Saturday, July 31, 2010

Please, Governor Jindal. Stop trying to help the environment

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.”


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, July 30, 2010

Friday Fish tank - a very sick Medaka

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

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.

Wednesday, July 28, 2010

I knew the story before I knew the story

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

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.

Saturday, July 24, 2010

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

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.

Thursday, July 22, 2010


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!

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

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?