Letter to a Biology Student

First of all, you have to check out this video. It pretty much sums up all of biology class. Here is the link:
https://www.youtube.com/watch?v=ap3QcPH6saA

I am Sandhya, a current freshman and I am 14. The classes I took this year are Journalism 1, English 9 MAP, World Geo/Health/DrEd, Espanol 2, Alegbra 2 Honors, and Biology. My interests in school are writing, science, math, english, and Spanish. I play the piano, sing, and play volleyball.

On the first day of class, I had this expectation that biology and just freshman year in general would be super hard. If this makes you feel better, it wasn't.

Mr Orre expects you to do your homework (the vodcasts) and the CFU's. If you pay attention to them and do the CFU's, you will be fine and you'll meet the basic expectations.

Here is a typical day in class. You come in, and get out your stuff. Then you will do a "golden moment" of mindfulness, and then you look at the board and do the DO NOW. Then, in your groups, you'll recap the vodcast and later Mr Orre will review it as well. The rest of class you could either be working on labs, blog posts, or projects.

Homework is a vodcast every class and sometimes unfinished work such as lab conclusions and projects. For example, I am in class right now. If I don't finish writing this now, it becomes my homework.

Tests are all straightforward and multiple choice. You will have to set up a notebook to use for the rest of the semester to have all of your vodcast notes and DO NOWs. You will also be required to keep a blog of all of the major things you'll do over the year in biology. My blog is called the Brilliant Biology Blog.

My favorite blog post is linked below:
http://brilliantbiologyblog.blogspot.com/2017/01/pglo-lab-conclusion.html
It's the pGLO lab, which was really fun because we got to make bacteria glow!

Over the year, I am now better at reflecting on myself, being mindful, and assertive.

Another project that takes up a lot of class time is the 20 TIME project. For this, we got to choose something we are passionate about and devote an entire project taking up the whole semester to that. Here is the link to my 20 time blog.
http://notjusttrash.blogspot.com/

Mr Orre's pet peeves include not cleaning up after a lab, talking while he's talking, not participating in mindfulness, not doing the CFU's, not doing the Do Now, not doing the Relate & Review, not having your notebook set up properly, etc. Its fairly simple to get a good grade- do the required work and CFUs, and study moderately- I wouldn't stress. As long as you put in the work and do the vodcasts, you will have a good grade. For tests, use the CFU's and Do Nows to study.

The most frequent mistake I made was publishing a blog post but forgetting to submit it in Canvas. I highly recommend that you don't forget this last step or your grade will suffer. Also, always do the CFUs because sometimes Mr Orre actually grades them based on participation.

Overall, biology is an interesting subject and some of the labs were very cool. I enjoyed doing labs such as the Pig Dissection, the pGLO, and the Hunger Games labs. I'm not sure how exactly I felt about the blended learning because it involved a lot more work at home than an ordinary class would, and it is hard to watch long videos distraction-free. I would rate this class as a 6/10. Next year I'm taking Chemistry Honors because I think I will really like the subject and I plan on going into a career involving science.

Remember, biology is not as scary as it is made out to be by science teachers in middle school. As long as you do your work and study, you'll be fine. Good luck!

~Sandhya

Pig Dissection Blog Post

Our Pig Dissection Video aka Jemimah the Baller!

The real deal (GOTTA WATCH!) : https://www.youtube.com/watch?v=aW1REKnDW6E

The purpose of the pig dissection was to see how the organs and systems of the body work together to maintain homeostasis. By dissecting the pig, we were essentially looking into ourselves, to learn how our own bodies work. In this unit we learned about the different systems in our body, the organs within them, and how homeostasis is maintained. In this dissection, we got to see the organs of the circulatory, respiratory, digestive, and endocrine systems. My favorite part of this dissection was cutting open the heart because it was really cool to see the arteries and veins. I think the dissection was a valuable experience, because I now have an idea of what my body would look like inside. It also helped me understand where all of the organs are located in the body. 

20 TIME Reflection: Not Just Trash Project

I chose to do my 20 Time project, the Not Just Trash Project, because I'm concerned about the direction we are heading in. Americans make so much waste compared to the rest of the world and it is going to hurt us in the long run. I wanted to inspire people with cool project ideas of how to convert trash into cool items. I want people to know that there are ways around throwing away everything.

My original plan was to create a blog and post frequently on it tutorials of converting trash into cool items. I thought of different ideas to convert small and large items into cool stuff and made a plan for my blog posts.

Getting the project started was slow because I had to make a plan of what I would do. Once I had the plan, I made some posts and did a lot of research. My project evolved from just the blog and posting tutorials, to also raising awareness about political issues relating to this topic. Overall, I think I now have a good foundation for the blog.

The challenging part was figuring out what to do in class. Unfortunately, my project made me do a lot at home and not much in class. I should've picked a different idea for 20 time because for this project, I needed time at home.

Through this project, I learned skills such as planning and scheduling. My project required a lot of pre planning and thought. I learned to plan in advance and put together a well thought out plan to look back at later on. I also learned that I needed to create a schedule for myself. This helped me be more productive.

Unfortunately, it was very hard getting viewers to my blog. I don't have many channels of outreach that I could use. Because of this, I'm not continuing my blog because no one will see what I post. However, I think this project has taught me to be more clever and reuse my own trash. I now know what it takes to actually create a blog and get an audience to it, and how hard it must be to actually be a successful blog.

I will still be encouraging people to reduce their waste and find ways to convert their trash into something useful.

Unit 9 Reflection

This unit was about how we classify life, and the evolutionary relationships of life's forms. We learned that taxonomy divided organisms by domain, kingdom, phylum, class, order, family, genus, species. The domains are archaea, bateria, and eukarya. Within eukarya, life probably started out as marine life, and eventually transitioned into land species, starting with the tiktaalik that could do a push up! Eventually, life evolved into amphibians, reptiles, birds, and mammals.



We also did the What On Earth Evolved Presentations. I thought my presentation went pretty well because I didn't read off the slides as much as I expected myself to. It was a fun experience over all because it was nice to hear information from other classmates rather than only the vodcasts. I think an area I could have done better in is speaking without filler words and "ums" and "likes". I really worked on that a lot for this presentation, but I should do that even more.  Link to my presentation is here.

It was really interesting to learn about all of the different organisms, especially the invertebrates. I didn't know that most of the invertebrates we learned about even existed. For example, the echinoderms, platyhelminthes, cnidarians, etc. I want to learn more hox genes because they seem very interesting and somewhat mysterious. I also want to learn about archaeopteryx because it was the transitional species between dinosaurs and birds. I also want to learn more about archaea, and the latest research.

archaea growing in a hot spring.

Over all, this unit was really interesting to learn about the vast diversity of life on our planet.
Link to previous reflection
Link to geologic timeline showing animal diversity on earth

Geologic Timeline Reflection

Three of the major events in Earth's history are the mass extinction at the end of the Cretaceous period, the appearance of prokaryotic cells 3.5 billion years ago, and eukaryotic cells 2.1 billion years ago. The extinction at the end of the Cretaceous period eradicated over 1/2 of the Earth's population, including but not limited to the dinosaurs. The appearance of prokaryotes and eukaryotes was important because there are many organisms now that are prokaryotes or eukaryotes including humans. These events are important because without them, the species that exist today wouldn't exist today. 

The majority of Earth's history was the Archean era and the Proterozoic era. What surprised me was how recently the dinosaurs existed. As humans, we feel they've been gone for so long but in the scale, they are very close to us. 

In such a short time, we've caused so much destruction to our planet with climate change and global warming. The earth has been around for 4.6 billion years, yet our impact has been the biggest.

I want to know about life during the Archaean period more. It seems so strange that there once was a world with barely any animals or even eukaryotes. How long is the Earth estimated to continue to have life?

Here is a segment of our timeline.

Unit 8 Reflection

This unit was about evolution, and how we, amongst many other species came to life on Earth. One of the main themes of this unit was natural selection vs. artificial selection. Artificial selection is how breeders, for example, are able to breed so many types of dogs with very different traits. Natural selection is what Darwin observed, which eventually weeds out undesirable traits in a population, eventually making the better traits more common.

 From there, we learned that evolution is the change in allele frequency in the gene pool over time. There is lots of evidence supporting evolution, but to me, the piece of evidence that stands out are the similarities in embryos. For example, the Hunger Games lab helped illustrate evolution, as the allele frequency of the species changed over time. 

The rise of new species contributes to evolution when members of a population are reproductively isolated. Other than natural selection, some other factors that also affect evolution are genetic drift, gene flow, mutations, and sexual selection. 

The best theory as to how life started is that first, macromolecules were formed, leading to protocells, eukaryotes, and eventually sexually reproducing organisms. The timeline of the Earth is broken into eras and periods, during which, the Earth and life underwent many changes and 5 mass extinctions.

I thought this unit was very interesting because I like to understand how humans came about, and the origins of life. I would like to learn more about vestigial structures and some examples because its really cool that there are evolutionary left overs. I also want to learn more about the age of the dinosaurs. 

On being more assertive, in the survey last month, I found out that I am slightly aggressive. I've been trying to give people in my group a chance to do what they want more because I usually take charge.
Image result for evolution gif

Hunger Games Lab Conclusion

1) In this lab, we saw natural selection in action, when we competed for survival and reproduction of an organism with 3 phenotypes: the stumpys, the knucklers, and the pinchers. Over generations, the allele frequency changed, simulating evolution.

2) The pinchers were the best at getting food because they could quickly and efficiently grab large amounts of food. 

3) The population evolved because the allele frequency changed. At the beginning of the lab, both of the alleles' frequencies were 0.5. By the end, the "A" frequency was 0.35 and the "a" frequency was 0.65. See the graph below. I apologize if you have to turn your head to do this.

4) Some of the events in this lab were random, such as the dispersion of food. In some areas, there was a greater concentration of food than in other areas. This affects the population by killing off certain phenotypes. Other events were non random, the more desirable traits continued to thrive throughout generations.

5) The results would have been different if the food size was different. For example, if the food was huge, it would be hard to pinch it. This is why organisms usually eat food that isn't too much bigger than them.

6) The results would have been slightly different, because the knucklers wouldn't exist, but the pinchers would still dominate. 

7) Natural Selection causes and contributes to the process of evolution. Organisms with more desirable traits tend to survive (which is natural selection), and over time, species evolve. 

8) In order to survive, people in this lab cheated, by grabbing food, and taking away food from others. Although for humans, cheating is considered morally wrong, in nature, organisms will do whatever it takes to survive. Thus, cheating plays into this. This changed the allele frequency in that those who cheated, got more of their alleles in the population. 

9) Evolution acts on populations, not individuals, and creates new species. Natural selection acts on the phenotype. For example, if a heterozygous individual had the same phenotype as a homozygous individual, natural selection would still act upon them both the same way. 

10) Has there been much natural selection in modern humans (homo sapiens)? How?

Unit 7 Reflection

This unit was about ecology and the main ideas behind it: homeostasis, interdependence, and cause and effect. Various biotic and abiotic factors make up habitats, which make up ecosystems. We learned that the food chain is made up of autotrophs, heterotrophs, and decomposers. Food webs show the passing of energy between levels more accurately. We also learned about the energy in the food webs, and that productivity is highest near the equators. 10% of energy is passed on to the next level. Higher level consumers exist in smaller proportions because of this. In population ecology, population is measured by density and dispersion. Factors that affect the population include immigration, emigration, births, deaths, disease, predators, abiotic factors. The 2 growth models are exponential (doubling), and logistic (rate of increase slows as carrying capacity is reached. Species inter depend on each other, resulting in boom bust cycles of the population. We learned about biodiversity, which is the number of species in an ecosystem. We are in the middle of the 6th mass extinction due to species loss. Species loss occurs from habitat loss, introduced/exotic species, over exploitation, and climate change. Some of the things we can do to curb this mass extinction is to identify and protect hotspots, protect what we already have, plan to have movement corridors, and restore habitats by jump starting succession.

Lastly, we also watched the documentary, "Bag it", which explained the magnitude of the plastic problem we have. I learned some interesting statistics, and realized that America, almost single-handedly causes this problem. Now, I actually know what it means when a water bottle says "BPA free" on the bottom. I hope I can use this knowledge and apply it to my 20 Time project (the Not Just Trash Project), and help people find ways to reduce their waste.

By taking the assertiveness and self awareness survey, I realized that my 2 highest numbers were assertive and aggressive. I think that in the Conservation project, I may have been aggressive on certain things that I could have just let go or worked out a compromise. I will try to work on being more assertive and less aggressive.

The hardest part of this unit was and still is really understanding what will happen when we eventually run out of resources. What will happen when we reach our carrying capacity? It is sad that the human race got ourselves into this mess, and I hope technology will improve so that some of us can move to different planets. Otherwise, life as we know it, may be gone. Actually, unless the TRAPPIST-1 planets could actually have life.

Here is the link to my first ever post on this blog on what biology is. A lot of it has to do with this unit:
http://brilliantbiologyblog.blogspot.com/2016/09/what-is-biology-collage.html

Unit 6 Reflection

Unit 6 talked about biotechnology, how it works, and its applications. 

Biotechnology itself is the study and manipulation of living things to benefit ourselves. Its used industrially, environmentally, Medically, Pharmaceutically, agriculturally and diagnostically. This includes fermentation, gene therapy, forensics and identification, and GMOs. 

Technologies include Polymerase Chain Reaction, Gel Electrophoresis, and Sequencing. PCR is used to yield millions of copies of a portion of DNA for it to be further examined. The strand is denatured and a primer is added to both ends. Then DNA polymerase yields the new double stranded DNA. This repeats itself. Electrophoresis runs a current through bands of DNA on a gel. The shorter bands move farther while the longer bands don't move as much. Sequencing determines the exact order of bases in a strands of DNA, resulting in an electropherogram. 

We also learned about recombinant DNA which is inserting foreign DNA into an organism. The DNA fragment is cut by a restriction enzyme and put into the plasmid, which is resistant to an antibiotic. The new bacteria is then grown and the protein is extracted. This created transgenic or GMOs.

Bioethics it the study of decision making as applied to biology. Based on your morals and values, you can take a stance on an issue. You use this to answer questions like: Is it okay to take extra napkins from a fast food restaurant?

Lastly, we did the pGLO lab, where we inserted a pGLO plasmid into e.coli. We placed them on different petri dishes and the dish with arabinose, broth, and ampicillin glowed under UV light.

Overall, this unit was a little tricky at first. I didn't understand recombinant DNA or the technologies until we did the labs. After doing the candy electrophoresis lab and the pGLO lab, it made much more sense to me.

I would like to learn more about the forensics side of biotech and agricultural applications. I also would have liked to do a lab that inserted DNA into a plasmid using restriction enzymes. I want to learn more about the successes and failure of biotech experiments, because I think it would be very funny and interesting.

pGLO Lab Conclusion

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 N/A  we didn't do this  not part of lab - pGLO LB/amp 0 no colonies no colonies + pGLO LB/amp 12 milky white milky white + pGLO LB/amp/ara 16 milky white neon green

2.	What two new traits do your transformed bacteria have?
	The transformed bacteria have the ability to glow under UV light and resistance to the antibiotic, ampicillin.
3.	Estimate how many bacteria were in the 100 uL of bacteria that you spread on each plate. Explain your logic.
	According to bio.net, bacteria with antibiotics divide every hour, and those without reproduce avery half hour. According to this method, that would result in 1048576 cells in a colony, multiply that by 16 and you get: 16777216
4.	What is the role of arabinose in the plates?
	Arabinose is the trigger that makes the growing fluorescent protein present.
5.	List and briefly explain three current uses for GFP (green fluorescent protein) in research or applied science.
	Scientists use GFP as a marker of proteins.They tag it to specific proteins in a cell and monitor the activity of it. It doesn't interfere with processes that occur within the organism but can be used to study the processes that occur. It is also used to track the spreading of a virus because the protein is inherited as the virus divides. It is also used commercially in pets like fishes to make them look interesting.
6.	Give an example of another application of genetic engineering. Genetic engineering is used in agriculture to create crops with more desirable traits. An example of this would be corn. It is modified to be resistant to a pesticide called herbicide glyphosate which is a weed killer.

Candy Electrophoresis Lab

1)
a. The dye bands looked about the same length as the reference bands, maybe a little bit smaller but not too much.
b. The dyes were the same colors as the reference band, but slightly different shades or hues.
c. The blue and yellow from the candies stacked up to form one band with the yellow on top and the blue below.
d. All of the dyes moved in the "right" direction.

These dyes might be slight variations in the specific candy used. Also, it could depend on how much of the dye you squirted into the gel, producing a bolder or lighter color.

2) Fast green FCF, and Citrus red 2 have similar structures to the dyes used in this lab, so they might migrate similarly.

3) Dog food manufacturers might put artificial food colors in dog food to appeal to the humans who are buying them. They don't appeal to the dogs because the dogs don't see the colors.

4) I think I eat mostly food that doesn't have dye in it, especially since I'm vegetarian. But food that I eat occasionally that have dyes in them could be chips, gummies, and cake.

5) length and speed control the distance that the colored dye solutions migrate.

6) and electrical current helps move the dyes through the gel.

7) Smaller molecules get more excited and move faster and farther. Larger molecules get less excited and move slower and less far.

8) They would separate in the following order from closest to farthest: 600, 1000, 2000, 5000.

New Year Goals

1) I will do my homework the day it is assigned rather than the night before to feel less stressed. I will do this by making better use of tutorials to get ahead on work and not using "I didn't have time" as an excuse.

2) I will not distract myself when doing homework and I'll finish it fast so that I can get to bed at a good time, and therefore be happier and more energized when I come to school the next day.