BIOL398-01/S10:Class Journal Week 2

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

• What was the purpose of this assignment?

The purpose of this assignment was to get some sort of comfort, by using the computers and getting a feel of what a biologist does. This assignment also showed in my perspective the degree of difficulty in finding certain answers with a program such as this.

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

I learned that it is a tough task to find an answer when it comes to looking for certain proteins that make a true breeding plant. It is not easy and it takes many tries until success is at hand.

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

At first I did not understand how to quite use the program, but as I tried I understood how. Based on the assignment that was done during lab I did not understand how do we get a certain color by changing some portion of the DNA sequence. --Salomon Garcia Valencia

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)

Week 2 Assignment

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?

The main purpose of the assignent was to use the Aipotu program in order to create a purebreeding purple flower. The assignment was also a good way to learn how to use OpenWetWare to take notes as if it was a real lab notebook. It also helped us learn how to deal with glitches and crashes that we faced while using the program.

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

I learned that it is very important to save my work often so that I don't have to start over if a program quits or freezes. I also reviewed what we learned in genetics in relation to the software, and used it to figure out the results of the lab. I started out a bit frustrated because of the crashes and not being exactly positive of my genetics knowledge, but once I got the hang of it the lab was actually really interesting.

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

I didn't quite understand when to take notes based on the lab, but once I just started typing out everything that I saw, it made discovering the results much easier for me to figure out. Also, I think I'm still a bit fuzzy on the different genetics terms used throughout the lab.

--J'aime C. Moehlman 20:29, 31 January 2010 (EST)

• Week 2 Assignment Page
• My Week 2 Journal Entry

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.

Week 2 Assignment

Individual Week 2

KP Ramirez

1. What was the purpose of this assignment?

• The purpose of the assignment centered on learning to use the program Molecular Genetics Explorer when given a specific task. In this case it was about finding a true breeding purple flower employing elements of genetics, molecular biology, biochemistry and how they function as a whole.

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

• This allowed me to get comfortable with this new tool, much like how i first learned to use GenMapp or MAPPfinder, it was interesting to learn how it could be used to solve problems like this. It was also my first experience working with new people in the class, which I felt was a good experience as both Jenelle and George were very active and worked very hard.

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

Janelle and I weren't exactly sure why adding certain amino acids produced the same color. (Jan 31 11:14pm)

Individual week 2

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.

Janelle N. Ruiz Assignment 2

Bobak Seddighzadeh

1. What was the purpose of the assignment? The purpose of this assignment was to show you how different fields of biology work with one another to further each other's understanding and progress in biology. In this lab we viewed the application of biology through molecular biology, biochemistry, genetics, and evolution. You were able to see a clear relationship between the different sciences and how each science takes a different focus or approach to examining a biological principle.
2. What did you learn from the assignment? I learned several things. First, I learned that if the selective advantage is for a recessive trait it only takes one generation time before the population all contains that recessive trait because the alleles for another trait do not exist anymore. This is very intuitive but it was something I had never thought about until the lab. Secondly, I learned that not all genetic mutations are equally likely to occur. There are certain mutations that are more likely to occur than others. Lastly, I learned that antibiotics, habit change, ect. do not induce the increased likeliness of a mutation and that all mutations are produced at random.
3. Do you have any questions about the lab? No I do not. I took molecular genome last semester therefore I have already developed a solid understanding of what was going on in this lab.

Amanda Wavrin

• Week 2 Assignment Page
• Week 2 Journal Entry

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)

• Week 2 Assignment Page

• Week 2 Journal

Links

BIOL398-01/S10:Week 2