Letter to a Biology Student

  Hey there biologists! That's something you'll get used to hearing, trust me!! Here you can see a video that will depict your entire year in biology. Anyway, I will be a sophomore when you are reading this, and I'll be 15 years old. I went to Redwood in 8th grade like many of you. In the beginning of the school year, I was really interested in almost all my classes, but like usual, my motivation and inspiration wore off with time(and homework). I play sports outside of school, and I am generally a good student that puts in a lot of effort. The first day of school, I expected the basic talk and syllabus, but it was the opposite. We actually did activities learning our way around the classroom(AKA the Rookie Module). It was really uncomfortable, but it was something unique. Even though it's the end of the year and people still don't know where anything is, Mr. Orre will still get upset if you act as a Rookie.
  Mr. Orre makes it clear what his expectations are, which I think is a good characteristic for a teacher. Have you ever done anything that upsets a teacher and have no idea why? Well, this won't happen in his class, because he makes it VERY clear what he wants out of us as students. The first thing you do when you come to class is work on the DO NOW/warmup, which reviews last night's homework. A typical class day involves reviewing the vodcasts, and working on a lab, project, or blogpost. If you haven't already guessed we blog in this class A LOT. At first it's kinda weird but eventually, you get used to it as you become more comfortable in the class. The labs are typically simple, it's ok if you do something wrong in your group, as long as you participate in some way, and write honestly in your blogpost, you will still get a good grade. If you haven't already noticed how weird this class has been so far, it's because it's different than others. Mr. Orre has a "flipped classroom" where we do the notes(vodcasts) at home for homework, and discuss and apply what we learn in class. I'm not gonna lie, it actually works pretty well, and these silly blog posts do too.Here you can read my Unit 9 reflection, we do a reflection for every unit and it really helped me capture the big idea of what we learned. But often that big idea is not at all what we are tested on. We are expected to understand the big idea, and be tested on small details in vodcasts and CFU's(a CFU is a small comprehension quiz that doesn't affect your grade, but you should ALWAYS do it. He will randomly give 100% in the test category for doing a CFU).
   To be honest, it doesn't really matter how you do on the tests, as long as you do homework, blogposts, and notebook checks well, you can have an A. The notebooks must be organized in a specific way, and if you forget to write the date on one vodcast, you will lose points for the whole category. I advise you to put a lot of effort in your notebooks for the first few notebook checks and build your credibility. Also, I know he says you should glue in your vodcasts, but don't use glue, tape is so much easier. There aren't any quizzes but there are tests for every unit, so luckily the class is really structured and predictable. This semester I got a B on every test, but I have a 96%, because it's the "learning process"(i mean this figuratively and literally because that's what it is called on canvas) that is worth the most. Your grade WILL go down if you don't do even 1 vodcast or blogpost. The homework usually takes from 20-40 minutes on average, because he will sometimes give you hand outs for notes, and sometimes he won't, so don't rely on having handouts for every vodcast.
   Again, to talk about the blog, you can kind of see it evolve over time in both content and writing style. By favorite blog post is about the river clean up service project, I wanted to do it for fun, and then I realized I could get extra credit and volunteer hours for health, so I got a lot done in one day. I felt really motivated to volunteer and help the environment after that one event. It's my favorite blog post because although it is simple, it shows my personal growth, and that is something Mr. Orre likes to hear about, especially in your blog. I changed over the year because I learned to practice little things like mindfulness, and recognize little things like learning preference and how to reflect on something. I feel like this class, although frustrating at times, has helped me grow a lot as a student, so my advice to you is to persevere.
  Some of Mr. Orre's pet peeves are when you treat him only as a teacher. He likes to ask how your day is going, and sometimes people don't answer because they are shy or tired or lazy, but he gets really upset. He will appreciate a little acknowledgment, like just saying good morning. Also, like I mentioned above, he doesn't like "Rookies." To earn a good grade on an assignment, you must be detail oriented and actually put in some effort. You can't just walk your way through this class, although tests don't make up your whole grade, you need to show that you've learned from vodcasts, labs, and classwork through your blog post.Homework is extremely important in this class, like I mentioned above you need to do all the vodcasts, because they will be the base of everything else you do in the class.  To get the most out of this class, you are going to need to make time to do the vodcasts, because rushing through them and scribbling them down in your notebook aren't going to teach you anything. You can get away with it, but just know that you will need to focus extra hard when we discuss it the next day.
  Also, don't be afraid to ask questions, even if they may seem stupid. In biology you'll probably pronounce a billion things wrong, and get tons of concepts mixed up, but so does everyone else. Asking questions that other people are afraid to ask will make your classmates appreciate you more because then Mr. Orre won't be in a bad mood thinking that people are ignoring him. Mr. Orre, if you're reading this, know that no one in this class was trying to be rude or ignore you when you asked how you were doing, we were just too tired to raise our hand. This class, although it's just a class, can teach you some grit, which is great when you start the day.
  I made a few mistakes this year, and I want to share my experience. First, I would advise you to be diligent, although Mr. Orre is usually pretty consistent, he is still human. Don't be afraid to talk to him if you think something in the grade book is wrong. He looks really intimidating, but he's actually really understanding. Second, turn in your assignments on time. This one is really important because even if you turn in a bad blog post, it's better than nothing. You do not want to have a 0/50 on something. A 50% on an assignment is better than a 0%. I know people who have had perfect grades in the class and forget one blogpost which makes them stressed out because they then have a borderline grade. The third thing I would advise is to listen to the non-academic things he has to say. He will go off-topic sometimes and show us how to decrease stress, and handle other things in the future. They are really interesting, and I think have been the biggest thing that has helped me grow as both a student and a person. Also, he likes people who aren't just about grades, so it wouldn't kill you to go to the weight room every once in a while and ask for some help.
  My overall rate for the class would be a 10/10, not because it was easy or fun all the time, but because I actually learned a new way to learn. It was really, and I mean really, hard to do finish blog posts before the deadline, or to do vodcasts when all you wanted to do was get some sleep, but it is worth it in the long run. This class, for me, has been the most memorable in my freshman year, because it's always been something to "Relate and Review" with other people, and joke about little things. Good luck this year, because it will go by really fast. :)

Pig Dissection Relate and Review

  This week we dissected fetal pigs in a span of 2 days. The purpose of this dissection was to explore the different organ systems in the pig and to relate them to our own human bodily functions. This dissection was a hands-on experience and really helped me understand what we discussed in the vodcasts of this unit more clearly. My favorite part of the dissection was finding the thyroid because, for me, the endocrine system is a really fascinating subject that I'd like to learn more about. It was fun doing a video tutorial because I felt like I got a deeper understanding of the organ systems I was speaking about. I think this dissection was a valuable experience and I was able to see what goes on inside of myself and other mammals.

Here you can check out our pig dissection video tutorial:

                                                                          Part 1:

                                         

Part 2:

Part 2:

20 Time Individual Reflection

  At first, Natalie and I wanted to work on 20 time about cat health, and then we realized we couldn't really test our ideas safely on our pets. Then we wanted to do nutrition, but we thought there wouldn't be much variation because our lifestyles are both similar. Also, it is hard to be consistent and rely on food as the cause and effect because things like sleep, and physical activity also come into play. We first thought about memes as a joke, but we were excited and determined to make this a great project when we got the approval.
  The goal of our 20 Time project was to prove how studying with memes makes student's more engaged and able to retain information. We decided to do this because we realized that students get bored easily, and give up on learning easily. Natalie and I wanted to provide an effective, yet an engaging way for students to be motivated to learn.
  Our initial plan was to create a booklet of memes for people to study with, and a booklet for notes for the other test group to study with. We soon realized that with the unknown number of people as well as with printing costs, that this wasn't going to workout. We ditched that plan and turned to the digital format, which is great because memes are usually digital. We did want to originally create a Kahoot! test for the experiment, and we ended up following through with that plan. Kahoot! also brings a fun, engaging, and competitive edge to learning. 
  We also learned that we should have contacted people earlier in the process about being test subjects. We made a Google form for people who were interested and we ended up with about 10 people taking the test. Also, some people showed up really late and didn't study, defeating the point of the experiment. Natalie and I both learned how hard it is to find people that fit exactly what you're looking for, and although those people will never exist, we learned how to deal with the chaos of running an experiment with so many teenagers.
   One of our biggest setbacks was finding a color printer to print out the memes for the posterboard. We went to various classrooms during multiple tutorials, and we ended up printing some at the journalism classroom, and most at my house. 
  I really liked doing this kind of project because I felt like I developed a lot of "soft skills" with all of the freedom we were given. Although we did encounter some ups and downs, we faced our problems head-on and came up with great solutions. Natalie and I worked really well as a team, and we learned to collaborate well and bounce ideas off each other. We learned a lot about time management because when we had such little time, we felt like planning wasn't enough. Later we realized that it was a big part of the process, and we did manage our time well and stay on task every time. 
  If I had the chance to do this project again, I would probably focus more on the technical aspect of the experimental test, just for accuracy. I feel like there were a lot of different variables, but some things were just out of our control. But our "big-picture" style of working was somewhat effective and helped us create a final outcome in the end.
  I learned about how myself, personally, am a visual learner, and I think that's why this project was so appealing to me. I was able to make facts that would usually feel boring, and turn it into something funny and memorable. We did set deadlines for ourselves, which we followed, but it was really hard making memes under pressure. Just making the memes was a learning process. Similar to how making a study guide can help you review and study what you need to know, making your own, original memes are more effective. Also, people might not have the same sense of humor as you, so it's better to just have your own unique way of studying. It would be really fun if everyone in the class could make a meme study guide for a test, and maybe see how it goes. 
  As for continuing this challenge, I would probably make little jokes and pneumonic devices to help me remember information because good memes do take a lot of effort and creative energy. But I will definitely share this experience with others because what I do know is that everyone's learning preference is different, but memes can help everyone learn. Even if they don't remember, they'll remember how it brightened up their day. 
  

River Clean Up Service Project

  This weekend I went to Calabaza Creek for 3 hours to do a river clean-up. It was a lot of fun, and I felt like I was helping the Earth just by helping out for a couple hours. I wonder how much less pollution there would be if everyone cleaned up for a couple hours every month. It was hard getting to trash that was stuck in hard to reach places. There were a couple items lodged between boulders that nobody could get out, and it was a bit disappointing.
  There wasn't as much trash as I thought there would be, but there definitely was some. What I commonly found was pieces of plastic and plastic bags and broken glass. I feel like now I am more aware of the materials I used because I don't really know where they will end up even if they are in the trash can. A lot of this experience related to BagIt, and it was really interesting to see the effect right in front of you.
  At the end, the program organizers had snacks and water for us and I thought it was really cool that they had us use reusable plastic cups rather than plastic water bottles. Although it was just a small act of community service for most, I really felt like I made a difference doing the river clean up. I know that difference was really small considering everywhere else in the world, but I think a small difference is better than no difference at all. I'm glad I seized the opportunity to help out the environment with the community because it was a really fun, rewarding, experience.

Unit 9 Reflection

 This unit was all about life, and how it is classified. Taxonomy is the study of the classification of organisms. We learned about the hierarchical structure and how life is classified through taxonomy. We also learned about binomial nomenclature, which is the widely accepted process of naming species and showing their relationships to the genus in an organized manner. It was developed by a Swedish botanist named Carolus Linnean, and this form of organization is now called the Linnean system. Here you can see a diagram of the different levels of classification in taxonomy.

   Why also learned about phylogeny, and how you can observe common ancestry through phylogenetic trees and cladograms. This relates to what we learned about in the last unit regarding evolutionary relationships. We then went into depth about each of the levels of classifications, and some real world examples that help us to remember.
  First, we talked about domains and kingdoms. There are 3 domains and they are based on biochemical and genetic differences. The first domain is Archea,  which are archaebacteria that are considered extremophiles. They can only survive in the most extreme environments, places that we would think no life could ever exist. I find this fact fascinating because it is a reminder that not everything is about humans and how they live, and that this world is a vast and diverse place. The second domain is Bacteria, and it's the base of all life. There are many types; symbiotic bacteria, cyanobacteria, and actinomycetes bacteria. The third domain is Eukarya, and it consists of plants, animals, fungi, and protists.

  We then learned about bacteria and viruses and established similarities and differences between the two. Bacterial cell wall composition can be used by scientists to classify bacteria into two groups; gram-positive (a lot of peptidoglycans), and gram-negative (little peptidoglycan). We also learned about bacterium and their anatomy, spirals, cocci(spheres), and bacilli(rods). We talked about their different conditions for living, and their metabolism.

• Chemoheterotrophs- heterotrophic bacteria take in organic molecules
• Photoautotrophs- use light to convert CO2 and H2O into carbon compounds
• Chemoautotrophs- use energy directly from chemical reactions involving ammonia, hydrogen sulfide, nitrites, sulfur, or iron.
• Obligate aerobes- must have oxygen to survive
• Obligate anaerobes-can't have oxygen, botulism from canned foods
• Facultative anaerobes- alternative between oxygen and fermentation depending on change in environment

  We also learned about viruses, and how they are small infectious particles, not living cells.We also learned about the composition of viruses, and how they consist of nucleic acid enclosed in a protein coat and sometimes a membranous envelope.
   We also learned about fungi, and the different examples. Fungal cell walls are composed of chitin, plant cell walls are made of cellulose and they absorb food through long strands of fungi known as hyphae. Mycelium is underground hyphae that resemble roots of a plant. They also have a fruiting body, an underground reproductive system. Spores, like gametes, are haploids(single cells), and they can develop into a multicellular organism without fusing. There are three main types of fungi, Sac Fungi, Bread Molds, and Club Fungi.
   The major plant phyla include Bryophyta(mosses), Pterophyta(Ferns), Gymnosperms(cone-bearing plants), and Angiosperms(flowering plants). There are two major types of Angiosperms, Monocots(single seed leaf), and Dicots (two seed leaves).
  The animal classes can be classified as invertebrates and vertebrates. There are many phyla of invertebrates, Porifera(sponges), Cnidaria(specialized tissue), Platyhelminthes(bilateral, flatworms), Annelida(earthworms), Echinoderms(starfish and sea urchins), and Mollusca(snails and oysters). Here you can see a diagram of the different phyla from the kingdom Animalia.

   There are 5 kingdoms in taxonomy, Animalia, Monera, Fungi, Plantae, and Protista.
We went deeper into the different groups and classes of each phylum, but mainly just emphasized the phyla their unique characteristics.

• Porifera-specialized cells but no tissues, sessile, no symmetry
• Cnidaria-specialized tissue, 2 body forms: polyps and medusas
• Platyhelminthes-bilateral animals, incomplete gut, parasitic
• Mollusca- complete digestive tract, 3 classes: Gastropods, Bivalves, and Cephalopods
• Annelida- segmented bodies, coelom, 3 groups: earthworms, marine worms, and leeches
• Arthropoda-exoskeleton of chitin, segmented bodies, and jointed appendages 
• Echinodermata-maternal skeleton made of interlocking ossicles, water vascular system, complete digestive system, most reproduce sexually
• Chordata-vertebrates and some invertebrates, endoskeleton made of bone and cartilage

   There are 7 classes of vertebrates: Agnatha(Jawless fish), Chondrichthyes(cartilaginous fish with jaws), Osteichthyes(bony fish with jaws), Amphibia(four limbs, water/land), Reptilia(amniote egg surrounded by membrane), Aves(birds, presence of feathers, also amniotes), Mammalia(mammals, presence of hair, also amniotes).
  Also, I was a bit overwhelmed with all of the different phyla and classes, so I decided to do the extra credit assignment. Below you can see the concept map I made that outlines almost everything we learned about in this unit. It has been a very useful studying tool so far, and it was really fun to make.

  I still wonder about some things, like all of the organisms that we haven't discovered. Over time will taxonomy change when we make new discoveries? I also wonder how what we learned about the last unit can relate to this unit. What kind of vestigial and homologous structures can we see between the different phyla and classes? I found it really fascinating what we watched in class, in "Your Inner Fish." Just to remember that we are all connected, and with the evolutionary evidence right in front of you, is mind-blowing.
  A big part of this unit was our "What on Earth Evolved?" Presentations. I did mine on Archaeopteryx, and I really enjoyed the process. My topic was something not many people knew about, and the toughest part was trying to describe a transitional reptile and bird fossil and keep the class engaged. I overcame this obstacle in 3 ways. I made sure I used good public speaking skills. I made my slides aesthetically appealing. I also related the facts to concepts we learned in class. It was a lot of fun, and I learned a lot of things. In the future, I now know I should elaborate on the topics that I find interesting and worth to share because that will also keep people interested. Although I enjoyed presenting my Archaeopteryx project, next time, I would challenge myself to do something different, like a physical project. Below you can see my presentation.

Works Cited

Kingdom Animalia. Digital image. Eduvictors. N.p., n.d. Web. 10 May 2017. <https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEim4uelG9fkMP0Nn8wbX1Jp5mCfVrgwerdNp9W8UmEGrBFP3LmhG9hrwDXcqgVRxXuye7qeKTLZsQAkqLrZToRkfX1VRDJGfPD_MpRByg_mFXXaxV3N3xhmRtJZxCMH14wf39WSpAZ8IsJU/s1600/cl9SciCH7Fig6.jpg>.

Levels of Classification. Digital image. Grade 11 University Biology. N.p., n.d. Web. 11 May 2017. <https://uoitbio2013.files.wordpress.com/2013/02/picture1.png?w=627>.

The Three Domains of Life. Digital image. N.p., n.d. Web. 11 May 2017. <http://www.windows2universe.org/earth/Life/images/domains_sm.gif>.

Geologic Time Line Reflection

  In this project, we worked as a group to create a geological timeline using components creatively to assist in better understanding major events that occurred in the history of the earth. We used 10 meters of register tape and labelled and colored major events for each era, period, and epoch of Earth's history. We used 2mm of register tape for every 1 million years, and it was shocking to see how a lot of the more major events occurred "recently" considering the geologic time scale. Things like human existence seem like a blink of the eye considering  the entire geologic time scale. What I noticed when working on the project, is that not much occurred during the longer, earlier periods, and only simple life forms like bacteria and algae dominated. I already knew from previous lessons about how long the precambrian era was, but actually physically drawing on this scaled timeline really showed me a new point of view.
  3 major events in Earth's history would probably be the rise of oxygen in the atmosphere, the dinosaur extinction, and the splitting of Pangea. As blue-green algae and cyanobacteria photosynthesized, the levels of oxygen on the earth increased immensely during the Precambrian Era. This is extremely important and contributed to the existence of oxygen dependent organisms like ourselves.  The Pangea was a supercontinent that used to be a large mass of land that covered roughly1/3 of the earth. It was broken up during the Mesozoic Era, and it was a big part of Earth's history because it created changes in the climate and atmosphere, and it also gave us all the different continents we have today.  Lastly, the end of the Mesozoic Era marked a mass extinction that wiped out the dinosaurs who previously dominated land on Earth. Earth today would be very different if dinosaurs still roamed the earth.
   Like I mentioned before, human existence is just a blink of an eye in terms of the earth's geologic history. In the considerably "small" amount of time we have been on Earth, we have done some major irreversible damage as a species. Although a lot of major life forms arose in the later epochs of the geologic time line, some other major events are currently occurring. We are in the middle of Earth's 6 mass extinction, and it is predominantly caused by humans. We have caused tremendous change to the Earth and we have caused global temperatures to soar off the charts. As humans, in our small amount of time, we can at least have some respect for our Earth to educate each other and make sure we do not create an end to this timeline. I feel as if it is our responsibility to take care of our Earth which is so often taken for granted.
  I wonder how much we can decrease our carbon footprint as far as we've come. Right now I'm typing on a computer that was shipped most likely using fossil fuels. I'm sitting with the light on, and hopefully the power plant where the electricity is coming from is not coal-based and rather runs on wind or water power. I know I can just sit here and rant all day about global warming and how we can never get everyone to stop living their lives, because we have become such a fast paced society so focused on work and life, but we never stop to realize where we actually are, or where everything we use is actually coming from. For now we can all take small steps to reduce our waste and reduce our carbon footprint just by being educated and aware about the issue.





Works Cited:
Geologic Timeline. Digital image. MBMG. N.p., n.d. Web. 20 Apr. 2017. <http://mbmg.mtech.edu/graphics/time-line.gif>.

Unit 8 Reflection

   This unit was all about evolution and the different ways it is studied. We first learned about artificial selection, or breeding for desired traits, which is used by humans for work and food purposes. We also talked about natural selection and Charles Darwin's observations and conclusions. He observed that:

1. All sexually reproducing species have high genetic variation
2. Traits are inherited from parents to offspring
3. All species are capable of producing more offspring than the environment can support
4. Competition is severe because of limited food and resources

   There are two types of competition, inter-competition that occurs between two different species and intra-competition that occurs between two of the same species.
   Darwin's first conclusion stated that there are "winners and losers" as better traits leave more offspring. His second conclusion stated that the "winners" were the population because beneficial traits become more common. Darwin's ideas on natural selection were displayed in our Hunger Games Lab. 
  The gene pool was also discussed, as it is the total of all alleles in a population for one trait. Allele frequency is calculated by dividing the total number of one allele by the total number of all the alleles. If allele frequency has changed over time, that indicates that the population has evolved. Lethal alleles, if recessive, can be hidden in heterozygotes, yet beneficial if conditions change. 
   Speciation was also a major topic we learned about this unit. It is the process of 2 or more species evolving from one existing species. It is caused by reproductive isolation, either temporal(timing), behavioral(courtship/attraction), or geographical(physical barriers).
   We also talked about how descendants of common ancestors have common traits. Embryology shows common ancestry. The patterns of speciation are as follows: Punctuated equilibrium, which occurs rapidly, or gradualism, which occurs slowly. Evo-devo is the study of the process of evolutionary development in multicellular organisms. Hox genes are relatively unchanged overtime(highly conservative), and they are responsible for turning on other genes during development. Vestigial structures are also known as evolutionary left-overs.




  Fossils are formed in these four steps:

1. Organism dies
2. Organism is covered in ash, sediment, or clay
3. Pressure and chemicals cause organism to become rock
4. Hard parts fossilize better than soft parts(fossil bias)

  Index fossils with known time periods are used for comparison. Relative dating is using the placement of fossils with sediment layers to estimate time periods of existence. Homologous structures are same structures, different functions. Analogous structures are different structures, same function. Convergent evolution is the process where unrelated organisms evolve similar structures.
  Natural selection occurs in 3 ways:

1. Directional selection-favors phenotype at one extreme
2. Stabilizing selection-favors intermediate/medium phenotype
3. Disruptive selection-favors phenotypes at both extremes

   Genetic drift is when a random event drastically changes a population and its allele frequency changes as a result. After genetic drift, genetic variation decreases, making populations less resistant to change. Genetic drift changes allele frequency due to chance alone by this random event.

Types of change include:

1. Genetic Drift-random event drastically changes population
2. Gene flow-move of alleles from one population to another
3. Sexual Selection-traits that improve mating success chosen rather than for survival
4. Natural selection-traits chosen advantageous for survival

   Lastly, the history of life was discussed in terms of the geologic time scale. Adaptive radiation is the rapid speciation from a common ancestor. First was the pre-cambrian era, then the paleozoic era which included the cambrian, ordovician, silurian, devonian, carboniferous, and permian periods. Then the mesozoic era occurred and it was known as the age of the reptiles, with the triassic, jurassic, and cretaceous periods. Then the cenozoic era occurred where mammals dominate, and the periods include tertiary(paleogene and neogene)and then quaternary. We are currently in the holocene era, but only a blink of an eye in terms of the earth's history.

  As for my self growth, I feel as if I am more assertive and I am speaking up for myself more. I am no longer hesitant to ask for something, because now I know that the worst possible thing that can happen is for someone to say no. I feel like I am more assertive socially, but personally I feel like I can improve and be more assertive with myself. I need to start being more assertive with myself so I can get work done when I need to to avoid procrastination.

Works Cited

A., Jonathan. Evolution. Digital image. Study Blue. N.p., 24 Mar. 2015. Web. 11 Apr. 2017.

Gradualism vs. Punctuated Equilibria. Digital image. American Museum of Natural History. N.p., n.d. Web. 11 Apr. 2017. <http://www.amnh.org/learn/resources/images/evolution_W4E3_punctuated.jpg>.

How Fossils Are Formed. Digital image. In. N.p., n.d. Web. 11 Apr. 2017. <https://image.slidesharecdn.com/fossilsppt-120502044843-phpapp01/95/fossils-ppt-6-728.jpg?cb=1335934187>.

Hunger Games Lab Final Analysis

1. In this lab we had 3 different species(pinchers, stumpys, and knucklers) compete for reproduction and survival with limited resources.
2. The pincher phenotype could capture food quickly and easily because fingers can pickup items easily rather than wrists and knuckles. 
3. The population evolved, because as shown in the graph and data table, the pinchers outlived the stumpys and knucklers overtime, dominating the population. In the end, the "a" allele frequency dominated the "A" allele frequency in a ratio of 77:23.
   
4. Some things in this lab were random, like the placement of food and number of food pieces necessary for survival. The non-random occurrences were the reproduction of individuals and deaths of individuals. Because of this, the pinchers evolved to dominate the population.
5. If the food was larger, then the stumpys would have the advantage over pinchers and knucklers. In nature, events like these could occur when a limited resource, such as food, changes. That change would affect the natural selection of the species. 
6. Without incomplete dominance in the knucklers, the species would eventually have reproductive isolation and grow apart because of disruptive selection. 
7. Natural selection goes hand in hand with evolution. It uses phenotypes of species best suited to survive and reproduce to change the genotype of the population over time. Ultimately, natural selection is one type of change that causes evolution. 
8. Different behavioral strategies were observed. A stumpy had sat on a pile of corks until everyone left.This stumpy was successful and survived. Also, some knucklers pushed away corks to form a pile hidden behind them, which was successful at first, but people soon discovered it. Also, people would use their bodies to guard food and block others from the source of food. Pinchers and knucklers put corks in their pockets and shirts as a container. These strategies increased the likelihood of survival and reproduction by allowing individuals to obtain more food. This would affect the allele frequency by keeping certain species alive longer than others, because of their strong desire to survive and reproduce. This often happens in nature, for example, many animals use a defense mechanism where they appear bigger to intimidate predators and competition and to protect their resources. 
9. In evolution, the genotype evolves after natural selection acts on the phenotype. The phenotype is what natural selection acts on for survival, but over time this changes the genotype of the species through evolution. 
10. If there was a human disturbance or natural disaster causing more limited resources, would behavioral strategies be the only way to survive, or would pinchers just completely dominate the population? Or is it just luck, like in genetic drift?

Unit 7 Reflection

   This unit was all about Ecology, and the different aspects and how they all affect the Earth. We talked about the difference between habitats, all aspects of where an organism lives, and niches, all factors that the species needs to survive. Biotic factors are living things, and abiotic factors are nonliving things. An important theme in ecology was homeostasis and interdependence. Homeostasis refers to the idea that environments are healthiest when in balance. Interdependence is a concept that all living things in an ecosystem rely on each other as well as abiotic factors for survival. Another key idea is that all energy originally comes from the sun, then to producers, and then to consumers. 

Diagram showing global productivity in different regions. 

   Producers(autotrophs) provide energy for other organisms in an ecosystem. Consumers(heterotrophs) are organisms that consume energy by eating other living, or once-living things. There are herbivores, omnivores, carnivores, and detritivores. Trophic levels are levels in a food chain that are based on what something eats. Food chains and food webs model the flow of energy in an ecosystem in different ways. 
   Energy pyramids show how energy is transferred up the food chain. Food web dynamics explain the domino effects that occurs when populations at the top and bottom of the food chain decline. Another important concept is the levels of organization: organism, population, community, ecosystem, biome, biosphere.
   The 10% rule states that of energy produced/consumed at each trophic level, only 10% of that energy is transfered up the food chain. This is because the other 90% is lost through heat and waste. In population ecology, terms like density and dispersion are used. Density refers to the number of individuals in a given area, and dispersion refers to the pattern of spacing among those individuals in that area. Some factors that can affect population size are immigration, emigration, births, deaths, disease, predators, limited resources and competition.
   Exponential growth in population is most common in bacteria and viruses and well as species rebounding from near extinction. Exponential growth cannot be sustained in any population because they reach limits known as the carrying capacity(K). Carrying capacity is the maximum population size and environment can support. In the logistic growth model, the rate of population increase slows down as carrying capacity is reached, it does not level off. 
   Another topic discussed was ecological succession, which is the sequence of changes in an ecosystem in response to a disturbance. Primary succession is when succession begins without soil to start. Secondary succession begins in an area where soil remains after the disturbance. The stages of succession are as follows: Pioneer species(grasses, lichen, moss), intermediate species(shrubs and tress), and climax community(trees at full maturity). 

Diagram showing the different stages of succession and examples of the types of plant species commonly involved. 

   The nutrient cycles include the water, carbon, phosphorous, and nitrogen cycles. Water is essential to all life. Carbon is the building blocks for all life. Nitrogen is essential to life in the form of DNA and proteins. Phosphorous is critical to life in DNA, ATP, and lipids. 

   Another topic discussed was biodiversity, which is the total number of species in an ecosystem. Genetic diversity is related to all the different genes within a population and between populations. Species diversity is the variety of species in an ecosystem or biosphere. Ecosystem diversity is the different types of ecosystems throughout the planet. An endangered species is in danger of becoming extinct, while a threatened species is at risk for being endangered. Mass extinctions are widespread, rapid, decreases in biodiversity. Only 5 in history have occurred, but we are currently in the middle of the 6th. This is related to the rapid pace of human population growth. Background extinctions are extinctions that happen normally. 

   The main causes of species loss can be traced to 4 major threats. The first, habitat loss, is caused by human farming and development. The second, exotic species, are caused by humans relocating species from their native location. The third is overexploitation, caused by human harvesting of wild plants or animals. The fourth is change in climate, because species are adapted to a specific range of abiotic factors by nature, and drastic changes outside of their niches causes species to die(especially plants i.e drought or excessive rainfall).

   Plants are the producers, or foundation for the entire ecosystem. From the sun's energy, they provide to the rest of the consumers in the ecosystem. Without them, there's nothing. I wonder how in the future, some super industrialized cities will have enough oxygen for humans to breath considering the few trees. Already, with fossil fuel pollution it is hard to breath in big cities, but will it get worse? How can this be prevented so we can take a step back from the industrialization and restore parts of our natural ecosystem?

   For our conservation biologist project, we easily came up our topic: the arctic tundra. We began our team contract and assigned roles for research with ease. But when it came time to condense our research and begin writing the slides, I ended up doing the entire thing. Luckily, we were able to finish our recordings in class, where Kai then volunteered to do the editing. Overall, it was a rocky experience, because it was difficult to contact people when I needed to, but I think it has made me more assertive. Overall, I think I had been more passive and patient with the group to an extent that was creating conflict for the terms of the project getting done. The experience has given me more of an active voice to listen to others, but make clear what I would like.
   We also watched the story of stuff videos and I posted on my blog a summary and reflection of another video, as well as notes and a response to a question about "The Story of Stuff." You can view it here: Story of Stuff and Story of Cosmetics

Works Cited

Carbon Cycle. Digital image. National Center for Atmospheric Research. N.p., n.d. Web. 8 Mar. 2017. <https://eo.ucar.edu/kids/green/images/carboncycle_sm.jpg>.

Global productivity and sunlight angles on earth. Digital image. Quia. N.p., n.d. Web. 8 Mar. 2017. <https://www.quia.com/files/quia/users/lmcgee/ecology/sun_angle_latitude.gif>.

Nitrogen Cycle. Digital image. Partnerships for Environmental Education and Rural Health. N.p., n.d. Web. 8 Mar. 2017. <http://peer.tamu.edu/curriculum_modules/Environ_Hazard/images/nitrogencyclesmall.jpg>.

Phosphorous Cycle. Digital image. Wordpress. N.p., n.d. Web. 8 Mar. 2017. <https://raceingminds.files.wordpress.com/2013/06/phosphorous-cycle.jpg>.

Stages of Succession. Digital image. Slide Share. N.p., n.d. Web. 8 Mar. 2017. <http://image.slidesharecdn.com/succession2009-110426161751-phpapp01/95/succession-2009-19-728.jpg?cb=1303834862>.

Water Cycle. Digital image. NASA Precipitation Measurement Missions. N.p., n.d. Web. 8 Mar. 2017. <https://pmm.nasa.gov/education/sites/default/files/article_images/Water-Cycle-Art2A.png>.

 

Story of Cosmetics

Summary and Reflection:

The story of cosmetics was about all the toxic chemicals that are put in everyday consumer products. Exposure to these toxins have been known to damage reproductive organs, and induce disorders like autism, and asthma. Many of these chemicals are known to be carcinogens, which are cancer causing chemicals. Also, it mentioned how the FDA does not even require all ingredients of these cosmetic products to be listed. The FDA doesn’t assess the safety of many of the ingredients in these products. Since 1938, they have only banned 8 out of 12,000 ingredients used in cosmetics. Because of the lack of regulation, cosmetics industries self-assess their products. The lack of government action has ultimately lead to the exposure of toxic chemicals in our daily used products.

Now I feel like I am more skeptical as to what I am putting on my skin, and more curious about what these things mean. I was always someone who would read the labels, but I didn’t do anything about it because I didn’t know what these things were. After all, they wouldn’t be allowed to buy if they weren’t safe right? The interesting statistics brought up about the lack of regulation in the FDA has me worried about everything I use. How do I know my toothpaste, deodorant, chapstick, and shampoo are even safe? Women use an average of 12 cosmetic products daily, while 6 for men. I hadn’t  even realize how many products I really use until I thought about all the chemicals in them. I think overall it has made me more aware of how many things I have, and how most of them are really harmful.

Story of Stuff

Notes:

• The materials economy runs through a process of extraction, production, distribution, consumption, and disposal.
• Every step has an interaction between the system and the real societies, cultures, and environments. 
• We are running out of natural resources, for a number of reasons. For example, the US has only 5% of the world's population but uses 30% of global resources. 
• In the Amazon Forest alone, we are losing 2,000 trees per minute.
• In production, toxic chemicals are added to the natural resources. 
• Externalized costs mean that the social cost is more taxing than the product's cost.
• 99% of items run through the system to later be thrown away after 6 months. 
• The average US person consumes twice as much as they did 50 years ago.
• Planned obsolescence are designed for the dump, so we throw things away and buy new ones.
• Perceived obsolescence convinces you to throw stuff away that us perfectly fine, 
• People in the U.S. see more advertisements in one year than people did 50 years ago in a lifetime.
• The average united states resident produces about 4.5 pounds of garbage per day.
• The garbage is dumped into landfills or incinerated, which both contribute to pollution and climate change.
• Recycling is not enough because many products are not designed to be recycled. 
• People united can change the way the system works. 

Q3: Annie says “recycling doesn’t get to the core of the problem.” Why not?

   For every one garbage can of waste, we put out, 70 other garbage cans of waste were used to produce the waste in that one garbage can. Also,  much of our garbage cannot be recycled because it either contains too many toxins, or it is designed not to be recycled. For example, there are juice boxes that are lined with layers of metal, paper, and plastic, so they cannot be separated for recycling. Although recycling is extremely important to help reduce waste and reuse products, the fact of the matter is that there are more things we can do to make a difference, because just recycling isn't enough. 

Unit 6 Reflection

This unit was all about biotechnology. The introduction of biotechnology discussed how it is known as the study and manipulation if living things in order to benefit mankind. This large field focuses on understanding DNA, proteins, and inheritance. There is a long timeline of biotechnology.

•  It began in 4,000 BCE in the classical biotechnology time period, where dairy farmers developed in the middle east and Egyptians used yeast to bake and learned to make wine through fermentation. 
• In 3,000 BCE Peruvians selected and cultivated potatoes.
•  In 2,000 BCE Egyptians, Sumerians, and Chinese develop techniques of fermentation: brewing and cheese making. 
• In 1500 CE acidic cooking techniques led to sour kraut yogurt- 2 examples of using beneficial bacteria to flavor and preserve food. Aztecs make a cake from spirulina algae.
• In 1861 french chemist Louis Pasteur develops pasteurization: preserving food by heating it to destroy harmful microbes.
• In 1910 American biologists Thomas Hunt Morgan discovers that genes are located on chromosomes
• In 1953 James Watson and Francis Crick Describe the double helix of DNA using x-ray diffraction patterns of Rosalind Franklin and Maurice Wilkins.
• In the early 1970's Paul Berg, Stanley Cohen, and Herbert Boyer develop ways to splice DNA, introducing recombinant DNA techniques.

A big emphasis in the introduction to biotechnology was the 4 real-life applications of the science and its effect. 

• Industrial and Environmental: Fermentation- the use of bacteria or yeast in an oxygen-free environment to convert sugars into acids, gasses or alcohol. (ex: food like yogurt, cheese, beer, wine, bread etc)
• Medical and Pharmaceutical: Gene therapy-putting a healthy copy of a gene into cells of a person whose copy is defective, Germ Line gene therapy- insert the gene into germ cells(sperm/egg), Somatic gene therapy- insert the gene into specific cells w/defective expression of the gene. 
• Agricultural: Classical breeding- individuals with desired traits are bred over many generations. GMO/Transgenic organisms are the product of recombinant DNA(Foreign DNA inserted in them)
• Diagnostic: Genetic testing- search for genes or DNA segments indicating risk for various diseases or disorders.

An interesting infographic about GMOs 

We also talked about the "technologies of biotechnology" and the different steps and procedures commonly used. We talked about Polymerase Chain Reactions (PCR) first, and then we talked about Gel Electrophoresis. We had already learned about gel electrophoresis when we did our Candy Electrophoresis Lab and our virtual lab.
   The lab was long, but it was lots of fun. It really helped me understand how gel electrophoresis really works. Although some errors got in everyone's way(as mentioned in the link), I feel like I have a better understanding of why each step in the procedure was there. Also, I learned how to use a micropipette to fill the wells of the gel after extracting the colored dyes from candies.

PCR: A procedure to amplify a specific DNA region that yields millions of copies of a sequence of DNA. It is the first step in preparing DNA for many experiments like gel electrophoresis and any other form of analyzation. The process makes millions of copies of the small DNA fragment so it is easier to study.
Check out this video that explains PCR: https://www.youtube.com/watch?v=3XPAp6dgl14

Steps of PCR:

1. Denature the double stranded DNA with heat
2. Anneal the primers to single stranded DNA above and below the region of interest. *A primer is a small fragment of DNA that bonds with a specific sequence.
3. Extend primers with DNA polymerase yielding new double stranded DNA. This cycle repeats steps 1-3 usually 20-40 times. The copies from PCR occur in exponential amplification which means after 30 cycles, DNA is amplified over a billion-fold. 

Helpful diagram displaying PCR

Gel Electrophoresis is the use of electricity to separate DNA fragments based on size. Large pieces travel slower than small pieces, and the results of distance traveled by the unknown lengths are compared to those of known lengths. It has many different applications such as forensics, biochemistry, genetic diagnosis, etc.

Sequencing was also discussed in the vodcast. Sequencing by definition is determining the exact order or sequence of a given DNA strand. DNA polymerase, primers, extra bases, and fluorescent dyes are all used to create copies. These copies are one base longer and contain fluorescent dyes attached. They are then electrophoresed and analyzed with a computer. The result is an electropherogram and the colored bases represent 1 of 4 bases. Finally, the sequence of bases is recorded.

Recombinant DNA was also discussed, where DNA of one organism is inserted into the DNA of another organism. Recombinant DNA or rDNA is also known as genetic engineering. The result of rDNA is GMO's (genetically modified organisms) or transgenic organisms. The steps followed to use rDNA technology in bacteria is as follows.

1. Gene of interest: know the location and sequence of your gene(above and below it)
2. The restriction enzyme cuts DNA wherever it reads a specific sequence. It latches onto the restriction site. Each restriction enzyme leaves a sticky end at the cut, which allows DNA to bond other DNA. 
3. Plasmids: circular DNA found in prokaryotes contains a replication gene that tells the plasmid to be copied. Typically it contains genes with antibiotic resistance that are small enough to be passed through pores of the cell membrane.
4. Ligase: an enzyme that re-attaches base pairs. 

The process of transforming bacteria to mass produce a protein product:

1. Isolate the DNA by finding the gene of interest and organism to insert the gene into
2. Get the plasmid, and know what antibiotic it is naturally resistant to
3. Digest  the DNA by finding a restriction enzyme that will cut the plasmid once above and below the gene
4. Mix the digested DNA(plasmid + gene)
5. Add ligase to attach sticky ends
6. Mix recombinant plasmid with the bacteria
7. Plate bacteria on agar with the antibiotic mixed in (only those with the plasmid(antibiotic resistance) will survive)
8. Grow the transformed bacteria and transfer to broth(liquid agar) to make many bacteria expressing the gene
9. Extract and purify the protein the inserted gene produced. 

Recombinant DNA technology has an interesting history. It was discovered when Herb Boyer and Stanley Cohen met at a conference. With their combined knowledge of restriction enzymes and isolating genes, they were able to work on the toad/bacteria rDNA together in the March of 1973. They discovered how DNA could be transferred between different species, and the world of genetic engineering was born. 

Another topic was the pGLO lab, which elaborated on the previous vodcast. It was about the bacterial transformation of an e.coli bacteria, using the presence of plasmid for a fluorescent glowing reaction.  My pGLO Lab Analysis and this video do a great job of explaining the process. Without doing the virtual lab, and the pGLO lab, I would have little understanding of how the procedure occurs, and why every step does what it does.  https://www.youtube.com/watch?v=OZyFX9megs8
   I learned how to predict which bacteria would glow, grow, or have nothing at all. For example, the plate with just LB, or lysogeny broth which makes the bacteria grow, would have bacteria on the plate. The plate with LB/amp (ampicillin, the antibiotic which the plasmid is resistant to) without the plasmid would not grow. The plate with LB/amp with the plasmid, would grow. Lastly, the plate with LB/amp/ara (arabanose is the sugar that acts as a promoter of the GFP gene, controlling its expression) would grow bacteria and glow with green flouresecnt protein. 

A picture of the results of another group in the class.

The last, most unique topic explored was about bioethics, and how we should answer not only ethical but bioethical questions. I feel like it has really opened my eyes to what my morals and values are, which will help me make ethical decisions in the future. The answer to ethical questions come from your morals(your justification of what is right or wrong), and your values(what is most important based off of your unique, personal experiences). The same approach is taken when you are faced with a bioethical question. You must first clarify your values, then identify the issue. Find as many options possible, and then list the pros and cons of each decision . Rank your ideas from best to worst, and once you've come to a decision, defend it. 

After reading articles in class, I wonder about all the infinite possibilities and ideas people can come up with to apply biotech. After listening to summaries of other classmate's articles, I was intrigued by the various fields and forms biotech took. I did further research on my own article about gene editing tools used to cure genetic diseases caused by mutations which you can find on my blog: Bioethics Reading. That's why it was a bit of a struggle for me to get started on my 20-time project, because I wasn't used to such vast boundaries. Usually, there is a set goal, but I think this free- thinking has really reignited my creativity. 

Lastly, I have been checking in on my New Year Goals, and I have found that I've been improving my studying skills. I can identify the forms of studying that are best for me, much quicker for each topic, but I still struggle with time management. As for drinking more water, I have bought a new water bottle, and I have been motivated to stay hydrated. I think overall, I am making good progress for both of my goals, but there is always room for improvement. 

Works Cited:

GMO infographic. Digital image. Kids Right to Know. N.p., n.d. Web. 31 Jan. 2017. <http://www.kidsrighttoknow.com/wp-content/uploads/2010/05/What-is-a-GMO.jpg>.

Polymerase Chain Reaction - PCR. Digital image. Wikimedia. N.p., n.d. Web. 31 Jan. 2017. <https://upload.wikimedia.org/wikipedia/commons/thumb/9/96/Polymerase_chain_reaction.svg/835px-Polymerase_chain_reaction.svg.png>.

pGLO Lab Analysis

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 0 tan tan - pGLO LB/amp N/A N/A N/A + pGLO LB/amp 1 tan tan + pGLO LB/amp/ara 4 tan fluorescent green

2.	What two new traits do your transformed bacteria have?
	The bacteria are now resistant to ampicillin(antibiotic), and glow fluorescent green under UV light.
3.	Estimate how many bacteria were in the 100 uL of bacteria that you spread on each plate. Explain your logic. Because each plate has 100 microliters of bacteria spread on it, the number of bacteria is the same for each plate. The volume of 1 E. Coli bacteria is about 1 micrometer cubed, which is equivalent to 0.001 microliters. 1 microliter(the volume of each bacteria) is equal to 1, 000 micrometers (or 1,000 bacteria). Since there are 100 microliters of bacteria spread on each plate, and 1,000 micrometers of bacteria 1,000x100 gives the answer of 100,000 bacteria on each plate. 100,000 bacteria(micrometers) is equivalent to the 100 microliters spread.
4.	What is the role of arabinose in the plates?
	The role of the arabinose sugar is the key component for making the bacteria on the plate (which were resistant to ampicillin, and contained the plasmid) glow. It is a promoter of the gene, allowing it to be expressed.
5.	List and briefly explain three current uses for GFP (green fluorescent protein) in research or applied science. GFP is a protein extracted from a jellyfish gene, which is commonly used to tag genes and cells of interest with its fluorescent properties. It can be used to identify expressed genes, making it easier for research scientists to observe their results. Some common applications are GFP being used to track and label cancer cells that can travel throughout the body. Some genetic engineers and breeders are also incorporating GFP into the cells of living things like fish(i.e. glo-fish).
6.	Give an example of another application of genetic engineering. The use of transgenic organisms, or creating GMOs (genetically modified organisms) in foods. A specific example is genetically modified foods. Some corn with GMOs can produce a poison to kill insects without pesticides. This contributes to the agricultural industry, making it a lot easier to produce mass amounts of crops without the conflict of naturally occurring environmental factors. Photos: Icing the tubes with transformation solution during the lab. Transferring the cold tubes to the heat bath. Incubating the tubes with and without the plasmid(-pGLO and +pGLO) Results after two days (under normal light0 Results after two days under UV light