Journal of Youths in Science
VOLUME 8 ISSUE 1
BIOPRINTERS AND ETHICS
THE ECOSPHERE CALCULATING THE ENERGY
THE FUTURE IN QUESTION
OF A CLOSED SYSTEM
JUAN FERNANDEZ
FIRECROWN
THE MAN WHO CAN
HEAR COLOR
Art by Connie Chen and Alexander Hong
ABOUT
The Journal of Youths in Science (JOURNYS), formerly known as Falconium, is a student-run publication. It is a burgeoning community of students worldwide, connected through the writing, editing, design, and distribution of a journal that demonstrates the passion and innovation within each one of us.
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All submissions are accepted at submit@journys.org. Articles should satisfy one of the following categories: Review: A review is a balanced, informative analysis of a current issue in science that also incorporates the author’s insights. It discusses research, concepts, media, policy, or events of a scientific nature. Word count: 750-2000 Original research: This is a documentation of an experiment or survey that you did yourself. You are encouraged to bring in relevant outside knowledge as long as you clearly state your sources. Word count: 1000-2500 Op-Ed: An op-ed is a persuasive article or a statement of opinion. All op-ed articles make one or more claims and support them with evidence. Word count: 750-1500 DIY: A DIY piece introduces a scientific project or procedure that readers can conduct themselves. It should contain clear, thorough instructions accompanied by diagrams and pictures if necessary. Word count: 500-1000 For more information about our submission guidelines, please see http://journys.org/content/procedures
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San Diego Local Section 2 | JOURNYS | WINTER 2016
CONTACT
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contents
WINTER 2016 Volume 8 Issue 1
CHEMISTRY 4 Complexometric Water Testing Kit | MINSEOK JEON 7 Florida Apple Snail | JESSICA YOUNG
BIOLOGY A Novel Approach to Treating Brain Disorders | NATHAN LIAN 10 Bioprinters and Ethics | JOANNE WON 13 Epigenetics| MELBA NUZEN 14 FoxP2 Analysis | SANJENA VWNKATESH 16 Juan Fernandez Firecrown | ERICA YEAWON HWANG 18 Lactic Acid Bacteria | MINCHUL SHIN 20
PHYSICS & APPLIED MATHEMATICS 22 Determining the Effect of Electromagnetism on WDM Systems | JOONHYUK LEE 24 Ecosphere: Calculating the Energy of a Closed System | ARPAD KOVESDY
PSYCHOLOGY The Biology Behind Behavior | IRINE THOMAS 26 The Effect of Listening to Heavy Bass Music | SANJAY KUBSAD 30 The Man Who Can Hear Color | ELLIE FLINT 34 Why Some People Remember their Dreams | ALINA LUK 36
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Complexometric Water Testing Kit for the Developing World MinSeok Jeon
Many countries in Africa and Asia are suffering from a severe lack of clean drinking water despite the existence of water-testing technology. Eighty percent of deaths in developing countries are linked to illnesses that originate from poor water and sanitary conditions.1 Currently, water-testing kits cannot be feasibly used in developing countries because they are extremely expensive and are difficult to use. This scarcity of clean water emphasizes the need to design a new water-testing kit that is both affordable and easy to comprehend. Finding the concentration of metal ions in a water sample is a major factor in water analysis because metal ions are one of the primary contanimants of water. An excess of certain metal ions in drinking water may be fatal to the human body. Manganese, for instance, can cause Parkinsonism, a syndrome characterized by erratic movement, while lead in even low amounts is known to cause central and peripheral nervous system damage in children. Some complexometric indicators were selected to compare against drinking water standard and transition intervals. By using the results of past experiments, as well as some widely-known information and indicators, an affordable and easyto-use water-testing kit was designed.
Figure 1: Water crisis in the world 1 (Charity Water, n.d.)
Art by Amy Kim
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Countless people in developing countries only have access to contaminated drinking water. Ordinarily, water that goes down the drain is treated through a sewer system that removes solid waste and contaminants. Up to 90% of wastewater in developing countries, however, is directly discharged into rivers, lakes or the ocean, without any sewage treatment,2 and the remaining contamination in the local drinking water may allow diseases to proliferate. As a result, about 3.6 million people die from water-related diseases anually worldwide, 98% of whom live in developing countries.3 Organizations such as the World Health Organization provide health guidelines regarding the safe levels of chemicals in drinking water.4 If drinking water is not well filtered, it is likely to exceed the recommended level of chemicals, causing illness. The following metals are major contaminants in the developing world: Arsenic: Arsenic poisoning can cause vomiting, abdominal pains, and diarrhea; its long-term effects include skin, bladder, and lung cancer. Arsenic has also been associated with neurotoxicity, diabetes, and cardiovascular disease.5 One of the biggest arsenic-related water crises is currently taking place in Bangladesh.6 Manganese: About 0.5 milligrams of manganese per liter of water can be a threat to humans. It can cause symptoms resembling Parkinsonism, potentially harming the nervous system.7 Copper: Short-term exposure to copper in drinking water can cause gastrointestinal distress, while prolonged exposure can result in liver and kidney damage.8 Lead: Lead in drinking water can delay the physical and mental development of children, leading to slight defects in their attention spans and learning abilities.9 Traditional water-testing kits are excellent for determining whether water is safe to drink, but are expensive and require sufficient experience in chemistry for proper usage. Instead of difficult electronic indicators, the kit proposed in this paper includes a complexometric indicator that changes color de-
Figure 2: Overall experiment method12
pendent on the containment of particular metal ions. Because only a small amount of chemicals and plastics are required to hold the chemicals used, the kit costs far less than current electric testing devices, affirming its efficiency and cost-effectiveness. The entire kit consists of a small, portable container that holds a small amount of indicators and a contraption into which potentially contaminated water may be poured. As water is poured, the user will shake the container to cause a chelating agent to remove metal ions from the water sample (if they exist), causing the solution to be a certain color that indicates the level of metal ion contamination. The indicator for the kit should change its color when a certain metal ion concentration exceeds the drinking water standard. The indicator should not change its color when a different metal ion concentration changes from the one that is intended to be measured is changed. The solution should be around a neutral pH, because an acidic or basic solution can be dangerous to use. In addition, the mixture of the indicator and buffer solutions should be stable enough to be preserved until the kit is used.
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The information from books Applied Complexometry by Rudolf Pribil and Complexation in Analytical Chemistry by Anders Ringbom were used instead of experiment results.10, 11 By comparing the titration intervals for indicators used in these literature with the drinking water standard, several possible indicators that could be used were found: Eriochrome Black A changes color when Mg2+ exceeds the drinking water standard at pH 8-9. Dithizone (diphenylthiocarbazone) changes color when Zn2+ exceeds the drinking water standard at pH 4. Zincon (2-carboxy-2’-hydroxy-5’-sulfoformazylbenzene) changes color when Zn2+ exceeds the drinking water standard at pH 7. Methylthymol Blue changes color when Mn2+ exceeds the drinking water standard at pH 8. The above indicators are suitable for the water-testing kit, because they change color when the concentration of metal ion in water approximately exceeds the recommended concentration in safe drinking water. Several indicators must be isolated in order for the user to note which metal is of excess in the tested water. A kit using the indicators tested in this research can detect magnesium, zinc, and manganese, but there are other metal ions that can be fatal. If more complexometric indicators that can detect other metal ions were added to the kit, it would be able to determine the safety of the water more accurately. To find additional indicators, further experiments must be conducted on conditions that change pH levels or mixing of complexometric indicators with special chemicals. The developed kit could then contribute to solving the water crisis around the world. Complexometric indicators were researched to determine whether they may be used for the water-testing kit. Eriochrome Black A, Dithizone, Zincon, and Methylthymol Blue were suitable for the kit, and could detect unsafe Mg2+, Zn2+, and Mn2+ levels. Using these indicators, we can design a water-testing kit that is affordable and easy to use. In addition, it is not necessary to have a deep knowledge of chemistry to use the kit; if the color of a water sample changes, the water is not safe. These two qualities pose significant advantages, since those who suffer from the lack of clean drinking water will most likely lack economic resources and education.
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REFERENCES
Charity Water. “Charity Water Facts.” http://www.futureinsights.com/display/ ShowImage?imageUrl=%2Fstorage%2Fcharity-water-facts1.png%3F__ SQUARESPACE_CACHEVERSION%3D1349722861888 (n.d.). 2 UNICEF. “Progress on Drinking Water and Sanitation” http://www.unicef. org/gambia/Progress_on_drinking_water_and_sanitation_2014_update. pdf (2014). 3 World Health Organization. “Safer Water, Better Health: Costs, Benefits, and Sustainability of Interventions to Protect and Promote Health.” http:// whqlibdoc.who.int/publications/2008/9789241596435_eng.pdf?ua=1 (2008). 4 World Health Organization. “Guidelines for drinking water quality, 4th edition.” 5 Center for Disease Control. “Center for Disease Control Fact Sheet.” http:// www.cdc.gov/biomonitoring/pdf/Arsenic_FactSheet.pdf (2009). 6 World Health Organization. “Contamination of drinking-water by arsenic in Bangladesh: a public health emergency.” (2000). 7 Department of Public Health. “Manganese in Drinking Water.” http://www. ct.gov/dph/lib/dph/drinking_water/pdf/manganese.pdf (n.d.). 8 World Health Organization. “Iron in Drinking Water.” http://www.who.int/ water_sanitation_health/dwq/chemicals/iron.pdf (2008). 9 EPA. “Basic Information about Copper in Drinking Water.” http://water.epa. gov/drink/contaminants/basicinformation/copper.cfm (2013). 10 EPA. “Lead in Drinking Water” http://water.epa.gov/drink/info/lead/index. cfm (2013). 11 Seeds, McKenzie. “McKenzie Seed” http://www.mckenzieseeds.com/product_ detail.aspx?productID=123847 (2014). 12 Grimason, Morse, Beattie, Masangwi, Jabu, Taulo, and Lungu. “Classification and quality of Groundwater Supplies in the Lower Shire Valley, Malawi.” (2013). 13 Pribil, Rudolf. Applied Complexometry – Pergamon Series in Analytical Chemistry Volume 5 (Pergamon Press Inc., New York, 1982). 14 Ringbom, Anders. Complexation in Analytical chemistry – A Guide for the Critical Selection of Analytical Methods Based on Complexation Reactions (Interscience, New York, 1963). 15 Roger A. Minear, Lawrence H. Keith. Water Analysis – Academic Press v. 1 (Academic Press, San Diego, 1983). 16 American Public Health Association, American Water Works Association, Water Environment Federation and managing editor, Mary Ann H. Franson. Standard Methods for the examination of water and wastewater – 18th edition supplement (American Public Health Association, Washington D.C., 1998). 1
Influence of Potassium Chloride and Temperature on the Development and Behavior of the Apple Snail By Jessica Young Abstract
The Everglades currently faces the obstacle of poor water quality,
which heightens chloride concentrations from fertilizers and saltwater intrusion. This has the potential to affect entire communities of organisms, including the Everglade snail kites (Rostrhamus sociabilis) and the affected Florida apple snails (Pomacea paludosa). Effects of raising snails in potassium chloride (KCl) levels reflective of and exceeding natural Everglade KCl concentration maximums were analyzed in conjunction with the impact of varying water temperature on the snails from an average temperature of 27.8°C. The experiments were performed to observe how the variables affected development of the snails and their ability to respond to fish kairomones, or chemicals indicating predation. Rearing snails in temperatures below 26.7°C and KCl concentrations 15 parts per thousand (ppt) and above resulted in reduced snail mass and response to predatory cues.
Introduction
The family Ampullariidae contains the species of Pomacea apple snails. These include the titan, island, spike-topped, and channeled apple snails, which are endemic to parts of South America, and the Florida apple snails, which are native to Georgia, Alabama, and Florida, including the Everglades ecosystem. The Florida apple snails currently face threats of degrading water quality due to agricultural, residential, roadway, and manufacturing activities as well as competition from the other exotic apple snails. Some believe the invasion of such non-native apple snails like P. insularum and P. canaliculata have directly benefitted the populations of R. sociabilis by providing an over-abundance of food, but others have concluded otherwise. Research indicates that non-native snails may transfer avian vacuolar myelinopathy, a lethal neurological disease, to birds 1. It has also been noted that large populations of apple snails in an area provide conditions that can promote the growth of dangerous Clostridium botulinum bacteria, the causative agent o f the potentially fatal paralytic illness known as botulism. The bacteria begin to create toxic spores in decreased oxygen levels
Art by Annie Zhou provided by decaying apple snails, which use up a great deal of dissolved oxygen in the water due to their large size. Once the C. botulinum bacteria have released the spores, the birds are then susceptible to developing botulism.2 Additionally, these non-native snails may prove difficult for kites to feed on, as their large size makes it harder for snail kites to carry their shells for long distances or extract from them.3 Anthropogenic effects, including the release of chlorides into the freshwater ecosystem from chloride-based fertilizers used in agricultural processes and saltwater intrusion, strain the Everglades ecosystem. Varying water temperatures also stand to create significant changes in freshwater ecosystems. In order to survive these threats, the snails must be able to communicate with their environment. Many do so through the use of semiochemicals, substances that regulate interactions between organisms. Fish emit kairomones, a type of semiochemical, when they find prey, enabling other organisms in lower trophic levels to determine that a predator is nearby and to react accordingly. Apple snails have very sensitive tentacles on the front of their bodies that they use to detect such predatory cues. For snails in particular, predatoravoiding responses are activated by a combination of fish kairomone and alarm cue detection. When such cues are detected in a compact timeframe, snails respond by hiding in their shells, crawling above the waterline to avoid aquatic predators, and burying themselves in the substrate to hide.4 This experiment tested how Florida apple snails’ olfactory senses may degrade with exposure to high concentrations of KCl or to temperatures that deviate substantially from their optimal range. It was predicted that if Florida apple snails were exposed to KCl or to water temperatures that differ greatly from 26.6°C, it would negatively affect the snail’s mass and ability to respond to predatory cues.
Method
To provide an accurate baseline for current chloride concentrations in the Everglades ecosystem, two water samples were collected from the nearby Grassy Waters Nature Preserve and subsequently titrated. To perform titrations, a 0.1 mol silver nitrate solution was prepared by dissolving 4.25 grams of solid AgNO3 in distilled water. A potassium chromate indicator solution was created by dissolving 1 gram of K2CrO4 in 20 mL of distilled water. Samples were prepared by measuring 20 mL of a water sample into a 100 mL beaker and adding 80 mL of distilled water. 10 mL of the diluted water sample was pipetted into a conical flask, and 50 mL of distilled water and 1 mL of indicator solution was added. Samples were titrated with an average 0.05 mL of the silver nitrate solution.5 One-hundred eighty-two Florida apple snails were obtained from 7 | JOURNYS | WINTER 2016
the Harbor Branch campus of Florida Atlantic University. The snails were divided into seven groups of twenty-six and then identified by a number written on their shell. Snails were then placed into seven tengallon tanks, with two groups of thirteen snails per tank. There was a control tank at 27.8°C and 0 ppt KCl, tanks with 0 ppt KCl set 28.9°C, 24.4°C, and 26.7°C, tanks with 5 ppt KCl set at 27.8°C and 27.8°C, and one tank with 30 ppt KCl set at 27.8°C. The mass of each snail was taken immediately before the experiment and every week during the experiment for three weeks. At the end of the three weeks, remaining snails were used in a series of behavioral trials. To make the behavioral chambers for the trails, two two-gallon tanks were used, and a T-shaped piece of PVC pipe 7 cm across with the opening facing downward was attached to each one 15 cm from the narrow edge of the tank and 6.5 cm from the wider edge of the tank. One of the other ends of each pipe was closed off to create a small hiding spot for the snails to take advantage of during the behavioral trials and assess predator avoidance behavior. Behavioral trials consisted of observations of a single snail in a behavioral chamber for an hour (Figure 2). Predation cue water was created by mixing 17 liters of water with two crushed snails (spire heights 26 mm and 18 mm) and holding a Rocio octofasciata in the water for two hours. Each of the behavioral trial tanks was filled with 4,365 mL of freshwater. One snail was placed in each tank at a time, and all snails were placed 6.5 cm away from both the short and long edges of the tank. To create a final concentration of 10% cue water, 485 mL of cue water was added to the behavioral chamber once the snail that was in the chamber was adjusted and showing activity. Observations about the snail’s behavior were recorded for one hour after the trial began. The total amounts of time (in seconds) the snail spent hiding, crawled-out above the waterline, or burying were recorded.
loss of mass out of all the groups, with a change in mass of -2.38 g between the initial measurements and week one, -2.00 g between week one and week two, and -3.25 g between week two and week three (Figure 1). A one-way analysis of variance (ANOVA) test showed that the results for the 30 ppt KCl, 15 ppt KCl, and 24.4°C were statistically significant (Figure 2).
Control snails spent an average of 44.6% of the time in the behavioral chamber conducting predator avoidance behaviors. The 26.7°C group and 5 ppt KCl group spent similar amounts of time conducting predator avoidance behaviors, but the 24.4°C group only spent an average of 26.3% of the time exhibiting these behaviors. The group raised in 30 ppt demonstrated these behaviors only 19.8% of the time (Figure 3).
Results
The control group showed an average change in mass of +1.85 g over
three weeks (Figure 4). The group exposed to water of 30 ppt KCl showed the greatest loss of mass out of all the groups, with an average change in mass of -2.54 g over three weeks. The 24.4°C group had an average change in mass of -1.17 g over the three weeks. The 26.7°C group gained 1.02 g, the 5 ppt KCl group gained 1.83 g, and the 15 ppt KCl group lost 0.75 g over three weeks. The control group showed a change in mass of +1.44 g from the initial measurements to the measurements taken during week one, +2.00 from week one to week two, and + 2.11 from week two to week three. The group exposed to water with a chloride concentration of 30 ppt KCl showed the most
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A one-way ANOVA test revealed that the lack of response by the 24.4°C, 15 ppt KCl, and 30 ppt KCl groups was statistically significant (Figure 4).
Titration showed chloride levels of 0.170 ppt in Grassy Waters, just above average chloride concentration of 0.140 ppt for the ecosystem. All snails in the 28.9°C experimental group had died within a week of starting the experiment, likely because the change to a higher water temperature was too stressful or because the water was too warm to hold enough dissolved oxygen to support all twenty-six snails in the tank (Figure 5).
REFERENCES
Byers, J., McDowell, W., Dodd, S., Haynie, R., Pinto, L., & Wilde, S. Climate and pH predict the potential range of the invasive apple snail (Pomacea insularum) in the Southeastern United states. PLoS ONE, 8, http://dx.doi.org/ 10.1371/journal. pone.0056812 (2013). Levin, P. “Statewide Strategic Control Plan for Apple Snail (Pomacea canalicula`ta) in Hawai’I”. http://www.hear.org/articles/pdfs/applesnailcontrolplanlevin2006.pdf (2006). Darby, P., Mellow, D., & Watford, M. Food handling difficulties for snail kites capturing non-native apple snails. Fla Field Nat. 35, 79-85. (2007). Dalesman, S., & Rundle, S. Influence of Rearing and Experimental Temperatures on Predator Avoidance Behavior in a Freshwater Pulmonate Snail. Freshw. Biol., 55, http://dx.doi.org/ 10.1111/j.1365-2427.2010.02470.x (2010) “Determination of Chloride Ion Concentration by Titration (Mohr’s Method)”. http:// www.outreach.canterbury.ac.nz/chemistry/documents/chloride_mohr.pdf (2007).
Data collected suggest that chloride levels in excess of 15 ppt and temperatures less than 26.7°C have the ability to inhibit the growth and development of Florida apple snails, as well as their ability to react to predatory cues. This trend could be explained by the change in the snails’ abilities to maintain homeostasis because of temperature differences between the external environment and the snails, as well as a change in the way ions were taken in by the snails, since the higher chloride concentrations might have changed the rates of diffusion. Results of titrations giving chloride levels at 0.170 ppt in Grassy Waters indicated that current levels of chlorides in the ecosystem are relatively close to expected average chloride levels of 0.140 ppt.
Discussion
Chloride levels above 15 ppt have the ability to inhibit growth and development of Florida apple snails, as well as their ability to react to predatory cues. Data collected illustrates how excess chlorides and increased water temperatures might affect wetland species in Florida, starting with the Florida apple snail. These results can be useful when considering the manufacture of fertilizers. Data collected from this study can also serve as an example of what occurs when saltwater intrudes into a freshwater ecosystem. Conservation of native snails is important, as other studies indicate the potential of non-native snails to significantly alter the ecology of the Everglades ecosystem by consuming native, helpful macrophytes and encouraging growth of phytoplankton, being possible vectors for Avian vacuolar myelinopathy and botulism, and limiting Everglade snail kite diet due to relative shell and beak size disparity.1,2,3 Understanding native snails’ thresholds for water quality can help people revitalize their population growth and offer possible solutions for control of invasive snails in the Everglades. 9 | JOURNYS | WINTER 2016
A Novel Approach to Treating Brain Disorders
by Nathan Lian Art by Jenny Li
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Our understanding of the relationships between the neural phenotype of the brain and the organization of the genome is impeded by several difficulties: (i) there exists approximately 22,000 structural genes in the human genome, of which several thousand have yet to be elucidated and (ii) the differences in sequences of mouse, rat, monkey, chimpanzee and human genomes are so small that genome evolution, as opposed to brain evolution, appears strikingly non-linear. A few plausible explanations for such non-linear evolution include: (i) the length of postnatal development—the period of development between birth and senescence, (ii) the selective stabilization and elimination of the synapse elicited by interactions with the social, cultural, physical and biological environment and (iii) chromatin epigenesis—functionally relevant changes to the genome that do not involve changes in the nucleotide sequence. However, for the purposes of the brain transcriptome, let’s just focus on sequential patterns in pre- and postnatal development. The best way to model the relationship between genotype and phenotype in multicellular organisms is based fundamentally on the extension of the bacterial operon scheme as described by Jacob and Monod—a method that utilizes bacteria to control gene expression by regulating mRNA transcription—to eukaryotic cell differentiation and embryonic development. Specifically, the bacterial operon scheme focuses on the use of transcription factors (TFs) in relation
to DNA and RNA polymerase and other TFs. Transcription factors serve as diffusible signaling allosteric proteins that bind to specific DNA elements in promoter regions, and in turn, triggering (or inhibiting) in cis—a molecular structure in which two particular atoms or groups lie on the same side of a given plane in the molecule—the transcription of adjacent genes by RNA polymerase.1 In other words, TFs determine which genes are turned “on” or “off” at any given moment. Studying them, therefore, would allow us to determine specific genes responsible for expressing a neural phenotype. Just as genes can be regulated by TFs, so TFs can be regulated by ligands and other TFs. When allosterically regulated by ligands, TF conformations are manipulated, thereby affecting their functional capabilities. TFs can also control the transcription of their own structural genes,2 which allows for the generation of autocatalytic feedback loops, wherein they may serve as gene switches in embryonic development. Since TFs have the functional capability of controlling other genes, including other TFs, we can generate hierarchical trees of gene-expression patterns throughout the course of development. However, the problem with applying this paradigm to brain genes and other relevant pathological phenotypes is not straightforward. Therefore, in order to identify the hundreds of genetic determinants that predispose to brain disorders, such as autism-spectrum disorder (ASD) and schizophrenia, an establishment between gene sets and brain connectivity is required. With that being said, leading scientists have been exploring a new method to treat these disorders based on a hierarchical network of TFs, specifically during pre- and postnatal brain development. Before discussing this new method, let’s first understand a few things. In order to evaluate DNA microarray data, we will begin by examining neural networks. In normal computers and technological systems, information is manipulated through discrete, rigid, sets of rules, and certain inputs to these rules always produce the same certain, calculated outputs. Computational systems follow linear paths and undergo procedural programs. However, neural networks manipulate data differently: instead of constricting inputs and outputs to separate, distinctly defined pathways, neural networks are composed of multiple interconnected neurons, or nodes, that each individually analyze data and work together to produce an output. In other words, neural networks process information on multiple levels of nodes, using inputs to influence many levels of modifiable processors, allowing for input “weights” to determine the mechanisms used to create an output, and allowing for neural networks to learn how to modify data by changing those input weights.3 Additionally, neural networks are able to learn from their mistakes, either by basing knowledge off of a definite set of inputs and outputs, inferring knowledge from an unlabeled set of data, or
by guiding the network to certain outputs by correcting incorrect pathways through supervised learning, unsupervised learning, and reinforcement learning.4 This separate method of data analysis, modeled off the information processing of the brain, allows for the processing of more abstract inputs, such as those seen in pattern recognition. One of the primary methods for clustering DNA microarray data is the self-organizing map (SOM) developed by Teuvo Kohonen due to its ability to cluster both genes and sample clusters (i.e. time points), while simultaneously taking into account the relationship between the two. Put simply, SOMs are unsupervised neural networks that allow for visualization of high-dimensional gene expression data through multidimensional scaling and data reduction.5 In order to generate a SOM, several parameters must be set: (i) the number of clusters that will be represented as a two-dimensional grid map, (ii) the number of training iterations and (iii) the assignment of neighborhood, learning factor, and distance metrics through the calculation of the Euclidean distances between nodes from a set of training data and nodes from a set of input data and the application of the Pythagorean theorem to determine the maximum radial distance from a best matching unit (BMU) to surrounding nodes. A BMU is essentially a “winning neuron,” or a node whose weight vector is the closest to the input vector being examined and whose neighborhood nodes are modified by a fraction of the difference between the old weight of the node and the input vector. As the SOM algorithm continues to run, the neighborhood begins to shrink exponentially, allowing for the creation of coherent gene groups (CGGs) and the placement of genes with minimal distance metrics in neighborhood vicinity, so that the only thing left by the final iteration is the BMU. By examining the generated CGGs, specifically in the hippocampus (HPC), cerebral cortex (CTX) and hypothalamus (HYP), a modified phylogenetic footprinting method6 can be used to search only for genomic DNA sequences that are conserved among species. A phylogenetic footprinting method is a technique used to identify transcription factor binding sites (TFBSs) within a non-coding region of the DNA of interest by comparing it to the orthologous sequence—sequences that are perceived to have been descended from the same ancestral sequence, separated only by a speciation event (vertical descent of a single gene from the last common ancestor)—in different species, which in our case, involves mice and rats. Through this modified phylogenetic footprinting method, the descent of brain disorders can be traced back to origins possibly existent in other species and allow for preliminary testing of pharmaceuticals before human-based clinical trials. While there is still a lot more to explore when it comes to utilizing SOMs, such as conventional signaling pathways and the development of the CTX and HPC in relation to 11 | JOURNYS | WINTER 2016
the HYP, the information that has been presented thus far is enough to be able to comprehend some plausible contributions of the TFs network to next generation pharmacological cures. It should be noted that all the elucidated TFs related to disorders participate in a broad set of regulations within the organism, especially those related to its development. Therefore, TF hierarchical networks can be used to generate concrete suggestions about a brain disorder’s genetic origin, as well as a potential design of pharmacological intervention at definite levels in these networks in order to prevent the emergence of pathological phenotypes. Each hierarchical network can be further divided into sublevels (and therefore even more TFs), but for the purposes of brevity and clarity, let’s just focus on three basic master TFs: the GATA-1 TF, a regulator of certain cell growth mechanisms wherein mutations in exon 2 can lead to Down Syndrome;7 the AP-1 TF, a Jun and Fos heterodimer responsible for regulating neuron and synapse development wherein mutations can lead to schizophrenia;8 and the E2F1 and HNF-1 TFs wherein mutations can lead to ASD. Interestingly, ASD and schizophrenia are disorders that start in the prenatal period, develop in the early postnatal period, and manifest themselves in the neural and behavioral phenotypes in the later postnatal period.9 Therefore, since there are temporal delays between the expression of the mutated TF and the manifestation of the behavioral defect, modern drug treatments tend to be inefficient. It should also be noted that the TFs involved in the control of CGGs grow exponentially as we progress down the levels of the TF hierarchy. With that being said, administration of drugs targeted to a given TF’s hetero-oligomer must coincide with the time of development when the TF of interest forms functional heterodimers—a protein dimer (protein quaternary structure) with two or more subunits—to bind to specific DNA sequences to prove effective. However, while this may be the case with modern drug treatments, a new approach has been synthesized that will utilize the information from CGGs in the SOM to synthesize compounds that are able to block (or enhance) in a steric (or allosteric) manner, the activity of a given TF in the hierarchical network. 12 | JOURNYS | WINTER 2016
Since there exists some common CGGs in ASDs and schizophrenia, if scientists can identify specific TF oligomers that can interfere with, and even restore, pathological evolution of mutated TFs in genetically predisposed patients, they may be able to use a single drug to downregulate the expression of a mutated gene significant to the progression of both diseases. The practical significance of this strategy is that it takes into account the genetic diversity within TFs, which can be anticipated, and even prevented, by their inclusion in common branches of TF development. This strategy also allows for the synthesis of new pharmacological agents that are strikingly different from commonly used agents for psychotic patients; meaning that instead of targeting the symptoms, we can finally target the cause. 1 .
References
Mannervik, M., Nibu, Y., Zhang, H. and Levine, M. (1999) Transcriptional coregulators in development. Science 284, 127-156. 2. Thayer, M.J., Tapscott, S.J., Davis, R.L., Wright, W.E., Lassar, A.B. and Weintraub, H. (1989) Positive autoregulation of the myogenic determination gene MyoD1. Cell 58, 24 3. Stergiou, Christos, and Dimitrios Siganos. “Neural Networks.” N.p., n.d. Web. 17 Apr. 2016. 4. Shiffman, Daniel. “Neural Networks.” The Nature of Code. S.l.: Selbstverl., 2012. N. pag. Print. 5. Eichler, G.S., Huang, S. and Ingber, D. E. (2003) Gene Expression Dynamics Inspector (GEDI): for integrative analysis of expression profiles. Bioinformatics 19, 2321-2322. 6. Halfon, M.S., Grad, Y., Church, G.M. and Michelson, A.M. (2002) Computationbased discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model. Genome Research 12, 10191028. 7. Grreene, M.E., Mundschau, G., Wechsle, J., McDevitt, M., Gamis, A., Karp, J., Gurbuxani, S., Arceci, R. and Crispino, J.D. (2003) Mutations in GATA1 in both transient myeloproliferative disorder and acute megakaryoblastic leukemia of Down Syndrome. Blood Cells, Molecules and Diseases 31 351-356. 8. Pennypacker, K.R. (1995) Ap-1 transcription factor complexes in CNS disorders and development. The Journal of the Florida Medical Association 82, 551-554. 9. Insel, T.R. (2010) Rethinking schizophrenia. Nature 468, 187-193.
Bioprinters and Ethics: The Future in Question by Joanne Won Art by Christina Patricia Ethical issues often arise with technological advancements. This is especially true in the case of the bioprinter, an emerging devicew built to print human organs using tissue engineering.1 Many proponents argue that bioprinters have the potential to significantly alleviate organ donor shortages; however, they also have the potential to do more damage than good. One major concern is that bioprinters could possibly contribute to the organ black market and increase the rate of illegal surgeries. Economically underdeveloped and war-torn countries are especially susceptible, since organ trafficking is endemic in developing countries throughout Latin America, Asia, and the Middle East.1 Bioprinting is a nontraditional technique in tissue engineering that allows scientists to print 3-D devices that deposit biological materials for medical purposes.2 The bioprinter originates from a traditional 3-D inkjet image printer often used to print documents. Organ printing, on the other hand, mimics embryonic cellular fusion by assembling tissues into 3-D patterns similar to the shapes of organs.2 The printer is able to create a variety of complex arrangements with precision and speed through regulatory structures in a normal inkjet printer.2 The bioink consists of nutrients and collagen that match the characteristics of the original organ structure. The biopaper, which is eventually removed from the construct, contains nutrients, collagen, growth factors, and other supporting agents vital to cellular life. Through specific computerized design instructions, bioink and biopaper have made it possible to use vascular tissue in complex organ production.2 The bioprinter has only existed for a little over a decade. Because it is so new, there are very few recorded cases of patients who have undergone transplants involving this technology. However, in one of the few known cases, an infant named Kaiba underwent a successful tracheal transplant at the University of Michigan in Ann Arbor.3 Kaiba possessed a disease called tracheobronchomalacia. This respiratory condition resulted in a collapsed bronchus and a deficiency of airflow into his lungs. To allow for sufficient airflow, a specifically designed tracheal splint (made from a biopolymer called polycaprolactone) was sewn around Kaiba’s airway to expand his bronchus and aid proper growth and was eventually reabsorbed by his body.3 Dr. Glen Green, an associate professor at the university, was able to create this custom-designed device by using
high-resolution imaging directly taken from a CT scan of Kaiba’s trachea. The scan was integrated with an image-based computer model enabled with laser-based 3-D printing. Dr. Green later stated, “It’s amazing. As soon as the splint was put in, the lungs started going up and down for the first time and we knew he was going to be okay.3” Bioprinting could very well change the world of medicine. Some critics are concerned that in the wrong hands, bioprinters and artificially-printed organs could thrive in the black market. However, it is actually quite the opposite: bioprinting can solve the organ-trading problem. Black market traders kidnap individuals for organ harvesting to satisfy huge demand and lack of supply, but the bioprinter could increase the supply of available organs.4 Bioprinting organs is a challenging endeavor, but the field of artificially-harvested organs is filled with innovative potential. Despite these benefits, bioprinting, like any other new form of modern technology, must continue to be monitored to ensure that it does not harm vulnerable patients. The longterm consequences of bioprinting are difficult to know exactly; hence, in the coming years, researchers must continue to ask important questions and modify the technology as needed. References 1
Mearian, L. “Bioprinting Human Parts Will Spark Ethical, Regulatory Debate.” (2015). 2 Ozbolat, I. T. and Yu, Y. Bioprinting Towards Organ Fabrication: Challenges and Future Trends. IEEE Trans. Biom. Engr., 60, NO. 3, 691-699 (2013). 3 Zopf D. A., Ohye, R. G., Nelson M. E. “Baby’s Life Saved With Groundbreaking 3D Printed Device from University of Michigan that Restored His Breathing.” (2013). 4 Boren, Z.D. “3D Printed Heart Saves Baby’s Life as Medical Technology Leaps Ahead.” (2014). 5 Nilsson, M., Forsberg, A., Lennerling, A., Persson, L. Coping in Relation to Perceived Threat of Graft Rejection and HealthRelated Quality of Life of Organ Transplant Recipients. Scandi. Jour. Caring Sci., 27, 935-44, 2014. 6 Ozbolat, I.T., Chen, H., & Yu, Y. Development of “Multi-arm Bioprinter” for Hybrid Biofabrication of Tissue Engineering Constructs. Robotics Comp. Int. Manuf, 30, 295-304 (2014). 7 Archer, D. M.D. “Body Snatchers: Organ Harvesting for Profit.” (2013).
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Revising the Consensus on DNA By Melba Nuzen Art by Alice Jin
Recently, epigenetics, the study of the epigenome,
has revealed that our lifestyles can affect our DNA. These changes do not alter the order of nucleotides in DNA - in fact, an individual’s DNA maintains its original sequence throughout his or her entire life, even after epigenetic changes affect the transcription and translation of those sequences.1 Epigenetic changes can occur in many ways, but the two major mechanisms are chromatin remodeling and DNA methylation. In the nucleus of eukaryotic cells, DNA is found wrapped around proteins for packaging and structure – this protein and DNA complex is called chromatin. The main element of this complex are protein molecules called histones. Groups of histones are bound by DNA molecules, forming clumps of DNA-histone units called nucleosomes. These nucleosomes are held together by more DNA, just like beads on a string. Additionally, histone tails extend from histones, allowing for chemical changes catalyzed by particular enzymes.2 Chromatin remodeling is regulated by the presence of chemical modifications to these histones. For example, the addition of chemical groups to histone tails can promote or inhibit DNA replication and transcription.3 But while mutations in genetic information are permanent, epigenetic changes are reversible. For example, adding acetyl groups to histone tails – histone acetylation – loosens the formation of chromatin, allowing DNA to become more accessible and easier to transcribe. Adding methyl groups – histone methylation – brings DNA closer together to inhibit transcription. Reversing these changes can be done by removing these chemical groups, a feat not so easily done in DNA. Since these biochemical groups do not change the actual content of DNA, they are considered to be epigenetic changes.4 In DNA methylation, the first discovered and most well-researched epigenetic change, a methyl group is added to cytosine, maintaining the condensed structure of DNA.7 The presence of this methyl group subsequently prevents transcription by physi14 | JOURNYS | WINTER 2016
cally blocking the passage of proteins used during transcription.5 Methylation is found across most of the genome in animals, with varying patterns and concentrations. For example, female bee workers and the queen bee are genetically very similar, but when methyl-adding enzymes are reduced in a sample of bee larvae, all of the larvae hatch as queen bees. The lack of methyl groups allows special genes to be read and eventually leads to the development of queen bees.6 Epigenetic processes vary in effects, from responses aiding development in the body to epigenetic changes due to pernicious conditions. As the body matures, epigenetic factors involve themselves in the specialization of cells, in addition to helping regulate gene expression. Epigenetic changes allow for the differentiation between identical pluripotent stem cells as they develop. Even though all the somatic cells in a person contain the exact same DNA, epigenetic processes make it possible for stem cells to differentiate into eye cells, muscle cells, or brain cells.8 Along with responding to stimuli from inside the body, the epigenome can respond to factors from outside the body as well. The two major factors in epigenetic response to external agents are nutrition and environment. Animal studies reveal that mothers with a low amount of methyl-donating nutrients in their body before childbirth can induce a methyl deficiency in their child’s genome.9 Exposure to cigarette smoke, ionizing radiation, and pesticides can also modify the epigenome. In vitro studies show that these types of exposure can result in hypomethylation, or a loss of methylation. Hypomethylation in DNA in exposed animals can be linked back to genomic instability – an increase in the likelihood of mutation in the genome.10, 11, 12 Furthermore, genomic instability is a “driving force for tumorigenesis,” or the formation of cancer.13 Typically, the pattern of methyl groups attached to DNA is mostly destroyed and then reformed during the formation of gametes.2 However, some research has found that alterations in the epigenome can be passed down from generation to genera-
tion. For instance, mice placed under stress can pass their epigenetic changes onto their offspring. In one study, scientists exposed a parent generation of mice to the smell of cherry blossoms, while simultaneously electrically shocking them. The parents consequently associated pain with the smell of cherry blossoms. When the parents had offspring, the mice pups responded anxiously and fearfully in the presence of cherry blossom scent, despite having never been exposed to cherry blossom scent in their life.14 Advances in the epigenetic field have paved the way for other opportunities for health improvements as well. The elucidation of the mechanisms of epigenetic changes can be useful in many different ways. Researchers are amassing evidence that epigenetics can be involved in mental disorders.15 And unlike genetic disorders, epigenetic changes are potentially reversible; techniques like exposure therapy, where an individual is subjected to the object of their fear to overcome their anxiety, are already being used to help treat patients with PTSD.16 Additionally, recent research has shown that aberrations in epigenetic mechanisms can contribute to the proliferation of malignant cells and subsequently lead to cancer. Data from Johns Hopkins School of Medicine Center for Epigenetics in Baltimore, Maryland suggests that epigenetic changes are seen in all cancers, and the epigenome is modified in most cancer mutations.17 With that in mind, the burgeoning field of epigenetic therapy involves drugs inhibiting enzymes that modify histones and is a promising new treatment for cancer.18 As mentioned before, the differentiation of cells comes mainly from epigenetic factors. Further investigation into this mechanism promises manifold prospects in regards to the production and development of stem cells, another reason as to why studies of the epigenome can play a vital role in future medicines and treatments. There are many positive reasons as to why the epigenome should be studied carefully: finding a cure for mental illnesses, understanding cancer, and possibly harnessing the power of stem cells, to name a few. However, there are also many concerns linked to epigenetic treatments, concerns that cannot be assuaged due to the relative novelty of epigenetic treatment, and its consequent lack of in-depth research. For example, the children of cancer and mental illness patients who undergo epigenetic treatment may undergo unforeseen effects, and even the process of artificially inducing epigenetic changes may have potentially dangerous and unknown repercussions. The science of epigenetic changes and epigenetic inheritance is still in its early stages. There are many challenges being faced in the study of the epigenome; the interdisciplinary nature of the science behind the epigenome makes research difficult. Even when manipulations of epigenetic mechanisms are successful, providing evidence for the fact that an in vitro epigenetic change might have caused a particular phenotype to be present in the organism remains a perhaps fruitless notion.19 Regardless, potentials and possibilities linked to the epigenome have already been discovered, with many more to come.
REFERENCES
1. Berger, S. L., T. Kouzarides, R. Shiekhattar, and A. Shilatifard. “An Operational Definition of Epigenetics.” Genes & Development 23.7 (2009): 781-83. Genes & Development. CSH Press, 2009. Web. 16 Apr. 2016.<http://data2discovery. org/dev/wp-content/uploads/2013/05/Berger-et-al.-2009-epigeneticsdefinition.pdf>. 2. Reece, Jane B., and Neil A. Campbell. Campbell Biology. Boston: Benjamin Cummings /Pearson, 2011. Print. 3. Glyphis, John. “NOVA ScienceNOW: Epigenetics.” PBS. PBS, Aug. 2007. Web. 15 Feb 2016.<http://www.pbs.org/wgbh/nova/education/ activities/3411_02_nsn.html#backgrou>. 4. Balogh, Peter, Dr., and Peter Engelmann, Dr. “Transdifferentiation and Regenerative Medicine.” Digitális Tankönyvtár. Educatio.hu, 2011. Web. 16 Apr. 2016. <http://www.tankonyvtar.hu/en/tartalom/tamop425/0011_1A_ Transzdifferenciation_en_ book/ch01s03.html>. 5. “DNA Methylation.” What Is Epigenetics. Whatisepigenetics.com, n.d. Web. 16 Apr. 2016. <http://www.whatisepigenetics.com/dna-methylation/>. 6. Cowell, Ian, Dr. “Epigenetics - It’s Not Just Genes That Make Us.” British Society for Cell Biology. N.p., n.d. Web. 9 Mar. 2016. <http://bscb.org/ learning-resources/softcell-e-learning/epigenetics-its-not-just-genes-thatmake-us/>. 7. “Epigenetic Modifications Regulate Gene Expression.” SABiosciences. QIAGEN, 2010. Web. 16 Apr. 2016. <http://www.sabiosciences.com/ pathwaymagazine/pathways8/epigenetic-modifications-regulate-geneexpression.php>. 8. “Epigenetics for Health and Disease.” Crg.eu. Centre for Genomic Regulation, 11 May 2011. Web. 16 Apr. 2016. <http://www.crg.eu/en/news/epigeneticshealth-and-disease>. 9. “Nutrition and the Epigenome.” Learn.Genetics. Genetic Science Learning Center, 22 June 2014. Web. 16 Apr. 2016. <http://learn.genetics.utah.edu/ content/epigenetics/nutrition/>. 10. Knopik, Valerie S., Matthew A. Maccani, Sarah Francazio, and John E. McGeary. “The Epigenetics of Maternal Cigarette Smoking During Pregnancy and Effects on Child Development.” Development and Psychopathology. U.S. National Library of Medicine, Nov. 2012. Web. 16 Apr. 2016. http://www. ncbi.nlm.nih.gov/pmc/articles/PMC3581096/>. 11. Merrifield, Matt, and Olga Kovalchuk. “Epigenetics in Radiation Biology: A New Research Frontier.” Frontiers in Genetics. Frontiers Media S.A., 4 Apr. 2013. Web. 16 Apr. 2016. <http://www.ncbi.nlm.nih.gov/pmc/articles/ PMC3616258/>. 12. Collotta, M., P. A. Bertazzi, and V. Bollati. “Epigenetics and Pesticides.” National Center for Biotechnology Information. U.S. National Library of Medicine, 10 May 2016. Web. 22 Feb. 2016. <http://www.ncbi.nlm.nih.gov/ pubmed/23380243>. 13. Shen, Z. “Genomic Instability and Cancer: An Introduction.” National Center for Biotechnology Information. U.S. National Library of Medicine, Feb. 2011. Web. 8 Feb. 2016. <http://www.ncbi.nlm.nih.gov/pubmed/21278445>. 14. Kim, Meeri. “Study Finds That Fear Can Travel Quickly through Generations of Mice DNA.” Washington Post. The Washington Post, 7 Dec. 2013. Web. 16 Feb. 2016. <https://www.washingtonpost.com/national/health-science/ study-finds-that-fear-can-travel-quickly-through-generations-of-micedna/2013/12/07/94dc97f2-5e8e-11e3-bc56-c6ca94801fac_story.html>. 15. Schmidt, U., F. Holsboer, and T. Rein. “Epigenetic Aspects of Posttraumatic Stress Disorder.” National Center for Biotechnology Information. U.S. National Library of Medicine, 2011. Web. 15 Feb. 2016. <http://www.ncbi. nlm.nih.gov/pubmed/21508512>. 16. “Prolonged Exposure Therapy.” PTSD: National Center for PTSD. U.S. Department of Veterans Affairs, 14 Aug. 2015. Web. 16 Feb. 2016. <http:// www.ptsd.va.gov/public/treatment/therapy-med/prolonged-exposuretherapy.asp>. 17. Taylor, Ashley. “Epigenetic Changes Can Cause Cancer.” TheScientist. N.p., 25 July 2015. Web. 16 Apr. 2016. <http://www.the-scientist.com/?articles.view/ articleNo/40592/title/Epigenetic-Changes-Can-Cause-Cancer/>. 18. Sharma, Shikhar, Theresa K. Kelly, and Peter A. Jones. “Epigenetics in Cancer.” Carcinogenesis: Oxford Journal. Oxford University Press, 13 Sept. 2009. Web. 16 Apr. 2016. <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2802667/>. 19. Bohacek, Johannes, and Isabelle M. Mansuy. “Epigenetic Inheritance of Disease and Disease Risk.” Neuropsychopharmacology. 2016 American College of Neuropsychopharmacology, 8 May 2012. Web. 16 Apr. 2016. <http://www.nature.com/npp/journal/v38/n1/full/npp2012110a.html>.
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FOXP2 ANALYSIS
By Sanjena Venkatesh
Art by Christina Patricia
Few genes have made as many headlines as the FOXP2
gene, one of the first genes to be associated with the evolution of human speech. The forkhead box gene is among the most important genes that separate humans from other primates. It is believed that the FOXP2 gene is crucial in the learning of language, allowing humans to make conscious associations in order to respond to external cues. Numerous projects are currently underway as scientists attempt to gain a better understanding of this gene. This article analyzes the relationships between the FOXP2 gene of Homo sapiens (Humans), Pan troglodytes (Common Chimpanzee), Gorilla gorilla (Western Gorilla), Pongo pygmaeus (Bornean Orangutan), Macaca mulatta (Rhesus Macaque), and Mus musculus (House Mouse) through the construction of a phylogenetic tree. The FOXP2 gene was chosen because it has little variation between members of the same species. In order to choose comparative species, the basic phylogeny of primates was first researched. This provided a fundamental understanding of their evolutionary history. The research was modeled after this diagram depicting evolutionary relationships The DNA sequences of the FOXP2 gene were obtained from a species in each of the first four groups: Homo sapiens (humans), Pan Troglodytes (chimpanzees), Gorilla gorilla (gorillas), and Pongo pygmaeus (orangutans). For the outgroup, the common house mouse, Mus musculus, was chosen due to research currently being conducted on mice. For instance, in one investigation conducted by researchers from MIT Figure 1: Phyologentic Tree of Primates. Image courtesy of Pearson Education and several other European universities, the scientists engineered for educational purposes mice to express humanized FOXP2. In turn, these mice were able to run the maze much more quickly than normal mice.1 By in-
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Figure 2: Phylogentic tree constructed in NJplot
vestigating this specific set of closely related organisms (with the exception of the mouse), the evolutionary changes occurring in the FOXP2 gene could be easily pinpointed. In the tree, the horizontal lines are branches, showing evolutionary change over time. The longer the line, the greater amount of genetic change has occurred. For instance, the species Mus musculus has undergone great change while Homo sapiens have undergone very little change according to the FOXP2 gene. Organisms closer together on the phylogenetic tree share greater genetic similarities than those farther apart. As the outgroup, Mus musculus differed greatly from the other species, diverging first. Subsequently, Macaca mulatta split off, then followed by Pongo pygmaeus, Gorilla gorilla, and Pan troglodytes. Clearly, Homo sapiens and Pan troglodytes share the most recent common ancestor, whereas Homo sapiens and Mus musculus only share a distant common ancestor. The results of this investigation corroborated the phylogenetic tree of primates shown in Figure 1. According to Your Genome, “the FOXP2 protein only differs from the human version by three amino acids,” while the difference between the human version and the chimpanzee version is only two amino acids.2 However, despite the similarity in the protein sequences, the DNA sequences of the FOXP2 gene vary enough to view distinct differences between species, as shown in the phylogenetic tree. The evidence obtained by researchers at NCBI also corroborate the results of this investigation. They state that “language is a uniquely human trait likely to have been a prerequisite for the development of human culture.3” The ability to develop articulate speech is dependent on vocal capabilities like fine con-
trol of the larynx and mouth that are not seen in other primates like chimpanzees and gorillas. This accounts for the divergence of humans from the chimpanzees and great apes in the phylogenetic tree. The researchers also sequenced the complementary DNAs that encode the FOXP2 protein in the chimpanzee, gorilla, orangutan, rhesus macaque and mouse, and compared them with the human DNA. In their investigation, they indicate that the FOXP2 gene found in human beings contains differentiations in amino-acid coding and a pattern of nucleotide polymorphism, which strongly suggest that FOXP2 has been the target of natural selection during recent human evolution.3 The FOXP2 gene has given homo sapiens an evolutionary advantage that distinguishes us from other species.
1. 2. 3.
References Trafton, Anne. “Neuroscientists Identify Key Role of Language Gene.” MIT News. N.p., 15 Sept. 2014. Web. 22 May 2016. Evolution of the human brain. (2015). Retrieved October 2, 2015, from Your Genome website: http://www.yourgenome.org/stories/evolutionof-the-human-brain Molecular evolution of FOXP2, a gene involved in speech and language (2015). Retrieved October 2, 2015, from NCBI website: http://www. ncbi.nlm.nih.gov/pubmed/12192408
Programs and Websites Used: ClustalX – (http://www.clustal.org/clustal2/) NJplot – (http://pbil.univ-lyon1.fr/software/njplot.html) NCBI – (http://www.ncbi.nlm.nih.gov/nuccore/)
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JUAN FERNANDEZ FIRECROWN Those who live by gardens can say that they know a
type of bird that hovers amongst the bees and butterflies: hummingbirds. These miniscule birds with needle-sharp beaks often have bright iridescent feathers and a heart rate of 1263 beats a minute, compared to the average human’s 70.1 During torpor, or the physical inactivity at night, the heart rate drops to 50 beats a minute in order to conserve energy. These small, seemingly restless birds have fascinated children as well as adults. However, of the 338 species, 34 are facing extinction.2 One such bird is the Juan Fernandez firecrown. The Juan Fernandez firecrown resides only on the island Robinson Crusoe, which is 667 kilometers off the coast of Chile and has an area of 47.94 square kilometers. Of this area, the Juan Fernandez firecrown’s habitat is limited to 11 square kilometers.3 Island Robinson Crusoe is part of the Juan Fernandez Islands, an island group unique for its rich biodiversity. However, this biodiversity can only be fully maintained if the Juan Fernandez firecrown continues to thrive.9 The island was first discovered in 1574, when a ship full of famished, disease-ridden British pirates wound up on its shore. The hotheaded Scottish navigator Alexander Selkirk demanded that his tyrannical captain Thomas Stradling leave him on the island, hoping that the rest of the crew would follow him and colonize. Unfortunately for Selkirk, the crew did not share his opinion. Selkirk was marooned on the island alone, but defied the odds when he survived and returned to England. Alexander Selkirk’s harrowing tale was the basis of author Daniel Defoe’s novel, Robinson Crusoe. Islands Robinson Crusoe and Alexander Selkirk are sister islands, both capable of supporting firecrown life. The Juan Fernandez firecrown, also known as the Sephanoides fernandensis, is about thirteen centimeters from head to tail tip. Males have a rusty orange-brown body with grey flight feathers and iridescent dark yellow crowns.3 Females, which are primarily green and white with iridescent blue crowns, have such a different appearance from males, that until the nineteenth century they were thought to be different species.5 These hummingbirds, once abundant centuries ago, are now critically endangered and face near-extinction. In 1969, there were only 459 birds on the island, a soberingly low amount.7 In 2008, there were 23 firecrown nesting pairs, 16 of which successfully raised young.6 Due to recent awareness and conservation efforts, the popula-
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tion has now risen to about 2500-3000 birds total, with around 17002000 at the age of maturity.3 This number, however, is decreasing at a rate of 1-9% every year.5 On Island Alexander Selkirk, the firecrown was last recorded in 1908 and is assumed to be extinct.3 These birds suffer mainly because of humanity’s lack of notice and care. Firecrowns are at risk due to the increase of invasive plants and the loss of their natural vegetation. While their natural vegetation includes Raphithamnus venustus flowers and Dendroseris litoralis flowers, the introduction of eucalyptus (Eucalyptus globulus) and garden flowers by humans throws the lives of the hummingbirds off-course. 75 percent of all native plants have disappeared due to burning, deforestation, and invasive species.3 Because invasive plants are being placed in Island Robinson Crusoe, the natural vegetation that the hummingbirds live off is vanishing. The ecological ruin is caused by the direct mass removal of vegetation and the introduction of herbivores such as rabbits and goats which cause environmental erosion.7 In fact, rabbits, which were introduced in 1935, are one of the main reasons for the lack of natural vegetation. They predate on native flora and desertify the soil, reducing the rich humus to dust.7 The number of rabbits is immense, with twenty rabbits a hectare, which is a thousand square meters.7 Carnivorous animals such as rats, cats, and coatis have been documented predating on the firecrowns and may play a cause in the decline of the species as well.3 Other birds on the island, such as the green-backed firecrown (S. Sephanoides) and the austral thrush (Turdus falcklandil) serve as a threat to the Juan Fernandez firecrowns. Thrushes predate firecrown nests, and green-backed firecrowns cause competition, but these serve as natural threats that would remain regardless of the introduction of invasive species through humans. When in torpor, these birds are very vulnerable because they are easy to approach and attack.3 However, the Juan Fernandez firecrown’s ability to defend itself may differ according to sex. The main competitor for resources is the green-backed firecrown. While the larger males are able to defend themselves, the smaller females suffer from interference. These two species prefer different nesting sites, but due to the lack of organic vegetation and nesting area, the green-backed firecrowns have relocated to the breeding areas used by the Juan Fernandez firecrown, thus causing significantly greater competition amongst the species.3 Due to recent notice, conservation actions have been set in place. The Juan Fernandez Islands were designated as a National Park in 1935 and an UNESCO Biosphere Reserve in 1977. Since 1997, several major campaigns have sought to restore the habitat. The Juan Fernandez Islands Conservancy, along with the American Bird Conservancy Conservation International, the Hummingbird Society, and the Royal Society for the Protection of Birds, are leading the attempt to save the firecrowns.
By Erica Yeawon Hwang Art By Amy Kim
Invasive species are being removed, and natural vegetation is being restored. In 2014, about four acres had all invasive species removed and natural vegetation planted for the benefit of the firecrown. Grazing restrictions for rabbits, goats, and cattle have been implemented, and native flowers are being planted in those areas. To prevent livestock from causing further erosion, 60 percent of the valleys and areas of natural vegetation are fenced.7 Rabbits are also being controlled by professional hunters. The reward for hunting a rabbit is 0.60 USD. By August 2001, at least 34,000 rabbits were captured.7 On the areas where the impact for erosion is greatest, trees have been planted for immediate, short-term relief. There have even been plans to control the native austral thrush if necessary. The Juan Fernandez Islands Conservancy has also made it a priority to rid the island of cats. With the creation of a “cat registration scheme,” owners and pet cats are identified and thus urge the owners to spay and neuter these cats to help the firecrowns. By the end of 2015, about 92% of all cats will be sterile.6 The people in the only village on the island, San Juan Bautista, are educated about the critically endangered birds; the children learn about the Juan Fernandez firecrowns at school and the importance of preserving biodiversity. All these actions have received support from people around the globe. In 2007, the Hummingbird Society, in association with the Clos La Chance Winery, created a wine called “Threatened Species” in order to help the firecrowns; this effort raised about 20,000 dollars.6 These conservation actions serve as the driving force for the preservation of all endangered species, including the Juan Fernandez firecrown. The preservation of this rare and beautiful species is vital to maintaining the colorful biodiversity on Earth, but it can only begin with humanity’s awareness. Though not everyone lives on the island of Robinson Crusoe, there are still ways to help. Though direct help by travelling to the island is the best way to help, one can also donate
to the Hummingbird Society, the American Bird Conservancy, or any other non-profit organization that funds the survival of the firecrowns. Because the firecrowns are unknown to most of the world, telling others about these critically endangered birds can serve as a milestone in their preservation. Endangered species need to be protected because they contribute to the lush biodiversity of Earth, and the Juan Fernandez firecrown in no exception.
REFERENCES
1. University of Mississippi. “Everything you wanted to know about Hummingbird Fun Facts.” http://home.olemiss.edu/~larryago/hummingbirds/ funfacts2.html (2014). 2. The Hummingbird Society. “Endangered Hummingbird Species.” http:// hummingbirdsociety.org/endangered/ (2014). 3. BirdLife International. “Juan Fernandez Firecrown Sephanoides fernandensis.” http://www.birdlife.org/datazone/speciesfactsheet.php?id=2021 (2009). 4. Selcraig, B. Smithsonian Magazine. “The Real Robinson Crusoe.” http://www. birdlife.org/datazone/speciesfactsheet.php?id=2021 (2005). 5. ICUN Redlist of Threatened Species. “Sephanoides fernandensis.” http://www. iucnredlist.org/details/22687863/0 (2013). 6. American Bird Conservancy. “Endangered Hummingbird Benefits from Conservation Efforts on Remote Island Chain.” http://www.abcbirds.org/ newsandreports/stories/081230.html (2013). 7. Cuevas, J.G. & Leersum, G.V. Project Conservation, Restoration, and Development of the Juan Fernandez islands, Chile. Scien Elec Lib Online. http://www.scielo.cl/pdf/rchnat/v74n4/art16.pdf 74:899-910 (2001). 8. Wildscreen Arkive. “Juan Fernández firecrown fact file.” http://www.arkive. org/juan-fernandez-f irecrown/sephanoides-fernandensis/image-G27961. html (2013). 9. Roy, M.S. Conservation of the Juan Fernandez Firecrown and its island habitat. Academia. http://www.academia.edu/1808270/Conservation_of_ the_Juan_Fernandez_firecrown_and_its_island_habitat 33(3), 223–232 (1999).
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An Application of Lactic Acid Bacteria: Eliminating Laboratory Odor Minchul Shin Lactic acid bacteria are known to be effective in removing odor causing substances found in animal pens. Is this method applicable to a more stringent problem, the odor of lab animal bedding? Introduction
Bedding for animal breeding is used to maintain the hygiene of the animal shelter by absorbing feces and increasing both habitability and heat-retaining characteristics. Typically, the unique bedding mix of paper, chip, bark, tree crumbs, and cone cup, when used with lab animals, should be changed once or twice per week, although it depends on the number of animals. Bedding for livestock also should be changed more than once a month. If not done, the bedding will produce a foul odor as a result of the anaerobic decomposition reaction of feces by microorganisms, and can harvest disease. Among the products of those reactions, volatile fatty acids, hydrogen sulfide, p-cresol, skitol, diacetyl, and ammonia have the strongest influence on the foul odor often found in animal pens. The research in this article applies a bio-control method of using the lactic acid bacteria Lactobacillus to remove microorganism metabolites that are harmful to animals. Yeast, Lactobacillus, and Bacillus subtillis are known to be effective in removing odor causing substances and have been added to bedding in order to limit the foul stench found in animal pens. However, this process may not be enough for bedding used to breed laboratory animals, which should have outstanding hygroscopicity, flexibility, and ability to preserve heat, and, if possible, the ability to be sterilized. Using probiotics would eliminate odor but could be potential sources of contamination. Through this experiment, it was determined that the most effective method of removing foul odor while maintaining suitable conditions for lab animal bedding was to coat the bedding with culture media that was sterilized after the cultivation of B. subtilis.
Methods
Separation of Lactobacillus
Parts of Korean traditional food, including kimchi, chunggukjang, daenjang, and sikhye, were cultured in MRS agar media, and 6 types of Lactobacillus, referred to below, were separated. Isolation of separated bacteria was requested from Macrogen, and their DNA was analyzed with the 16s rRNA method; if its composition was under 99% pure, a new sample was supplied by the Korean Collection for Type Culture (KCTC) . 20 | JOURNYS | WINTER 2016
Art by Alexander Hong Table 1 List of bacteria originated fermented food
Bacteria
Origin
DNA Purity
Bacillus sonorensis
Daenjang
99%
Enterococcus faecium
Chunggukjang 100%
Bacillus subtilis
Kimchi
100%
Bacillus tequilensis
Kimchi
100%
Lactobacillus sakei
Kimchi
100%
Lactobacillus plantarum KTCT 3103
-
Antibacterial Effect of Media with Cultured Bacteria
Each type of lactic acid bacteria was injected into MRS broth media and sterilized at 121â&#x201E;&#x192;, 1.2atm. Sawdust polluted by mice was placed into culture media at 30â&#x201E;&#x192;. Its absorbance was measured at 630nm of UV wavelength with a UV spectrophotometer.
Removal of Foul Smell of Lactic Acid Bacteria Culture Media and Antibacterial Effect of Coated Sawdust
After sawdust was put into lactic acid bacteria culture media, the odor was measured by a halitosis machine and the human olfactory sense. The level of the foul odor was ranked from 1 to 5, 5 being the most severe. Sawdust was also cultured in NB media, and its absorbance was measured.
Results
Antibacterial Effect of Media in which Bacteria Were Cultured
When polluted sawdust was cultured in Lactobacillus culture media and its absorbance was measured, E. faecium media (E. faecium M) had 55.7% higher absorbance than the control group. B. subtillis
M had 43.5% lower absorbance than the control, which suppressed the proliferation of bacteria from sawdust. B. sonorensis M showed 85.7% of decreasing level, thus suppressing a significant amount of bacteria. Fewer colonies proliferated in B. subtilis M and B. sonorensis M than had proliferated in the control group when they were cultured in nutrient agar (NA) media as well. Almost no colonies appeared in B. sonorensis M.
Figure 3 Odor level according to measuring method
Figure 1 Absorbance of sawdust bacteria in lactic acid bacteria cultured media
Figure 4 Absorbance of bacteria from sawdust coated lactic acid bacteria
Figure 2 Growth of bacteria from sawdust in lactic acid bacteria cultured media
Conclusion and Discussion
Removal of Foul Smell of Lactobacillus Culture Media and Antibacterial Effect of Coated Sawdust
Media sterilized after culturing Lactobacillus contains mixture of dead Lactobacillus their secreted proteins. In this study, 6 types of Lactobacillus were cultured and subsequently coated with sawdust that had been used for mouse breeding. After adequate time was allowed, the level of malodor and proliferation of bacteria caused by the feces contamination was measured. B. subtilis removed the foul smell and suppressed the proliferation of bacteria effectively.
Polluted sawdust was put into the Lactobacillus media, and after culturing, the level of odor was measured. The halitosis machine measured that odor was less severe when cultured in B. tequilensis and B. subtilis. Afterward, the Lactobacillus culture media was coated with sawdust, and the absorbance of bacteria that appeared in the sawdust was measured.. B. tequlensis suppressed bacteria by 25.4%, and B. subtilis suppressed 63.3%, thus confirming that coating Lactobacillus culture media on sawdust maintains its effect.
21 | JOURNYS | WINTER 2016
D etermining the E ffect of Electromagnetism on By Joonhyuk Lee WDM Systems Art by connie Chen Abstract
Fiber optics, at its core, involves using thin glass fibers to transmit large quantities of information in the form of light signals.1 Modern fiber optic companies use wavelength-division multiplexers (WDM’s), devices that combine multiple light signals (multiplex) into one, in order to send multiple streams of information at the same time on a single device, thus maximizing efficiency. However, despite the ubiquity of fiber optics systems, the potential influence of variables such as electromagnetic fields (EM fields) on WDM system performance is currently not well understood. The goal of this project was to discover how EM fields affect light and, as a result, WDM system performance. It was hypothesized that due to the disrupting effects of electromagnetic fields on light waves, WDM systems “exposed” to a simulated EM field would suffer from more errors when compared with non-EM WDM systems. This experiment was performed using the network simulation framework OMNet++. The simulation was run several times with millions of signals sent across four trials to ensure an accurate bit-error rate (BER), or the percentage of signals lost or rendered incorrectly during transmission. Then, the same simulation was performed with the WDM systems, except with a C++ code designed to simulate an EM field. Between each trial, the channel spacing (amount of “distance” between signals) was changed. The results showed that WDM modules that were exposed to EM influence had an increased number of errors compared to the control group.
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Introduction/Background
Results & Conclusion
Methods
Discussion
Currently, fiber optics technology is the preferred method of signal transmission for the vast majority of long distance communications services.2 Fiber optics offers many advantages when compared to copper wire, such as relative immunity from interference, faster transmission speeds, and easier modification of existing communications structures.3 To further enhance the advantages of fiber optics, many communications companies use wavelength-division multiplexers, or WDMs, which divide data into multiple channels based on wavelength of light in order to facilitate the simultaneous transmission of many different packages of data. However, WDMs are not without their potential disadvantages. As the primary mode of signal transmission in fiber optic systems is light, environmental factors such as EM fields, which can alter the light signals conveying information, could affect WDM efficiency.4 The goal of this experiment was to determine the effects of EM fields on WDM performance through computer-based simulation.
To perform the experiment, OMNet++, a simulation framework designed specifically for simulation of networks of various kinds was used. Using C++, various modules of four different wavelength-division multiplexers were created, then assembled using NED, an OMNet++ specific language. These four different WDM modules each had different numbers of channels, or number of signals being multiplexed at once. Using OMNet++, the transmission of millions of packets of data was simulated for each WDM module to obtain a consistent and accurate BER, or bit-error rate. Afterwards, NED code was used to artificially impose an electromagnetic field on the WDM systems. Based on existing research,5 the polarization angle of light signals traveling through the WDM modules was changed to reflect the Kerr effect, and the procedure used to calculate BER for the control group was repeated. The intended result of the changes in polarization angle was to alter the amount of chromatic dispersion, double refraction, and other errors to accurately simulate the host of light signal changes a real EM field would induce.
The results consistently showed an increase in bit-error rate for WDM systems exposed to EM influence when compared to the control systems. For example, System B, with 16 channels, had a BER rate of 3*10-7 when not exposed to EM, but had a rate of 5*10-7 when exposed (regular channel spacing). Although all systems showed a small decrease in efficiency when exposed to EM, WDM systems with the lowest amount of channels showed the smallest increase in BER. System D, which only had 4 different channels, had a net change of 1*107 BER following the addition of a simulated electromagnetic field. On the other hand, System A, which multiplexed 32 channels, recorded a net change of 7*10-7 BER. In all systems, the results also showed a strong reduction in net BER change when the channel spacing was doubled. In conclusion when WDM systems were exposed to a simulated EM field all systems showed an increase in BER and systems with less channels and greater channel spacing were affected to a lesser extent.
The initial hypothesis of this experiment predicted that due to the disrupting effects of electromagnetic fields on light waves, WDM systems “exposed” to a simulated EM field would suffer from an increased bit-error rate when compared with non-EM WDM systems. The results of the experiment found this to be true across all of the WDM systems tested. Larger channel spacing had a dampening effect on the influence of EM, while larger amounts of channels led to a more pronounced net increase in BER. These results may become more relevant in the future as WDM design parameters trend toward a greater emphasis on a large number of channels accompanied by lower channel spacing. Although the intent of these parameters is to maximize efficiency, considering the growing proliferation of fiber optic networks around the world, it will be important to keep in mind the potential impact of EM fields on these critical components of the world’s communications systems.
REFERENCES
1. “What is Fiber Optics?”. http://www.f-n-t.com/whatisfo.htm (2011) 2. “What Do We Use Fiber Optics For, Anyways?”. http://www.cableorganizer.com/articles/fiber-optics-tutorial/fiber-optic-technology.html (2016) 3. “Comparison of Optical Fiber to Copper Wire”. http://lasermotive.com/wp-content/uploads/2012/12/Fiber_vs_Copper_summary2013Jan.pdf (2013) 4. Porins, J., Supe, A. Interaction Between Electromagnetic Field and Optical Signal Transmission in Fiber Optics . Elec. And Electric. Eng. 122, 83-86 (2012) 5. Porins, J., Ivanovs, G. & Dzerins, O. Influence of External Electromagnetic Disturbance on the Optical Fiber Properties in WDM Systems. Elec. And Electric. Eng. 92, 57-60 (2009)
23 | JOURNYS | WINTER 2016
TC he Ecosphere E C alculating the
nergy of a
losed
INTRODUCTION Several years ago, NASA presented a small glass globe, which it called the “Ecosphere.” The Ecosphere consisted of a closed glass ball filled with stones, sea water, photosynthetic marine plant, and couple little shrimps. This little glass globe was intended to be a souvenir, but there is a scientific significance to it – the glass ball is a microcosm of planet Earth. Like the interaction of organisms within the ecosystem of our planet, the krill shrimp does not die even if without food input since it feeds on the aqua plant. Similarly, the aqua plant grows by photosynthesis, providing more food to the krill shrimp to an extent that the plant itself does not die. In this research, we try to analyze the Ecosphere using biological, chemical, and mathematical modeling under certain assumptions. We introduce a new constant, k (calories needed per day for a certain organism), which we call the “organism constant” obtained from the modeling and will try to further investigate the significance and application of the constant.
Materials and Methods Here, we created a formula for the maintenance of a small, closed system that incorporates the number of plant and animal organisms as variables. The first step is to calculate the total solar energy that enters the ecosphere. Under the assumption that: A. The sun changes its direction π radian per day. B. The sun shines on the ecosphere for 13 hours per day on average. We use the solar constant I (1.946 cal/cm2∙min) to integrate the total energy input during the total 13 hours: “A” stands for the total surface area of the plant. Since The integration can be converted into: Calculation yields the total energy, which is: Next, we calculate the total carbohydrate produced by the system (by plants) by using the chemical formula of photosynthesis, which is: Considering that 28 moles of ATP is used up to produce 1 mole
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System of C6H12O6 and under the assumption that: C. The energy efficiency of photosynthesis is approximately 40% of input The total energy produced and stored by plant organisms would be: Then, setting n as the number of plant organisms within the ecosystem, N as the number of animal organisms within the ecosystem, and k as a constant that represents the required calories a certain animal organisms need for metabolism for a day, we can make three possible states of the ecosystem: i) 38.65∙A∙n>k∙N ii) 38.65∙A∙n=k∙N iii) 38.65∙A∙n<k∙N State i) represents an ecosystem where plants outgrow animals, resulting in a collapse of the ecosystem. State ii) represents an ecosystem with perfect balance, similar to that of the Ecosphere. State iii), consequently, represents an ecosystem where animals outgrow plants, resulting in a collapse of ecosystem. When the ecosystem is designed to be in the state ii), we can calculate the constant k for certain organism, where Now we investigate the further possible application of constant k in ecosystem equilibrium by improving the simple formula obtained above by incorporating food web, growth, reproduction, and lifespan of organisms into calculation. Imagine a circumstance in a closed system with plant species 1 and 2. There will be animal organisms that have biological constant k1 and k2 that eats only plant 1 and 2, respectively. There will be predators of higher rank to the mentioned animals, with biological constant K1 and K2 that feed on animals with constant k1 and k2, respectively. Then the previous formula changes into: If the higher predator needs Ki calories per day, it needs to predate on numbers of low rank predators. Additionally, since the 10% law states that only 10% of the energy from the lower level in food pyramid goes up to the next level, the higher predator needs to predate on 10 numbers of the lower rank predators. That changes the formula into: Where M is the number of higher rank predators within the ecosystem. Now we incorporate the reproduction of plant and animal species and growth of the plant species. Let the reproduction rate of
By Edward Yoon Ki Joo Art by Alexander Hong and Connie Chen 1
2
3
17
Height (cm)
14
16
13
Table 1. measurements of the initial height of the plants.
Change (cm)
+5
0
-4
Height (cm)
1
2
3
9
16
Table 2. measurements of the initial height of the plants.
each species noted as: This changes the previous formula into: Letting the growth factor of plant to be “Gi”, corresponding constant “Ci”, and lifespan of an animal species to be “Ti” then since the death of animal serves as a fertilizer for the plant,
to be perfect equilibrium and will collapse in the long run. Plant in tank 1, in contrast, grew to a degree that it will serve sufficient amount of energy for the animal organisms after the Gymnocorymbus ternetzi reproduce, maintaining the ecosystem. Considering tank 1 as an ideal ecosystem, we measured the total surface area of the plant leaf in order to use the formula To calculate constant k. We found out the total surface area of the plant to be 312cm2, and since the number of plant species (n) was 1 and animal species (N) 14, the constant k for Gymnocorymbus ternetzi is 861 cal/day.
Discussion and Conclusion That leads to a final formula for ecosystem equilibrium,
Where b is a constant for the lifespan of an animal species. We will now show our experiment, which was making three Ecospheres in order to calculate the constant k. We used Gymnocorymbus ternetzi for marine species and plant species bought from an aquarium. We varied the number of fish within the tanks. We observed the ecosystem for 2 weeks to figure out which tank provided nearly perfect ecosystem equilibrium. A perfect equilibrium would, after 2 weeks, show a degree of growth of the aqua plant, since the fish will need more food after reproducing. An ecosystem that would collapse will show no growth or too much growth of plant, which would result in overgrowth of animals species and overgrowth of plant species, respectively. At the first day of observation, we recorded height of the plants. The measurements were recorded as in Table 1 (above). After two weeks, we re-measured the height of the plants. The re-measurements were as in Table 2 (also above). Two weeks of observation showed that the plant in tank 1 grew, the plant in tank 2 had no change, and the plant in tank 3 shrunk in its height. This indicates that tank 2 and tank 3 was not maintained
In this research, we showed methods to calculate k and presented a formula for an appropriate numbers of each photosynthetic and heterotrophic organism to bring a closed ecosystem into equilibrium. The method we used to drive a formula was to use math modeling based on information provided in biology and environmental science textbooks. Methods we used for experiments were making a small closed system with plant and animal organism, measuring the height of the plant after two weeks of observation to determine which tank was in perfect environmental equilibrium. This research can be applied to planning a certain environmental habitat, such as building a national park. The formula will tell what should be the adequate number of each plant and animal species in order to make a sustainable ecosystem. This formula could serve as a basis for more complex ones. If fully applied in the future, it might also be used as the basis for the creation of large-scale closed ecosystems, potentially allowing scientists to turn inhospitable planets such as Mars into environments capable of sustaining human life.
REFERENCES
1. “EcoSphere Care.” EcoSphere Closed Ecosystems. N.p., n.d. Web. 07 Oct. 2016. 2. “The Magic of Photosynthesis: How Plants Turn Sunlight into Energy.” About.com Education. N.p., 28 Apr. 2016. Web. 07 Oct. 2016. 3. “Ecological Collapse by Lisa Rayner.” Ecopsychology. Gatherings, n.d. Web. 07 Oct. 2016.
25 | JOURNYS | WINTER 2016
THE BIOLOGY BEHIND ABSTRACT
Using brain imaging techniques to understand the relationship between neuroscience and psychology could lead to breakthrough revelations for diseases such as Parkinsonâ&#x20AC;&#x2122;s, Alzheimerâ&#x20AC;&#x2122;s, and autism, as well as psychological disturbances including schizophrenia and depression. We have long known that the brain is the control center of the mind and body, but it is still unclear how physical brain damage can result in behavioral, psychological damage. Using neuroimaging to identify biological roots to behavioral problems could allow us to predict any potential psychological trouble before their onset. Understanding the discrepancies
26 | JOURNYS | WINTER 2016
and overlaps between neurology and psychology would allow for medical advancements in treating multifaceted diseases. In addition, by acting as a bridge between neuroscience and psychology, neuroimaging would help to combat stigma surrounding mental disorders.
BEHAVIOR
BY IRINE THOMAS ART BY ALEXANDER HONG
Before neuroimaging, neurology and psychology were both
widely considered inferior as scientific fields. Due to the lack of high quality technology, neurology was a highly obscure field of study. Because of the limits of past technology, psychology could not support its assertions about the nature of mental problems with hard, cold facts, and it was not truly considered a science until modern times (“Scanning the brain”, 2014). As a result, severe psychological disorders, especially schizophrenia, were significantly socially stigmatized. In the absence of a verifiable biological basis in the brain, mental illness was thought to be the result of divine punishment, demon possession, and other supernatural interventions (Foerschner, 2010). At one point, neuroscience and psychology employed separate methods of uncovering new information about the human brain. However, the emergence of brain imaging in recent years has permanently altered this bond, allowing for a complementary relationship between the two fields. Neuroimaging has introduced the imminent need for a reevaluation of the relationship between neuroscience and psychology. Neuroscience uses deductive methods, analyzing the activity of specific neurons and pathways (Ginger & William 2011), and then applies these observations to a larger scale. Psychology takes the opposite approach to the same subject matter. Psychology studies behavior to understand the nature of the mind, such as in the case of Phineas Gage (Kean, 2014). Gage was a miner who was severely injured by a metal rod that went through his brain and caused both physical damage and drastic personality changes. Originally a mild-mannered man, Gage developed more violent tendencies. Using psychology, overall behavioral patterns were analyzed to pinpoint the corresponding disturbances in his mind. Despite their seemingly incompatible differences, the characteristics of neurology and psychology, share a complementary relationship and each contributes to the other. Neural activity in a subject’s brain correlates to the behavior produced as a result of changes in mental state (Aguirre, 2002). In other words, changes in mindset or mood produce altered behavior, which can then be traced back to changes in brain activity, which can then be measured using brain imaging. The visualization of pathways in the brain allows researchers to predict specific behaviors in people. For example, in 2014, The Center for BrainHealth conducted a study on the neuroscience behind poor decision making, specifically in risk-seeking teenagers. Functional magnetic resonance imaging (fMRI) was used to measure the differences between the risk-taking and non-risk-taking group. They found that connections between certain regions of the brain are amplified in risk-taking teenagers. These connections make up the emotional-regulation network, which controls emotions and therefore influences decision making. (Center for BrainHealth, 2014). This discovery led psychologists to question whether risk-taking behavior is a predisposition in teenagers, or if it is a result of environmental effects on the brain. In either case, the study establishes an irrevocable connection between biology and behavior. As seen in the aforementioned study, environmental impacts are the most important during childhood and adolescence. A person’s psychosocial influences can have visible anatomical effects on the brain, especially at an early age (Dryden, 2012). According to this argument, the people and situations one surrounds him or herself with
have the ability to alter both their behavior and brain structure. These changes can be detected in the modern day by brain MRIs, which display the anatomy of the central nervous system. The neurologists of Washington University School of Medicine used neuroimaging to explore the impact of the quality of parenting on the mental stability of their children. Brain scans have shown that school children who received more attention from their mothers had a larger hippocampus, a region of the brain involved in learning, memory, and stress response (Dryden, 2012). In this study, it is clear that outside influences can impact a person’s biological makeup, in both positive and negative ways. Imaging allowed these neurologists to bridge the correlational relationship between the quality of parenting and the size of a child’s hippocampus, which supports the role of nurture over nature. Brain imaging, specifically functional magnetic resonance imaging (fMRI) and positron emission tomography (PET), has been the main connection between neuroscience and psychology. Functional magnetic resonance imaging detects changes in blood flow, which corresponds to changes in the activity of neurons in the brain. For example, fMRI technology is being used to connect the experience of reward to motivational behavior. Scientists used a variety of experiments on a large amount of people and found that differences in a single gene could cause noticeable changes in how individuals weighed their choices and addressed their preferences. (Nauert, 2008). Here, brain imaging is used to answer the nature versus nurture question. Behaviors that may have perceived as psychologically produced are now being observed to have neurological origins. A research study conducted in 2013 used fMRI to examine the activity of the prefrontal cortex and the basal ganglia, which supplies most of the brain’s dopamine, in both schizophrenic and healthy individuals. Schizophrenia expresses many psychological disturbances, one of them being psychosis. To test this connection, schizophrenics and non-schizophrenics were asked to complete a memory task. The results showed that patients with schizophrenia have increased activity in the basal ganglia, decreased activity in the prefrontal cortex, and very little connection between the two areas. This is consistent with the role of dopamine in preventing psychosis. (Yoon, Minzenberg, Raouf, D’Esposito & Carter, 2013). This research contributes to the decrease in stigma that disorders like schizophrenia have endured, and shows how visualization of brain activity can affirm the contribution of neuroscience to understanding mental illnesses. Neurological diseases often have psychological symptoms and side effects, and psychological disorders often have neurological symptoms and side effects. Alzheimer’s disease is a neurological disease accompanied by cognitive decline and fluctuating psychological disruptions (Thompson, 2009). These include depression, irritability, delusions and long term memory loss. Studies about the famous injuries and survival of Phineas Gage have led researchers to believe that his drastic change in behavior was due to damage to his frontal lobe. Similarly, damage to the frontal lobe in stroke and Alzheimer's disease may eliminate a human aspect of their victims (Kean, 2014). Drawing these psychological connections among very different neurological diseases makes it possible to isolate the causes and effects of injuries like Gage’s, and perhaps predict the severity of the effect of such disturbances. Another disorder that straddles the line between 27 | JOURNYS | WINTER 2016
neuroscience and psychology is autism.While autism is sometimes considered a neurological disorder due to symptoms such as epilepsy, it also has psychological ramifications including social and behavioral disabilities. Calcium imaging to measure neuronal activity in certain areas of the brain that are implicated in autism (Dolen, 2014). Autism always has both psychological and neurological sides to it, dependent on severity, which contributes to the connection between biology and behavior. While neurological disorders emphasize biological problems over behavioral side effects, psychological disorders are known for behavioral problems, but also have previously unrecognized neurological bases. Schizophrenia is an example of a rare mental illness which is characterized by symptoms such as hallucinations, hearing voices, disorganized behavior, and problems with speech. Patients with schizophrenia have increased activity in the basal ganglia, decreased activity in the prefrontal cortex, and very little connection between the two areas (Yoon, et.al., 2013). This shows a clear neurological basis for a psychological disorder. One study conducted on healthy and affected subjects that were shown a “funny face”. Healthy children responded to it in a normal way, while affected individuals showed no response whatsoever. In schizophrenic patients, connections between certain regions of the brain are dulled, which leads to distorted experiences (Nauert, 2009). This conclusion is supported by the correlation between a lack of response and communication between two regions of the brain. Depression is another psychological problem that can be a symptom or a side effect of another disease. Depression is a psychological side effect of neurological diseases like Parkinson’s, and it has a neural basis, often connected to serotonin and dopamine ([18F]-FDOPA PET, 2014). Again, neurotransmitters play a role in individuals’ psyches. Researchers used brain scans on the children who had depression and those who were mentally healthy. The participants with depression who were nurtured had hippocampi that were 10 percent larger than those of the depressed children who were not nurtured (Dryden, 2012). This use of brain imaging reveals the impact of a mental illness (depression) in combination with psychosocial influences (nurturing) on brain structure.
DISCUSSION AND CONCLUSION
The growing connection between neuroscience and psychology has resulted in a decrease in the stigma surrounding mental disorders, better treatment for those problems, and heightened knowledge of the human mind for experts in both fields. Imaging has played a large role in forming and maintaining this bond, as it permits the visualization of brain activity in different people, which can eliminate the guesswork or speculation in diagnosis and treatment of both neurological and psychological disorders. This complementary attachment allows society to see the complexities of the brain from multiple perspectives, and to pursue a more whole understanding of the biology behind behavior.
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REFERENCES
[18F]-FDOPA PET. (2014). PET scans highlight the loss of dopamine storage capacity in parkinson’s disease [Image]. Retrieved from http://feinsteinneuroscience.org/wp-content/uploads/Parkinsons_ compare_437px_2col_large.png Aguirre, G. K. (2002). Functional imaging in behavioral neurology and cognitive neuropsychology. Behavioral Neurology and Cognitive Neuropsychology, 1-24. Retrieved from http://ccn.upenn.edu/home/news/events/aguirre_ inpress.pdf Autism fact sheet [Fact sheet]. (2009, September). Retrieved November 19, 2014, from National Institute of Neurological Diseases and Stroke website: http://www.ninds.nih.gov/disorders/autism/detail_autism.htm Center for BrainHealth. (2014, August 15). Brain imaging shows brain differences in risk-taking teens. ScienceDaily. Retrieved October 15, 2014 from www.sciencedaily.com/releases/2014/08/140815102326.htm Dolen, G. (2014, October 9). Research project information request [E-mail to the author]. Dryden, J. (2012, January 30). Mom’s love good for child’s brain. Neuroscience News. Retrieved from http://neurosciencenews.com/moms-love-goodchild-brain-nurture-hippocampus-volume/ Foerschner, A. M. (2010). The history of mental illness: From “skull drills” to “happy pills”. Student Pulse, 2(09), 1-4. Retrieved from http://www. studentpulse.com/articles/283/the-history-of-mental-illness-from-skulldrills-to-happy-pills Ginger, & William. (2011, February 4). Psychology and neuroscience [Online forum post]. Retrieved from Brain Science Podcast Discussion website: http://www.goodreads.com/topic/show/486708-psychology-andneuroscience Heeringen, C. V. (2003). Understanding the suicidal brain. The British Journal of Pyschiatry, 206(1), 282-284. http://dx.doi.org/10.1192/bjp.183.4.282 Hiss, K. (2014, September/October). The beautiful life of your brain. Reader’s Digest, 76-85. Kean, S. (2014, May 6). Phineas gage neuroscience’s most famous patient. Slate. Retrieved from http://www.slate.com/articles/health_and_science/ science/2014/05/phineas_gage_neuroscience_case_true_story_of_ famous_frontal_lobe_patient.html McLeod, S. A. (2007). Nature Nurture in Psychology. Retrieved from http:// www.simplypsychology.org/naturevsnurture.html Nauert, R. (2008, August 7). Brain imaging helps explain behavior. Retrieved from http://psychcentral.com/news/2008/08/07/brain-imaging-helpsexplain-behavior/2712.html Pruessner, J. C., Champagne, F., Meaney, M. J., & Dagher, A. (2004). Dopamine release in response to a psychological stress in humans and its relationship to early life maternal care: A positron emission tomography study using [11C]raclopride. The Journal of Neuroscience. http://dx.doi.org/10.1523/ JNEUROSCI.3422-03.2004 Scanning the brain. (2014, August). Retrieved November 19, 2014, from American Psychological Association website: http://www.apa.org/ research/action/scan.aspx Thompson, D., Jr. (2009, January 14). Psychological therapy in alzheimer’s treatment. Everyday Health. Retrieved from http://www.everydayhealth. com/alzheimers/alzheimers-treatment-psychological-therapy.aspx Yoon, J. H., Minzenberg, M. J., Raouf, S., D’Esposito, M., & Carter, C. S. (2013, February 26). Mapping brain circuitry provides clues to schizophrenia, earlier detection of psychosis. Retrieved October 15, 2014, from National Institute of Mental Health website: http://www.nimh.nih.gov/news/sciencenews/2013/mapping-brain-circuits-provides-clues-to-schizophreniaearlier-detection-of-psychosis.shtml
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The Effect of Listening to Heavy Bass Music on Reaction Time Abstract Decades of research have gone into understanding the effect of music on the brain7. However, only a few studies , highlight the effect of music on reaction time. This research tested the effect of heavy bass music on reaction time among teenagers (ages 15-18). The subjects (n=30) were counterbalanced as they listened to bass boosted music and control music without heavy bass influences while they completed a reaction time test. The results were statistically insignificant (p>0.05), so it was concluded that heavy bass music does not affect reaction time. Upon further reflection, the reaction time test used was deemed ineffective in determining an accurate reaction time due to an inaccurate method of calculating averages, namely it did not account for early clicking. Further studies must be conducted utilizing an accurate reaction time experiment to better assert this conclusion.
Hypothesis
Sanjay Kubsad Mead Senior High School
Art by Jenny Li
Null Hypothesis: Listening to heavy bass has no effect on reaction time of an individual. Alternative Hypothesis: Listening to heavy bass increases reaction time of an individual. The final result is most likely the conclusion that listening to heavy bass music increases reaction time. If we see this result, further studies can be conducted into different forms of popular music to see if other types of popular music might impede daily life by increasing reaction time.
Purpose Electronic music uses artificial and acoustic sounds to create musical pieces. Often times, heavy bass is electronically synthesized to create sounds that cannot be created with musical instruments. Thus, in amidst the birth of this new genre, it is necessary to establish a link between heavy bass and the brain’s response. Particularly, one such response that should be evaluated is reaction time. People often listen to music while driving. Hence, it becomes necessary to evaluate whether listening to such music increases or decreases the reaction time of those operating the vehicle. If this experiment succeeds in proving that listening to heavy bass music negatively impacts reaction time, a link can be made between such music and roadside accidents; prevention techniques could be put in place to combat such events be it through education or transit safety measures.
Literature Review Reaction time has been one of the most important aspect of the human brain. Reaction time is more than just the speed the brain takes to respond to stimulus; it is a measure of how fast a brain analyzes a perceived action and how quickly it can convert this realization into a bodily response. During the caveman era, life or death revolved around how quickly one responded to a problem whether it was fighting off an attack from a carnivorous wild animal or hunting for prey. A slow reaction time could have resulted in losing the prey or getting eaten. Reaction time is still critical today. A fast reaction time is often an indicator of proper brain development. According to Dr. Christiane Lange-Kuttner, “reaction times are an indicator of the neural 30 | JOURNYS | WINTER 2016
maturity of children’s information processing system.”1 Although reaction time is controlled by many parts of the brain, specifically the corpus callosum is believed to be a major player in reaction time. In fact, according to Rachael Seidler Ph.D, “slower reactivity is associated with an age-related breakdown in the corpus callosum.”2;3 The health of the corpus callosum is an important indication of proper cross-talk in the brain. Although past studies have been conducted regarding the effect of music on the brain, none address the impact of heavy bass on reaction time. But there is no doubt that music has a strong correlation to brain activity. In fact, according to Claudia Hammond from BBC, “a meta-analysis of sixteen different studies confirmed that listening to music does lead to a temporary improvement in the ability to manipulate shapes mentally”6 . Furthermore, A popular study conducted in October 1993 first described what is now known as the Mozart Effect. Researchers split thirty six students into three groups. Each group was offered a pre-test before the experiment began to test whether the experiment would result in an increase in IQ. Then, one group listened to music by Mozart, the other listened to white noise, and the last group did not listen to anything. After another IQ test was performed, it was revealed that the Mozart group resulted in an average increase of 9 IQ points compared those who listened to white noise or nothing. The increase in IQ, however, was transitory,
the effects fading in ten to fifteen minutes. Regardless, this study was important in establishing the link between music and brain reaction. A definitive link between reaction time was established by researchers at Winona State University. Researchers tested sixty-one subjects and played a variety of popular and unpopular forms of music. This study also spotlighted the effect of different types of music on reaction time. From this study, it was concluded that reaction time was lesser when listening to unfamiliar music when compared to familiar music.8 This study focuses on the impact of heavy bass on reaction time. The study’s implications are tangible. When driving, many drivers listen to heavy bass. We can see evidence of this in the growth of the electronic music sales industry, and the outfitting of popular branded bass stereos in cars such as Bose and Beats. Perhaps nowhere is reaction time most important than when driving. According to the American Automotive Association, “the average driver makes about 20 major decisions during each mile driven - and often has less than one-half second to react to avoid a potential collision.5” Determining whether or not listening to heavy bass while driving reduces reaction time is essential to prevent collisions. There are many gaps in existing research regarding this question. There have not been reliable and conclusive studies on the effect of heavy bass music and reaction time. Answering this question further aids us in understanding the effects of music on the brain.
Methods Bass music, for the purpose of this study, was any music with a prominent bass frequencies, specifically bass boosted dubstep music. The songs chosen for this experiment was a bass boosted version of “Reptile” by Skrillex and a condensed version of “Symphony No 6” by Beethoven, which served as the control. Equal numbers of males and females were used to ensure that this effect was not due to gender differences. Each subject sat in one minute of silence to get comfortable with the environment. The subject then listened to music without prominent bass music, the “Symphony No. 6.” At the two minute mark, the subject took a reaction time test while continuing to listen to the music. Then the subject, after one minute of silence to relax, listened to heavy bass music, the Skrillex piece. At the two minute mark, the subject took a similar reaction time test while listening to the music. This procedure allowed for only one independent variable to be tested — music with different amounts of bass. The reaction time test that was used was a one minute reaction time test published in the British Broadcasting Corporation, where the the participant was required to press a button every time an object moved9.The results were averaged for the average reaction time. This procedure was counterbalanced to prevent the data from being skewed due to the subjects getting comfortable with the reaction test. The subjects were taken to a quiet and undisturbed location to prevent noise pollution from affecting the results of the reaction time test. The music was played at one consistent volume to prevent the introduction of another variable.This experiment was conducted with headphones and music player. Headphones were used to minimize the effects of noise pollution on the experiment. The data collected was analyzed with a t-test to determine if
the results were significant. Based off the results from the t-test, the null hypothesis could be accepted or rejected.
Research Design Twenty students from various debate and biomedical classes participated in the test. Each participant was tested one at a time for an eight minutes (one minute period of silence, three minutes of music with prominent bass including one minute of reaction time test, another minute of silence, three minutes of music without prominent bass including one minute reaction time test). The results from the reaction time test were recorded. Standard deviation and statistical variance was calculated for the reaction times of both samples and were used to find the t-value. The t-value was calculated using a one tailed t-test to determine whether the data was statistically significant and whether the alternative hypothesis can be accepted and the null hypothesis rejected. A one tailed t-test was used because the experiment is directional. The results of this experiment fall short in that they test the effects of only one type of bass prominent music and one type of music without prominent bass sounds. Thus, further study is necessary.
Project Schedule Tasks
Start Date
End Date
Find Mentor
12/19/2014
1/16/2015
Start test
2/24/2015
3/13/2015
Record data
2/24/2015
3/13/2015
Statistically analyze data
3/14/2015
3/14/2015
Accept/reject null hypothesis
3/14/2015
3/14/2015
Present findings
4/21/2015
4/21/2015
Sample Data Table Subject Number
Gender
Date, Time
Avg. RT w/ heavy bass
Avg. RT w/o heavy bass
Comments
Materials List Heavy Bass Music: “Reptiles” by Skrillex (Bass Boosted version) https://www.youtube.com/watch?v=uTF-fj1tigg Low Bass Music Beethoven’s No 6 symphony https://www.youtube.com/watch?v=s6SSM2vl6AU One minute Reaction time test http://www.bbc.co.uk/science/humanbody/sleep/sheep/reaction_ version5.swf Headphones Music Player
Results Through a numerical, graphical and statistical analysis of the experimental results, it was deemed that heavy bass music does not affect reaction time. A frequency graph was used to graph the average reaction time, and boxplot graphs were used to identify outliers. 31 | JOURNYS | WINTER 2016
Figures Figure 1: Bar graph depicting average and median results
Figure 2: A box plot of reaction time with heavy bass music
Figure 3: Box plot of reaction time without heavy bass music
A one-tailed paired t-test was used to determine statistical significance because the same group of people were tested twice. Intermediate values used in calculations: n = 40 d = 0.006010 t = 0.0602 df = 38 Standard error = 0.100 The two-tailed P value equals 0.9523. By conventional criteria, this difference is considered to be not statistically significant. The presence of heavy bass music thus does not increase reaction time. (I believe a greater number of people should have been used for this test to begin with. Experiment design also needs some work before concluding statistical significance and making a conclusion).
32 | JOURNYS | WINTER 2016
Analysis
Appendix
The null hypothesis was accepted, and it was determined that the amount of bass in music does not affect reaction time. Although there was a slight increase in reaction time associated with listening to bass music, the increase is small enough to be disregarded. Listening to heavy bass music does not prove as a greater risk to drivers over music without bass influence. There were however many discrepancies. There existed many outliers as indicated in Figure 2 and Figure 3 due to the nature of the reaction time test. The reaction time test automatically docked three seconds if the user hit the button early. This three second addition on to the reaction time heavily influenced the average reaction time of the data. It is important to note that some users, by clicking the button early affected the results. This study should be repeated once more with a different test to reduce this discrepancy and allow for the collection of better data. Additionally, the counterbalance did not work effectively. Upon examination of Table 1, it can be seen that in a majority of the cases, when the reaction time test was performed a second time, reaction time decreased. This shows that a bias was introduced in the test where the subject performed better because the subject was better aware of the test.
Table 1: Raw Data for the Experiment
Conclusion For this experiment, the null hypotheses stating that listening to heavy bass has no effect on reaction time of an individual was accepted. Although there was a slight increase in reaction time associated with listening to bass music, the increase was deemed statistically insignificant. Listening to heavy bass music thus does not prove as a greater risk to drivers over music without bass influence. The data of this experiment has shown very interesting parallels to a past experiment. In this experiment, the participants were often familiar with heavy bass music, but unfamiliar to Beethoven’s Symphony No. 6. When comparing the average reaction times, those who listened to the unfamiliar music had a lower reaction time than those who listened to the more familiar music. This connects to the research conducted by Mjoen and Fried where the researchers tested sixty-one subjects and played varieties of popular and unpopular forms of music. From this study, it was concluded that reaction time was lesser when listening to unfamiliar music when compared to familiar music.8 My data further buttresses the conclusions of Mjoen and Fried. There were sources of error in the experiment. There existed many outliers as indicated in Figure 2 and Figure 3 due to the nature of the reaction time test. The reaction time test automatically added three seconds to the average if the user hit the button early. This three second addition on to the reaction time heavily influenced the average reaction time of the data. This study should be repeated once more with a different test to reduce this discrepancy and allow for the collection of better data. Furthermore, participants did better when they were more familiar with the test. Although the subjects were counterbalanced, it is important that future experiments make their participants better aware of the reaction time test used to avoid confounding variables. If listening to heavy bass music does affect reaction time, further studies can be conducted with other genres of popular music. Due to the errors inborn in the experimental design, it is important to conduct another experiment.
Subject Number
Gender
Date, Time
Avg. RT w/ heavy bass
Avg. RT w/o heavy bass
Comments
1
F
5 Mar 12:53
.2964
.2768
B
2
F
5 Mar 1:02
.3538
.8442
B
3
F
5 Mar 1:10
.3532
.3202
S
4
F
5 Mar 1:18
.344
.2906
S
5
F
5 Mar 1:23
.8696
.8098
S
6
F
5 Mar 1:50
.8328
.3502
B
7
F
5 Mar 1:55
.3466
.2864
S
8
F
5 Mar 2:01
.3090
.3866
B
9
F
5 Mar 2:08
.2872
.8304
S
10
M
6 Mar 12:50
.2694
.833
B
11
M
6 Mar 12;57
1.3904
1.3668
B
12
M
6 Mar 1:14
.3134
.2664
S
13
M
6 Mar 1:20
.2636
.3004
B
14
M
10 Mar 1:03
.3736
.2802
S
15
M
10 Mar 1:10
.217
.2894
B
16
F
10 Mar 1:18
.3206
.8942
S
17
M
10 Mar 1:28
.2836
.2694
S
18
M
10 Mar 1:43
.7834
.2438
B
19
M
10 Mar 1:47
.8262
.2906
S
20
M
10 Mar 1:51
.8032
.2874
B
The order of the track can affect the result, and in order to reduce experimental bias, a counterbalance was added. In the comment section, the “B” and “S” refer to the order that the experiment was conducted. “B” means that the Beethoven track was played first. The “S” means that the Skrillex track was played first.
References
1 “The Importance of Reaction times for Developmental Science: What a Difference
Milliseconds Make.” The Importance of Reaction times for Developmental Science: What a Difference Milliseconds Make. Web. 18 Jan. 2015.. 2 “As We Age, Loss of Brain Connections Slows Our Reaction Time.” Psych Central. com. Web. 18 Jan. 2015. 3 University of Michigan. (2010, August 19). Brain connections break down as we age, study suggests. ScienceDaily. Retrieved January 29, 2015. 4 “The Importance of Football Reaction Time.” LIVESTRONG.COM. LIVESTRONG.COM, 01 Nov. 2013. Web. 18 Jan. 2015. 5 ”Reaction Time | SeniorDriving.AAA.com.” Reaction Time | SeniorDriving.AAA. com. Web. 17 Jan. 2015. 6 ”Does Listening to Mozart Really Boost Your Brainpower?” BBC Future. 07 Jan. 2013. Web. 18 Jan. 2015. 7 ”The Mozart Effect: A Closer Look.” The Mozart Effect: A Closer Look. Web. 17 Jan. 2015. 8 “Music on the Mind: Cognitive Recall and Reaction Time.” WSU Psychology Student Journal. Web. 20 Jan. 2015. 9 “Sheep Dash Reaction Time Test.” British Broadcasting Company. Web. 20 Jan. 15.
33 | JOURNYS | WINTER 2016
by Ellie Flint Achromatopsia is a visual disorder which causes the absence of color vision and a decrease in light sensitivity. This disorder is caused by an interference of phototransduction, where photons are transmitted to electric signals via the retina to the brain. In bright light, cones are the source of vision and also provide the ability to see color. People with achromatopsia have non-functioning or partially-functioning cones which causes their colorblindness. Achromatopsia affects 1 in 33,000 people worldwide; Neil Harbisson is one of those people.1 In 2004, Harbisson was presented with an cybernetic antenna (embedded in his brain) that would allow him to hear color. The inventor, Adam Montandon, met Harbisson while he was speaking about cyborg techniques. Harbisson’s unique situation incited Montandon’s sense of innovation. Because sound and light both travel in waves, they are compatible for a color-to-sound scale that would allow Harbisson to hear different light frequencies. Harbisson’s musical talent allows him to perceive different notes that would be indistinguishable to the untrained ear. Living in a world of grey, Harbisson accepted the responsibility of becoming a cyborg, a being with both organic and biomechatronic body parts. This new identity would open doors for him creatively and color his black-andwhite world. Sounding like something straight from a sci-fi movie, the “eyeborg” was created and permitted Harbisson to realize his destiny as an artist and cyborg activist.2 Another hope lingered in the evidence of a newly defined phenomena: synthesia, or the unification of the senses. People who have this sensory condition often experience a blending of various sensations, which are ordinarily separated. For example, a person might feel musical sounds on their body or have a taste evoke a lucid color, such as “steak producing a rich blue.7” The most common 34 | JOURNYS | WINTER 2016
art by Annie Zhou occurrence is colored hearing, which is what Montandon was attempting to produce for Harbisson through technology. To understand how the device works, it is important to know that color has three components: hue, saturation, and light. The gadget identifies the hue, color or shade, and converts the photons, recognized as light, to a sound frequency heard as a musical note. Wavelength is inversely proportional to frequency, making the conversion of light to sound effortless. Saturation is also translated into volume: when the color is more concentrated or vibrant, the sound will be louder, and when the color is dull a softer note is produced. Additionally, colors such red, with low frequencies on the color spectrum, have lower tones while a color like violent, at the opposite end, is a high tone. Harbisson can identify 360 hues, ranging from frequencies of 384 units to 718 units, in addition to ultraviolet and infrared light. This is another aspect where being a cyborg has enhanced him; his newfound awareness can help him to avoid potentially detrimental UV rays, known for their ability to cause cancer.3 Though there are many variations of infrared light: near, middle, and far, and two types of ultraviolet light: near and far, the camera is limited to solely near.8 For Harbisson, near-infrared and
near-ultraviolet are both expressed within the same octave as the other colors, starting at an F note. Before the surgery, his use of the “eyeborg” was limited to when he was wearing headphones and using a computer screen. As an artist prior to the surgery, he only utilized black and white when painting because of the distance he felt towards the other colors he could not appreciate or fully understand. Now, the “eyeborg” is implanted into the back of his skull, and he is able to receive messages from the camera through bone vibrations
processed as sounds. The picture below illustrates his technology, with the long, skinny wire protruding from the back of his head (where the chip originates) to the camera that rests just above his eyes. A wifi connector inside the chip allows him to hear images sent from his phone.3 Although it was not initially apparent to him, Harbisson realized he was a cyborg after hearing electronic sounds in his dreams. He then accepted that his body had given him a new sense; he had evolved.5 Unfortunately, due to his “eyeborg,” Harbisson encounters problems socially. Because of the obvious camera connected to the antenna dangling from his head, he is denied access of entry to movies because people assume he will record the show. Also he is gawked at or seen as a threat because of his misunderstood technology. Very recently, however, he was granted permission to wear his “eyeborg” in his UK passport picture, explaining that it was not merely technology, but an extension of himself. Injustices such as these that came about with becoming a cyborg drove Harbisson to create the Cyborg Project which aims to educate the population about this new “era” of technology, the cyborg transition bound to be felt within
the next few decades, and create rights for this developing class of people.4 Some examples include Jesse Sullivan, and amputee who has a bionic arm and Jens Naumann, “the first person in the world to receive an artificial vision system.9” Harbisson explained in a Ted Talk how his life has changed as a result of becoming a cyborg. For example, art galleries have become concerts because of their endless plethora of color, and he dresses in a way that sounds good (that day it was C major: pink, blue, and yellow). He is also able to eat his favorite song and create “sound portraits” by writing down the various notes heard upon appearance. Harbisson also states that regular sounds elicit the colors in him, for example the telephone sounds green while Mozart sounds yellow. He has even translated famous speeches into art, as seen to the right: one being Martin Luther King Jr.’s “I Have a Dream” (right) and the other written by Adolf Hitler (left). Surprisingly, most people assume that the
speeches are reversed, with King’s speech on the left and Hitler’s on the right. However, color has nothing to do with content; it is merely an interesting observation of a color’s implicit meaning for people with vision. For Harbisson, this grave consciousness of what he should be versus what he is can be perceived as a stark dichotomy, compelling him toward all-encompassing tolerance. Instilling his passion on any listener he states, “becoming a cyborg is not about becoming like a machine, it’s not about becoming less human, it’s about
bringing us closer to other animals and to nature; it’s about awakening our senses, our instincts, our intuition… qualities that we seem to have lost due to our constant use of technology as an external tool, and not as part of our body.6” Ethically, this topic is extremely controversial, yet it is fascinating to consider the new definitions that could be formed from this technology if society would allow for it. Because of technological innovation, a man was able to discover and understand something as abstract as color without ever actually seeing it. When humans embrace new ideas and combine science with creativity, they can immerse themselves in a heightened realm of reality, one that just might make history.
REFERENCES
“Achromatopsia.” Genetics Home Reference. U.S. National Library of Medicine, 21 Mar. 2016. Web. 24 Mar. 2016. Williams, Amanda. “Colour Blind Artist Becomes World’s First ‘eyeborg’ by Having Antenna Implanted inside His Skull so He Can ‘hear’ Colours.”Mail Online. Associated Newspapers, 16 Mar. 2014. Web. 24 Mar. 2016. Yasenchak, David. “Filling the Colorless Void: The Cybernetic Synaesthesia of Neil Harbisson.” Filling the Colorless Void: The Cybernetic Synaesthesia of Neil Harbisson (n.d.): n. pag. Valley Humanities, 2013. Web. 29 Mar. 2016. “Cyborg Project.” Cyborg Project. Espill Media, n.d. Web. 24 Mar. 2016. Harbisson, Niel. “I Listen to Color.” Neil Harbisson:. TED Conferences, June 2012. Web. 24 Mar. 2016. Harbisson, Niel, and Mariana Viada. “Niel Harbisson- A Cyborg Artist.” (n.d.): n. pag. Cyborg Foundation, 2013. Web. Carpenter, Siri. “Everyday Fantasia: The World of Synesthesia.” American Psychological Association. American Psychological Association, Mar. 2001. Web. 11 Oct. 2016. “Neil Harbisson Interview – Part 5: Beyond Hearing Color | Munsell Color System; Color Matching from Munsell Color Company.” Munsell Color System Color Matching from Munsell Color Company. N.p., 20 Nov. 2014. Web. 12 Oct. 2016. Nelson, Bryan. “7 Real-life Human Cyborgs.” MNN. Mother Nature Network, 25 Apr. 2013. Web. 12 Oct. 2016.
35 | JOURNYS | WINTER 2016
WHY SOME PEOPLE REMEMBER THEIR DREAMS AND what they mean Written by Alina Luk Art by Christina Patricia
Everyone has been startled awake from a nightmarish dream before. Dreams have always preoccu-
pied the minds of humans and aroused many questions. Although not everyone remembers his or her dream, the meanings and causes of dreams have become a topic of compelling research. Research experiments exploring the nature of dreams often ask why some people remember their dreams and what these dreams really mean. Scientists have come up with multiple theories on why people dream. The most commonly proposed theory dictates that dreams occur to help understand and reflect human knowledge, emotions, and worries.1 The human brain undergoes five stages of sleep, which represent different levels of depth. REM (rapid eye movement) sleep is the fifth and deepest stage, which is characterized by dreaming. During this stage, the brain emits alpha waves and the neurotransmitter dopamine, which is a chemical responsible for transmitting signals between nerve cells. Several parts of the brain are also activated during REM sleep, including the limbic and paralimbic systems, medial and orbital frontal cortex, extrastriate visual cortex, right parietal cortex, and motor cortex. 2 The other systems and areas of the brain account for consciousness and other features of dreams. These fascinating neural characteristics shape the brain of a dream-recaller.4 A “dream-recaller” refers to someone who remem36 | JOURNYS | WINTER 2016
“Scientists have proposed theories about dreams, including that dreams try to reflect human emotions and problems.”
bers his or her dream after he or she wakes up. A study conducted by Perrine Ruby and her team have shown that while dream-recallers are sleeping, they have higher amounts of alpha waves and increased activity of sense, vision, and hearing in the medial prefrontal cortex and temporo-parietal junction, which is located between the parietal and temporal lobe of the brain. Increased levels of these neural factors promote a deeper impression of the dream in a person’s mind, resulting in the person being able to remember the dream even after waking up. The study used tomography, which uses X-rays or ultrasound to display cross sections through the human body, to study the brain activity of two groups of people: high dream-recallers and low dream-recallers. The study attempted to
determine the cause of why some people remember their dreams more than others. All twenty-one high dream-recallers were more likely than the low dream-recallers to respond to sounds and wake up during sleep. The experiment’s results revealed that the higher activity in the aforementioned areas of the brain contributed to the high dream-recallers’ ability to recall dreams and that “high dream-recallers [were] more reactive to environmental stimuli, [awakened] more during sleep, and thus better [encoded] dreams in memory than low dream-recallers.” 5 Besides this connection to brain function, possible reasons for why some people remember their dreams more than others may be a result of mental and physical restrictions including stress, alcohol, drugs, or traumatic events.6 The answer to how dreams work, and why some people dream more than others prompts people to ask what dreams symbolize. Scientists have proposed theories about dreams, including that dreams try to reflect human emotions and problems. Recurring objects in dreams represent the manifestations of these theories. The most common symbols include fire, water, disasters, travel, flying, and clothing. Disasters could represent a form of stress, possibly due to concerns and anxieties felt during conscious hours. Flying could represent a feeling of accomplishment and confidence. When interpreting dreams, details are important; whether one is floating or drowning in water could be a representation of two vastly different parallels to reality.7 Therefore, it is possible to interpret dreams based on any concerns or feelings that are developed in reality. According to Jeremy Taylor, an employee of the DreamTime magazine, “dreams are frequently unusual… dream images are ‘not yet speech ripe,’ however over time, with practice, we can learn how to remember those odd dreams and grasp them long enough to be able to record them.” 6
Although there is much more to learn about dreams and their purposes, the knowledge already uncovered has helped many people sort out their emotions and problems and discover more about themselves. In short, some people who display higher brain activity recall dreams, which reflect the daily lives, more frequently. As mysterious as dreams are, scientists are learning more and more about their nature. The discovery of connections between dreams and reality provides maps for future research and can even chart the complete analysis of the human brain and its capacity to dream. REFERENCES:
1. “Why Do People Dream? Meaning Behind Dreams.” Why Do People Dream? Meaning Behind Dreams. SBI, 2011. Web. 27 Jan. 2016. <http://www.dreaminterpretation-dictionary.com/ why-do-people-dream.html>. 2. Mastin, Luke. “Sleep - Dreams - How Dreams Occur.” Sleep Dreams - How Dreams Occur. N.p., 2013. Web. 27 Jan. 2016. <http://www.howsleepworks.com/dreams_how.html>. 3. McNamara, Patrick. “Dopamine and Dreams.” Psychology Today. N.p., 08 Jan. 2016. Web. 27 Jan. 2016. <https://www. psychologytoday.com/blog/dream-catcher/201601/dopamineand-dreams>. 4. Hoss, Robert J. “Science of Dreaming - Section 3.” Science of Dreaming - Section 3 - Robert J Hoss. N.p., n.d. Web. 27 Jan. 2016. <http://www.dreamscience.org/idx_science_of_ dreaming_section-3.htm>. 5. Chan, Amanda L. “Is This Why Some People Are Able To Remember Their Dreams Better Than Others?” The Huffington Post. TheHuffingtonPost.com, n.d. Web. 12 Dec. 2015. <http:// www.huffingtonpost.com/2014/02/21/remember- dreamsbrain_n_4809360.html>. 6. Brucker, Amy E. “Why We Forget Our Dreams.” The DreamTribe. N.p., n.d. Web. 12 Dec. 2015. <http://thedreamtribe.com/whywe-forget-our-dreams-2/>. 8. “Dream Themes: Flying and Other Common Dream Themes.” Dream Themes: Flying and Other Common Dream Themes. SBI, 2011. Web. 04 Feb. 2016. <http://www.dreaminterpretationdictionary.com/dream-themes.html>.
37 | JOURNYS | WINTER 2016
LETTER FROM THE PRESIDENT
Dear Readers, As you’ve flipped through the pages of our 8.1 issue, I hope something has caught your eye, sparked an interest, or made you stop and think about a concept from a new vantage point. If it has, then we at JOURNYS are one step closer to accomplishing our goal: inspiring scientific passion and encouraging innovation. Now nine years from our founding, JOURNYS has had tremendous growth and we hope to continue expanding our supportive community of student STEM aficionados while building stronger connections with the professional world. Locally and internationally, JOURNYS has found a welcoming audience in the many who recognize the ever-increasing importance of the youth voice in STEM, which has a unique perspective and much to share in both research and writing. Our student contributors also continue to have a great resource in collaboration opportunities; language, location, and experience are no barriers. Instead, being a member of the JOURNYS community means being able to communicate and work with peers from areas as diverse as Korea, Mexico, and Taiwan, and gaining feedback and advice from professionals in universities and companies, all while being connected by a common enthusiasm for scientific discovery and progress. In particular, JOURNYS is honored to begin a new partnership with the San Diego American Chemical Society this issue. SDACS, with its expertise in chemistry and related fields, represents another wonderful addition to our community and opens new doors for our student members. As to the months ahead of us, I look forward to sharing much more of our work with you. But it is our hope that you join us, for the invitation to the JOURNYS community is always open. Sincerely, Caroline
LETTER FROM THE EDITORS-IN-CHIEF
Dear Readers, Thank you for taking the time to pick up this issue. It’s made up of articles from JOURNYS’s past and present, as we look towards the future. The staff of JOURNYS has been working to put this issue together since the beginning of the school year, and we hope that you’ve enjoyed reading these articles as much as we did. Each of the articles you see today was included in this issue because it embodied a unique approach to a specific field of science. Now more than ever, scientific discoveries and innovations are being made by young people. It’s become increasingly important to keep an eye on the work of teenagers, or “youths in science.” The work included in this issue is a combination of original research and scientific review. Students around the world are working hard to develop sanitary experimental conditions for laboratory pigs, but they are also shedding light on the plight of endangered species like the Juan Fernandez firecrown. Many of our original research articles focus on the benefits of scientific discovery-- the possibility of clean water in developing countries, or the development of life on other planets. This is the first issue published by the 2016-2017 JOURNYS board, and as a team, we’ve had our trials and tribulations. But we’ve carved out our own identity. The Letter from the EICs and the Letter from the President are just two of the ways that we have been able to enact change. Each year brings new leadership, and with each new administration comes new ideas, new methods, and new ways of looking at the world. That’s why we’d like to end by thanking everyone who contributed to this issue, whether through writing, editing, drawing, or designing. JOURNYS prides itself on being a student-founded and student-run organization, providing a platform for original and collaborative work for high school students. JOURNYS hopes to foster interest in scientific research and innovation, but we also want to foster cooperation and proficiency in writing among our staffers and contributing authors. Achieving in science is impressive, but achieving in science while writing at a professional level is impactful. Whether we’ve caught your interest because of our material or our art and design, we assure you that the magazine you see here is our best work-- the product of months of input from different and unique voices. We hope that yours might soon be one of them. Sincerely, Jessica and Alexander
38 | JOURNYS | WINTER 2016
STAFF POSITIONS EDITORS IN CHIEF Jessica Gang, Alexander Hong
PRESIDENT Caroline Zhang
ASSISTANT EDITORS IN CHIEF Maya Kota, Stacy Hu
VICE PRESIDENTS Grace Lee, Frank Lee, Kalyani Ramadurgam, Erica Hwang
SECTION EDITORS Stacy Hu, Jonathan Kuo, Maya Kota, Anisha Tyagi MEDIA MANAGER Maggie Fang GRAPHICS MANAGER Connie Chen GRAPHIC ARTISTS Connie Chen, Alexander Hong, Jenny Li, Alice Jin, Annie Zhou, Christina Patricia, Amy Kim DESIGN MANAGER Dimei Wu DESIGNERS Dimei Wu, Alexander Hong, Kiya Klopfenstein, Maggie Fang, Sumin Hwang COPY EDITOR Maya Kota CONTRIBUTING AUTHORS Joanne Won, Nathan Lian, Minseok Jeon, Joonhyuk Lee, Yoon Ki Joo, Melba Nuzen, Sanjena Venkatesh, Erica Hwang, Minchul Shin, Jessica Young, Irine Thomas, Sanjay Kubsad, Amruta Ponugupati, Ellie Flint, Alina Luk STAFF ADVISOR Mr. Brinn Belyea
COORDINATORS Mihika Nadig, Jonathan Wang, Maggie Fang, Jacey Yang, Emily Zhang SCIENTIST REVIEW BOARD COORDINATOR Kalyani Ramadurgam SCIENTIST REVIEW BOARD Dr. Aaron Beeler, Dr. Akiva Cohen, Dr. Amiya SinhaHikim, Mr. Andrew Corman, Dr. Aneesh Manohar, Dr. Arye Nehorai, Dr. Benjamin Grinstein, Mr. Brooks Park, Dr. Bruno Tota, Mr. Craig Williams, Mr. Dave Ash, Mr. Dave Main, Mr. David Emmerson, Dr. Dhananjay Pal, Dr. Erika Holzbaur, Dr. Gang Chen, Dr. Gautam Narayan Sarkar, Dr. Greg J. Bashaw, Dr. Haim Weizman, Dr. Hari Khatuya, Dr. Indrani Sinha-Hikim, Ms. Janet Davis, Dr. Jelle Atema, Dr. Jim Kadonaga, Dr. Jim Saunders, Dr. Jody Jensen, Dr. John Allen, Dr. John Lindstrom, Professor. Joseph Oâ&#x20AC;&#x2122;Connor, Ms. Julia Van Cleave, Dr. Kathleen Boesze-Battaglia, Dr. Kathleen Matthews, Ms. Kathryn Freeman, Ms. Katie Stapko, Dr. Kelly Jordan-Sciutto, Dr. Kendra Bence, Dr. Larry Sneddon, Ms. Lisa Ann Byrnes, Dr. Maple Fung, Mr. Mark Brubaker, Dr. Michael Plewe, Dr. Michael Sailor, Mr. Michael Santos, Dr. Reiner Fischer-Colbrie, Dr. Ricardo Borges, Dr. Rudolph Kirchmair, Dr. Sagartirtha Sarkar, Ms. Sally Nguyen, Ms. Samantha Greenstein, Dr. Saswati Hazra, Dr. Simpson Joseph, Dr. Sunder Mudaliar, Dr. Sushil Mahata, Ms. Tania Kim, Dr. Tanya Das, Dr. Tapas Chakravarty, Dr. Tapas Nag, Dr. Thomas Tullius, Ms. Tita Martin, Dr. Todd Lamitina, Dr. Toshinori Hoshi, Ms. Tracy McCabe, Dr. Trilochan Sahoo, Ms. Trish Hovey, Professor. Xin Chen, Dr. Yifeng Xiong
39 | JOURNYS | WINTER 2016
Journal of Youths in Science
2016-2017