship between blogging and traditional forms of journalism can be deliberately cultivated". Another of the tirades to which I regularly subject longsuffering friends and relatives concerns the accuracy of science reporting. It seems that every time I see a mainstream media story about a subject I happen to know in some depth, the reporter gets important details wrong -- which does not inspire confidence in stories concerning the many subjects about which I know squat. This (411blog) is an attempt to connect reporters to bona fide experts who are self-selected for an interest in outreach and science communication and who are available on, essentially, a minute-by-minute basis via the web. I hope it succeeds; I'm going to nominate a bunch of folks from my blogroll.

Dear CBS,

there is apparently a campaign under way to get you to sack Dan Rather. Don't do it! Mistakes happen; Dan got punk'd, no one got killed and he owned up -- when will GWB admit even one of his many, far more costly, mistakes? If unscrupulous liar Lisa Myers still has a job, honest Dan should get to keep his.

Don't can Dan!

----

Feedback to CBS via the link at the bottom of this page; the above is the letter I sent them.

(I seem to be recycling a lot of links from the spousal unit lately.)

Media Tenor International claims to be "the world's leading provider of international media content analysis". I can't really judge that claim, but I like their Slant-o-meter because the September 21 edition cheered me up considerably:

It's not clear to me how they derive the numbers; for instance, of 120 statements regarding Crusader Codpiece by ABC news, "the share of negative reports exceeded the share of positive reports by 32.5%". So then

POS + NEG = 120
POS/NEG = 1.325

solves to NEG = 51.6. If NEG = 52, I get POS/NEG = 1.308. But never mind all that maths bollocks, look at the pretty picture! Fox "News" doesn't count, because they are the broadcast arm of the RNC. ABC news is strongly pro-Kerry and even NBC and CBS, despite being "more negative" about Kerry than about Bush, talked more about Bush and so made more negative comments about the Chicken-in-Chief than about THE NEXT PRESIDENT OF THE UNITED STATES OF AMERICA, JOHN F KERRY. Ahem. 'Scuse me.

I would wonder whether there is something to all that whining about "liberal media bias" after all, except if you're talking about Chimpy it's impossible to say much positive without telling outright porkies (like, say, Fox). So maybe the US mass media is showing a teeny bit of spine after all.

(Via the spousal unit's sidebar.)

This may be a bona fide breakthrough in virus detection: a Harvard group has reported specific detection of individual virus particles using silicon nanowires coupled to virus-specific antibodies. The article in Proc Natl Acad Sci is open-access, so anyone can read the whole thing and I don't have to feel bad about swiping their cartoon, which explains the principle at a glance. The authors use simultaneous electrical and light microscopy monitoring of individual nanowires to demonstrate that the changes in conductance are due to binding/unbinding of single virus particles. They show that the duration and magnitude of the conductance changes are characteristic of specific binding events, which are easily distinguished from diffusion events; together with antibody specificity this means that detection is highly selective and the false positive rate extremely low. Multiple viruses (well, at least two, but the system should scale readily) can be detected in parallel in a single sample. These features of the system offer a solution to the problem of antigenic variation that plagues other antibody-based detection methods, since multiple antigens can be targeted simultaneously and molecules other than antibodies, such as cellular virus receptors (e.g. CD4 for HIV), could also be used. The size of the detection units means that multiplex systems will not be physically unwieldy: a tiny array much like a computer chip could contain thousands of different detectors. Virus was detected with similar specificity and selectivity in purified and "unpurified" samples, but the latter just means allantoic fluid so it remains to be demonstrated that the method is robust enough to screen, say, body fluids directly. It's also not clear from the paper what sort of equipment is involved and whether it will adapt readily to fieldwork, though it's basically just a bunch of transistors so I don't imagine it's intrinsically fragile. The authors don't discuss virus quantitation, either, but that would seem to be a relatively straighforward issue (they show that event frequency is directly proportional to virus concentration in one figure).
The extreme sensitivity of the method offers hope of detection in the very early stages of infection. This alone could mean many years and much improved quality of life for millions of HIV patients, since it is much easier to maintain than to rebuild the CD4-positive cell population. Furthermore, very early detection may open a window onto a period of viral vulnerability in which medical intervention will be more effective than in later stages. In addition to detection, the method will be readily applicable to the study of viral binding kinetics and possibly to high-throughput screening for drug discovery. (via Eurekalert)

I think there is a strong possibility of malfeasance in the upcoming US election, particularly in respect of electronic vote counting (or not counting, as the case may be). WorldChanging (also here) and For The Record have good coverage of the background, and you can take action and learn more at Black Box Voting and Verified Voting.

One of the simplest actions voters can take is to use a postal ballot. This may not be necessary where you are, and it's certainly not a good long-term solution, but for many US voters it may be a good way to sidestep, and register dissatisfaction with, e-voting in the upcoming election. Overseas Vote 2004 is a good way to obtain the necessary paperwork and check the registration deadlines. Beware of state laws regarding eligibility for postal ballots, though: if your vote can be challenged, it will be challenged if the election is at all close.

While I'm at it, don't forget Project Vote Smart, one of the best political resources online.

Don't screw this up, America.

Oh my. Ask MetaFilter goes where few others would dare.

Sometimes, you just gotta do the experiment, even if it means a swimming pool full of snot.

This site has GM MIDI files of algorithmic music determined by mathematics and the musical preferences of a human. Insert obligatory Philip Glass joke. (via BoingBoing, which probably should carry a NSFW label these days)

Growth industry: New Zealand scientist Christopher Anderson is sowing corn and canola and reaping gold, mercury and other toxic contaminants from small-scale mines. Metals recovered from the plants are used to pay for cleanup and local programs to combat poverty. (via jwz)

Of, like, pertaining to, resulting from, resembling. Be sure to check out the rest of the Phrontistery as well. (via kindall)

What with all the Patriot Act insanity going around, amateur photographers might want to carry the Photographer's Bust Card with them. Especially if they're, you know, brown.

For the nerd who has everything: cufflinks with embedded instrumentation. (also via BoingBoing)

Graham's right, this animated gif is hypnotic.

Ever notice how things that "everybody knows" are usually wrong? Here's another one (from here, concerning this paper):

It is an established fact that 98 percent of the DNA, or the code of life, is exactly the same between humans and chimpanzees. So the key to what it means to be human resides in that other 2 percent.

Argh. Actually, it's an established fact that this meme, or trope, or whatever you want to call it, is bollocks. Individual human genomes vary by about 0.08% at the single-nucleotide level, whereas human and chimpanzee genomes differ by about 1-1.5% at the same level. This is misleading, because single-nucleotide comparison means aligning comparable sequences base-by-base and counting the differences. In order to line up the two sequences in the first place, however, you have to introduce gaps into each sequence to allow for insertions and deletions. Like this:

actgccggctaac-----gtaccTgtcaactggcatgcatgcaagtacc
actgccggcGaacggtccgtacccgtcaac--gcatgAatgcaagtacc

In this made-up example, three bases out of fifty are different (6%) but the gaps account for a further 7 bases' worth of difference (14%). Do this with enough regions of each genome to get a representative sample and you can estimate the degree of sequence identity between the two genomes. Of the optimally-aligned sections of our genomes, we share about 98.5-99% with chimps, but taking the gaps into account produces a rather lower figure of about 95%, something Roy Britten showed in 2002.

What both figures overlook, and tend to obscure, is differences in the organization of large sections of the genetic information: duplications, inversions, recombinations between and within chromosomes, insertions of retroviral sequences, and so on. I wrote earlier about a method that allows us to measure such differences. Variation between individual humans on this scale seems to run at about 1.5% (cf. 0.08% at the nucleotide level); it will be interesting to see a ROMA-based comparison between humans and chimps. It is on this organisational scale that the real clues to the inscrutable Decree will be found.

Corner Seat

Suspended in a moving night
The face in the reflected train
Looks at first sight as self-assured
As your own face—But look again:

Windows between you and the world
Keep out the cold, keep out the fright;
Then why does your reflection seem
So lonely in the moving night?

Museums

Museums offer us, running from among the buses,
A centrally heated refuge, parquet floors and sarcophaguses,
Into whose tall fake porches we hurry without a sound
Like a beetle under a brick that lies, useless, on the ground.
Warmed and cajoled by the silence the cowed cypher revives,
Mirrors himself in the cases of pots, paces himself by marble lives,
Makes believe it was he that was the glory that was Rome,
Soft on his cheek the nimbus of other people's martyrdom,
And then returns to the street, his mind an arena where sprawls
Any number of consumptive Keatses and dying Gauls.

Aubade

Having bitten on life like a sharp apple
Or, playing it like a fish, been happy,

Having felt with fingers that the sky is blue,
What have we after that to look forward to?

Not the twilight of the gods but a precise dawn
Of sallow and grey bricks, and newsboys crying war.

The Sunlight On The Garden

The sunlight on the garden
Hardens and grows cold,
We cannot cage the minute
Within its nets of gold,
When all is told
We cannot beg for pardon.

Our freedom as free lances
Advances towards its end;
The earth compels, upon it
Sonnets and birds descend;
And soon, my friend,
We shall have no time for dances.

The sky was good for flying
Defying the church bells
And every evil iron
Siren and what it tells:
The earth compels,
We are dying, Egypt, dying

And not expecting pardon,
Hardened in heart anew,
But glad to have sat under
Thunder and rain with you,
And grateful too
For sunlight on the garden.