Unit 8 Reflection

This unit was about evolution and how it occurs in our everyday lives, and what factors effect evolution. The themes of this unit were evolution, and how evolution is connected with geology and the geological timeline. The parts of this unit include natural and artificial selection, allele frequency, speciation, the structural evidence of evolution, and how populations evolve. Natural and artificial selection act on the phenotype of different individuals, who must adapt to constant changes within their environment. Natural selection acts on these phenotypes  and in the process decrease the allele frequency within the population. This allows for speciation, in which related species no longer are able to reproduce with each other, and thus evolve into new species. The types of change that cause evolution within populations include genetic drifts, gene flow, mutation, natural selection, and sexual selection. These all change the allele frequency and affect evolution. Another theme that we learned about was how populations evolve. The three types of change are directional change, stabilizing change, and disruptive change. These show how the genotypes and phenotypes change, and are caused by the different types of change. Another theme we learned about was earths geological history and how earth formed. Earths history was caused by many major events, which include mass extinctions and adaptive radiation, in which their is rapid speciation from a common ancestor. Scientists use radioactive dating of radioactive isotopes in the rocks to determine age. Earths history is split into Eras, Periods, and Epoch's. This unit greatly relates to our previous units about genes, since evolution affects phenotypes, but has a greater impact on the genes of individuals. The labs we did in this unit include the:

• Hunger Games Lab
• Bird Beak Lab 
• Geological Timeline Reflection

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In my Unit 7 Reflection, I learned about my conflict style and found that my dominant style was assertive, though my second one was passive aggressive. I have taken steps to be more assertive in projects by making sure that I am not overpowering or aggressive to my teammates and to make sure that all people win, and that I am a good teammate. 

Geologic Timeline Individual Reflection

       Three of the most significant events that have occurred in earths geological history are the "Cambrian explosion:, the Permian extinction, and the Cretaceous extinction. The Cambrian explosion is the time period where a large amount of new species arose, and the diversification of current species rapidly grew. It created a prosperous time for new animals and allowed for a diversification in sea life, which led to the Permian era. Without the Cambrian explosion, much of earths current life would be non existent, and the Permian era sea life growth would never have occurred. The Permian extinction was the largest mass extinction ever, and caused the destruction of 70% of all species. This extinction caused decimated the large amount of aquatic species on earth, and created a niche for the Dinosaurs and other animals to step into. The Permian extinction is thought to be caused by a drastic increase in temperature, which caused many glaciers to melt and allowed for the continents of Pangea to dry up. with this extinction, Earth would still be largely aquatic and have much larger glaciers. The Cretaceous extinction is the third significant event because of its lasting effect on humans and its destruction of the Dinosaurs. Without this extinction, the earth would still be ruled by the Dinosaurs, and humans would hav
e never found and inhabited their niche.

http://www.basfeijen.nl/evolution/pic/cambrianfauna.jpg

     Despite the scale of earths history being so large, what surprised me is how little time humans have been on earth, and how in the grand scale of time, our actions and lives have had a minuscule effect on what has occurred over time. As seen in the Cosmos video, if earths history was a calendar year, we take up the last second of the last day, which truely shows how small we are in the grand scale of things. Despite us having been on earth for such a short time, we have had a large impact on our planet. From global warming to the extinction of many species, we have caused much harm to our earth and have created a lasting impact. With continued increase in temperature, we may be causing our own extinction.

https://spongebobquh.wikispaces.com/file/view/geological_time.jpg/128735281/geological_time.jpg

Hunger Games Lab Analysis

1. In this lab we simulated evolution and natural selection through the process of feeding and reproduction. We had the population split evenly among three different phenotype and had the different groups feed and gain as much cork as possible to simulate feeding. After the birds who gained enough food survived they reproduced and created a second generation which continued the process of feeding and reproduction.
2. Pinchers were the best phenotype at capturing food because they had the use of there oposable thumbs and were allowed to reproduce the most. Contradictory to these results, knucklers continued to reproduce the most and had the largest population due to sexual selection, in which people were more likely to mate with knucklers rather then pinchers despite the data and phenotypic advantages.
3. The population evolved from natural selection because of a change in allele frequency. After the first round, the allele frequency changed greatly in that the A gene dropped in percentage while the a gene rose, showing a change that fit the pattern of phenotypes and how they work in the lab. The percentage of A gene started as 52%, while a gene was at 48%. After the first round, the A gene dropped to 31%, while a gene rose to 69%. After this round, the ratio stated constant and the a gene greatly outnumbered the A gene. This shows how the population evolved quickly and that there was a change in allele frequency.
4. The random events that occurred in this lab were sexual reproduction, the food placement, and the method in which mates were chosen. The non-random events included where people were placed on the line towards the food and phenotype of every bird. These random events had a large effect on the evolution of the population since mating was random and not chosen based upon successful phenotypes, which allowed unsuccessful genotypes to live through sexual reproduction, which slowed evolution of the gene pool. Food placement also affected evolution since individuals closer to food piles survived and gained more food through sheer luck, so natural selection was unable to take place.
5. If the food was larger or smaller, the results would have been different because the different phenotypes would have to adjust to this change, so the data would change based on which phenotype was best suited. If the food became smaller, chances are that the pinchers would be best adapted due to there maneuverability, while stumpys would adjust to larger foods best. This would change the data, as the Stumpys became endangered with the current food size. This is similar to nature in which natural events change the availability of food, so animals must adapt to new foods, which allows the population and gene pool to evolve.
6. If there was no incomplete dominance, the results would be different since knuklers would become stumpys with a higher chance of reproducing, so the population would not evolve due to the stumpys continuously living.
7. Natural selection acts on the phenotypes of individuals, and in turn changes there genotype and decides weather they will survive. This alters the frequency of this genotype in the gene pool, which is evolution, the change of gene frequency in a population.
8. Some strategies that individuals adopted included mating with exclusively pinchers or by having a very aggressive approach to mating. Pinchers had the best equipped phenotype, so only mating with them increased your chance of survival and created offspring that could survive.This relates to nature, where certain individuals only mate with those who have the best traits for survival rather than sexual reproduction, which change the gene frequency and selectively breeds to evolve the population.
9. In evolution, populations evolve, and the frequency of alleles changes. Natural selection acts on the phenotypes, but through acting on the phenotype changes the genotypic frequency for the population. 
   

Bird Beak Lab Analysis

In part one of our lab, our claim was that "Individuals with better traits leave more offspring". The evidence of this occurrence is that the tweezer and spoon had 22 and 23 chicks respectively (shown on graph), while the scissors only had 14 chicks. This is because the tweezers and spoon were easier to use with the given materials and thus were the better trait, allowing them to leave more offspring.

Another claim of ours was that "Populations begin to look more like winners."The evidence of this occurrence is that the tweezer and spoon had 39% and 37% of the population, while the spoon only had 24% of the population. This is because the tweezers and spoon were the "winners" in terms of the amount of chicks they had and the quality of their traits were better then that of the scissors. This increase in the amount of chicks allows them to have a larger amount of the population and thus, the population reflects them.

In part two of this lab, we asked the question of "If natural selection occurs in a population, how do changes in selective pressures affect the evolution of that species?" Our hypothesis was that if natural selection occurs within a population and selective pressure mainly effects traits that are not suited for it, then only the traits that are suited to survive a certain selective pressure will continue the process of evolution. The scenario assigned to us was that we were only able to use 1/4th of our food source, which made food very scarce and allowed instruments that pick up large amounts at a time to survive. Our claim was correct since the tweezers and spoon were able to intake large quantities at a rapid pace, with a respective 12 and 11 chicks born between the two. On the other hand, the scissors, which take time to gain food, were unable to compensate in either loading capabilities of speed, and thus only had 7 chicks. This result is likely caused by how the traits adapted to the selective pressures, and those that were less suited had a lower chance of survival.

While our hypothesis was supported by the data, there have been errors due to first, the uneven partition of our food supply, and second, the differences in the techniques for using certain beaks. The cause of the uneven food partition was human error, as we partitioned it through the eye test rather than quantitatively partition it, which may have allowed for a wrong amount of food to be used in the test. This could have effected the number of chicks hatched and changed the effect of the selective pressure itself. The cause of the difference in technique was also human error. One example of this was the spoon, which was used by some to push food against a wall and collect it, which was easier that outright collecting food. The effect of this was that the number of chicks hatched for the spoon may have been altered due to an illegal advantage. Some solutions to these problems include using a scale or another type of quantitative measurement and to clarify instructions over the usage of the different beaks.

This lab was done to demonstrate the process of natural selection and two of Darwin's main principles, which are that individuals with better traits leave more offspring, and that populations begin to look more like winners. From this process I learned how different traits survive in a population, which helps me understand the concept of natural selection, where only certain traits are able to survive selective pressures and control the majority of the population. This relates back to the vodcast called "change, its all natural" where we learned about the basics of Darwin's conclusions and to 7th grade science, where we learned the concept of natural selection, but never experienced a life like example of it. based on my experience from this lab, I know how to create an experiment through the use of competition and how to change variables but still keep the same principle concepts.

Unit 7 Reflection

This unit was about ecology and how different factors and decisions affect the biological lives of different species. The parts of this unit include energy movement, food webs, succession within ecosystems, and conservation biology. Energy move throughout the ecosystem through the use of the food web. The layers of the food web include: primary producers, primary consumers, secondary consumers, and tertiary consumers. They also consist of herbivores, omnivores, carnivores, and decomposers. The health of an ecosystem changes greatly based in a number of factors, including population, birth and death rate, and succession. Succession in the process in which new species will enter the ecosystem after the destruction of itself. A major theme of this unit was how everything about ecology connects to our everyday lives and how our ecosystems are threatened and that we should do something about it. One thing I want to learn more about are the solutions to many problems facing our environment and how everyday people can do their part in solving them. I wonder about why our government hasn't passed more laws concerning the well being of our planet and why we ignorantly continue to allow our plant to be destroyed. The content within this unit was easy to understand as the majority of it was big picture thinking or review from previous years, but it challenged me in more of a personal way in how all of the things i have learned affect me everyday and the impact they have on my life.

http://eschooltoday.com/ecosystems/images/Levels-of-Organization-in-an-Ecosystem.jpg

The main project we worked on in this unit was the Conservation Biologist project, in which we looked at the in-depth problems facing a specific biome. My group consisted of Andrew Gao, Sam Tiles, and Pranay Jalan and we focused on the African Savanah and the poaching problems facing this region. It was fun collaborating with others as I had the ability to bounce back ideas and have people to review my work and offer constructive criticism on my work. It also allowed my to focus more on my individual part knowing that others were taking care of theirs. It was a little hard mixing the multiple personalities, and the team contract was more of a burden to fill out rather than a tool to ensure proper collaboration, but it helped me learn how to deal with others and properly work together to achieve a common goal.

Link to Project: African Savanah Conservation Biologist Project

After taking the self assessment test to identify my preferred method of conflict management, I found that I was generally assertive, while my secondary response was to be aggressive or passive aggressive. I should try to be more passive at times, as that will help my assertiveness and tone down my aggression when working with others.

https://media.licdn.com/mpr/mpr/shrinknp_800_800/p/3/005/0b9/1e4/32af486.jpg

Unit 6 Reflection

This unit was about the technologies in biology and their different applications in everyday life. Biotechnology is the study of the manipulation of living things and how they are changed in order to benefit mankind. The four applications of biotechnology are: industrial and environmental; agricultural; medical; and diagnostic research. Despite the many benefits that these four applications have given to mankind, there are many questions that are posed about the bioethics of gene manipulation and weather they fit our values and morals as a species. This part of biotechnology is important since scientists are constantly creating organisms and making different discoveries, but weather the applications of these discoveries the moral thing is something that must always be asked in science that changes the natural order of things. We also learned about recombinant genes, and how they are used to mass produce and create bacteria with a desired protein to be extracted. This involves extracting a gene using a restriction enzymes, inserting it into a plasmid, and mass producing the plasmid in order to create and extract the protein that is created from the gene. The three main technologies used in biotech are Polymerase Chain Reactions (PCR), Gel Electrophoresis, and DNA Sequencing. The process of PCR is to denature strands of DNA with heat, add a primer to specific DNA sequences, and to use DNA polymerase to read the DNA and mass produce it, creating multiple copies for analysis. Gel electrophoresis is when DNA is placed into a gel and ran through with a an electrical current, which separates the DNA by size and allows for them to be more easily analyzed. DNA sequencing is used to determine the exact sequence of a gene and uses DNA polymerase and dyes to allow a computer to read it and analyze it. This was a fast paced unit and I had a hard time understanding some of the concepts until we did the labs, which gave us hands on experience and allowed us to truly see how the technologies are used and their  applications in real life.

We did three labs in this unit which all helped me understand the concepts behind the different technologies. In the Recombinant DNA lab, we used paper models to help us understand the role of restriction enzymes and how they cut plasmids and DNA to allow them to combine together. In the Candy Electrophoresis Lab, we ran different dyes in candy through a gel electrophoresis and analyzed them next to sample dyes, which helped us understand how gel electrophoresis is used and how it separates DNA by size.  In the pGLO Lab, we did the replication and combing part of Recombinant DNA, by combining DNA and plasmids through a process of cooling and heating and then mass producing the plasmids inside of bacteria to see how they are actually created and combined.

Links to Labs:

• Recombinant DNA Lab Analysis
• Candy Electrophoresis Lab Analysis
• pGLO Lab Analysis

I want to learn more about the industrial applications of biotechnology, since we learned about the diagnostic and medical applications through the pGLO lab and how that technology can be used to mass produce insulin and other medicines and how gel electrophoresis can be used to study DNA, but not about how biotechnology can be used in the industrial setting.

My goals from the New Years were to gain a 4.0 GPA in the second semester and to final in at least one speech and debate tournament by the end of the second year. I have yet to complete the first goal, but am making good progress towards the goal. The second goal is also incomplete but I have come very close in many tournaments, I need to continue practicing and become more knowledgeable on the analysis of current events in order to complete this goal and achieve future success.

Recombinant DNA Lab 

Gel Electrophoresis Lab 

pGLO Lab

pGLO Lab Analysis

pGLO Observations , Data Recording & Analysis

1.

Obtain your team plates.  Observe your set of  “+pGLO” plates under room light and with UV light.  Record numbers of colonies and color of colonies. Fill in the table below. Plate Number of Colonies Color of colonies under room light Color of colonies under   UV light - pGLO LB Lawn White None - pGLO LB/amp 0 + pGLO LB/amp 6 White Purple White + pGLO LB/amp/ara 2 and Satellite Colonies White Green White

2.	What two new traits do your transformed bacteria have?
	The two traits that the transformed bacteria have are resistance to the antibiotic ampicillin, and the inclusion of the GFP gene in the bacteria.
3.	Estimate how many bacteria were in the 100 uL of bacteria that you spread on each plate. Explain your logic.
	We estimate that there were around 5000 - 10000 bacteria since their were about 15 bacteria colonies in every unit, and those have a multitude of bacteria, and because many bacteria died due to the ampicillin, there are approximately that many bacteria at the beginning of the lab.
4.	What is the role of arabinose in the plates?
	The arabinose is a promoter for the GFP gene, and it is needed in order for the RNA polymercase to be allowed to read the GFP gene and express it.
5.	List and briefly explain three current uses for GFP (green fluorescent protein) in research or applied science.
	It is used in many animals alongside another resistance gene to test whether it has actually entered the organism and is active inside of it. It can be used to track organisms since they glow under UV lights and can properly be used to check where they are in a contained environment. It is used in monkeys to track the entrance of diseases into the monkeys brains can better help these diseases be studied.
6.	Give an example of another application of genetic engineering.

Another example of genetic engineering is the introduction of pest resistant genes into plants in order for them to better grow in impoverished areas and to yield better crop results.