So begins the hand-wringing about mad biodefense scientists

As I mentioned in my two previous posts about the Amerithrax suspect, (here and here), the entire country will soon be all tits-a-flutter about the looming threat of mad biodefense scientists.

Science magazine joins in with this article and soundbites from Gerald Epstein and Jonathan Tucker.

Biodefense researchers were pondering today whether there might be a backlash to their field if the worst bioterror crime in U.S. history was indeed committed by a scientist who had spent a career developing countermeasures against anthrax. But the fact that Ivins won’t face trial also raised the uncomfortable specter that the full truth about the case may never come out. “We may never know for sure whether he did it or not,” says virologist Thomas Geisbert, a former USAMRIID researcher now at Boston University.


The death–and presumed involvement in the anthrax letters–puts the biodefense research community in a tight spot, says Gerald Epstein, a biosecurity expert at the Center for Strategic and International Studies in Washington, D.C. “From the very beginning, there has been speculation that the attacks were carried out by a biodefense zealot who wanted to prove that bioterrorism was a serious problem,” says Epstein. If true, that could give the public the impression that “biodefense research is a giant fraud,” he says. “It would be unfortunate if the message people take away from this is that the only individuals we should be concerned about are deranged biodefense scientists.”


Jonathan Tucker, a specialist on biological weapons control, says the incident is bound to evoke new concerns about “insider threats” at government and university labs. Officials may be compelled to further scrutinize researchers who work with select agents, Tucker says, adding that some questions have already been raised about “the adequacy of the screening process” used by the FBI to determine if a scientist should be allowed to work with a dangerous pathogen.

Where the bad bugs are

Where bad bugs are

This issue has been debated for a long time. Several years ago I would have pooh-poohed the idea that highly trained and vetted scientists would present such a risk.  But for at least the last couple of years I’ve felt that the expansion of biodefense labs is related not to research need but to homeland defense money.  If you build it they will come, and a couple of them might be frakking nuts.  Do we not now have enough investment in the study of the most dangerous, but least likely threats? How much more likely do these threats become, due to expanding the numbers of labs people handling them?

On the other hand, if Ivins was our guy, he’s been working in biodefense for nearly 20 years. Who knows when he could have gone over the edge? Would anyone have known? His coworkers seem to have liked him and don’t believe he was responsible, by the statements we’ve seen so far.

It may be that the risk of a deranged scientist is one that we’ve already taken all possible precautions against.  Screenings, protocols, security policies, all of these are already in place. There’s been some discussion of inculcating a “life scientist’s code of ethics” at universities—a noble initiative but will have zero effect on someone who is already there intending to become an insider threat.

I don’t know the answer, but I know that you’re going to be seeing a lot of this hand-wringing in the days and weeks to come.


UPDATE: More opinion at Wired Science and Danger Room.

Healthmap redux

See, folks, if you stick around and read my blather you’ll hear what’s in the news like a year and a half ahead of everybody else. For instance, here’s my post from November 4, 2006…


Who’s catching what, and where? Here’s a handy tool at www.healthmap.org.


Kind of chaps my %@#. But I guess this tool hit the news big recently because it’s had some nice feature updates.  Check it out, it’s much better these days.

BTW, did you hear about the recent Marburg case in the Netherlands? Tourist brought it back in her from Uganda, after having contact with cuddly bats.  She died a liquefacted hemorrhagic death on July 11.  You tell people not to play with the African bats, and you tell them over and over, but they just won’t listen.

And hey, don’t play with the SE Asian bats, either.

A new kind of Frankenfood: the tomato vaccine

Korean scientists have performed some promising tests using GM tomatoes that grow their own edible vaccines. In this case, against Alzheimer’s disease. And why not – the idea’s not a new one (although this guy notes a rather important reason why edible vaccines would be “a disaster” – each tomato would produce a variable level of the vaccine).

We already eat specific foods precisely for their purported health benefits. We’ve created other foods that produce desired substances, for example, the golden rice that produces large quantities of beta-carotene.

Still, something about it makes me leery. Kind of like “meatri” – synthetic meat. I’d know it was real meat, grown by the same biochemical mechanisms that animals use to grow their own meat. But I’d feel kind of hesitant to eat it, at least the first time. There’s a yuck factor.

From my own perspective of course, I also wonder how might this be used as a threat. A vehicle for biowarfare? Well, I imagine there are all kinds of toxins and such that food could be engineered to express. But there would be no reason to go to all that trouble when there are far more productive, established methods to crank out and deliver weapons. So this will no doubt remain in the realm of sci-fi for the foreseeable future. Could make for a great short story, though.

Using the homeless as vaccine test subjects in Poland

The homeless in Poland may have more hazards than the elements to deal with—it seems some unethical scientists viewed them as easy pickings for tests. Oh, and don’t take any ambulance rides there, either.

I figure this story deserves passing along in its entirety because it’s short, and it’s weird enough on its own without any commentary from me. I added the italics.

Homeless people die after bird flu vaccine trial in Poland

By Matthew Day in Warsaw
Last updated: 11:17 PM BST 02/07/2008

Three Polish doctors and six nurses are facing criminal prosecution after a number of homeless people died following medical trials for a vaccine to the H5N1 bird-flu virus.

21 people died after being given the vaccine

The medical staff, from the northern town of Grudziadz, are being investigated over medical trials on as many as 350 homeless and poor people last year, which prosecutors say involved an untried vaccine to the highly-contagious virus.

Authorities claim that the alleged victims received £1-2 to be tested with what they thought was a conventional flu vaccine but, according to investigators, was actually an anti bird-flu drug.

The director of a Grudziadz homeless centre, Mieczyslaw Waclawski, told a Polish newspaper that last year, 21 people from his centre died, a figure well above the average of about eight.

Although authorities have yet to prove a direct link between the deaths and the activities of the medical staff, Poland’s health minister, Ewa Kopacz, has said that the doctors and nurses involved should not return to their profession.

“It is in the interests of all doctors that those who are responsible for this are punished,” the minister added.

Investigators are also probing the possibility that the medical staff may have also have deceived the pharmaceutical companies that commissioned the trials.

The suspects said that the all those involved knew that the trial involved an anti-H5N1 drug and willingly participated.

The news of the investigation will come as another blow to the reputation of Poland’s beleaguered and poverty-stricken national health service. In 2002, a number of ambulance medics were found guilty of killing their patients for commissions from funeral companies.

Interesting new vaccine production method

There’s a lot of innovative work being done to develop new ways to jumpstart our immune systems, both in the “immune system trigger” part, and the packaging. For instance, there are efforts focused on virus-like particles (VLPs), liposomes, and various nano-structures (a couple of examples). This week in Science, a team including Eckard Wimmer, famous for de novo synthesis of poliovirus, reports its work in exploiting “codon pair bias” to create weakened poliovirus strains with great vaccine potential. Science mentions two teams currently exploring this method—Wimmer’s at Stony Brook University, and a team led by Olen Kew at the CDC.

We currently have a live poliovirus vaccine that is not without risk of causing the illness it is supposed to prevent. The thinking on this new strategy is that the genetically crippled virus could never mutate in such a way to overcome all of its flaws; further, the methodology could possibly be applied to any virus to create new vaccines.

Here’s the abstract:

Virus Attenuation by Genome-Scale Changes in Codon Pair Bias

J. Robert Coleman,1 Dimitris Papamichail,2* Steven Skiena,2 Bruce Futcher,1 Eckard Wimmer,1† Steffen Mueller1

As a result of the redundancy of the genetic code, adjacent pairs of amino acids can be encoded by as many as 36 different pairs of synonymous codons. A species-specific “codon pair bias” provides that some synonymous codon pairs are used more or less frequently than statistically predicted. We synthesized de novo large DNA molecules using hundreds of over- or underrepresented synonymous codon pairs to encode the poliovirus capsid protein. Underrepresented codon pairs caused decreased rates of protein translation, and polioviruses containing such amino acid–independent changes were attenuated in mice. Polioviruses thus customized were used to immunize mice and provided protective immunity after challenge. This “death by a thousand cuts” strategy could be generally applicable to attenuating many
kinds of viruses.

Because everyone wants to coin a catchy phrase I guess, they call the method “synthetically attenuated virus engineering” or SAVE. The paper sums the potential benefits:

…these results suggest that synthetic attenuated virus engineering (SAVE) could play a role in creating new vaccines for various types of viruses. By deoptimizing codon pair bias, one could systematically attenuate a virus to variable but controllable and predictable extents. This approach has four key features: (i) It produces a virus encoding precisely the same amino acid sequences as the wild-type virus, and therefore eliciting the same immune response. (ii) It is a systematic method apparently applicable to many viruses, and possibly not requiring detailed, virusspecific research. (iii) The attenuation is not subject to reversion, simply because of the sheer number of mutations. (iv) It can be combined with other attenuating changes (such as amino acid changes from adaptation of the virus to low temperatures or alternative species) or with other synthetic biology approaches to attenuation (18, 19), thus taking advantage of additional modes of attenuation while providing the unique advantage of limited reversion.

Codon pair bias is a little more complicated twist on codon usage bias (or just codon bias) which is a principle that has been applied in codon optimization for synthetic genes. Greatly simplified, in the genome there are multiple three-letter codons that can result in single amino acids, but some just seem to translate better than others. This preference can be used to promote high levels of gene expression in a selected organism, for instance. If you do the opposite, though, you can produce an organism that the body recognizes as a threat, but it really isn’t because it just can’t quite get the job done. It’s like an instruction manual written in Engrish. You know it’s an instruction manual but damned if you can understand it.

Here’s another writeup at ArsTechnica.

DNA testing is risky business for all concerned

I’ve been reading a flurry of posts and news stories over the past several days (see the latest at Wired Science) about California’s attacks on DNA testing businesses like Navigenics and 23AndMe. In what could be the opening salvo of a long and expensive battle, California’s health officials have issued cease-and-desist letters to up to 25 biotech companies that offer direct to consumer genetic testing. California says only a doctor can order a genetic test—under no other circumstances should this be available to consumers. Health Dept. official Karen Nickles made the spurious justification for this action,

“The public demand around access [to genetic information]… has created the worried well,” Nickles declared, noting that the results could be difficult for consumers to understand or act upon. “Once they get the results, they don’t know what to do about it.”

As always, the excuse is that the public is stupid and must be protected from itself. Or could it be that certain erstwhile links in the DNA chain of custody are a bit miffed about missing out on the money/data/privacy of consumers? Such as, oh, I don’t know, doctors, labs, and insurance companies who desperately want to have your genome on file? Not that they would ever use it against you—perish the thought! If you can just pay cash directly to some biotech company and get the results delivered to you, that’s a threat.

Indeed, an individual representing one of the targeted companies noted that although the health department feebly claims that its action was spurred by “multiple consumer complaints,” it’s more likely to have been spurred from within the (profit-motivated) health industry, to which I would add let’s not forget the insurance industry.

“If we could find out who put the bee in their bonnet, my guess it’s the medical community,” Greenspan [partner at DNATraits] said. “I think that the medical community doesn’t want to lose control of who orders the test.”

A couple of comments from Wired readers I thought worth repeating here….

“One (this one) wonders if insurance companies put this ‘Bee’ in the bonnet. If the individual orders the test, it does not go into the medical record, and insurance companies can not use said data to provide or deny their services. Mandating testing through medical professionals could be the first window to genetic discrimination by insurance companies…” – Matt

“Given the privacy-hostile nature of the US corporatocracy, you’d have to be crazy or incredibly stupid to hand over your genetic data to companies not bound to abide by even the token protections of HIPAA.” – realitydose

Yes, I think until a whole lot of things get figured out, I’ll stick to my policy of not handing out my DNA to anyone. Period. You’d be well advised to do the same, unless you have a very good reason to seek genetic testing at this time. If you’re just curious and have $1000 to blow, quite frankly, at this time no one can foresee what kind of risks you may be taking by enabling the collection of this data.

That’s nice, but you still can’t have my DNA

Wired Science reports that our Dear Leader signed the Genetic Information Nondiscrimination Act (GINA) law today. Theoretically, you now can’t be denied a job or insurance based on the titillating secrets hiding within your DNA. I’m sure there will be plenty of creative ways around that within 10 years or so. Further,

“GINA’s not perfect: The law doesn’t specifically keep genetic information out of third-party hands. It also doesn’t apply to the military. (So actually, you still might be denied entrance to Gattaca based on a genetic test.) And some people say health insurance won’t ever be fair without a pricing structure that makes discrimination impossible.”

The GINA law is a good thing. A great thing, even. It’s good that they can’t say, “Hmmm, looks like you’ve got a 28% chance of having clogged arteries by the age of 45, so we’re not going to insure (or hire) you.” But there is no way in hell I’m ever going to have my genome sequenced and entered into some medical record that frankly, I have zero control over. Laws change, and corruption happens. Government and businesses work out ways to do and get what they want, not to mention the fact that data of all kinds is stolen and sold on a regular basis.

I’m not trying to sell tin foil hats here, folks, but in the case of genetic data we simply do not know what the world is going to be like within 20-50 years. No, I don’t think individuals are going to be secretly “targeted” in some way but I do think genetic information will just be another way that people will be grouped and categorized, probably right out in the open, and to some end that a lot of them will be unhappy about. Since we do not yet know what we will be able to learn from or do with the genome in the future, how could we possibly know how releasing or even (supposedly) securely storing your genetic data might come back to you in the future? There could even be some sort of disadvantage to your kids who aren’t even born yet. Just a thought.

On the “open genome” side of the aisle, there are a few adventurous people so far, like Craig Venter and George Church, who are happy to have their genomes published in the name of science. Better them than me, but I guess only time will tell whether my paranoia was a waste of neurotransmitters or not.

Another $55M for biological agent countermeasures

And with my last post in mind, HHS has announced another $55M to fund countermeasures against anthrax, plague, and tularemia. From the press release:

The Department of Health and Human Services (HHS) announced today the award of contracts totaling $55.3 million to four companies for the advanced development of anthrax antitoxins, therapeutics and antibiotics for use against plague and tularemia.

The new Biological Advanced Research and Development Authority (BARDA) and NIH’s National Institute for Allergy and Infectious Diseases (NIAID), provided funding for the new contracts. Through an agreement with BARDA, NIAID will manage the contracts.

The companies receiving contracts are:

* Nanotherapeutics Inc. of Alachua, Fla. — $20 million for a plague and tularemia antibiotic development;
* Emergent BioSolutions Inc. of Rockville, Md. — $9.5 million for anthrax immune globulin development;
* PharmAthene Inc. of Annapolis, Md. — $13.9 million for anthrax antitoxin development [Note: I've posted about PharmAthene before—they're also developing recombinant human butyrylcholinesterase, or "Bioscavenger"]
* Elusys Therapeutics Inc. of Pine Brook, N.J. — $11.9 million for anthrax antitoxin development.

“These contracts will help speed the development of new interventions against anthrax, plague and tularemia, three diseases considered to be important bioterror threats,” said NIAID Director, Dr. Anthony S. Fauci. “The ‘pipeline’ of candidate bioterror countermeasures is fuller than ever, which bodes well for our ongoing efforts to protect Americans from those who would do us harm with biological weapons.”

Yes, the pipeline of candidate bioterror countermeasures is fuller than ever, because as I’ve said, that’s where the cash is. It would be reassuring to know though, that out of all this effort there are technologies and methodologies being developed that will help fight diseases that are arguably greater global health threats.

UPDATE: 8Oct07 – For another point of view on the issue, see this post at the Armchair Generalist.

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