Tracing Resistance

Happy Earth Day

2011-04-22T11:05:00.002-04:00

Friday Fish Tank - The Doctor

2011-04-01T09:50:00.005-04:00

Introducing The Doctor, my new red dragonscale halfmoon betta. He's most likely a plakat as well, but still a little too young to predict how large his fins will grow.

They glowed like ghosts

2011-03-29T12:40:00.005-04:00

There could be no better time for Deborah Blum to recall the story of the Radium Girls. With fears rising about radioactivity in Japan and spreading elsewhere, it’s easy to forget that we once held radioactive elements as miracle medical cures and items of high fashion. It’s astounding to learn how naively we treated these elements less than a hundred years ago. Compare that to today where the news is abuzz and the public in panic at any detection of radioactivity above background level, even if the levels detected are of no harm.

At the time, radioactive elements were just discovered and businessmen were quick to find ways to utilize them. One property that made radium so intriguing was its otherworldly glow, an eerie blue green shimmer. While today we take for granted our digital watches with luminescent faces, in the early 20^th century there was no such technology. And one popular application of these wondrous new elements was self-luminescent paint, used to make the dials and numbers of watches and other interments visible in the dark. Of course these details had to be painted on by hand, where workers had to craft a fine tip to their brush with their lips between strokes…

“The painters were teen-aged girls and young women who became friendly during the hours together and entertained themselves during by breaks by playing with the paint. They sprinkled the luminous liquid in their hair to make their curls twinkle in the dark. They brightened their fingernails with it. One girl covered her teeth to give herself a Cheshire cat smile when she went home at night. None of them considered this risky behavior. Why would they when doctors were using the same material to cure people, when wealthy spa residents were paying good money to soak in the stuff, when the popular tonic Radithor was promoted by neighboring company? No one – certainly not the dial painters themselves – saw anything to worry about it.

Until, one by one, the dial painters began, mysteriously, to fall ill. Their teeth fell out, their mouths filled with sores, their jaws rotted, they wasted away, weakened by an apparently unstoppable anemia. By 1924, nine of the dial painters were dead. They were all young women in their 20s, formerly healthy, with little in common except for those hours they spent, sitting at their iron-and-wood desks at the factory, painting tiny bright numbers on delicate instruments.”

It was not known at the time but radium is treated by the body as calcium and is incorporated into the bones. The girls’ severe anemia was caused by a degradation of their bone marrow from the radiation. And with each breath they took, they poisoned themselves further. As radium decays, it breaks down to radon, a gas which is also radioactive. With a constant inhale and exhale of lethal air, the girls withered away as their eventual legal fight ensued.

“Katherine Schaub’s jaws were starting to break apart; as she told her lawyers, she hoped the money – they were asking $250,000 each – would pay for her funeral. “If I won my $250,000, mightn’t I have lots of roses?””

The whole story is recounted by Blum brilliantly in this three part series (Part I // Part II // Part III) which is also found in her book, The Poisoner's Handbook: Murder and the Birth of Forensic Medicine in Jazz Age New York. I encourage everyone it up as it is easily the best popular science book I have come across. It is especially interesting to me, as it shows the birth of my whole field, toxicology, something that I had not realized was such a recent branch of science. The book details the work of the two most steadfast scientists, Charles Norris and Alexander Gettler, transforming not only the reputation of the notorious New York Medical Examiner’s Office but also building the foundations of an entirely new field of science. Thorough their endless experimentation and the constant battle against sheer bloody-mindedness of political corruption at the time, Norris and Gettler were unmatched in their novel thinking and perseverance. It was actually quite inspirational to read the lengths and sacrifices these two went through to convince the scientific, legal and political communities that toxicology was a field on its own and worthy of respect. The most amazing part of the book is Blum’s engrossing storytelling as you can glean from the excerpt above. The whole book reads like fiction but it is entirely factual.

So after the next apocalyptic scenario you hear about Japan's radiation reaching American, think back on the Radium Girls and a time when radioactivity was so poorly understood.

Yellow is the new Green

2011-03-19T10:32:00.002-04:00

While on the topic of heavy metals...

"A group of scientists from Brazil have discovered that minced Banana peels rather quickly and efficiently removed toxic metals from wastewater. In fact the method was found to be more effective than conventional water treatment plans. Moreover the same bunch of peels can be used up to 11 times....The results obtained showed that Banana peel was 20 times more effective than other substances."

Very cool. And the best part, banana peels are readily available and can be used in small scale operations where large commercial treatment centers are not present.

Friday Fish Tank - Angelfish

2011-03-18T22:07:00.003-04:00

Why Miley Cyrus and Shrek are toxic to your kids

2011-03-18T22:06:00.001-04:00

They have both been in the news recently but not for the reasons you may think.

Companies like Wal-Mart and McDonalds were forced to recall thousands of items, such as Miley Cyrus jewelry and Shrek promotional glasses, because of the presence of cadmium. And it’s not too uncommon now that you hear on the news of some product made in China tainted with a toxic heavy metal like lead and cadmium. The most common culprit? Cheap jewelry, specifically, children’s jewelry. But is the cadmium present in these items bioavailable? Meaning, what is the risk to the consumer and just how much cadmium in these products can be potentially taken up by the user’s body? Researchers asked just that.

Cadmium (Cd) has broad industrial applications so it is a common environmental contaminant that is studied. Chronic cadmium exposure in humans can lead to kidney damage as well as osteotoxicity, where the bones become soft and less dense leading to increased fractures as well as general pain and weakness. Chronic exposure at any level is likely unsafe because it is not readily removed from the body and bioaccumilates, persisting in the body for a very, very long time. For example, the half-life of cadmium concentration in the kidneys is between 10 to 30 years. Yikes!

Certain cohorts tend to be more sensitive to cadmium as well. Smokers for example directly absorb cadmium from the inhalation of cigarette smoke, leading to a much more direct route of exposure. The group of most concern through is children. Children have been shown to have increased gut absorption of cadmium compared to adults, especially females (anyone know the reason for this? I’d be interested to know). However current guidelines for safe levels of cadmium exposure do not exist for children, so using the recommendation for adults (0.1 µg/kg bw/day) is likely an overestimate of safe levels for a child. In addition, there are no regulatory limits for cadmium levels in jewelry products.

To test whether there is a risk of cadmium exposure from children’s jewelry, in a coming issue of EHP, researchers went out and bought a bunch of cheap bracelets, charms and pendants. No more than $12 an item, most under $10 and many of the items manufactured in China. In order to determine the risk associated with these items, researchers had to simulate the most common pathways a child would be exposed to the cadmium found in these products and determine whether or not the metal is bioavailable. To simulate a child mouthing or sucking on their jewelry, the items were placed in saline for 6hrs. And to simulate the swallowing of one of these items, the jewelry was placed in HCl for on average 24hrs. The US Consumer Product Safety Commission (CPSC) recommends a maximum cadmium level of 18 µg/6hr saline extraction and 200 µg for the acid extraction.

Of the 612 pieces of jewelry purchased for this experiment, more than 270 contained more than 10,000 ppm (1%) cadmium, with 70 of those containing more than 10% cadmium. There did not seem to be any correlation between the amount of cadmium present in the items and the amount of cadmium extracted from the above methods. This is likely due to the different manufacturing of each item (different items made of different alloys, different coatings etc.) which also lead to a high variability between items. But none the less, both extraction methods yielded very high amounts of cadmium. In the mouthing scenario, up to 2200 µg Cd was leached into saline, and 10 of the 48 items tested were above the 18 µg CPSC recommended threshold.

The HCl extraction yielded even more interesting results because the amount leached into the acid increased linearly over time, tested up to 96hrs. A third of the jewelry tested leached more than the 200 µg recommended amount after just 24 hrs and the highest content measured at 20,000 µg. In addition, some jewelry that was damaged with 1-2mm cutss to simulate normal wear yielded 30 times more cadmium than undamaged replicates. But the differences in damaged versus undamaged jewelry were item specific in both the saline and acid extractions which just highlights the difficulty and complexity of trying to simulate and ultimately regulate the risk associated with cadmium tainted jewelry.

The authors raise an interesting point about whether the time points which are recommended are representative enough of actual ingestion exposure. In another study of children swallowing foreign objects, the “transit time through the digestive tract” (read: poop) was 6 days, but varied from 1 to 46 days (eewww). So maybe 6 or 24hrs time points are not long enough to replicate potential absorption. It would appear to me that the acid digestion utilized in this study would only account for cadmium leached while in the stomach and may not take account any enhanced absorption while passing through the intestines. But there are limitations on any simulation.

Overall though, this study really shows how difficult it is to calculate bioavailability of cadmium when the application and usage is so diverse, even when dealing with a specific subset of products like cheap children’s jewelry. But still, researchers were able purchase items that were both really high in cadmium content but also leached about to 100 times the recommended amount. So the danger is out there on the store shelves right now. As if the dreadful pop music and animated movies weren’t enough reason to avoid Miley Cyrus and Shrek, exposure to toxic cadmium can now be added to the list.

When a Project Meets a Personality…Does Success Follow?

2011-03-18T18:16:00.002-04:00

The longer my tenure as a grad student, the more and more I realize that it is a total learning experience. It is not enough for me to only learn the intricacies of select HIV/SIV proteins or the phylogenetic trees of viruses, humans and, non-human primates. I must also figure out what type of scientist I am and what type of project is best for me.

As I mentioned in my last post, thesis project #2 died in late August. As with thesis project #1, it was well thought out and based on good data and better ideas. However, things simply did not pan out, think of it as a “miscarriage of science.” The real question is what did I learn?

Sure I increased my depth of literature read, I learned and got close to mastering some techniques in lab. However, the true value of what I learned is that a project has to have a little bit of your personality in it. If the project is not a good fit how can you possibly be motivated to work hard on it, especially since a good project that is a good fit will test a student’s resolve at times.

Some scientists have amazingly good technique. You can say that they pipette excellence every time they change tips. The lab slang for these prodigies is that they have “very good hands.” Someone with hands of gold can get away with smaller more elegant experiments or using very technical assays to create beautiful data. A scientific paper tries to tell a story, it makes life a lot easier when you have beautiful figures to convince the reader your are right. Unfortunately for me my hands are average at best. Admittedly, had either project panned out I would have had to do some technically challenging assays that would have been hard for me to do well.

So, at the end of August I had to ask myself, what then are my strengths? If I don’t have great hands how can I ever hope to graduate? It was at this point that I had to step back and remember what had gotten me this far, the brute force approach. Whether it was my running or studying in college or basically any other aspect of my life I have always tried to outwork or do more then my “competitors.” Why then would grad school be any different?

The new project has a lot of my personality in it. I am a competitive person and we jumped into a competitive area with this one. I see the project as a race against the other groups. Just like running a race, with science there is no prize for second place. I try to work in lab with that in mind. We are also trying to answer a very complicated question; it does not lend itself to very elegant targeted experiments. Instead it requires me to approach question with a sledgehammer and learn all I can from the pieces. What this means on a daily basis is that I need to generate as many mutant viruses as I possible can as quickly as I can.

I have to say I am very happy with this approach and importantly it keeps me motivated in lab. Will success follow, I am not sure, but so far it has been one hell of a ride so far.

Tracing Updates

2011-03-13T18:57:00.002-04:00

This blog has been dead for quite some time, but Master John has brought us back from the brink. I’m going to ease back into posting with a few updates. (I promised to have a post done by the end of the weekend but I am still running around lab and really need to figure out my taxes)

The Second Demise of TR: August and September became very busy months both John and myself. After months of trouble shooting Master John got things working in lab and was busy trying to get everything together to graduate. At the same time my thesis project number 2 did not pan out. The last time I lost a thesis project I stopped blogging as well… Third time is a charm anyone?

Positive outcomes: John completed his masters and is now working on a paper for publication. He will be the first one out of us to get a paper \m/. I will refer to him as Master John in all posts from here on out….that is unless/until he threatens me with physical harm for doing so.

I have been working quite hard on thesis project 3 and it appears to be working. There will be a few posts about that coming soon.

Possible Rebirth of TR? I really hope that this time the both of us can sustain semi-regular posting on the blog. During our down time one of my friends got his blog on Scienceblogs which is a huge accomplishment….actually I still owe him a drink for that. Every day I watch the news or see CNN’s main page I am reminded at how desperately scientists need to improve scientific communication with the public. As budget cuts loom I think scientists will face a challenge communicating the reasons and importance for basic research. I hope that this blog helps me prepare for such a scenario.

Other updates:Despite our absence from blogging we are still 4^th on the internet for all things crocodile poop Please help us become number 1! We really need to be good at something.

Friday Fish Tank - Sterbai Corys

2011-03-11T15:27:00.003-05:00

A wild blog post appears!

2011-03-11T14:07:00.005-05:00

What is this, a new post??? Only the finest of science smack-downs and political snark could manage to wake this blog out of its state of hibernation. It was just too good not to share.

It was actually a combination of two news events that got me in the blogging mood. The first; BP-apologist, climate change denialist, Rep. Joe Barton (R-Texas), defending the continuation of billions in tax credits and subsidies for oil companies, specifically Exxon. His argument, without government support, these companies would go out of business. Yes, Exxon, the company that in 2008 made the highest quarterly profit for any corporation, ever. $11.68B in a single quarter. And this is person that has been placed in charge of the House Energy and Commerce Committee.

Really doesn’t give you much hope for a clean energy future, does it?

Especially when that same House Committee has proposed a bill sponsored by Chairman Fred Upton (R-Mich.), Rep. Ed Whitfield (R-Ky.) and the Sen. Jim Inhofe (R-Okla.) to block the EPA from regulating greenhouse gases as part of the Clean Air Act.

But during a hearing on the legislation yesterday, there was a moment of absolute glory. Rep. Ed Markey (D-Mass.) spoke out against this Triforce of Stupid, with delicious amounts of science-laden snark. Either he really knows his science or he watches too much Futurama, doesn't matter, Rep. Markey wields science like a hammer against the anti-science kooks he calls colleagues.

From the Wonk Room:

"Mr. Chairman, I rise in opposition to a bill that overturns the scientific finding that pollution is harming our people and our planet.

However, I won’t physically rise, because I’m worried that Republicans will overturn the law of gravity, sending us floating about the room.

I won’t call for the sunlight of additional hearings, for fear that Republicans might excommunicate the finding that the Earth revolves around the sun.

Instead, I’ll embody Newton’s third law of motion and be an equal and opposing force against this attack on science and on laws that will reduce America’s importation of foreign oil.

This bill will live in the House while simultaneously being dead in the Senate. It will be a legislative Schrodinger’s cat killed by the quantum mechanics of the legislative process!

Arbitrary rejection of scientific fact will not cause us to rise from our seats today. But with this bill, pollution levels will rise. Oil imports will rise. Temperatures will rise.

And with that, I yield back the balance of my time. That is, unless a rejection of Einstein’s Special Theory of Relativity is somewhere in the chair’s amendment pile.”

A perfect response. Because really, when faced with such gross and proud ignorance and denial of science, ridicule is the best remedy.

Friday Fish tank - Shark attack pt II

2010-09-11T23:10:00.001-04:00

So yeah, a day late and I don't have any new pictures. This should do as a substitute though.

Friday Fish tank - Red-eared Sliders

2010-09-03T10:55:00.003-04:00

Bring it, Earl!

2010-09-03T09:07:00.003-04:00

2010-08-30T14:20:00.001-04:00

That is all.

Agent Orange: time to pay up

2010-08-30T08:46:00.004-04:00

The headline on POLITICO this morning features a lengthy article covering the long awaited bill the government will have to pay to Vietnam veterans exposed to Agent Orange.

"It’s a world turned upside-down from decades ago when returning soldiers had to fight to get attention for deadly lymphomas linked to the herbicide. Now the frailties of men in their 60s — prostate cancer, diabetes, heart disease — lead the list of qualified Agent Orange disabilities, and the result has been an explosion in claims — and the government’s liability.

The latest expansion, approved by Veterans Affairs Secretary Eric Shinseki in October, adds ischemic heart disease and Parkinson’s and will cost at least $42 billion over the next 10 years. The VA estimates 349,000 individuals are already receiving Agent Orange disability benefits and that number could soon reach 500,000 — or one out of every four surviving Vietnam veterans by the VA’s count."

Agent Orange is something we all learn about one point or another in toxicology research. Not only because a large number of people were exposed and but also because we can still observe the toxic legacy of Agent Orange today - whether it be development of cancers in exposed veterans or the nearly 500,000 Vietnamese born with birth defects. Since I work on environmental contaminants (which include a large variety of herbicides), we also focus on the manufacturing process. Because anytime you combust hydrocarbons at high temperatures in the presence of halogens (like chlorine) you are likely going to form some really nasty dioxins.

In the case of Agent Orange, a chlorinated herbicide, the manufacturing process lead to the contamination of one form of Agent Orange with 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD). TCDD is especially important in our field because it is such a potent inducer of the aryl hydrocarbon receptor (AhR), which triggers a cascade of reactions to metabolize and detoxify foreign chemicals. In fact, the toxicity of other organic contaminants are measured as ratio of their AhR induction compared to that of TCDD. In other words, the toxicity of TCDD is the measuring stick in which we compare the toxicity of other relevant chemicals to. This ratio is known as the toxic equivalent factor and can be a useful tool in environmental risk assessment.

But bringing this back to the veterans, there is still hesitation from both politicians and scientists to support the newly added diseases to the veteran compensations.

"The VA had contributed an important piece with a 2006 study analyzing the incidence of heart disease among Vietnam veterans who had served in the Army Chemical Corps. And Shinseki, who himself served in Vietnam, found that this built on well-established evidence that dioxins present in Agent Orange could damage blood vessels. “Veterans who endure health problems deserve timely decisions based on solid evidence,” he said.

Nonetheless, the leader of the IOM panel, Dr. Richard Fenske of the University of Washington, told POLITICO that he was “surprised by the speed” with which the VA decided to add the presumption for heart disease. And Weidman argued that the department repeatedly ignores what he sees as a central tenet of the 1991 law: that more should be invested in scientific studies of veterans themselves.

“The whole concept of the 1991 law was to leave it to science, not politics, but we haven’t invested in the science in the 20 years since,” he said. In a shot back at Webb, he added: “If you want more scientific data, fund the damn science.”

For all the debate over Agent Orange, what’s most surprising is how little or no effort has been made to track down specific infantry units that operated in the widely sprayed areas of Vietnam."

Kind of sad really. Though one thing the article ends with that I can agree with; this kind of retroactive tracing of exposure is slow and inaccurate and just further emphasizes the need for electronic medical records. Not only useful for civilians but for military personnel is could easily be used to track from the time of enlistment to retirement which individuals were exposed to what chemicals, the exposure level, and what health effects develop later in life.

As best said by German thrasher Tom Angelripper, "Agent Orange - the fire that doesn't burn!"

Friday Fish tank - Shark attack!

2010-08-27T10:51:00.004-04:00

I'm a little late for Shark Week but anytime of the year is great for some shark trivia. And even better when its in infographic form! Plus, I always knew there was something wrong with the way that Megashark attacked...

Click for the full image.

“Bow down fools! My name is Tyrone”

2010-08-21T13:11:00.004-04:00

I have covered atrazine before (here and here) and highlighted some of the back story of the lead scientist leading the charge, Tyrone Hayes, against atrazine manufacturer, Syngenta. Now, Syngenta has filled an ethics complaint against Hayes for sending Syngenta employees “explicit and obscene” emails over a period of several years. Hayes regrets if he offended any friends with his language but remains unapologetic, saying his emails were in response to verbal threats and abuse by Syngenta.

Syngenta has compiled these emails into a 102 page document posted online. And they are worth a read. Come on, how awesome is it to have a scientist end an email with “word to your mother.” It’s pretty much 102 pages of Hayes jive talkin’ and smack talkin’ Syngenta.

Some highlights:

“my abstract for e.hormone below. ...

"strike like lightening

voice like thunder

i hear the fear when you call my name

oh so frightening

makes you wonder

if the second coming done already came

tyrone

WHERE MY DAWGS AT? ATRAZINE AND THE FALL OF MAN”

and...

“you thought you hit a nerve

but i threw a curve

and sho' cold busted a vein//see the man in black just keeps coming back

while you flushin yo money down the drain

so go'head, bring "your boys"

cuz i'm bringing the noise

i told ya, you can't stop the rage

you been braggin but we'll see who's tea baggin

when TDawg hits the stage”

This isn’t the first time Hayes has been known to talk in rhyme, such as the Atrazine Rap:

Reading the taunting emails, I have to award Dr. Hayes a few internets for his grade A trolling. Pretty much, I just picture this:

Friday Fish tank - American Eel

2010-08-20T09:49:00.001-04:00

Get out of my killifish traps you stupid eel!

What I did today

2010-08-17T00:09:00.003-04:00

Thanks for the picture Anne Cooper!

Friday Fish Tank - I need to take more pictures...

2010-08-13T21:10:00.002-04:00

...I'm running out of my old ones.

Tracing Resistance: Your one stop resource for....Crocodile Poop?

2010-08-07T19:57:00.008-04:00

A while ago I wrote a short post about a fascinating archeological discovery entitled "Shark-Bitten Crocodile Poop Fossils Found (No, Really)". Of all my posts, this one has generated the most hits from Google searches. These people searching crocodile poop are not discrete about their searches. In fact, they are quite open about the fact that they want info on Crocodilian poop. Terms have included "CROCODILE POOP" and "where crocodile goes poop" and the simple non-yelling "crocodile poop". I was totally unaware of the fact that there people out there in desperate need of crocodile poop information. The real shock came when I googled the term "crocodile poop". This is what google returned.

Thats right!!!! Our blog is the #5 resource on the internet for crocodile poop! This made me realize there there is an unfulfilled need for accurate and reliable crocodile poop reporting on the internet. I mean if our little blog is number 5 what does that say about humanity as a whole? How could such a fundamental issue be ignored by the entire internet. I think John and I have a new goal, TO BE THE NUMBER ONE WEB RESOURCE ON CROCODILE POOP! Let's face it, we are not good or unique enough to be #1 at anything else on the internet. I think have a really good shot at this one. I mean look at the number one link, we can do so much better. I ask all of our followers and readers to help us with our goal to be the # 1 internet site for crocodile poop!

PS. Even more perplexingly all of these hits have come in the past week or so, if anyone out there knows why there has been such a rush on the search term "crocodile poop" let me know. I want to cover it.

Kevin's Review of House of Numbers

2010-08-07T18:53:00.003-04:00

After my involvement in a lengthy debate on the House of Numbers (HoN) Facebook page I wanted to watch the film for myself. But I was stuck in an unfortunate catch-22. I wanted to see the film but in no way wanted to contribute to funding of its message. Luckily, some others in the HIV dissident community made it possible for me to watch their copy. I am very thankful.

I have been trying to figure out how to write about the film. I saw it three weeks ago and right now I am wishing I had taken some notes. I think my overall impression of the film may actually be shocking, I did not think it was that bad. In fact I agree with a few points. I was really expecting a parade of pseudoscience, blatant denialism, questionably edited clips, and just plain misinformation. Although, the documentary is defiantly biased, I thought it was going to be A LOT worse. Maybe that’s why I do not think it was that bad. Either way, I am jealous of Brent Leung (pictured left) for talking science with some of the leading names in HIV. I wish I could have had the opportunity to meet with his interviewees. I would have put that time to better use too.

Overall, Mr. Leung puts his own stamp on HIV dinialism. While some argue that thevirus does not exist, the virus does not cause AIDS, or the virus is harmless and the drugs cause AIDS, the main message of HoN is that the testing and diagnoses are inherently unreliable and that poverty is the real issue at hand

I do not disagree with him on the last point. With poverty comes a lack of education, nourishment, medical care ect.. I agree with his point that we simply cannot combat HIV in Africa without addressing the issue of poverty; unfortunately right now both of these are “incurable.” Does more need to be done about poverty? YES! Poverty and infectious disease are inseparable they each contribute to the other. No one can deny that the number of people who are in desperate need dwarfs the number of people living with HIV. If you combine poverty related ailments such as starvation, malnutrition, deaths from preventable/treatable illnesses, water borne illness, and deaths due to lack of sanitation or medical care that number would again dwarf the 30-35 million estimated people living with HIV (UNAIDS 2007). Malaria alone caused 190 - 311 million clinical episodes in 2008 (WHO). In the USA these problems sound foreign but for millions, if not a billion people, they are a daily reality.

To this extent I accept the poverty argument. However, Mr. Leung conveniently ignores poverty’s influence of the very thing he attacks- HIV testing and diagnosis. A significant portion of the film is dedicated to testing/diagnosis and how it is part of some big consperiency. From Leung’s experience at a free HIV testing kiosk in South Africa, to reviewing diagnosis criteria for remote African locations, to interviews with some individuals who may have had a false positive (emphasis on may), Leung tries to imply that the testing/diagnoses are fundamentally flawed and biased by some unknown hand.

The most glaring example of the omission of poverty as a factor for the “correct” HIV/AIDS diagnosis came from the criteria used by remote African doctors. Numerous times throughout the film the stringency of these criteria are compared to those in developed nations, however, WE ARE NOT TALKING ABOUT DEVELOPED NATIONS. When doctors lack basic supplies like gloves, clean instruments, antiseptic, antibiotics and a dying patient comes in, confirming a 100% positive HIV/AIDS diagnosis is not as important as easing the pain or saving/extending the life. I am sure mistakes are made, but what would doctors rather do, spend what little money they have on sophisticated tests to confirm an HIV diagnosis or use their meager funds to buy supplies to save many more lives? Seriously, what good does a highly accurate test do for a person dying of AIDS? Sure, you can accurately tell them exactly what they are dying from, but you can also tell them that they are shit out of luck when it comes to morphine to dull the pain from the many systematic infections ravaging their bodies. POVERTY COMPOUNDS EVERYTHING, IT IS THE THEME OF THE ENTRIE MOVIE! WHY IS THIS CONVENIENTLY LEFT OUT?

Another large segment of the movie was dedicated to Mr. Leung taking an HIV test at a free testing kiosk in South Africa. In 2007, UNAIDS estimated that around 11% of the total population was HIV positive. With an instance of infection that high, getting people to know their status is VERY important. What Leung fails to tell the audience is that there are nearly 50 million people in South Africa. Testing a significant portion of the population (possibly testing people more that once) is a massive undertaking. It would be a massive undertaking in the USA, just look at the great lengths the government had to go through to get people to fill out a 10-question census. Now think about getting people to consent to a blood test that could give you some very bad news. South Africa is not a particularly wealthy nation. They need a very cheap, easy to administer (anyone can be trained to do it), and easy to analyze (no expensive or sensitive reagents or equipment). It is possible that a test that meets these criteria sacrifices some small amount of precision. Leung attacks the fact that they confirm a positive result from a marginally less accurate test with a more accurate (probably more expensive) one. However, isn’t this good medicine? They are making sure they do not accidently give someone the wrong diagnosis. Wouldn’t anyone want to be tested again?

The idea of confirming a life-altering diagnosis with multiple tests is a controversial idea in this film. This is a luxury that people have in highly developed nations. There are many ways to test for HIV, antibody, antigen, viral load, and each has positive and negative qualities. Importantly, each test tests for a different marker; immune response, viral protein, and viral genome respectively. Different tests have different levels of accuracy, which are stated in the testing material. No test would be approved by the FDA unless it was pretty damned accurate. Since a positive test is a HUGE deal, tests manufactures commonly suggest that you take another test to confirm the diagnosis. Isn’t it only natural to ask for a second opinion when confronted with some other life changing diagnosis, why not HIV?

Overall Mr. Leung makes some valid points. If the movie argued that we needed to combat multiple ailments instead of focusing on one virus, I would support it. If the movie talked about trying to combat poverty through education and development programs, I would support it. However, these are not the messages of the film. This documentary is simply another attempt at advancing an HIV denialist agenda. I CANNOT SUPPORT THAT. If they were being open minded why would they intentionally omit so many facts? HIV deniers live in a House of Glass and they should not throw stones.

Friday Fish tank - Jack Dempsey Cichlid

2010-08-06T16:16:00.003-04:00

My latest additions, a pair of Jacks! Expect more pictures, my camera battery decided to die after taking just this one.

AGW - a theory not in crisis

2010-08-03T11:53:00.006-04:00

To all the climate change denialists - eat it.

The 2009 State of the Climate report released today draws on data for 10 key climate indicators that all point to the same finding: the scientific evidence that our world is warming is unmistakable. More than 300 scientists from 160 research groups in 48 countries contributed to the report, which confirms that the past decade was the warmest on record and that the Earth has been growing warmer over the last 50 years.

Where will the goal posts be shifted to next? Humans aren't the cause, we're coming out of an ice age, or some other distorted amalgamation of pseudoscientific jargon. Whatever your flavour of denialism, the scientific consensus remains remains the same. And until a substantial body of evidence is produced to overturn it, the theory of AGW holds true.

Please, Governor Jindal. Stop trying to help the environment

2010-07-31T22:54:00.004-04:00

Of all the characters that have to come to the light during the Gulf oil spill, one of the biggest “winners”, if you could really call them that, has been Louisiana governor, Bobby Jindal. And I give him some credit; he’s been out there on the beaches from the start getting as much face-time as possible with those impacted. He’s also been one of the most vocal people decrying the inaction of the government. He demanded immediate action, and if government wasn’t going to do anything, than he would.

And this earned the Governor some serious credibility in the media. His main proposal, the construction of artificial barrier islands made from dredged sand, became a rallying point for both news outlets and politicians. The whole project however, reeked of demagoguery. The reason the government wasn’t building sandberms was because, quoting one coastal geologist, “I have yet to speak to a scientist who thinks that the project will be effective.” The EPA too stated, “there is no evidence the project will stop oil from entering marshes and estuaries.” But heated political pressure trumped science, and the federal government caved in, authorized the funding for this estimated $340 million project. And just as the scientists predicted, the berms aren’t doing a damn thing. Well actually they are, they’re washing away into the ocean, (click here for pictures).

But learning today, this isn’t the first time during this crisis that Jindal rushed into an absolutely idiotic idea to make it seem like he was doing more than the federal government.

“In May, a few weeks after the Deepwater Horizon rig exploded and began leaking as much as 60,000 barrels of oil a day into the Gulf of Mexico, Gov. Bobby Jindal ordered the opening of many of the state's massive Mississippi River diversions, hoping that the torrent of fresh water would drive the oil back into the sea.”

….*blink*….really?

Govenor Jindal clearly does not understand how the tides work. Though I guess his sand island project was testament enough of his oceanographic ignorance. There are many species that can only thrive in the brackish environment of coastal marshes. Suddenly hitting the marshes with a deluge of freshwater is a great way to disrupt this delicate ecosystem. For one, oysters harvested from the marsh are a $300 million industry for Louisiana. Scientists are now reporting up to 80% oyster mortality in areas flooded with Mississippi water. And it may take three years until the oyster stocks recover, if they recover.

Seriously Governor, you’re taking an environmental disaster and just making it worse.

Friday Fish tank - a very sick Medaka

2010-07-30T15:39:00.005-04:00

Sometimes my results aren't so pretty. He's alive by the way. And that long clear tube below the eyes, that's the heart. Slowly, erratically, twitching.

Only In Science

2010-07-30T11:20:00.001-04:00

You know you are becoming a scientist when certain strange or extraordinary things become routine. For example, I conjure up boatloads of HIV anytime I need some from nothing more than some DNA and cells. I then proceed to work with a lethal virus at all hours of the day and night, even before meals without so much as an afterthought (although I do wash my hands). If you think this is crazy wait until the day you hear what John does in his lab. It scares the shit out of me.

Recently I have been growing a bunch of cell lines for my project. Really all I have been thinking about for the past few days is OMG I have to take care of more of you little needy bastards with all of you different growth rates and different requirements. Before the coffee hit my brain this morning as I checked to make sure I did not screw something up that killed half of my cells overnight I starting thinking of the collection I had going. Growing in my incubator was

53 year old male

14 year old boy

A human embryo with a cold

An African Green monkey (unknown species atm) edit: I think its a vervet

2 humans fused together

Another human of unknown age and sex

2 rhesus macaques

This is starting to be quite the collection. I was thinking of writing something about a family at the Bronx Zoo watching monkeys while pushing their conjoined twins around in a stroller, however that may be a little morbid considering that all of the people and monkeys have died thus allowing me to have these cells. Now I feel like a jerk. Science is truly a strange profession. Any way I am off to tend my growing army of cells while thinking about how utterly strange growing a zoo can be.

I knew the story before I knew the story

2010-07-28T12:32:00.010-04:00

Its been a big month for asbestos news. Featured as both the cover story of the latest Environmental Health Perspectives issue and the topic of a 9 month joint research piece by the Center for Public Integrity's International Consortium of Investigative Journalists and the BBC, I can’t say the news is good.

Honestly, I didn’t know much about asbestos before reading up recently, so what may be shocking to me may be old news to others. Pretty much the extent of my knowledge is that asbestos exposure, mainly occupational, can lead to mesothelioma, at least that’s what I gather from the daytime lawyer ads that run during the commercial breaks of the Price is Right. But occupational health and safety is something I’ve been getting more interested in, so now looks like the perfect time to look a little further for some hard numbers. And it seems pretty clear; asbestos exposure leads to cancer among other adverse health effects. Not only is asbestos one of the most commonly encountered carcinogens in the workplace but as the World Health Organization noted, asbestos related cancers account for half of all occupational cancers worldwide.

This leads into one of the scariest conclusions from the latest investigative report. It is estimated, that by 2030, asbestos related deaths worldwide will have reached 10 million.

10,000,000 deaths. Preventable deaths.

Such deplorable numbers give EHP good reason to renew the battle cry for banning the use and trade of asbestos. While over 50 countries have banned the asbestos and found safer alternatives, the United States is not among them. Ah, glorious American Exceptionalism at work! And international attempts to ban the trade of asbestos have failed repeatedly. Mainly because the amount of money being dumped in by the industry to oppose any sort of regulations of asbestos. Since 1985, roughly $100 million dollars have been spent by industry groups to keep the asbestos flowing. Asbestos is big business after all, with over 2 million tons being traded annually. And despite the well understood toxic effects of asbestos exposure, in developing industrial countries, asbestos use is on the rise. So like coal, the use of asbestos in the biggest growing economies like China and India are only climbing. Experts are warning of a looming cancer epidemic in these and other nations but the demand is high and the industry in strong.

Asbestos is a known human carcinogen yet an estimated 125 million workers are at risk of exposure. Why are we knowingly putting so many in danger? It’s insidious enough that the United States hasn’t banned its use but its other countries, like Canada, carrying out to villainous degree the export and opposition to regulation which keeps this industry alive. Public pressure has led Canada to ban the use of asbestos domestically but that hasn’t stopped them from shipping it overseas. Too toxic for their own people but perfectly safe (as they claimed when battling the World Trade Organization against legislation which eventually led to an asbestos ban in the EU) when its being sold to developing countries. It’s exploitation and a flagrant disregard for the safety and health of workers worldwide all in the name of making money.

I always feel my closing sentiments in a post are nearly identical when writing about widely used toxic chemicals. And seriously reading up on asbestos for the first time, it’s deflating to run into the same story I’ve seen before, again and again. We know X is toxic, we have alternatives for X and yet, attempts to regulate X are faced with fierce, well-funded opposition from industry. The richest countries keep selling to the poorest countries, and we are ineffective at protecting the health of those most at risk. Enough already.

Sleep and Science

2010-07-28T10:18:00.003-04:00

I try not to talk about my research too much on the blog, mostly because it is in a sub-niche of a sub-niche of a topic related to HIV and well, there may be like 100 people in the world who would find it interesting. Of those 100 people none of them know about the blog and most certainly are not one of our 12 die hard followers (thanks guys). I will try not to bore all 12 of you with the hard-core details of my work. However, I have come up with an interesting observation.

I ended up working 25 hours straight in lab Sunday-Monday to try to get a result, an inconclusive result (shakes fist). However, I must say that following this result I had one of the most satisfying sleeps ever in the history of sleep. Seriously! I was up for over 30 hours then took a 4 hour nap (ok sleep) and then went to bed around the time I normally do. During those 8 hours I got 8 hours of possibly the most intense sleep ever. I woke up and almost needed a cigarette because it was so satisfying. Think sleep+crack+crystal meth+winning the lotto and an olympic medal at the same time and that may get you close to the way I felt Tuesday morning.

This marks a milestone in my research. Normally my research has a dramatic negative impact on my sleep. Whether it is because my mind is going at escape velocity thinking science, stressing about some negative result, a coffee overdoes or that can’t sleep like a kid on Christmas eve in anticipation of a result. All of these lead to positive feedback loop of caffeine overdose (sleepy=bad when working with a virus that can kill you) and even less sleep. Waking up Tuesday morning marks the very first and possibly the last time science has ever drastically improved my sleeping; actually it took it to the next level. This is in spite of having to repeat the assay, but after a sleep like that I honestly don’t care right now.

HIV vaccines cause 50 percent false positive rate in HIV tests-OMG!

2010-07-24T09:43:00.010-04:00

Since it has been so long since I actually posted anything of merit, here is a quick update. The “documentary” House of Numbers has been released, it is now available for purchase on DVD or on demand. I know everyone is really excited about that news. I actually lucked out and was able to watch it without having to pay for it (there was no way I was actually going to give them a cent). I was wondering if I would have the chance to see it since I caused such a stir on their Facebook page a few months ago. I was planning on opening up our revamped blog with a review of the movie, but I came across this note from the House of Numbers blog that has bothered me a lot more than the movie.

For anyone keeping score at home HIV dissidents belong to many schools of thought ranging from the virus does not exist, the virus may exist but has not been isolated, the virus exists but does not cause AIDS and the House of Numbers opinion that the testing is flawed. Now, none of these arguments rest on scientific fact, however this note is noteworthy for its blatant disregard for facts (presented in the original article that they actually linked at the bottom) and its lack of scientific comprehension. What really bothers me is that someone actually took the time to twist the facts and make HIV vaccine work sound like a major conspiracy. I suppose HIV vaccine trials must account for the 30+ million people that are estimated to be infected.

Here is a sample of the first few paragraphs, I encourage you to read more.

Tuesday, July 20, 2010

HIV vaccines cause 50 percent false positive rate in HIV tests

(NaturalNews) It may come as a big surprise to most people, but HIV tests given to people today don't actually test for the presence of the HIV virus. Rather, they test for the presence of HIV antibodies that the immune system creates to defend itself against HIV. And just because you have HIV antibodies doesn't mean you actually carry HIV. In some circumstances, up to 50 percent of HIV positives are false, causing havoc with the lives of those patients who are falsely accused of being "HIV positive."

This startling fact was revealed in a recent study that's being published in the July 21 issue of the Journal of the American Medical Association. It shows that patients who are recruited for HIV vaccine trials often end up testing positive for HIV even though they were only exposed to the vaccine, not the virus.

"Almost half of HIV-negative people who participate in clinical trials for HIV vaccines end up testing positive on routine HIV tests -- even though they're not actually infected" reports US News & World Report.

Some vaccines caused a false positive rate of over 86 percent.

I will give your brains a moment of recovery…how about now?,. Oh a couple more seconds? I understand…. Lets now look at the first couple paragraphs from the original source which is a recap of a scientific article, I am glad people feel safe getting their health information form third hand sources like House of Numbers. I am sure that means everyone feels comfortable buying underwear from thrift stores too. Any way here is the original article’s intro….

SUNDAY, July 18 (HealthDay News) -- Almost half of HIV-negative people who participate in clinical trials for HIV vaccines end up testing positive on routine HIV tests -- even though they're not actually infected, a new study shows.

The reason: They underwent what experts call "vaccine-induced seropositivity/reactivity" (VISP), meaning that they possess immune system antibodies to the virus but not the virus itself. That's an important distinction, since routine HIV screening looks for virus antibodies only.

Experts pointed out that the results are not new or surprising, but simply underline the delicacies of conducting trials into HIV/AIDS.

"You need to make sure to use other forms of testing for HIV, for example, viral load or p24 antigen, not just HIV antibodies. And people who've been in trials need to know their antibody status by the end of the trial," said Dr. Michael Horberg, director of HIV/AIDS at Kaiser Permanente in Santa Clara, Calif. "If it is a false positive but they do not have HIV infection, that would be very important for them to know, especially if they do repeat testing as part of good preventive health.

Hopefully you recognized two totally different points of view. The (non)issue at hand here is that people who participate in HIV vaccine trials may test positive for the presence of antibodies that specifically recognize HIV. This is a fact that no one is trying to cover up. Many vaccines have been developed to illicit an antibody response. The hope is that if the right type of antibodies are made, a person would be relatively resistant to HIV infection. From the scientist’s point of view having people develop such responses is a very good thing. This is EXACTLY WHAT THEY ARE TRYING TO DO, IT IS NOT SOME CONSPERIENCY IT SAYS SO IN THEIR PAPERS AND GRANTS AND TALKS! In fact this process is measured in a way that nearly identical to the antibody based HIV test. Again, this is in their methods sections, it is not hidden. For whatever reasons the House of Numbers crew thinks this is evidence that the testing is flawed. If anything, this observation supports the idea that HIV is in fact a real virus. We can take viral proteins, proteins that are identical to those in infected individuals, inject them into healthy subjects and get an antibody response. However these people do not develop AIDS. People normally do not develop auto reactive antibodies (antibodies that attack oneself), so this in some ways rules out arguments that AIDS is caused by some internal factor. Importantly, the fact that a test subject may test positive is disclosed up front at the enrollment step and measures are in place to show this person participated in a vaccine trial. I really cannot understand what the House of Numbers people are doing with this post. Honestly, this may quite possibly be the worst argument against HIV and HIV testing that I have ever read.

To put this in perspective anyone who has received the BCG tuberculosis vaccine can relate to what is going on here. Although receiving this vaccine is rare in the USA, it is standard in many parts of the world. If you take a "normal TB test” in the USA after receiving the BCG vaccine you will test positive. I have seen this happen with European friends. Does this mean that the testing is flawed? No! Every test has its limitations and those are disclosed. Are there plans in place for this very scenario? Yes! Sound familiar? In this case a simple chest X-ray can show the lack of lung damage that is a hallmark of TB infection. Along similar lines, a viral load test or antigen HIV test can rule out the possibility that an HIV vaccine trial subject has the virus. What do you think they use in clinical trials when they look at how well a vaccine protects an individual? Again these tests are outlined in the methods section of numerous papers. Maybe the House of Numbers of people missed that concept along with many other facts.

I think this note proves a point. House of Numbers and related entities do not care about facts…at all. This is one of the weakest, nonsensical arguments that has ever been written. Either the author has no concept of basic science or they choose to ignore/distort basic facts. These facts go well beyond the bounds of the “HIV industry,” they are fundamental concepts that have been in place before the first HIV patient was ever diagnosed. This also shows how utterly desperate AIDS dissidents have become to try to advance their points of view. Regardless, this note only panders to people’s insecurities and fears in an attempt to advance an agenda of AIDS denialsim and not the open mindedness they claim.

Friday Fish tank - Festivum Cichlid

2010-07-23T10:35:00.002-04:00

100!

2010-07-22T23:02:00.002-04:00

Well this is our 100th Post. I have no idea why typing this is so scary, but John and I wanted to do something special for this one. At first we mocked each other about who was going to do it, but neither of us felt worthy to type the 100th post for our 12 diehard followers. The result was an epic spell of inactivity. During this time science and life got in the way and the 100th post still loomed. The longer we went without a 100th post the more important this one had to be. In our quiet period, there has been good data, bad data, conferences, an environmental disaster, crazy denialists and too many cool papers to blog about. With each one we reassured ourselves that once the 100th post was done, blog posts would flow out of our fingers like oil out of BP’s well in the Gulf. EPIC BLOG FAIL!

Ironically, our total lack of activity for the last two months has finally given us a reason to write the dreaded one hundredth post…….WE ARE RELAUNCHING THE BLOG! We are opening up with a new look and commitment to blog more frequently. Some posts may not be as long, but we are going to try our hardest to stay current and hopefully more entertaining. John is going to get us started with post 101, consider this post and many more will follow. Sorry to everyone who actually checked our blog and have been disappointed to see nothing has changed.

Kevin and John

BP will not be outdone!

2010-07-22T20:02:00.006-04:00

Ok, that was probably in bad taste. But, China's current oil spill, the worst in the nation's history, is growing. The NYT reports, "an official warned that the spill posed a 'severe threat' to sea life and water quality. " Too bad we won't be getting much more information than that considering China's state controlled media. Greenpeace has released several images of the oil spill and cleanup efforts including the one above (sans Kanye), which are frankly, pretty horrific.

Nuclear Fallout

2010-07-22T19:14:00.007-04:00

Since the detonation of the first nuclear device, new forms of elements have been introduced into the environment. Certain radioactive isotopes that are characteristic of nuclear fallout, previously unseen in nature, could now be detected globally. And while this sounds bad, the detection of these isotopes can act as useful and reliable markers for scientists. In other words, if we can measure these isotopes in our sample, we know that whatever it is we are measuring, dates no further back than 1945.

So say for example, you’re a billionaire and you just spent half a million dollars on wine that is said to have been owned by Thomas Jefferson. You’d probably damn well want to know whether or not you just bought yourself a couple bottles of counterfeits. Just ask bazillionaire Bill Koch, because he did just that. After purchasing the wine he grew weary of the seller’s credibility and sent the bottles off for a battery of tests. One of which included testing the bottles for traces of Ceasium-137, an isotope not naturally occurring but rather a product of nuclear fallout. After a week of tests in a detector surrounded by walls of 10in thick lead, the tests came up negative for Cs-137. The wine was at least bottled before the atomic age. But other tests for authenticity did not come back as promising…

…alright, I’ve gone off track, back to radioisotopes! Ok, they aren’t as exciting as stories about billionaires, rare wine, and deception but I shall proceed anyway. What else can radioisotopes be used for in terms of environmental science? Since we know when they first entered the atmosphere (which then takes about 10 years to equilibrate with the ocean) we can use their detection as a way to measure the patterns and rates of ocean circulation by seeing where and how far they penetrate the depth the of the water column. For example, the figure on the left shows how the concentration of bomb-produced C14 (different than naturally occurring C14) in the oceans varies with depth. The three depths, top-to-bottom, being 0, 1200 and 3500m. And what we see is very high radiocarbon in surface waters with highs around the 30° latitudes where convergent wind patterns cause the air to sink over the ocean. But as you go down with depth there is a much higher amount in the North Atlantic compared to the Pacific, and in general, the C14 is higher in the Atlantic with depth. This match up with the model scientists use to map ocean circulation, often simplified into the well known “conveyer belt model”. Seen below, the areas where deep water is formed are the North Atlantic and the Southern Ocean around Antarctica. In these areas, the surface water becomes sufficiently cold and salty that its density rises enough to make the water sink. This newly formed deep water is “young” by comparison since it has been recently re-oxygenated. This young water can then be tracked by tracers, such as radiocarbon, as it moves South. So we can determine the rate at which the currents flow and in which direction based on the concentration of our tracer. The older water, which moves sluggishly northward in the Pacific along the ocean bottom has the least amount of radiocarbon because this water has been not been near the surface for a very long time. It takes roughly a 1000 years for the ocean to turnover. So that C14-rich water in the North Atlantic, as it sinks and travels globally, it won’t see the surface again for another 1000 years.

But back to the bombs. The bombs are the reason we now have these tracers at our disposal. It’s great that along with nuclear energy, radioisotope tracers and everything else that came out of this original technology, nuclear proliferation arose out of the desire to destroy other humans. And nuclear weapons performed this task with such gusto that we are now capable to demolishing nations in the most excessive and terrifying fashion we’ve ever known. Just how many bombs were dropped in the name of testing and political posturing? Watch the video below, it starts slow, but just watch it. Every nuclear weapon detonated from 1945-1998. After the 3 minute mark, the grim horror and reality begins to onfold.

Quoting the Bad Astronomer, “what the hell were we thinking?”

The demonstrations of power between nations is clear. But to the absurd degree in which it was carried out, it appears the Cold War was nothing more than a glorified penis waving contest between the US and USSR. Probably a far more apt description would be from Carl Sagan who said "[the nuclear arms race was like] two sworn enemies standing waist deep in gasoline, one with three matches, the other with five." Sagan was an outspoken critic when it came to stockpiling of nuclear weapons and he had the ability to communicate this deathly growing and irrational problem like no other. Read the following passage from Sagan’s “The Nuclear Winter” and then watch that video again.

“Except for fools and madmen, everyone knows that nuclear war would be an unprecedented human catastrophe. A more or less typical strategic warhead has a yield of 2 megatons, the explosive equivalent of 2 million tons of TNT. But 2 million tons of TNT is about the same as all the bombs exploded in World War II -- a single bomb with the explosive power of the entire Second World War but compressed into a few seconds of time and an area 30 or 40 miles across …

In a 2-megaton explosion over a fairly large city, buildings would be vaporized, people reduced to atoms and shadows, outlying structures blown down like matchsticks and raging fires ignited. And if the bomb were exploded on the ground, an enormous crater, like those that can be seen through a telescope on the surface of the Moon, would be all that remained where midtown once had been. There are now more than 50,000 nuclear weapons, more than 13,000 megatons of yield, deployed in the arsenals of the United States and the Soviet Union -- enough to obliterate a million Hiroshimas.

But there are fewer than 3000 cities on the Earth with populations of 100,000 or more. You cannot find anything like a million Hiroshimas to obliterate. Prime military and industrial targets that are far from cities are comparatively rare. Thus, there are vastly more nuclear weapons than are needed for any plausible deterrence of a potential adversary.”

Indeed, what the hell were we thinking?

The Cybermen don't stand a chance against him

2010-05-28T07:05:00.005-04:00

...the Daleks, maybe.

From the video description:

"ArcAttack employs a unique DJ set up of their own creation to generate an 'electrifying' audio visual performance. The HVDJ pumps music through a PA system while two specially designed DRSSTC's (Dual-Resonant Solid State Tesla Coils) act as separate synchronized instruments. These high tech machines produce an electrical arc similar to a continuous lightning bolt and put out a crisply distorted square wave sound reminiscent of the early days of synthesizers."

Friday Fish Tank - Feed Me!!!

2010-05-28T06:48:00.003-04:00

The sight that greets me anytime I open up the Captain's tank. He's so spoiled that he will only eat if he's hand fed. Little brat.

These photographs speak for themselves

2010-05-26T10:36:00.003-04:00

View the whole collection here.

Your sperm is safe

2010-05-25T16:26:00.003-04:00

One of the biggest concerns surrounding BPA is that it is a known endocrine disruptor (ED) and acts as both an estrogenic and anti-androgenic agent. Now for us macho men this can mean some pretty bad things. For example, based on occupational exposure levels of BPA, factory workers with increased exposure were found to have a lower sex drive and higher rates of erectile dysfunction (the other-ED). The levels of exposure faced by these workers though were much higher than anything we would come across on a daily basis. But we are still constantly exposed to BPA, with over 90% of the population having measurable BPA in their urine.

So how do these everyday levels correlate to sexual effects in a normal healthy male? A new study in EHP attempts to answer just that. By measuring BPA urinary concentrations, the researchers sought to see how they measured up with semen samples collected from 375 men. I quite enjoyed how they chose these participants. What better way to determine if you got a healthy reproductive system than if you just impregnated your partner. Internet high-five to all 375 of you.

So, to get to the answer of the original question, the researchers conclude:

“Our results suggest that, in fertile men, exposure to low environmental levels of BPA may be associated with a modest reduction in markers of free testosterone, but any effects on reproductive function are likely to be small, and of uncertain clinical significance.”

Whew, your sperm is safe. But still, that doesn’t mean you shouldn't limit your exposure to BPA since as its been shown again and again, BPA is toxic to humans.

Atrazine still shown to be toxic to amphibians

2010-05-25T12:20:00.002-04:00

Oddly, the post we’ve gotten the most comments on here is my atrazine article awhile back. So I figure now would be a good time to see if there have been any new research in support of or in opposition to atrazine’s (ATZ) toxicity to amphibians.

And in last month’s EHP ( I tend to stick to this journal for a lot of my posts since its readily available and deals with the “big” environmental issues that are easier to blog about) there was another paper linking atrazine exposure to sexual disruption in frogs. Interesting. So what makes this paper stand out? Well since a lot of the conflicting reports on ATZ toxicity are between laboratory studies this new paper analyzes a commercially prepared ATZ mixture and with exposure at environmentally relevant concentrations using outdoor mesocosms. And in addition, the study analyzed a native frog, R. pipiens, to the region where the study was performed. So from all that, looks like whatever the results might be, they will better mimic the potential toxic effects to amphibians compared to the laboratory results which have been so controversial. There were further lab exposures as part of this study but I’ll just focus on the mesocosms since I find that portion then most novel.

Using 100gallon containers furnished with leaves and other organics and filled with groundwater, tadpoles reared from locally collected egg mats were added to each mesocosm. ATZ was tested at a both 0.1ug/L and 1.8ug/L concentration and against 1.5ug/L 17α-ethinylestradiol (EE2) which serves as a positive control. ATZ concentrations tested were selected to mimic the concentration measured in the local river and streams (and it was detected in every stream tested) which ranged from 0.01-1.6ug/L. And even at these very low concentrations, tadpoles were affected by the presence of the herbicide. In the high concentration ATZ group, survival rate was significantly less compared to the control, 66% and 79% respectively. So that shows ATZ is toxic, but is it the notorious endocrine disruptor its made out to be?

There are some indications, that yes, ATZ exposure induces sexual disruption. The first being metamorphosis. Whereas 76% of control tadpoles achieved metamorphic success, only 45% of the low ATZ group and 50% of high ATZ group were successful. Surprisingly in this measurement, ATZ seems to be a more potent estrogen mimic compared to the positive control, in which 55% of EE2 treated tadpoles completed metamorphosis. Furthermore, the high ATZ group shifted the sex ratio to a female bias (1:1.4 male: female) while the control embryos exhibited a male bias population (1:0.6) which is comparable to sex ratios of adult frogs populations at the collection sites.

Now, here is where things get a little tricky and authors are sure to hedge their results. Unlike my last post on atrazine, no frogs from either ATZ treatment showed signs of intersex while 22% of EE2 treated frogs did. But differences between gonadal studies the authors suggest, may come down to differences in experimental design and choice of frog species tested. The authors also tested for a variety of gene expression and enzyme levels but many showed no difference from the control. Chronic low level ATZ exposure did however alter brain estrogen receptor activity and altered activity of liver enzyme that is thought to be related to feminization. These two changes may be responsible for the metamorphic interference observed, but it is still unclear.

So looks like atrazine will remain somewhat controversial. There have been some definite observations of function responses to environmentally relevant concentrations of ATZ but the mechanisms which induce endocrine disruption by way of ATZ cannot yet be confirmed. But, this study does offer a picture of real world chronic exposures which are experienced by amphibians. Atrazine, once again, has been shown to be toxic and should be of serious environmental concern.

---------

Langlois VS, Carew AC, Pauli BD, Wade MG, Cooke GM, et al. 2009 Low Levels of the Herbicide Atrazine Alter Sex Ratios and Reduce Metamorphic Success in Rana pipiens Tadpoles Raised in Outdoor Mesocosms. Environ Health Perspect 118(4): doi:10.1289/ehp.0901418

Things just keep looking worse for BP

2010-05-25T09:03:00.000-04:00

Visit msnbc.com for breaking news, world news, and news about the economy

Ok, one more post of gloating.

2010-05-24T18:11:00.004-04:00

Another day in the lab, another day of inconclusive data. Yay grad school! So after slinking home I found a package at the door...

hmm? from the Dept. of Ecology & Evolution at the University of Chicago...from Jerry A. Coyne?

Jerry A. Coyne???

SQQUEEEEEEEEEEE!!!!!!!!!!!

You see, a few weeks ago on Jerry Coyne's blog, he called for submissions for a spring reading contest. The objective was to recommend a nonfiction book using only three sentences. And as it turns out, my entry for Douglas Adam's Last Chance to See took first place. Better yet, after reading it himself, Jerry Coyne gave it two thumbs up. Even still better yet, I was to be the recipient of a signed copy of Why Evolution Is True, probably the best book I've come across that lays out the evidence for evolution.

So yes, I'm having a total nerdgasm right now.

OMG! Wait…OMV… well maybe not…just yet...

2010-05-22T15:23:00.002-04:00

Like many this week, I was stunned with the news that Craig Venter had done the impossible. With headlines proclaiming Venture created the first synthetic life or first synthetic cell, how could I not be excited. Obviously, as word buzzed through my research complex people were saying OMG. It was then that I realized that maybe Venter had achieved “oh my Venter status”, OMV.

Within a few hours of hearing the news, my excitement over this event felt hollow. It was almost like my first Christmas after finding out that Santa was not real. There was something that was missing. Unfortunately, once again the media ruined this moment for me. I had just elevated Venter to OMV status, when I began to look beyond the headlines to find out about the god-like accomplishment he achieved. I soon realized that this was just another logical step in science combined with a neat trick, albeit on a Venter scale.

Maybe it is because I am a virologist but I am not shocked at creating a replicating entity from synthetic DNA. In true Venter Institute fashion they increased the scale by over 1000x, but they were not the first. Eckard Wimmer at SUNY Stony Brook (w00t) was the first to create a “synthetic” virus, polio, back in 2002. They even made it all in cell free systems. Obviously reconstituting a virus that can self assemble and replacing the genome in a cell are two different things. It would have been really cool if they could have assembled a cell in vitro around their synthetic genome but that is beyond our capabilities right now. I expect this may be the direction they will be going though. There will be more OMV days to come.

Genomic replacement is nothing new. Dolly the world’s first cloned animal in 1996 was produced from nuclear replacement. Actually, genomic replacement and nuclear replacement are governed by similar rules. The most important is that the new genetic material has to interact with the cellular machinery. DNA by itself is inert; it is like the tape inside a cassette. You need the tape player, speakers etc to actually use the information that is embedded within it. The Venter group had to chose two closely related organisms for the swap. Otherwise the DNA would stay inert, since it could not fully tap into the cell’s machinery. It will take a greater understanding of cell-DNA interactions to begin to plan on accomplishing this trick with a truly synthetic genome representing the world’s first true intelligently designed species.

This accomplishment is not synthetic life, it is photocopied life. DNA is a chemical polymer, it is not alive, whether it is made in a cell or in a test tube it is identical. The Venter group copied the genome (this is still a big accomplishment) from one organism and put it in another. They did not engineer a new organism, they did not make a new species, what they did was equivalent to installing Linux on computer that was running Windows 7. It is far different from coming up with the new operating system that some headlines proclaimed he did.

After going over why my excitement has been tempered, you may be wondering why I am giving this attention, or even why was this published in Science? It is because of the scale at which it was done. While many well funded labs today still weigh the cost and benefits of synthesizing DNA constructs instead of cloning them through traditional means, Venter through money out the window and showed what is possible. He has once again dared the scientific establishment to dream big. In the age of tight funding where taking the next incremental step is more desirable than shooting for the stars, Venter thumbed his nose at the establishment and grant reviewers. More importantly Venter has now established the platform, protocols, techniques, and troubleshooting, so that others can now propose to do similar things and hope to get funding instead of a big “lolz that’s impossible.” He has once again pushed the envelope of current technology and dared the rest of the world to come with him.

Now that Venter has shown this is possible, what would be the first thing you would like to see happen with this technology, comments encouraged.

A post in which I gloat

2010-05-17T16:21:00.006-04:00

I'm sitting right now on a king sized bed, sipping scotch, at a resort on Lake George enjoying the amazing view from my window. This Solid Waste Management conference ain't so bad.

Took these pics with my cellphone and sent them to Kevin. He replied, "View from my bench, you win."

RIP Dio

2010-05-16T20:29:00.003-04:00

Stomach cancer has just claimed the legend, Ronnie James Dio. Fuck.

CONCERNS OVER POSSIBILITY OF HURRICANE-OIL SLICK COMBINATION

2010-05-14T15:43:00.004-04:00

I has been a long time since I posted. I have been coming up with a new project and trying to get it off the ground. More on that will come later; right now I am going to try my hand at steeling some of John’s thunder (I am a little tired of my own research topics right now.)

In between incubation steps or papers in the lab I have been reading up on the gulf oil spill. Lets just say that the news consistently worse than my attempts at getting this project going full steam, and that is saying a lot. I have been fearing the worst ever since the explosion and somehow reality has always trumped my pessimism. With that in mind, I was still not prepared for this article.

CONCERNS OVER POSSIBILITY O F HURRICANE-O IL SLICK COMBINATION

Louisiana has made headlines for two recent tragedies, Hurricane Katrina and the current oil spill. Now imagine if a hurricane and the oil spill collided. Disaster films have combined some of the most remote possibilities and SyFy has brought us giant squid vs mega shark. I am pretty sure no one has thought of this mega disaster, and the scary thing is there is a real possibility it can happen. We are heading into hurricane season and there is no fix in site for stopping the leak. Even if they can manage to do that oil will undoubtedly be floating around there for weeks (more likely months).

This article only hints at a dismal picture. The oil from this spill has been largely kept in open ocean, a hurricane could change all of that in a hurry. Minimally the storm would disperse the slick and force it up on shore. However, there is an even more frightening possibility, aerosolized oil. If the winds are strong enough some speculate that the oil could be sucked up, aerosolized and carried onto land. The results on the environment and human health could be catastrophic, lets face it “fumes” or “residues” that smell toxic usually are hydrocarbons have a bad habit of sticking around.

Friday Fish Tank - How fish breathe

2010-05-14T10:12:00.002-04:00

For more fake science posters, click here.

"The Gulf appears to be bleeding"

2010-05-12T14:51:00.003-04:00

I felt hopeless watching the Congressional hearing yesterday. Hearing BP blame Transocean, Transocean blame Haliburton and Haliburton blame BP. And yet, this video managed to drop my spirits even more. This spill is worse than we thought and worse than we are being told.

You must cut down the mightiest tree in the forest with...

2010-05-12T10:03:00.003-04:00

...a HERRING!

Probably wouldn't be too bad if I could use the frozen King of Herring, or Oarfish, found off of Sweden this week. The dead specimen they found measured 3.5 meters (11 feet) and was the first time an oarfish has been found around Sweden in 130 years. The problem with deepsea species, like giant squid, is that so little is known about them because we can only study what gets washed up or caught accidentally. The oarfish caught though was nothing (though its missing a good chunk of its body), they've been known to grow to 12m and are the largest bony fish in the ocean.

A toxic cleanup

2010-05-07T13:13:00.006-04:00

The first rule of working as an undergrad in my lab is wash your hands before putting your hands in the fish tanks. And never, NEVER, ever, wash your hands or any glassware with soap.Soap, a surfactant, is highly toxic to aquatic organisms. So good thing we’re dumping tons of it in the Gulf, right?

Oil spills are really nasty environmental disasters. One of the main reasons being, as much as it kills anyone to say, sometimes the best remediation effort is to do nothing at all. This was true for example in the Exxon-Valdez spill where to clean the coast of oil, clean up workers used high powered hoses and blasted the rocks with scalding hot water. Sure, it made the rocks on the surface clean, but it actually drove the oil deeper below the surface, into the crevices of the rocks and sands where it could not be broken down by sunlight. In addition, the hot water killed any coastal flora and fauna living on the rocks and also destroyed the bacteria that would degrade the oil. This is but one example where the remediation effort actually worsened the environmental state after an oil spill.

Another example is the use of dispersants. If used properly they are an effective way of reducing the size of an oil slick. The dispersant which contains surfactants, bind to the oil and form little tiny globs that sink from the surface.By breaking the slick into smaller units, or in this case, billions of tiny oil blobs, there is more surface area per volume for bacteria to breakdown the oil and also further aids the spilt and dispersal in the water by wave action. But there comes a cost, these chemicals are toxic, and should never be used in very near shore environments (100m). The risk of it washing on shore and poisoning the coastal ecosystem is too great.

But what if the slick we’re using it on is moving closer and closer to the coast? The Gulf oil spill is by no means small and dispersants have not been used before on a spill of this magnitude. The NYT reports that so far 160,000 gallons of dispersants have been used on the surface and another 6,000 gallons below. The main chemical being used is Corexit.What are the active ingredients in Corexit? Wish I could tell you.It’s a trade secret and since its under a proprietary name like, Coca-Cola, they don’t need to tell you what’s in their product.Hmm…ok then. Well is it safe at least? No, says the British government, which denied approval for its use because it was found to be toxic to coastal invertebrates. Nalco, the company that manufactures Corexit, has released a 10 page report which lists the health hazards of their product which states it can cause skin and lung damage on contact and poses a “moderate” environmental risk.

There’s a 230,000 gallons of Corexit on tap and further production has been commissioned by BP. Wired reports though that a safer alternative is available but not being used. Dispersit was tested against Corexit by the EPA and while Corexit could breakdown Gulf crude oil 54% of the time, Dispersit had a 100% success rate. That alone seems like a good reason to switch, but what about toxicity? Using both a vertebrate (silver fish) and invertebrate (shrimp) model organism, both dispersants were also tested.Corexit was 3x more lethal to fish and 2x as lethal to shrimp compared to Dispersit. I’m guessing this is not the news Gulf fishermen and shrimpers want to hear.

Jeremy Jackson - How we wrecked the ocean

2010-05-07T09:23:00.001-04:00

Friday Fish Tank - Festivum cichlid spawn

2010-05-07T08:37:00.002-04:00

There most be something in my water...

National Day of Prayer

2010-05-06T14:28:00.001-04:00

Let us join with Monty Python and give thanks to the Lord above on this most sacred day.

"All things dull and ugly,

All creatures short and squat,

All things rude and nasty,

The Lord God made the lot.

Each little snake that poisons,

Each little wasp that stings,

He made their brutish venom.

He made their horrid wings.

All things sick and cancerous,

All evil great and small,

All things foul and dangerous,

The Lord God made them all.

Each nasty little hornet,

Each beastly little squid--

Who made the spikey urchin?

Who made the sharks? He did!

All things scabbed and ulcerous,

All pox both great and small,

Putrid, foul and gangrenous,

The Lord God made them all.

Amen."

Media Watch catches denialist in a lie

2010-05-04T14:44:00.005-04:00

The ABC calls out climate change denialist, Ian Plimer, for his false claim that volcanoes dwarf humans in their annual CO2 emissions. Watch the video to see this debunked and to learn just how the emissions from the Icelandic volcano, which grounded flights across Europe, measure up to the CO2 generated by airplanes.

Stop peeing in the damn pool...

2010-05-01T10:32:00.003-04:00

…you’re giving me cancer. Seriously.

Summer is coming up and I’m sure some of you are looking forward to taking a dip in the pool. Swimming is America’s second favorite exercise after all. So, in order to ensure the health of swimmers, disinfectants are added to the water to prevent the outbreak of infectious diseases. Especially for public pools, just think about the amount of disinfectants that have to be added to keep the water sterile.

I’m studying the toxicological effects of disinfectants in the environment for my thesis, so when I came across a paper about disinfectants and human health, I thought it was worth the read. While most people are interested in whether there are health effects from disinfecting our tap water (as opposed to not??), studying these chemicals in swimming pools and water parks are actually the perfect place to start, because they are disinfected to the extreme. It’s not so much the disinfectants themselves (chlorine, bromine etc.) we are worried about, it’s after they interact with organic matter, they form disinfectant byproducts (DBPs) which can be toxic.

Back to the pool…ok, so you’re wading around, think of the organic soup you are sitting in. Its probably a lovely mix of dirt, skin, hair, and sweat. Mmmm. But it gets better, don’t forget about all those pool pissers and bathers wearing sunscreen and lotions. The urine and personal care products are especially important because they are rich in nitrogen. And nitrogenous disinfectant byproducts (N-DBPs) are known to be mutagenic and specifically, cause bladder cancer, the sixth most common cancer in the US.

In order to quantify the toxic potential of recreational swimming pools, researchers collected water from different facilities that all use a common tap water source. The goal being to see which method of disinfection utilized lead to the least genotoxic water, rather than characterizing the individual DBPs present in the samples. This was done by exposing Chinese Hamster Ovary cells (CHO) to whole water samples and measuring DNA damage of individual cells through a comet assay.

The results below show that compared the tap water, all other water samples collected elicited a higher genotoxic response in CHO cells. The most genotoxic sample by far was S4, the only water site that was disinfected with bromochlorodimethylhydantoin (BCDMH). As BCDMH reacts with water, it slowly releases chlorine and bromine, which disinfect the water. However these halogens can react with organic matter and form cytotoxic and genotoxic N-DBPs. The reason for such high genotoxic response from S4 is also to due to the total organic carbon (a measure of organic matter) being incredibly high, 125mg/L, yuck! More organic matter the disinfectants can interact with, greater the chance toxic DBPs will form.

The best disinfectants to have in place are UV+chlorine which had significantly lower genotoxicity compared to pools disinfected with chlorine alone. UV treatment may be important in breaking down the N-DBPs and thus lower genotoxicity. Measuring the N-DBP, nitrosamine, outdoor pool concentrations were 5 times lower than in indoor pools, probably do to UV and solar radiation.

Some other recommendations may be to shower not just after you take a swim, but before as well. Washing away lotions or any other personal care products on your skin will reduce the chance they will form mutagens once in contact with treated water. Also, stay away from that uncomfortably warm spot next to the 6 year old in swimmies…

-----

Genotoxicity of Water Concentrates from Recreational Pools after Various Disinfection Methods

Danae Liviac, Elizabeth D. Wagner, William A. Mitch, Matthew J. Altonji, Michael J. Plewa

Environmental Science & Technology 2010 44 (9), 3527-3532

Friday Fish Tank - I'm being watched

2010-04-30T19:47:00.001-04:00

Offshore energy

2010-04-28T14:46:00.003-04:00

That exploding oil rig in the Gulf made for a rather awkward Earth Day. With Obama recently lifting the ban on off shore drilling, this event should give us a pause to the potential human and environmental hazards that come with operation of oceanic oil wells. And the situation isn’t looking good either. The slick is currently 80 miles long and 40 miles wide with 42,000 gallons of crude oil leaking a day. Containment efforts have not yet been successful and BP estimates 90 days until the leak can be shut off. The Coast Guard has gone ahead and made the decision to burn the oil. Risky business, this is first time setting fire to an oil slick will be utilized for such a large spill. But the alternative being letting the oil reach land, it may be the best chance to curb the environmental impact.

Is it safe? More than 90% of the oil will be converted to carbon dioxide and water through combustion. But the plume of black smoke generated will contain plenty of toxic chemicals. Crude oil is primarily a nasty mix of hydrocarbons and including many carcinogenic PAHs, and burning of the oil will only result in the formation of pyrogenic contaminants and volatile organic compounds as well. As the plume of smoke is carried into the atmosphere, local weather conditions will be the controlling factor for the human and environmental health impact. This is definitely a news story that you will want to keep your eye on as the situation changes daily.

..sigh…

Anyways, there is some good off-shore energy news. The US has just approved the construction of the first offshore wind farm. Located 14mi off of Massachusetts, the 130 turbine station will generate enough power for 3/4^th of Cape Cod, or about 225,000 residents. Energy production could start as soon as 2012.

Wind power is one of the cleanest sources of renewable energy. It requires no fuel to run, releases no emissions and has a minimal environmental impact. Offshore farms are particullaly appealing because their prohibitive set up cost is offset by high energy yields. Because the ocean surface is smooth compared to land, sustained wind speeds are on average much greater. It’s rather disappointing that the US is only now jumping on this. Off shore wind power could potentially be great additions to energy grid in coastal regions (see pic), and for this reason, I wish the Mass. farm great success. Hopefully it will encourage lawmakers to allow construction of additional wind farms around the country (I’m looking at you, Long Island).

James Randi on TED

2010-04-23T13:10:00.002-04:00

Despite being 79 when this was recorded two years ago, the ever more gnome-like, James Randi, is as brilliant as always.

Friday Fish Tank - Albino BN Pleco

2010-04-16T12:43:00.001-04:00

Another image of one of my favorite fish.

RIP thesis project

2010-04-13T14:36:00.003-04:00

Sorry, for not blogging for a while, I have been tied up in lab running many important controls for an observation I based my thesis on. It did not turn out the way I would have liked..... stupid controls. Sorry I can't say what the western blot below is. Let today mark the tragic death of my thesis project.

PS. My backup idea about a small trend in some other data did not pan out with a larger data set either. Science-2 Me-0.

Sarah Palin and the politics of reality

2010-04-11T19:19:00.004-04:00

Belched out of the intellectual black hole that is Sarah Palin, comes this breathless bit of populist posturing:

"We should create a competitive climate for investment and for renewables and alternatives that are economical and doable and none of this snake oil science stuff that is based on this global warming, Gore-gate stuff that came down where there was revelation that the scientists, some of these scientists were playing political games."

Emphasis mine.

Damn those elitist scientists!

Palin continues on (see video) by bemoaning America’s current energy woes. But don’t worry! America is going lead the next global energy revolution because we are the leaders in scientific innovation, according to the former governor. Sorry Mrs. Palin, you can’t have it both ways. You cannot extol America’s scientific ingenuity while simultaneously giving a big greasy “fuck you” to the science community, climate researchers or not.

All this does is further sensationalize and distort a non-issue. By referring to climate change as “Gore-gate” only goes to show how little denialists understand the issues on hand. They seek to characterize scientists as cultists affixed on protecting the image of their sacred idol, whether it be Al Gore for climate change or Darwin for evolution. This is not how science works. But it gives denialists and their followers something easy to latch on to, an easy target. It fires them up, like in the video mentioned, hear how her listeners bray at the sheer mention of Gore’s name.

I think Phil Plait over at Bad Astronomy said it best:

“the far right in this country have been beating the pulpit to a bloody mess with their distortions and noise-making. They will do or say just about anything to distract people from the real issues. As long as people are scared to death by this noise, they won’t think about issues, they’ll react to them.”

Accompanied in his post is a brilliant segment by Rachel Maddow (reposted below). While it covers many issues that fall outside the realm of science, she does discuss “climategate” and how tortuously it was paraded around by the right - never mind the fact independent investigations found nothing that undermines the scientific backings of climate science.

Visit msnbc.com for breaking news, world news, and news about the economy

And rightfully so, Maddow calls “bull” on these politicians.

Phil again:

“Global warming is real. Evolution is real. Vaccines do not cause autism. Homeopathy doesn’t work. These are facts, and they don’t care whether or not denialists spin, fold, and mutilate them. Until we face up to reality, however, they will spin, fold, and mutilate us.”

Friday Fish Tank - Bolivian Ram

2010-04-09T10:04:00.003-04:00

Happy Easter!

2010-04-04T00:00:00.000-04:00

Friday Fish Tank - now with more fish!

2010-04-02T20:39:00.007-04:00

Seems I've gotten behind on this series since I lost all my fish pictures with my laptop. Now that I've finally found my camera software CD, I bring you, pictures!

First, the oldest fish I currently own, or rather the fish I've had the longest, my cory - Podgy. He has endured all my stupid mistakes as a fishkeeper and has grown quite fat over the year and half since I've gotten him. So maybe I'm doing something right.

Next, an update on my Laetacara curviceps spawn. Well, they're at it again. After losing the first spawn (I'm looking at you, Mr. Moustachfish) they've decided to give it another go.

If you look at the bottom right of the video, you'll see a yellow and black snail amidst the corpses (er...empty shells) of several Malaysian Trumpet Snails. I was being overrun by the MTS, so what cooler way to solve this problem them by getting a snail to eat the other snails.

You're a cold blooded killer!

Continuing Discussion About the Existence of HIV

2010-03-30T11:12:00.002-04:00

If anyone is interested about reading about the ongoing discussion I have been having with the Perth Group here are some helpful links.

I initially posted a long message on a Facebook discussion page here. The post is about half way down the page under the name Kevin Sullivan.

The Perth Group sent an official reply to me in a PDF format that can be found downloaded here

It took me a little while (I was pretty busy with other things) but I recently got a repose back to them, and they kindly made the PDF public here.

2010-03-29T08:56:00.000-04:00

Opinion: HPV Policy

2010-03-27T20:03:00.002-04:00

With all the HIV talk and my laborious posts on restriction factors I think this article is a good opportunity to branch out a little bit. Lets talk a little HPV policy.

Fighting viruses is tough. They don’t play by the same set of rules that other pathogens play by. At some point during my first semester in gradschool while drinking with fellow virologists we drafted a poem about the epic journey gradschool was going to be (yes ,we really are that lame, please facepalm for us….now). One of the last stanzas is.

For the virus is an awesome foe

Against which mankind has little to show

For how much time must mankind give

To finally kill that which does not live

Although corny, it is true, we have had trouble fighting viruses. The distribution of Cervarix from Glaxo Smith Kline and Gardasil, from Merck are one of the highlights of virology in the last 10 years. Not only is it a vaccine against a virus, it is a vaccine against cervical cancer. The Merck vaccine also has the added benefit of protecting against some types of genital warts, this may not be a lifesaver but from what I have seen in high school health class, that is one hell of a benefit.

Vaccinology can bridge the gap between bench science and public policy. Lets face it, public policy can be a complicated thing. Since men lack a cervix this vaccine was not initially approved for them (in the USA), many doctors do not stress its importance for men and I am not sure if it is even covered by most insurance companies yet. Despite the fact that something that would protect me from warts down there would be much appreciated (yes I had to link it). I am sure the cost benefit analysis has a little something to do with the decision, these vaccines are expensive to make.

It has been my opinon (I am not a doctor) that it is stupid not to vaccinate men. We sometimes forget in our self-centered society that vaccines are not for the individual. Vaccines do not do too well if most of the population is not vaccinated, especially when dealing with pathogens that can mutate quickly. Vaccines work best through herd immunity. Aggressive vaccination and high compliance rates protect the whole population, including those who have not received the vaccine. This is how smallpox and hopefully shortly polio will be eradicated.

Although, men cannot get cervical cancer from HPV 16 and 18, they can carry the virus and not even know it. Unless 100% of women get the vaccine before they become sexually active (putting a good age on this has been problematic) then women will still die from a preventable form of cancer. Things like that really bother me. Now, if you vaccinate both the carrier (men) and the women you lower the chances two individuals will transmit the virus. The occurrence of infection goes down over time in the population and the chances an unvaccinated person becoming infected rapidly decrease. Unfortunately, policy does not always work that way.

It is more unfortunate that the rise of another form of cancer may help me get my wish. It turns out that HPV 16 and 18 can cause another type of cancer, and it is on the rise. This one knows no gender barrier. Rates of HPV positive oropharyngeal squamous cell carcinoma (OSCC), a so called “head or neck cancer” have gone up by 70 percent in Stockholm since the 1970s and by 50-100% in the last 10 years in the United States. Oral sex is thought to account for the increase.

These findings are going to force the policy makers to reconsider a lot of positions. First, they are going to have to decide if men should be strongly encouraged to be vaccinated. They are also going to have to wrestle with the question of at what age the vaccine should be administered to women (hopefully men too) to insure they receive the series of shots before they become sexually active, including oral sex. Many have oral sex before having other more penetrative forms of intercourse. For OSCC prevention it may turn out to be too late for teenage and young adults, particularly men. Hopefully policy goes at a faster pace than science.

“What is WRONG with you people!”

2010-03-24T13:14:00.008-04:00

So my See no SIV post got some comments on another forum. This is one from Claus Jensen

“Kevin Sullivan,

What is WRONG with you people!

You post a couple of EMs, claim that we're looking at "SIV" because they look the same when they are cloned or something like that. Zero references. Montagnier also has an EM of budding "HIV", and you know what, when the genetic material was "cloned" and the particles from transfected cells were EM'ed they looked fairly similar to that original EM.

What exactly do you think are you adding with your SIV analogy ?

Your so-called "SIV" seems to cause disease when it is injected into a different monkey species, "HIV" doesn't seem to do very much when injected into chimps.

How exactly does that support your argument from analogy?
Let me tell you what would be nice: a couple of references where they inoculated a monkey with their deadly "SIV" or better even "SHIV", let him loose in a captive (has to be captive because it doesn't happen in the wild, coincidentally) colony and watched how the new monkey plague spread and decimated that colony via unprotected sex.

Can you do that, master analogist? Then maybe we can finally get somewhere.”

Claus, yes I put a couple of EM pictures of the pre cloned and cloned virus. I am sorry my brief referencing format author’s last name in year. I will gladly give you the pubmed links to the articles you request.

The EM of in the lymphnode of Macaque239 is from this paper titled “Isolation of T-cell tropic HTLV-III-like retrovirus from macaques” Daniel et al. 1985 in the journal Science.

The EM of cloned SIVmac239 is from this paper “The SIVmac239 Pr55Gag isoform, SIV p43, suppresses proteolytic cleavage of Pr55Gag.” Nicholson et al., 2007 in the journal Virology.

I brought up this point because somewhere some of the criteria of the PG called for was that there be an EM before and after isolation and they must look alike. These pictures validating that point. Dr. Turner states the following

“ To prove the existence of a new (“novelty”) retrovirus first you must:

1. Have proof for the existence of particles bearing all the morphological characteristics of retroviruses.

2. Prove the particles have unique biochemical constituents (proteins and RNA but no DNA).

3. Prove the particles are infectious, that is, the introduction of particles into a cell culture results in the appearance of particles with the identical morphology and biochemical constituents (proteins and RNA) as the parental particles.”

Thank you for agreeing that some of this has already been accomplished, particularly part 3. “Montagnier also has an EM of budding "HIV", and you know what, when the genetic material was "cloned" and the particles from transfected cells were EM'ed they looked fairly similar to that original EM."

You state “Your so-called "SIV" seems to cause disease when it is injected into a different monkey species, "HIV" doesn't seem to do very much when injected into chimps.”

My argument is not about chimps. I talk about SIVmac in macaques from a virus that has been shown to come from a sooty mangabey, the same monkey that gave rise to HIV-2 in humans. Not all HIVs are the same, hopefully you appreciate this (or at least allow this distinction). I will discuss the macaque data here. I will discuss this topic first and once sufficiently debated by both sides we can move on to the chimps you are so interested in. Mind you I want to finish my longer reply to the PG fist as they are patiently waiting.

“Let me tell you what would be nice: a couple of references where they inoculated a monkey with their deadly "SIV" or better even "SHIV", let him loose in a captive (has to be captive because it doesn't happen in the wild, coincidentally) colony and watched how the new monkey plague spread and decimated that colony via unprotected sex.”

I will provide you with some links to papers for what you request, papers on the natural circulation of SIVmac in cohorts of macaques across the United States. This is from retrospective analysis. Keep in mind since we cannot ask the monkey, I cannot tell you whether transmission occurred through fighting, breast feeding, birth, or sex or any other route. We can show the virus was circulating before it was isolated, even before the discovery of HIV. SHIVs are artificial and do not replicate as well as SIVmac in macaques. There are no free circulating strains because this could cause problems at primate centers. If you want to get into the molecular biology of SHIVs I suggest we do so later as it is a very complex and technical area.

One theory of how SIV from a sooty mangabey got into captive macaques is presented by Christian Apetrei, I would consider him an expert on the free circulation of SIVs in captivity. This is an opinion piece as some important data was not taken or has been lost to time.

“Kuru experiments triggered the emergence of pathogenic SIVmac.” Journal AIDS 2006

That hypothesis came from his careful work on the natural circulation of SIVs in macaques and sooty mangabeys. He traced the spread of SIVmac from the Davis primate center across the country. The paper is titled “Molecular epidemiolo gy of simian immunodeficiency virus SIVsm in U.S. primate centers unravels the origin of SIVmac and SIVstm.” Journal of virology, 2005.

Here is a map and timeline of the spread. (for facebook viewers see linked blog at bottom of the post for all images)

Work at tracing the spread of SIV in the cohort of macaques at the New England Primate Center first was done by. Dr. Daniel “Prevalence of antibodies to 3 retroviruses in a captive colony of macaque monkeys.” International journal of cancer, 1988

This was followed up by Dr. Mansfield “Origins of simian immunodeficiency virus infection in macaques at the New England Regional Primate Research Center.”Published in the Journal of medical primatology in 1995. If you want to see the timeline of the New England outbreak I can scan the document and upload it to my blog.

The passage history of the SIVmac251 and SIVmac239 can be found in Ringler et al. “Simian Immunodefficiency Virus-Induced Meningoencephalitis: Natural history and retrospective study” Annals of Neurology 1988 . Again if you are interested in the figure I can put it online.

When you ask “What exactly do you think are you adding with your SIV analogy?”

I am presenting a case where a virus which is strikingly close to HIV-2 causes immunodeficiency in macaques. The sooty mangabey SIVs got into both humans and macaques and caused similar diseases. Your group makes the clam that HIV does not exist, due to the failure of its isolation and a few other sticking points. Animal data clearly proves beyond any doubt that SIVmac239 is an immunodeficiency virus. When similar sequences (coming from the same natural reservoir) are found in humans with the same immune problems your group claims it does not exist. No one has come out and explicitly stated the Perth Group’s opinion on these viruses. I believe that this is because it is a difficult subject to discuss as it forces them to either accept or deny this animal data and commit to a specific point of view. I cannot say that SIVmac is the smoking gun to prove HIV exists. You are right. However examples of the smoking gun in science are rare. Normally theories are built up and refined over time slowly. This is just another piece of evidence to my argument. Is it required, no, but it does help make my point. Hopefully, some neutral bystanders will agree.

Also I hope these links on the natural spread of SIVmac are sufficient. There are a few others. I would suggest using NCBI Pubmed to find others.

Don't worry Michael, I would have facepalmed too

2010-03-23T23:30:00.010-04:00

I had reservations about watching Nightline's debate, "Does God have a Future?," featuring Sam Harris and Michael Shermer versus Deepak Chopra. The reason being, anytime Deepak Chopra opens his mouth, a frantic word salad of scientific sounding new agey tripe is released. This places any rational listener at risk of severe and permanent brain dysfunction after hearing just a few sentences of this vacuous crap. I'm glad I watched. Not just because Harris and Shermer were brilliant and eviscerated everything Chopra said, but rather because Chopra's composure implodes under the weight of his own massive ego. Shermer especially gets under Chopra's skin which was hysterical to watch. Chopra had to result to talking over everyone with clear indignation and frustration when his arguments were laughed at for what the were, complete bunk.

There was one exchange that literally had me in stitches, and I've taken the liberty of taking screen shots. This is the actual dialouge.

(Discussing how Deepak Chopra hijacks the word "quantum mechanics" to claim everything is connected and everything relies on observer experience, Shermer goes... )

Deepak Chopra has simply outdone himself.

Yellow: its worse than you think

2010-03-23T12:13:00.002-04:00

Look around you, do you see something that's yellow? Just on my desk I have: post-it notes, a week old McDonald's coffee cup, a crinkled up Shop-Rite bag and all the pages in my lab notebook. I really dislike yellow too, its loud and obnoxious, but regardless, its all around us. But now, I have a new reason to add to my "why I hate yellow list," it contains PCBs.

Ah crap.

Polychlorinated Biphenyls (PCBs) were produced for roughly 50 years in the making of electrical capacitors and industrial lubricants before they were banned in the late 1970s. During that time, over a million tons of PCBs were produced which has lead to widespread environmental contamination. Due to their persistent nature, they act as a legacy contaminant, remaining in the environment at trace levels and being transported globally. Bad stuff huh? PCBs are also one of the most common contaminants we deal with in environmental toxicology because they are toxic and have the ability to become stored within fatty tissue leading to bioaccumulation within organisms and biomagnification within the food chain.

There are 209 congeners, or forms of the compound, that are classified as PCBs. Our scientific knowledge is mainly concerned with those congeners that were manufactured under PCB's trade name of Aroclor since these tend to be the most environmentally relevant. But in 1998, the NY DEC found a relatively unknown congener, PCB 11, enriched within New York Harbor wastewater. The researchers were able to trace this back to a pigment manufacturing plant which made paints. So it was thought these PCBs were either being released from paint production or from paint vapors.

But it turns out, PCB11 is from a specific pigment, called diarylide which is used to make the color yellow. New research in ES&T shows scientists were able to measure PCB11 in newspaper, yellow shopping bags and cereal boxes; pretty much anything except plain white paper. And its not just limited to physical products, PCB11 is ubiquitous. It is in the air, the water, sediment, and organisms. Things just keep looking worse. Within New York Harbor, it was measured at the part per billion (ppb) level which is quite significant. The same applies for the Delaware River, except, there are no pigment manufacturing plants that discharge into this waterway, meaning PCB11 is leaching from our garbage (paper and plastics) and contaminating the water.

PCB11 may prove to be a major obstacle in environmental remediation of areas effected by PCB contamination. For example the Hudson River which was infamously contaminated by two GE plants has just recently begun dredging of PCB-laden sediments. But in lower Hudson NY/NJ harbor, PCB11 remains both high and variable so even the removal of toxic sediment upstream will not make the Hudson PCB-free as long as there are other congeners being constantly released. Still, little is known about PCB11, including its toxicity, so we really don't know what we're setting ourselves up for in the future.

The story ends with some quotes that pretty much encapsulate the whole struggle of environmental toxicology.

"But PCB 11 is also symptomatic of a larger problem. “There are more chemicals being produced and invented than we’re able to analyze in environmental samples. At some point, you have such a mixed soup that the synergistic effect is greater than the individual chemical effect,” says Glenn Milstrey, director of the New York State Department of Environmental Conservation’s Bureau of Water Assessment and Management. “We are addressing legacy pollutants [such as dioxins and PCBs] that were discharged a generation ago,” says Scott Stoner, who heads the department’s Pharmaceuticals Work Group. “Let’s not let today’s emerging contaminants become the legacy pollutants that we leave to our children.”"

Words of Wisdom

2010-03-22T16:22:00.004-04:00

So today I am sitting in my office with not much real science to do. Hopefully my cells are busy cranking out tons of HIV for later in the week. While talking to a post doc in the lab on an equally slow day he provided me with some words of wisdom, "science is like a pregnant woman, it takes so long to deliver." And there you have it, I think this best describes science. I can be fun to start, then you may regret it, you have to gut it out for a long time before you reach the end. Thats deep.

Shark-Bitten Crocodile Poop Fossils Found (No, Really)

2010-03-21T16:43:00.005-04:00

For the most part I think that this blog sticks to pretty defined areas of interest, mainly HIV/viruses and pollution/marine science. However, a science story comes about that just need to be told, this is one of those cases. Thats right, although highly improbable someone found a fossilized crocodile poo that bears the wounds from an encounter with an ancient shark. Lets think about this, first someone had to find a rock that had a strange pattern of holes it it. See below.

Then they had to bring it to someone to ask about them. That person had to have been bored enough to take a casting of those holes and then compare those to castings of modern day shark teeth. The conclusion, these holes were made by a shark that was a decedent of modern tiger sharks. Against all odds, this story is turning out to be pretty neat.

This discovery leads to many interesting questions. The one that came first to my mind was "what was an ancient shark doing munching on poop?" Followed by, "no wonder this species of shark went extinct". Fortunately, my burning yet sophomoric questions were answered by SCIENCE! It turns out the depth of the tooth holes are not even. This lead the team doing the investigation to speculate that this piece of preserved fecal matter was originally in the colon of some poor crocodilian that was attacked by shark. First, this is why I <3 science. Second, I felt satisfied with this answer. Third and most importantly, I wish I could have seen this prehistoric battle royal go down. Luckily for us all of us, this article included an artist's representation of what this battle may have looked like.

All I can say is badass \m/, I wish this picture was on a T-shirt

Friday Fish Tank - Figure 8 Puffer

2010-03-19T08:23:00.000-04:00

The Gasm

2010-03-17T14:31:00.003-04:00

Breaded chicken, mozzarella, thick-cut bacon, cole slaw and Russian dressing. Coupled with half iced tea/ half lemonade.

Fuck yeah.

Two drunks drinking from the same cup of stupid

2010-03-17T10:47:00.005-04:00

Sean Hannity is anti-science. I know, this will read like a story that ends with the punchline, "in other news, dog bites man," because its so damn obvious. But thanks to Sean Hannity's brave mavricky investigation, him and his lapdog Tucker Carlson can now report that stimulus money given to the NSF, is now being used for...get ready for it...grants! I'm sure when this story aired on Fox News this week, many a pearls were clutched and fainting couches were quickly deployed. But to everyone else in the reality based community, these two just look like a couple of fools who fell from the top of the stupid tree and hit every branch on the way down.

So what was the big deal here? The NSF granted Michigan State University over $187,000 to build new storage systems for their famous arthropod collection. Their old storage units were inadequate and were in danger of losing their specimens to other insects. Trying to save dead bugs from bugs. Hilarious right? Carlson sure thought so. He yipped with glee as he reported back to his owner as if he had exposed some know-it-all scientist. I could easily go through a line-by-line dissection of this since each sentence uttered drips with smug stupidity, but it would just be too infuriating.

You can just read the transcript of the segment here and see what I mean.

There is this part here that deserves some attention:

CARLSON: So four students are working on this collection who would not be working on it otherwise.

COGNATO: Correct.

CARLSON: How much are they getting paid?

COGNATO: They get paid between $8 and $10 an hour.

(END VIDEOTAPE)

CARLSON: So four kids are making eight bucks an hour to move dead bugs from old trays to new trays. This is the job-creation engine of the Obama administration.

An employee of the company benefiting from this grant showed up in the comments:

"My job is one of the many that were either created or saved by this particular grant. I work for BioQuip, the company, based in California that manufactures the drawers and unit trays that MSU purchased with their stimulus money. Our company employs 27 people and we purchase wood and other supplies used to construct said drawers from other American companies and those companies purchase lumber harvested and milled in the United States by still more American workers. There is also the local, US based glass company that manufactures and cuts the glass that we use on the tops of the drawers. All of these materials then have to be trucked to us by still more US workers, employed by US freight companies, and then the finished products have to be shipped to MSU, again, using a US freight company which employs American drivers. I could continue on and include the mechanics who work on the trucks used by the freight companies and so on and so forth but I think you get the idea. When you take the time to really examine the facts, this $200,000 stimulus grant has benefited the US economy, created and maintained American jobs and businesses on a level far greater than 4 jobs at a single university."

So Mr. Hannity, Mr. Carlson, why do you hate America?

Happy St. Patrick's Day

2010-03-17T08:47:00.001-04:00

Ignorance is fish

2010-03-16T12:04:00.004-04:00

So what do you do when the world's largest importer of seafood does not understand the concept of sustainable fishing? Actually, its worse than that. What happens if they are completely unaware of the concept of sustainable fishing? Well, the answer is that our fish stocks look a lot like they do now. Though it may seem obvious, a survey conducted of Japanese shoppers has shown that they haven't heard of sustainable fisheries and show little concern for fishing's environmental impact.

The Japanese are fairly notorious for their ravenous consumption of fish which fuels fisheries in all the world's seas. The spoils are shipped to Tsukiji Fish Market in enormous quantities and fetch unimaginable prices. Whether buying the fattest tuna for status or for food, the Japanese continue to oppose international trade regulations and fishing quotas. Even this week at the CITES convention, Japan stands in strong opposition of a bluefin tuna ban supported by the US and EU. Furthermore, their lobbyists have been threatening developing nations into siding against the ban.

So if the government is willing to stand in the face of all fishery science and international support, what does this mean for the Japanese consumer? Misinformation and unsustainable consumption. There is a dangerous mix of ignorance and hubris involved here. As quoted from the first linked article:

"[Japanese shoppers] were sceptical about how humans could ‘manage’ fish stocks and one woman shopper told researchers: 'There can’t be a shortage of fish – just look at how much there is in the supermarkets.'"

"Associate Professor Yuko Onozak of Stavanger University told the Seafood Summit in Paris: ' The Japanese are not aware of any problems with the sea. They don't see it. They don't hear it. They don’t think it is their problem.'"

These sentiments can also be found in the survey results which looked at the seafood concerns of 3,700 Japanese primary household shoppers. As seen below, less that 7% consider the environmental impact of how their fish was harvested very important. With more than 35% considering it unimportant. There results are similar for traceability, or where the fish came from. This is important for determining whether a fish has come from well-managed stock or not. This is bad news for fish stocks since of those surveyed, more than three quarters purchased fish at least once a week, and over half, multiple times a week.

The survey also showed that there was a lack of information available to Japanese consumers and a lack of understanding of what it even meant to manage fish stocks. Some never thought about it and others were unfamiliar with any of the eco-labels that are used to identify fish caught from sustainable fisheries. The phrase 'eco-' in Japan is only used for pollution and recycling, so for many, eco-friendly fish simply did not make sense. But probably the most frightening finding was that, out of the 3700 surveyed, NONE thought that overfishing was occurring.

Those surveyed did respond well to information that was provided to them with respondents willing to pay more for fish if it carried an eco label. But internationally, there really is no lack of information. The results showed that shoppers were more likely to trust the government regarding seafood information, and least likely to trust an NPO. What this just goes to show is that there really is no hope to change Japanese consumer perceptions untill the government actually acknowledges there is a problem. With the Japanese government strong-arming its way through another international conference, tuna and all other vulnerable fish stocks remain at risk from this arrogant over-exploitation.

Restriction Factor-Tetherin: Not so fast you little virion

2010-03-14T16:08:00.005-04:00

It is time to move on from all things TRIM related and I am going to take things in a different direction. Rather than talking about viruses getting in, I am going to be talking about getting out. BST2/Tetherin has a cool story to tell.

Although, scientists talk a lot of game with our technical jargon we do like to keep things simple (because even simple hardly ever works). For example when you want to know what a gene/protein is doing, the easiest way to figure it out is to get rid of it. When scientists deleted the Vpu gene of HIV-1 they saw something weird. First their cells made less virus. Naturally, they wanted to know what part of the viral life cycle was disrupted. It turns out the virus could do everything it needed to, except new viruses could not detach from the cell surface (see picture bellow from Neil et al., 2008). The conclusion was that Vpu was required for proper budding. The funny thing was that if you put SIVs into some human cells a similar thing happens. No one could figure out why but the story stopped there. Surly some grad students and postdocs got burned on this one.

The answer was only recently revealed. Vpu was not actively involved in the budding process at all, instead it was actively opposing a restriction factor that prevented budding. This factor makes a protein string preventing the new virus from leaving the cell. Previously named BST2 the factor was renamed Tetherin because it could “tether” a virus to the cell surface. The ability of a virus to get around this block is species and virus specific. HIV-like viruses, primate lentiviruses (PLVs) that make a niche in one species have a protein to take care of that specie’s Tetherin. If you put the virus in another species it has trouble getting around it.

If viruses had brains this is the sort of thing that would drive them crazy. Look at it from the virus’ point of view. It flies around an organism till it finds the right receptor. It dodges TRIM, it finds a nice spot to integrate into the genome, it makes all the proteins it needs before the cell kills itself or goes into lockdown mode, and now at the very last step the cell gets the last laugh and says…. gotcha bitch. Tetherin is basically a bungee chord preventing the virus from blasting of from the cell. The cell can then reel the virus back in and destroy it.

Insights Gained from the discovery

When one aligns Tetherin sequences from a few species you notice something very quickly, there is a lot of diversity. This is because this protein has been locked in an arms race against viruses, emphasis on viruseS. This protein is not only active against HIV when it is missing its Vpu, but if it were not counteracted it would work against HIV-2, SIVmac, SIVcpz, many other SIVs, Ebola, Marburg, at least one Arena viruses and KSHV. It is beginning to appear that Tetherin is active against just about any virus with a membrane, which begs the question how do other virus get around it?

The most stunning evidence of this arms race comes from how viruses have adapted to counteract Tetherin. I mentioned before that the effects of Tetherin are only observed either when a virus loses a gene to that takes care of Tetherin, or the virus finds itself in a cell that has a different type of Tetherin. The primate lentiviruses have jumped from species to species and they have utilized many proteins to counteract Tetherin. The Vpu of HIV-1 counteracts human Tetherin, but remember that virus came from a chimp virus SIVcpz. In a chimp the virus uses its Nef protein to do the same job. SIVmac in macaques also uses its Nef protein, while some types of the closely related HIV-2 use their envelope protein. This underscores a fundamental property of the PLVs, they are vey plastic, when presented with a challenge they will find a way to evolve around it. Arguably, solving the same problem independently with multiple solutions is one strong case against intelligent design.

Chimps and Humans are quite similar and the PLVs infecting them only diverged in an evolutionary blink of an eye. So why does one type of virus use Vpu while the other uses Nef? Again the answer is evolution. At some point after the two species diverged the human protein lost 5 amino acids in its tail. The amazing thing is that these amino acids are in the exact spot that some SIV Nef proteins recognize Tetherin. Nef basically grabs the tail of Tetherin, pulls it off the cell surface and marka it for destruction. The missing 5 amino acids protect human tetherin from Nef. Sadly, HIV evolves so quickly that it just switched to Vpu in humans to do the same task. The missing amino acids are common to all humans. The obvious question to ask is what virus selected for this? Was it the same virus that selected for only one version of Trim5 in humans? These are all interesting questions that make me want to build a time machine and find out.

Interesting Story

2010-03-13T22:41:00.002-05:00

Last night I went out to dinner with a few friends. While waiting for a table we got a few drinks at the packed bar. As I was trying to wiggle my up to the bar for a refill, a man struck up a conversation with me, he had more than a few. After a little bit about his life he asked what I did. I told him I was a grad student and it came out I was doing HIV research. His reply was a little unexpected. He gave me a big hug and said thank you. I think this has to be the first thank you I have ever received for doing research. It was totally unexpected and I was more than little taken back. He explained how in his social network, some of his friends had tested positive. He began to tell me how he gets regularly tested and takes all the precautions he can. He recounted how nerve racking the testing processes is every single time he has it done. I tired to tell him that what I was doing was basic research and would likely not amount to much in the way of a cure or treatment. That did not curb his enthusiasm. He was very happy to meet someone that cared and was “doing something about it”

When you are a grad student locked away in a lab somewhere you are not exposed to many people like this. I think it is every easy to isolate yourself behind your bench or stacks of papers. The science is tough enough on you, but when you mix in being stereotyped as the typical egg headed, nerdy, socially awkward science guy by most outsiders and the news have more coverage vocal opponents to science than expert opinions, you sometimes get the feeling that no one appreciates or understands what millions of people around the world are doing. When I wake up tomorrow with one hour less sleep on a cold, wet, stormy Sunday, (the type one would rather lay in bed all day) to put in a full day of lab work, I just may have a little more pop in my step, or at least not hit the snooze more than once.

Maybe we need a national Hug a Scientist day.

Friday Fish Tank - Angel spawn

2010-03-12T11:28:00.003-05:00

Ok, not the best picture by any means. My laptop died so I lost all my good fish pictures. Here though is an old pic taken with my cell phone of my blushing koi angelfish pair protecting eggs they had laid on a leaf of java fern. Despite guarding them constantly throughout the day, they were no match for my psycho yoyo loaches. They must have gotten to the eggs at night because I came back to the office the next morning and the yoyo's had some big bulging bellies. Clearly, someone had a midnight snack.

Hear no SIV, See no SIV, Speak no SIV

2010-03-11T13:56:00.009-05:00

It is no surprise that in this blog space, there is absolutely 0 doubt that HIV exists. I think denying something with that much scientific evidence without presenting actual data of your own is a little silly.When asked on a Facebook discussion about where the Perth Group stood on SIVs we were met with this answer from an important player in the group, Valendar Turner (or at least someone claiming to be

him).

"Yes, “SIV is not HIV” and you cannot know how closely they are related unless you first have proof for the existence of both. And you cannot have animal models and all the rest unless you first have proof for the existence of HIV. And to paraphrase Professor Weiss, you don’t prove the existence of HIV by proving the existence SIV.”

Aside from dodging the question about how the Perth Group stands on SIV, and a lot of circular reasoning I can see why they make this point. The problem is that they cannot offer an opinion either way. The virus is trap to their ideology. Saying” yes”” they believe it exists, or “no” it doesn’t will compromise their argument either way. The best they can do is not answer the question. This is because of the history of SIVmac.SIVmac (our HIV/AIDS model in macaques “mac”) came from the cross species transmission from an SIV from a Sooty Mangabey to macaques, in captivity. It is a really cool story I will have to share some time. Most people talk about HIV coming from chimps. This is true of HIV-1, the more common form that has become pandemic around the world. However, HIV-2 arose form the cross species transmission of a Sooty Mangabey SIV to humans. This is more common in western Africa where the Sooty Mangabey’s natural habitat is. The virus appears to be less pathogenic and less easily spread. Nonetheless it is a human immunodeficiency virus that has a brother in macaques. Because of some careful work, SIVmac239 fulfills a lot of the criteria the Perth Group uses to claim HIV-(1?) does not exist. There are EM pictures of the virus budding from a lymph cell of macaque 239-82.

(Daniel et al., 1985)

(Nicholson et al., 2007)

The virus was cloned after culture (sequence here) and the virus by the clone looks the same (above). Furthermore this virus does fulfill Koch’s postulates. Monkeys that were given infected blood from macaque 239-82 (example macaque 316-85) and the virus caused the same immunodeficiency, and the virus was isolated to make the infectious clone SIVmac316. The SIVmac239 clone can also be used to infect other animals, which present the same immunodeficiency symptoms. These experiments could never be done in people. Basically this virus rocks their argument.

The fact that it is so closely related to a similar HIV virus in humans makes the Perth Group walk a fine line. Because of the overwhelming evidence that SIV is a real virus (the animals are not given any drugs so its not the treatments, they are well fed no so starvation or oxidative stress, monkeys are not in any risk group so they are not IV drug users or hemophiliacs and although I never ask I would think most are not gay) so to deny this virus exists just makes them sound crazy. Yet if they do say this virus exists it opens the possibility of saying HIV-2 exists since both viruses have a common not so distant ancestor in Sooty Mangabeys. Now I cannot prove HIV exists by proving SIV does, but its presence cannot be dismissed either.

Whales are the “forests of the ocean”

2010-03-08T10:27:00.003-05:00

Well here’s a weird little article from the BBC. Researchers from the Gulf of Maine Research Institute have calculated that a century of whaling has released a large amount of carbon into our atmosphere. The use of whale oil has released equivalent amounts of carbon to burning 130,000km^2 of temperate forests, or running 128,000 Humvees continuously for 100 years. Still pretty small compared to the annual anthropogenic input, but this highlights a larger issue.

From the biggest whales to the huge schools of harvestable fish, they are all made up of carbon, lots of it. And whenever we remove biomass from the oceans for our land use, we are reducing the amount of carbon that would otherwise sink to the ocean floor when the organism dies. Previously unaccounted for, the amount of carbon that can be sequestered to the deep ocean by large organisms may be significant. The new research suggests that megafauna aren’t just important an important flux of organic matter which feeds the ocean’s carbon cycle, but they may also be a manageable global carbon sink.

If the amount of carbon contained within a stock of whales or fish could be calculated, the researchers suggest a carbon credit system could be put in place to encourage nations to not fish. This could work in much in the same way as carbon credits are issued for trying to reestablish forests. Keeping marine carbon in the ocean…seems like an interesting way to address the issues of conservationism, climate change and dwindling fish stocks simultaneously.

Friday Fish tank - Laetacara curviceps

2010-03-05T00:00:00.002-05:00

It's ironic. I can't get any eggs in the lab and yet fish in my home tanks are spawning, and the angelfish in my office tank were going at it today. Here is Laetacara curviceps, or dwarf flag acara. An extremely pretty fish with each scale an iridescent green or blue. However, when in spawn mode like above, they turn a dark purple, almost black. Pictured is the female guarding her spawn. They are almost ready to become free swimming fry, with a few hopping up every now and then. The male and female take turns protecting the spawn and will occasionally carry them by mouth to a new location. The brooding behavior has been very entertaining to watch. Hell, I didn't even know I had a male and female, I assumed both were male since they were so colorful.

Since the photo was taken, the pair has moved the free swimming fry into a shallow pit dug out in the substrate and are dropkicking any fish that gets close. Ok, they're not being that aggressive, but everyone else is keeping away from that side of the tank.

Inspiration

2010-03-04T23:38:00.005-05:00

Grad school is a strange beast. Nothing can be more exciting and rewarding while at the same time so defeating as John pointed out. I chose to study virology because I wanted to make a difference. I thought that there was no better way to impact as many lives as possible than working on infectious diseases, especially viruses which lag behind bacteria in treatments. I was young bright eyed and optimistic, probably a little too young, too bright eyed and too optimistic. Many seasoned grad students and PhDs who talked to me would agree. I respected the fact that science moved at a time scale only slightly faster than a geologic one, but I was not prepared for the rollercoaster that is grad school. I have to say through classes and rotations I felt like anther cog in a massive machine. I never saw how anything I worked on could ever make a slight impact on the world or be of the slightest interest to anyone aside from 10 other people in the world. It is really a quite humbling and depressing realization. Scientists are born asking question, so it comes at no surprise that we usually question ourselves, our motives, our skill, our qualifications and our goals and ambitions. If I had a quarter for every time I questioned myself I could fund my lab. The most important and frequent question I ask myself is “is it worth it?” On my worst days when my western blot has failed every day for the second week in a row, I almost say no. Caught in a moment of hopelessness I question how much more failure I can take, how on earth can I continue in a career of failure, and most critically how can I fulfill those wild dreams of making a difference in the world. I refuse to let grad school take that goal away from me. Its on days like that when seeing something like this (see below), makes me proud of what I am doing, strengthens my will, and motivates me to step outside the confines of my lab and actually try to make a difference.

Letter From JW. Tested HIV Positive. What do you suggest I do from here regarding further testing? I don't know what to beli...

Today at 12:01pm

Date: Sun, 31 Jan 2010 07:01:08 -0800
To:
Subject: House of Numbers: Tested Positive - Film Availability

I am a 34 y/o gay male who recently tested positive in December. I had three tests - two rapid (oral and blood) and one Western Blot and they all (shockingly) came back positive. I don't understand how this is possible because I've only had oral sex and never let anyone intentionally cum in my mouth. However, it has happened a couple times. That's the only "exposure" I can assume in my case. However, even then it's very rare according to what I've researched.

I'm supposed to have a viral load test to confirm this is in fact HIV. I just don't trust the process anymore and the "meds" have always been a fear of mine years before testing positive. I just knew in my spirit that they're poison and I believe your film (like the others) confirms that.

I recently watched AIDS, Inc and another similar documentary. They're both dated films but very informative and have led me to question HIV/AIDS diagnosis. More specifically the testing process.

I'm really looking forward to viewing House Of Numbers but unfortunately I discovered your documentary after it already screened in Los Angeles. Is it possible to purchase an advanced copy or screener? Is it available to view (PPV) online?

What do you suggest I do from here regarding further testing? I don't know what to believe anymore and it's very uncomfortable not knowing what to do.

Thank you for your time and your courage in creating this film.

Respectfully,
JW

Updated 9 hours ago · View Original Post · Report Note

Sheila Dvorak If you can send this message to JW - PLease contact the organization Alive and Well. They will be able to help you from here. http://www.aliveandwell.org/

2 hours ago · Report

Andres Marroquin Hi Dear JW, my suggestion for you, is not to rely on beliefs, this is mostly a matter of educating your self about real facts, behind HIV=AIDS hypothesis, I would strongly recommend if you study the scientific literature from great and highly credible people, who spent years, making research on this matter, read Inventig the Aids Virus from Dr. ... See MorePeter Duesberg, also Origins, Failures and persistence from HIV=Aids hypothesis from Dr. Henry Bauer, Goodbye Aids From Aids trap surviver Maria Papagiannidou, go and visit the following websites, rethinkingaids.com, aliveandwell.org. I am sure that you will get a conclsuion after reading this material, stick with that, forget about your test result, there are many conditions well documented that can produce those results, the manufacturers from these kits, recognize that there is no standard to determine based in a serological result the presence or abscence of HIV, and please, do not take ARV therapy, a lot of people die from complications associated with it, specially liver failure. Change your beliefs and fears and make a transition in knowing facts from responsible and well condiucted science, mind is very important on this issue, take care and God bless you, you are fine!

2 hours ago · Report

Lishui K Springford

check out www.newmedicine.ca

about an hour ago · Report

Now, I seriously hope that the letter is from someone trolling instead of someone looking for help during the worst time of their life. Sadly, to think that this is not happening (if not here then elsewhere) would be like denying HIV exists. My work on HIV in lab may never result in a cure, or even amount to a drug that can extend lives. However, all those papers and seminars I attended were not a waste. Knowledge is the currency of science and I have a lot in the bank to fight these dangerous people who call themselves HIV dissidents. I can’t change the minds of hard-core dissidents, but maybe I can prevent needless suffering for people like JW by taking on their campaign of misinformation with real facts. Although, seeing things like this makes my blood boil I will try not to let my emotions get the best of me. That is what these people thrive off of, they want to make scientists throw their hands up in frustration. That is what they get when they argue with a famous and often busy PI. What they forget is that I am a grad student, I have an iron will, and I am not afraid to bash my head against a wall for years to get a result if need be. The internet has given people unparalleled access to information and dissident groups of all types have taken full advantage of it, its time to remind them that the internet works both ways.

TrimCyp-Crazy Convergence

2010-03-03T16:47:00.006-05:00

A few weeks ago I started a series on host restriction factors. So…the Trim5alpha one may have been just a little too technical, sorry about that, I get carried away some times. I am going to try to increase the awesome evolutionary insight to boring biochemistry ratio in this post.

So last time I mentioned that Trim5alpha was made up of two major units, the recognition domain (SPRY) and the effector domain (TRIM). TrimCyp is a protein where the recognition domain has been replaced with a cyclophilin domain. It is an entire cyclophilin A molecule stuck to the TRIM part. Once HIV-1 gets into a cell it binds to cyclophilin A proteins. The cool part is that HIV actually needs cyclophilins to achieve maximum infectivity. So here we have a case where evolution has taken one of the things a virus like HIV-1 needs and fused it to the thing that helps chew HIV up…genius right! You can’t create a better thing. So how did it get there? A cyclophilin mRNA got picked up by some retrotransposition machinery and inserted it right in the Trim5a locus on the chromosome, poly A tail and all. A few splice site mutations sealed the deal for making a potent new restriction factor. Events like this are quite rare and the fact that it was maintained and selected for is pretty cool.

The really wild part of the story is the fact that it has happened twice independently.....on two different sides of the world....in two totally different species. Talk about convergent evolution. It happened once in South America in owl monkeys and it probably did a good job because all 12 species of owl monkey only have this variant. Who knows maybe it saved the species. The second example is in macaques where it is distributed at different frequencies in at least 3 species ranging from about 10-100% . Again one would like to think this protein must have kicked some ancient viral ass. We know they were independent based on where they inserted into the genomic DNA, the macaque insertion is after the SPRY domain while the Owl monkey one comes before it.

If it is one thing evolution likes to do it is improve upon a good idea. It turns out mutating amino acids near the part that binds to HIV-1 changes its specificity for viruses. In the macaque protein these changes cause the loss of recognition for HIV-1 but the gain of recognition for HIV-2. That is a neat trick. Recent work actually shows that this switch is controlled by a singe amino acid change. One could imagine scenarios where at a population level the protein could flip flop specificities fairly quickly in response to new significant threats. There is a similar pattern of changes in the owl monkey version but no one has attributed any functional differences to it.

Personally I think the coolest part of the whole story is where the in the mutations in macaque and owl monkey proteins fall. The mutations that likely change binding specificity occurred just opposite each other! That was a WOW moment for me. These two species probably were faced with similar threats, solved the problem independently in a similar yet distinctly unique way!

I took this image of human cyclophilin A (same sequence as the macaque one) (PDB C3YS) colored it in PyMOL. Light blue is The cyclophilin A protein. The yellow ring is a drug cyclosporine that is bound to the active site, this is where it also binds to HIV. I colored the changes from human sequence to owl monkey in red. The orange ones are the macaque changes. Think of cyclophilin holding that ring like a whole hand gripping a ball. If you were to hold a ball in your hand and look down at it, the mutations in the owl monkey protein would be in the thumb and the macaque ones on the pinky. If you were to mutate “move” either finger you would change the grip on the ball. How cool is that?? I love evolution.

Atrazine: more controversy and sexually confused frogs

2010-03-03T14:19:00.005-05:00

Ooh! It’s not every day I get to see an aquatox issue covered in the news. CNN is carrying the headline “Weed killer 'castrates' male frogs, study says” and before even clicking the link, I knew it was going to be about atrazine. Hmm, this isn’t exactly news to us. Atrazine and endocrine disruption/teratogenic effects have been studied in frogs and fish for over a decade now. Amphibians seem to especially sensitive. So what’s this all about now?

Skimming through the CNN article there is this nice gem,

“Syngenta, a Swiss company that is the largest manufacturer of atrazine, has challenged the validity of Hayes' study.

"We haven't seen these kinds of responses that Dr. Hayes reports," said Keith Solomon, an environmental toxicologist at the University of Guelph in Ontario, Canada, who has served as a consultant to Syngenta. "Some of these studies are poorly conducted and are entirely inconsistent."”

Uh oh, looks like another spat between Hayes and Solomon, who have a pretty good history of butting heads. Solomon says the Hayes’ science is poorly designed, and Hayes says Solomon only finds negative results when his studies are funded by Syngenta. Anyways, ignore the drama for now, let’s see what this study says to warrant its publication in PNAS.

Actually, I guess a little background is in order first. Atrazine, the most commonly used herbicide in the US, with over 80 million pounds applied on the ground yearly. Yikes! It is also the most commonly detected pesticide as a groundwater contaminant. The EU has gone as far to ban its use and while, as mentioned above, the effects are slightly controversial, the new administration’s EPA has ordered a review of atrazine’s environmental impact.

Hayes’ new study started out with a 100% male group of African clawed frogs (Xenopus laevis) and exposed them to 2.5 parts per billion (pbb) atrazine from development through as far as 3 years. So while most previous amphibian tox studies looked at developmental disruption, this new study examines how chronic atrazine exposure can lead to detrimental adult reproductive function.

90% of the males were morphologically male when examined. Wait, only 90% of males were males? The other 10% had become morphologically female. They exhibited a pronounced cloacal labia, and upon dissection, they possessed ovaries and a lack of male features. Figure 1 shows the difference in cloaca in unexposed males compared to a “female.”

Furthermore, those females who were not dissected were allowed to live and ended up reproducing with males (Figure 2), even producing viable eggs which were reared to adulthood! And yet, based on chromosome analyses, these “females” were still genetically male. Ack! It’s quite extraordinary that the degree of hermaphroditism observed led to complete feminization.

Of the 90% of that remained males, what of them? Well, two-thirds of them had become essentially, chemically castrated. This was due to for example, lower testosterone production and underdeveloped testes. And compared to unexposed males, atrazine exposed males had a lower libido and were outcompeted by unexposed males in breeding. The comparison in Figure 3 showing a control frog’s gonads compared to an exposed frog’s gonads.

The results from this study do seem pretty jarring, especially considering the low concentration they were exposed to, which in some areas is environmentally relevant, meaning they are equivalent to a chronic exposure organisms are already experiencing in the wild. It would be interesting to see what the critics have to say regarding this study and whether these results really are replicable. Another nail in the coffin for atrazine? Could be. I eagerly await the EPA’s finding regarding their ongoing critical review of atrazine’s environmental impact.

----

Hayes, T. B., V. Khoury, A. Narayan, M. Nazir, A. Park, T. Brown, L. Adame, E. Chan, D. Buchholz, T. Stueve, and S. Gallipeau. Atrazine induces complete feminization and chemical castration in male African clawed frogs (Xenopus laevis). Proceedings of the National Academy of Sciences. PNAS published online before print March 1, 2010, doi:10.1073/pnas.0909519107

Protection Agency in Name Only

2010-03-02T10:50:00.002-05:00

Its shaping up to be a bad year for the EPA. Last month, I covered a story about the lobby opposition to regulating CO2 under the Clean Air Act. But now, a new investigative report by the New York Times has found the Clean Water Act has been essentially gutted in recent years. Makes you wonder, what’s the point of having regulatory agencies if they keep getting stripped of their regulatory power?

The latest issue arises from a Supreme Court ruling that scrutinizes the language limiting regulation to “navigable waters.” This has historically been interpreted to include ecologically important wetlands and tributaries that connect to major bodies of water, like rivers. But of course, the lobbyists would have none of it!

The NYT reports:

“If you erase the word ‘navigable’ from the law, it erases any limitation on the federal government’s reach,” said Mr. Parrish of the American Farm Bureau Federation. “It could be a gutter, a roadside ditch or a rain puddle. But under the new law, the government gets control over it.”

…

“’If you can get Glenn Beck to say that government storm troopers are going to invade your property, farmers in the Midwest will light up their congressmen’s switchboards,’ said the coalition member, who asked not to be identified because he thought his descriptions would anger other coalition participants. Mr. Beck, a conservative commentator on Fox News, spoke at length against the Clean Water Restoration Act in December. “

Ugh.

The new rulings find that “waterways that are entirely within one state, creeks that sometimes go dry, and lakes unconnected to larger water systems may not be “navigable waters” and are therefore not covered by the act — even though pollution from such waterways can make its way into sources of drinking water.”

So what does this mean for our environment? Well, according to EPA reports, up to 45% of major polluters might now be out of regulatory reach. Whole water ways are now vulnerable and in some states, Clean Water programs are essentially being shut down. Here in New York, many of our watersheds that feed our drinking water supply are now unprotected.

This is not environmental protection. The change in interpretation of the language has caused some 1,500 major pollution investigations to be dropped in the last four years. This can only mean the future holds more incidents of pollution, more environmental degradation, more threats to public health and far less governmental power to stop the perpetrators.

Research and helpless frustration

2010-03-01T10:54:00.002-05:00

I’m used to the constant disappointment of experiments flopping, of waking up in the middle of the night during those dreadful hours with the excessive fear you did something wrong with your research. These all seem to be the norm for grad school - a rewarding yet absolutely spirit breaking process.

Though I may soon face something I hoped not to encounter. The slinking horror that all my research just ceases. Coming off a great week of experiments that worked wonderfully showing very promising results that may soon lead to rapid progress, I have hit a wall. For inexplicable reasons, my fish have stopped producing eggs, meaning no embryos to run tests on. Though egg production has been capricious in the years past, I have managed to turn around our aquaculture system into a booming egg factory. But now I’m at a loss, I know how difficult it can be to get everything back into working order again and who knows how long this delay will last and what it will cost me.

With the clock ticking and grant funds dwindling, an impasse in my research is the last thing I can afford at this time.