Letter to Biology Student

Dear Biology Student,
Hi, I my name is Rohan and I was a 9th grade Biology student in the 2016-2017 school year. I took Algebra 2 Honors, English 9, Spanish 1, Freshman Band, Band P.E. (for first semester only), Biology, and Geography/Health and Drivers Ed. I took part in the Saratoga Marching Band which lasted from August to the end of October. I then took Winter Percussion which started late November and lasted until April. I was generally nervous about what high school would be like and how strict and difficult the teachers might be like.
 My third period was Mr. Orre's Biology Class. Mr. Orre uses a flipped classroom which means that we learn from home in "vodcasts," which are lectures that Mr. Orre makes that explains important topics in class. Usually, Mr. Orre assigns a vodcast for homework, and we have to take notes in our Biology notebook. We come to class the next day and take out and read the Do Now, written instructions of what to do when you enter the classroom. It is usually a question about the vodcast that is due that day. While we are doing our Do Nows, Mr. Orre checks our notebook to make sure we have done our vodcast notes. After this is done, we go over the vodcast in our table groups and then review it with the entire class. What happens for the rest of the class varies from day to day, but we usually do a lab that relates to the unit we are learning. There are some things in Mr. Orre's class that differs from other Biology classes. One is the biology notebook. This notebook is organized and is set up in a very particular way. The way we take notes of our vodcasts is also done in a very particular way and you must do it this way to receive credit. Another difference is our biology blog. We rarely turn in paper to Mr. Orre because all our reflections are in our biology blog. This blog is used to show all your work of the school year. One important thing you will encounter next semester is the 20 Time Project. In this project, Mr. Orre gives use 20% of all class time to work on our own personal project. It could be on a wide range of topics, but it must relate to science and you should have something to show that you have accomplished something. Mr. Orre will make us right a few blog posts about our project and our progress in it. By the middle and end of the project, you will either have an interview with Mr. Orre or write a blog post giving yourself a score that you think you deserve, and then justifying it with evidence.
Mr. Orre's class can be very easy, or very difficult depending on your approach to his class. If you want to get a good grade, you must complete all your homework and classwork on time. You could ace all your tests and still have a failing grade if you don't complete your classwork on time. Mr. Orre expects everything other than vodcast notes to be on time. Submitting something late will give you half credit first semester and no credit second semester. One thing Mr. Orre does not like is excuses. Do not try to negotiate with him about giving in late work unless you have a dire situation. If you were absent and never asked him for makeup work, then you will get a 0 on that assignment. You have to ask him for the makeup work. Mr. Orre also expects us to be independent and does not like giving directions to you when you are given a procedure for a lab. Mr. Orre does not like repeating himself and if a lab takes too much time because we weren't listening to him, then he won't let us go until everything is cleaned up. He also wants you to respect him and your other classmates so you shouldn't talk out of turn. My best advice would be to do exactly what he tells you and be attentive in class. If you follow this, then the class will not be a challenge for you.
Overall, I am glad that I got to have Mr. Orre as my Biology teacher. It is a good class if you pay attention and you will learn a lot. Mr. Orre teaches us many concepts to try to help us in not only his class, but in all of school. This includes actively studying, having a growth mindset, being assertive, etc. If you use the work ethic that he teaches you through the school year, and apply it to all your other classes, you will learn more from those classes and get better grades. I hope you enjoy your freshman year and time with Mr. Orre in his Biology class, and I wish you well through you journey into high school.
Sincerely,
Rohan Joseph

Pig Dissection

Here is the link to the pig dissection video: https://www.youtube.com/watch?v=5paw1BRoIHg

In this unit of biology, the main lab was the pig dissection video. In this lab, we got to cut open a pig fetus to see the anatomy of the pig. Pigs are somewhat similar to humans because they are both mammals, so looking at the anatomy of a pig is similar to looking to the anatomy of a human. We strapped the pig down to the tray and laid it on its back. We then cut the pig open through the center to expose its internal organs. We had to make a video showing all the essential organs to the pig. This related to our unit because we had learned about many of these organs and their functions.  The purpose of the lab was to find the different structures in the pig fetus and better understand how these organs work and how they look like inside a body. My favorite part of the dissection was opening the pig for the first time because it was surprising to see how similar it looks to a human body. The structures of the pig look like miniature versions of the human organs. I believe that the pig dissection is valuable because it is the best way to show how the different organs play together in a body. You can't truly understand how these organ systems work without seeing it in person. 

River Clean Up Reflection

Over the weekend, I along with other students from SHS cleaned up litter from a creek for National River Clean Up Day. We picked up garbage that was scattered on the floor for 3 hours. The purpose of this is to prevent the ecosystem from being hurt by garbage. Animals could eat the garbage mistaking it for food, or it might not decompose. Most of the garbage was small plastic bags and fragments of soda bottle glass. This was an opportune time to clean the creek because most of the water was gone meaning we could easily clean the bottom. We found some miscellaneous items in there such as a scooter and metal pieces that were lodged in the rocks. I liked this project and hope it happens often so that the creek doesn't become covered in litter. I have seen places in India where the creeks and rivers are covered in garbage, and I hope this doesn't happen to creeks in California.

Unit 9 Reflection

    In this Unit, we learned about the taxonomic classification of animals. Taxonomy is the classification of animals into groups that start broad and become more refined. Taxonomy helps us see the evolutionary relationships of different animals because animals that share more taxonomical levels will be more closely related and have a more recent common ancestor. The Taxonomic levels are the following: Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species. This is the current organization of animals; the original system was created by Carl Linnaeusus in the 1700s, meaning that microscopic organisms weren't considered life. The original system divided all living things into plants and animals. Another major change was the discovery that bacteria and archaea. We then learned more about Bacteria and Archaea. Eukarya was divided up into talking about the different kingdoms. We spent a vodcast looking into plantae and learning the different classifications such as mosses (bryophyta) that are nonvascular and don't have seeds, pterophyta (ferns) which are vascular but have no seeds. We also learned about plants that have vascular systems and seeds such as the angiosperms and gymnosperms, the prior having seeds dispersed in fruit and the latter having seeds dispersed in cones. Angiosperms can be divided into monocots and dicots depending on how many leaves sprout first and their structure. We then learned about Animalia. This was divided into 2 vodcasts on invertebrate which account for 98% of all animals and 2 vodcasts on chordates.
    I would want to learn more about Archaea because we didn't learn much about them and they don't seem different enough from bacteria to be a separate domain. I would also want to learn about the split from bacteria and archaea. I would want to learn more about the main kingdoms and phylum in bacteria and archaea like we did with Eukarya. I would like to learn more about protista, fungi, and plantae because we learned more about Animalia. I would want to learn more about the evolutionary timeline of the organisms we learned about and when they evolved and split from their ancestors.

    One of the main projects of this unit was the what on Earth evolved presentations (you can see mine right here). In this projects, we got to pick an important organism, and give a 4-8 minute presentation on all the information of the organism. For my organism, I chose Australopithecus, a genus of hominids that gave rise to the genus homo. I talked about the many species in the genus and their differences. The most important characteristics of this organism is that it was the first bipedal hominid and gave rise to the homo genus which eventually evolved into modern day humans. I learned a lot about my topic, but my presentation wasn't clear and I had to read off my notes. Instead of writing a post it note of what I should say, I had an entire script in my hand and made no eye contact. I should try memorizing my presentation better so that I could make more eye contact and be more engaging. I was able to not procrastinate and give late work this unit, but I am concerned about this upcoming test because of all the information condensed in this unit. Overall, though, I am happy with my progress in this unit.

Geologic Timeline Reflection

The first major event in Earth's history was the cyanobacteria oxygenating the atmosphere. This radically changed the composition of Earth's atmosphere and is the reason most current life exists. There was a mass extinction event that killed off the obligate anaerobes. This probably caused life on land to appear. This also allowed stimulated evolution to survive in oxygen rich environments. The next most event in Earth's history was the Permian extinction event. This was the deadliest mass extinction event in Earth's history killing 90% of marine organisms and 70% of terrestrial organisms. It is speculated that it was caused by an eruption or release of gas from the ocean. It ended the paleozoic era and made way for the mesozoic era. It took 30 million years for life recover and there is a gap in the fossil record because of the event. The last major event was the Cretaceous mass extinction. It was the last mass extinction and well known for ending the dinosaurs and mesozoic era. A giant meteorite crashed onto Earth's surface killing three quarters of all life on Earth. It is very important because it ended the dinosaurs and let mammals take over which would eventually give rise to humans. The scale of Earth's history is impressive and makes you realize how insignificant you are in a grander scale. I was surprised that  the Precambrian lasted so long and that we have a lot of blanks for information on the Precambrian. The Precambrian stretched most of the room while the rest could fit on a table. Many scientists say we are in the middle of the 6th mass extinction event because our killing of species through deforestation is killing many species. Many mass extinctions take thousands of years and if we don't change, we could be the cause of a mass extinction that will probably lead to the end of humans. I want to know more about the early Precambrian and how life formed because it seems strange how such complicated life could come from random assortment of chemicals. click here for picture

Unit 8 Reflection

Unit 8 was about the constant change of species. We started this unit learning about artificial selection, the process in which humans choose the best traits from the gene pool of a species, and purposely mate them with others with the same traits to produce individuals with the best traits for their tasks. This is used livestock by creating the hugest turkey or cattle so that it can produce the most meat and food. The next vodcast was about Charles Darwin's discoveries and theory of evolution. He traveled to the Galapagos islands and recorded four major observations. The first was that sexually reproducing species tend to have higher genetic variation. The second observation was that traits are inherited from parent to offspring. The third observation was that all species are capable of growing exponentially, beyond their carrying capacity. The last observation was that competition is stiff and not all offspring survive because of limited food and other resources. He concluded that individuals who inherited traits that help them survive better and reproduce more tend to leave more offspring than other individuals. The second conclusion was that the unequal ability of individuals to survive and reproduce will result in the better traits becoming more common in the population over generations. He came up with the idea of natural selection, the process of weeding out traits in a population that don't help individuals survive leaving trait that are neutral or do help survive. We next learned of the gene pool, the collection of all alleles in a population. Allele frequency is the frequency of an allele in the gene pool when compared to the other alleles. Speciation in when one species becomes two new species. This means neither can reproduce with the other one. This is caused by behavioral, geographical, and temporal isolation. We then learned of the structural evidence that evolution has occurred such as vestigial structures, remnants from our ancestors that we inherited and do not use anymore, as well as other techniques scientists use in trying to find evidence for evolution. We then learned of three ways populations tend change in allele frequency: directional selection, stabilizing selection, and disruptive selection. We also learned of genetic drift and other ways evolution occurs. We finally learned of the history of life according to evolution. We of the eras and periods the history of life is divided into and theories in how life started.
I want to learn more about the Precambrian era because I still have a lot of information I want to know about it. It is the largest era in terms of time and is when life emerged which is vitally important if we want to understand how life came to be, yet we know the least about this era. This unit has been successful in completing my beginning of the year goals because I have been more on time with my assignments and doing the CFU's more regularly. I need to work on being assertive and haven't worked on it because I haven't seen many opportunities where it is essential to be assertive. I will try to be more assertive in the next unit. You can look at my Unit 7 Reflection here.

Hunger Games Final Analysis

1. In this lab, we divided ourselves into three groups: the stumpys, the knucklers, and the pinchers. This simulated three different alleles in a population. We had to collect as many corks as possible in a limited amount of time which represented collecting food.We needed a certain amount of corks to survive and reproduce, and we got to choose whom we would reproduce with. This process simulated evolution and natural selection because only the strongest survived.
2. We found that the pinchers were the best at collecting food because they could use their entire hands which made it easier to collect a lot of food at a time.
3. Evolution is defined as a change in allele frequency, which means that in our simulation, the species evolved. By the first two trials, the frequency of recessive "a" alleles grew from 52% to 96.67% which is a clear change in allele frequency.
4. One non-random factor was that the everyone tried to mate with the pinchers so that their offspring was more successful. This made the evolution to pinchers much faster. One random factor is the distribution of food across the field. Stumpys made a comeback because they had food closer to theme but this was not because they were better at surviving.
5. If the food was larger, the knucklers and stumpys wouldn't have had as hard of a time to pick up food which would of made the allele frequency closer to 50%. If it had been smaller, the pinchers would have been the only ones that could survive and the other populations might have completely died out.
6. There would have been more pinchers because "Aa" is a pincher. Stumpys would have died out.
7. Natural Selection favors individuals who are the best at surviving and reproducing which means that they have more alleles and the allele frequency increases. This means evolution has occurred.
8. In the beginning, everyone wanted to mate with the pinchers so that there would be more pincher offspring. This is why in the first two trials, the other species almost went extinct. Stumpys made a comeback, however, because people wanted there to be more successful. This could be related to sexual selection because people wanted to mate with a certain individual not because of their survival skills.
 9. Natural Selection works on phenotype because you can be heterozygous but the natural selection only cares what trait you have and not the alleles. Evolution occurs in populations and not individuals because individuals stay with whatever alleles they have but because there is a preference of a certain allele to survive, populations tend to look like the most successful individual over time.
10. I still wonder how this simulation can become more realistic such as how to make more species and have more people do the lab.

Unit 7 Reflection

In this unit, we learned about Ecology. Ecology is the study of organisms interacting with each other. There are 2 big ideas in ecology: Homeostasis, and Interdependence. Homeostasis is the concept that environments and ecosystems are healthiest when they are in balance. We learned the difference between a habitat and a niche, a niche being the ideal factors for a species to survive in an environment, while a habitat is all the abiotic and biotic factors that affect an organism where that organism lives. We leaned abiotic factors which are nonliving, and biotic factors, which include other organisms. We then learned about the 6 levels of organization: Organism, Population, Community, Ecosystem, Biome, and Biosphere. We then learned about food chains and food webs. A food chain is a way that energy is passed from organism to organism. A producer like a plant makes energy from abiotic factor. Then, Something eats the producer, and something eats that consumer and so on so forth. There are 4 types of consumers: Herbivores, Carnivores, Omnivores, and Decomposers. Food chains are inaccurate because it only shows one possible scenario of transfer. A food web shows you all the possible ways energy is transferred from one organism to another. The energy going up the pyramid decreases by a factor of 10 as it goes up the pyramid. For example, a producer can make 100,000 units of energy (like Joules) and the 3rd level above it would only have 100 units of energy. This is why there are less predators than prey. Population Ecology is the study of populations of organism reacting to their environment. Two important concepts are the difference between exponential growth and logistic growth. Exponential growth is when a population is growing at an increasing rapid rate. Logistic growth who's how after some time of near exponential growth, the curve plateaus. It plateaus when it reaches its carrying capacity, or the amount of organism the environment can support. Factors for this carrying capacity include the following: Immigration, Emigration, Births, Deaths, Disease, Predators, Abiotic Factors, and Population Density and Dispersion. A healthy ecosystem is shown by the amount of tertiary and quaternary consumers there are. Biodiversity is essential for maintaining a healthy ecosystem. Habitat Loss, Introduction of exotic species, overexploitation, and climate change are all causes of species extinction and endangerment. We must protect Biodiversity hotspots through conservation because we need to save them from species loss. Sustainable Development is essential for this to be true. Our group project was a success and we worked together as a team. There was barely any fighting or disagreement and everyone did what they had to do. I hope to learn more about realistic solutions to conservation that can be applied fast. Overall, this unit has been pretty strong for me and I am meeting my goals.

Story of Stuff

We live in a market economy which is a system that is dependent on us buying things. It starts with us extracting natural resources from the Earth. Then, we manufacture goods in factories. These goods are sent to stores for people to buy. People buy these goods to use for a short amount of time. This is then disposed of by piling it all in one place, or incinerating it. This process is unsustainable because it is linear and not a cycle. A linear system is infinite, but we do not have an infinite amount of resources. There are many flaws in this system. Extracting natural resources causes a lot of harm to the environment and destroys the local ecosystems. Manufacturing uses thousands of chemicals that could be harmful to make products cheap. Both of these steps are usually in a third world country with lax human rights laws which allows kids younger than I to work in unsafe toxic conditions for many hours and very low wages. Buying things in stores is because of the massive propaganda through advertisements that convince us that the more new things we have, the better our lives are. Once problem is the meeting with corporations and the government in the 1950s under President Eisenhower. He wanted to encourage growth in the economy, and he figured the best way would be creating a need for short term goods. This would be achieved by convincing people to keep on buying goods that would need to be replaced in a few months. This would create and endless cycle of buying that would push our economy forward. By making products either look outdated, or making their lifespan short, we would create this constant demand for new products. This is also coupled with the constant bombardment of advertisements that condition us to think that we need new things and it creates societal pressure for us to conform and be a part of the endless cycle of buying. If we have outdated products, we will be scorned by society because it is outdated, regardless of whether or not is still functions. Another issue is external costs. When we buy a product, it is usually a lot cheaper than it should be. The example shown was a radio that costs about 5 dollars, even though there are a vast amount of products used to make it found on opposite sides of the planet shipped from one place to another. This product should realistically cost a lot of money. We keep prices cheap by sacrificing parts in the other steps of the cycle. Examples of this is the poor working conditions of workers and child labor. Disposing is also a problem because leaving it in one place will destroy the ecosystem that live there and incinerating will force us to inhale the chemicals in our products. Recycling can work in a small scale, but it is inconsequential compared to what manufacturing produces in waste. In summary, the material economy has many flaws and is unsustainable.

Unit 6 Reflection

Unit 6 was about biotechnology. We first learned about the history of biotechnology from its roots 6000 years ago. We learned about many of the applications like gene therapy and classical breeding. In the next vodcast, we learned about more modern technologies in biotech such as polymerase chain reaction ( pcr), gel electrophoresis, and sequencing, and there applications. In the last vodcast, we learned about bioethics, a field of ethics that involves biotechnologies. We learned about ethics in general and some of the main issues that involve bioethics. Some examples include cloning and genetically enhancing humans. My strength was the process of gel electrophoresis because I learned about it in the 7th grade. My weakest topic was probably the PCR because I hadn't previously known about it and it wasn't given as much attention as gel electrophoresis. The two labs that we completed for this unit were the candy gel electrophoresis lab and the pGlo lab. In the first lab, we extracted the dyes from candy and tried to determine what there basic chemical compounds were based on running it through a gel and comparing it to known samples. The pGlo lab was to show the process of giving one trait to another organism, in this case, giving the E. coli bacteria the ability to be immune to ampicillin and glow under UV light. I want to learn more about PCR because it wasn't my strongest topic. I would also want to learn more about DNA sequencing because I want to see whether you could completely predict the traits of a person based on their DNA. I have a few unresolved questions about bioethics because there is no clear answer. Most of these questions are relevant because they are in a gray area, and it is hard to determine which side is correct. I still need to work on my procrastination because it is still causing problems. I hope to do better at accomplishing my new year goals next unit.

pGlo Lab

1. The first colony had about 100 colonies. It glowed orange under Uv light. The second plate had about 120 colones, but it didn't glow under Uv light. The third one didn't have any colonies.
2. The transformed bacteria now glow under a Uv light, and are resistant to ampicillin (the antibody.)
3. I think we had very few bacteria put onto the agar plates because there are a lot that could die in the process. You only need 1 to survive for there to be colonies.
4. Arabinose is able to make the E. coli survive the ampicillin and grow colonies in its presence.
5. GFF is being used in science for multiple research reasons. One use is to test whether a plasmid has successfully been inserted into another bacteria. Another use is to use it as a marker when doing tests in bacteria. One example of its use is when they inserted it into a parasite and infected another organism. They would easily be able to tell if the host was infected if it glows because of the gene.
6. One application of genetic engineering is using the E. Coli gene to cure malaria. They made the E. coli get a gene that makes it harmless and cures malaria for a much cheaper cost. This is a very important technology is third world countries stricken with malaria as the treatments that used to cost $50 are now $5.

New Year Goals

I will do better on the tests of this class. I will do this by studying more for the tests. This means that I should take better notes and relate and reviews. I should study the CFUs and do them more often because they appear on the test. I need to listen to the vodcasts more thoroughly because the specific details are important to.

I will stop procrastinating. This hurts my performance in school and other activities so stopping this would be is very important to help my grades, increase time for studying, and reduce stress. I will make sure to do my homework as soon as possible and not make any excuses for not doing it.