science surf

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.
Sowerbys.jpgStudent 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 p56lck (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.