Letter to Incoming Biology Student

Dear incoming biology student,

First off welcome to Saratoga High! I am Jeffrey Xu; at the time that you'll be reading this, I'll be a sophomore on my first day of school. As a freshman, I have taken English 9, Trig-Precalculus H, Journalism, and obviously, Mr. Orre's biology class. Aside from academics, I play the piano, play badminton in Saratoga's varsity team, and eat lots of food.

Honestly, on my first day of school, I wasn't worried too much about classroom procedure, but rather, that I wouldn't end up with a lot of friends in my classes. You're probably in a similar situation. I wouldn't worry about it too much, think of not ending up in the same class as your friends an opportunity to make new ones.

Mr. Orre is a strict teacher. For late work, most of the time, he just gives a zero, unless it is a vodcast. Vodcasts are nightly homework assigned for your learning purposes, so there's no reason to discourage turning it in after it's late, so Mr. Orre gives full credit for late vodcasts. I suppose if your after school life is very packed, you can do the vodcasts at a later date, but make sure you do them before the end of the unit!

In my opinion, the tests are the hardest category in biology, and I really wouldn't worry too much if you don't meet your expectations on them. Instead, try to make sure you do well on labs and let labs and projects carry your grade. You will have a biology notebook in this class, but it is almost more like a textbook. You must be highly organized, with a table of contents, and there will be notebook checks before every test to make sure that you have kept yourself organized.

One of Mr. Orre's biggest pet peeves is people not following easy directions and making what he calls "rookie mistakes." Make sure you always turn papers into the correct turn in box, and not the handout station. Also, he is big on cleaning up after labs. If you don't clean up well, you will have to stay in for precious tutorial time. Finally, always make sure to do your Check For Understanding quiz (CFU) online after you watch your vodcast, as Mr. Orre will sometimes turn these in for a real grade. I speak from experience so don't make the same mistakes that I did!

Overall, I actually really enjoyed this class and learned a lot. In my studying for the SAT II Biology subject test I was taking, I found that this class actually helped quite a bit. I like the fact that it relies on the student to be more responsible for their own learning, taking good notes instead of just being fed information by a teacher. Next year, I am taking Chemistry Honors, as recommended by Mr. Orre. So yeah, on top of what I already said, take advantage of this flipped classroom, keep yourself organized, and get the points on labs and projects that you should be getting.

Oh right, here's my biology blog. I'm actually pretty proud of it: http://jeffyx.blogspot.com/

Good luck,
Jeffrey Xu

Pig Dissection Lab Write-up

I think the purpose or essential question was to find out if dissecting a pig can help identify internal structures and organs learned in class. This dissection definitely related a lot to this class because we had already learned a lot about the different organ systems in the human body, and finding those internal organs in a pig, a fellow mammal of the humans, helped us to further understand the function and importance of these organs and organ systems.

My favorite part of the dissection was, to be honest, scraping off membranous material to uncover important organs, because it just felt satisfying. 

I do think this dissection was a valuable experience because it really practiced hands-on skills as well the skill of teaching other people via a video, just like Mr. Orre! 

This was a pretty fun lab, perhaps the most fun lab of the year--besides the hunger games lab obviously. I had already learned a lot of knowledge regarding the digestive, circulatory & respiratory, nervous, and endocrine systems, but I felt that it was pretty hard to grasp when everything seemed pretty abstract and far away, but this lab really brought everything to real life. 

Above is the video of our tutorial.

20 Time Individual Reflection

This is my first time talking about 20 Time on this blog, so let me explain what it is. The idea behind this is that employees or students or anyone, can take around 20% of time out of their normal working hours to instead work on something else, something special and interesting to them, a passion project. In Google, these so-called passion projects led to ingenious inventions such as Gmail, Google Shopping Express, and many other world changing inventions.

For my 20 Time project, I investigated a phenomenon that affects many teens schoolwide, and probably worldwide. I did experiments about procrastination. I chose this as my research interest because procrastination is also something that affects me, and is often times my biggest adversity. In doing research on how to combat procrastination, I was actually able to help myself battle it.

You can get to my 20-Time blog right here: http://jeffrey20time.blogspot.com/

What I planned to do was to test various procrastination-combatting tips/methods and test it on some of my peers and myself. I thought that in this relatively large amount of time, I would be able to get a control experiment finished as well as perhaps 20 or so methods. That was rather optimistic of me.

I didn't realize that for each individual method, large amounts of testing was required to ensure accuracy of results. After I realized that just testing 1 or 2 methods took almost a month to complete, I readjusted my goals and thought that testing 5-10 tips in total was an achievable but also quite challenging goal. I finished testing 7, which I am pretty happy with. Another roadblock that came my way was that when I would tell my peers what methods to try out while doing homework, sometimes they would forget to use them or do something completely different! So I fixed this by creating a Facebook group chat (teenagers always are on Facebook these days) and I communicated with them through this helpful medium.

I made a data spreadsheet documenting the different times of finishing homework for me and my peers and you can help yourself in your procrastination by looking at some of these tips. The link is right here

One thing I learned from this project is that although people share many similarities in working habits, they are way more differences. Some of the methods I tested, I expected everybody to improve their working efficiency, but instead, some still were slower. Also, for the methods that I thought were probably not going to make a huge difference or be a burden on doing homework, they actually were able to drive some of my peers to finishing their homework hours earlier!

I also picked up some soft/process skills. Cutting up the workload and time management were quite important for me. Sometimes, I would fall behind schedule due to limited time at school or other groups pestering me to help them, but I would always go home afterwards and find time to catch up and get ahead.

If I could change this project in any way, I would definitely make it larger scale. The only people I was able to document in my studies were just me and 4 of my peers that took part in the experiment. Perhaps next time, I could do polls and surveys on the SHS Facebook group and allow for a broader scope of views on procrastination.

I learned something about myself along the way. I tend to work much better under deadlines. Towards the beginning of the project, I was lagging pretty behind in terms of goals, but as deadlines approached, I was much more insistent on my peers to finish their tasks and would almost work on 20 Time at home on a daily basis. It turns out, this worked well, as I finished about a day early compared to most of the other students in the class.

I'm not sure how I could continue this project in any way, but one thing is for sure. I will apply what I learned from this lab as much as I can in my life. This way, I'll be much more effective at finishing schoolwork and be able to put in more time to other things that I enjoy doing, going beyond just school, and sports. In my opinion, being effective at getting work done not only enhances your work ethic, but allows for a more enjoyable life.

Unit 9 Reflection

The title of this unit was: What on Earth Evolved? As you can probably tell from the title of this unit, we learned about the different groups of organisms that evolved on Earth and the order in which they evolved. So starting off, the most primitive life on Earth began with unicellular prokaryotes like bacteria and archaea. Some may argue that viruses are living, but they don't have many of the characteristics of life.

Then, there evolved the domain Eukarya, when prokaryotes began living inside each other as symbiotic organelles. In the domain Eukarya, there were four kingdoms, namely: Protista, Animalia, Fungi, and Plantae. In the kingdom Animalia, we humans belong to the phylum Chordata, class Mammalia, order Primates, and so on. We are considered one of the most recently evolved organisms. A good way to see how new traits evolved and created new groups is a phylogenetic tree. Below I have attached an image of one regarding all the organisms within phylum Chordata.



One of the major projects in this unit was the What on Earth Evolved? presentations. My presentation went quite well, and I attribute my success to the fact that I practiced a lot in front of the mirror, my parents, my brother, even my dog! I got feedback from the mirror by making sure my posture was good, and that I didn't sway. My parents gave me helpful feedback by suggesting certain topics I should include in the presentation to make it more engaging and interesting. This made my presentation not only get a good grade, but I was able to enjoy the process of presenting something that was quality. In the future, I will always make sure to overprepare for such presentation, as the payoff is always worth it.

The link to the actual slideshow can be found right here. The topic of my presentation was the Human Immunodeficiency Virus (HIV)

Although the Geologic Timeline assignment was a Unit 8 assignment, we only completed it during the beginnning of this unit, so I would like to attach the link to my reflection right here. If you really think about it, the Geologic Timeline actually ties in quite a bit with taxonomy, because it shows us the huge amount of time that Earth was inhabited by only unicellular organisms, and how long it took to evolve complex organisms, and that we humans only occupy a tiny sliver of time compared to life on Earth.

This unit has definitely helped me grow as a person. Being put in front of a classroom of 30 students and presenting really pushed my out of my comfort zone. I feel a lot more comfortable now speaking in front of large audiences. However, one thing I still struggled with this unit was trying to pay better attention to other people's presentations. I need to improve my active listening so I can learn more.

Here is a photo of a chart I made for the taxa observation of organism to help me better understand common characterstics.

Geologic Timeline Individual Reflection

3 of the major events of Earth's history include the Cambrian Explosion, the Permian Extinction, and the Cretaceous extinction. The Cambrian Explosion was highly significant and is often referred to as the most significant evolutionary event on Earth due to the rapid appearance of many animals with mineralized, fossilized remains. The evolution of skeletal structures that leave behind fossils is essential to the study of fossils. The Permian Extinction is highly significant because it was the largest extinction event in all of Earth's history, with 96% of all marine species becoming extinct. The Cretaceous extinction is also very significant because without the extinction of the dinosaurs, mammals would have never radiated and humans would have never came to be.

Earth's history relative to human history is much more grand than I had first expected. On the timeline extending from one end of the classroom to the other, our little sliver of time is absolutely negligible.

However, despite this short period of time that humans have been on this planet, they have had massive effects. Ice caps are melting, many places are flooding, nature all around us is being destroyed and used instead for industry. At this rate, I feel that the human population will not be able to sustain itself for much longer until we choke ourselves to death.

One question I wonder about is why it took so long for humans to evolve, to come to be. So much of Earth's history involved only single-celled organisms, which seems a bit counterintuitive as multicellular organisms seem more likely to dominate.

Below I have attached a couple photos of the timeline:
 

Unit 8 Reflection

I always like to start off with the title of the unit. This unit was called Constant Change. This makes a lot of sense because evolution is all about how populations are always changing. 

But how exactly does evolution work? There are many mechanics involved in evolution, but one of the main causes is natural selection. In order for natural selection to occur within a population, there must first be variation. Variation is created through mutations and sexual reproduction. Natural selection favors individuals with traits that help them survive better, causing them to better produce more offspring, so that over time, the population begins to look more like these individuals. An interesting lab we did to demonstrate this concept was the hunger games lab. Other factors that can cause evolution include gene flow, genetic drift, sexual selection, and mutations. 

Speciation is one of the causes of evolution. As two populations of the same species have reproductive isolation, they begin to evolve differently based on their different ecological niches. Soon, they become so different that they can no longer reproduce with each other anymore. This is when one species becomes two. 

There is a lot of evidence to back these ideas up. First and most obvious is fossils. Fossils found in the earth can tell scientists a lot about when and what individuals looked like. By carefully studying the differences from fossil to fossil, it is pretty clear how and when a population evolved. Also good evidence is the fact that many organisms that are very different (i.e. birds and flies) can evolve analogous and homologous structures. 

One thing that I wonder a lot about is that although it appears that many populations of organisms like animals and plants are evolving, I feel that the human population appears to be still quite the same as before. Why is that? Hmmm.

Below, I have attached some images that I feel highlight some of the key ideas of this unit:

Hunger Games Final Analysis

1. In this lab, each person had to grab as much food as they could based on their phenotype and try to reproduce by the end of the round. This lab simulated the workings of evolution on a population. 

2. The phenotype which was best at capturing food was the pinchers, because of the fact that they could grab lots of food quickly with their opposable thumbs and index fingers. 

3. The population did evolve because the allele frequency changed. At the beginning, the frequency of the "a" allele was only 48%, but by the end, it had already reached 78%. See the graph below for intermediate changes and you will be able to see the rate of change better.

4. Some events in this lab that were random were the placement of the food, the amount needed to survive, the coin-flipping that would determine the offspring. Some things that were not random were the possibilities of the offspring and the methods that we used to pick up food. This affected the evolution because some rounds had way more deaths than others because of these arbitrary conditions. 

5. The results would definitely have been more different if the food was larger. The knucklers definitely and the pinchers perhaps would have a more difficult time picking up the food in between their little fingers. This can also happen in nature where changes in external conditions can be advantageous for some and disadvantageous for others. 

6. Yes, the results would definitely have been more different. Without incomplete dominance, there would be no knucklers, only pinchers and stumpys. This probably would have resulted in more stumpys initially as the homozygous genotype would still create a stumpy.

7. The relationship between natural selection and evolution is that natural selection acts on the favorable phenotype, allowing it to survive and reproduce better, and as natural selection occurs over longer periods of time, the population will gradually change to look more like these organisms with the favorable trait. This gradual change in a population over time is evolution. 

8. The stumpys, although not necessarily best suited for survival, were very good at strategizing and teaming up. In my opinion, it looked like they only mated with each other to produce "the superior stumpy race." This seemed to cause a bounce-back in the population of the stumpy, and I congratulate them for not dying out. 

9. In evolution, it is the population that evolves. Natural selection acts on the phenotype, as that is what directly affects the organism's ability to survive. To further elaborate, in the case of complete dominance, a homozygous dominant and a heterozygous will have the exact same phenotype, so their ability to survive will be pretty much equal. As you can see, the genotype is not the whole story in this case. 

10. I still have one burning question though: If evolution is by definition a change in allele frequency, then isn't evolution occurring every second (each time an organism dies, the allele frequency changes a bit) and not really a "gradual change over time?"

Unit 7 Reflection

Unit 7 was titled "The Study of House." What this is referring to is ecology. This name actually makes quite a lot of sense because in studying ecology, we study the mechanics that take place within the biosphere, which is the "house" in which we live. Some topics we covered in this unit include food chains, food webs, ecosystem energy, populations, ecosystem conservation, and much more.

At first, these topics may seem to be very different, but looking at the larger scope of things, these topics are actually quite interrelated. For example, within the food web, energy is transferred from lower trophic levels to the higher, and this energy is actually what is needed to maintain an ecosystem's health and to keep its populations balanced. Personally, my favorite part of this unit was population dynamics, as the behavior of populations as they reach the carrying capacity K and the oscillations about K seemed very intuitive and mathematical, and math is sort of my thing. In this unit, we also watched The Story of Stuff, which I took some pretty decent notes on. You can access my notes here.

So I'm pretty familiar at this point with ecology concerning organisms, populations, communities, and ecosystems, but I've also heard of another type of ecology called landscape ecology and am pretty curious to maybe find out about what that is in the future.

One big project that we did during this unit was the Conservation Biologist Project (link to the video). This project really opened my eyes and really put things into perspective, the fact that ecosystems are something undeniably real and close to us. It is our duty to protect and conserve these ecosystems as as of right now, Earth is our only home (house). Some things I felt that our group did really well was the fact that we had really good communication and everybody did what they pledged to do. However, I feel that with a little more time, maybe we could have touched up the slides, recorded perhaps a bit more attempts, and also modify the content a bit more.

Overall, this unit was one of my favorite units, and I really learned quite a bit about our house, Earth.

Below I have attached a picture of logistic growth:

Story of Stuff

• Using up resources occurs in a linear fashion, however, this linear fashion cannot continue indefinitely because of the fact that we only have a limited amount of resources on this planet
• Stuff moves through a system that starts with extraction, then production, distribution, consumption, and finally, disposal
• However, this doesn't tell the complete story as many different phenomena happen along the way
• Many people live under crazily bad conditions, like for example, when their own environments can no longer sustain them, they take jobs even for crazy low pay and harmful working conditions such as toxins in the air, etc
• The government is almost as if it's under the big corporations
• The system is set up in a way that encourages people subliminally that consuming is the most important thing that somebody can do.
• However, truth to be told, many of our natural resources are running out because of the reckless rate at which we are consuming.
• The U.S., which only accounts for about 5% of the world's population, actually consumes 30% of the resources. If everybody consumed as we did, we would need an additional 5 Earths.
• Many of the chemicals used in production haven't been tested
• 99% of consumed goods are thrown into the trash and disposed of within six months of use
• Many people are influenced to keep on buying new things because items are designed to lose effectiveness in a short period of time, or people are pressured by those around them to shop for things to "stay in trend"
• Interestingly enough, the national happiness factor is still not quite as high as the 1950s because this constant cycle of shopping, feeling depressed, working etc. leaves barely any time for people to spend time on things that actually matter, such as friends, family etc.
• Incinerating trash creates really bad toxins
• Although recycling helps, it is for sure not enough to get to the core of the problem
• However, since this heavily flawed system was created by people, it means that it is definitely possible to stop it, since we are people as well. If we can come up with a large-scale solution, this problem (at least in my opinion) can definitely be solved, we just need to raise awareness and educate the others out there

Unit 6 Biotechnology Reflection

In this unit, we learned about biotech and the different possibilities and applications it might offer to humanity. There are four main fields of biotech, namely: agricultural, industrial, medical, and investigation. These fields of biotechnology offer amazing abilities and powers that we humans can wield, such as the power to clone, to heal using recombinant DNA, to optimize crop growth and food output, the possibilities are practically endless. However, there is also the issue of bioethics, which puts for the question: Just because we can, should we?

In this unit, one of my main strengths was being quick to understand how the two labs pGLO and dye electrophoresis would work. Because of this, I was able to push my groupmates in a positive to direction to work quickly, efficiently, and at the same time, closely following the procedure. However, one of my weaknesses in this unit was the recombinant DNA vodcast. I didn't quite understand the process of extracting DNA using restriction enzymes and cutting it, and then pasting it into other organisms.

I really liked the pGLO lab because it was a great demonstration on how recombinant DNA could be used by letting E. Coli pick up the plasmid that would make them resistant to ampicilin and even cooler, it would make them glow in the presence of arabanose sugar. However, I still hope to learn more about recombinant DNA and find out about even more of the possible applications that it could offer to humanity.

As for my New Year's goals, I feel like I have been doing really well. I carefully watch the vodcast and take notes closely, and even replay parts of the video to help better broaden my knowledge. I have also cut down on the procrastination and have been studying for the unit test throughout the unit instead of all on the night before. In general, I am really excited about biotech and hope to see where this technology will take us in the future.

Below I have attached some pictures that highlight some of the labs we did in this unit.

pGLO Lab

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 20 tan/white violet - pGLO LB/amp 0 the color of nonexistence "" + pGLO LB/amp 10 tan/white violet + pGLO LB/amp/ara 6 tan/white bright glowing green

2.	What two new traits do your transformed bacteria have?
	These bacteria are now resistant to ampicillin and will glow in the presence of arabanose sugar.
3.	Estimate how many bacteria were in the 100 uL of bacteria that you spread on each plate. Explain your logic.
	After two days, there were about 100 billion bacteria. Assuming the bacteria divided once and hour, a pretty typical rate, the amount of bacteria in the original 100 uL would be around 100 billion divided by 2^24 or about 6000
4.	What is the role of arabinose in the plates?
	It reacted with the pGLO to make the plate of bacteria glow a bright, florescent green.
5.	List and briefly explain three current uses for GFP (green fluorescent protein) in research or applied science.
	Used to label spermatoza, too help see microorganisms better, and it can be used as a reporter gene.
6.	Give an example of another application of genetic engineering. It can be used in agriculture, to make crops pick up DNA that can make them resistant to certain plagues, therefore having a positive effect on the harvest.

Editing the genes of embryos: a most debated question

It all began when Chinese scientists reported taking 86 human embryos and attempted to modify the gene that causes beta-thalassaemia, a deadly blood disorder. They did this by using a new gene-editing technology known as Crispr-Cas9, a machine that can make extremely precise edits to DNA. Now, Britain wants to do the same thing, except this time, to research the development of a healthy embryo and the possible causes of miscarriage. This technology can be used to cure many diseases that may be genetically inherited and may show some of the possible causes of miscarriage.

Clearly, this new technological and biological revolution has the potential to bring about many benefits. First off, using this gene-editing technology can cause genetically inherited diseases to be wiped off the face of the earth. Secondly, such edits can cause aging to be much slower, letting us humans live much longer, and healthier lives. Finally, such gene-editing technology can end the "gene-lottery," where the babies that have favorable traits are completely randomly chosen. Now, everyone will have desirable traits and nobody will have any unfair advantage over another.

However, such gene-editing technology can also prove to be very ethically problematic.  First off, there could be an accidental, "off-target" mutation caused by gene editing on a different part of the genome, which could have fatal effects. Also, gene-editing could cause the creation of "designer babies", babies whose traits have been carefully selected to be superior in looks, height, intelligence, and other different areas that aren't actually necessary for medical purposes. Even leaving it up to the "gene-lottery" is better than creating a race of perfect humans, where there is little genetic variation when it comes to different natural talents. Finally, this gene-editing of embryos could lead to a scary methodology called eugenics, the racist idea of creating a superior race with specific traits like for example, with the Nazis, was the Aryan race, a race purely made of people with blond hair and blue eyes.

In conclusion, I must say that I stand on the side of not supporting such technology, or at least limiting it purely to medical purposes, and not for genetic enhancement. This is because even with all the possible benefits it could introduce to make life much easier for everybody, it takes away the aspect of life which is that hard work is the key to success. In a world where gene-editing is possible, those with enhanced genes will clearly have an unfair advantage. This is why I feel that modification of the genes of embryos, or any human for that matter, should not be done, or at least limited to medical purposes only.

Above shows how the Crispr-Cas9 genetic editing technology works

Works Cited:

Savulescu, Julian. "News and Articles on Science and Technology." News and Articles on Science and Technology. Science X Network, 3 Dec. 2015. Web. 26 Jan. 2017.

Page, Michael L. "How Do We Weigh Benefits and Risks of Human Gene Editing?" Genetic Literacy Project. N.p., 17 Mar. 2015. Web. 26 Jan. 2017.

Candy Electrophoresis Lab

1. When we analyzed the results, all of our test dyes matched the four reference dyes except for one. When we extracted the dye from the orange skittle, it didn't match any of the reference dyes in both color and distance traveled. It almost seemed to split into red and yellow, except that since they weren't fully split and were still partially combined, the didn't quite match the red reference die or the yellow reference dye.

2. I think that betanin, the beetroot red, and citrus red 2 will likely match or at least be pretty similar to the red 40 reference dye. However, I think that betanin will be slightly darker and citrus might be a bit lighter.

3. These dog food manufacturers likely put colorful dyes in dog to make it more attractive to the consumer.

4. One reason why artificial dyes might be more preferable than natural dyes is the fact that artificial dyes can be mass produced. This makes it a lot easier to make and makes it a lot more mainstream.

5. The size and time it travels.

6. The negatively charged end (the anode) attracts the dyes and causes them to start moving through the holes towards the end of the gel.

7. The component that causes the molecules to separate by size is the fact that there are holes within the gel. Larger molecules move a lot slower through the holes while smaller molecules move quick and easy through them.

8. The molecule(s) with weight of 600 daltons will go the furthest, then followed by 1000 daltons, 2000 daltons, and 5000 daltons will travel the least distance.

In this lab, we asked the question: How can we use electrophoresis to identify the dyes in candy? We found that we were able to do so by comparing the distance traveled by our candy dyes to that of the reference dyes. The dye from the red skittle matched red 40, the dye from the green skittle successfully separated into yellow and blue, and matched the yellow and blue reference dyes, and so did the dye from the yellow skittle. However, the orange skittle wasn't able to completely split into red and yellow, so it ended up halfway between the two reference dyes for red and yellow. This supports our hypothesis because we thought that it would indeed be possible to identify the dyes used in the candies, and we were right.

While our hypothesis was supported by our data, there could have been possible errors due to the fact that we were at an assembly while we ran our gel. This could have caused the dyes to move without supervision, and anything could have happened to alter the results and we wouldn't have known about it. Also, when we used the micropipet to transfer the reference dyes and our candy dyes into the wells, there were a couple of times where we missed some dye, so that could've also affected the results by changing the amount of dye that was actually running through the gel. Due to these errors largely being affected by not having enough time, I suggest that in the future, this lab be split into two days: one for preparing the dyes and the second day for running them.

This lab was done to demonstrate how electrophoresis could be used to identify different dyes. This lab helps me better understand the concept of how similar molecules will travel similar distances through the gel because of their similar size. Based on what I learned in this lab, I think I can probably do gel electrophoresis for DNA as well.

New Year Goals

This year, one of my two SMART goals is to spend much less time on my phone or my computer, watching videos and procrastinating on work. It might seem a bit overzealous, but I will cut down my daily usage of these things to one hour at max. This way, I can get my daily workload finished much earlier and more efficiently, therefore allowing me to go to sleep earlier and to be even more productive the following day. This creates a positive cycle of becoming a much more aware and focused student.

The second of the two SMART goals I set is to pay much more attention to the vodcasts. A lot of the time, I would usually skip through the vodcast, purely copying down what was written on the screen, and therefore getting my homework done in a really short period of time, but in turn, not actually learning much. This would usually come back to get me when studying for the unit test later on, because I would have to cram all the things that I missed from the vodcast into the brief studying time I would have right before the assessment.

These are my two goals for the new year and I intend to pursue them with motivation.

Unit 5 Reflection

In this unit, we learned about the central dogma. The central dogma says that information travels from the DNA to the RNA to the proteins, which make up the physical traits that we have. This process can be broken down even further into two steps: transcription and translation. Transcription is the process in which DNA unzips and RNA is made to match the spare nucleotides to make messenger RNA (mRNA). In translation, mRNA arrives at the ribosomes, where the codons are translated into a code for proteins, which are produced and make up our physical traits. There are also mutations and different things that can regulate gene expression, but those are rather slightly less relevant to the central idea of the unit.

One of my main strengths in this unit was that I was able to easily translate and transcribe different DNA pairing, RNA sequences, and going from codon to protein, This made the protein synthesis lab quite easy for me, as I was done in less than 10 minutes. However, one of my weaknesses was not being able to visualize things. When Mr. Orre called on students to walk up to the board to label the different items related to regulating gene expression, I was not even able to identify a single one. Thank goodness I wasn't called up!

Yet still, I have many questions. Mr. Orre said that this unit would bridge the gap between how our chromosomes affected our traits, but I still don't quite get how different alleles correspond to different base pair codes and how the types of proteins can create so many different combinations that affect our physical traits.

As a student, I feel like I have definitely grown after this unit. DNA had always been one of the most puzzling concepts for me that I couldn't quite grasp. However, I feel that after this unit, especially after creating the DNA model, my understanding of the structure and function of DNA has definitely expanded. Also, my learning skills have definitely improved. I used to rush through my vodcasts with haste, focusing more on completing the task rather than actually trying to learn more as a biology student. Now, I listen carefully and try to pick up on as much detail as possible, even referencing the textbook when the vodcast is unclear. I feel like this time, unlike the others, I will not be cram-studying the night before the test because I think I already have ample knowledge to do well on the final. I might study a little bit here and there and review my peer study guides, but I will definitely be getting a good night's sleep this time.   

Protein Synthesis Lab

In this lab, we asked the question: "how does the body produce proteins?" In the process of protein synthesis, RNA polymerase reads the DNA and transcribes it into a code for the messenger RNA (mRNA). Then, the RNA travels to the ribosomes. They bond, and the mRNA is read, each codon representing a specific protein. Finally, the protein is made based on the code read from the mRNA.

Frameshift mutation seemed to have the greatest effect on the proteins, and yes, it does matter where the mutation because an insertion or deletion near the beginning of the sequence can offset the entire rest of it, but one of these at the end might not do much. If the T was at the end, it would not have affected the sequence before it. However, in some cases, substitution can cause a huge change in protein as well.

In step 7, the mutation I chose was a simple substitution on the 6th base. A substitution at the end of a codon may seem like nothing at first, but the change was actually pretty massive. This simple substitution caused the second codon to go from a Tyr protein to a Stop protein. So effectively, the new sequence literally became just start-stop. Quite a difference with such a small substitution. And yes, of course, like always, the spot where the mutation occurs definitely matters when choosing the mutation that will create the biggest or smallest change.

Mutations can affect our lives because if a section of our DNA is deleted, inserted, or substituted for, it could cause a drastic change in the protein that is made, and in some cases, will cause some pretty significant changes in our phenotype. A mutation on a section of DNA that controls the proteins that make up eye color can cause heterochromia. In heterochromia, spots of irregular shape appear around the pupil that are a different color than the circular ring that is around it. Perhaps a mutation on the DNA caused a different protein to be made in the eye cells, which caused this variance in color. 

Human DNA Extraction Lab

In this lab, we asked the question: How can DNA be separated from cheek cells in order to be studied? During our research, we learned that the protocol for DNA extraction involved three basic steps: homogenization, lysis, and precipitation. We found that it was made possible by means of scraping our cheek cells with our teeth in the presence of Gatorade, adding salt, soap, and pineapple juice, and then finally applying a layer of cold alcohol at the top. The DNA floated to the alcohol with ease.

In order to break down the cell walls/membranes, plasma membranes, and nuclear material in the first step homogenization, the cell tissue must be submerged in a polar liquid, which in our case, was Gatorade. Inside the mixture of our saliva, Gatorade, and cheek cells, we could see the DNA a little bit better because of the breaking down of the cell membranes, plasma, and nuclear material. After adding soap, salt, and pineapple juice to the mixture, 95 percent isopropanol alcohol is layered carefully to the top of the mixture, and since alcohol is nonpolar and DNA is polar, the DNA falls out of the solution as a precipitate at the interface of the two solutions. After pulling it out of the alcohol layer, our DNA has been extracted.

While our hypothesis may have been supported by our data, there could have been possible errors due to the fact that many of the steps didn't have exact amounts of materials we were supposed to add. This could have affected the results because if we didn't have the right amount of something to add to the solution, the DNA may have not been able to be extracted properly. Also, we were supposed to come up with the procedures by ourselves, so if we did something that was not in the correct order, that could have messed up the process of extracting the DNA properly. I think that next time, maybe more precise amounts should be added to the procedure and the students should actually get the full procedures to prevent the possibility of just wasting materials by not being able to do the actual procedures.

This lab was done to demonstrate how DNA could be extracted from cheek cells and that DNA is not as complicated and unreachable as we may think. From this lab, I learned about concepts such as homogenization, lysis, and precipitation, which helps me better understand the concept of DNA as a whole. Based on my experience in the lab, if cloning is invented, I would definitely know how to extract my DNA to create a clone.

Unit 4 Reflection

In the coin sex lab, we simulated gamete formation by flipping coins to determine which of the two in the allele pair would make it to the sex cell. Then, we simulated sex, by adjoining the results of the coins to determine the genotype of the offspring. The expected result in our double heterozygous dihybrid cross was two have two double homozygous babies. One of which would be double homozygous dominant and the other recessive. However, it turns out that in this dihybrid cross, we got none of these. We can attribute these results to the working of random chance; even as the expected result is for two, we still cannot predict what the genes of the actual outcome will be. This is the limit of using probability to predict our offspring's traits. We can determine the possible traits they will have and their likelihoods, but we can never know for sure. In life, there are many things which we can estimate the probability of, but in the end, we can never predict for sure.

This unit in general was about sex and how great it is. It creates offspring that are part of the new generation so that species don't die out and go extinct. Some essential themes included that alleles would randomly separate during meiosis and join during fertilization for recombination, making the genotype of the offspring completely random and unpredictable. However, it is possible to determine the possibilities and the probability of those possibilities. In a monohybrid cross, there are only four squares in the Punnet square, making the results very limited and easy to find the probability of. We also learned that there are two different types of inheritance: X-linked inheritance and autosomal inheritance. Since I'm pretty good at math, one of my main successes was being really quick at finding the probabilities of certain outcomes when there were crosses.

Before these previous experiences, I had always had built in impressions that inheritance was both straightforward and intuitive. However, after learning about the different possible complications, incompletions, and exceptions, it is not quite as straightforward as I thought. However, it feels like the possibilities with genetics are endless and this was definitely one of the funner units.

Even after this unit, I still have many questions. What are the causes behind these different mutations and complications? I was almost aborted because my parents thought I had Down Syndrome, but in the end, they still decided to keep me and I turned out to be a normal, healthy baby, which makes me wonder: Is it just by random chance that we are born? If everything is just random chance, what's the point. I wonder about this often and I have never found an answer.

Here is a link to an infographic I created on genetics: https://magic.piktochart.com/output/17957312-why-is-sex-so-great

Is sex important?

There are definitely many benefits to reproducing sexually. One of the benefits is that sexual reproduction shuffles the genes of individuals from those of their parents, making the entire species as a whole less susceptible to mass extinction by a disease or mutation, as stated by the armadillo. However, there are also some downsides to sexual reproduction as well. Trying to survive the dangers of predators in the while makes it hard for an organism to find a mate at the same time, as said by Olivia Judson. It is often hard to impress the opposite gender, making successful sexual reproduction quite difficult.

There are also some benefits and costs of producing asexually like the E. Coli. Producing asexually only requires female organisms, eliminating the need for males, argued Miss Philodina. Also, unlike in sexual reproduction, where it takes two children to balance the population, asexual reproduction only needs one offspring to equalize population. However, one of the downsides of asexual reproduction is that all organisms have the same DNA, so anything like a disease can wipe out an entire species, and also, mutations will be passed onto future generations, causing more and more of the population to be mutated.

I don't have many questions regarding this topic, but I guess my one burning question would have to be: What causes us to be so eager to mate?

Unit 3 Reflection

In a nutcell (nutshell), this unit was about cell structure and function, photosynthesis, and cellular respiration. Some of the themes included the process by which a protein is created, a tour of the cell, the reactants and products of both photosynthesis and cellular respiration, etc.

Although many of the concepts and skills required in this unit were already fairly familiar to me, I had quite a bit of trouble memorizing and fully grasping all of the structures and functions of all the organelles within a cell as well as many of the complex steps in the reaction of cellular respiration.

I am definitely a better student now than I was at the beginning of the unit. I have learned many new skills such as focusing a microscope on the specimen much more quickly, I also learned how to make cool labels on Google Drawing. But most importantly, I started to get more accommodated to working with my tablemates and getting to know them better, making our labs much more efficient and at the same time, fun.