Pig Dissection

In this lab we dissected a fetal pig. The purpose of this lab was for us to understand the physiology of another organism and see how it their organs and organ systems relate to those of humans, as they are both mammals. I was able to learn a lot through this lab, and it really helped me compare the pig’s anatomy to a human’s anatomy, and relate the concepts learned through this labs to the vodcasts that we are currently doing in class.

The external anatomy of the pig contained its wrists, shoulders, digits, thoracic cavity, and abdominal cavities. THis is similar to our external anatomy, as our wrists and shoulders are used for the similar purposes and we have fingers like the pig’s digits. We also have thoracic and abdominal cavities. In regards to the digestive system, we have nearly all of the same organs as the fetal pig, included the esophagus, stomach, liver, pancreas, small and large intestine as well as the rectum. There are a few differences between the liver of humans and pigs - The human liver has 4 lobes, while the pig liver has 5. Interestingly, there is no food in the stomach of the pig, mainly because it is a fetus.

This is similar for the respiratory, circulatory and reproductive systems. All the primary organs of these systems, ie. the lungs, diaphragm, heart, coronary artery, kidneys ureters, bladder, etc. This is mainly how I relate to what we have learned in this unit, and the striking similarities between the pig and human anatomy, solidified my understanding of the material taught.

My favorite part of this lab was probably analyzing the pig and its organs. It was really interesting to see what was in some of the organs that the functions of each part. Inside the heart we were able to see the ventricles and atria. In my opinion this dissection is a very valuable learning experience for many students, because it really helped me connect the dots of everything that we have been learning throughout our unit vodcasts.  

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20 Time Project Individual Reflection

For the past two months, we have developed an experiment, for a “20 Time Project” in our science class. The goal of the 20 time project was first displayed through’s google’s pact to their employees. Google wanted their employees to spend 20 percent of their time, doing what they enjoyed, and what they wanted to bring to Google’s variety of products. Some products that came out of this new philosophy were Google News, GMail and even AdSense, google’s highest grossing products.

Our science teacher replicated this, for the classroom, in which we got to design an experiment in which we were learning something about science, more specifically biology, while also having fun, and doing something that we were interested in. That’s why we chose to do an experiment about music, and how it can affect your neural performance - in layman’s terms, Can music help you study and learn the material better, and if so what type of music and at what volume?

I chose this experiment because as a student I always was interested in study tips and what can make you a better overall learner. There are numerous studies, that take many different stances on this topic - Some suggest that music enables you to create a pace to your studying, and even relaxes your brain making it more susceptible to understanding information. On the other hand, experts say that music can distract you from learning information and can be detrimental to your overall understanding of concepts.

With many differing views, I wanted to devise an experiment that would be able to tell which of these views were right, and also give me an idea of what music to listen to, in order to study. This would be able to benefit many students who were interested in learning how to study better. To see the results of what genres of music paired with what volumes improved/deterred studying, wait for our 20-time Write Up, coming soon.

We tested the main 4 genres of music, hip-hop, pop, classical and country, against 6 different brain factors: speed of processing, memory, attention, flexibility, problem-solving, and reaction time. Speed of processing was divided into 3 subdivisions, information processing, spatial reasoning, and visualization. Flexibility was split into task switching, response inhibition, and verbal fluency. Memory was divided into working memory and recall. Attention was divided into divided attention, selective attention and field of view. Problem-solving was split into reasoning, planning, and numerical calculation.

We decided to test this experiment while also having a little fun along the way, to make our experiment more desirable to participate in. Rather than taking tests or answering questions to determine improvement of performance, we decided to play games and look at cumulative scores to see whether music helped or hurt the subject’s performance. We did this through a subscription brain games model, called Lumosity. In each game, lumosity tested a number of different factors, including the speed in which the game was completed, the accuracy and other factors for each specific game.

In order to achieve the desired results for our experiment, we had to create a plan that would not take into account the subject’s own intelligence as a factor into what improves performance. This is why we had each subject play the brain game without any music to get a baseline score. From then on, every time the subject played a game while listening to music, we recorded the difference either positive or negative from their baseline score to determine the effect that music had.

Throughout the experiment, we executed our plan nearly flawlessly, with one main difficulty. Certain subjects that were either smarter or that appreciate different kinds of music were scoring differently based on these factors. We didn’t want a subject’s personal characteristics to affect our experiment’s results, so we had to figure out a way to test the subject's without taking into account how smart they were or what music they liked. Thus, we randomized the subject pool and had different subjects play the games each time, thus there would be no bias in the experiment to people that appreciate certain kinds of music, or subjects that were just simply smarter.With different subjects testing different parts of the experiment, we got results that purely indicated what effect the music had, and not other outlying factors.

One of the things we did really well, was finish testing, quickly and effectively. With 4 genres of music at three volumes, testing 16 different subdivisions, we needed to perform nearly 200 different tests to get all the results we needed. This was not a really easy task to do, especially with the time crunch we had, along with the restraints on class time we sometimes had.

Nevertheless, we were able to test both in class and outside of class, and do not have to cut down an experiment at all. In some cases, all of the types of music improved performance, in other cases only some improved music, and music did not help in only very few of the categories. The fact is, music mostly helps improve performance, given that you listen to the right kinds of music while doing the certain activities.

During this experiment, I was able to learn multiple skills, primarily working to finish an experiment with a partner. I am generally a person who likes to get everything right, especially when doing a project and sometimes fear that others involved might screw it up. Because I wanted to get better at overall collaborative work, I decided to work with a partner for this project. This decision was quite a risk as I didn’t know what working with a partner on such a big assignment might entail.

However, Justin has been a very supportive partner, and what we both share in common is our ability to get things done in an effective and timely manner. Because we both understood the experiment very well and loved the concept behind our testing, we were always on top of our working, making sure to meet deadlines in order to finish all the testing we needed by the end of the semester. Because of this, I was able to take a backseat in some other testing and need not worry about everything getting done perfectly.

Another soft skill that I learned through this endeavor was meeting deadlines, as aforementioned. Because of the constant time crunch that we were on, and such a big experiment to complete, we needed to set deadlines for ourselves, and we needed to make sure that we met all of them despite any other circumstances. We did this for most of the project, however, sometimes we need to push our deadlines, which was manageable, mainly because of the small increments we did our testing in. Additionally, we helped each other out whenever needed, allowing us to focus on other activities as well, without being stressed out about finishing our testing.

If I had a chance to do this project again, there isn't much that I would change, mainly because our experiment went nearly flawlessly. I might want to dig a bit deeper into why the brain reacts to music in the way it does, and why certain types of music help certain areas of the brain function while others don't. For now, we were only able to use previous research and information about the brain to answer these questions at a surface level. However, to get a deeper understanding about this, we would need much more costly materials as well as much more time to analyze results better.

I learned a lot about myself while doing this project. I primarily noticed that when I am more relaxed while doing a long term project, it tends to yield more results. Further, our good organization and ability to divide the experiment and testing into small increments allowed us to both take our time while testing each part and test each part correctly and effectively. I learned the value and importance of collaboration and organization.

We have exhausted all we can do for this experiment without much more funding and knowledge. However, I am interested in doing similar projects that I find interesting and that relate to science.

Unit 9 Reflection

Unit 9 was about what on earth evolved. The very first concept we learned was about classification and evolutionary relationships. Taxonomy is the study of naming and classifying organisms, with the purpose to avoid confusion with common names. Carolus Linnaeus a Swedish botanist who live in the early 1700s originally classified all life as plant or animal and create the 7 levels of organization including the scientific name, known as the binomial nomenclature. The binomial nomenclature is a two name system to name organisms made up of the genus and species names. There are certain rules to the name process; If you discover the ograms, you name it. It must the underlined or italicizes, the genus name is capitalized and the species name is lowercased. It is based on Latin. Phylogeny is the evolutionary history and relationships of species using taxonomy The phylogenetic tree shows shared ancestry. Node,s where th branches meet, present a common ancestor. There are 7 main taxonomic levels: Kingdom, Phylum, Class, Order, Family, Genus, and Species.

The second concept we learned about was Kingdoms and Domains. Taxonomic groups go from broad to narrow are domain, kingdom, phylum, class, order, family, genus and species. There are three main domains, Archaea, Bacteria, and Eukarya. In the Eukarya domain, there are 4 main kingdoms - protista, fungi, plantae, and animalia. It is really fascinating to see that we are only 1 of the 800,000 species in the Animalia kingdom, and there are 799,999 other consumers and heterotrophs that are in the same kingdom The Archaea domain live near hydrothermal vents, hot springs, digestive tracts of animals, anoxic muds and marshes and petroleum deposits. . The protista are very diverse, while fungi are decomposers and heterotrophic, while plantae come in both vascular and nonvascular forms

Next, we learned about Bacteria and Viruses. Earth’s first organisms were likely prokaryotes, and most prokaryotes are unicellular. There are three common shapes of of bacteria, spheres (cocci), rods (bacilli) and spirals. Bacterial cell walls contain peptidoglycan, a network of sugar polymers cross linked by polypeptides. Scientists use the gram stain to classify bacteria by cell wall composition. Gram positive bacteria have simpler walls with large amount of peptidoglycan, and gram negative bacteria have less peptidoglycan and an outer membrane that can be toxic. Most mobile bacteria propel themselves by flagella scattered about the surface of concentrates at one of both engs. Chemoheterotrophs: Heterotrophic bacteria that take in organic molecules. Ex: Staphylococcus aureus in undercooked food Photoautotrophs: Use light to convert carbon dioxide and water into carbon compounds. Ex: cyanobacteria Chemoautotrophs: Use energy directly from chemical reactions involving ammonia, hydrogen sulfide, nitrites, sulfur, or iron. Obligate aerobe: Must have oxygen to survive. Ex: Tuberculosis - Mycobacterium tuberculosis Obligate anaerobes: Can not have oxygen. Botulism from canned food. Ex: Clostridium botulinum Facultative anaerobes: Alternate between oxygen and fermentation depending on change in environment.

We also learned about viruses in the same lesson. Viruses are not cells, it is a very small infectious particle consisting of nucleic acid enclosed in a  protein coat and in some cases, a membranous envelope. Viral genomes may consist of either double or single stranded DNa or double or single stranded RNA. A capsized is the protein shell that encloses the viral genome. Some viruses have membranous envelopes that help them infect hosts called viral envelopes. They are derived from the host cell’s membrane and they contain a combination of viral and host cell molecules. Once a viral genome has entered a cell, the cell begins to manufacture viral proteins. The virus makes use of host enzymes, ribosomes, tRNAs, amino acids, ATP, and molecules. Viral nucleic acid molecules and capsomeres spontaneously self-assemble into new viruses. Lytic Infection: Virus enters a cell, makes copies of itself, and causes the cell to burst. Lysogenic Infection: A virus integrates its DNA into the DNA of the host cell, and the viral genetic information replicates along with the host cell’s DNA.

Next, we learned about fungi and plants. Plants and fungi have different traits. Fungal walls are made of chitin, while plants cell walls are made of cellulose. PLants have chlorophyll and photosynthesis while fungi absorb food through hyphae. There are three main types of fungi - sac fungi, bread molds and club fungi. Fungi Can also act as mutualists - lichens form between fungi and algae while mycorrhizae form between fungi and plants. They are useful in several ways, as food, antibiotics, and as model system for molecular biology. They can also cat as pathogens, preventing human diseases including ringworm and athlete's foot, and plant diseases including Dutch elm disease. Plants, first grew at the edges of water, and evolved through natural selection. Bryophytes are the mosses, and their relatives are the seedless nonvascular plants. Pterophyta are ferns and they are seedless vascular plants. Their vascular system allows them to get off the ground resulting in more photosynthesis. Roots allow absorption of water and nutrients, while the leaves allow for more photosynthesis. Gymnosperms are cone bearing plants which their seeds in cones. The cone is the reproductive structure of most gymnosperms. There are three major phyla -  Cycads, Ginkgos and Conifers. Angiosperms are flowering plants with seeds enclosed in the fruits. It is one phylum and it is the largest in the plant kingdom. There are two major types of angiosperms, monocots and dicots.

After plants, we learned about invertebrates which make up 97 percent of all animal species. Difference in their body plants result from different in expression of Hox genes, which tell embryonic cells which body part or\to become. Animals are grouped using a variety of criteria -body plan symmetry, tissue layers and developmental patterns. Major Invertebrate phyla include sponges, phylum Porifera, cnidarians, flatworms, and mollusks. Sponges are the most primitive species of Earth and share common characteristics - they are sessile ad have no symmetry. They reproduc eboth sexuall and asecxually and their cells work together to filter feed. Flatworms have a solid body and an incomplete or absent gut, many are parasitic. Mollusks are bilateral animals and have a  complete digestive tract. Annelids have segmented bodies and a coelom. Arthropods are the most diverse of all animals and their features are highly adapted. They have an exoskeleton made of chitin, jointed appendages and segmented body parts. Arthropods also have an open circulatory system. Insects are the dominant terrestrial arthropod, they have three pairs of legs and one pair of antennae. Their body has three parts - the head thorax and abdomen. Crustaceans are a diverse group of ancient arthropods, and they share several common features. They have two distinct body sections and one pair of appendages per segment. Echinoderms are on the same evolutionary branch as vertebrates - they have radial symmetry, they have an internal skeleton and a water vascular system.

Chordates are all vertebrates and some invertebrates. An endoskeleton allows vertebrates to grow to large sizes. There are seven main classes of vertebrate chordates. Agnatha, jawless fish, chondrichthyes, cartilaginous fish with jaws, osteichthyes, bony fish with haws, amphibia, four limbed animals that can live on water and land, reptiles, lay eggs surrounded by membranes, aves, birds, and mammals, hairy animals. There are only two classes of Agnatha that still exist, lampreys and hagfish. Amphibians evolved from lobe finned fish and a number of adaptation allow them to live on land. They have large shoulders, mobile and muscular tongues, and they breathe through skin or with gills. The amniotic egg allowed vertebrates to reproduce on land. Reptiles are a diverse group of amniotes that share several characteristics - ectothermal, covered with scales, three chambered heart, and cloaca. Birds evolved from theropod dinosaurs and they share several anatomical features - hollow bones, fused collarbones and rearranged hip muscles. Mammals are the dominant terrestrial arthropod.

There are a few unanswered questions that I have. Of the many phylums, which do scientists study the most and what organisms have the best medicinal uses. I really enjoyed learning about invertebrates and I would love to learn more about them

This is my presentation for what on earth evolved. I loved the presentation as I was able to learn more about the organism and practice speaking about a topic. I could have practiced a bit more and even changed my slides to include less information so I could have talked more about the species rather than reading off the slides. I hope to do more presentations like this one in the future especially in science topics as it really helped me.

Geologic Timeline Reflection

While working on a timeline to represent the full history of earth, we were asked to reflect about our learning, and provide 3 significant events that impacted Earth's history. I found that the mass extinction during the Triassic period, also known as the End-Triassic extinction was one of the most impactful events in Earth's history. In this one mass extinction, approximately, 252 million years ago, nearly 76 percent of all marine and terrestrial species on the face of the earth were wiped out, along with over 20 percent of all taxonomic families. This event was impactful to Earth’s history primarily because it changed the dynamic of the earth. Although not all, most of the dinosaurs were wiped out, and this allowed mammals to radiate. The cause of this mass extinction is very debated by scientists, but many believe that climate change was the root cause, as some of the species were not able to adapt to the rapidly changing climate.

The second event that is really significant in Earth’s history is the Cambrian Explosion, which was when fossil records of complex animals suddenly appeared. This is considered by many as the most important evolutionary event in Earth's history as it accounted for most of the diversification of life over Earth’s history. It happened nearly 540 million years ago, and it is extremely important to Earth’s history because the diversification of life is necessary for life on Earth.

The last event that is extremely important to Earth's history was the development of cyanobacteria, as it enabled the oxygen levels on earth to rise, allowing for more complex species to live on earth. Many of the current species today rely on oxygen to produce energy and survive, and without the development of cyanobacteria most of the species that currently live on earth would not have been able to live.

Earth’s history spans approximately 4.6 billion years, and what really surprised me is how short, comparatively, humans have lived on earth. On our timeline, every million years was 2 millimeters, and humans were only on earth for barely 1 millimeter. Additionally, there were not many events earlier in earth’s whereas there are many major events happening fairly recently. This would make sense, and goes to show that evolution of earth is picking up as years go by.

Despite being on earth for such a small amount of time compared to Earth's full history, humans have managed to make a powerful impact. In our time on this planet, we have managed to take over it entirely, living on almost every part of it. Further, we have increased climate change, and constantly worsened the overall environment.

I still wonder about what happened during the early years after Earth’s formation. If nothing really happened, I wonder why the major events in Earth's history started happening so late.   

Unit 8 Reflection

Unit 8 Reflection

This unit was all about evolution. The very first concept we learned about was variation and artificial selection. Variation is any difference of traits within a population. Variation exists because of crossing over, meiosis, mutations, and sex, and it is extremely important within a species. It accounts for all the genetic differences within any species, and without any genetic diversity, all species would quickly become extinct. With no genetic variance, all species will be exactly the same, and if there was ever an event that killed one of the organisms, all of the organisms would die. We also learned about artificial selection, which is the process of humans breeding organisms together for our purposes. A perfect example of this are dogs, which are bred for different purposes. For instance, collies are bred for sheep herding, chihuahua are bred to be guard dogs and pit bulls are bred as fighting dogs.

Next, we learned about Charles Darwin and his observations and conclusions about natural selection. Charles Darwin was the scientist who discovered that evolution is caused by natural selection. He made 4 main observations on this subject: First, all sexually reproducing species have high genetic variation - variation in traits. Second, traits are always inherited from parents to their offspring. Third, all species are capable of producing more offspring than the environment can support. Fourth, Competition in any population is stiff and not all offspring can survive because of the limited food or other resources. Darwin described this competition and survival of the fittest because only the best of the species survive. From these observations, Darwin made 2 main conclusions. First, individuals how inherited traits that are favorable for their survival help them reproduce and those organisms tend to leave more offspring than other individuals. In other words, this means that there are winners and losers in this population, and the winners reproduce more. The second conclusion that Darwin made was the unequal ability of individuals to survive and reproduce will result in better traits becoming more common in the population over generations. In simpler terms, the population begins to look like the winners. Based on this, natural selection is the process of weeding out traits in a population that DO NOT help individuals survive, leaving traits that are either neutral or favorable to individuals. Natural selection causes populations to evolve over time.

In our third vodcast, we learned about gene pools and the basic concept of evolution. The gene pool is the total of all alleles in a population. Genetic variation is stored in the gene pool, and gene pools change as new allele combinations form when individuals of the population have offspring. Allele frequencies measure genetic variation. The allele frequency is how common an allele is in a population. We can determine allele frequency by adding up all alleles in a population and adding up the total of each type of allele. For each type of allele, you divide by the total, getting a decimal allele frequency. Natural selection favors certain phenotypes, and those with the better phenotypes survive and reproduce. These “winners” pass their alleles to their offspring. Evolution is a change in allele frequency over time. As natural selection favors specific phenotypes, those alleles will become more common in the population. Therefore, the population, or gene pool, evolves over time. Lethal alleles stick around by being the recessive allele in the population. In heterozygotes, that have the favorable phenotype, the recessive allele is still in their genetic makeup. Thus, because of their phenotype, natural selection favors them, however, they can still pass on their recessive allele to their offspring. This can be beneficial for populations in conditions, especially environmental conditions change.

In the fourth lesson in our unit, we learned about speciation, and where new species come from. A species is a  group of individuals that can reproduce and have fertile offspring. Speciation is the rise of 2 or more species from one existing species. This takes a long time, usually many generations. Speciation is caused by reproductive isolation. Reproductive isolation happens when a population is split into 2, and eventually, the 2 populations can’t reproduce with each other when they meet again. There are 3 main causes of speciation: behavioral isolation, temporal isolation, and geographic isolation. Behavioral isolation is caused by changes in mating behaviors or occupying different niches. Human barriers and natural barriers can also geographically isolate a population. A population may be split into two because of the formation of a mountain or a natural disaster, and if there is no gene flow between the two populations, geographic isolation occurs. The two new species will adapt to their environment and thus there is the possibility of separation. Temporal isolation happens when timing prevents reproducing between populations. Species are related based on a  common ancestor - Over a very long period of time, new species arise, and new species arise for earlier species. All these species share a common ancestor. Descendants of common ancestors have common traits. There are two patterns of speciation, gradualism and punctuated equilibrium. Gradualism happens when speciation occurs slowly, but over many generations, many new species arise. The evidence of gradualism is ancestor fossils on bottom layers when descendants fossils are on top layers with transitional pieces in between. Punctuated equilibrium happens when new species arise “suddenly.” In this scenario, speciation occurs extremely fast, usually due to sudden reproductive isolation. There are no transitional forms and there are big differences between layers.

Our fifth vodcast was all about the structural evidence to support the theory of evolution. There is a ton of developmental evidence of evolution. Embryology is the form of evidence when similar stages of embryo development suggest common ancestry. Evo-devo is the study of the evolution of developmental processes in multicellular organisms. Another compelling piece of evidence that supports evolution are fossils. Fossils form when organisms die, and they are covered in sediment, clay or ash, and does not decay. There is a fossil bias, however, to organisms with bones or shells. Unicellular, soft bodied invertebrates, plants and insects are less likely to have fossils. Fossils tell us that animals and plant forms have changed over time. Fossils also tell us that extinction is the fate of most species that have ever existed. Homologous structures are another piece of evidence. Homologous structures are the same structures used in multiple organisms for different purposes. This suggests a common ancestry. Analogous structures are kind of the opposite, when species use different structures for the same function. Covert evolution is the process where unrelated organisms evolve similarly or analogous structures. For example insect wing, bird wing and batwing are all used to help organisms fly but they all that different structures.

Our sixth lesson was about evolving populations and what factors can cause a population to evolve. Natural selection can change the distribution of traits in three main ways. Directional selection, stabilizing selection and disruptive selection. Directional selection happens when natural selection favors phenotypes at one extreme. This causes the population to begin to look like the extreme phenotype because it proves beneficial for survival. Stabilizing selection happens when natural selection favors the intermediate phenotype, and the population will thus “stabilize” on the middle phenotype. Disruptive selection happens when natural selection favors both extreme phenotypes for survival. This might cause the population to split into two because only the two extremes are beneficial for survival, and thus the intermediate phenotype will no longer exist. Although this does not guarantee speciation is could be the beginning of species. There are 5 types of change in populations, with only one being natural selection. Genetic drift happens when a random event drastically changes a population and results in a change in allele frequency. In other words, genetic drift changes allele frequencies due to chance alone. Gene flow is the movement of alleles from one population to another. Gene flow could be the prevention of speciation. Mutations produce new genetic variation that natural selection can act on, leading to evolution. The final type of change in sexual selection, which selects traits that improve mating success, but don;t help organisms survive better AT ALL.

The last lesson in our unit about evolution was on the History of life. Life formed on earth when chemical and physical processes on early Earth may have produced very simple cells through a sequence of stages: Abiotic synthesis of small organic molecules, the joining of these small molecules into macromolecules, the packaging of molecules into protocells, and the origin of self replicating molecules. Earth’s history is broken into groups of time-based on major events in the fossil record. There have been 5 mass extinctions in Earth's history and the eras of Earth history are divided by mass extinctions. The precambrian era accounts for 88 percent of Earth’s history, starting 4.6 billion years ago to 542 million years ago. In this era, the oldest fossils of prokaryotes were found, the concentration of oxygen in the atmosphere increased, and the oldest fossils of eukaryotic cells appeared. In the next era, the paleozoic era, which was 542-251 MYA, has 3 mass extinctions, and included the colonization of land by plants and animals, the diversification of vascular plants, and age of fishes and amphibians, the origin of reptiles, the radiation of reptiles, and the origin of insects. The next era, the mesozoic era was from 251-65.6 MYA, and was the age of reptiles. The last era the cenozoic era is the current era we are in, starting from 65.6 MYA. The mammals have got the upper hand in this era.

Personally, I enjoyed this unit probably more than any another unit so far, because of the way in which the material was taught. Through main interactive labs and analysis, I was able to understand all the concepts while still being able to apply the concepts to real-world examples. My favorite lab all year has been the hunger games lab, in which we simulated natural selection by competing for food. It was clear the population began to look like the most beneficial phenotype, and this lab helped me understand Darwin's two conclusions. The analysis for this lab can be found here.

This is one the units that I found most interesting, but I really wanted to learn more about the history of life and what caused some of the mass extinctions, and the process in which organisms rebounded from those mass extinctions. How did the mass extinctions happen and did the way it happens give certain types of organisms an upper hand in the next era of earth. What caused the rise and fall of certain species and how exactly those species contributed to the rise and fall of new species? These are all unanswered questions I have, and evolution is a topic that I really want to learn more about.

Throughout this unit, I feel that I have really grown as a student, especially becoming more assertive. The main principle that I learned the last unit that I have strived to follow in this unit was to fake it until you make it. Throughout our projects in this unit, I have always tried to take on a leadership role, making sure that everything ran smoothly, and everybody was doing something at all times. However, I still need to make sure that everyone is enjoying what they are doing, trying to make everything a win-win situation like any assertive person does.

Hunger Games Lab Analysis

1. In the Hunger Games lab, we learned about how natural selection acts on beneficial and harmful traits in a population. There were three main phenotypes, stumpys, knucklers, and pinchers. The pinchers had to pick up food with their index and thumb fingers, the knucklers had to pick up food with their knuckles and the stumpys had to pick up food with their wrists. Each of these organisms had to pick up food with their given traits, and thus, it simulated natural selection.

2. The phenotype that was best at capturing were the pinchers, as their method of getting the food was the most effective not only because it was the quickest, but it also ensured that you could pick up multiple pieces of food at once. This is shown in evidence as in each generation, there were always more pinchers that survived to produce offspring than any other species. This was also the reason that the A allele was the prominent allele, as the genotype of pinchers was AA.

3. In this lab experiment, populations evolved in every generation. Never were there the same number of organisms in two consecutive generations, or in any two generations at all. Evolution is a change in allele frequency and since in every year there was a change in allele frequency compared to the previous year, evolution occurred. The graph of the allele frequency is shown below: The blue line represents the frequency of the "A" allele, while the green line represents the frequency of the "a" allele. As you can see, both started out at a similar frequency, but because the "A" was a beneficial trait, while the "a" was a harmful trait, the "A" allele became more common throughout the experiment and was always more common that the "a" allele.

4. In this lab there were many factors that affected the evolution of the population - some were random, while others were not random. Generally, in nature, the distribution of food occurs randomly, however, in this experiment, Mr. Orre distributed the food in different ways every year. This stimulated the randomness of food distribution in nature and thus affected our results. For example, if a pile of food was placed in front of a stumpy, the stumpy would be more likely to succeed in getting more food, thus have a better chance at survival, which leads to an opportunity to reproduce, and thus they would have a chance to pass on their traits, despite their unhelpful traits, solely because of the random food placement in nature. Another factor that affected the evolution of the population was the reproduction and mating between species. This was a factor that was not random and purely chosen, just like it is chosen in nature. In this lab, we stimulated sexual reproduction by choosing a mate and tossing a coin up to see what would be the genotype of the offspring.

5. If the food in the experiment was larger, it would have given the stumpys an advantage when searching for food. Knucklers and pinchers had the advantage in the lab, solely because their method of collecting food was quick and effective because the food could fit in their knucklers and fingers respectively. However, if the food was larger, it might not have been able to be picked up by knucklers or pinchers, and thus would have given the stumpys an advantage, as the wrist can grab larger food amounts. On the other hand, if the food was smaller it would be the complete opposite. The trend in the phenotype and genotype would continue, and it would favor knucklers and pinchers even more than in the status quo. The stumpys struggled to pick up the food in the lab because it was too small, if the food was made smaller, the stumpys might not have survived while the pinchers and knucklers would be able to use their effective collecting method to collect for more. This is like what may happen in nature, as many different organisms might have trouble picking up food in certain sizes. If this is the case, the population will quickly begin to look like the organisms who had the favorable and beneficial traits.

6. If there was not incomplete dominance the results would have varied. If all knucklers had been either pinchers or stumpys the pinchers would have evolved much quicker, and the stumpys would not have been able to rebound from extinction. Because of the knucklers recessive allele, it was possible for them to mate with each other and produce a stumpy, because they had the "a" allele. However, if this did not happen, by the end of the experiment, the only allele in the population would have been pinchers, and the extinction of the stumpys would have happened much quicker.

7. Natural selection is the process when nature chooses which traits of an organism gets passed on to the next generation. If traits are favorable to an organism and help them survive in nature, then those organisms with the favorable traits are more likely to be passed onto the next generation. This leads to the species looking more like the favorable traits as those are the traits that are constantly passed on. Because those are the traits that are passed on, there is a change in the allele frequency of the gene pool, as less and less of the unfavorable traits are being passed onto the next generation, and more and more of the beneficial traits are being passed on. Because of this change in allele frequency, evolution occurs.

8. In the experiment, the stumpys could work amongst themselves, and sometimes with the knucklers to help their population rebound from extinction because of the recessive alleles in knucklers. The stumpys adopted a mindset to band together as a group and succeed, like what we see in nature when herds work together to improve the chance of survival for everyone in the herd. This behavior affected the allele frequency of the population because it allowed for more “a” allele to be passed onto the following generations. We see constantly in nature this happening, as groups of organisms always try to do what's best for their organisms and their species, like what we humans call "family."

9. In evolution, the gene pool and the population evolve. The population evolves by a change in allele frequency, also known as a change in the amount of any allele in the gene pool. This causes the entire population to begin to adopt similar traits that are beneficial for survival. Natural selection acts purely on the phenotype of an organism because the phenotype is the only one that can determine an organism's chance of survival in a population. In nature, the genotype is never seena, and thus cannot affect ad organism's survival. For example, if a chameleon needs an "A" allele to catalogue, both the Aa and AA organisms will have the same chance of survival, because they are both able to camouflage in nature, something that the ones with aa can't do. It did not matter that the Aa organisms had one recessive allege their dominant allele - phenotype, allowed them to survive.

10. I still have some unanswered questions about the food distribution. I understand that in nature food is distributed randomly, but I am extremely intrigued to find out how food is placed and what factors might affect this. Also, are organisms with favorable traits, generally closer to the food supply because of those favorable traits?

Unit 7 Reflection

Unit 7 was all about ecology. Through vodcasts, class discussions and textbook reading, we learned about the main themes and concepts of ecology. We started the units with the main basics of ecology, talking about habitats, niches, biotic and abiotic factors. Habitats include all aspects of the area in which an organism lives, including all abiotic and biotic factors, while niches include all the factors a species needs to survive, stay healthy, and reproduce. Biotic factors are like plants animals, fungi, and bacteria, while abiotic factors are air, temperature, light, soil, etc. We also discussed the levels of ecosystem organization, starting with organisms, going a population, to a community, to an ecosystem. to a biome, then to a biosphere.

Next, we learned about food chains and food webs. Producers, or autotrophs, provide energy for themselves and make their own food from abiotic factors, and consumers, or heterotrophs, get their energy by eating other living or once-living resources. A food chain is a linear network of links that come from a food web. A food web is a diagram that shows energy transfer between different organisms in an ecosystem. The arrows on a food web point to where the energy is going. We also learned about trophic levels, which are levels in a food chain based on what organisms eat. There are five main trophic levels: Quaternary consumer, tertiary consumer, secondary consumer, primary consumer, and primary producer.

We also learned about ecosystem energy, and how the energy that is available in an ecosystem affects the populations at different trophic levels. Interestingly, only 10 percent of the energy that is produced at each level is passed on to the next level. 90 percent of the energy is lost as waste, heat, feces, etc. The way to show this transfer of energy between different trophic levels is through energy pyramids. Energy, which originates from the sun, is passed from producers up the food chain to top-level consumers.

Our next main concept in the unit, and the one that I found the most interesting was ecosystem recycling. We learned about how different cycles contribute to the stability and health of ecosystems. Ecological succession is the sequence of community and ecosystem changes after a disturbance. The order of succession begins with pioneer species after the incident, moving on to intermediate species, then to a climax. There are 4 main nutrient cycles. The water cycle, which consists of the processes of evaporation, transpiration, condensation, precipitation, and movement through surface groundwater. The carbon cycle moves carbon from the atmosphere, through the food web and returns to the atmosphere. Both the nitrogen and phosphorous cycle are also essential to life.

One of the last concepts we learned in our unit was about ecosystem health, and why ecosystem health is extremely important not only for animals and other species but for humans as well. Healthy ecosystems have large populations of tertiary and quaternary consumers and diverse communities of producers and decomposers. Healthy ecosystems also have high biodiversity, includes genetic diversity, species diversity, and ecosystem diversity. In the United States, 25 percent of prescriptions contain substances originally derived from plants, thus overall ecosystem health is important for human life. There are 4 main causes of species loss. Habitat Destruction, Introduced/exotic species, overexploitation, and change in climate.

I really wanted to learn more about the benefits and costs of having great biodiversity on our planet. We had an ecosystem health vodcast about it, and I was extremely intrigued. I found it fascinating that 25 percent of all prescriptions that are made in the United States contain substances that are originally derived from plants. Not only that, I did some research fo my own and found that plants are used in other medical situations as well, and are not just limited to prescriptions. Plants are currently being used to help treat diabetes and cancer, and are likely to be one of the main ingredients if we were to come up with a cancer cure.

Throughout our unit, we did a conservation biologist project, in which we, as groups, set out to solve the major problem treating a particular biome or ecosystem. Our group took on the task of fixing the root causes behind the Great Pacific Garbage Patch. Collaboration is our group was nearly flawless, as each group member not only did his work but helped others whenever he/she could. Working as such an on-task, and effective group, allowed us to finish our work swiftly with little problems. Nearly everything went well, and I learned as long as everyone in the group knows their role and tries their best to execute their part, the group should do great.

Great Pacific Garbage Patch

Unit 6 Reflection

This Unit in our Biology class was all about biotechnology. This unit was probably the best unit we've done this year, and by far, the one I found the most fun. It was particularly interesting because of the rapid developments of biotechnology currently happening around the world. For example, in an article I read for one of our assignments, I learned that a company called Pembient is attempting to help stop animal trafficking - starting with one of the most lucrative poaching markets, especially in Asia - Rhino Horns. The article explained that rhino horns contain the exact same materials as the hair fibers and nails of humans, and thus Pembient is creating genetically identical duplicates of these rhino horns. These duplicates come in at around 20 percent of the cost, with higher quality, and less risk of transmitted disease, and thus will take the poachers out of business extremely quickly. Furthermore, this new rhino horn made by Pembient, is in large supply, and thus Pembient is teaming up with beer and other alcohol companies to use these genetically identical rhino horns to make hangover cures. 

We started of our unit by learning the basics of biotechnology. Biotech in is simplest form is just the manipulation of living things, including their cells, tissues or organs, to benefit humankind. Biotech generally focuses on the understanding of genetics, proteomics, and genomics. The 4 main applications, or domains, of biotechnology are industrial and environmental biotechnology, medical and pharmaceutical biotech, agricultural biotech, and diagnostic biotech. 

We continued to learn about the technologies of biotechnology, such as the polymerase chain reaction, or PCR, gel electrophoresis, and sequencing. PCR is a procedure to amplify a specific region of DNA, and it yields millions of copies of a sequence. Gel electrophoresis is a method using electricity to separate DNA fragments based on length. Larger pieces travel slower than smaller pieces through the gel - and after using a known fragment length as a ruler, we can determine the exact length of the unknown fragments. The last main tech used in Biotech, is sequencing, which is used to determine the exact sequence, or order, of a given DNA strand. Each copy of the sequence is one base longer and contains a florescent dye attached to it. 

Next, and probably most importantly we learned about recombinant DNA - which is basically inserting DNA of one organism into DNA of another organism and is often called genetic engineering. The result of recombinant DNA is a transgenic organism or GMO. Restriction enzymes are an essential part of any recombinant DNA - restriction enzymes are enzymes that cut DNA whenever it reads a specific sequence. 

The last main ideas we learned in this unit was about bioethics - something that has really come into the limelight over the last decade - with technology rapidly advancing. There will always be two sides of any arguments, and this vodcast helped me understand which path to take, by using my values and morals to make these decisions. In the vodcast, we learned a mature, easy way to handle these sorts of bioethical decisions, and just ethical decisions in general. The first step is to clarify the values at hand pertaining to the ethical dilemma, then you must identify the problem or issue and why it is a problem or issue. Once doing this, you move on to the crucial step of exploring all alternatives and other solutions. Once you complete that step, and are not able to find a better alternative, you must identify the pros and cons of adopting to the solution, or each of the multiple solutions.

We did multiple labs in this unit, my favorite probably being the pGLO lab. Find a pic from the lab below: 

Another one of the labs that we did in this unit, was the candy electrophoresis lab, in which we got DNA fragments from different candies and ran them through gel to compare their lengths:

I learned a lot from the 2 labs pictures above, not only content and concept wise, but also in another way. I learned that I must follow directions carefully, especially in high level labs. In the candy electrophoresis lab, I was forced to check the directions after every step, because of the complexity of the project. In my unit 5 reflection, which can be found here, I vowed to improve my group work habits, and to try to become a better group mate, helping people out whenever they do not understand something, as well as making sure that our entire group is constantly on the same page. I feel that this semester, has been much better for me in this regard, as my group has been able to finish labs constantly working together in an amazing way. We could all make sure that each other had the right idea in mind, and any confusion was swiftly solved and our group would not move on, even if one of us had a shadow of a doubt about the next step.

This brings me to my strengths and weaknesses of this unit. I feel like my main strength in this unit was me and my group's success and understanding of all the lab content. We could flawlessly work together with rarely any disagreements, and we were all able to come out with a pure understanding of the concepts, something that I could not say for previous units, or previous groups. Just minor changes in my group dynamic, really helped solve many of the problems I had misunderstandings from in previous units - it just shows you how important the people you associate with yourself are - the adage goes, "A man is only as good as the company he keeps."

My main weakness in this vodcast, in my opinion was interpretation of data and understanding of some lab questions. Especially in the pGLO lab I misunderstood one of the blog questions about bacteria, confusing during what time the question was asked about, and I received a completely different answer than those of my group mates. I also at first found the arabinose and ampicillin a bit confusing and hard to distinguish between what does what, and to what extent, however, at the end of the unit I could clear up all my questions and make sure that I go into the unit test with an exceptional understanding of all the concepts.

I really wanted to learn more about current biotech developments and what type of technology we could see soon. How close are we to genetically modifying people? How close are we to making sure that no one will ever get disease? Furthermore, I wanted to have a bioethical debate about some of these questions and about some of the current uses of biotechnology in our world. For example, we could debate whether removing disease for everyone in the world is a good thing, or is it a bad thing because it messes with the natural selection of our world.  

Earlier this semester, I made a News Years Goals post, talking about the two main goals that I wanted to strive toward accomplishing over this semester. My first goal being to better improve my time management, and I have seen a drastic increase over the past month. I organized all my activities into one calendar, and I am now able to see whenever a conflict presents itself and make sure to plan with all parties involved well in advance. I have been able to juggle, speech and debate, mock trial, basketball, boy scouts and schoolwork, primarily because of my new time management approach.

My second main goal for this year was wot more effectively improve my studying habits for assessments by learning what type of studying work for me and better implementing them into by regular studying routine. I have started to make progress to this goal by using the VARK questionnaire as well as other platforms to find out that I am a visual and reading learner and thus I have really improved my test scores. Last semester, in some of my classes, my test scores were the category pulling my overall grade down, and this semester, because of the changes I made, I feel as if the test scores category is the one that is holding my grades together. I hope both these tends continues and stay tuned for more updates in future blog posts.

pGLO Lab Write Up

pGLO Observations , Data Recording & Analysis


1. Obtain your team plates. Observe your set of “+pGLO” plates under room light and with UV light. Record numbers of colonies and color of colonies. Fill in the table below.

Plate	Number of Colonies	Color of Colonies under Translucent Room Light	Color of Colonies under UV Light
- pGLO LB	1 large colony	Gray	Gray
- pGLO LB/amp	0	N/A	N/A
+ pGLO LB/amp	Approximately 80	White	White
+ pGLO LB/amp/ara	Approximately 50	White	Green

2.  What two new traits do your transformed bacteria have?

Our new, transformed bacteria, are now resistant to ampicillin, and they glow green (as shown in the picture above) in the prescence of arabinose sugars.

3.  Estimate how many bacteria were in the 100 uL of bacteria that you spread on each plate. Explain your logic.

An Escherichia coli cell (a single bacteria) has a volume of approximately 1 micrometer cubed. And there are 1,000,000,000 (1e9) cubic micrometers (e-coli cells) in one micro litter. Thus, if the plate is 100 micro liters, there are 1e9 * 100 bacteria on the plate. 

There arer 100,000,000,000 - 100 trillion bacteria in the 100 micro liters on the plate.  

4.  What is the role of arabinose in the plates?

The arabinose is a sugar that triggers a fluroscent green dye in the bacteria that makes the bacteria glow green.

5.  List and briefly explain three current uses for GFP (green fluorescent protein) in research or applied science.

Green fluorescent protein can be used to make transgenic pets. For example, in a french laboratory, Alba, a green-fluorescent rabbit was created using GFP.  This could be used for to save animals, like rats, by making them easier to see, on roads and freeways. 

GFP can also be sued for macro-photography. For example, the spread of virus infections can be tracked by using GFP.  This could help us stop contagious diseases from spreading.

GFP can also serve as a reporter gene, which attaches to a sequence of another gene. GFP can be heritable, and thus allowing for long term studies.

6.  Give an example of another application of genetic engineering.

One example of genetic engineering is how dragonflies are currently being genetically engineered to become cybernetic drones, for surveillance. This could be really helpful for intelligence gathering operations, and it also has other uses.