DNA-MX Spring 2022 by mxscimag

Dna-MX SPRING 2022

Inagural Issue of the Middlesex Science Magazine DNA-MX (Dynamics)

SUMMARY 4

The Stress Epidemic

Genetic Mutations of COVID-19

Mushroom Materials: an eco-solution

The Himalayan Glaciers are Disappearing

Human Genome Completed

Detection of Shoreline Erosion using Satellite Image and Machine Learning

Navigating the Pros and Cons of Internet Cookies

Nuclear Fusion: What, How, and Why?

The DNA Q&A with Dr. Erickson

DNA-MX Magazine Editors in Chief Mae Rusconi Jasmine Li Layout Editor Lucas Mylon Section Editors Laura Hoffman Madeleine Godfrey Megan Shi Peter Favero Tem Taepaisitphongse

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EDITORIAL

Our First Issue

We are thrilled to introduce the first ever issue of the Middlesex Science Magazine, DNA-MX [pronounced ‘dynamics’]. Through this publication, we aim to encourage more student involvement in STEM disciplines. In and out of the classroom, Middlesex students are keen to ask hard questions, attack difficult problems, and seek out challenges to learn and grow. Our fellow classmates have diverse interests and knowledge related to science, technology, engineering and math that are not highlighted often enough. Merging writing skills with scientific research and scholarship, we hope to spotlight our fellow student and faculty scientists. We aim to spark creativity, curiosity, and wonder. Articles in this issue are a mix of informal and formal science writing—ranging from a look into the make up of COVID-19 variants to the science of stress. We hope you will enjoy this issue, seek out our writers for any further discussions, and consider contributing to the next DNA-MX issue come Fall. Sincerely, Jasmine Li & Mae Rusconi

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FEATURED I

The Stress Epidemic LAURA HOFFMAN

s schools become increasingly rigorous and competitive, students are left overwhelmed to meet the insurmountable expectations and pressures felt both internally and externally. We know that the levels of stress felt by students right now are greater than ever before, and the result of these unprecedented stress levels negatively affect students’ mental health, social life, and wellbeing. However, there are many ways that, through education and the help of institutions, students can create healthy routines and strategies to help cope with their stress. The Science of Stress The greater the level of stress, the greater the effects it has on the brain. In Harvard Health Publishing, Dr. Ressler explains that while the different parts of the brain all are important for different functions and tasks, they all work together. In this sense, if someone is under chronic levels of stress, one part of the brain is engaged more, and, therefore, other parts of the brain are left with less energy. This explains why greater levels of stress negatively impacts memory and thinking. Additionally, the brain is composed of both gray matter and white matter: in short, gray matter is for processing and white matter is for channels of communication. During chronic times of stress, white matter can be overproduced and gray matter can be underproduced and these changes can be permanent. The excess of myelin from the excess of white matter can, in theory, leave the brain more susceptible to mental illness. The Journal of Organizational Behavior Management revealed that stress levels also suppress the immune system, leaving people susceptible to getting sick as well as

anxiety and depression. However, according to stressed they choose to not attend social activiDr. Kashouty, moderate stress can actually be ties and events. beneficial, strengthening the connection between neurons in the brain, helping to improve memory and attention span, thus increasing productivity. The problem is that students who Ways to Decrease Stress face chronic levels of stress encounter more of the consequences rather than the benefits. There are science backed ways to decrease stress. For example, Dr. Ressler suggests that The Middlesex Stress Epidemic students create an attainable routine that can be stuck to every day for while stress isn’t preWhile it is commonly understood that dictable, having a routine to rely on can help stress is bad, the severity and prevalence of students maintain control in their life and is students’ stress is less commonly recognized or good for development and health. Lack of sleep acted upon. In a voluntary response survey, a worsens the effects of stress, so prioritizing a sample of 25 Middlesex students, selected from good night’s sleep is crucial. Maintaining orvarious grades using convenience sampling, ganization through list making, effective time were asked to rate their level of stress at school management, and timelines prevents students on a scale of 1-10. The average rating was an from getting overwhelmed and gives the brain 8.6. This number would categorize the avera- one task at a time. Meditation is a proven, efge Middlesex student as having chronic levels fective, and accessible way to lower our perceiof stress, and therefore, negatively impacting ved levels of stress and builds skills on how to students in all the ways mentioned above. manage stress - so channel your inner Doug! While there are resources on campus such as the meditation classes and counseling, Sophia It’s evident that Middlesex students are struFawcett a junior at Middlesex believes there is ggling with their levels of chronic stress and a lack of direct education to the students on that there are scientific ways to decrease levels strategies and routines to reduce stress sug- of stress in the body. Still, in the past three gesting that “the school could give a lot more years the school has only had one speaker talk input and talks to the students about how to about the effects of stress. While the education manage stress.” Similarly, school president on the startling effects of stress is available and Aarav Mehta reflected his high stress levels commonly understood, there seems to be a “can lead [him] to not really being able to en- lack of action taken in response to these facts. joy what [he’s] done or achieved because [he’s] Whether or not schools decide to begin to prioalways thinking about the next thing.” Middle- ritize their student’s stress levels, remember sex Junior Rachel Solomon believes that her that some resources are always available: reach high stress levels negatively impacts her social out to Ms. Cohane, Krystin Willis, Doug Worlife, admitting that “the stress of Middlesex can then, Molly Gerrity, your advisor, or a friend to often put strains on relationships.” Solomon is find ways to reduce your stress levels. one of thousands of students who feel this way for 53% of students nationally report feeling so

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FEATURED II

Genetic Mutations of COVID-19 MADELEINE GODFREY

ALPHA

DELTA Omicron

BETA

VARIANTS?

hroughout the COVID-19 pandemic, not only has the virus rapidly spread across the globe, it has appeared to supernaturally evolve in order to maximize its risk of contagion and prevent its extinction. Luckily, the virus is not a superhuman being: it is merely undergoing genetic mutations as it rapidly replicates itself. But what causes these mutations, and what are their effects on vaccines? Analyzing influenza virus mutations is helpful to further understand these mutations. To be clear, although both the influenza virus and coronavirus are contagious respiratory illnesses, they are caused by completely different viruses; however, they mutate similarly. Influenza viruses mutate in two main ways: antigenic drift and antigenic shift. Antigenic drifts involve multiple genetic copying errors accumulating over time (which, in reality, often happens quickly as viral cells replicate at an extremely rapid rate). A genetic mutation in a viral cell provides the RNA coding for slightly different spike proteins and antigens—substances on the surface of the virions that cause your body to build antibodies against them—until eventually your existing antibodies are no longer effective against the new antigens. Vaccines target spike proteins, and thus, even if you’ve gotten a flu shot, you can still get a mutated strain of the flu. While most antigenic drifts are benign, antigenic shifts can cause more rapid genetic changes to the virus. With the influenza virus, antigenic shifts occur when two different strains of the virus attempt to inhibit the same host cell at the same time, causing both strains’ RNA strands to mix in a process called reassortment. COVID-19 virions contain only one long strand of RNA, but they undergo a similar process: when two virions try to inhibit the same host cell simultaneously, their RNA strands recombine to make a new one. In both cases, the resulting “novel” virus often contains a new different combination of spike proteins and antigens. Thus, as it has spread and replicated across the globe, coronavirus has had the opportunity to undergo a multitude of mutations. The most drastic of these mutations is the Omicron variant. According to the Center for Disease Control (C.D.C.), “the Omicron variant is characterized by at least 30 amino acid substitutions, three small deletions, and one small insertion.” Omicron virions have an increased ability to bind to angiotensin converting enzyme-2 (ACE-2) receptor proteins, which is DNA-MX

where coronavirus virions can dock, and are more capable of staying put, making the variant highly transmissible.

Can vaccines effectively respond to novel COVID variants? Different vaccines protect us from the coronavirus in different ways. The Pfizer and Moderna vaccines are mRNA vaccines, meaning they contain viral material that teach cells to make a harmless copy of a COVID spike protein. After creating the protein, T-lymphocytes and B-lymphocytes (our defensive white blood cells) destroy it, and will be prepared to do so again in the future if infected with the actual virus. The Johnson & Johnson vaccine is a viral vector vaccine, meaning that injects a modified version of a different virus containing material from the coronavirus within it. Then, once again cells will make copies of the protein and the body will be prepared to fight actual infection in the future. Inevitably any COVID-19 vaccine’s effectiveness will wear down over time, and while that gradual decline in effectiveness occurs, it may seem extremely concerning that variants as wildly altered from the “original” coronavirus as Omicron are popping up across the globe. Yet vaccines are still proving to be largely effective, even against Omicron, as there are still many similarities among the spike proteins on the surface of different variants. That said, getting a booster shot will definitely help “re-jog” the memory of your T-lymphocytes and B-lymphocytes, and it is likely that as time goes on and coronavirus variants presumably become even more mutated, we may continue to need regular vaccinations to make sure our immune system is able to effectively recognize and destroy any new version of the coronavirus spike proteins. 05

BIOLOGY

Mushroom Materials: an Eco-solution MAE RUSCONI

s cardboard products accumulate in landfills, a new sustainable alternative is gaining momentum: mushroom materials.

Yes, you read that correctly. In the past decade, scientists and designers have engineered mushroom houses, furniture, and clothing. More recently, companies such as IKEA and Dell began using fungi-based packaging. But what exactly is this mysterious fungus medium, and how can we continue to apply it? A mushroom is the fruiting body of a fungus. Underground, fungi are composed of mycelium, a white tissue made of continuously branching filaments called hyphae. Flexible and intricate, this root-like network facilitates nutrient absorption and decomposition. For their role connecting trees and plants throughout the forest, mycelial networks have been coined the ‘Underground Internet.’ Fungi-webs extend far beneath our feet, spreading for kilometers. In fact, one of the largest organisms in the world is a fungus. Mycelium is strong and resilient. It can break through concrete and survive off of minimal resources. When grown on an organic substrate, mycelium forms a strong biocomposite material.Myco-materials are lightweight, with insulation rates comparable to hardwoods. One study found that their compressive strength is “fully competitive” with that of standardized materials such as Styrofoam™, paperboard and cardboard (Girometta et al.). The material can be grown into any form, from bricks to poles. Mycelium materials are so promising that NASA is currently funding a myco-architecture project in Silicon Valley, exploring the use of mycelium buildings for Mars colonization. A more immediate usage for mycelium is as a sustainable single-use material. Mycelium biocomposites are far more environmental than cardboard and paperboard. The material’s production requires low energy and

no high carbon processes, and involves the recycling of agricultural waste products such as plant fibers. Mycelium has an infinite growth capacity, does not depend on deforestation, and is 100% biodegradable (Jones et al.). With proper sterilization techniques, just about anyone can cultivate mycelium materials. Production and experimentation is inexpensive and innovative. Given these green incentives, in 2021 Jasmine Li and I conducted a fungi-biocomposite research project to test a new product: mycelium-based cup sleeves. Single-use paperboard cup sleeves are victim to discard culture; in 2018, 99.75% of paper cups world-wide were not recycled, implying that a large amount of accompanying cup sleeves were not recycled either (Team). Although compostable alternatives such as Starbucks’s EarthSleeves™ exist, all paperboard products rely on deforestation and industrial processes that emit carbon dioxide. A mycelium biocomposite sleeve appears to be an apt eco-solution. The research process consisted of three phases: modeling, cultivating, and prototype testing. We constructed a reusable cup sleeve model out of cardboard, and used coffee chaff (the flaky husk of coffee beans) as a substrate. While growing mushrooms can be difficultwith variable factors of humidity, darkness, and mold- growing mycelium is far easier. We attained Blue Oyster mushroom grain spawn, sterilized our substrates by bringing them to boiling point, then layered the models as if baking a coffee-fungi cake. After two weeks, the mycelium threads began to poke through the substrate in wispy white strands. Without any additional water or nutrients, the fibers soon wove into a dense, opaque material. Once removed, the cup sleeves were well-formed, with a smooth surface and snug fit. The mycelium resembled rubber: white and firm with a subtle earthy scent.

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In our study, the biocomposite cup sleeves exhibited equal thermal resistance to paperboard cup sleeves. There were, however, several product disadvantages; the mycelium material was rigid, thick, and took 3 weeks to grow. Nonetheless, at a manufacturing plant these challenges could be resolved with advanced cultivation methods and technology. Companies such as Mylo™ Unleathered, for instance, use mycelial cells with extra polymers to achieve a flexible material. Finer substrates and isolated growing chambers can speed up growth. These home-grown mushroom cup sleeves add to the list of inventive, slightly wacky, yet purposeful fungal designs. As consumer culture begins to prioritize sustainability and companies search for practical cardboard and styrofoam alternatives, mushrooms may emerge MVP. Green biocomposite products are likely key to fighting climate change, deforestation, and waste accumulation globally. Afterall, as many mycologists and the occasional T-Shirt will tell you, the Future is Fungi.

BIOLOGY

The Himalayan Glaciers are Disappearing MEGAN SHI

he majestic ice caps of the Himalayas are melting at a horrifying rate. The Himalayan mountain range is home to the third largest amount of glacier ice, after Antarctica and the Arctic, and is often referred to as the Third Pole. However, recent research suggests that “the massive ice sheets in the region have shrunk 10 times faster in the past four decades than during the previous seven centuries,” and these glaciers have lost about 40% of their area in the last couple centuries, amassing to an estimated 390 to 586 cubic kilometers of ice. Here are the reasons behind why glaciers are melting and the impacts this event has on the human population and the environment.

THE EFFECT ON OURSELVES AND THE ENVIRONMENT

The increased speed at which the Himalayan glaciers are melting has led to increased sea levels, endangering coastal cities and increasing the risk for saltwater intrusion in aquifers and farmland irrigation. Historically, glaciers melt partially in the summer and grow back in the warmer months, but as summers become warmer due to global warming, glaciers are melting faster than they can grow back. This occurrence has had devastating impacts on those who depend on the glacier melts as a source of water. Moreover, the newly released fresh melted water impacts ocean currents, and if the currents change, weather patterns and the distribution of heat are also disrupted. THE SCIENCE BEHIND IT The thermohaline circulation that drives water The current rate of glacial melting is at least throughout the world is altered because the ten times higher than the average rate over the new addition of fresh water disrupts the usual past centuries. Studies show that glaciers with system involving saltier, colder water sinking. significant amounts of natural debris are melting faster, contributing to around 46.5% of the total volume loss despite only making up 7.5% of total glaciers. Pollutants like volcanic ash, soot, and dust gather on the surface of the ice and absorb sunlight, increasing the rate at which the glaciers are melting. While pollutants are certainly a major factor of melting ice, the biggest culprit of our melting glaciers is global warming that stemmed from the industrial revolution. The greenhouse gases that the revolution unleashed upon our world like carbon dioxide and methane trap infrared radiation that the Earth reflects back to the atmosphere, slowly increasing the world’s temperature. Glaciers that once melted during the summer and returned to their original size in the winter are no longer re-forming due to these harmful gasses. As shown in the graph below, almost all of the Himalayan glaciers are losing mass year after year, and that increased melted water has consequences on humans and the environment.

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For humans, coastal populations may be forced to relocate from vulnerable areas or experience more extreme temperatures due to the change in thermohaline circulation. These massive glaciers melting is just one of many pieces of evidence that global climate change is not to be taken lightly, and must be combated by all countries in order to effectively diminish its effects. More international agreements like the Kyoto Protocol and the Paris Climate Agreement must be passed in order to combat this environmentally devastating occurrence. Global leaders like the United States and China need to take the lead in promising emission reductions and contributing to the United Nations’ global fund in order to help lift developing nations out of poverty and decrease reliance on industrialization. If nations do not collaborate and find compromises to minimize the effects of climate change, the glaciers melting, though in of itself having detrimental effects, would just be the beginning of our problems.

TECHNOLOGY

Introducing

HUMAN GENOME PROJECT

TEM TAEPAISITPHONGSE

On April 14, 2003, the International Human Genome Sequencing Consortium announced that the Human Genome Project was complete: they had successfully mapped the first complete human genome. Twenty years later, the Telomereto-Telomere (T2T) consortium has announced that they have mapped a truly complete sequence of the human genome. Although the Human Genome Project accounted for an impressive 92% of the human genome, their sequence could only be considered “essentially complete.” With the help of new technologies, however, the T2T consortium has been able to fill in the missing gaps and make corrections to the initial human genome sequence.

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apping the complete human genome took over three decades to accomplish— why did it take so long? The sheer amount of DNA that makes up the human genome alone posed a significant challenge. The limits of technology meant that researchers could not simply read the entire human genome at once. Instead, they had to determine sequences of shorter, random pieces of DNA and identify overlapping sections before incrementally piecing the pieces together for a more complete picture of the human genome. Moreover, many sections of the human genome are repetitive with near-identical sequences, making the task infinitely more difficult. At the time of the Human Genome Project, researchers were only able to read about 500 bases at a time. Currently, researchers are able to read up to 100,000 bases at once. The increased perspective researchers part of the T2T consortium got from longer sequences allowed them to more easily detect these repeating sequences and to then fill in missing pieces. DNA Sequencing The Human Genome Project utilized Sanger sequencing, also known as the chain-termination method, to sequence the human genome. Sanger sequencing consists of three main steps: chain termination PCR (polymerase chain reaction), size separation by gel electrophoresis, and determination of the DNA sequence. PCR is a method based on DNA replication that allows researchers to copy small segments of DNA in large amounts. In standard PCR, the two strands of the target DNA are separated using high temperature. Primers (sequences which serve as the starting point for DNA synthesis) are then bound to the ends of these separated strands. A polymerase enzyme is attached to the primer and begins to synthesize new complementary strands of DNA by adding dNTPs. Chain termination PCR differs from standard PCR in that chain-elongating inhibitors of DNA polymerase, ddNTPs, are mixed in with the dNTPs. Therefore, when the polymerase enzyme randomly adds a ddNTP instead of a dNTP, chain synthesis is terminated, resulting in DNA strands of varying lengths. In gel electrophoresis, the strands are placed on one end of a gel matrix, an electric current is applied, and the negatively-charged DNA is attracted towards the positive electrode on the opposite side of the gel. Smaller fragments will move faster than bigger fragments, meaning the strands will be arranged from smallest to largest from bottom to top. Finally, the gel is read to determine the DNA sequen-

ce. As each terminal ddNTP corresponds to a specific nucleotide in the original sequence, researchers are able to determine the sequence of the original DNA strand. Although Sanger sequencing is time consuming and costly, it is the gold standard for DNA sequencing. 454 sequencing, or pyrosequencing, like Sanger sequencing, begins with dividing the DNA sequence into fragments and using PCR to create copies of each fragment. Fragments of the same type are put into a well and incubated with various substances. One of the four types of nucleotides are added to the wells and then are incorporated onto the single-strand DNA fragments by the polymerase enzyme. The pyrophosphate released from this process is converted into ATP, and following a series of reactions, a light of intensity proportional to the amount of ATP produced is emitted. This process is repeated until the complementary strand is completed. A detector picking up the intensity of light emitted throughout the process determines the number and type of nucleotides added. While pyrosequencing is much more cost-effective and accurate than Sanger sequencing, it can only read short sequences. Researchers are now working on third-generation sequencing which will allow them to read longer sequences. There are two main types: nanopore sequencers and single molecule, real-time sequencing (SMRT) platforms. Nanopore sequencing utilizes the differences in size and electrical properties of each nucleotide base, measuring the electrical current changes to determine the DNA sequence. The SMRT platform detects fluorescence events that correspond to the addition of specific nucleotides. Each nucleotide is labeled with its own color. Every time the polymerase enzyme adds a nucleotide on a single-stranded DNA, a camera takes a picture. The different colors then allow researchers to determine which base was added. However, third-generation sequencing platforms are still expensive and lack the same accuracy as Sanger sequencing. Nevertheless, these advances in DNA sequencing technologies have allowed for great breakthroughs in science, including the complete sequencing of the human genome.

“It’s a history book - a narrative of the journey of our species through time. It’s a shop manual, with an incredibly detailed blueprint for building every human cell. And it’s a transformative textbook of medicine, with insights that will give health care providers immense new powers to treat, prevent and cure disease.” Francis Collins, 2001 Former Director of National Human Genome Research Institute

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TECHNOLOGY

DETECTION OF SHORELINE EROSION USING

SATELLITE IMAGING & MACHINE LEARNING TOMMY LI

horeline erosion is a very serious problem that we face as we try to protect the environment. It is caused by the increase in sea level due to global warming. The typical consequences of shoreline erosion are the receding of coastlines and decreases in landmass. There are many island nations in the middle of the ocean; for example, the Maldives are suffering from this problem. Ultimately, if severe enough, loss of landmass due to shoreline erosion will completely take away islands and cause the loss of ecological habitats. According to a data source online, be-

tween 1984-2016, about 24 percent of beaches underwent erosion at a rate of .5m/y. Thus, it is necessary for us to prevent further erosion from taking place. In order to do this, we must understand how the shoreline has changed throughout the past years as well as predict their future erosion. Although efforts are currently underway to measure shoreline erosion, most of the methods employed by scientists are not accurate or efficient enough.

An example of an image that is not clear enough.

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An example of an expectable data.

I used Google Earth (an easily accessible and public online data source) to collect raw data of satellite images of coastal areas. Google Earth Engine contains satellite images of all areas within the world. It has been widely used by researchers and scientists for detecting changes around the world. There were several problems during this process. Since it was not always sunny, there were clouds that interfered with the shoreline when we tried to detect it. To ensure accurate measurement of the shoreline, I used the “check_detection” model within CoastSat which allowed me to manually check image quality and keep only high-quality images. I implemented the machine learning model within Coastsat on the raw data from Google Earth. First, I imported all packages from the conda environment for further usage. Then, I set up a couple of improvements beyond the original function of Coastsat, including hyperparameter tunings, batched training to save data storage, beaching classification, and so on. I used the code “coastsat_retrieve_data” to get the image of the selected area. Then, I input the collected data into the machine learning model. In this process, the data goes through a neural network classifier with many layers. The model starts by classifying the images into many different colors and different features with different intensity. It then labels the images with different classes: sand, water, white-water, and other land features. The second step of the model (the most crucial one) is the MNDW1 model which was used to detect the boundary between sand and water.

MNDWI =

SWIR1-G SWIR1+G

An example of how the model will be influenced by the image quality.

Square algorithm to detect a contour as the shoreline. The post process of the algorithm also required some work, tidal correction being a major part of post-processing. Since the images were not guaranteed to be taken at the same time of the day, they were influenced by the tide and thus led to variation in the data collected. I put together all the detected shorelines into a graph with matplotlib (a python package) and manually plot 5 transections on the graph to visualize the difference within the same shoreline between different time periods. Ideally, the transects on the graph would be perpendicular to the detected shoreline. I labeled the position of the shoreline relative to others on another graph to visualize the change of the shoreline. The position of each shoreline relative to others would be reflected through a graph with the x-axis as time and the y-axis as position. The graph showed all the shoreline’s position compared to other shorelines and provided a better visual for the shift within the shoreline. The last step was to use Python to find the mean and median value of the position of the shoreline so I could evaluate whether or not there was any change in shoreline with the calculated results. This step eliminated small errors in the data that were caused by weather or tide. Conclusion From the data collected and the research I have committed, I conclude that there was indeed a change in the shoreline position during the time period I modeled, and that the shift is not very significant. However, due to data scarcity during the early time period and the short expanse of data, it was difficult to reach a conclusion with certainty. Despite this, machine learning has proven to be a better and more accurate model compared to the traditional method of shoreline erosion detection.

SWIR1 is the shore-wave infrared band (the output value will be between -1 and 1). A histogram was produced to show the value of different features. The water had a negative value while the sand had a positive value. The model then imposed the Otsu threshold algorithm to find a value that maximized the variance between sand and water. The final algorithm of the model was to use the iso-valued “sand/water” threshold with the Marching

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TECHNOLOGY

The importance of examining the downsides of the internet. PAETYN NAIDOO

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henever you click into a website, a prompt asking you to accept cookies would likely pop up. These messages about cookies, though annoying, are generally perceived as harmless. But, what are cookies? And why are they everywhere? Named by Lou Montulli, a cookie is a piece of information that a web browser collects from you. There are three types of cookies: session, persistent and third-party. Session cookies are used to customize user experiences in online sessions and to permanently erase data when the active browser is closed. Persistent cookies, like their name suggests, track user’s online preferences and store the information they give their browsers for a long period of time. This type of cookie collects data like language preferences and website bookmarks. Third-party cookies collect users’ data and sell it to advertisers in order to target people with relative advertisements. Though extremely useful for online convenience, internet cookies, particularly third-party cookies, invoke questions of privacy.

rience to be personalized. Many websites rely on information provided by cookies to find their target consumers for certain products. When advertisers get to understand what products a user may be interested in from their internet activity, they can choose more personalized advertisements for users to see. For example, after you look up a picture of a bike, you will begin to see advertisements for bikes on various other websites. Cookies can also make a user’s online experience more enjoyable. Online shopping websites use cookies to keep track of user actions in a specific session, from favoriting products to making purchases. Without these cookies, you would be unable to save products you like, and the shopping experience would be drastically more difficult. On the one hand, it may be terrifying that websites and companies have so much access to users’ personal information. On the other hand, this information is often used to make users’ online experiences easier. Ultimately, as the world continues to evolve into a place where all information is accessible, it is most important to be aware of how your personal information can be used.

Each and every internet user has a digital profile created for them, made up of all the information they have ever given to their devices. Think about the amount of information your phone has about you: your full name, address, credit card information, clothing size, food and restaurant preferences, hobbies, skills, relationships, weird random google searches, etc. For many people, realizing how much the internet knows about you can be terrifying. Things like identity theft and credit card fraud are real dangers that are only helped by the amount of personal information that lives online. Yet, for most of these same people, the conveniences cookies offer outweigh their risks. Internet cookies allow for a user’s online expe-

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TECHNOLOGY

NUCLEAR FUSION: What, How, and Why? KWAME ADDISON

If you were to ask google what nuclear fusion is, you would get this result: Nuclear fusion is a reaction in which two or more atomic nuclei are combined to form one or more different atomic nuclei and subatomic particles (neutrons or protons). While the definition for all intensive purposes is correct, it is overly simplified and does not assist in building any deeper understanding. Let’s look at nuclear fusion here in more detail, and hopefully change that.

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uclear Fusion in the practical, real world sense is the smashing together of heavy hydrogen (Deuterium and Tritium) isotopes to form helium, as done in the sun, in an exothermic reaction where the mass lost is converted into energy, and MASSIVE amounts of energy are released. Einstein’s famous equation E = M(C2) gives the amount of energy released from a given mass M when turned into energy as E, where C2 is the square of the speed of light, an incomprehensibly huge number. A single D-T reaction, the fusion of one atom of deuterium and one atom of tritium as pictured below, releases 17.6 MeV for the consumption of 8.35*10-27 kg of deuterium and tritium fuel, at a fuel efficiency 400 million times that of most fossil fuels and 4 times as efficient as the common nuclear fission used in nuclear reactors today. Fusion produces very little and very short-lived radioactive waste, is effectively 100% green, as it produces no greenhouse gasses and the fuels necessary are effectively completely renewable and very easy to obtain. Fusing just 42 kg of deuterium and tritium would be enough to power the US for an entire year, and would be almost 100% clean, if it were at all feasible. So, how do we make it feasible? There are many ways to achieve fusion, but the most promising methods demonstrated in recent science come from a trial

How Does it Work? Inertial Confinement Fusion at the NIF “Blast it with lasers” is what the scientists say when they attempt the process of Internal Confinement Fusion at the National Ignition Facility in Livermore, California, representing the most promising and currently most successful method of nuclear fusion within the scientific community to date. The NIF was primarily constructed at an experimental facility to examine the viability of fusion energy in a real fusion reactor using lasers to heat and compress hydrogen into extreme enough conditions for it to fuse. The facility uses a set of 3070 42-kg plates of laser glass – the strongest laser ever produced in human history – to heat and compress a tiny plastic bead (the size of a grain of rice, as pictured above) filled with frozen deuterium and tritium such that it could fuse. The bead is placed on a “target” of sorts, and then instantly hit with such a massive influx much heat and laser-energy that it instantly implodes due to massive external pressure. Imagine what would happen to a soda can if it got compressed by a sonic boom – this is like that but 100 times stronger. The laser compresses the plastic capsule around the fuel speeds of up to 350 m/s and raises its fuel’s density by a factor of well over a thousand in a matter of trillionths of a second. Again, there is no human analogy which can express how extreme this process is. This radical compression and the influx of energy from the laser heats the plasma instantly raises the plasma to conditions that rival the core of the sun, heating it to hundreds millions of degrees, fahrenheit or celsius, while the center of the sun is only 15 million ºC, causing the plasma to instantly fuse and release massive amounts of energy. While this process only lasts for about 100 trillionths of a second before the plasma explodes, it should be enough to release

(PHOTO)

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of large scale D-T fusion in a small “artificial sun” (called a Tokamak reactor) done on January 10th, 2022 in China and a trial of small scale D-T fusion through a process called Inertial Confinement at the National Ignition Facility (NIF) on August 8th, 2021. We aren’t going to discuss Tokamak fusion here, as this article is already too long. To further a deeper understanding of Inertial Confinement Fusion, however, let’s examine it in detail here. How does it work, how did its recent trial go, and what does that trial mean for the future of energy in our modern society?

massive amounts of clean, usable energy, in theory, due to the massive latent potential energy fusion is tapping into. So, what did scientists in the lab observe in practice? How Did It’s Trial Go? August 8, 2021 Unfortunately, what scientists observed in the lab was anything but “massive amounts of clean, usable energy,” a result which the researchers at the NIF actually expected due to the totally experimental nature of the project. The entire experiment generated a total amount of energy valued at just over 3 cents – only 1.3 megajoules or 0.366 kwh, enough to power an average American desktop for a couple hours or power an average American household for 1/80th of the day. This is not a large amount of energy, so what went wrong? Can fusion be something we look forward to as a clean energy source in the near future. The answer right now is no, and this article isn’t going to explain why because it’s too long already, but I encourage you to do your own research – these concepts are fascinating if you get into them. In essence, the problem is that the technology isn’t there yet, and just powering up the laser that the scientists used 477 megajoules of energy, far outweigh the costs of what was produced for the sake of research in an experimental setting – again, read some articles about it, the simultaneous massive promise and total inviability of fusion energy is both interesting and a hoot. However, the achievement of fusion like this at the NIF presents a faint glimmer of hope that economically viable fusion might be viable in the future, and can motivate future scientists to study physics in order to theoretically make this alluring dream of practically viable fusion possible. Maybe someday, powering our society with the fusion of deuterium and tritium will finally be possible.

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What originally got you into science and why did you want to be an organic chemist?

The DNA Q&A with

Dr. Erickson PETER FAVERO

I interviewed Dr. E to find about his success in science and gain insight on how students can better pursue science in the future. Dr. E is a PhD organic chemist who has acquired multiple patents and now teaches chemistry and physics.

What was it like working in a lab? I was among undergraduates with graduates looking after us, guys who are getting PhDs and stuff. So they inspired me. And there’s a lot of good stories. There’s a lot of kind of community built around the lab group. They really had a good, good tight bond with everybody. There were challenges, but I got to do some interesting reactions, and that really got my interest going.

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I had a really dynamic and kind-of inspiring high school chemistry teacher, so that made me want to go into chemical engineering in college. I got there, and my path veered a little bit from engineering to life sciences – I actually thought I wanted to go to medical school – but then I came back to organic chemistry after a great internship with a professor at the end of my sophomore year. It was a NSF research grant, and I was paid a stipend. And I did research and that, really, that’s where my interest really took off. I got interested in organic chemistry at that point. How was the transition from the corporate world to teaching? For a couple of years it was rough, I’m not gonna lie. It was hard to scale down because I’ve been working at a pretty high level as an organic chemist. So and then I had to scale that down to general fruit, you know, software, General Chemistry. That was hard. And, then I also had to teach physics, and I had to relearn physics because I had studied it for years. So yes, it was hard, but in the end it was rewarding.

How was the process of transitioning from college to the corporate world? Also, once you were there, I heard you acquired a patent – how did that process go?

Favorite lab story or favorite chemical reaction? The reduction reactions of lithium aluminum hydride are very exciting. It’s also really dangerous to work with. It’s very reactive, and will catch fire in air and water for sure. One of the scariest moments I had in the lab was after a reduction with lithium aluminum hydride, So I’d set up a reaction the night before, I got home, back of my house, whatever. And the next morning, I came to the lab, and there were fire trucks there. And it was cordoned off with yellow tape. Okay. Every window of the third floor – which I had been working on – was blown out. Yeah, it exploded, there had been a big explosion in my lab. And so, for a while, I feared that it had been my reaction that I’d set up the night before, and I was gonna get blamed for this, but, long story short, it turned out it was one of the graduate students. He put a giant beaker full of a very volatile solvent and one of the refrigerators filled it up with vapor. And then the one the motors in the fans of the fridge triggered and set off a spark. So yeah, it blew it all up. It was explosive. The refrigerator looked like a giant marshmallow. It was round, and it blew all the windows out and it caught fire to the lead. So yeah, it was exciting. So I was relieved that it wasn’t me.

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Working in a corporate lab was very different. Like I said, it moved very slowly. Through a lot of meetings, a lot of planning, a lot of meetings. That seemed less exciting than the kind of the collegial atmosphere that was in graduate school, like the group I worked with was more distant, a little more positive. So that wasn’t quite as nice. And the chemistry wasn’t that exciting? Well, it wasn’t, you know, if you do chemistry, in graduate school, you’re like, on the cutting edge, you have, like, you’re doing stuff, it’s never been done before. And industry, you’re probably doing some derivative of, although I did, you know, do have original patents. Acquiring a patent was rewarding for a lot of aspects, because you’re working on getting something developed to the point where it was commonly useful and could be used to benefit society. That was the good part of it. The bad part of it was that the process was very slow, very slow. It took years and years to make it happen. So I think in the end, I grew tired of the slow pace, and that’s what brought me out of corporate science, and the reason I chose teaching was because both my parents were teachers. I saw Middlesex as a parent because both my kids were here. So I saw Middlesex through their eyes, came over, and felt like I could fit in. And I’ve never had any regrets.

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Tips for students to easily do better in science classes or things students easily miss?

Favorite element of teaching? ` My favorite moments are when I see, after kind of trying to get something across, I see kind of the light bulbs go off in people’s eyes. I see them having an aha moment where it all makes sense. Yeah, that’s very rewarding. It’s awesome. Do you have a least favorite element of teaching? I don’t like grading lab reports. It takes about 20 minutes to 30 minutes per lab report, and if I have 20 of them, that’s a lot of time. Knowing that it’s often hard to start, because I know I have like six hours of grading ahead of me. And they get better over the course of the year, but the first ones are really bad. Yeah. They’re really bad. So it’s really like pulling out your hair. Mostly, it’s mostly, they take a lot of time. But lab reports are important, because I think a good skill that everyone should have is being able to communicate in a clear manner.

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Paying attention to units.

Tips for students looking to do well in higher level science in the future? Curiosity and engagement, I think, are the two key things. You’ve got to be curious, and you gotta be invested in learning. And it’s hard to be invested in learning if you’re not curious, if you’re not asking questions all the time, and without that you’ll never have success in science.

DID YOU ENJOY THIS MAGAZINE? CONSIDER WRITING FOR THE DNA-MX MAGAZINE!

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SOURCES

Genetic Mutations of COVID-19

Mushroom Materials: an Eco-solution

“COVID-19 Vaccines Work.” Centers for Disease Control and Prevention, www.cdc.gov/coronavirus/2019-ncov/vaccines/effectiveness/work. html. Accessed 28 Apr. 2022.

Girometta, C., Picco, A. M., Baiguera, R. M., Dondi, D., Babbini, S., Cartabia, M., . . . Savino, E. (2019). Physico-Mechanical and thermodynamic properties Of Mycelium-Based Biocomposites: A review. Sustainability, 11(1), 281. doi:10.3390/su11010281

“How Viruses Mutate and What It Means for a Vaccine.” Pfizer Incorporated, www.pfizer.com/news/articles/how_do_viruses_mutate_ and_what_it_means_for_a_vaccine#:~:text=As%20a%20virus%20 replicates%2C%20its,virus’%20surface%20proteins%20or%20antigens. Accessed 28 Apr. 2022.

Jones, M., Mautner, A., Luenco, S., Bismarck, A., & John, S. (2020). Engineered mycelium composite construction materials from fungal biorefineries: A critical review. Materials & Design, 187, 108397. doi:10.1016/j.matdes.2019.108397

Maragakis, Lisa Lockard. “COVID-19 vs. the Flu.” Johns Hopkins Medicine, www.hopkinsmedicine.org/health/conditions-and-diseases/ coronavirus/coronavirus-disease-2019-vs-the-flu.

Team, R. (2018, April 17). Plastic recycling: Why Are 99.75% of coffee cups not recycled? Retrieved February 25, 2021, from https://www. bbc.com/news/science-environment-43739043

“Science Brief: Omicron (B.1.1.529) Variant.” Centers for Disease Control and Prevention, www.cdc.gov/coronavirus/2019-ncov/science/ science-briefs/scientific-brief-omicron-variant.html. Accessed 28 Apr. 2022.

Images Photo by Christopher Cassidy on Unsplash; https://unsplash.com/photos/EYlS8SiHcYg

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“Understanding Viral Vector COVID-19 Vaccines.” Centers for Disease Control and Prevention, www.cdc.gov/coronavirus/2019-ncov/vaccines/different-vaccines/viralvector.html. Accessed 28 Apr. 2022.

Human Genome Completed

Images Photo by CDC on Unsplash; https://unsplash.com/photos/w9KEokhajKw

Adams, Jill U. “DNA Sequencing Technologies.” Nature News, Nature Publishing Group, https://www.nature.com/scitable/topicpage/ dna-sequencing-technologies-690/. “A Brief Guide to Genomics.” Genome.gov, https://www.genome.gov/ about-genomics/fact-sheets/A-Brief-Guide-to-Genomics.

The Himalayan Glaciers are Disappearing

Green, Eric D. “Completing the Human Genome Sequence (Again).” Scientific American, Scientific American, 31 Mar. 2022, https:// www.scientificamerican.com/article/completing-the-human-genome-sequence-again/.

Emma Newburger. (2021, December 20). Himalayan glaciers are melting at an extraordinary rate, research finds. CNBC. Retrieved April 12, 2022, from https://www.cnbc.com/2021/12/20/himalayan-glaciers-melting-at-extraordinary-rate-research-finds-.html#:~:text=Researchers%20found%20that%20the%20Himalayan,levels%200.92%20to%201.38%20millimeters.

Greenwood, Michael. “What Is Pyrosequencing?” News, 31 Oct. 2018, https://www.news-medical.net/life-sciences/What-is-Pyrosequencing.aspx.

NASA. (2014, September 16). How does debris influence glaciers? – climate change: Vital signs of the planet. NASA. Retrieved April 14, 2022, from https://climate.nasa.gov/news/712/how-does-debris-influence-glaciers/

Hartley, Gabrielle. “How Scientists Finally Completed the Human Genomic Puzzle.” PBS, Public Broadcasting Service, 1 Apr. 2022, https://www.pbs.org/newshour/science/how-scientists-finally-completed-the-human-genomic-puzzle.

ScienceDaily. (2021, December 20). Himalayan glaciers melting at ‘exceptional rate’. ScienceDaily. Retrieved April 14, 2022, from https:// www.sciencedaily.com/releases/2021/12/211220083104.htm

“Sanger Sequencing Steps &amp; Method - Sigmaaldrich.com.” MilliporeSigma, https://www.sigmaaldrich.com/IS/en/technical-documents/protocol/genomics/sequencing/sanger-sequencing.

World Wildlife Fund. (n.d.). Why are glaciers and sea ice melting? WWF. Retrieved April 14, 2022, from https://www.worldwildlife. org/pages/why-are-glaciers-and-sea-ice-melting

Sharman, Sarah. “Piecing Together the Genome: The Long and Short of It All.” HudsonAlpha Institute for Biotechnology, 3 Feb. 2021, https://www.hudsonalpha.org/piecing-together-the-genome-the-long-and-short-of-it-all/.

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Images

“What Is PCR (Polymerase Chain Reaction)?” Facts, The Public Engagement Team at the Wellcome Genome Campus, 21 July 2021, https://www.yourgenome.org/facts/what-is-pcr-polymerase-chain-reaction.

Photo by Aryan Singh on Unsplash; https://unsplash.com/photos/WBcpokx6FgA

Images Photo by Warren Umoh on Unsplash; https://unsplash.com/photos/-qycBqByWIY https://en.wikipedia.org/wiki/Human_Genome_Project#/media/File:Logo_HGP.jpg

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Detection of Shoreline Erosion using Satellite Imaging and Machine Learning

Cookies Caccavale, Michael. “Council Post: Bye Bye, Third-Party Cookies”. Forbes, 2022, https://www.forbes.com/sites/forbesagencycouncil/2021/04/13/bye-bye-third-party-cookies/?sh=33543be03788.

Bennett, M. K., Younes, N., & Joyce, K. (2020, August 28). Automating drone image processing to map coral reef substrates using Google Earth engine. MDPI. Retrieved February 17, 2022, from https:// www.mdpi.com/2504-446X/4/3/50/htm Choung, Y.-J., & Jo, M.-H. (2017, May 14). Comparison between a machine-learning-based method and a water-index-based method for shoreline mapping using a high-resolution satellite image acquired in Hwado Island, South Korea. Journal of Sensors. Retrieved February 17, 2022, from https://www.hindawi.com/journals/ js/2017/8245204/

“COOKIES AND SIMILAR TRACKING TECHNOLOGIES”. CNN, 2022, https://edition.cnn.com/cookie. “How Computer Cookies Affect Your Online Privacy | CRU Solutions”. CRU Solutions | Cleveland Managed IT Services & IT Support, 2022, https://crusolutions.com/blog/how-types-of-computer-cookies-affect-your-online-privacy/. “Internet Cookies”. Federal Trade Commission, 2022, https://www.ftc. gov/policy-notices/privacy-policy/internet-cookies.

Dwarakish, G. S., & Nithyapriya, B. (2016, July 9). Application of soft computing techniques in coastal study – A Review. Journal of Ocean Engineering and Science. Retrieved February 17, 2022, from https://www.sciencedirect.com/science/article/pii/ S2468013316300109

Support, Product et al. “What Are Cookies? What Are The Differences Between Them (Session Vs. Persistent)?”. Cisco, 2022, https://www. cisco.com/c/en/us/support/docs/security/web-security-appliance/ 117925-technote-csc-00.html.

Goldstein, E. B., Coco, G., & Plant, N. G. (2019, April 23). A review of machine learning applications to coastal sediment transport and Morphodynamics. Earth-Science Reviews. Retrieved February 17, 2022, from https://www.sciencedirect.com/science/article/abs/pii/ S001282521830391X

Images https://www.relationshipone.com/wp-content/uploads/2016/11/Internet-Cookies-Blog.jpg

Kumar, L., Afzal, M. M., & Afzal, M. S. (n.d.). Mapping shoreline change using machine learning: a case study from the eastern Indian coast. Retrieved February 17, 2022, from https://www.researchgate.net/publication/342563133_Mapping_shoreline_change_using_ machine_learning_a_case_study_from_the_eastern_Indian_coast

Nuclear Fusion

Kupilik, M., Witmer, F., MacLeod, E.-A., Wang, C., & Ravens, T. (2017, December 4). Gaussian process regression for Arctic coastal erosion forecasting. arXiv.org. Retrieved February 17, 2022, from https://arxiv.org/abs/1712.00867

“Fuelling the Fusion Reaction.” ITER, www.iter.org/sci/FusionFuels. “How NIF Works.” National Ignition Facility & Photon Science, Lawrence Livermore National Laboratory. https://lasers.llnl.gov/about/how-nif-works

Luijendijk, Arjen, et al. “The state of the world’s beaches.” Scientific reports 8.1 (2018): 1-11. Luijendijk, Arjen, et al. “The state of the world’s beaches.” Scientific reports 8.1 (2018): 1-11. Ye Yincan et al, in Marine Geo-Hazards in China, 2017

“Laser Glass.” National Ignition Facility & Photon Science, Lawrence Livermore National Laboratory. https://lasers.llnl.gov/about/how-nif-works/seven-wonders/laser-glass.

Rachid Amara, ... Baghdad Ouddane, in World Seas: an Environmental Evaluation (Second Edition), 2019 “Nuclear Fusion Power.” World Nuclear Association, Last Updated August 2021. https://world-nuclear.org/information-library/current-and-future-generation/nuclear-fusion-power.aspx “U.S. Energy Information Administration - EIA - Independent Statistics and Analysis.” Use of Electricity - U.S. Energy Information Administration (EIA), www.eia.gov/energyexplained/electricity/ use-of-electricity.php. “What is a Tokamak.” ITER, https://www.iter.org/mach/Tokamak. Images https://www.pinterest.com/pin/853009985659403386/ https://byjus.com/physics/nuclear-fusion/

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Cover Photo by Lucas Mylon

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