Wednesday, January 27, 2010

Congrats John!

Congrats for getting your proposal accepted. The tracing resistance team is done with classes and proposals, now we can just focus on being jaded bitter grad students.

\m/ to John

Tuesday, January 26, 2010

Finding God in Haiti

Listening to the radio to and from lab each morning, every news program has had at least one segment on Haiti. Certainly a grave tragedy that deserves the world’s attention and charity. What I don’t understand however, is the amount of coverage given to people finding God amidst the rubble and piles of bodies, and clergy men praising God for his mercy in sparing those who were not crushed. This raises one of the most fundamental arguments against God – the problem of evil. And what everyone from simple believers to intellectual theologians have turned to in these times is theodicy. These are the mental acrobats needed to justify or explain away a benevolent god in a world filled with evil.

Probably the most notable of commentary was from the maw of Pat Robertson, calmly stating that the people of Haiti brought this upon themselves by making a deal with the devil. And no sooner did he utter these repugnant words did the faithful back peddle away from them.

Thankfully, there are those willing to call out such hypocrisy. In recent op-eds, Dan Dennett, Richard Dawkins and James Wood have all stepped up to denounce this type of thinking. All of these are worth reading in their entirety (especially the usually mild Dawkins who writes with viciousness and eloquence like no other), but here some quotes to give you an idea.

From Dennett:

"The idea that God is a worthy recipient of our gratitude for the blessings of life but should not be held accountable for the disasters is a transparently disingenuous innovation of the theologians. And of course it doesn't work all that well. The Problem of Evil, capital letters and all, is the central enigma confronting theists. There is no solution. Isn't that obvious? All the holy texts and interpretations that contrive ways of getting around the problem read like the fine print in a fraudulent contract--and for the same reason: they are desperate attempts to conceal the implications of the double standard they have invented."

From Dawkins:

"Educated apologist, how dare you weep Christian tears, when your entire theology is one long celebration of suffering: suffering as payback for 'sin' or suffering as 'atonement' for it? You may weep for Haiti where Pat Robertson does not, but at least, in his hick, sub-Palinesque ignorance, he holds up an honest mirror to the ugliness of Christian theology. You are nothing but a whited sepulchre."

From Wood:

"Terrible catastrophes inevitably encourage appeals to God. We who are, at present, unfairly luckier, whether believers or not, might reflect on the almost invariably uncharitable history of theodicy, and on the reality that in this context no invocation of God beyond a desperate appeal for help makes much theological sense. For either God is punitive and interventionist (the Robertson view), or as capricious as nature and so absent as to be effectively nonexistent (the Obama view). Unfortunately, the Bible, which frequently uses God's power over earth and seas as the sign of his majesty and intervening power, supports the first view; and the history of humanity's lonely suffering decisively suggests the second."

There have also been responses printed to Wood that are also worth reading. They too show how the faithful claim that God is unknowable and mysterious and yet suspiciously, they claim all he does is with love and good in mind. Pure theodicy.

Monday, January 25, 2010

Physics of the Megashark

Sitting in my Netflix queue waiting to be watched is “Megashark vs. Giant Octopus.” A movie who’s title alone guarantees cheesy entertainment and terrible science. One infamous scene has the Megashark leaping out of the water and taking down an airplane. Yes, an airplane. Absurd as that sounds, the physics required for such a feat are even worse than you can imagine. Luckily, there’s a nice infographic demonstrating this point.

Click here for full size pdf.

Sunday, January 24, 2010


Unlike many things in life, science is self correcting at every step of the publication process. Generally a researcher gets data and goes to some type of advisor and they discuss the interpretation of the result. That result can lead to a publication, which is then sent to a journal. The journal sends that out for independent review by experts. Those experts review the work, make suggestions, and often ask to see additional data. Only after the editor of the journal is satisfied does a worthy article get published. Other groups will then read the paper and if they disagree with the result they can write a letter (with data) to the journal or publish a paper with opposing results. Other groups will then weigh in and eventually the right result will become an accepted fact. Disagreements are commonplace and debates can go on for an entire scientific career.

Although many do not think it, scientists are people too. At some point in a career a decision has to be made and a topic or problem becomes your life’s work. So what happens when two groups of scientists disagree? Normally the debate is carried out in journals and meetings, and yes emotions can get the better of people. What happens when scientists get involved in an emotionally charged topic? The debate is taken up in journals, meetings, the media and in the public. That is exactly what has happened with the report XMRV was not detected in chronic fatigue syndrome (CFS) patients in England. I think people should get involved in scientific debate, however there is so much misinformation and arm chair scientists out there, true facts are hard to come by. Science moves much slower than the 24 hour news we have grown accustom to. I think Vincent Racaniello’s blog and Abbie Smith’s erv blog have done a good job of covering the developments and offer a good cross section of the internet debaters. Unfortunately, CFS suffers and their families will likely have to wait years for conclusive experiments to be done by a number of groups for there to be any scientific consensus about XMRV and CFS.

This debate reminds me of a personal problem I had. I found out that I have celiac disease last year. Although I do not know when this disease began, I believe that it went undiagnosed for a fair amount of time. I was asymptomatic and some other complications revealed it’s presence. I ran track and cross country in college and suffered from recurrent injuries, lack of energy, and repeated inconsistencies in my training. The result was little improvement in 4 years. Did my disease contribute to this? I would think it is likely, but I will never know for sure. Do I wish I found out earlier, yes. There were a number of times I felt like something was not right and talked to my coach and medical staff and they could never find anything wrong, which was frustrating. In a way the diagnosis was a moment of validation for me, I could point to something and say, hey maybe this was the problem all along. From reading comments on blogs from CFS patients it looks like they really want that ah-ha moment too. I would urge them not to jump too quickly onto XMRV being the cause of their ills. If the idea that gluten was the trigger of celiac disease symptoms was controversial, I could change my diet without significant impact on my life. If I found out gluten was not the trigger I would be pissed about not enjoying my favorite foods years, but at the end of the day I can live with that. If we rush too quickly into accepting XMRV causing CFS, patients may be prescribed harsh antiviral drugs that carry very unpleasant side effects. From what I read about CFS and the side effects of antiviral drugs, the combination of the two sounds unimaginably unpleasant. Although it is unfair, humans and science have different time scales, this is a case where scientists are working as hard as they can and the rest of us are going to have to wait.

Friday, January 22, 2010

DDT in Africa

Back when it was released in 1962, Rachael Carson’s Silent Spring was a major jolt to the public consciousness towards pesticides and the environment. The outcry helped found the environmental movement and pushed towards banning the use of DDT in the US in 1972. Unfortunately back then, we didn’t realize to what extent chemicals can remain persistent in the environment long after their discontinuation. And in areas where use was once heavy or heavily contaminated, like a Superfund site, the land remained noxious.

In the early 90s, DDT became a major issue again because it was found that DDT degradation products were toxic to wildlife, particularly alligators. So what kind of group breaking finding could suddenly get the public into a furor and into action once again?

“Abnormally small phalli.”

Aaah, one of my favorite bits of information. Nothing grabs the public’s attention more than a couple of small dicks. Much like BPA, which I talked about earlier this week; DDT and its metabolites are endocrine disrupting chemicals. They act as estrogen mimics leading to feminizing effects in male populations.

This isn’t so much a problem in US but in other parts of the world, DDT use remains high. DDT is so far, the most effective and inexpensive methods for controlling malaria in Africa, where more than 700,000 children die each year (though efficacy is decreasing as mosquitoes are developing resistance). Because of the high exposure to DDT, such as through household spraying, the incidence of urogential defects is incredibly high. Out of more than 3300 African boys studied, 11% were found to have at least one such urogenital defect (which I’ll spare you the details of) compared to the world average which is around 2%. The study found mothers exposed to household spraying were 33% more likely to have a son with such a defect compared to mother unexposed to DDT.

But, mother from villages that do not spray were found to have sons with similar morbidity being at 10%. One explanation is this may be due to DDT residue on food consumed by both villages. It also suggests DDT having generational effects. Most of the villages studied were sprayed between 1945 and 1979, meaning intergenerational impacts may be significant. DDT and its metabolites are known to be passed through breast milk and can remain persistent once in the body. The mother’s body burden, whether exposed directly through spraying or from breast milk, may be leading to the deformities in their sons.

DDT use in Africa remains highly controversial. Persistent organic pollutants such as DDT and PBDE are known to cause chronic toxicity. But how do you weigh out these negatives against the lives saved each year by their use?

Tuesday, January 19, 2010

Host Restriction Factors: Intro

Now that I passed my qualifying exam it is time to get back to blogging. This post is going to be the first in a series about my thesis work on host restriction factors.

Under Pressure- Constant Retroviral Assault: One of the most potent driving forces behind evolution is selection pressure. There is no lack of evidence of macroscopic forces shaping the morphology of organisms, for example the convergent evolution giving sharks and dolphins similar shapes because the environment imposes the same hydrodynamic constraints. Similarly, microscopic factors, like viruses have shaped cellular evolution. Central to the survival of the cell, organism and species as a whole is the preservation of genomic integrity, a process retroviruses directly oppose. The human genome chronicles a long history of retroviral infection, exemplified by 8% of our genome consisting of endogenous retroviruses. This represents a finite percentage of all retrovirus-cell interactions, as these invaded the germ line, became inherited and preserved. Accordingly, some primate genes owe their present form to the intense selection pressure imposed by viruses.

The Red Queen- One can think of the interaction of viruses with the hosts they infect as an evolutionary arms race. The host wants to stay healthy so it can pass on its genes, while the virus wants to infect the host so it can copy its genome. Every time one gains the upper hand the other faces intense selection pressure. For example when a species gets better at resisting a specific virus, the virus must adapt to get around the block or face extinction. Now that the virus has gotten around this defense, the pressure to evolve is passed to the host species. This relationship will continue until one side “wins” or “moves on”. In evolutionary biology this is called the Red Queen Hypothesis The term is taken from the Red Queen's race in Lewis Carroll's Through the Looking-Glass. The Red Queen says, "It takes all the running you can do, to keep in the same place.” Both the virus and host have to evolve rapidly just to maintain the same relationship. This applies to many systems, but for this blog I am going to limit most of what I talk about to the retroviruses, specifically viruses like HIV and its brothers and sisters in the primate world the simian immunodeficiency viruses SIVs. Study of SIVs in their native hosts and those that successfully crossed-species to give rise to the global HIV pandemic and our HIV models in macaques have revealed the presence of a subset of genes termed host restriction factors. In the coming days (who am I kidding, at the rate I blog weeks) I am going highlight the major anti-retroviral host restriction factors and their interesting evolutionary insights. You can expect to see posts on my personal favorites Trim5a and TrimCyp along with others like Tetherin/BST2, the APOBEC family.

To me this is exactly what tracing resistance means. My work is focused at studying how restriction factors work and how they evolved.

Monday, January 18, 2010

BPA shown to be toxic to humans (again!)

I pee Bisphenol-A (BPA). I’m sure you do as well. About 90% of Americans have measurable concentrations of BPA and its metabolites present in their urine.

BPA is one of the world highest produced chemicals (>2 million metric tonnes produced in 2003) and we have a nearly ubiquitous exposure to it daily. Because BPA is so water soluble, the half-life for human oral intake is only a few hours. So the fact we are measuring it in urine means we have a nearly constant exposure to BPA. Exposure to BPA comes mainly through dietary means since it is a constituent of plastics and used as a lining for canned goods (so the food doesn’t actually touch the metal).

There are many health concerns though about BPA because it is a known endocrine disruptor, acting as both an estrogen mimic and androgen antagonist. Anytime chemicals alter hormonal function, it can often lead to a cascade of effects. With BPA this includes liver and pancreatic dysfunction, thyroid disruption promoting obesity and also feminizing effects in males studied. More so, these effects are observed at daily intake concentrations lower than the recommended safe exposure level. Never a good sign.

And producers of BPA and BPA-containing products have gone through great lengths to try and cover up these findings and try and sell BPA as if it were safe product. Such findings come from minutes and memos from closed door BPA industry and advocacy groups:

“Internal notes from the meeting obtained by the Post state that industry representatives discussed "using fear tactics [e.g. 'Do you want to have access to baby food anymore?]." The notes also state that the group focused on "befriending people that are able to manipulate the legislative process. According to the Journal-Sentinel, industry officials "hammered out" a public relations strategy they hoped would include the "holy grail" of "showcasing a pregnant woman to talk about the chemical's benefits.”


These letters gained the attention of both Connecticut and California whom are both considering bans on BPA with the Conn attorney general concluding:

“The chemical industry used "confusion and concealment" and possibly violated Connecticut law in its unsuccessful attempt to kill legislation banning the use of bisphenol-A in baby bottles and infant food jars, Attorney General Richard Blumenthal charged Monday.

Blumenthal, during a news conference with legislators and environmental and public-health activists, said he was concerned by an apparent strategy that was developed during a meeting of packagers and chemical lobbyists in Washington early this year. Misleading consumers, he said, is a violation of state law.”

Just this month however, a new study published in PLoS one confirms a previous survey that elevated BPA urinary concentrations are associated with heart disease. The previous study, National Health Nutrition Examination Survey (NHANES), a large scale and high quality dataset representative of the US adult population, for 2003/04 was the first association found between BPA exposure and coronary disease, diabetes and an increase in specific liver enzymes. Such important findings needed to be confirmed by independent data however.

With the NHANES 2005/06 report just released, looking for the same associations and adjusting for the same variables as the 2003/04 survey, BPA urinary concentrations were again found to be associated with heart disease. Using an independent survey group than the 2003/04, the new study found the overall urinary concentrations to be lower but the heart disease correlation remained virtually the same. BPA exposure and incidence of diabetes and liver enzymes did not prove to be significant in the new data set (though diabetes was sooo close, but alas, not significant). In the pooled data between 2003/04 and 2005/06, heart disease, diabetes and increased liver enzymes were all significant.

While this is confirmation that BPA may cause heart disease further testing is needed. These new findings do however add to the growing body of literature that shows the adverse health effects of BPA exposure.

It’s about time we phase this chemical out.