Dobzhansky and anthrax

| 28 Comments

The Washington Post today reminds us that there has been little progress in uncovering the source of the 2001 anthrax attacks.[1]

Why is this news for Panda’s thumb? Read on…

First, a disclaimer. I’m not an “evolutionary biologist,” per se. I have what is I swear the longest job title ever–molecular infectious disease epidemiologist. As such, I often get asked, “what’s the relevance of evolution to your work?” Or, I’ll read editorials such as Dr. Skell’s recently in The Scientist[2] questioning the use of evolutionary theory in experimental biology, and be disheartened. Yet the method of investigating the anthrax attacks shows once again just how relevant evolutionary theory is to all areas of biology, and how Dobzhansky’s famous “Nothing makes sense…” comment once again ring true.

There are several clues regarding the 2001 attack (for those unfamiliar with the story, the background can be found here)[3]. Some are in the packaging of the material: the writing on the envelope, the location of the postmark, the mailbox where the letters were dropped. Others are in the processing of the anthrax: the spores were finely milled, so as to be more easily aerosolized. Finally, there are clues in the bacteria themselves: in their genetic makeup. Early on, they looked at the molecular profiles of the anthrax and compared them to known strains, zeroing in on the Ames anthrax strain.

This is a good thing, because the Ames strain is fairly rare in nature–making it more likely that the anthrax was obtained from a laboratory. The problem with anthrax, however, is that as a species, it is very homogeneous: there isn’t a lot of variation in the DNA sequence. Fingerprinting techniques like pulse field gel electrophoresis (PFGE), which uses restriction enzymes to cut the bacterial chromosome into smaller pieces to be run out on agarose gels, work well for pathogens like E. coli and Staphylococcus aureus, but isn’t nearly as useful in anthrax due to the low level of sequence diversity. This makes it necessary to use more sensitive techniques to identify the bacterium, bringing us back to the characterization of the 2001 bioterrorist strain as the Ames anthrax strain.

What is the “Ames strain,” exactly? In a 2001 Science article[4], it was noted that

Over the past 2 decades, the U.S. Army Medical Research Institute of Infectious Diseases [USAMRIID] in Fort Detrick, Maryland, sent the Ames strain to several research labs. And as it was passed around and grown in different labs, it may well have accumulated minute new changes.

Researcher Martin Hugh-Jones noted, “The Ames strain can be many different things. A very detailed fingerprint could reveal very very minor variations.”

Therefore, it’s the accumulation of these mutations–from a common ancestor, the original “Ames strain” (sound familiar?)–that may allow for a more specific determination of the origin of the 2001 strain, shedding light on the most notable biocrime in recent history. I’ve not seen a published comparison of the whole genome sequences of the various Ames strains, but that seems like the logical way to proceed in this (apparently stalled) investigation–go right back to that “useless” evolutionary biology to save the day.

References

[1] Lengel, A. “Little progress in FBI probe of anthrax attacks.” Washington Post. September 16, 2005. [2] Skell, PS. 2005. “Why do we invoke Darwin? Evolutionary theory contributes little to experimental biology.” The Scientist. 19:10. [3] http://en.wikipedia.org/wiki/2001_anthrax_attack [4] Enserink, M. 2001. “Taking anthrax’s genetic fingerprints.” Science: 294; 1810-2.

28 Comments

I’ve not seen a published comparison of the whole genome sequences of the various Ames strains

I don’t think you’re likely to see that any time soon. For security reasons, not technological ones.

Ken Ham: (Inser thick Australian accent here) But this is all just variation within the Anthrax kind. No new information is produced. You see when God created the Anthrax kind.…..wait, did I say God?

(Sound of running footsteps recede into the distance)

SSCP is a simple straightforward screening technique to locate single nucleotide substitutions. It’s sensitive and inexpensive, and with a 4.5mb genome it just a lot of gel rigs and technicians which the army is good at (NCBI list the Y. pestis biovar Medievalis sequencing center as the Academy of Military Medical Sciences).

Id proponents can also participate. Since IC structures will allow little if any modification without losing function (they couldn’t evolve to begin with), genes encoding components of these structures will not have to be screened for sequence variants since the number of nucleotide substitutions will be lower (mostly third position) and uninformative. For the same reason, identification of IC structures will also allow biowarfare antiterrorism experts to cross off those structures in their threat analysis assessments of mechanisms to weponize microorganisms.

Delta Pi Gamma (Scientia et Fermentum)

I don’t think you’re likely to see that any time soon. For security reasons, not technological ones.

Actually just go to:

http://ncbi.nih.gov/genomes/lproks.cgi

and you can download 3 B. anthracis strains, including the Ames ‘ancestor’, the senate strain and one other.

Bruce, that is very clever. It goes to show that ID proponents care about ideology, and can’t even consider consequence.

Thankyou

Perhaps this should be mentioned to the president and homeland security.

Delta Pi Gamma (Scientia et Fermentum)

W is a creationist and doesn’t believe in scientific mumbo jumbo. Just ask Marburger, the National Weather Service and the National Hurricane Center.

I’d be careful about labeling W as a creationist. His religious background (Episcopalian and Methodist) doesn’t suggest that he’d be one. Furthermore, he refused to answer a question from a reporter on whether he was a creationist. When was the last time a creationist politician refused to answer such a question? The best way to answer the question would be to determine what his Texas church’s opinion of evolution is.

One of the graduates of my department works at one of the Army science genetic labs. He gave a talk at our silver anniversery symposium last year. Their main job is to genotype remains, but they do other research. I can’t remember if anthrax was involved.

Actually I’d expect a non-answer from W, regardless of his real views on the subject.

Openly supporting creationism thrills the theocrats, but alienates key swing voters. Openly opposing creationism reassures same key swing voters, but angers the theocrats.

I don’t think you’re likely to see that any time soon. For security reasons, not technological ones.

Actually just go to: …

The “security reasons” are not to keep the genetic sequence of anthrax from terrorists, it is to keep anyone from finding the actual purpetrators (the CIA). Go back and look at how all the right-wing talking heads and pundits were worrying about anthrax attacks, coincidentally just before they actually occured. This is characteristic of most known admitted CIA operations that fits those particular crimes. The patern is: get people worrying about the theoretical “threat”, make the “threat” real (while blaming someone else of course) thus justifying whatever draconian “protective” measures are necessary to face the “threat”. Typically it’s done outside the U.S., but the 9/11 terrorist attacks didn’t seem to be quite enough to get the powers they wanted, so an extra “push” was in order.

All of the evidence points to the culprits, yet the case is “stalled” because nobody will follow where the evidence leads.

I think you’re letting Skell off way too lightly. That was a particularly stupid article, and an NAS member should have known better. I can only speculate that it was a combination of being far outside his area of expertise, combined with the tendency of people, when they’re elected to NAS, of automatically assuming they have God-like wisdom about any area of science.

Skell, BTW, hasn’t published a real paper since 1990, and from his CV looks like he did some very routine organometallic chemistry. Anyone have any idea how he got into the Academy?

The conspiracy theorist complains: All of the evidence points to the culprits (the designer) , yet the case is “stalled” because nobody will follow where the evidence leads. italics mine

The refrain of ID.

You comment will generate a post on Dembski’s blog. Something to the effect of:

“The patern is: get people worrying about the theoretical “threat” anti Darwinian forces, make the “threat” (ID) real (while blaming someone else of course) (school boards in Kansas and Dover) thus justifying whatever draconian “protective” measures are necessary to face the “threat”.” (italics mine)

If I apply this logic to ID, then I and my fellow IDT (interior design trailer) spooks are secretly assisting ID. We at Delta Pi Gamma (Scientia et Fermentum) have better things to do. It’s Friday night and we’re low on beer.

Gerard Harbison:

Skell, BTW, hasn’t published a real paper since 1990, and from his CV looks like he did some very routine organometallic chemistry. Anyone have any idea how he got into the Academy?

He may not have published a real paper because he is retired, having done his major work in the fifties. In the fifties he was central in the development of “carbene chemistry” (if that means anything to you, it doesn’t to me). With relation to Carbene chemistry, he formulated the “Skell rule”, which rates a paragraph in an introductory university level text on organic chemistry I picked up. That, I presume, is why he is a member of the NAS.

Now, unfortunatley, he is simply a fruitcake. He has one very weak argument against evolution, refuses to enter meaningfull debate and on internet fora would be considered a joke even by creationists except for those wonderful credentials that are used to give weight to vacuous comments.

Now, unfortunatley, he is simply a fruitcake. He has one very weak argument against evolution, refuses to enter meaningfull debate and on internet fora would be considered a joke even by creationists except for those wonderful credentials that are used to give weight to vacuous comments.

Fred Hoyle (another good-scientist-turned-fruitcake), at least, had the redeeming value that he thought creationists were utter idiots.

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THis is really sad. How many scientists does it take to find a more variant region of the genome and do a few PCRs? I haven’t read the ASM paper mentioned, but honestly this should not be a difficult puzzle to solve. Use the three published genomes to find less conserved regions. And by the way, while more important pathways (which are not the same as IC or more complex) would have lower deviation, there are many other parts of the genome. Genomes often have hypervariant low complexity regions. And also, 3rd position nucleotide variants would be informative enough if there were a couple or few of them near eachother. A mere four years later they are close to finding SNPs with which to identify the strain of origin. Grr.

The refrain of ID.

Actually, I am a firm believer in evolution and it was quite rude of you to claim that changing “CIA” to “designer” was only italics.

In case it wasn’t clear, CIA means Central Intelligence Agency. I firmly believe that the closest available ancestors to the antrhrax used in the attacks belong to the CIA. However nobody will ever get a true sample from the CIA stock, but it is quite probable that the CIA obtained their source much more recently from Ft. Detrick than most other labs did. Thus the true sequence from the attack samples will be very uncomfortable for the government to reveal. Most participants in the coverup will be of the belief that they are saving the emberassment of revealing that somebody stole some of their anthrax, but the actual truth is much more damning than that.

I think it would be possible for Dembski to launch a bogus argument similar to that which you constructed around the CIA methodology, however if it claims specific reports from evolutionary biologist warning that a theory of ID would arise and threaten education before the IDsts organized, that will be false. Of course Dembski is a liar so he would just lie about that. However I did not. There are in fact quite a number of newspaper, radio and television commentaries specifically warning that the U.S. was vulnerable to an anthrax attack immediately preceeding the actual incidents. Go check and see for yourself.

Actually, I am a firm believer in evolution and it was quite rude of you to claim that changing “CIA” to “designer” was only italics.

Once again, in the world of literary currency I’ve short changed myself.

The utility of offering conspiracy theories in a discussion of evolutionary topics is not very fruitful. In contrast, a testable hypothesis is.

Delta Pi Gamma (Scientia et Fermentum)

The utility of offering conspiracy theories in a discussion of evolutionary topics is not very fruitful. In contrast, a testable hypothesis is.

That seems to be a higher standard than the general discourse on PT, but I’ll play the game.

Hypothesis: The CIA was the source for the actual anthrax attack materials.

Prediction (1): Efforts to sequence the entire genome of the attack materials will be frustrated.

Prediction (2): Should the attack material DNA sequencing ever be completed, the sequence will be classified.

Either these predictions will be falsified, or not. If they are not, then I invite you to find a simplier hypothesis to explain the (then evidence) predictions.

By the way, I was impressed with:

For the same reason, identification of IC structures will also allow biowarfare antiterrorism experts to cross off those structures in their threat analysis assessments of mechanisms to weponize [sic] microorganisms.

It would indeed be a good thing to frustrate the government’s efforts to weaponize microorganisms. Sadly I fear they will instead use real science.

As for “fruitful utility”, it’s certainly possible that some of the actual lab researchers who have access to samples of the attack materials and are actually frustrated that their recommended analysis aren’t being pursued might read PT. If they hear a hypothesis (conspiracy theory) as to why “there is no budget for that” or some such, maybe they will find a way to overcome obstacles; you never know. It might bear some bitter fruit.

Actually, this discussion highlights one core problem with ID: it is useless.

An evolutionary biologist would tell you effectively the same thing about most of the genetic sequences you would call IC: namely that they are strongly conserved because they are subject to stabilizing selection in most if not all environments in which the bacteria would find themselves.

ID adds nothing new here.

Furthermore, ID is fundamentally useless because it provides no causal mechanism for the origin of biological complexity. Even if there are biological complexities that evolution cannot explain (something I am not convinced of), the logical step here would be to attempt to formulate new theories or new extensions to evolutionary theory to account for them. If such an extension of theory became necessary, I would start looking from the perspectives offered by this kind of stuff:

http://mitpress.mit.edu/books/FLAOH[…]ml/home.html

(Of course, that kind of stuff is already yielding insights into how evolution works. Evolution is evolution, not “Darwinism,” and it has progressed considerably since the 19th century.)

ID simply tells us to stop looking and say Goddidit. It’s useless. Imagine if physics had, upon encountering the anomolous orbit of Mercury, simply concluded that “Newtonism” had been discredited and that goddidit. We would never have had Einstein.

Dubious explicitly advocated teaching of creationism on a par with evolution while he was mis-Governor of Texas

One does not have to be a creationist to think that equal time should be given to “both views”.

Most participants in the coverup will be of the belief that they are saving the emberassment of revealing that somebody stole some of their anthrax, but the actual truth is much more damning than that.

Thanks! I’ve been wondering what the “actual truth” was. Did you get this via divine revelation?

Go back and look at how all the right-wing talking heads and pundits were worrying about anthrax attacks, coincidentally just before they actually occured.

Yeah, come to think of it, that sounds an awful lot like this whole Hurricane Katrina thing - warnings in the years and days before it happened, and then the actual event.

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Mr Cartwright,

GW Bush’s church in Midland, Texas are “Born-Again” or Evangelicals.

The fundamental tenet of the creed is a “personal relationship” (carnal or not) with Jesus.

A super-majority of evangelicals believe in the literal truth of the Bible, and so, would be creationists of some stripe or another.

However, as someone recently pointed out to me, GW Bush has repeatedly references “good people of no faith at all,” making him rather progressive in his propaganda (embracing atheists).

Apparently I lost my earlier post attempting to use kwikXML, so I won’t do that agin.

Mr. Cartwright said:”One does not have to be a creationist to think that equal time should be given to “both views””.

This is technically true, although the correlation between the groups is extremely high.

Mr. Ierymenko said: “Actually, this discussion highlights one core problem with ID: it is useless. An evolutionary biologist would tell you effectively the same thing about most of the genetic sequences you would call IC: namely that they are strongly conserved because they are subject to stabilizing selection in most if not all environments in which the bacteria would find themselves.”

While he doesn’t approve of ID theory, he still gives it too much credit in his assessment. They don’t have a list of IC objects. They just have untested algorithms that even they won’t go applying universally. As far as I know, they only have the flagellum, and they claim the eye and blood clotting systems. But there is no reason to assume that an “IC” systems gene sequences will be more conserved than any other given coding region. In fact, a few quick BLAST alignments would probably show us that genes for these are not among the most conserved in the species they inhabit. Using the flagellum as an example, when a wild pathogen is cultured in the lab, it is not uncommon for it to lose motility, as this trait does not improve fitness in plate or broth culture. Evolutionary theory would predict that these sequences, without selective pressure, would be highly mutable. In short, IC does not equate to stabilizing selection. ID theory, as it stands now, is both unable to discern the so-called irreducibly complex structures at the crux of their theory, and unable to tell us any predictive characterists of said structures if they could. That’s a double-whammy of uselessness.

sanjait Wrote:

THis is really sad. How many scientists does it take to find a more variant region of the genome and do a few PCRs? I haven’t read the ASM paper mentioned, but honestly this should not be a difficult puzzle to solve. Use the three published genomes to find less conserved regions. And by the way, while more important pathways (which are not the same as IC or more complex) would have lower deviation, there are many other parts of the genome. Genomes often have hypervariant low complexity regions. And also, 3rd position nucleotide variants would be informative enough if there were a couple or few of them near eachother. A mere four years later they are close to finding SNPs with which to identify the strain of origin. Grr.

They do have a number of variable regions (several were known before the genomes were published; others have been increasingly investigated since their publication) and, as noted above, a few complete sequences. But I’d think with something this important, sequencing a number of different “Ames” strains and doing a comparison would be high priority, and could re-start the stalled case.

I think a crisp rejoinder to Skell and other naysayers concerning the utility of evolutionary biology is to point out that there is a well-known historical incident that shows us what happens when a government decides to politically mandate the content of evolutionary biology and adopt a teleological view of adaptation instead. The U.S.S.R. did just that under Trofim D. Lysenko, and paid for it. They paid for it in the lives of researchers who, at a minimum, had to give up their lines of research, or be jailed, or executed outright for adherence to “bourgeois” science. They paid for it in famine and food shortage. They paid for it, literally, with their economy. Part of the reason that there is no U.S.S.R. right now is because they crippled themselves by denigrating evolutionary biology and adopting pseudoscience in its place. So when the next know-nothing comes along claiming that evolutionary biology is of no practical value, you can smile at his touching ignorance, not just of the state of evolutionary biology today, but also the documented history of the relative merits we accrued in the west by its adoption, and the hardships encountered in the east by its diminution.

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This page contains a single entry by Tara Smith published on September 16, 2005 10:58 AM.

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