Human Papilloma Virus (HPV) is in the news lately because its maker Merck is marketing a vaccine against it which they bill as the first anti-cancer vaccine. It may be effective against HPV, one of the main risk factors for cervical cancer, but it isn't the first cancer vaccine. The hepatitis vaccine gets the honors there. The HPV vaccine has become controversial in part because the risk factor it is preventing is infection with a sexually transmitted virus. Anything to do with sex is controversial in the US.
There's another sexually transmitted disease, much better known: gonorrhea ("the clap"). There's a lot of it around. More than you know. Apparently more than anybody knows, because there are now strains that aren't showing up with the usual tests:
"Stealth" strains of gonorrhoea that fail to show up in tests are on the rise across the world, researchers have discovered, because the tests used by doctors to identify the bacteria look for an enzyme no longer present in those strains.
The rising prevalence of these strains was found in Australia, New Zealand, England, Scotland and Denmark. The findings should prompt clinics to change practice and use at least two tests that work in different ways to detect the infection, the scientists say.
The prolyliminopeptidase (PIP) enzyme was previously thought to be present in all strains of gonorrhoea and was therefore used in many diagnostic tests. However, mutations or deletions in the PIP gene that prevent the production of this enzyme had been identified in some strains. Gonorrhoea is known for its ability to mutate throughout its entire growth phase. (New Scientist)
PIP negative gonorrhea strains are now showing up in many places, apparently the offspring of some original ur-mutant. Isolates from New Zealand, Scotland and Australia are almost identical to those from England and Denmark and are thought to have come from a single ancestor. All are sensitive to antibiotics, but if you aren't diagnosed you won't be treated, so the loss of PIP could be thought of as a novel form of antibiotic resistance.
Gonorrhea is rarely fatal but it causes a significant amount of serious pelvic inflammatory disease and can result in infertility. You'd think that we'd have this one pretty well figured out. But the bug seems to be smarter than we are.
That is, if you can ascribe intelligence to a bacterium. And if you can ascribe intelligence to us.
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You could just look at the evolution of stealth gonorreha as part of the everlasting cycle - like the cheeta and the antelopes they prey on. Humans have intelligence, scientific method, exosomatic tools, and bacteria and viruses have time and lots of progeny. Hearing about hsi reminded me of the work being done at MSU Digital Evolution Laboratory http://devolab.cse.msu.edu/ using Avida software to simulate evolution digitally. Amazing stuff from digital constructs. Link to the full article at the end.
When I read about it this part especially struck me.
"Ofria has been finding that digital organisms have a way of outwitting him as well. Not long ago, he decided to see what would happen if he stopped digital organisms from adapting. Whenever an organism mutated, he would run it through a special test to see whether the mutation was beneficial. If it was, he killed the organism off. You'd think that would turn off any further adaptation, he says. Instead, the digital organisms kept evolving. They learned to process information in new ways and were able to replicate faster. It took a while for Ofria to realize that they had tricked him. They had evolved a way to tell when Ofria was testing them by looking at the numbers he fed them. As soon as they recognized they were being tested, they stopped processing numbers. If it was a test environment, they said, 'Let's play dead,' says Ofria. There's this thing coming to kill them, and so they avoid it and go on with their lives.
http://www.carlzimmer.com/articles/2005/articles_2005_Avida.html
K: Thanks for the link. This is fascinating. Carl Zimmer is now at ScienceBlogs (The Loom), but I hadn't seen this.
Your welcome Revere - I first read of it in Discover a year or so back - I thought it was fantastic.
Very interesting! But after all, the basic method of evolution is more-or-less "there are no rules, try anything and see if it works".
Thanks, K.
The irony is delicious, of the creationists helping to debug avida. Helping to breed a more dogma-resistant robust evolutionist program.
I wonder, can we use the program to investigate pandemics or public health systems? The evolving programs, inside, are claimed to be Turing-equivalent, so the theoretical answers are, yes. Is somebody clever, or lucky, enough?
"... (HPV) is in the news lately because its maker Merck ..."
Revere, I agree the pharmacorps salivate at the profit potential of plagues and pestilences. I am surprised that you would state without a great deal of careful evidence that they have created one.
I know : 7:31 AM.
Greg: Not sure what you mean. HPV has been around for a long time, but it is in the news because of Merck's antics and the FDA approval. The Gardasil issue is interesting and I am taking a hard look at it, but I certainly never said Merck created the problem, unless by the problem you mean the bad appearance of lobbying a corrupt governor, who may have done the right thing for the wrong reasons (or maybe it isn't the right thing). Mandatory vaccination for minors might very well be the way to go here, but there are a variety of unknowns that make taking a sober look at this reasonable. If my daughter were of the right age I would have no hesitation having her vaccinated. But that's a somewhat different thing than a mandatory program for an extremely expensive vaccine whose length of protection is in doubt. It is not the public health no-brainer it seemed to be. Obviously for me it has nothing to do with abstinence, a failed policy. It has to do with risk reduction, effectiveness and probably other things we are just figuring out. Some critical thinking would be useful.
Anyway, the post was about something else. It was just my mind wandering in the opening sentence. You know, 7:31 am.
"... (HPV) is in the news lately because its maker Merck ..."
Grammatically, "its" refers to the virus, both according to number, and according to phrase structure.
I thought, when I first read it, that you had revised your sentence incompletely, leaving Merck as maker of the virus, where an earlier version had had Merck as maker of the vaccine.
Now, I think, in light of your reply to my comment, that "news" might be regarded as singular in your region; however, I would still claim "its" refers to the virus according to phrase structure. Alternately, you might have conflated Merck's antics with news about the virus.
I thought that you had done something similar to the latter, in an earlier post. It may be that you have a grammatical idiosyncrasy of your very own. One which we must accept and allow for.
Grammar and the way people make it fascinate me.
Also, the notion that the drug industry would, like the tobacco industry, harm its customers for profit, is too delicious to let pass. Although, obviously, it should not be allowed to appear too frequently, here.
Yes, your post is about something else, equally fascinating.
If you can speculate that microscopic creatures like bacteria or virus ar inteligentWhy not say that the entire planet is an inteligent lifeform and bacteria and virus are its form of a defence mechanisims against harmefull life forms like the human race.
Perhaps humans are about to be culled using these propertiess in the same way we cull an animal population if it is at a point where its overpopulation is at a point where it is harmfull to our enviroment.
Anything is possible .It was not too long ago when humans believed with all there heart that the earth was flat.
Greg: Oh, my. You are quite right. That's really bad writing on my part. What's worse, I still didn't see it even when you pointed it out to me.
Wayne: I am genuinely interested in what "life" means and I think digital life forms have a good claim to being "alive" in the usual sense. When it comes to aggregates like a species or a planet I suppose there is a sense where thy are also "a life form" but it is not anywhere near the same as for the individuals and I would tend not to use the word that way. Transferring meaning by analogy can be quite dangerous because you assume that a logical implication on one side implies a logical implication on the other and it is frequently not the case. We see the same thing with "models." The solar system model of the atom doesn't imply that there are people living on the third electron from the nucleus. Etc.
Loss of PIP by N. gonorrheae could be a novel means of antibiotic "resistance" if it actually prevented the infections from being treated. However, the diagnosis is based on the clinical presentation and other diagnostic info like Gram stain (result: Gram-negative diplococci) or nucleic acid amplification test (NAAT) with a target like the 16S ribosomal RNA, which unlike PIP is essential. At that point, clinicians treat, usually with a single-dose cephalosporin or fluoroquinolone.
Final ID by culture, sensitivities, and enzyme expression (including PIP, if it's used) occurs later. Though PIP negative strains seem to have created significant problems in terms of case definition, it's unclear to me how diagnostic info that arrives after the treatment decision can confer a selective advantage.
Other studies reporting PIP-negative strains in the Journal of Clinical Microbiology comment on the fact that either pts were empirically treated or that results of PIP activity were not relevant to treatment. Also, PIP-negativity seemed to peak and then fall.
PIP loss does seem to be more common in fluoroquinolone-resistant strains common in homosexual men. Since there doesn't appear to be any clear advantage/disadvantage of PIP-negative strains in terms of growth or infectivity, it could just be a marker. One important point regarding diagnostic testing, then, is that one should choose an essential gene/gene product target if possible.
Relevant links:
CDC Treatment Guidelines for gonococcal urethritis and cervicitis
http://www.cdc.gov/std/treatment/2006/urethritis-and-cervicitis.htm#uc6
Two prior articles on PIP-negative N. gonorrheae from J Clin Microbiol (free full text)
http://jcm.asm.org/cgi/content/full/43/8/4189?view=long&pmid=16081973
http://jcm.asm.org/cgi/content/full/44/4/1400?view=long&pmid=16597868
Revere, I have a bad habit of obliquity when pointing things out.. and other occasions. I shall try to be more direct next time, I suppose, unless there is a side issiue to inflate.
I find I am disappointed not having a new grammatical quirk to explore.
It occurs to me that other pathogenic bacteria might be using similar mechanisms to avoid detection.
Consider cases of illnesses where there is no obvious causal organism, at least, not obvious in routine testing. I suspect many of these cases involve test-evading mutant strains.
This new strain of the clap should be a warning sign, and a prompt for further research across the spectrum of infectious diseases.
It is a warning that becoming ill is NORMAL. Instead of going to work to share, we ought stay in bed for a day or two, let our bodies handle it.
Yeah, Yeah. There are exceptions. If we had a decent health care system, we would know what they are, when they are. If we had a decent economy, instead of sacrificing our lives for the bosses' profits, we would stay home when needful.