Letter to a Biology Student

Dear biology student,
   My name is Sophie. I was 15 at the beginning of this school year and starting my sophomore year. I went to Redwood Middle School prior to coming to Saratoga High School. I was very interested in my English class this year because it was more challenging than my freshman English class. But my favorite class this year was newspaper because it is extremely difficult and takes up a lot of time and energy, but it is all worth it because looking at the finished product is so satisfying. I am very interested in writing so my first elective is newspaper and my second elective is Spanish. I approached my sophomore year surprised that the difficulty level had increased a lot more than freshman year. I participated in Cheer and learned that I really love throwing people and yelling. I expected my first biology class to be difficult and intense, but it ended up being very informative and welcoming.
   Mr. Orre expects you to listen very respectively. You should refrain from conversing with your table partner while he is talking. NEVER talk when he is talking. Once you enter Orre's class, you are expected to stop talking, sit down, get out your notebook and look at the Do Now and start writing the assigned task. A typical class day includes going over last night's Vodcast asking Mr. Orre questions, discussing in a group to review it,  then doing a lab or class work that has to do with what has just been learned. The homework takes about 30-45 minutes to take thorough notes of a Vodcast + the CFU. There are no quizzes, only tests. The tests are very fair and only ask questions about the topics that have been covered and thoroughly discussed in class. The notebook is your most prized possession. It is where you keep all of your assignments organized and it is was truly helps you study. You have to keep each assignment organized and listed in your table of contents. REMEMBER to put the date on each assignment to receive full credit in the notebook check. Your biology blog is where you write about labs and reflections for the unit. The blog posting was difficult in the beginning of the year, but it progressively became an easier task. My favorite lab/blog post here This is my favorite blog post ever because it includes my best friend John, the fetal pig my group dissected. I had the most fun during this lab because we all worked together to create our own Vodcast about our pig. My blog evolved over time because I figured out how to explain labs more concisely.  I personally changed over the course of this year by taking a LOT more naps, not procrastinating, eating healthier, and making my main priority school. Another important thing to know about the class is that sometimes there are moments of silence where Mr. Orre rings a bell or chime thing which is a signal for everyone to be quiet and compose themselves into relaxed human beings. It is important for you to use this silence to clear your mind and ready yourself to learn biology.
    Some of Mr. Orre's pet peeves are unnecessary noises being made such as the click of a pen, tapping of a foot, humming, or whistling. It takes a lot of time and effort to receive a good grade on an assignment. You can't just bs your way through homework, you have to really make an effort to understand what you are writing. It takes a lot of studying and listening to achieve a good grade on a test. Retaking the CFU's is very helpful. To get the most out of this class, a student can participate, listen attentively, absorb the information, and ask questions. Three mistakes I made this year were talking, not checking canvas, and not forgetting to put one Vodcast notes into my notebook.  I was caught talking once and it angered Mr. Orre so I refrained from having side conversations the rest of the year. My second mistake was that I turned in one of my labs late because I thought I had an extra day to complete it. If you turn in a lab late you receive zero points out of fifty. I never turned a lab in late again. My third mistake was forgetting to glue one of the vodcast notes into my notebook because it was a separate piece of paper. During the notebook check, I received no credit for the Vodcast notes because I forgot to glue in the notes for that ONE Vodcast. I never forgot to glue in Vodcast notes after that. I grew from these experiences and did not repeat them, making me a better student.
   I would rate the class a 9/10 because I really enjoyed the flipped classroom. It allowed more time for labs, and the labs we do are very fun. I am either taking Chemistry or Physics next year. To sum it up, do all of your homework on time, don't talk while Mr. Orre is talking or make any unnecessary noises, and lastly, try to enjoy the class and really absorb the information. By listening, you will get the most out of this class. What you learn is more important than the grade.

Sincerely,
Your Homie Sophie Z

20 Time Individual Reflection

I chose to research and base my 20 time project on Green tea because I truly do have a love for green tea. It is just such a fascinating substance that I want to continue finding uses for.  I was focused on spreading awareness of the positive affects of green tea. My initial plan to achieve my goal was to do plenty of research about green tea to find out which rumors were true and which were false. After educating myself about the topic, its origins, and effects, I decided to conduct an experiment. My experiment involved two test subjects drinking green tea daily to see the affects of the substance. It went very well, I learned that I it can improve skin quality and even help with weight loss. I did have a setback when one of my test subjects forgot to drink green tea one day, which led to the experiment restarting because of that mistake. I learned that it can be hard to conduct experiments alone and to keep data organized. At times it was difficult because this project did not have a set of instructions, so it was hard to figure out what my next steps should be. I am still very interested in green tea and how exactly it has such positive effects on people. I plan on continuing my research and I will be continuing my love for the healthy tea.

Group 6 Pig Dissection

The fetal pig dissection was a very new and enjoyable experience. At first, the thought of even making physical contact with the pig made me cringe. Watching Mr. Orre's demonstration of how to make the first few incisions made me feel more comfortable, so immediately after being instructed on what to do, I turned around to my group and said "I WANT TO MAKE THE FIRST CUTS." I went from completely disturbed by the pig to completely in love with it. At first it was hard to figure out how deep each incision should be, then we finally got the hang of it. Each of my group members and I tried to be extremely careful that we didn't accidentally cut an organ. Breaking the ribs was kind of difficult, breaking the jaw was easier. I specifically liked the texture of the liver. On the second day I was suffering from a cold and did not want to go near the pig so Gabbi and I did most of the paperwork, figuring out the function of each part of the pig. It was really interesting to me that the intestines are very tightly together, and not actually able to fall out of a stomach if a person was stabbed. The overall experience was very fun, and my favorite part was holding the pig's hoof. I'm glad I got to experience this because it opened my eyes to new possible career options.

Here are some photos I took: 

Unit 9 Reflection

Unit 9 taught me about taxonomic rank and the different levels and groups belonging to each. The order goes Domain, Kingdom, Phylum, Class, Order, Family, Genus, then Species. One species I learned about was the sponge. The sponge belongs to the Phylum Porifera because sponges have specialized cells but no tissues. Every organism can be classified into a Phylum for a specific characteristic it has; yet the protist group is miscellaneous. 

https://upload.wikimedia.org/wikipedia/commons/thumb/7/71/Taxonomic_Rank_Graph.svg/2000px-Taxonomic_Rank_Graph.svg.png

Next I learned about Anthropods, a type of invertebrate which has an exoskeleton made of chitin,  with joining appendages and segmented body parts. Anthropods are classified into five groups: Trilobites, Crustaceans, Chelicerates, Insects, and  Myriapods. Trilobites are extinct bottom feeders. Crustaceans live in oceans, streams, and on land. Chelicerates have specialized dagger-like mouthparts(Scorpions). Insects have 6 legs and usually live on land. Myriapods have long bodies with many pairs of legs (Milipedes). 

https://pixabay.com/p-87721/?no_redirect

I want to learn more about sand dollars because I don't completely understand how they function. Sand dollars have always interested me and I used to collect them. I wonder who thought of the idea to base kitchen sponges off of the actual sponge creatures living in the sea. 

My What on Earth Evolved Presentation was done about Roses. I truly enjoy public speaking so I liked getting a chance to share and teach the class about my topic. My presentation went well I'd say, I could have gone more in depth about the anatomy of the flower to make my presentation longer.

Sophie Z

I am very happy with how the presentation went well because I spent a lot of time researching. It is actually very difficult to find information about the origins of roses and how they evolved. During this presentation, I started connecting the rose to modern day movies to explain and show the relationship of how people view these flowers. I am going to try to make more connections in my presentations in the future.

Geologic Timeline Individual Reflection

In the Hadean eon, Earth was formed, along with the first life forms. In the Archeozoic period shows the earliest evidence of plate tectonics, as well as organic carbon. The Cambrian period has a diversity in which fossils have been recovered. It surprised me that there was evidence of plate tectonics in the Archeozoic period. It is amazing how much humans have impacted the Earth over time. I wonder how old the oldest rock is.

Hunger Games Final Analysis

To simulate the affects of natural selection, my class stood in a circle and fought for our survival by attempting to collect as much food as possible while being 3 different phenotypes: "stumpys," "knucklers," and "pinchers." The "Knucklers," who had to pick up food between their second knuckles of their index and middle fingers, ended up being the most successful with their survival. The "Stumpys" started dying out around trial 4. The population evolved to consist of "Knucklers" and "Pinchers." The results would be different if the food was smaller because it would allow the different beaks to pick up pieces faster. This relates to the real-world because in nature sometimes food becomes larger or smaller. When this happens certain species that don't have large or small enough beaks to pick up the food, die out. The relationship between natural selection and evolution is natural selection is necessary for evolution to occur. Individuals started cheating by turning around to see where the food would be located, as well as picking up food with their hands and not their correct beak form. This behavior could occur in nature if an animal hid or hoarded all of the food from the rest of its kind. In evolution, natural selection acts on both the genotype and phenotype. Positive or negative traits can be inherited that are not physically seen, such as an allele for a disease. Phenotype can also be affected, causing members of a species to have a certain beak. I wonder what kind of bird has the best beak to eat any kind of food.

Unit 8 Reflection

This unit was mainly about speciation. Isolation is necessary for speciation to occur. The three factors that contribute to speciation are behavioral isolation, geographic isolation, and temporal isolation. Behavioral isolation is where there are changes in mating behavior. Geographic isolation is where a physical feature separates a species into groups. Lastly, temporal isolation is where reproduction is prevented because of the timing. 

https://upload.wikimedia.org/wikipedia/commons/thumb/f/f3/Mutation_and_selection_diagram.svg/2000px-Mutation_and_selection_diagram.svg.png

This unit also taught about Darwin's conclusions. Darwin's first conclusion is that there are winners and losers in the natural world. His second conclusion is that due to natural selection, populations usually end up looking like the winners. An essential theme for this unit is that natural selection causes evolution. I want to learn more bout birds and why some have very colorful feathers, such as parrots, while others have bland colors, such as crows. In an attempt to be more assertive, I have been trying to sit up straighter and make more eye contact. My goal is to very assertive by June.

Below are Darwin's finches.

https://upload.wikimedia.org/wikipedia/commons/a/ae/Darwin%27s_finches_by_Gould.jpg

Story of Cosmetics

After watching this video, I learned that there are toxic chemicals linked to cancer is brands I have at home and use everyday before going to school. This was quite shocking to me because I didn’t know there weren’t strict laws about what can and what cannot go into a product. Even soap made specifically for babies contains chemicals that are linked to cancer and even neurotoxins, which damage the brain. In the end, there is nothing we can do except convince the business people controlling this entire industry that consumers want to buy SAFER products that aren’t linked to cancer. People can also take it up with local governments to try and get a bill created that has more narrow restrictions on what can and cannot be placed inside of products for human use. Annie Leonard says that we are  basically just test subjects being experimented on with various chemicals not knowing the effects. That is really scary to think about. This video was very similar to the Story of Stuff video because they both point the leading cause of the problem to the big industry owners at the top, deciding what/how products are made. I plan on using this information to safely buy makeup and hair products that have the least amount of toxic chemicals inside of them. The video refers to safecosmetics.org, so I decided to check it out. I learned about how products that are marketed as “anti-aging” contain chemicals linked to breast cancer. L’OREAL’s products contain chemicals linked to cancer as well. The website was very informative and I am going to remember what products not to buy.

Unit 7 Reflection

 A few major themes we talked about during this unit are biodiversity, ecology, and food webs/chain. Biodiversity is how the diverse species on Earth provide us with food, industrial products, and medicines. Ecology is the study of interactions between organisms and their environment. Food webs/chains consist of producers and consumers than can be herbivores, which are plant eaters, carnivores, which are meat eaters,  omnivores, which are everything eaters, or detrivores/decomposers, which eat decaying/non-living things.

I want to learn more about how to save endangered animals. Threats such as disease are a large factor that contributes to the death of animals such as the Tasmanian devil in Eastern tropical Australia. I wonder how many endangered species there are on this planet and if there are common threats which made those species endangered.

Since I am quite an assertive person, I found collaborating with my group members in the Ecology Conservation project fairly easy. The project was a success because we each individually completed our assigned work. No one completed anything late. All of our personalities somehow meshed, making it easier for us to problem-solve and find solutions.

I learned about how threats such as deforestation and mining destroy the environment and its animals. Construction also plays a role in the endangerment of animals, since in many cases animals fall into trenches, to their death. The ecosystem is very fragile and we must do what we can to protect it. My group came up with the solution to create more national parks to protect animals and the land around them.

I learned from the video that my dominant personality is being assertive. I am a fairly confident person and this helped me share my ideas to my group members because I wasn't afraid to speak up. Things I could do to be even more assertive would be to sit up straighter and try harder on maintaining good eye-contact.

Reflecting back on my New Year's Goals, I have started getting 7 hours of sleep every night, which is an improvement from last month.

Unit 6 Reflection

The overall topic of this unit was Biotechnology, which is the study and manipulation of living things in order to benefit mankind. Biotechnology covers a large field that generally focuses on understanding DNA, proteins, and inheritance of genetics. The four applications of biology that we learned about in detail are industrial and environmental biotech, medical/pharmaceutical biotech, agricultural biotech, and diagnostic research biotech. Industrial and environmental biotech is the fermentation of foods and beverages, biodegradable plastics, and bio fuels. Medical/pharmaceutical biotech has to do with the medicines from plants, fungi, animal vaccines, and gene therapy. Agricultural biotech is the breeding of plants and animals and the transgenic organisms aquaculture. Diagnostic research is about DNA identification and comparing and contrasting the DNA of organisms. We also learned about Gel electrophoresis which is when a mixture of DNA fragments is placed at one end of a porous gel, then has an electric voltage applied to the gel. Recombinant DNA is produced by combining DNA from different sources. Next I learned that PCR stands for polymerase chain reaction. PCR is used to detect diseases, green bone marrow and organ compatibility, identify human remains, paternity testing, cloning of genes for medicines, genetic engineering, to identify species and alleles, and to analyze DNA. Sequencing is the determination of the exact sequence of a given DNA strand. I then learned about bioethics which has to do with what each individual person feels is right based on his or her own personality and experiences. Lastly, I learned about pGLO and the steps to properly complete the pGLO lab we did in class. The Vodcast I watched beforehand was very helpful.

 My strengths in this unit were understanding gel electrophoresis and the study of bioethics. I found that learning about Gel Electrophoresis through a virtual lab made it easier for me to understand the concept. We went really in depth on the topic which made me have a much better understanding of it. It was mentioned in the "The 'technologies' of Biology" Vodcast and the pGLO pre-lab Vodcast. The repetition of it helped me better understand it. I understood the topic of bioethics very easily because it is mainly about the different ways someone could have biased views towards something based on his or her background and beliefs. My weakness in this unit was learning about sequencing which is the determination of an exact sequence, or order of a given DNA strand. It just confused me a bit at first, but by learning more details about it, I figured out exactly what it is.

I missed but fully understand everything that happened during the Candy Electrophoresis Lab. In this lab I learned that the two factors that control the distance the colored dye solutions migrate are the length and the charge of the dyes. The longer the length, the slower it travels. The shorter the length, the faster it travels. In the pGLO Lab, I learned how to transform bacteria. It was cool to see the colonies under a UV light because they glowed yellow and green.

I want to learn more about medical/pharmaceutical biotechnology because it interests me how medicines can come from plants. I wonder who discovered that bacteria colonies can glow under UV light.

I have been sticking to the healthy diet I planned out in my first goal. Occasionally I do cheat if I go out to a nice restaurant or eat a slice of cake. But so far I have cut out sweets and normal Carbohydrates out of my diet and have been trying as hard as I can to maintain this. My next steps would be to not cheat with any foods at all. My second goal was to get more sleep, which I am slowly achieving. Recently I was very ill and it was extremely difficult for me to sleep at all. But just this week I found that reading a few chapters of a book before going to bed helps me clear my mind and allows me to sleep around 10 or 11pm. I will try to sleep at 10pm as often as I can during the school week.

pGLO Lab

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 room light Color of colonies under   UV light - pGLO LB none none none - pGLO LB/amp none none none + pGLO LB/amp 39 yellow yellow + pGLO LB/amp/ara 31 yellow green

2.	What two new traits do your transformed bacteria have?
	One plate was empty, but there were dots on the two other plates.
3.	Estimate how many bacteria were in the 100 uL of bacteria that you spread on each plate. Explain your logic.
	I think there were about two colonies of bacteria because we got only a small amount of it.
4.	What is the role of arabinose in the plates?
	The arabinose activated the gene, allowing it to glow.
5.	List and briefly explain three current uses for GFP (green fluorescent protein) in research or applied science.
	GFP has been used as a reporter gene, a cell maker, and a fusion tag. A reporter gene can be attached to a regulatory sequence of another gene. A fusion tag is a protein.
6.	Give an example of another application of genetic engineering. Genetic engineering is also used to make genetically-modified crops.

Candy Electrophoresis Lab

I, myself, was absent from the lab, but I was given information from the two people in my group who were present that day.  When the gel results were analyzed, the dyes matched with the reference dyes. Our dyes were a bit more circular shaped than the reference dyes which were more rectangular. The two dyes that came out ended up being purple and yellow. A bit different from the reference dyes which happened to be blue, yellow, orange, and red. Since it has a negative charge, I think the fast Green FCF is most similar to my dye. Dog food manufacturers could possibly be adding artificial food colors into dog food to make it more appealing to dog owners who buy it. Maybe the dyes are used to match the meaty flavor and make it seem healthier for the dogs, attracting more dog owners to purchase artificially dyed food. The two factors that control the distance the colored dye solutions migrate are the length and the charge of the dyes. The longer the length, the slower it travels. The shorter the length, the faster it travels. Electricity is the force that helps move the dyes through the gel. The gel lanes and the electric current which runs through the gel are the component of the electrophoresis system that causes the molecules to separate by size. This is because it controls how the dyes move. I would expect DNA molecules with molecular weights of 600, 1000, 2000, and 5000 daltons to separate so that the molecule which weighs 600 would be the first and furthest from the wells. Since 600 is the lowest weight, it would be the fastest. Then the 1000 dalton molecule would be next, then the 2000 dalton molecule, and lastly the 5000 dalton molecule would be the heaviest, causing it to be the slowest and closest to the wells.

1. 
   

New Year Goals

One of my goals for 2017 is to consume only healthy foods, such as fruits, vegetables, and complex carbohydrates. I will also only eat home-cooked meals instead of going out to eat. That way, I know every ingredient and seasoning put into my food. First, I will stay strong and not eat any of the girl scout cookies my sister is selling. Next, I will stay away from unhealthy eating environments, such as going out to cheap fast food with my friends. Ultimately, I will eat healthy all throughout 2017, and live a healthy lifestyle.

My second goal for 2017 is to get more sleep. My goal is to get at least 8 hours of sleep every night, as opposed to 6. I will achieve this by having the will power to not click "watch next episode" when watching Netflix, and putting my phone away early in the night. I currently have the horrible habit of sleeping at 12 am and waking up at 6 or 7 am. I will gradually start to sleep earlier and earlier. First, I will aim to sleep at 11 pm. My ultimate goal is to sleep by 10 pm, allowing me to receive 8 hours of sleep if I continue to wake up at 6 am.