BIOL398-01/S10:Class Journal Week 2

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Contents

Kristoffer Chin

Week 2 journal Entry

Lab Reflection

  1. The purpose of this assignment was to apply the understanding of biology through genetics, biochemsityr, molecular biology, and evolution for critical thinking and problem solving. Using the genetics explorer allowed us to see how the smallest change in any of these empahsis of biology can change the overall organism
  2. The assignment has showed me how very specific biology is in application. I can understand now why biologists need to be perfectionist in their work in research. The smallest mistake can change the outcome of a project that has been worked hard with. I was a little frustrated at first in trying to figure out how to make the true breeding purple, but adding that amino acid sequence made it easier, but it was only through trial and error.
  3. What i did not understand yet in the assignment is how do you know which amino acids have to deal with making pigmentations in the flower. I know that an error in the sequence can cause no pigmentation in the flower leading to white, but is there to way to know how to make a purple, green, or any other color in the flower pigmentation without needing to do it through trial and error. I guess there might have been a pattern in all the allele sequences, but I am still not 100% sure about it.

--Kristoffer T. Chin 00:10, 31 January 2010 (EST)

Salomon Garcia

  • Week 2 Entry

Angela Garibaldi

  1. What was the purpose of this assignment? The purpose of this assignment was to refresh our minds of important realms of Biology that we may have taken a break from over winter vacation. Moreover, my group's specific purpose was brush up on evolution and hardy weinberg and to see how the population dynamics are related to and affected by the molecular biology, biochemistry and genetics of the individuals.
  2. What did I learn from this assignment (head, hands, heart)? From this assignment, I foremost learned which biological topics I should brush up on. I also learned that formatting for numbering on wiki is not as flexible as I would like it to be. I finally figured out that I had to use the entire line to avoid breaks and ,therefore, avoid discontinuities in the numbering. I'd prefer to be able to use bullets and indentations with more freedom without having the numbering discontinuities. I also realized how great it is to work on these assignments in groups even though we do individual work. It really helped orient me especially since I haven't worked with wiki before this class.
  3. What did I not understand (yet) about this assignment? At the end of the assignment, there wasn't much regarding the assigned exercises on evolution that I can say I don't understand. Although, I'm sure if I were to have had the Biochemistry assignment, there may have been some things I'd be more unclear on and would have to brush up on to understand. Angela A. Garibaldi 03:06, 31 January 2010 (EST)

Alex George

Assignment Questions

  1. The purpose of this assignment was to use and understand the Molecular Genetics Explorer by tackling a problem (finding a true-breeding purple flower) using principles from Genetics, Molecular Biology, Biochemistry and evolution.
  2. This assignment gave me a basic knowledge of the "Biochemistry" aspect of Molecular Genetics Explorer. Also, I learned to appreciate the interconnectedness of the sciences. All of the branches encompassed in the assignment were tools in finding the ultimate solution. Finally, I learned the aromaticity of protein side chains can affect phenotypic color.
  3. I didn't (and kind of still don't) understand how the addition and subtraction of amino acids in the protein chain can produce the same color. For example, we found many amino acid sequences that produced a purple color. How can all of these mutations result in the same phenotypic result?

Alex J. George 20:25, 27 January 2010 (EST)

J'aime Moehlman

1.What was the purpose of this assignment? 2.What did I learn from this assignment (head, hands, heart)? 3.What did I not understand (yet) about this assignment?

Michael Piña

  1. What was the purpose of this assignment?
    • The purpose of this assignment was threefold. Firstly, it was in exercise in computers to get our feet wet. As a Bioinformatics Lab, we will obviously be working intensively with computers and so we need to get used to quirks and bugs (large or small) that may arise. Secondly, this assignment allowed us to see and reinforced the interconnectedness of various aspects of Biology from a broad view seen in Genetics and Evolution, to a more detailed look in Biochemistry and Molecular Biology; they are all important. Lastly, this assignment got us to think like scientists. The answers in research aren't always so easy, and they aren't always there. Finding a true breeding purple flower was great mental exercise.
  2. What did I learn from this assignment (head, hands, heart)?
    • In terms of my head, I think that this assignment was a lesson in critical thinking. The goal of finding a true breeding purple flower was not clear cut so you really had to think about it.
    • With my hands, I learned that the Aipotu program likes to have its Greenhouse files in specific locations. Also, I've been refreshing myself with wiki code.
    • I didn't learn too much in terms of my heart this week. The assignment was group based but we also needed to arrive at a solution on our own to be able to understand it. It is also nice to have a partner though to work through problems.
  3. What did I not understand (yet) about this assignment?
    • I mostly used the Genetics and Molecular Biology tabs for this assignment, so I'm not quite clear on the Biochemistry and Evolution functions of the program.

KP Ramirez

  1. What was the purpose of this assignment?
  2. What did I learn from this assignment (head, hands, heart)?
  3. What did I not understand (yet) about this assignment?

Janelle N. Ruiz

  1. What was the purpose of this assignment?

The purpose of this assignment was to learn how to work with the computer and a new software system, including learning to deal with a software program which experiences frequent crashes and possesses imperfect design components.

  1. What did I learn from this assignment (head, hands, heart)?

I learned tips and tricks of working with the wiki site. I learned the importance of saving "early and often". I gained review some of the basics of biochemistry as well as genetics. I learned that I am going to need to adjust my note-taking habits and my work habits to fit with this course. For example, I prefer doing most of my work outside of class and on an individual level, but it is becoming apparent that with the unfamiliar and complex software/assignments we will be doing in this class, I will need to not only take advantage of class time to complete the assignment, but I will also need to utilize both the professor and my peers for assistance.

  1. What did I not understand (yet) about this assignment?

I do not understand some of the patterns and anomalies I am observing with regards to amino acid sequence and allele color.

Bobak Seddighzadeh

Amanda Wavrin

  1. What was the purpose of this assignment? The purpose of this assignment was ease us into the lab work and to give us a general biology review. It was a good genetics review for me. It was also to introduce us into different types of software, such as Aipotu. This software was diffucult to work with because it crashed a lot but it forced me to keep working no matter what happens.
  2. What did I learn from this assignment (head, hands, heart)? With my hands I learned how to use Aipotu website, I learned how to take notes in my online journal while conducting experiments, and I learned how to better use the computer in general. With my head I got a very nice genetics review. This lab forced me to call upon my previous knowledge of genetics and forced me to apply that knowledge in order to understand my results. With my heart I learned to be persistent. As much as I wanted to quit every time the system crashed, I knew that I had to keep going and finish my work.
  3. What did I not understand (yet) about this assignment? This assignment was tough to get started with but once I began to get the hang of things and understand the website and the note taking, it became much more interesting. I think what held me back the most was my poor memory of genetics. The observations were easy to make but interpreting them was more difficult. I found I was making some things much more complicated than they had to be but it was just because I was confused and frustrated sometimes. During lab I was having a tough time remembering the difference between codominance and incomplete dominance and this made interpreting some of the data more difficult.

Amanda N. Wavrin 19:35, 31 January 2010 (EST)

Ryan Willhite

  • What was the purpose of this assignment?

The purpose of the assignment was to to explain biological processes utilizing genes. My group was particularly interested in finding out how flower color is inherited. Overall, the assignment in its entirety, was to utilize previous knowledge of biochemistry, genetics, as well as molecular biology in order to explain biological phenomena such as how flower color is derived either occurring naturally or through mutations and how different levels are affected due to those mutations.

  • What did I learn from this assignment (head, hands, heart)?

I learned a lot from this assignment. My main understanding by utilizing this program is that computer are not very reliable. Several times we have lost data due to computer failure. It was quite hard to remember and try and continue with the program shutting down every time several mutations were made. Through my head, I learned the connection between sciences such as the three I listed above. I also understand how scientist can work together by using different specialties and focuses for a common goal. Through my hands, I learned how to work the program and with all of the difficulty with the computers, I had to really be able to navigate my way through the program in order to save data and keep at least some of my findings still there. In my heart, I feel as though I can eventually reach a goal no matter what hurdles may come my way just like in the real world of science.

  • What did I not understand (yet) about this assignment?

I did not understand that the computers would be so hard to deal with at times.

Ryan N. Willhite 16:48, 31 January 2010 (EST)

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BIOL398-01/S10:Week 2

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