Remote Sensing

Finding water on Mars

by Gen Itorocketphys

What are worlds outside of Earth like?

Many readers today probably can imagine some kind of extraterrestrial scene when asked this question. You might have seen a photo of a landscape of Mars captured by the recent rover, Curiosity, or perhaps astronauts walking on the Moon from Apollo missions. Others might recall images from science fiction books and movies, such as the recent film Interstellar. We live in a society now where basic space and planetary knowledge has become part of common life.

Mars Rover Selfie photo credit NASAJPL_CaltechMSSS

On the surface of Mars, the rover Curiosity takes a selfie! NASA JPL/Caltech MSSS

This was not always true; much of the universe was unknown. For example, we did not know much about the water content of Mars, number of near-Earth asteroids, or methane on Titan. Scientists in the space and planetary field have been working to
understand more about the universe in which we live. They use a variety of methods to
study space and planets, including a technique called remote sensing, which looks at (“senses”) something from far away (a “remote” place). The power of remote sensing lies in the fact that it canbe used to study places on a global scalewithout physically going to those places, and is therefore widely used for studying the planets in our Solar System. A research group at Stony Brook University, headed by Dr. Timothy Glotch, builds models that enhance the remote sensing application to amarscropreas of Mars that have been difficult to understand in the past. These models could pave the way for more efficient exploration of planetary bodies in the future.

Instruments used in remote sensing are frequently carried on satellites. These instruments contain optical devices similar to telescopes that look down at the ground instead of up at the stars, and the optical devices are combined with sensors that detect light. The type of light detected is not just normal light that we can see with our naked eye, but rather infrared light. Infrared light, although we cannot see it directly, is actually all around us. One example of visualizing this form of light is the use of night vision cameras. Night vision cameras work by detecting infrared light that is emitted as heat (e.g. body heat released from humans and animals). The same physics behind night vision cameras are also understood by remote sensing scientists, and they can use infrared light to study physical and chemical properties of materials. Remote sensing scientists analyze infrared and visible light that comes from the planetary surfaces to understand what the planets are made of, what they looked like in the past, questions about the existence of life, or where a safe and scientifically interesting place to send the next rover may be.

Mars Reconnaissance Orbiter space com

A satellite above the surface of Mars images the surface for further analysis back on earth. & Mariola Sznek

Remote sensing is a useful tool to study distant planets, but it is not perfect. One major limitation is accurate detection of planetary surfaces that are covered by fine particles, like dust on Mars. The interaction of infrared light with fine particles is complicated and makes accurate data interpretation difficult. This is problematic because Mars has many dusty regions. When trying to analyze the composition of an area that may be tied to past water activity, for example, remote sensing cannot provide accurate results if the area is covered by dust. Dr. Glotch’s group at Stony Brook University tries to push this limit by building light scattering models of the interaction of infrared light with fine particles. These models provide firm understanding of the pattern of infrared light affected by fine particles. The models are based on one of the most fundamental concepts in physics, Maxwell’s equations. Maxwell’s equations mathematically describe the behavior of electric and magnetic fields. By solving Maxwell’s equations, the models simulate the paths of infrared light as it goes through clusters of particles that resemble a dusty planetary surface. The outputs from these models provide detailed parameters that describe the behavior of infrared light as it interacts with fine particles, and this leads to better understanding of data acquired by remote sensing. From the scattering parameters, we will be able to understand how much of the infrared pattern was caused by fine particles and how much was caused by the composition of the surface itself. This understanding is important because having accurate compositional interpretationwill help answer big questions like whether life on Mars is possible. Building light scattering models enhances remote sensing application to areas of Mars that have been difficult to study, and with more accurate remote sensing capabilities, we will be able to more efficiently explore planetary bodies.

Issue 1, October 2015 


Tracking the Shark Fin Trade

Protecting the sharks from us

by Amanda Levine icon_gentics_10

There are over 100 million sharks killed every year to fill bowls of shark fin soup in China. That’s more than 3 times the population of the state of New York! Before the year 2000, shark fishing activities went largely unnoticed. Many species of shark were caught all over the world, their fins removed and shipped to Hong Kong. Since the fin was the only part of the shark deemed “valuable” to the fisherman, the shark’s still living body would then be thrown overboard to die a slow death.


Photo Credit: Mark Conlin, SWFSC

This disgusting act known as “finning” was practiced throughout the world to support the huge demand in China. Although the media has famously portrayed sharks as dangerous man-eaters in movies like Jaws, scientists have a very different view of these incredible animals. Their existence is vital to the ocean, as loss of sharks can result in the degradation of aquatic habitats, especially delicate locations like coral reefs and seagrass beds. The loss of these fragile places decreases local fish populations, which increases economic strain on coastal communities. Today a number of shark species are internationally protected to combat this decay. In order to truly protect sharks and promote conservation efforts, organizations and governments need to know which species are being affected the most.

The conservation of sharks is not easy. The first step in protecting sharks is identifying at-risk species being sold in Chinese fish markets, a process filled with obstacles. It is difficult to even acquire the fins to be identified, due to the high costs and extreme measures that many of these Chinese fish markets go to in order to stop anyone attempting to get samples. Even when samples can be acquired, the identification process can be complicated. Shark fins tend to look alike, making it nearly impossible to distinguish them by sight. Scientists, however, are capable of discriminating between the species by the fins’ DNA (genetic code), which is unique to each species. They use a technique called polymerase chain reaction to amplify certain pieces of the DNA, which is then analyzed to identify the species.

Unfortunately, the DNA in shark fins on the market is often degraded after having gone through chemical baths and processing. These roadblocks have prevented the scientific community from adequately protecting sharks or even identifying if current conservation methods are working.


Graphic: Melissa Hoffman

Dr. Demian Chapman and Ph.D candidate Andrew Fields of Stony Brook University’s School of Marine and Atmospheric Sciences have devised a solution for identifying these shark fins more effectively. During a trip to Hong Kong, they found that some shark fins were cut up into smaller, potato chip-sized pieces and sold cheaply in mixed bags. By buying these “off-cuts” they could buy lots of samples for a fairly low price; however, the DNA was still degraded, complicating the identification process. They had to invent a brand new method to identify the fins. They tweaked the current technology used to amplify DNA, so that only a smaller section of a specific gene, the cytochrome oxidase I gene, had to be amplified. By using this method, they could identify even the processed fins!

Unfortunately, it seems that the shark fin trade is bigger than was previously thought. After using this test on hundreds of off-cuts, Fields says, “There seems to be no safe group [of sharks].” Small and large sharks from all over the world, from the tropics to the subarctic seas to the deep sea, have been identified. Most shocking of all is the presence of internationally protected species in these samples. Hammerhead sharks were recently added to the Convention on International Trade in Endangered Species, or CITES, and seeing them pop up in the shark fin trade through this research has shown that these conservation efforts may be failing. Now that scientists can identify shark species at risk, we can continue to shine a light on these issues and help protect our oceans.

Issue 1, October 2015


Genetically Modified Organisms

The science behind our creation and use of GMOs for food

icon_gentics_10by Julia Budassi 


Genetically modified organisms (GMOs) are living things that have had a change engineered into their genome, or DNA. DNA is the molecule that describes the specific traits and characteristics of an organism; things like what an organism’s eye color or blood type is, how good it may be at digesting lactose, or how susceptible it may be to certain diseases. The information contained in DNA is decoded within an organism’s cells to produce its observable characteristics. The genome, the entirety of an organism’s DNA, is ultimately what distinguishes one organism from another. For example, the difference between humans and corn is a difference in the number, identity, and expression of the genes within their genomes. If you think of the genome as a cook book written in the language of DNA, the genes are single recipes for certain traits. The genome of a GMO has certain recipes that are changed artificially, meaning that recipes within the book are added, removed, or altered.

Graphic: Mark Mace

Graphic: Mark Mace

When GMOs are discussed in the news, genetically modified crops are most often the topic of the discussion. With this understanding of what a GMO is, you may be wondering why anyone would want to change the cookbooks of our crops to begin with. There are many benefits to genetically modifying crops, including improved shelf life, nutritional content, flavor, color, texture, and “farmability”. Improving shelf life is becoming increasingly important because of the global trade of crops, which requires produce to travel long distances before it reaches its consumer. The nutritional quality and farmability of plants is also crucial for nourishing a growing global population in economic positions spanning from third world to first world countries. While changes to crops that produce these effects are economically necessary, the question that we should be asking ourselves is the following: are they safe for humans to eat and for the environment to sustain? If there are risks involved with crops containing some altered genetic recipes, are the modifications truly yielding beneficial results that outweigh these risks? These big questions about GM crop growth show that the matter is of significant importance to public welfare and the agricultural industry. At the same time, trying to answer the questions reveals that there is an intimidating volume of information on the subject accessible to people. The best way to sift through all the literature and develop a well-informed opinion on the issue is to truly understand the science behind GMOs.

Scientists use plasmids for genetic modification because plasmids are naturally occurring molecules meant for the relatively simple exchange of genetic information. If a bacterium’s genome, or its cook book, lacks a gene, or recipe, scientists can use plasmids to send over the new recipe and have it added to the book. Plasmids with genes inserted into them are called recombinant plasmids. The recombinant plasmid is like a Trojan horse since the cell takes it up not knowing that it contains something foreign to it. The foreign content, however, does not ultimately attack the cell but is incorporated into its regular activities. The bacterium doesn’t mind cooking up whatever its new recipe calls for, it doesn’t know any better.

Once the plasmid is inside the plant cell, getting the recipe added into the cookbook is more complicated than it is in bacterial cells. As a result, recombinant plasmids are made not only by adding the gene scientists want to see the plant express, but also by adding a number of other DNA sequences that make the plasmid more compatible with the plant genome. There is a compatibility problem because plasmids, naturally occurring in bacterial cells, are written in the style of bacterial cookbooks. While plant cookbooks are written in the same language as bacterial cook books, the language of DNA, the writing style is a bit different. It would be like giving an American chef who is used to tablespoons and ounces an English chef’s recipe written in grams and milliliters. It is all the same language, but there is a conversion issue that would look suspicious to the plant cell chef resulting in the denial of the recipe’s addition to the book. The extra sequences inserted into the recombinant plasmid used for transforming plant cells are like a conversion chart that will make the new recipe compatible with the plant cookbook, and therefore an acceptable addition to the book.

Aphids Photo Credit: Alvesgaspar & Corn Photo Credit: IRRI Images & Graphic: Mark Mace

Aphids Photo Credit: Alvesgaspar & Corn Photo Credit: IRRI Images & Graphic: Mark Mace

The transformation process occurs in plant cells that scientists grow in petri dishes. The cells that successfully incorporate the recombinant plasmids into their genomes are identified, isolated, and grown into whole plants. The seeds of these plants will contain the recombinant DNA. When those seeds are grown in the soil, as opposed to starting as cells in petri dishes, they will produce plants that also contain the recombinant DNA, and can grow to create a family line of plants with the new gene.

When addressing crops with new genes, the question of whether the new genes change how safe the crops are is a complicated and crucial one. The most important issue to address is human health. The comparison of GM crops and their non-GM counterparts is in their chemical compositions and amounts of different molecules like proteins, carbohydrates, and lipids, the different molecules our bodies obtain from food for nutrition, as well as other nutrition related compounds like minerals. Modified corn and canola seeds, for example, contain amounts of certain classes of nutritional molecules that vary from their non-modified counterparts. Sometimes molecules were found in greater quantities in the modified crops, sometimes in lesser quantities, others were found not to have changed. The conclusions of these studies were simply that there were chemical differences between some modified crops and their non-modified counterparts, but not that the differences resulted in any sort of toxicity or danger to human health upon consumption. Furthermore, a 2008 article on GM crop safety reported that in the fifteen years of GM crop consumption prior to the article’s publishing, there have been no reported ill effects or successful legal cases related to the effects of GM crops on human health.

Environmental safety is another consideration that cannot be overlooked when discussing agricultural issues. A common genetic modification made to crops is the addition of a gene which produces a molecule that targets and kills specific pests. Adding this gene to crops allows the crops to protect themselves, eliminating farmers’ need to use chemical pesticides. Pesticides are used to kill specific pests, but the problem with any sort of pesticide, whether it be chemical pesticides or the molecule that comes from the gene used to modify the crops, is the depletion of biodiversity due to some degree indiscriminate, as opposed to targeted, killing of wildlife. A diverse population of insects and soil bacteria is important to the health of the environment because of the different roles they play in the food chain and in natural cycling of organic and inorganic resources. To assess GM crops’ effect on the environment, a study was conducted measuring the size of the population of organisms in crop fields that are not the targets of the plants’ genetically produced pesticides. These non-target populations were monitored in fields where GM crops were grown, in fields where chemical pesticides were used on non-GM crops, and in fields where no pesticides were used at all and the crops grown were also non-GM. This particular study concluded that GM crops are safer than using chemical pesticides to protect crop growth, but more harmful to the environment than not protecting crop growth at all.


Graphics: Melissa Hoffman & Mark Mace, See Photo credits in footnote*

Another environmental concern is the risk of crossbreeding between the genetically modified crops and wild relatives. This type of crossbreeding may develop super weeds that could, as a result of overgrowth, impact the soil ecosystem; a problem which currently exists and has been reported on in the past. While GM crops are safer to the soil ecosystem than chemical pesticides, a weed which does not have its growth controlled and confined like crops do could have a greater impact on non-target species than the crops containing the same foreign gene. With this in mind, there are a number of strategies implemented when growing GM crops to prevent gene flow to the wider environment. These include breeding the crops in isolation and growing seeds in isolated greenhouses or in fields that do not grow any weeds or crops related to the GM plant, eliminating the chance of crossbreeding.

While there is some environmental risk related to the cultivation of GM crops, there have been studies conducted that demonstrate the benefits reaped by growing these crops. The implications of these results are not trivial; increased crop yield could be extremely helpful for developing countries both in the way of food for the population and economic stimulation from selling the crops. On top of that, decreased use of pesticides is positive for both the health of the people and the environment. Countries with people who cannot afford much food other than the staple crop of the region could benefit from modifications that improve certain nutritional aspects of the crop by getting a more complete diet from the one food item they can afford.

GMOs are a scientific achievement that has been applied to modern agriculture with the goal of improving crop quality and yield. While GM crops are known to be chemically different from their non-GM counterparts, there has been no documented evidence of their danger to human health. There are serious environmental risks associated with the cultivation of GM crops, but with tight control, they are an effective method of increasing crop quality and yield and are less harmful to the environment than other methods of improved crop yield like the application of chemical pesticides.

Issue 1, October 2015

Photo Credit: United Soybean Board,, Pingpongwill, Uwe Hermann, flickr users nociveglia Rosana-Prada Kimberly-Vardeman geishabot