Libya vs. Evolutionary Science: Will the Tripoli Six be sentenced to death by firing squad?

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Oliveiria_etal_2006_HIV_phylo_Tripoli6_Fig2.jpgBecause I’ve apparently been living in a cave, I only just heard the full story of the “Tripoli Six”: five foreign nurses and a doctor that the Libyan government has imprisoned for seven years, tortured, and sentenced to death by firing squad for allegedly causing an outbreak of 400 cases of AIDS in a Libyan children’s hospital in 1998. Apart from the problems with torture and firing squads, the major problem here is that these poor people didn’t do it. The infections were caused by poor hygiene practices, like reusing needles, that existed at the hospital long before these nurses arrived in 1998. But the Libyan government is scapegoating some foreigners to distract the populace from the fact that the government is the real criminal here.

What does this have to do with evolution, you ask? Well, out here in the real world (outside of Libya and creationist circles), the way you tell where an HIV strain actually came from, and when, is by doing a standard molecular phylogeny. If you are a creationist who doesn’t believe in this sort of thing then you should really just stuff it, because the criminal courts, relying on their “beyond reasonable doubt” standard, have been using phylogenetic methods as forensic evidence for years (so much so that an HIV phylogeny was used on the TV show CSI).

The co-discoverer of HIV, Luc Montagnier, and other scientists, have already told the Libyan court that the Tripoli Six couldn’t possibly be responsible, since the HIV infections occurred both before 1998 and after the Six were arrested (Nature has Montagnier’s report online (free PDF)). The first time this happened, in 2003, the Libyan court ignored their report and sentenced the Six to death anyway. Their lives were saved, temporarily, because diplomatic pressure forced the Libyan government to throw out the original trial and give the Six another chance. So a second trial was held this year, again with scientific testimony, and the verdict and sentencing are scheduled for December 19 – only 12 days from now.

Just yesterday, Nature, which has been beating the drums about this since September, published (free PDF) a fast-tracked paper from the lab of evolutionary biologist Andrew Rambaut of the University of Edinburgh, formerly of the Oxford Evolutionary Biology Group.

Basically, with molecular phylogenetics and statistical modelling, Rambaut and co. were able to prove that each of the various HIV-1 strains found in the Libyan children had a common ancestor that predated March 1998, the time when the foreign nurses arrived. More than that, all of the 95% confidence intervals for the estimated date of common ancestry of both the HIV-1 virus, and three strains of HCV (Hepatitis C), another blood-born pathogen which was co-infecting patients, all fall months-to-years before March 1998. This means that nosocomial (hospital-acquired) infections had been occuring for years.

Here is the chart:

Oliveiria_etal_2006_HIV_phylo_Tripoli6_Fig2.jpg

Unless you are a creationist, this quantitiatively proves that these strains were being passed around at the hospital before the foreign nurses were even in the country. This result, from an independent lab, confirms what Montagnier and others have already testified to.

The Scottish newspaper The Herald has a really incredible story reviewing the whole situation and the evolutionary science involved. Here is a quote:

The last-ditch bid to save the Tripoli Six by James Morgan

[…]

In desperation, human rights organisations launched a last-ditch appeal to scientists around the world to find definitive evidence that would exonerate the group. Today, with just 12 days until the verdict, that call has been answered – thanks, largely, to the ingenuity of an Edinburgh scientist.

Dr Andrew Rambaut had only just arrived in his new office at the Institute of Evolutionary Biology in October when the telephone rang. It was Professor Tulio de Oliveira, Rambaut’s former colleague at Oxford University, who had been asked to head up a coalition of international experts to provide the missing evidence: the precise date of the HIV outbreak in the Libyan hospital, a secret hidden within the DNA of the virus itself.

[…]

He set out to date the outbreak using a technique similar to that used by taxonomists to date the evolution of a species. His program began comparing HIV samples taken from 51 of the 426 children. Each child had a slightly different lineage of virus, but each lineage had evolved from a common ancestor – a single strain of virus with a single DNA sequence.

Over two fraught weeks, the program was able to determine the original virus sequence, and reconstruct the exact phylogeny, or family tree, of the outbreak. Each new branch in such a tree is due to a mutation – a tiny change in the virus DNA sequence as the virus transmits from person to person.

Now, here comes the clever part. The rate of these mutations is almost constant – so regular that you can mark time by it. Thus, by beginning at the children’s HIV sequences and travelling backwards through the branches, the computer was able to count the mutations and thus determine the length of time that had passed since the first infection in the hospital.

It showed that the strain of HIV with which the children had been infected was a West African subtype, which had clearly been present and spreading locally in the mid-1990s, long before the medics arrived. If the “molecular clock” was stopped on the day they arrived, in March 1998, it would show that the original virus had already branched into many, many different viruses – a sign that it had already been transmitted many times between people within the hospital.

The findings, published today in the journal Nature, provide independent genetic confirmation of Montagnier’s testimony.

The journal’s editors have fast-tracked publication to make this new evidence available before the verdict – but whether that will be enough to save the Tripoli Six from the firing squad is a question no computer program can answer.

“It’s not my place to comment on the outcome of the case,” says Rambaut. “But I’m hopeful that something will come of this.”

The bloggers at scienceblogs.com have already been raising a ruckus over this. Go here for all the links, and go here to find out what to do – write a letter to your representative at least. If Libya doesn’t let these people go I think we’ll be seeing protests outside the Libyan embassy and calls to cut off scientific and educational contacts with Libya (if there were any to begin with).

And yes, promoting evolutionary biology is a distant second here compared to the primary issue of saving innocent human lives, but it is worth pointing out that the question of ignoring evolutionary science really can be a matter of life and death.

28 Comments

Nature reports further on the paper:

Other phylogenetic analyses of HIV have been used in court cases involving allegations of HIV infection. The first was in 1991, when a Florida dentist was shown to have contaminated his patients. The technique has since been accepted as evidence in dozens of cases involving rape, hospital infection transmissions and people with HIV knowingly exposing others in Sweden, France and elsewhere.

Thomas Leitner of Los Alamos National Laboratory in New Mexico has provided forensic HIV evidence in more than 30 such cases over the past 15 years. He describes the de Oliveira paper as “compelling evidence that the outbreak had started before the accused could have started it”, a view shared by every expert that Nature contacted (see ‘Expert opinion’).

Leitner points out that calculating evolutionary timescales is tricky, but that because HIV has such a fast mutation rate, even recent events can be pinpointed quite accurately. “De Oliveira et al. have tested and evaluated the clock and its uncertainty using several methods,” he says. “I find their analysis well done and timely, and hope it will affect the judgement in the Libyan court.”

They have a sidebar with the opinions of other experts:

The following scientists have all previously testified in court cases involving HIV molecular evidence. They assess the new data.

“This study is an impressive statistical analysis. It shows clearly that the hypothesis of deliberately injecting children with HIV in 1998 should be rejected.”

Philippe Lemey, expert on HIV evolution, Rega Institute for Medical Research, Belgium.

“This is exactly the kind of objective phylogenetic analysis needed in this case. The results clearly show that the health workers were not responsible for the introduction of these HIV strains.”

David Hillis, expert on viral phylogenies, the University of Texas, Austin.

“This kind of analysis has been approved by courts around the world. This is a case of [hospital] infection with multiple, independent sources, a pattern most easily explained by sloppy or inappropriate practices at the hospital.”

Fernando González Candelas, evolutionary geneticist, the University of Valencia, Spain.

“The existing epidemiological data are already enough to demonstrate that the accused medical staff cannot be the source of the contamination. De Oliveira’s analysis is completely independent, and yields the same conclusion. The court cannot pretend to be impartial if it refuses to hear any competent scientist from abroad.”

Michel Milinkovitch, evolutionary geneticist, the Free University of Brussels, Belgium.

“They have used state-of-the-art methods to estimate divergence and dates of events in this outbreak. The analysis shows compelling evidence that the outbreak had started before the accused could have started it.”

Thomas Leitner, expert in HIV evolution, Los Alamos National Laboratory, New Mexico.

Scientists could have stopped AIDS in its tracks and saved millions if they hadn’t be so worried about gay bashing.

As far a Libya, shall we INVADE and LIBERATE the prisoners?

If Nick is correct that this is a matter of political expediency, then the only way all these studies can make a difference is if enough Libyans are aware of them to change the political motivations. And if any serious AIDS prevention program is going to require a lot of money or the sort of political reorganization where people lose genuine power (whereas the current scapegoating is increasing their power), that’s not going to be easy.

Blairs Bitch said: “Scientists could have stopped AIDS in its tracks and saved millions if they hadn’t be so worried about gay bashing.”

Yeah, right. How do you figure? Good luck containing a virus that is already dispersed by the time you realize it is a virus.

Is this trolling? I honestly can’t tell.

In the comments why don’t we focus on solutions to getting the Tripoli Six out of that situation?

Thank you, Nick, for blogging about this. I’ve called for another round of letters to the government. I don’t know what else to do, unless people have some other ideas. Suggestions?

I don’t know what else to do, unless people have some other ideas. Suggestions?

As interesting as the science is, I think at this point the trial has nothing to do with evidence anymore. The situation is purely political, and I have no idea how I could influence Lybia.

Anyone from Lybia here?

Is there an e-mail address for a Libyan embassy where everybody can post a protest?

U.S. Embassy Tripoli Contact Information

General [Enable javascript to see this email address.] 218-21-335-1848 Public Affairs Section [Enable javascript to see this email address.] 218-21-335-1831 http://libya.usembassy.gov/contact.html

thank you katarina

Cotton Mather was very concerned that he burned witches after a “fair trial.”

Why would supporters of the “home team” care that this is brought into the 21st century.

Is there an e-mail address for a Libyan embassy where everybody can post a protest?

The only protest that would matter is one from the U.S. government, accompanied by economic (or physical, but let’s not go there again) threats. So we should really be writing to our representatives, not to the Libyans.

Bloody hell,

To the Honorable Wait Winthrop Esq;

Sr.

By the special Disposal and Providence of the Almighty God, there now comes abroad into the world a little History of several very astonishing Witchcrafts and Possessions, which partly my own Ocular Observation, and partly my undoubted Information, hath enabled me to offer unto the publick Notice of my Neighbours. It must be the Subject, and not the Manner or the Author of this Writing, that has made any people desire its Publication; For there are such obvious Defects in Both, as would render me very unreasonable, if I should wish about This or Any Composure of mine, O That it were printed in a book! But tho there want not Faults in this Discourse, to give me Discontent enough, my Displeasure at them will be recompensed by the Satisfaction I take in my Dedication of it; which I now no less properly than cheerfully make unto Your Self; whom I reckon among the Best of my Friends, and the Ablest of my readers. Your Knowledge has Qualified You to make those Reflections on the following Relations, which few can Think, and tis not fit that all should See. How far the Platonic Notions of Demons which were, it may be, much more espoused by those primitive Christians and Scholars that we call The Fathers, than they see countenanced in the ensuing Narratives, are to be allowed by a serious man, your Scriptural Divinity, join’d with Your most Rational Philosophy, will help You to Judge at an uncommon rate. Had I on the Occasion before me handled the Doctrine of Demons, or launched forth into Speculations about magical Mysteries, I might have made some Ostentation, that I have read something and thought a little in my time; but it would neither have been Convenient for me, nor Profitable for those plain Folkes, whose Edification I have all along aimed at.

Why worry about religious murders (many daily) when we can rant about “evangelical atheists?” I think that such wise-men as Ed Brayton should make their side totally clear that they are supporters of this killing. After all we must not criticize religious fanatics, they might be offended.

I’m not sure if you’re aware, but you’re in august company - well over 100 Nobel laureates, no less. See this for more http://www.iht.com/articles/2006/11[…]s/nurses.php

Btw, look at the guard on the right: his vision and hearing obscured by his clothing and stance. Not a good omen, but what a telling comment on both Libya’s judicial system and the mental attitude of fundamentalists of all stripes.

Btw, look at the guard on the right: his vision and hearing obscured by his clothing and stance. Not a good omen, but what a telling comment on both Libya’s judicial system and the mental attitude of fundamentalists of all stripes.

That guard is a woman I’m sure, just with a head covering. Various shots of the Tripoli Six have female guards with various head coverings.

Why worry about religious murders (many daily) when we can rant about “evangelical atheists?” I think that such wise-men as Ed Brayton should make their side totally clear that they are supporters of this killing. After all we must not criticize religious fanatics, they might be offended.

Um, we all criticize religious fanatics. The thing we object to is treating religious moderates like religious fanatics.

“That guard is a woman I’m sure, just with a head covering. Various shots of the Tripoli Six have female guards with various head coverings.”

Woman? Could have fooled me (and, in fact, did). Still, with female defendants I suppose a female guard is obligatory. Nonetheless I maintain that that court is blinkered and deafened to evidence and reason - and, indeed, to reality.

The thing we object to is treating religious moderates like religious fanatics.

That’s foolish of you, since they are like them, for certain values of “like”.

Speaking of foolish, what quantitative values of “like” are you referring to?

Nick, as I recall, you studied the distribution of some plants as a graduate student. Your boss is a physical anthropologist, so I doubt that she has ever done ethnographic fieldwork; live a few years in some little village where they think you are weird and they sacrifice animals to gods you have never heard of before.

You watch, take notes and hope they never ever takeover your home town. They are still your friends, but …

Creationists are not any different from the religious fanatics of thousands of years ago. Religious “moderates” are merely those people who have not made up their minds.

Personally, I am a strong agnostic; Science can not tell if god(s) exist, and neither can you! (generic “you”)

Dogma is deadly. Religion is murderous. If we could only deny the benefits of medicine, and advanced agriculture, and chemistry to the assholes that will gladly murder us for not worshiping their delusions, they would be dead right soon. Saddly, we are much more ethical than they are.

If we could only deny the benefits of medicine, and advanced agriculture, and chemistry to the assholes that will gladly murder us for not worshiping their delusions, they would be dead right soon. Saddly, we are much more ethical than they are.

Who, exactly are you talking about so self-righteously?

So we should really be writing to our representatives, not to the Libyans

The embassador in our US Embassy in Lybia is an American, as are the rest of the staff. They communicate regularly with Washington. It would be good to write both to representatives and the embassy. Senator Lugar of Indiana is on the Foreign Relations committee, I will call him on Monday.

I wondered why I hadn’t heard about this on the news. Then I read the original Herald article by James Morgan:

“Five Bulgarian nurses and a Palestinian doctor”

I realised then why it hasn’t received the press coverage it should be getting. I suppose the BBC will cover the story when it’s too late.

Who, exactly are you talking about so self-righteously?

yes, it does appear that US foreign policy sometimes follows Gary’s darker visions.

Pressure on UN reproductive outreach programs, AIDS investment in Africa, and other things come to mind.

but overall, the idea that there is a prevailing ethos to help where possible is correct; it just gets lost in the political shuffle and right-wing religious mindset a bit too often.

the funny thing is, if we view our own relgious fundamentalists in the way Gary puts it, you could make an argument that their impacts on foreign policy are merely attempts at self preservation!

For their own reasons, either good or bad, Libya has been working hard to get in the good graces of the western world over the past three or four years. A protest from U.S. citizens probably will get at least a hearing.

For what it’s worth, this issue has been covered regularly, if not in great depth, by major U.S. and European media. The thing that brings it to the fore right now is the rapidly approaching deadline for execution, and the news from Scotland that scientists have evidence that should exculpate the accused.

Can’t say why others are feeling crabby today (I’m tired, too) – but why not shoot off an e-mail or letter or two, and see whether there is any effect? What does it hurt?

Sir_TJ,

but overall, the idea that there is a prevailing ethos to help where possible is correct; it just gets lost in the political shuffle and right-wing religious mindset a bit too often.

In general I respect your views, but you gotta be kidding me. Democrats have been almost as bloodt-hirsty in matters of foreign policy as Republicans have. Don’t forget that Clinton dropped bombs on Iraq too. Don’t forget the long years of sanctions, whose victimis are primarily sick children. Please let’s not start on this. Makes my blood boil thinking about it. Ethics has not a damn thing to do with our international affairs.

I wrote:

The embassador in our US Embassy in Lybia is an American

I was speaking generally, but now I realize that an ambassador hasn’t been assigned to that embassy yet. It is open and staffed, and I think still worth contacting, but there is no ambassador yet!

From what I understand Lybia needs to be part of the international community pretty badly, and that process is underway despite failure to free the prisoners, and despite their being sentanced to death. I’m not sure why the diplomatic efforts failed, but the Nature article mentioned something about realpolitik, having something to do with looking the other way. I am surprised the Nobel letter didn’t help, but I think it’s worth keeping the pressure up.

We need talking points, 3 or 4, and maybe ask people to pick a few and compose an original e-mail based on them. I wasn’t familiar with this case until Nick posted it, but it shouldn’t be too complicated.

Where did Lenny go? Oh yeah…:(

Libyan court condemns all accused to death for infecting children with HIV:

TRIPOLI, Libya (AP) - A court on Tuesday convicted five Bulgarian nurses and a Palestinian doctor of deliberately infecting 400 children with the HIV virus and sentenced them to death, provoking condemnation from Bulgaria and shouts of joy in Tripoli.

“God is great!” yelled Ibrahim Mohammed al-Aurabi, the father of an infected child, as soon as the presiding judge finished reading the verdict in the Tripoli courtroom. “Long live the Libyan judiciary!”

Bulgaria swiftly condemned the decision, and reiterated its belief that the children were infected by unhygienic conditions in their Benghazi hospital.

“Sentencing innocent people to death is an attempt to cover up the real culprits and the real reasons for the AIDS outbreak in Benghazi,” said Bulgarian parliamentary speaker Georgi Pirinski.

The five Bulgarians and the Palestinian sat stony-faced and made no reaction as the judge finished delivering the verdict.

“God is great!” yelled Ibrahim Mohammed al-Aurabi”

Yeah! Go god! Allah suckmybar!

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This page contains a single entry by Nick Matzke published on December 7, 2006 10:22 PM.

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