Letter to Biology Student

To whom this may concern;

My name is Shiv Paul Gupta, and when I first started 9th grade, I was 13 years old. I loved history and Spanish. I also enjoy wrestling, basketball, soccer, speech and debate, and reading science fiction. As a freshman, I took Geometry Enriched, English 9, World Geography and Health/Driver's Ed, Spanish 2, PE/wreslting, and this biology class. In general, I approach school like it is my one and only mission. As a teenager who lives in the bubble of Saratoga, I don't have many responsibilities, unlike my parents. Doing well in school is my one job, and I pride myself in my work. I strive for all A's and learning the material. It does not matter if I don't like it or if I don't want to do it. I have to.  The first day of Mr. Orre's class was a mystery to me. I did not know what to expect, but he jumped straight into biology. He explained how his class worked, what he expected, which was a mature student who listened the first time he or she is told, and he especially wanted us to learn. He made it clear that the grade was not his priority, nor should it be ours. He cares more about actual learning and growth.

Like I just said, Mr. Orre's most significant expectations are actually learning, listening the first time, and following deadlines. He runs his class similar to a college course. When we first walk into class, we sit down in assigned seats and then look at the corner board. There, we have the agenda, the essentials for the unit, and the DO NOW. This is a short answer question based on the previous night's vodcast. There is usually one everyday excluding days with large labs. Mr. Orre holds a flipped classroom. This means that you watch online lectures, or vodcasts, as homework and we expand on the lectures or learn more during class. Our class time consists of in class projects, labs, or other activities. The homework is a vodcast every night. The tests and quizzes are out of both the textbook and the vodcasts. It is essential for you to read the textbook as your chances of success go down dramatically. Many problems come from the textbook. One major part of this class is your notebook. You must keep it organized and up to date in order to succeed in the class. There are routine checks after every unit, and there must be every single component otherwise you lose all points in the category of the check. Our biology blog is the journal of the year. We write down lab reflections, unit reflections, and project reflections. Every major event that happens in the class is put on that blog. The blog improves exponentially because you get a grasp on what happens and what you are supposed to do overtime, along with your writing improving. This was my favorite reflection because it covered evolution, my favorite unit: http://shivpaulgupta.blogspot.com/2017/05/unit-9-reflection.html
Over the course of this year, I matured as a student because I had to stay within the boundaries of this class with no room to move. I learned to stick to the rubric or what I am supposed to do and then finish it. The only project I got to do on my own and really express myself was the 20Time, which was our project to control.

Mr. Orre's biggest pet peeve is not putting things away after a lab. One time, someone broke a test tube on a chair but she didn't clean it up. Mr. Orre exploded because it was an extreme safety hazard. After another lab, one group forgot to put the microscope away, and that sent Mr. Orre to the moon and back. We had to write a 500 word essay on the dangers of a lab environment. In order to get a good grade in the class, you must do everything Canvas says. You must also follow Mr. Orre's instructions to the letter. Straying off course the slightest bit will cost you greatly. Homework is essential to earning a good grade in the class as it makes up 35% of the total grade. In order to get a good grade on tests, you must find a smart way to study. It is all about how you learn. Studying smart is more important that studying hard. In order to get the most possible out of this class, you must watch all the vodcasts and read the textbook. The textbook is your best friend in this class. The final is all off the textbook. I have made many mistakes in this class. One was not putting everything away during a lab, and that caused everyone 5 extra minutes after school ended. I learned to be more careful about everything I do in wherever  I go and to put things back where I found them. Another mistake I made was bad-mouthing Mr. Orre while changing for PE. After I finished, and my friends and I walked out, he opened the door for us and said "It is really easy to hear in the locker rooms...". This mistake made me think about everything I do carefully before I do it.

In general, this class is a class. That is it. It is not fun. It is for learning and maturing. I did not like the class in terms of looking forward to going, but I enjoyed what I got out of the class. Next year,  I am taking chemistry honors. I am taking this class for the honors credit. I don't necessarily love science but I feel I will enjoy chemistry more than biology, mostly because it is more hands on. This class is a class of growth and reflection. It is not a fun class but a class that will help you greatly in the future.

Pig Dissection Reflection

Last week, we dissected a fetal pig. We received a male pig, that was about 38 cm long. The purpose of this lab was to apply what we learned in the past two units. We actually saw the evolutionary components that we learned about. We saw what made us the latest evolutionary piece. We saw the lungs, the 4 chambered heart, and many other body parts that made humans humans. Our vodcasts in the physiology unit that we focused on during the dissection included the digestive, the respiratory, the circulatory, and the endocrine systems. There is a major difference between learning about evolution with a vodcast and probing around and feeling the parts.

My favorite part of the dissection was the probing of the inside. I felt a weird satisfaction when I snapped the ribs in half and then scraping out the connective tissue. Although satisfying, the most interesting things was seeing the inside of the pig and then discovering things like the diaphragm and the kidneys.

Here is the link to our Pig Dissection Vodcast: https://www.youtube.com/watch?v=jLEIk-TFP18&t=1s

20 Time Reflection

When Mr. Orre first mentioned 20 time to me, I sighed with despair. I was practically done with large projects. When I read the guidelines, I just thought it was gonna be a boring assignment that would take up 20% of class time. However, I soon realized that I am gonna do this whether I like it or not, so I might as do something worth my time. That is when I teamed up with Joelle and we started thinking. Our first idea was surrounding phobias and dreams. However, we got the feeling that the idea would turn into a research project. That is when Jayne came to Joelle and asked to be her partner. At the time Alex was also looking for a partner, which is when we decided to switch. That is when I birthed the idea of a cancer awareness project. This was not going to be an average cancer awareness project, but one that is less common but more lethal, the EGFR NSCLC. 

As I have said in my previous blog posts, my grandfather was diagnosed with the epidermal growth factor receptor mutation of the non-small cell lung cancer about 12 years ago. He defeated the cancer, or so he thought. About a year ago, it resurfaced, but it grew more advanced. We used two types of chemo drugs, but this mutation grew resistant to both medications. The mutation, Alex and I found out, is a new discovery in the field of lung cancer, but it is one of the most deadly. The mutation is becoming more common, and it is occurring without a cure or survival rate. This is the reason we wanted to spread awareness. The best word to describe cancer is "bastard". Our goal is to change that.

Alex and I had a very rough outline on what our plan was. The first part of the plan was getting in contact with Dr. Heather Wakelee, the head of oncology at Stanford. This was the toughest part of the whole process as she is probably the busiest person I know. She oversees every single patient in the oncology department. It was easy to contact her through email, but we wanted to get a conference call with her to ask her suggestions for where exactly the money should go and how. Once we got in contact with her and held the conference call, it was rather smooth sailing. She recommended that we donate the money to Max Dienh, the head of a research team exploring the resistance of the mutation through blood work. We took this advice and started our campaign on gofundme. After creating the basic fundraiser, we began sharing it witch everyone we knew. We went on every social media form we knew including Facebook, Instagram, Twitter and Snapchat. We even reached out to celebrities hoping we could gain popularity or start a trend. Our end goal was about $5000, but we knew this would not be reached and expected about $1000. In the first week, we raised about $500, which was a great start, but then nothing happened. To this day we have only raised $500, and achieved only about 25 shares.

Although the fundraiser was not what we had hoped, it was a great experience because I learned more about time-management and work ethic. Time management was a weakness because it took us about a month to schedule a conference call with Dr. Wakelee, and that scared us as the deadline crept up on us.

We finished what wanted to and met the deadline, but this will hopefully become a long-term project and maybe even a club at school. I am very interested now about the topic of fighting the mutation and I am also very enthralled in the subject. I have not stopped the fundraiser, but I will do so once we reach our goal. The greatest thing I learned about myself is that I underestimate my abilities. When I first thought of the idea, I thought this would be too much for me to handle and recruited Alex, but as we worked on the project, I realized I could have easily done this by myself and I would have felt more accomplished at the end. I think I can make this small project into a large movement or club.

Unit 9 Reflection

In the past two units, we zoomed out of the microscopic view of what we had previously learned. We first focused on ecology. This unit, we learned about Earth's animal population, its evolution, and taxonomy. Along with the traditional vodcasts and notes, we were tasked with a small presentation on a certain animal. This presentation was almost stress-relieving because it was a project, but we had the power to choose what we wanted to put. We did not have any other labs or projects.

https://docs.google.com/presentation/d/1MBv4B7VQrq3Jxy0raEQ_UJpPckNFZYN5mk-YhTZWI3E/edit?usp=sharing

Taxonomy is the naming and classifying of organisms. This study and classification was created to avoid confusion, as the same organisms have many different names and descriptions in different environments of the world. It was created by Carolus Linnaeus, a Swedish botanist in the early 1700s. He created the seven levels of organization with proper classification and the binomial nomenclature system. Phylogeny is the evolutionary history and relationships of species using taxonomy. It is represented using a phylogenetic tree. In the phylogenetic tree are the levels of taxonomy: Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species.
https://upload.wikimedia.org/wikipedia/commons/7/70/Phylogenetic_tree.svg

Then we jumped into the Kingdoms and Domains. There are three domains in taxonomy, and those are the Archaea, Bacteria, and the Eukarya. Inside these three domains there are four kingdoms, the Protista, the Fungi, the Plantae, and the Animalia. The Protista is is very broad and considered the junk drawer, where all the hybrids and mismatches go. The Fungi's defining characteristic is that the kingdom is filled with decomposers. The Plantae kingdom's defining characteristic is that they all photosynthesize. Animalia's defining characteristic is that they are only heterotrophic.

Bacteria and Viruses were the first "animals" we looked at. Bacteria have been that 1% of all species that survive the test of time and have been alive for billions of years. The are about 1/2 a micrometer. They also have cell walls made up of peptidoglycan, which is a network of sugar polymers cross-lined by polypeptides. They move using the flagella, which spirals around forcing movement. Bacteria is important because they are decomposers, nitrogen fixers, and they help in the biotech industry. Viruses are considered nonliving. They latch onto a host cell and take over all machinery. Once a viral genome has entered the cell, the cell begins to manufacture viral proteins. The virus either uses the cell and then kills it, a lytic infection, or it uses it to make copies of the virus, and keeps it alive, a lysogenic.

Fungi used to be considered plants, but they are very different. Once main difference is that plant cell walls are made up of cellulose while fungi cell walls are made up of chitin. Fungi don't photosynthesize either. Fungi are useful for food, medicine, model systems, etc. However they can also be pathogens causing ringworm or athlete's foot, and also Dutch elm. Plants used to be water-dwelling organisms only, but they slowly evolved to land, which gave them a great advantage because they could now reproduce easier and less competition. Cuticles allowed plants to stay hydrated on land, and a vascular system allowed plants to grow off the ground. There are two majors types of angiosperms: monocots and dicots. Monocots have leaf veins that are parallel, have flowers in multiples of 3, and have a bundle of vascular tissue scattered in the stem. Dicots have netlike leaf veins, have flower parts in multiples of 4, and have bundles of vascular tissue in rings of stem.

http://images.wisegeek.com/leaf-diagram.jpg

Invertebrates are diploid and usually reproduces sexually. Most animals have HOX genes, which control early development. They tell the body what to do, when to do it, and how. Instead of talking about every class, I will choose the most significant and explains why. Sponges (Porifera) were the earliest with specialized cells but no tissues. They are immobile and can repoduce sexually and asexually. The Cnidaria phylum has the oldest existing animals, such as jellyfish, sea anemones, coral, hydra, and box jellies. Annelida have segmented bodies, and they have a coelom, which is a fluid-filled space completely surrounded by muscle. The arthropods share many highly adapted features such as chitiin, jointed apendages, and segmented bodies. It is split into 5 groups - the trilobites, the crustaceans, the chelicerates, the insects, and the myriapods. Crustaceans are very diverse and have 2 distinct body sections, a cephalothorax and an abdomen. They also have a pair of appendages per segment. Echinoderms are on the same evolutionary branch as the vertebrates. They have radial symmetry, and use a series of water-filled canals to move around. They also have a complete digestive system. The classes in this reflection are significant because they highlight the evolution of invertebrates in the increasing complexity of the organisms. We first talked about sponges who were filter feeders and weren't even made up of tissues, and then we went all the way to echinoderms, who have a very advanced form of movement along with a complete digestive system. The annelids and mollusks were the middle stages, as we could see the formation of a digestive system.

The Chordata phylum includes all vertebrates. The first is the jawless fish, the Agnatha. These were the first recognizable vertebrates. However, these gave way to the condricthyes and the osteicthyes. These fish had a skeleton made of cartilage or a full bony skeleton, respectively. They also had gills which was huge as it made breathing much more efficient and easier. The last of the aquatic only vertebrates were the lobe-finned fish. These had a pair of pectoral and pelvic fins that were round. They were not as maneuverable, but they could support their own weight, which allowed for adventures onto the shore. The final step to land was the class of Amphibians. They evolved from lobe-finned fish and were tetrapods.  They breathe through their skin, and can lay eggs on both land and in water. Along with the evolution onto land, there came major adaption for reproductive systems. The amniotic egg is a completely waterproof container that holds the embryo and keeps it safe. All amniotes have 2 circuits of blood vessels. The class Reptilia share characteristics such as having a 3 chambered heart, being covered with dry scales, and being an ecotherm. Class Aves are birds that evolved from theropod dinosaurs. They have hollow bones and fused collar bones for flight. These major adaptions allowed for flight. Lastly, the class Mammalia share characteristics such as hair to retain heat, mammary glands, a middle ear, and chewing jaw.

This unit is very tough as we need to not only memorize the taxonomy but also understand the defining characteristics. This is because there is overlap, and you must be able to differentiate. This unit reminded me of the mitosis and meiosis unit because that unit was the hardest for the first semester. We had to memorize, understand, and differentiate for that unit as well.
This was that unit review http://shivpaulgupta.blogspot.com/2016/11/unit-4-reflection.html

Geologic Timeline Individual Reflection

The first of the three major events that occurred is the formation of Earth. This is considered a major event because this is where it all started. There is not much evidence necessary for both an obvious and a significant event. The earth was created 4.6 billion years ago by the collision of dust particles until this grew into a planet. The creation of Earth is what allowed this all to happen. It is why I am able to type this reflection, and why you are able to teach me at all, let alone about the event. The second event we will be focusing on is the Cambrian Explosion. This was a sudden and rapid growth of a variety of organisms. The Cambrian Explosion is important because it was the start of many animal groups according to fossil records. This means that without the Cambrian Explosion, many of the life forms we have today would not exist. Finally, the end of the Cretaceous Period. The end of the period was brought by a mass extinction, which was caused by an asteroid about 6 miles in diameter. The mass extinction not only rid the Earth of about 3/4 of it's life, but it also opened the door to mammals. Before the extinction, dinosaurs ruled the land and only small mammals could survive in the beasts' shadow. However, the small mammals were some of the few that survived the collision, which allowed for evolution into larger mammals, and eventually us. These three major events all lead to the creation of mankind.

In our geologic timescale, 1 million years was represented by 2mm. When we first looked at this, we thought that we were going to have trouble measuring such small measurements. However, after we calculated the length of the each period, we discovered that the measurements would not be as terrible as I thought. What surprised me is the amount of time Earth went without any life at all, and then still took time for the Cambrian explosion to take place. What also surprises me is that such small events like asteroids colliding during the formation of Earth could change the course of the planet so greatly. Just imagine if an asteroid hit Earth during formation "the wrong way" or another hit causing a mass extinction. There would be a high chance we would not be here or Earth as we know it would not exist. It is beyond interesting just thinking about how perfect Earth is.

Human impacts on Earth have been great for humans. We have made life luxurious for ourselves. We have technology. No other known species has technology, let alone to our complexity and ability. However, in the perspective of nature and Earth, we are equivalent to the devil. We have taken from Earth and its resources without giving back. Humans have ruined Earth. It is a terrible reality, and there is always talk of changing, but there is no solution for years. Yes there are Teslas and solar energy, but that is lest than half a percent of what we need. Some scientists say we are already beyond the point of return.

I don't have any questions. I understood this unit and project rather well. The only thing is that there is so much to think about. Like I said previously, there were so many possibilities for Earth's life and path. How did Earth become what it is today? What stopped another asteroid from hitting Earth or falling into its orbit and becoming a second moon?

I couldn't get any quality photos of my own timeline, so I will post a photo of a geologic time scale in general.
      

Unit 8 Reflection

This unit was all about Evolution. We were first introduced to the unit with a vodcast on artificial selection, and in my opinion, it is summed up in one sentence: Artificial selection is survival of the fittest based on skewed criteria, which is based on human needs or desires.  This breed is a product of artificial selection to improve its speed and look.
 We were then introduced to Darwin, who laid down the foundation of the study of evolution. Darwin made observations and then conclusions which allowed future scientists to make the progress they have made. We then learned about evolution, specifically natural selection and the gene pool. Like we know, natural selection is survival of the fittest, and the gene pool is what the population is made up of. However, the most significant topic is what evolution is. Evolution is a change in allele frequency. Speciation is literally the process of creating two species. It is the visual effect of evolution. It is when two populations of the same species grow beyond capable of interbreeding with each other. In other words, they have become 2 new species from that one original. After we leaned what evolution was, we learned about the proof that evolution was true. We learned about embryology, evo-devo, vestigial structures, fossils, analogous/homologous structures, and convergent evolution. Out of all of these processes, the strongest evidence we have in support of evolution is vestigial structures. It is literally visible proof of how populations are in the midst of evolving beyond the use of some bone. However, the evolution has not completely occurred, which is why the structures still show up in some organisms only. The weakest evidence we have, in my opinion, is fossils. Although fossils tell a story, it is too easy to miss a chunk of information/history because one year or one generation didn't fossilize correctly or completely. Evolving populations was all about the types of evolution that occur. There are 5 main types: natural selection, sexual selection, mutations, genetic drift, and gene flow. However, gene flow stops evolution from occurring, as it is the movement of organisms between populations. This means that the organisms still breed with each other and speciation does not occur. The most interesting one is genetic drift. It is when an unexpected disaster strikes and put a dent in a species' population. This also leaves who survives up to chance, so it is not always that the superior trait with survive. We lastly learned about the history of life on earth. This was an interesting vodcast, because even though we learn about the eras in every science class, this is the first time I learned about and RNA based world. I did not realize how important RNA was. I though it was simply RNA, but I would have never guessed it would help create the world we live in so dramatically. 
In the middle of learning all of this, we did a couple of fun labs. We did the bird beak one which showed the best bird beak out of a spoon, scissors, tweezers, and a binder clips. It was obviously the tweezers. However, the best lab was the Hunger Games Lab. This lab really made evolution of a population clear. The population grew, shrunk, changed in allele frequency, and many other things. This was also the most fun lab.

The only question I have left is: Where do the new alleles come from in the first place? I understand the original, and how evolution occurs, but where does that new or different allele in the allele frequency change come to be?

I really enjoyed this unit because I am very intersested in evolution and animals. I love studying about what once ruled the planet and what happened. In my opinion, this was my best unit yet on understanding the concepts and participating in class. I was active every class and was doing all my assignments to the best of my ability. I think I did well in being assertive and not aggressive, especially when it came to the Geologic Timeline. This was one thing I wanted to continue to work on. Of course I will still work on it, but I would really like to focus on my studying techniques. I felt confident on the test and did not study as much as I should. Even though I didn't have any problems with the test, it is not a good study habit to not study because you think you know everything.

Hunger Games Conclusion Analysis

1. In this lab, we were assigned a phenotype, stumpys, knucklers, or pinchers. These were all phenotypes of birds. The objective of the lab was to pick up enough food to both survive and reproduce. The amount of food, which was represented by wine bottle corks, needed to survive and reproduce changed depending on the year. stumpys could only pick up food with their wrists. knucklers could only pick up their food in between their knuckles, excluding thumb. The pinchers could pick up their food by pinching the corks in between their thumb and index fingers. This lab simulated natural selection by highlighting which phenotypes could survive and reproduce most.

2. The knucklers were the best at capturing food because they had a large and flexible mouth in which multiple pieces of food could fit. One of the most efficient tricks to picking up food as a knuckler was to stack pieces of cork on top of each other picking up 2 pieces of food at a time. This would double the amount of food picked up, and lead to a flourishing population.

3. I found that the population greatly evolved in favor of the little "a" allele, which was the knucklers and pinchers. In the first 3 years, there was a constant increase in the "a" allele, and a constant decrease in the "A" allele. The "a" allele frequency after the first trial, second year, jumped from 0.5 to 0.67, and then even further up to 0.72 in the third year. The "a" allele rose to almost 75% of the gene pool, and stabilized at that level. This causes evolution, because evolution is a change in allele frequency.

4. The location of food was random to an extent. For some trials, the food was all placed in a pile, where the fastest of all participants would reach the food the quickest. For the most part however, the placement of the food was random. This was similar to genetic drift, where the location of the food would affect the population, whether it be drastic or minuscule. Sometimes there would be a major decrease in population, or even phenotype size due to the placement of food. When the food was spread out over a wide area, stumpys had great difficulty picking up food, but knucklers and pinchers had great success. If the food was in large piles, then the knucklers and pinchers had less of an advantage over the stumpys.  Another random factor was the amount of food necessary to survive and reproduce. This also included whether or not there was plastic among the food. The participants never knew how much food was needed or whether or not they would survive. The one year there was a spike in plastic in the food source, there was a drastic change in the population. The population decreased by over half. However, a non-random factor was who mated with who. This was a form of sexual-reproduction, since participants usually mated with friends rather than strangers. Based on this factor, what phenotype their offspring had was totally random, which sometimes stopped the population from evolving. Even if two pinchers mated, there was chance of having a stumpy. This prevented evolution, which would have gotten rid of stumpys.

5. The results would have been very different if the food was a different size. Depending on how much the food size is increased, the stumpys would have less to no disadvantage, considering that it is much easier to pick up larger food with your wrists. The pinchers and knucklers would also lose their advantage, and if larger enough, the food would be too big for their mouths to pick up. If the food was smaller, then the pinchers and knucklers would have even more of an advantage. This means that the stumpys would go extinct much quicker, and the pinchers would rise to the top of the food chain. In nature, evolution occurs throughout the food chain, which means that predators must deal with different size foods. As the food evolves, the predators must evolve to eat this food. This occurs by change in phenotypes. Some phenotypes go extinct while others flourish.

6. The results would have been very different if there was not incomplete dominance. If there was natural evolution, then the population would have been void of stumpys within the first 4 years. The knucklers would have also dominated the population by the fourth year. This would have lead to evolution that favored the knucklers.

7.  Natural selection causes allele change, and evolution is allele change. In other words, natural selection causes a change in the gene pool. The change favors the alleles that help the organisms survive and reproduction. This change in allele frequency is evolution.

8. I am not sure of any strategies that pinchers used, but as a knuckler, I doubled my food intake by grabbing two pieces of cork, one after the other. Instead of picking up each piece and saving it, I would do something similar to stacking them on top of each other. This doubled my food intake and helped me survive and reproduce all seven years. Stumpys, on the other hand, had trouble picking up any food in general. This is where they adopted the strategy of covering the food from competition, and waiting until it was safe to pick up their food. This helped a few organisms survive, but that phenotype was at a disadvantage.

9. The population evolves into organisms with the desirable traits that help it survive and reproduce. Natural selection acts on both the genotype and the phenotype. Natural selection affects both the genotype and the phenotype. The genotype's physical expression is the allele, which is the phenotype.

10. The only question I have is where to the alleles come from in the first place. If a population is made up of organisms with a certain allele, where does the new allele come from when evolution occurs. I know it comes from certain organisms with that new allele, but where did that organism get that new allele?