Human Muscle Regenerated With Animal Help

Andrew Lemberger 9/24/12

Core Bio Honors, Davies

Fountain, Henry. "BODY BUILDERS; Human Muscle Regenerated With Animal Help." The New York Times. The New York Times, 17 Sept. 2012. Web. 24 Sept. 2012. <http://www.nytimes.com/2012/09/17/health/research/human-muscle-regenerated-with-animal-help.html?ref=research>.

            For returning vets of the war in Iraq and Afghanistan, who were crippled or received severe muscle damage, there is hope. Thanks to a material called extracellular matrix, scientists are able to help people grow muscle back through this thin sheet found on pigs. Extracellular matrix is the natural scaffolding that underlies all tissues and organs, in people as well as in animals.  Scientists have recently found that this scaffolding not only holds muscle in place but to their surprise also signals the body to grow and repair those tissues and organs. Due to an explosion and subsequent rounds of surgery sergeant Strang, 28, a marine, with a huge divot in his upper thigh could not move his leg.  But now two years later he walks with barely even a limp, can run on a treadmill, and is planning on becoming a police officer. This technique that was performed on Strang though still in development holds promise for treatment of current and future vets. The doctor behind this Astonishing discover is Dr. Peter Rubin, a plastic surgeon at the university of Pittsburgh medical center.  Peter being the leader of the study discovered that patients specifically sergeant Strang were showing signs of spurring muscle growth from the animal scaffolding.   About a month before Peter had scraped the scar tissue from Strang’s leg and placed the extracellular matrix from a pig bladder onto what good tissue was left. Strang’s body immediately began to break down that scaffolding and began to recruit stem cells to begin to come to the site and form into muscle cells. Now two years later Strang is able to run and do things that he would never have been able to do without this amazing advancement.   

             For me this article is exactly why science is such a interesting thing in my mind, the fact that everyday new things are discovered or created to help others or further a cause. The reason I chose this article was because not only did it talk about a new creation that betters the lives of people who have been in horrific accidents or have been injured serving our country, but also it also just amazes me what people can do when they focus on one goal and accomplish that goal.  Its great to know that in a few years maybe Men and women coming home from a long fought battle with a missing leg muscle or bicep can have it replaced and continue to live an almost normal life. 

            Overall I thought this article was written fantastically, there was great insight and detail. The author was able to create and emotional connection to the story through a touching and heartfelt story of a man who lost something and then got it back.   He provided good background details, getting into the process and studies of Dr. Peter Rubin and how he came to create this animal scaffolding. 

New Cervical Cancer Screening

Do It Yourself Cervical Cancer Screening

http://www.nytimes.com/2012/09/25/science/cervical-cancer-el-salvador-gets-a-screening-test-that-women-can-administer-at-home.html?emc=tnt&tntemail1=y

Cervical cancer is caused by the human papilloma virus, a sexually transmitted infection. It was a leading killer of women in the United States until the George Papanicolaou invented the Pap smear, which involves swabbing the cervix. But the test is expensive and requires a trained cytologist to read the cell smears. This article describes a new test that is so simple, a woman can do it herself at home. And its affordable and effective. This test will now be administered in El Salvador where most people can't afford the expensive Pap smear. This will likely save thousands of women's lives over the years to come.

Imagine if this test had been around when Henrietta Lacks was alive? Perhaps her condition could have been caught sooner and spared her life. I believe that this is the new frontier of medicine: affordable, easy to administer healthcare. With the majority of the world's population in poor and developing nations, scientists should turn their attention to serving those most at risk: those who can't afford the latest advances in Western medicine. This kind of research takes funding from charitable organizations, not big pharmaceutical companies that are only interested in profit. This new cervical cancer screen was funded by the Bill and Melinda Gates Foundation.

I am happy for the women of El Salvador who will doubtless benefit from this research, and I hope that the test spreads to other poor regions of the world. However, the question still remains if the women who get the test will be able to afford the follow-up procedures necessary to treat cervical lesions.

A Robot With a Reassuring Touch

Kylie Kardos                                                                                                                     

September 24, 2012

Core Biology 1 Honors / C-Block, Davies

Current Event Report: A Robot With a Reassuring Touch

Markoff, John. “A Robot With a Reassuring Touch” New York Times Online. 18 Sept 2012.

http://www.nytimes.com/2012/09/18/science/a-robot-with-a-delicate-touch.html?ref=science&_r=0moc.semityn.www

            Today’s robots are no longer isolated carefully inside glass cages safely and securely from humans. This was done because they were so dangerous, precise, and extremely quick that they could squish flat any human that got in their way. Recently, advancements have allowed for a significant development in the robotic systems. This article concerns creating new robotic technology that is safe to work with humans. The first product of Rethink Robotics, Baxter, a friendly two-armed robot, is evidence that future robots will be safe to work with humans. For example, besides being moderately slow moving and imprecise, Baxter is also fully equipped with a large range of safety mechanisms and sensors in order to protect the human workers it assists. Rodney A. Brooks, the roboticist who founded Rethink, proves Baxter’s safety by placing his head in the range of Baxter’s arm while it transports objects on an assembly line. And if that doesn’t totally convince you of its safety, it also has a computer-screen face that turns red in the presence of workers to let them know it is aware they are nearby. Each is even equipped with a large red “e-stop” button that will cause it to shut down immediately when pressed. Rethink calculates that the new robots can work for the equivalent of $4 an hour performing repetitive tasks for manufacturing lines and assembly.

            This article is important to society because it shows how technology has advanced to the point where we are able to construct robots that can work effectively and efficiently in the same environment as humans and not harm them. I have always been interested in technology, and it is fascinating to me how robots are now sophisticated enough to be put to work, let alone work with humans. I chose this article because it stood out to me the most - I couldn’t wait to read it.

            This article was really well written and descriptive. An important point that the author emphasizes is that employees whose tedious tasks are done by robots are not going to be laid off. Instead, these employees are going to be assigned to jobs that call for higher ability, such as training the robots for working on manufacturing lines. Also interesting is a statement made by Mr. Movellan, director of the Machine Perception Laboratory at the University of California, San Diego, “For humans it is very difficult to repeat the same movement twice. If they grasp an object, they will do it differently each time.” This shows how robots are perfect for working on assembly and manufacturing lines, as they are able to replicate the same movements infinite numbers of times - something humans cannot do. This article also compares this new robotic technology to Apple products. For example, Tony Fadell, the former Apple executive who oversaw the development of the iPod and iPhone states, “It feels like a true Macintosh moment for the robot world.” I wish that the author, John Markoff, had included more points about how this new technology was developed, instead of focusing on points about how these robots will be able to safely work with humans. I wanted to learn more about how these robots were created, and the process of designing them and how long it took. Otherwise, this article is a good read, and left me wanting to learn more about this amazing technology.

Current Events

Meghan Mitchell                                                                                         9/24/12

            The article starts out talking about how many animals, such as deer and bears, are having trouble finding food. Bears have become the biggest problem as they come to campsites and mountain towns in search of food. Sheriff Bill Masters of San Miguel County in southwest Colorado describes the situation as, “My god they’re everywhere. A lot of them just don’t seem to care anymore.” Many bears have even come into homes in their search for food, climbing through windows or open doors. But the problem isn’t only in Colorado but stretches to Montana, Kentucky and parts of the Appalachians. The shortage in food is due to the drought that has impacted around 63% of the country, a number that hasn’t been that high since 1934. And with fall coming, the bears are going to have to eat even more to prepare for hibernating.

            This problem of drought, which connects to global warming, affects humanity greatly. The people in the area with this problem have had to adapt and change with the environment. Global warming is becoming a factor in everyone’s lives as it becomes more discussed. Also, the problem with animals becoming comfortable in our society is becoming a bigger issue. People in areas such as Colorado have to be aware of their surroundings more and make an effort to save these animals that don’t have enough food.      

              I thought the article was good. It had many facts and didn’t go too in detail about anything. Also, this article was very easy to understand and was to the point. I liked how there were charts on the left-hand side having to do with drought and the visual was really useful. I didn’t like how the article ended however. It didn’t really have a strong conclusion or any closure. Overall, the rest of the article made up for this and it was really well written.

Article- Healy, Jack. "Their Food Scarce from Drought, Animals Dine in Town Dine." New YorkTimes; 6 Sept. 2012.Web.<http://www.nytimes.com/2012/09/07/us/their-food-scarce-from-drought-animals-dine-in-town.html?ref=animals&_r=0moc.semityn.www.

How to Build A Dog

Matt Drygulski              September 24, 2012

Core Biology I Honors/C-block Ms. Davies

Ratliff, Robert. “How To Build a Dog” National Geographic Online. Feb2012.

<http://ngm.nationalgeographic.com/2012/02/build-a-dog/ratliff-text>

Dogs are the most diverse animals on the planet. Dog shows, such as the Westminster Kennel Club Dog Show, is the perfect opportunity to display the great variety of canine breeds in one place. The array of different shapes, sizes, and colors is almost endless. From the great size and strong legs of a Doberman, to the small size and stubby legs of a dachshund. But how did dogs become so diverse?

According to scientists, evolution of wolves into dogs started almost 20,000 years ago. The first semi-domesticated wolves were mixed by humans to create a new type of wolf that is built for specific tasks, creating the modern dog. Of course, it took many, many generations to achieve even the smallest change. At first, dog-wolves were bred for hunting, guarding, and companionship. Thousands of years later, the process somehow jump-started to create the specific dog for a specific purpose by mixing and matching breeds. In only a last couple hundred years, breeders created 350-400 new breeds of dogs. For example, to create a dog for the purpose of cornering badgers, some kind of hound was combined with a terrier to create a new variation of a dog with stubby legs and a rounded body that allowed it to chase the badger into its burrow. This dog is known today as the dachshund.

This human interference with dog evolution changed the genes of canine anatomy. Scientists believed that this diversity led to genetic diversity. However, surprisingly there are only a few genes that control a dogs shape, color, and size.   

According to recent studies, there are certain genetic codes that can change a dachshund to a Doberman. It was discovered that the variety amongst dogs is decided by only a small amount of specific genes. Slight variations and switches of 50 genes cause the size, color, hair length, shape, fur type, nose shape, and ear positioning of a dog.

          However, this variation is something specific to dogs, as being the most diverse animals. Normally a trait or disease is caused by a combination of many genes, but in dogs, it is caused by only a handful of them. This discovery can be very important, as it helps us to understand genetic disorders shared between humans and dogs. Scientists can see what genes cause these disorders in dogs and then look for it in humans, as dogs have much simpler genetic codes than us.  

            I chose this article because I love dogs and I was always very interested in learning about them. I also find the study of genetics very interesting. The more I read, the more fascinated I was. Anyone who has a dog would be surprised to see that their Chihuahua is the same as a Great Dane, except with some simple genetic switches. The article also has relevance to the human world as scientists are using these canine genetics to understand disorders shared between humans and dogs. This discovery in dogs can revolutionize the study of genetic disorders in humans.

            The article is very informative. An outside connection is made, examples are given, and a bit of history is shown. I am impressed by the information and how it relates to humans. The article, however, needs some kind of background on genetics for someone who does not fully understand the notations of genetics and how genes work. This could be more valuable in the understanding of the main idea of the article. Overall, however, the article conveys its meaning and displays a very interesting discovery in the world of genetics.  

Jack Boyd

Ancient flower lives only on two Spanish cliffs, and uses ants to survive
This story begins with a cliff-hanger. On the Spanish side of the Pyrenees mountains, around 850 metres above sea level, two adjacent cliff faces hold the entire population of Borderea chouardii – one of the world’s rarest plants. It’s a small herb that grows into crevices in the rock. Its leaves are heart-shaped and its flowers green and unassuming. There are around 10,000 individuals here, all growing on a square kilometre of vertical rock.

Now, Maria Garcia form the Spanish National Research Council has discovered the plant’s survival strategy, which involves three different species of ants. Through these multiple partnerships, B.chouardii quite literally clings to existence.

The plant is a relict, an ancient hanger-on from a time just after the death of the dinosaurs, when the Pyrenees enjoyed a tropical climate. It was discovered in 1952, and Garcia started studying it in 1993 by request of the Regional Government of Aragon, which is responsible for its management. Since then, she has regularly returned to the site by herself, and monitored all the accessible plants. “It’s not easy fieldwork, I can tell you, but exciting and fun,” she says.

Borderea plants are either male or female and not both. They need some way of carrying pollen from male flowers to females. They live high in the mountains, so wind seems like an obvious candidate. But when Garcia placed several sticky microscope slides next to a male flower, none of them picked up any pollen at all. So, not wind.

What about insects? Between 2008 and 2009, Garcia spent 76 hours just watching B.chouardii to see which insects visited its flowers. The majority were ants: Lasius grandis and Lasius cinereus in particular. That seems to fit, for B.chouardii has many of the traits you’d expect of an ant-pollinated flower. Low-growing, nectar-filled flowers that can be reached by a non-flying insect? Check. Small flowers that aren’t attractive to bigger insects? Check.

The ants are rare visitors but effective pollinators. Across 17 years of observations, Garcia has found that around 83 percent of the female flowers eventually bear fruit. But the plant then has another problem: How does it disperse its small, yellow seeds? It can sow itself: Borderea grows away from light, and some the fruits end up headfirst in new crevices. Two-thirds of the seedlings germinate in this way. The two ants that pollinate B.chouardii might also contribute, since the plant has been found growing from their nests. But the main seed disperser is another species of ant entirely – Pheidole pallidula. Garcia demonstrated this by setting up seed “cafes” – plastic seed-filled vials that were glued to the cliff. Only P.pallidula visited the vials, and dragged the seeds off to nearby crevices. It prefers the seeds of B.chouardii to those of related species, and it eats two thirds of the seeds it collects. The rest are left to germinate.

Garci’s careful observations suggest that Borderea takes part in a “double mutualism” – partnering up with some ants to both pollinate its flowers and another to disperse its seeds. It’s a risky strategy. Even though three species of ants are involved, Garcia says that the plant is “putting all its stakes on just one kind of mutualist.” If ants disappear, perhaps if the surrounding cliff-sides become unsuitable for them, then B.chouardii would go extinct. “It is difficult to imagine other animals playing the ants’ role,” says Garcia.

But Borderea has another trick to mitigate its risk of extinction: an extraordinary lifespan of up to 300 years! In 17 years of monitoring, Garcia and other scientists have only counted 139 seedlings – just 8 per year. This is a plant that lives life in the slow lane. Its population is small and grows at an infinitesimal rate, but it’s in no rush.

The cliffs it hangs from are inaccessible to grazing animals, sheltered from the excesses of the elements, and constant in their climate.  Few new individuals are born each year, but few survivors die. Several were lost to public works before Garcia came on the scene, but she soon set up a management plan that prevented further losses. She has also started a programme to grow them in 2 new sites. Will she succeed? We cannot say. This story ends with a cliff-hanger.

Summary:

            The Bourderea Chourardii is a plant that hangs from the side of a cliff vertically. It has an interesting reproductive strategy. It has ants pollenate other plants for them. They area accessible to non flying insects, don’t have large enough leaves to attract other bugs and have a sweet nectar that comes from it. All these make it a  preferable meal for an ant.

Once the plants are pollinated, seeds are created and another ant drags the seeds back into his crevice, where the plants grow best. He eats a third of the seeds and leaves the rest to germinate. They don’t reproduce a lot of other plants. Only eight plants a year but their lifespan is a staggering 300 years. This plant has been found nowhere else in the world besides these two cliffs in the Pyrenees.

This adaption has helped the plant to survive in a very hostile environment. This truly is one of the miracles of evolution in action.

Owen Balseiro                                                                                                9/11/12

The article that I read was New Breed of Robotics Aims to Help People Walk Again, and it was about how companies like Ekso are researching and creating robotic machines to help people with physical disabilities walk again. With funding from the military and collaborating with Berkley University they have 15 rehabilitation centers around the country that help people with these new technologies. Though no one is able to have one for themself yet, progress is being made towards having this idea realized.

            Other research is also being put towards military bionic suits that allow soldiers to carry up to 200 pounds in equipment over varied terrain. The suit can also be used to protect soldiers from the injuries of heavy lifting including spinal injuries.

            Another problem with the bionic design of the Esko is that it is not yet ready for use at home and with all the materials that are used to make the suit, it is going to be hard to bring the price down. But if the military starts to use the suit more widely the price could go down.

If the suit does overcome all of these hurdles this could be new great invention of our time. Just having thousands of disabled war vets, or people from car accidents or people being born with disabilities, being able to walk. Their lives could be changed forever and no longer living a limited life because of their disabilities. This technology could also spread to people who could be given an artificial limb that moves just like their old one. The possibilities are endless. This suit is a great advancement in the medical field of our time and let’s hope that the suit gets by all boundaries so it can help the lives of thousands.  

http://www.nytimes.com/2012/09/12/technology/wearable-robots-that-can-help-people-walk-again.html?ref=science&_r=0moc.semityn.www

Suburban Lions Present a Conundrum

 Biology                                                 Spencer Cox
Current Events                                        9/10/12

The article I chose to read was about how a lion and two of her cubs escaped into the suburbs of Kenya for four months where they survived and remained remarkably fit.  When the Kenyan wild life rangers finally were contacted by one of the residents about one of the lions and how it and its cubs had been found in his backyard by his dog, they quickly came to deal with the situation.  Very little is known about how lions act in suburban environments because usually once they have either wandered into a residential area or escaped there from their protected reserve they usually are killed quickly by vehicles.  However this time around a great deal of information was gathered on how these animals act in suburban environments due to the way that the animals weight had increased and what it had been eating showed how it had survived in the suburbs.  The article then goes on to talk about how lions are an important part of the wildlife in Africa as they bring in large amounts of money from safari tours and tourists.  Many scientists and people were amazed that the lion was able to survive in an urban environment for such a long period of time and the fact that the lion also remained in good health.

The information from this article affects my life particularly because I would have never thought a lion would be able to survive in possibly one of the most dangerous places for and not only survive but thrive for a period of four months before it was finally noticed.  Personally if a lion was walking around my neighborhood I would notice pretty fast and I'm sure everyone else would to.  I have always been interested in lions ever since I first saw them at the zoo when I was little.  I always wondered how they would live it they had to be around humans constantly except they weren't in a closed environment like they are in a zoo.  I never thought that a lion would go to such a dangerous area once it had escaped its already secured habitat.  I would expect it to instead go back into the wild rather than go into an area that would have even more people in it following them and trying to catch them.

I felt that the article could have done a better job of explaining where the lions were originally from and what they did while they were in the suburbs and what they ate while they were there and if they ever made contact with people before they were caught.  Although the article did miss these key and important points I still found it to be an amazing in the knowledge and depth that it went into when talking about how the animals managed to survive in this urban environment while others had been unable to before them.

http://www.nytimes.com/2012/09/11/science/suburban-lions-present-a-conservation-conundrum-in-africa.html?_r=2      

Plasma Gasification: From Garbage to Clean Energy

Plasma Gasification: From Garbage to Clean Energy

Caroline DePaul

September 12, 2012

Core Biology I Honors / C-Block, Davies

Current Event Report- Plasma Gasification: From Garbage to Clean Energy

Leonard, Randy. "Plasma Gasification Raises Hope of Clean Energy from Garbage" New York Times Online. 11 Sept 2012. 

<http://www.nytimes.com/2012/09/11/science/plasma-gasification-raises-hopes-of-clean-energy-from-garbage.html?pagewanted=all> 

            David Robau is an environmental scientist for the Air Force who has been traveling throughout the United States trying to push for and publicize plasma gasification. Plasma gasification is a method of discarding garbage, developed by the Air Force, and is an alternative to typical incinerations. Plasma gasification, in addition to getting rid of trash, creates clean energy from garbage, recycles metals, eliminates toxic impurities, and makes enough electricity to power the entire system. As stated by Randy Leonard, the article's author, plasma gasification, “sounds too good to be true.” Currently, this system is being put into action at Florida’s Hurlburt Field Air Force base. The process of plasma gasification starts out with garbage being cut into very tiny pieces. These pieces are then fed into a gasification chamber, lacking in oxygen and hotter than nine thousand degrees. It is here that ionized particles called plasma heat the garbage to the point where only a pool of liquid oxide remains, with metal left sitting at the bottom. The metals are separated and later recycled for steel and other products. Also in the chamber, organic gases are decomposed into a fuel called synthesis gas, or syngas. The gas leaves the furnace, passes through a plasma torch polisher, and is cooled to two hundred degrees with injected water. It later passes through three filters in order to dispose of any other contaminants still left. The resulting syngas is as clean or even cleaner than natural gas and can be used to power the system. An additional result is that less dioxin, a toxic substance, is created than in normal incinerations, proving plasma gasification to be quite earth-friendly.

            The development of plasma gasification, if accepted and used by other waste companies, could create significant improvements in the environment and greatly affect humanity. It is a lot cleaner than incineration, and thus, a lot better for the environment. However, some scientists worry that by being able to completely get rid of all trash could potentially discourage recycling and the creation of renewable products. However, I believe this argument is weak when put in contrast to all the plus sides of plasma gasification. With this new technique and process of waste disposal, three hundred fifty kilowatts of electricity will be created from about ten tons of garbage every day. On top of this, metals will be recycled, less toxic substances will be created, and there will be a great decrease of emissions in the atmosphere.

            I feel the author, Randy Leonard, did a sufficient job at writing this article. He was successful in his description of the process of plasma gasification, going through each of the steps and using a lot of detail. On the other hand, I lost interest towards the end of the paper when the writer started veering off and talking about other facilities handling waste in similar ways to the plasma gasification method David Robau is promoting. Although this information is relevant, I feel the article could easily stand without this section. Also, I did not especially like how the article ended with the quote, "They're not even at the point where they should be thinking about waste-to-energy," from a scientist named Allen Hershkowitz  . In my opinion, the article should have ended with a positive note on plasma gasification and not with a statement from someone who opposes the idea. 

Clean Energy From Garbage

Andrew Dent September 10, 2012

Bio/ block c odd Ms. Daviss 

 Leonard, Randy. “Plasma Gasification Raises Hope Of Clean Energy From Garbage.” New York~.11 sept 2012, sec D: 3

This article is about a new way to dispose of our trash in an environmentally safe way. In order to do this we would need to do this we would need a machine that would break down the gas so it does not let bad fumes into the air. Mr. Robuau, environmental scientist, thinks he solved this problem. He is working along with the air force in florida creating a machine that safely way to dispose of trash without having to use unsafe chemicals or burn the waste. Many environmentalist are worried that this will discourage recycling. To this he says, “This is not incineration. This is gasification.” (par 5) By this he means that it does not destroy the garbage it just safely disposes of the gas as to know harm the environment. Left over medals are melted down and reused for steal. As well as disposing of garbage it also creates energy. 350 kilowatts of energy were created by 10 tons of garbage. the way this machine works is the pieces of garbage are cut by a mechanical shedder into two inch pieces. They then are moved to a oxygen poor chamber where the temperature reaches up to 9000 degrees and the garbage is instantly turned into a gas. The medal falls into a mullein pool which instantly cools the medal and creates ionized particles known as plasma. These particles heat the chamber to help break down the harmful gasses formed by the garbage. The cooled medal is taken and used as steal or other products. In the chamber with gasses that are from the garbage there are broken down carbon and hydrogen monoxide. These gases are the components of synthesis gas which is the gas found in furnaces. The gas goes through the plasma touch polisher which breaks down any remaining complex molecules. The synthesis gas is cooled to less then 200 degrees which purifies the gas. This gas comes out cleaner then the air we breath. The article goes on to say that this has interested many other companies in places like Japan, Texas, and New York. The addition of this green device might save the planet. 

The importance of this article is to show a better way to dispose of trash. The less trash in the ground the better it is for the society. Also the less bad fumes we release into the atmosphere the better it will be for the world. I chose this because it intrigued me that we can take something and completely get rid of  any existence of a think. 

The problem with article was that they never actually talked about how much it will cost to found this machine. They also never talked about how long it would last and what kind of backup plan was there if it failed. 

DNA Junkyard Turns Treasure-Trove

Ms. Davies

September 9, 2012

Core Biology I Honors / C-Block, Davies

Current Event Report: DNA Junkyard Turns Treasure-Trove

Kolata, Gina. “Bits of Mystery DNA, Far From ‘Junk,’ Play Crucial Role” New York Times Online. 5 Sept 2012. <http://www.nytimes.com/2012/09/06/science/far-from-junk-dna-dark-matter-proves-crucial-to-health.html>

            The human genome is about 3 billion (3 x 10⁹) nucleotide base-pairs long. (U.S. Department of Energy Genome Programs, 2008) However, until now, scientists thought that only about 1% of the DNA had any function. This is because the approximately 20,000 genes sequenced by the human genome project in 2003 make up about 1% of the DNA. The rest of the DNA is referred to as “junk” or “noncoding DNA” in most textbooks and was thought to have little to no useful function. It was often thought to be left-over garbage from our evolutionary past, such as bits of ancient genes that have since lost their function. It was also posited that the DNA “junk” helped to protect the important information coded in our genes by providing a sort of buffer zone between genes and protecting them from the wear and tear that happens in the DNA replication in mitosis. For example, as we age our telomeres wear down with edge, encroaching on the important information coded in chromosomes. The gradual wearing down of our telomeres is thought to have something to do with the aging process. However, the hypothesis that “junk DNA” was simply there as a buffer, or a vestigial evolutionary remnant, is now “junk” itself. Now, thanks to research from project Encode, Encyclopedia of DNA Elements, which is providing a sort of roadmap of how genes are interconnected, scientists have discovered that “at least 80 percent of this DNA is active and needed” and “at least four million gene switches reside in bits of DNA that one were dismissed as ‘junk.’” (Kolata 2012)

                This finding has enormous implications for many genetically-linked diseases. Although some genetic diseases have a simple genetic cause (such as Huntington’s Disease or sickle-cell anemia), for a long time scientists have realized that some diseases have a genetic component, but one that is influenced by the environment. The field of epigenetics is the study of how genes are switched “on” and “off” by other genes or environmental factors. Many “switches” for genes are being discovered in the dark matter of DNA that was thought to have no function. This can lead to insights for complex diseases such as autism, psychiatric disorders, and cancer. Scientists have often been flummoxed by the complicated genetic components of some cancers. Cancer-linked genes can be switched on and off in a way that is not fully understood. Learning more about the dark matter of DNA may help shed light on epigenetic changes that contribute to certain cancers. As a genetic cancer researcher myself who focuses on epigenetics of pancreatic cancer, this discovery has major implications for my own research. I have been focusing on genes in stretches of DNA that are methylated (epigenetically modified) in unusual frequency in pancreatic cancer, to discover which genes might be important in the progression and treatment of this cancer. However, what I have failed to ask is HOW these genes get methylated in the first place. Perhaps it is due to unknown switches in the DNA formerly known as “junk.”

            Although I am aware that the New York Times is for a generally lay audience, I felt that the author, Gina Kolata, could have done more to explain some of the basic science behind this significant discovery. First of all, Kolata failed to mention project Encode, until the tenth paragraph, and even then, failed to describe exactly what the project is doing except by analogy. I would like to know more about the actual science behind project Encode, and what techniques make it more sophisticated that the Human Genome Project. Secondly, there was no mention as to how this new understanding will affect our perception of evolution. Junk DNA was often used as one of the pieces of evidence for evolution, and I question how evolutionary biologists and genetics will now reevaluate “junk DNA” in light of these discoveries. There were many other important ideas mentioned in this article, but none of them were discussed at length. Perhaps with over thirty scientific papers being published on this topic, it was simply too much to be encapsulated in one New York Times article. I hope that the New York Times will continue to print more on this discovery, and do it justice, as this is a virtual revolution in our understanding of genetics. With this discovery all of our biology and genetics textbooks are out of date and will have to be rewritten. The name “junk DNA” should be stricken from every index and in place a new term will have to substitute. Some have suggested “dark matter DNA,” however as we learn to unravel the mysteries of this region that comprises the majority of our DNA, perhaps we can come up a better term that better captures its importance.

U.S. Department of Energy Genome Programs. “The Science Behind the Human Genome Project.” 26 Mar 2008. <http://www.ornl.gov/sci/techresources/Human_Genome/project/info.shtml>