Seriously, North Carolina? Seriously?

I am outraged about a new proposed law in North Carolina (< link to actual legal text); I feel as if this proposed law is infringing on free speech. Ok, not quite, but it is very similar. Basically it wants to limit how scientists are going to calculate sea level rises. Here's an excerpt from the bill-

The part highlighted in blue is rather disturbing to me. This proposed law wants to define how sea level rise rates can be calculated (and by whom as well).

Any data collected prior to 1900? Throw it out the window, according to this. Apparently it's not relevant. Who the heck came up with that idea? Certainly not a competent scientist. It's always in the best interest of gaining an accurate understanding of the dynamics to increase your sample size. If the data are there, why not use it?

Also notice the part about extrapolating data linearly. What if the line of best fit is exponential?

Why are lawmakers making making decisions about how to perform the scientific process? Leave the science magic to the expert scientists in the field. They know what they are doing, and the best way to do it.

Sediment Analysis of Long Swamp Creek

For my Environmental Forensics class, we have to complete a mini research project. I choose to analyze sediment from the brook behind my house, Long Swamp Creek. Long Swamp Creek is a tributary of the Toms River, and is, according to the EPA, "moderately biologically impaired." There are a number of commercial properties and housing developments. Long Swamp Creek has looked pretty yucky from time to time, and I've seen a lot of garbage in it, so I am really excited to see what fun chemicals are lurking in the sediment.

So far only a few samples have been analyzed. I can preliminarily report that there are petroleum biomarkers, or as my colleague, Kevin, put it, "it looks like you had an oil spill back there."

I'll be sure to have an update with the full details of what was found as soon as they come in!

Hiding in Plain Sight

It seems that news articles come in with regularity about new species that are discovered in places such as the remote jungles of Indonesia, or the little explored dark abyss of the ocean. It's not often that you hear of a new species being discovered in an urban area. But that is precisely what has recently happened.

A doctoral student from Rutgers University, Jeremy Feinberg, heard a frog call that he was unfamiliar with back in 2009, in Staten Island. It was similar to the well known southern leopard frog, which has a repetitive nature to its call, yet the call that the doctoral student heard was not repetitive. After lab tests and field work, Feinberg and his team of other scientists have made the conclusion that there is a new species of leopard frog among us here in the tri-state area. Genetic analysis shows that the new frog is indeed a different species, despite looking so similar to the northern and southern leopard frogs that are known to inhabit the area.

The new species, which has yet to receive a name, has a range that is believed to be within the "commuting distance to mid town Manhattan."

Picture from the NYT

Original article from the New York Times

Cool Place of the Week #9- Lake Vostok, Antartica

Picture from this article.

Lake Vostok is one of about 150  subglacial lakes located in Antarctica. It is covered by over 2 miles of ice. Scientists have been trying to drill through the ice to the lake since 1998- the project has been plagued by funding shortages, equipment failures and harsh environmental condtitions (we're talking temperatures hitting -128 degrees Fahrenheit). Another big issue that slowed the project was the possibility of contaminating Lake Vostok with drilling fluids (kerosene and Freon), which has been isolated for millions of years (between 15 and 34 million years).  It is quite possible that the lake contains new life forms unknown to science. On the other hand, it's possible that the lake is devoid of life, due to its super high oxygen levels. Even if that were the case, that would make Lake Vostok the first water body on Earth to contain no life.

Russian scientists have confirmed a few days ago that they have successfully reached the lake, just before being forced to pack up for the harsh Antarctic winter.

I am really excited to see what is found. This is ground breaking science here, having possible implications for extraterrestrial life It goes without saying that I will be sure to keep you posted on any developments!


Contributing articles from: The New York Times and The Week.

An Update on "An Unusual Bacteria"

Last week I wrote an article ("An Unusual Bacteria") about a potentially ground breaking finding that a bacterium had been found to be using arsenic in its DNA structure. A few days ago I came across an article in Scientific American about a follow up study that was performed.

The follow up study grew the bacteria , GFAJ-1, in arsenic and very little phosphorus, like the methods used in the original paper. The DNA of the grown bacteria was then purified and sent off for analysis using a caesium chloride gradient and then a mass spectrometer. The results showed that no arsenic was found in the DNA.

However, these results have yet to be published in a peer-reviewed scientific paper, so this new finding must be taken with a grain of salt. The author of the original paper about GFAJ-1, Felisa Wolfe-Simon, countered that perhaps the caesium chloride gradient made any arsenic-containing DNA too fragile, and broke apart, and not appearing in a significant way in the results. Also, it could be argued that the follow up study did not starve the bacteria of enough phosphorus so that it would start using arsenic.

My Awesome Research Trip to the Virgin Islands

My amazing professor/advisor/mentor, Dr. Bologna, has given me and his other students so many wonderful opportunities to get out and do research. My favorite, and probably the favorite of many others, is the 10 day stay on the beautiful island of St. John.

We departed on January 3rd- most of the group left from Newark Airport, but I was leaving from JFK because the tickets had been cheaper. So for the first leg of our journey, I was travelling alone. This was the first time I was travelling so far from home on my own. It was exciting and nerve-wracking at the same time. I was especially nervous because only 9 days prior, someone had tried to blow up a plane with an underwear bomb. Being that the incident had just occurred, I figured security would be extra tight.

Air travel has always bothered me a little bit, even before 9/11; I was always worried the plane would crash, and I have a slight fear of heights.I reassured myself that with the number of planes flying everyday, that the percentage of incidents occurring is extremely low. Despite a small fear of heights, I love looking out of the window. I love looking at the clouds, and I took about 100 pictures of just pretty cloud formations.

The flight went mostly smoothly- there was only some slight turbulence. It felt like a bumpy car ride. But when you are 40,000 feet off the ground.... it's different. As we descended I could make out some sea grass beds and and the waves on the water. Lower and lower we crept, until I could really see the waves well, and I felt like we were going to land on the water we were so low. Then, all of a sudden, the runway came into view underneath me and a split second later we touched down onto the island of St. Thomas.

I met up with my group at the airport and we all piled into a large open air tour bus and drove across the island of St. Thomas... on the left side of the road. Even though the U.S. Virgin
Islands are a territory of the United States, they drive on the left side of the road; if I remember correctly the islands were once held by the British.

This took getting used to.

Our drive across St. John.  Notice the sharp turns.

We took the ferry out of Red Hook Bay in St. Thomas over to Cruz Bay in St. John. Finally! St. John! But our travel wasn't over yet... we still had to drive to camp. On the way we saw numerous houses still decorated for Christmas, which was weird, given the palm trees and ambient air temperature around 80 degrees.
Our loyal bus driver, Hamilton, picked us up, and drove us along the steep wind-y road to our camp. When I say steep and wind-y, I mean really steep and hairpin turns. Sometimes there were steep hairpin turns. It was quite nerve-wracking.  The sun was setting as we drove across the convoluted way to camp (see the picture above). We finally arrived at the Virgin Islands Environmental Resource Station (VIERS) after dark. It was so noisy, with all of the bugs and frogs making noise, but it was so beautiful. We went down to the dock for a swim in the ocean. It was amazing to float on my back in the warm water, looking at the stars- which were brilliant, by the way.

The night sky was amazing! Photo by Mike Schmid.

In the morning I got my first good look around, and I fell in love. Nestled among the trees are a ring of screened in cabins for lodging, a mess hall and open air showers. There are critters all over the place- most noticeable are the numerous hermit crabs walking around all over the place (one morning I found a hermit crab in my shoe that I had laid out overnight to dry). There are also a lot of anoles sneaking about.

Hermit crab at VIERS.

Anole at VIERS.

We went down to the dock to start  off the day with a lesson on snorkeling. I had never gone snorkeling before, although I had gone scuba diving once in someone's pool. I had trouble learning to breathe through my mouth instead of my nose, and what I ended up doing for awhile was inhaling through my mouth and exhaling through my nose, which wasn't too good because over time my mask filled with water. I grew up having swimming lessons, so that was no issue for me. Within a few minutes, I was one of the 4 or 5 students out in the open water. I love how much easier wearing fins makes it to swim.

View from the dock.

We got right into starting our research; that was the reason we were there, after all. We had a few projects lined up- assessing sea urchin size and density, investigating the relationships between sea urchins and a few other creatures that hide among the sea urchin's spines, and testing mysid shrimp to see whether or not they respond to the "scent" of a fish. This work involved a LOT of snorkeling. We would be in the water for 2-3 hours at a time.  The first few days we were there, the waves were really rough, so after getting out of the water, we all had a phantom feeling of still being tossed around by the waves, much like how you still feel like you're moving after getting off a treadmill.

But I wasn't complaining about all of the swimming. The water was the perfect temperature, and I loved being submerged into the ecosystem. One time while snorkeling I found myself in the middle of a huge school  of tiny fish. It was so amazing. They swam around me for a few minutes before moving on. Another time I had a tiny fish swimming along side me for a few minutes, I imagine for the same reasons that remoras swim along side of sharks- for protection and scraps of food. This little fish was quite clearly following me, it was so cute!

We took a day off to go out hiking to explore the Pre-Columbian petroglyphs (rock carvings) at a nearby waterfall. I unfortunately became stricken with blisters early on in the hike, so it was a bit of a challenge to get there. I had to wear flip flops on the way back, my feet hurt so much! I ended up with a pair of nasty blisters on both of my heels.We also took another day off to go sailing. We went to two locations and went snorkeling, but my blistered feet only let me go snorkeling at one location.

The petroglyphs are right above the water line.

The day before we left, January 12, the earthquake in Haiti occurred just before we sat down for dinner. I was 500 miles away from the epicenter, but I heard the ground rumbling and the camp director actually felt the shaking while he was standing on the steps of his office.

St. John is a wonderful island, and I would highly recommend staying there. In my opinion, it is much nicer than St. Thomas, because St. John is so much less built up. In fact, almost 2/3 of the island is protected as a national park! There are a number of hiking trails, ruins to explore, and plenty of places to snorkel! There is even an underwater snorkeling trail!

Moving On Up In My Academic Career

Yesterday was the first day of the spring semester at Montclair State University! I had a busy day on campus meeting with some of my advisors and going to class. The class I'm taking is called Environmental Forensics, and as my professor told me, it's the first of its kind in the country. The class is about using chemistry techniques to answer questions about environmental contaminants, such as what the contaminant is, where it came from and how long it has been in the environment. I'm very excited to take this class. While thinking about thesis topics, one of the things I considered doing was an analysis of contaminants in the small stream behind my house. It has a number of discharge pipes and has a bunch of garbage thrown in there, and I would be really surprised if it is not contaminated.  The big project for the class is a small scale research project, so I think I will use that idea for my project.

Speaking of my thesis, I spoke with my thesis sponsor yesterday (the wonderful Dr. Josh Galster) and he says I'm ready to sign up for my thesis credits this semester! Even though I have been working on my thesis proposal and taking graduate classes for awhile, it has really hit me now that I am actually a graduate student. It's a very exciting and daunting task at the same time.

My thesis project was inspired by my time working for the Ocean County Mosquito Commission. I noticed during the summer of 2010 that despite there being a drought, there seemed to be a lot more West Nile Virus activity than the year before, when there was a lot of rain (I worked at the OCMC during the summers of 2009 and 2010). Was there something about there being a lack of rainfall that made the virus transmit easier? It was in this observation that my thesis project was born.

I got a glowing letter of recommendation from my boss.

I am hypothesizing that droughts influence an increase in the amount of West Nile Virus activity (basically, the number of birds and mosquitoes that test positive for the virus). This does seem counter-intuitive, since mosquitoes lay eggs in water, and more water equals more mosquitoes. However, when there is a drought, the water resources become limited, leading to clustering of birds and mosquitoes. Being in close proximity enables an increase in the rate of transmission of the virus, and voila! more West Nile Virus activity!

An Unusual Bacteria

Mono Lake in California is not your traditional lake; it is in what's known as an endorheic basin, meaning that there is no outflow of water from the lake to the ocean. As a result, Mono Lake has accumulated a lot of dissolved salts and is very alkaline; it is also naturally high in arsenic. Despite those harsh conditions, Mono Lake is thriving with life, and is also an important stop over for migratory birds.

A paper was published in December 2011(here is a link to the paper) about a potentially unique strain of bacteria found in Mono Lake. The bacteria, called GFAJ-1 (I read in an article a while back that it stands for "Give Felisa A Job," Felisa, being the lead researcher. I can't find the original article that says that though) not only survives in an enviornment with high arsenic levels, but is also thought to utilize arsenic into its DNA structure. You know, arsenic, the toxic heavy metal? Wait a second....

Transmission electron micrograph of the bacterium

 GFAJ-1.  Credit: Science/AAAS.

What the research team proposed is that this bacteria is using arsenic in its DNA instead of phosphorus. On a strictly structural basis, this would be possible for a few reasons- Both arsenic and phosphorus are in the same column of the periodic table and thus have the same number of valence electrons, meaning that they both can make the same number of bonds. Arsenic and phosphorus also have similar atomic radii. And it turns out that they both have almost the same electronegativity (arsenic is 2.18 and phosphorus is 2.19) which is just a fancy term for the affinity of an atom to attract electrons (and thus make bonds). However they have different ionization energies (the energy required to remove an electron), though in comparison to the other elements, the two are rather close.

The research team brought the bacteria back to the lab, and did some experiments growing the bacteria in a phosphorus limited environment (no added phosphorus, only what was originally present in the samples), and found that GFAJ-1 grew fine- that the arsenic was definitely not impeding the growth. The team also did experiments to find evidence that GFAJ-1 was actually incorporating the arsenic into its own biomolecules, by tracing radioactive arsenic. The results indicated that GFAJ-1 was actually using the arsenic in its DNA.

This finding rocked the scientific world, because it was a generally accepted fact that the elements necessary for life included carbon, hydrogen, oxygen, nitrogen, phosphorus,and sulfur. So to find that an organism was using arsenic instead of phosphorus was has huge implications for understanding different life forms, both here on Earth and in space. Perhaps there are other instances of elemental substitution that make life possible on other planets?

As with any radical idea, this finding has its critics. There is a lot of skepticism about how the samples were analyzed and the conclusions of the research team. It's an interesting find nonetheless, and I look forward to seeing what further research has to find on the idea!

St. John: A Fluctuating Ecosystem

It was two years ago exactly, that I was on the most amazing trip that I have taken thus far in my life- to the island of St. John in the U.S. Virgin Islands to do research. I'll probably talk about that trip in a separate blog post.

A group of film students also went on the trip and this is one of the videos that they made, about some of the environmental problems in St. John, and a little bit about the research we did.

I proudly present to you "St. John: A Fluctuating Ecosystem" by Joe Marquet.

Well Isn't This Ironic?

I found an interesting article about a study (also contains link to original research article) conducted on habitat fragmentation and selective logging and their effects on ecosystem functioning. (In case you are not familiar with the term, habitat fragmentation is when natural or man-made barriers form within a habitat. A typical example would be a road). These human disturbances are associated with loss of biodiversity (genetic transfers are impeded by barriers) and loss of habitat (especially detrimental for species that may prefer certain sizes or species of trees).  Loss of biodiversity and habitat are then usually associated with negative impacts on ecosystem functioning.  So I was especially surprised to see a study that reported no effects and even increases in ecosystem functioning.

Some of the findings:

• human disturbance hardly affected the number of species
• community composition of some groups of species was affected by fragment size
• selective logging did not affect number of species or community composition but increased some ecosystem processes

Wait, what?

So what's going on here? A few things need to be considered:

• The study only looked at one forest, in Kenya
• Once a certain number of species were included in the study.
• The fragments of the forest were still rather large.
• The ecosystem functions measured were animal-mediated (pollination, seed dispersal, seed predation, decomposition, army-ant raiding and antbird predation) which logical would increase with the extra movement of species caused by logging activity.

There are sometimes some silver linings to environmental changes, but you have to remember to look at the big picture- is the fragmentation and selective logging really benefiting the ecosystem? Probably not.

I would be interested to see further studies done in other areas to compare, and other studies done to look at other aspects of this ecosystem in Kenya.