Friday, May 28, 2010

The Cybermen don't stand a chance against him

...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!!!

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.

Wednesday, May 26, 2010

Tuesday, May 25, 2010

Your sperm is safe

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

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

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Monday, May 24, 2010

Ok, one more post of gloating.

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???


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.

Saturday, May 22, 2010

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

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.

Monday, May 17, 2010

A post in which I gloat

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."

Sunday, May 16, 2010


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

Friday, May 14, 2010


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.


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

For more fake science posters, click here.

Wednesday, May 12, 2010

"The Gulf appears to be bleeding"

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...

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.

Friday, May 7, 2010

A toxic cleanup

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

Friday Fish Tank - Festivum cichlid spawn

There most be something in my water...

Thursday, May 6, 2010

National Day of Prayer

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.


Tuesday, May 4, 2010

Media Watch catches denialist in a lie

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.

Saturday, May 1, 2010

Stop peeing in the damn pool...

…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