Letter to a Biology Student

Hello Biology Student,

I am in the 9th grade and when I was starting this class like you I was 14 years old however I turned 15 in a week of school. I was interested in Biology so I took this class. My general approach to school is to do as well as I can and to learn as much as possible. Outside of this class I play the trombone in Band and am a member of the Robotics Club. On the first day of class I expected to take notes in class and review the topics for homework. BUT NO, the classroom was flipped so we took notes in vodcasts outside of school.

Mr. Orre expects us to finish the homework on time and to be respectful and attentive in class. The first thing we do when we come to class is get out our vodcast notes so that they can be checked. After that we write and answer the Do Now. Once we have finished that, someone in the group reviews the vodcast and the Do Now. After that, on a typical day, we do a lab or write something on blogger. On occasion we will have a test with a notebook check prior to it. And sometimes we will work on a project during the class period. On a typical lab there is a small packet where we fill in our data and observations, this packet also contains information on the procedure, or other background information. Once we finish the lab, we normally write a reflection on the lab on a blogger post. We have vodcasts, which are online videos we take notes on, almost every block day. This homework takes usually about 40 minutes. Around once a month, we have to take notes on sections in the textbook. This takes around 1 and ½ to 2 hours, however we usually have a few weeks to work on these notes. The tests and quizzes are normally multiple choice and if you study for them they shouldn’t be too difficult. We write all our notes and Do Nows in our notebook which is organized by page numbers and a table of contents, you will learn more information on this in the vodcasts in the rookie module. Over the year, we record lab reflections, and unit reflections on our blog. Mr. Orre expects each blog to be better than the one before it and an improvement over the course of the year. Over the second semester, we work on our 20-time project. The goal of this project is to spent 20% of our class time working on something we find interesting. Although I did not finish a prototype of my project, the research I did taught me and my partner many concepts. My favorite blog post is my 20-time Individual Reflection.

One of Mr. Orre’s pet peeves is presentations that contain too many words on the slides and not enough visuals. If you have the chance to make any kind of presentation for this class or different class, I would highly encourage having limited words on the slides and orally explaining the content in detail. Also having visuals that relate to the topic is also helpful. On my What On Earth presentation I tried this and it turned out very well. To earn a good grade on an assignment, you must give effort and time to the assignment. Homework is important for receiving a good grade in the class, not only because it makes up a large chunk of the grade, but because it helps you know and understand the topic that you will be assessed on in the test. To get a good grade on a test you must review your vodcasts and other notes before the test. Also, make sure that your notebook is always organized because many times the notebook check is worth more points than the test. To get the most out of this class I would suggest trying to make sure you still understand the concepts even after you have been assessed on it, because they will likely show up again in other times of your life. One mistake I made this year is I would sometimes get lazy and not do the CFUs, which are mini online quizzes after each vodcast. Since the CFUs are occasionally graded and many of their questions show up again on tests, I could have had more points if I had done them. Another mistake I made was not spending enough time on the conservation biology project. Although I met all the standards I failed to go above the average. One last mistake I made was forgetting to write a relate and review for the textbook notes a couple times. Although I knew I was supposed to do it, the fact it was different from a vodcast made me sometimes forget the write the relate and review. From these mistakes I have learned how to be a better student both in biology and in other classes.

Overall I would rate the class as a 10 out of 10. I liked it because I learned a lot about biology and other science topics. Although the vodcasts can be kind of tedious they are full of useful information. Next year I am taking Chemistry Honors because I want to learn more about science. Overall give your best effort and you will have a great year!

Sincerely,

Connor Galvin

Pig Dissection

The Pig Dissection was engaging and educational. The smell of the preservatives was very pungent, however from this experience I learned a lot about the parts and functions of the body. The plasticiser helped show where the veins and arteries where by color coding them. With a few differences, pigs are very similar to humans so this helped show how human anatomy would be without actually dissecting a human. This dissection helped me relate concepts learned in vodcasts in the Physiology unit to real life applications. It was especially interesting how we could see the digestive system in a way other than a diagram. Most of these ideas I knew before hand in theory however this dissection helped me learn how to identify the organs on an actual organism.

20-time Individual Reflection

Equation we used for calculating lift.

   In this project we chose to do a project to build a RC hot air balloon, we chose this because the project was going to last the whole semester so we wanted to try to do something that would take a lot of time and be hard. The focus of this project was to create something that hadn't been made too often so we could see what we could do to perfect it's design.

   The initial plan to achieve the goal was to have a couple months of research and then the rest of the semester we would work on building it.

Idea for built in remote control electrophoresis for
hydrogen balloon. (to dangerous to test on a large scale)

   As we started the project, we soon realized that this would require much more research than we thought we would need. Our choice of balloon envelope material changed from plastic bag to nylon to silicone coated nylon to paper to urethane coated nylon to thin plastic bag and so on. We also researched in the use of hot air, helium, and hydrogen for lift. My robotics and planning for my eagle scout project took more time than I anticipated so I had less free time to work on the project than I thought. However in researching the project I learned many new things about physics, material properties, and electronics. We would first research something and then test it for effectiveness, like putting it over a candle to test it's heat resistance. All class time for this project was used efficiently and out of class research time was used also. Overall I think this was a successful research project, however we are not yet finished with building a prototype.

   While doing this project I learned many process skills by working with my partner Will. We communicated together both in and out of school to collaborate on our research for the project. If I had done this project again I would have started with a smaller scale. I have learned that I sometimes try to be a bit too ambitious, however I think this project is achievable with a bit more time.

Diagram of simple hot air balloon idea

   Over this summer, Will and I will continue to work on this project in building a physical prototype for the RC hot air balloon. Since we have already done so much research on this topic we know what works well and what works bad, so it is just the building we need to do now. The research we have done was a good learning experience and I can't wait to make a physical prototype of our ideas and designs.

Unit 9 Reflection

  This unit was about the classification of species, and the characteristics by which they are classified. Species where originally classified into 7 levels, however nowadays we classify into 8 taxonomic levels. The levels from broadest to smallest are: Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species. The Bacteria and viruses vodcast explained how Bacteria can be classified as gram-positive or gram-negative, and viruses infect cells and force the cell to create more of the virus. The fungi and plants vodcast explained their properties and how they are classified. In the many vodcasts about chordates and invertebrates we learned the characteristics of many phylums and classes in the kingdom Animalia. Classification might seem tedious and useless, however it is significant in sharing scientific observations and understanding genetic relationships. I want to learn more about the classifycation of different species and their characteristics so that I can better understand their evolutionary relationships.

Budding video used in What on Earth Presentation

   In this unit we also did a What on Earth Presentation. We had the ability to choose our own organism to research and do a presentation for in front of the class. My presentation was on yeast and it can be viewed below. The requirements for this project where more vague and allowed us the option to research and report on what we thought was important on the topic. This gave us more freedom to choose what we presented about. For my project I did a lot of research however I only presented the parts that I thought where useful and people would like to know, instead of putting in all the information that I could find. For the slides I used less wording and more pictures because it was a presentation and not a report so people would look more at the pictures instead of the words. To enhance people's understanding of the topic of budding I added a time-lapse of the budding process that I found on YouTube to the presentation. To make the presentation more apparent to everyday life I spent most of the presentation describing how yeast is used in everyday things such as bread, alchlohal, or root beer. Overall I think that the presentation went well and in the process I learned how to make a presentation accurate and engaging without incisive guidelines.

Geologic Timeline Reflection

   One major event in earth's history was the Cretaceous-Tertiary Extinction. The Cretaceous-Tertiary Extinction was when the last of the dinosaurs exception of birds went extinct. This extinction is a significant factor in the transition from the age of the dinosaurs to the age of the mammals eventually creating human. Another major event in earth's history was the appearance of cynobacteria. Cynobacteria helped to change the atmosphere into one with a higher concentration of oxygen. This oxygen was then toxic but it was later used by more advanced organisms in respiration, like humans. And a third important event in earth's history was the Cambrian explosion. The Cambrian explosion was the relatively sudden appearance of advanced organisms in the Cambrian era. These organisms created in the Cambrian explosion would later evolve into all the multi cellular plants and animals in geologically a relatively short amount of time.
   On our 10 meter long geologic time line of earth's history almost all of the major events happened in only the last 2 feet. This is surprising in how little amount of geologic time it took for much of evolution to take place. And what's even more important about this geologic timeline is that we as the human species can greatly change the face of the earth over only a few thousand years and at a more significant rate over only a couple hundred years. And this is relative to 4.5 billion years that the earth has existed as a planet. The vodcasts and our geologic timeline where very full of information therefore I have no unanswered questions.

Unit 8 Reflection

Hunger Games Lab

   In this unit we learned about how over time artificial and natural selection cause evolution, and also how this evolution is shown and how it can be proven. In the Change, It's all natural and Very Gradual Change you can believe in vodcasts we learned how both natural and artificial selection over time cause a population to evolve. The swimming in the gene pool vodcast explained how this evolution happens over time more statistically by showing allele frequencies and population numbers. We later simulated this process in the hunger games lab in which natural selection played on a population causing the population to have a higher allele frequency of the allele that resulted in a beneficial phenotype. The speciation vodcast explained how a species splits into 2 different species because of behavioral, geographic, or temporal reasons. Evidence for evolution can be shown in embryology, vestigial structures (evolutionary left overs like the human tailbone), Fossils, homologous structures (same structure of bones but different function), or in analogous structures which is the opposite of homologous structures. And finally the origin of life vodcast the possible theories for how life first formed are explained.

    I would like to learn more about the causes and effects of evolution over time and the specific species that where created and how they came to be. This unit was very full of information and left me with no unanswered questions. I wonder about what species existed on earth before and later when extinct and how some of their traits are shown in our modern species.

    In the Unit 7 Reflection I reflected on the topic of being assertive. We watched a video and did a survey on how assertive I am. Most of the points I got on the survey showed that I was assertive. Over this unit I have kept being assertive and helpful in our timeline project.

Hunger Games Lab

1. In this lab we simulated natural selection by having three prototypes: Stumpys, Knucklers, and Pinchers. Stumpys could pick up food with their wrists, Knucklers could pick up food with their knuckles, and Pinchers could pinch the food to pick it up. The Stumpys where homozyguous dominant, the Knucklers where heterozyguous, and the Pichers where homozyguous recessive. In each round the organisms would fight over corks which would be food. The organisms that got enough food to survive would reproduce and create another organism with a phenotype determined by each mating organism flipping a coin with their alleles on each side. Then we would repeat this process 8 times.
2. The Pincher phenotype was the most effective at capturing food because it could get the best grip on the corks.
3. The population evolved because over time more of the other phenotypes died out while the pincher phenotype survived and grew. This is known because over time the knuckler and stumpy populations decreased while the pincher population grew. This is shown in the data where the allele frequency goes from around 50-50 to about 75-25 and 75 being the "a" allele which makes up the picher's homozyguous genotype. 
   
4. This lab was in some ways random because the mating choices are random and also some of the less advantageous organisms could have still survived by being very aggressive.
5. If the food was smaller it would benefit the pincher phenotype even more, and if the food was larger it would benefit the knuckler and stumpy phenotypes more. Over time this would make the A allele more common and the a allele less common.
6. If there was not incomplete dominance this would cause there to be many more Stumpys because they had the dominant allele. However over time the Pinchers would start to take over the population, however they would have to only mate with other Pinchers to make the process faster.
7. Natural Selection causes evolution because natural selection will kill of the bad phenotypes and only the beneficial phenotypes would live to reproduce, this over time would cause there to be more of the phenotypes beneficial to survival to exist in a population. This is evolution.
8. The stumpy population after almost dieing out completely decided to work together and keep the population strong. This occurs in nature when organisms with less beneficial genotypes will work together in a herd.
9. In evolution a population evolves over time, not an individual organism. Natural selection most directly acts on phenotypes for survival. However the corrosponding genotype for the phenotype will be passed on to the offspring. And that offspring's chance of surving to reproduce will be determined by it's phenotype which is determined by the genotype it got from it's parent.
10. The one question that I still have would be why the populations of the different phenotypes first follow directional selection in the first half but then in the second half it seems to follow disruptive selection more?

Unit 7 Reflection

   This unit was about Ecology and how it effects us and how we effect ecology. In the Food Chain vodcast we learned how food chains and food webs transfer energy from organism to organism in an ecosystem. The ecosystem energy vodcast taught us how in energy pyramids the amount of calories in each tropic level decreases by 10 times as it gets higher. This is important because it shows how wasteful it is to eat animals on higher tropic levels. In the population ecology vodcast we learned how certain populations grow exponentially and others grow logistically when they get closer to the carrying capacity. The human population is growing at very high rates and is expected to reach carrying capacity soon.

   I want to learn more about ecology in the future and how plant and animal populations are dependent on each other in an ecosystem. I have no unanswered questions because the vodcasts explained everything I needed to know.
  The Conservation biology project went well and there was no problems with the collaboration. The one problem we did have was that while we where filming a series of things happened that unfortunately made the audio quality poor. Firstly, near the beginning there where some construction sounds, and halfway through the video one of the classroom doors nearby was opened creating more sound. These problems would have been avoidable if we could do another recording of the project, however I had to go to jazz band photos during tutorial so we couldn't work on it then. However the group collaboration was fine and I think our slides where great. In the self assessment we did at the end of the unit I got the most points in assertive which is good.

Unit 6 Reflection

   In this unit we learned what biotech was and how it is applied for use in biotechnology. The candy electrophoresis lab demonstrated how gel electrophoresis is used to sort DNA strands by their lengths by using the dyes in candy. Later in the pGLO lab I learned how to use plasmids to transform the bacteria E. coli to glow under UV light. In this unit I learned many things about biotechnology and how it is applied to real life. Although most of the dyes ran off the gel in the candy electrophoresis lab due to a school assembly, in the pGLO lab our E. coli was successful in taking in the plasmid and glowing.
 
   In the candy electrophoresis lab we extracted the dyes from the candies and then used a centrifuge to concentrate the dye. After that we placed the dyes into the slots and compared how far each band traveled. Unfortunately, an assembly started when we where running the gel and once we got back the dyes had run off the gel! There where 2 blue strands still remaining on the gel so I observed these strands.

In the pGLO lab we got E. coli to take in a plasmid that would make it create glowing proteins. First we dissolved a E. coli colony each into 2 different vials, one containing the plasmid that would make the cell make glowing proteins and one without. The vials where then cooled then heated then cooled again. Eventually the solution was spread out onto 4 separate petri dishes. The petri dish that had the E. coli in the broth, ampicillin, and arabinose glowed when placed under an ultra violet light.

I want to learn more about biotechnology and it's applications in the future. I understand all the topics in the vodcast and how all the experiments worked in the labs. However I wonder what the results of the candy electrophoresis lab would have been like had the experiment not failed. As far as my New Year's goals go, I am currently on track.  My notebook is nice and organized and I have made sure that I understand each topic.

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 76 76 0 - pGLO LB/amp 0 0 0 + pGLO LB/amp 0 0 0 + pGLO LB/amp/ara 13 13 13

2.	What two new traits do your transformed bacteria have?
	The transformed bacteria have the 2 new traits of glowing under UV light and ampicillin resistance.
3.	Estimate how many bacteria were in the 100 uL of bacteria that you spread on each plate. Explain your logic.
	I estimate that the amount of bacteria inside the 100 uL was roughly the same amount as the amount of colonies there where. This would be because once a bacteria landed on a certain spot it would multiply exponentially and create an entire colony.
4.	What is the role of arabinose in the plates?
	The role of arabinose was to create a nutrient rich environment for the glowing bacteria so it could have all the nutrients needed for a bright glow.
5.	List and briefly explain three current uses for GFP (green fluorescent protein) in research or applied science.
	Tagging certain genes so their expression in certain cells will be known. Acting as a biosensor or cell marker when studying protein-protein interactions. visualizing promoter activity.
6.	Give an example of another application of genetic engineering. Other kinds of plasmids could be used to change certain genes and gene expressions in order to make organisms that produce certain kinds of proteins that can have benefits to health or sustainability. For example a plasmid could be used in bacteria to create a foe meat or other kind of food.

Candy Electrophoresis Lab

The results of our experiment.

In our experiment there where no dyes that had visibility have different lengths than the reference dye. This might be because there was only 2 blue dye bands that where observed because the rest ran off. Our dyes ran off because we had to go to an hour long assembly while the electrophoresis was only supposed to run for only 15 minutes.

Electrophoresis system before running current.

The dyes that where observed where blue colored and since they where the only ones on the gel after the current being applied for about an hour they where very slow. These blue dyes would likely be either Carminic acid or Betanin since they have long molecules.

Manufacturers put food coloring in dog food because the colorful treats look better to the owners who buy them. Also since there are likely less restrictions about food coloring in dog food manufacturers would be allowed to use cheaper but more unhealthy food coloring.

The distance the colored dye solutions migrate could be determined by the length of the dye molecule, the amount of time it is running, and the voltage of the electrolysis machine.

Centrifuge used to concentrate dye solution.

The force that moves the dyed through the electrolysis machine is the electricity. When the molecules in the dye get charged they are pulled through the pores in the gel by an electrical attraction to the other side.

The electrophoresis system separates  molecules by size because the smaller molecules move much faster through the gel than the larger molecules. So in the end the bands that traveled farther are the smaller molecules and the ones that traveled less are the larger molecules.

Candy the dye came from.

If DNA molecules have molecular weights of 600, 1,000, 2,000, and 5,000 Dalton, the 600 Dalton molecule would travel the farthest. In second would be the 1,000 Dalton molecule. Third fastest would be the 2,000 Dalton molecule. And the slowest molecule would be the one that is 5,000 Dalton.

New Year Goals

   In this new year I will put more effort into this class. This will be done by first studying at least an hour or two longer for the tests in biology. Making sure that my notebook is always completed and organised not only to the amount needed to get a 100 on the notebook check, but more. Even if it wouldn't change my grade it would still add to the organisation and make things easier to find when studying. In labs I will spend time giving more complete and detailed analysis. If I accomplish this the accomplishment of this alone is enough of a reward for the needed motivation.

   Also in English class I will also put more effort into the assignments. On the projects I will spend more time perfecting them and find more collaborative group members. I will make sure that the product of the project is to the best of my ability. On tests I will study for at least an hour longer and use study tools like flashcards to help me learn the concepts. If I complete all of these I should be able to not only increase my grade but feel more confident in my school work.