World's Longest DNA Sequence Decoded

Michael Grieco

AP Biology

Current Event 8 - Review

November 14, 2018

Davison, Angus. “World's Longest DNA Sequence Decoded.” BBC News, BBC, 31 Oct. 2018,

<www.bbc.com/news/science-environment-46046024>.

This article by Angus Davison from the University of Nottingham talks about a new breakthrough in
DNA sequencing methods. UK scientists decoded a human DNA strand of 2.3 million bases in one read.
It gives context on this ongoing “competition” that will end when scientists decode an entire genome. The
method the scientists used was called nanopore sequencing, which is a simpler and more cost-effective
method compared to the current sequencing methods. This new method also reduces the cost of
replicating a human genome from one million dollars to one thousand dollars. The article states that this
reduction arises from the increased length of a single read. In the past, even with technological
advancements, the only ways of sequencing a genome was in smaller pieces. And after this, scientists
would have to piece together the sequences, a complicated process that the article compared to a jigsaw
puzzle. Finally, the article discusses the applications of this breakthrough, such as further advancements
in cancer research.

As stated above, the extension of sequenced DNA strands can help cancer research, which studies the
rearrangement of DNA. By removing the need to rearrange smaller strands, scientists can increase the
accuracy of studies. With this advancement, we can apply similar tactics to processes such as CRISPR
in order to eliminate disease and increase the quality of life for humans. Additionally, because this
process can be applied to other organisms, we can study evolution to a further extent, allowing us to
understand the history of life on Earth.

This article explains the new study in a very detailed manner. It includes lots of information, regarding
the history of DNA sequencing, how this new method is different, and the potential applications of it. I
believe that the author could have included information regarding how the process actually works. This
could further the understanding of the importance of the study. And by giving the inner workings of the
nanopore sequencing, we could compare it to past methods not just based on efficiency.

How the Jumping Spider Sees Its Prey

Alisa Kanganis

Current Event 8

Gorman, James. “How the Jumping Spider Sees Its Prey.” The New York Times, The New York Times, 6 Nov. 2018,

www.nytimes.com/2018/11/06/science/spider-vision.html?rref=collection%2Fsectioncollection%2Fscience&action=click&contentCollection=science®ion=rank&module=package&version=highlights&contentPlacement=2&p.

This article, “How the Jumping Spider Sees Its Prey”, by James Gorman describes the different aspects of jumping spiders eyesight. Jumping spiders leap to attack their prey, but how do they know where their prey is? To answer this, Elizabeth Jacob, a spider biologist, decided to look deeper into spiders vision. She even built a custom spider eye tracker, which is used to follow their gaze. This is one of only two spider eye trackers in the world! A jumping spider has 8 eyes in total, 2 of which pick up color and detail, 2 more look backwards, another 2 detect motion, and the function of the last 2 has not yet been determined. Using the spider eye tracker, Elizabeth Jacob and her team were able to conclude that jumping spiders have tunnel vision. Their sight is like shining a beam of light into a dark room. What can be more interesting than that? Well, it turns out that the pair of eyes that detect motion let the spider know where to look! When their motion eyes are blinded, the spiders are left clueless. The main takeaway is that these pairs of eyes, which are physically separate, work together.

This discovery does not impact society greatly. However, the scientists do plan on continuing research. They want to know how the spiders tiny brain can manage information from both sets of eyes simultaneously. This can be important in understanding spider cognition, which opens a whole other door to spider biologists, like Elizabeth Jacob.

Mainly, I wish that the author included more scientific information in his article. For instance, how is a spider eye tracker built and what does it look like? Or what is the significance of this study? It would even be interesting to learn more about how the spider eyes actually work. I would like to know how some eyes are designed only to see color and detail and other eyes are designed to see motion. Why did jumping spiders vision evolve like this and is it different from other spiders? Some contextualization would be a good touch as well, as most people do not have much background information on spiders.

Raphael Munchenbach

5/11/2018

Cohut, Maria. “Cancer: How Close Are We to Curing It?” Medical News Today, MediLexicon International, 2 Mar. 2018, www.medicalnewstoday.com/articles/321106.php.

In her article, Maria Cohut discusses a much anticipated scientific development: a cure for cancer. She begins by putting cancer into context, listing shocking statistics which help put the issue into perspective. Then, she lists some already known and widely used treatments for cancer. Then, she introduces the idea that other treatments, which are still being perfected, are currently in the works, and seek to better defeat the deadly illness. The first method which she discusses is immunotherapy, or the bolstering of the body’s immune system against cancer. She then lists a flaw in immunology: that certain more aggressive cancer cells tend to develop resistances against the body’s immune system. However, she then reassures her readers by presenting a study which discussed how scientists were able to work around the more powerful cancer cells, by blocking certain signaling pathways. The second method she discusses is therapeutic vaccination, which consists of injecting “therapeutic viruses” into the patient’s body, which are helped by artificial receptors to help the therapeutic virus identify and destroy the cancer cells. Cohut does recognize a possibly destructive downside to this method, that it is difficult to control, and the supposedly helpful viruses may also certain important components of the human body. She then states a way that scientists have found to mitigate this issue, through a bioresponsive scaffold system, which makes it easier for the treatment to be controlled. She then brings up a relatively new method: nanotechnology. These are very small particles which can be programmed to target cancer and ignore the rest of the body. However, as nanotechnology is fairly new, scientists do not know the full extent of its potential, or possible downsides which may arise from it. The fourth method she discusses is “starvation” of tumors, by preventing tumors from feeding on glutamine. As this method is fairly new and unexplored, scientists must conduct more research before formulating a definitive solution. The final method she discusses is epigenetics, which is the manipulation of gene expression to eliminate possible risks of cancer. However, this is apparently harder to do in a shorter term, emergency situation and is best used years in advance. Then, she ties it all together, saying that although these methods can seem promising, they are fairly new, and it won’t be for some time that they become viable for widespread usage. She ends on a positive note, however, that every day, our knowledge progresses and we have more ways of fighting this disease.

The impact on society of these methods is fairly obvious, as cancer is one of the world’s leading causes of death, and it is the medical world’s utmost priority to find ways to combat it.  These new methods of cancer treatment have worlds of potential, and can be applied to fields even beyond the medical world. New breakthroughs such as nanotechnology seem to hold nearly unlimited potential, which brings humanity ever closer to defeating cancer.

The article has very clear strengths: it lists a variety of methods to potentially cure cancer, the contexts in which they are used, and any downsides or limitations of the treatment. This is all presented in well organized chunks, which allows readers to easily sift through each method and be certain of the proper location of these elements. She also very efficiently includes information directly from cancer researchers and studies in the field. However, Cohut’s article suffers from a lack of clarity. The language can seem oversaturated to the average reader, making it very difficult for one to follow the course of the article. Explanation for some of the more technical terms in the article would have been invaluable,  and would make the article easier to digest, and place every reader on equal footing when reading the article.

The Appendix May Play a Role in Parkinson's Disease

Anna Normand

AP Biology

Mr. Ippolito

4 November 2018

Cunningham, Aimee. “The Appendix May Play a Role in Parkinson's Disease.” Science News, 2 Nov. 2018, www.sciencenews.org/article/appendix-implicated-parkinsons-disease?tgt=nr.

The scientific article I read this week described an apparent connection between the appendix and the development of Parkinson’s disease. Parkinson’s disease is a neurodegenerative disease that affects movement, coordination, and balance, and affects more than 10 million people worldwide. Although the exact cause of the disease is unknown, but a marker of the disease is the death of neurons (nerve cells) in the area of the brain which controls movement. The subject of this article is a study done through analysis of nearly 1.7 million Swedish people throughout their lives, sometimes for over 50 years. The lead researcher, Viviane Labrie, a neuroscientist at the Van Andel Research Institution, and her team, discovered a possible connection between the removal of the appendix and the risk of developing Parkinson’s. The finding showed that removing the appendix was associated in a 19% drop in the risk of developing the disease. The researchers also studied the differences in urban areas vs. rural areas, and found that rural residents are more at risk for developing the disease. The researchers attributed this risk to possible pesticide exposure in rural areas. The researchers believe that Lewy bodies, or clumped up bits of a protein, can travel from the gut up the main nerve that connects to the brain. Because Lewy body buildup is associated with Parkinson’s, the researchers believe that the markers of Parkinson’s disease may show themselves first in the gut.

The scientific importance of this new connection should not be underestimated. Parkinson’s disease is mostly a mystery to modern scientists, and its causes have not yet been determined. Because of lack of knowledge on how to prevent the disease, most research is focused on treatment. This new information could be the key to developing early or even preemptive treatments for Parkinson’s. Researchers believe that by preventing buildup of Lewy bodies in the gut, they could possibly prevent the spread of the bodies from the gut to the brain, and thus prevent the disease.

I thought this article presented information in a concise and understandable way. Their research, although very complicated, was presented so that someone without medical education could understand, and I liked the way that the information was given and conclusions drawn. However, I thought that the article did not touch enough on the possible treatments stemming from the connection to the appendix. Personally, I am wondering if appendix removal will be considered as a preemptive treatment for those who may develop Parkinson’s, or if removal of the appendix can slow the spread of the disease once contracted. I would have liked if the author had drawn more conclusions from that discovery. I think that if the author gave more information on how this research would change the care and treatment of those with Parkinson’s, the article would be more complete and more informative.

Human Pressures Have Shrunk Wildlife Populations by 60 Percent.

Anabel Maldonado

Ippolito C Even

Current Event Review

November 4th, 2018

Waldman, Scott. “Human Pressures Have Shrunk Wildlife Populations by 60 Percent.” Scientific American, Scientific American, 31 Oct. 2018, www.scientificamerican.com/article/human-pressures-have-shrunk-wildlife-populations-by-60-percent/.

This year I have learned a lot about the problems our world faces with the environment. However, Scott Waldman article refreshed my memory on these topics. He clearly summarizes our problems with biodiversity and our land usage. He explains that our demand for food, medicine, land, energy and other resources, result in more environmental issues. This is proven, as he states “Humans have wiped out about 60 percent of the world’s wildlife populations in the last four decades, a new report has found.” His main purpose of this article is to explain how our human activity affects the wildlife around us. Waldman states that these events occur because of the deforestation, agricultural uses and overexploitation of animals. He later goes into much more in depth as to specific examples that have been affected such as “Shallow-water coral reefs have been cut in half in the last 30 years, and about 20 percent of the Amazon rainforest has disappeared over the last 50 years, the authors found.” His explanations and examples are suppose to send the audience a message stating that these problems are increasing as more time passes.

Some may argue that our world already knows all of this information. However, Waldman's article reminds his readers about these severe problems - that need to be fixed. The issues our world faces with our environment are very significant. If this trend continues then our world’s rates of deforestation and endangered species will increase. As a result, our “desire for resources” will put more wildlife in danger; and as more time passes we will continue to spiral out of control. If these problems continue to occur then our ecosystem will change, which puts our lives at risk. Yet, this topic is, also, very fixable as he explains that we should stop hunting as much, cutting down more trees, and ultimately be much more respectful of our environment.

One thing that Waldman succeeded with was explaining the relationship between this topic and his audience. He made his audience feel as if they could make a change. Also, Waldman wrote in a very persuasive tone by presenting a lot of evidence. For instance he stated “The population of polar bears is expected to drop 30 percent by 2050 as global warming shrinks the ice they need to hunt for food.” However, he did not state the sources he used to find facts such as these. I believe this was his major weakness. In order to improve upon this, he should include all sources he found. In addition, I noticed that Waldman did not state his stance or opinion on the topic. If Waldman where to personalize his article, his audience would have been more convinced to make a change.

Tiny Nanoparticles to Treat a Huge Problem: Snakebites

Cassidy Mullen

Mr. Ippolito

AP Biology C Even

11/3/18

Mcneil, Donald G. “Tiny Nanoparticles to Treat a Huge Problem: Snakebites.” The New York Times, The

New York Times, 12 Oct. 2018,

www.nytimes.com/2018/10/12/health/snakebites-treatments-nanoparticles.html.

“An Epi-Pen to treat a snakebite?” New York Times Health columnist Donald G. McNeil writes, capturing the attention of his readers and making them question the possibility of this new idea. In his article Tiny Nanoparticles to Treat a Huge Problem: Snakebites, McNeil discusses the idea that a recent study by Dr. Shea in PLOS Neglected Tropical Diseases could change the way that snakebites are treated for not only a few unlucky people in America but for people in the tropics of Africa, Asia and Europe where over 2 million people are bitten each year. Antivenins have been used to treat these snake bites in the past but they are expensive and potentially dangerous, therefore they are rarely used in poor countries where snake bites are a prominent issue. Few drug companies make Antivenins because they are expensive, must be kept refrigerated and they are difficult to make. They contain sheep and horse proteins which can also trigger life-threatening symptoms in the body. Victims often die before they can reach hospitals once they are bitten by venomous snakes. Dr. Shea’s lab is creating hydrogel nanoparticles coated with polymers (the building blocks of plastics) small enough to attach to proteins. He isolated some nanoparticles which bind with and neutralize two poisons produced by snakes like cobras, kraits, sea snakes and mambas. These solutions did not seem to interfere with normal proteins or cause dangerous allergic reactions, so the goal is to put these particles into a handheld injector, like an Epi-Pen, which does not have to be refrigerated, is relatively inexpensive, and can be carried into the field. The particles can be injected into the site of the snake bite to stop the poison from spreading and would buy time to reach better treatment.    

This discovery is important for society because snakebites are a large but overlooked problem in the community of Global Health. About 10,000 people year die from snake bites while another 400,000 are left with serious disabilities which include amputations or nerve damage so extensive that a leg or hand is permanently useless. Right now there is no accepted explanation of how anecdotes to treat snake bites are working or if they are working, therefore it is important that this problem, which is killing so many, is researched. There are many Global Issues in the world that are prevalent, but the groups that are in need of treatment are often poor, therefore there is limited funding for global projects. Author McNeil acknowledges that there is a lack of funding for this project even though the military and veterinary industry have shown interest.  

Donald G. McNeil Jr. does a very good job writing this article. He explains the basis of this advanced contemporary idea and the research that shows mice have been protected against tissue damage from spitting-cobra venom without allergic reactions due to the treatment using nanoparticles. McNeil also explains the technical issues of the project, explaining that the project has no further funding at the moment while also addressing the possible future of the project and the groups that are interesting in funding the project. McNeil does a thorough job of expressing why this project is critical to society and writes this article to raise awareness about the project. The one topic I think that could have been addressed to a further extent is the fact that the Nanoparticles are not a full solution because they only stop the poison from spreading and buy time, but this makes the reader question what the next course of treatment is after the nanoparticles reduce tissue damage but do not eradicate the poison.

Startling New Research Finds Large Buildup of Heat in the Oceans, Suggesting a Faster Rate of Global Warming

Joseph Daher

Mr. Charles Ippolito

November 1, 2018

AP Biology D-Even

Mooney, Chris, and Brady Dennis. “Startling New Research Finds Large Buildup of Heat in the

Oceans, Suggesting a Faster Rate of Global Warming.” The Washington Post, WP

Company, 31 Oct. 2018,

www.washingtonpost.com/energy-environment/2018/10/31/startling-new-research-finds-large-buildup-heat-oceans-suggesting-faster-rate-global-warming/

In a surprising study published in the popular science journal Nature on October 31st, geoscientists at Princeton University concluded that Earth’s oceans had retained 60 percent more heat than previously predicted. According to Laura Resplandy, who led the study, “We thought that we got away with not a lot of warming in both the ocean and the atmosphere for the amount of CO2 that we emitted”. The study was more accurate than previous studies because it measured the volumes of gas that have recently escaped the ocean instead of measuring the ocean temperature directly. This method is a more reliable indicator of ocean temperature change because it reflects a fundamental behavior of a liquid when heated; because gases tend to be less soluble in warm water.
Wednesday’s study carries important policy implications for modern society because it leaves nations even less time to dramatically cut the world’s emissions of carbon dioxide to abide by the Paris climate agreements level of 1.5 Celsius.
Mooney and Dennis, the authors of the Washington Post article, conclude that more rapidly warming oceans mean will result in faster rising sea levels, while also meaning that more heat will be delivered to critical locations susceptible to warming already, such as coral reefs in the tropics and the rapidly shrinking ice sheets of Greenland and Antarctica.
Mooney and Dennis’ article was an accurate summary of the recently published Princeton study and additionally provided a larger context for global ocean warming. The structure of the article is a little confusing, since the study is introduced immediately but is only clarified upon much later on. The article jumps between the science of global warming and its geopolitical implications; a more organized progression from the actual science to the international response to it would have been clearer. Otherwise the article once again shines light on one of the defining challenges for humankind in the 21st century; global warming. As the article points out, only unprecedented international cooperation against climate change can ever hope to limit and plateau global warming. And beyond the long-term implications of warmer oceans, even small changes in ocean temperatures can affect weather in specific places over the short term, making weather much more pertinent.