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.

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.

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)