# BIOL398-03/S13:Class Journal Week 2

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## Contents

# Week 2 questions

## Reflection on Work

- What was the purpose of this assignment?
- To understand the math behind the chemostat and improve our MATLAB skills.

- What aspect of this assignment came most easily to you?
- Understanding the math and biology of the chemostat.

- What aspect of this assignment was the most challenging for you?
- Doing anything in MATLAB I do not understand it other than the most basic things shown in the tutorial. Working with the computer, I do not like computers and I really very much do not enjoy writing code and working with computer programs.

- What (yet) do you not understand?
- MATLAB.

## Read and Reflect

- What distinction does Lander draw between modeling to "discover new knowledge" and modeling for "understanding"?
- Lander clearly favors modeling with the purpose of understanding, and comments on how it is seen as trivial when compared to the discovery of new knowledge. While discovery of new knowledge is finding bits and pieces of information accepted as "facts", truly understanding includes taking those facts and connecting them to other knowledge (the metaphor of the hairball, the nodes would be facts while the edges are understanding).

- Which point of view resonates with you more?
- I find that I get more out of understanding then I do out of straight facts. Knowing the facts is great, but without the anchor of understanding, facts will quickly exit one's memory. I know this from experience. I remember biological processes much better when I actually understand them for example, I really understand the Krebbs cycle because I can draw it out and explain every part of it, not just because I have memorized the diagram.

Kevin Matthew McKay 22:39, 23 January 2013 (EST)

## Kasey E. O'Connor Week 2 Journal Entry

##### Reflection on Work

- What was the purpose of this assignment?
- What aspect of this assignment came most easily to you?
- What aspect of this assignment was the most challenging for you?
- What (yet) do you not understand?

##### Read and Reflect

- What distinction does Lander draw between modeling to "discover new knowledge" and modeling for "understanding"?
- Lander states that discovering new facts, while it can be exciting, is much different than actually understanding what you are presented with. He clearly favors modeling for understanding, and claims that the majority of biologists would feel the same. He says that there will always be a need for models for understanding, and the notion that models can only be used to make predictions is not entirely correct. It is with all of the models that understanding can be found.

- Which point of view resonates with you more? Why?
- I found that the models for understanding resonate more with me. There is much more to learning than just memorizing facts. Especially in math and biology since they are subjects that constantly build upon each other, having an understanding it necessary. In order to be able to correctly explain biological systems, or even some mathematical problem solving techniques, an understanding of the process and/or model that goes with it is going to be much more beneficial.

## James P. McDonald Week 2 Journal

### Reflection on Work

- What was the purpose of this assignment?
- To further understand the nature of a chemostat. We can understand how cell populations will increase or decrease in the chemostat depending on different conditions, such as nutrient supply. Also, to use mathematical equations to account for how the chemostat behaves in different situations. This allowed us to observe the behavior of the cell populations and nutrient concentration when various constants were changed.

- What aspect of this assignment came most easily to you?
- The aspect that came the easiest to me was understanding the physical and biological behavior of the chemostat. I am familiar with population dynamics so I was able to understand what was taking place in the chemostat. Also, I am able to understand growth rates, death rates and understand cell growth or decline in the presence or absence of nutrients.

- What aspect of this assignment was the most challenging for you?
- The aspect that was most challenging to me was using the mathematical equations. I have not taken a math course in three years so I am hazy on my understanding of differential equations. I find that I am able to apply math equations much better when I fully understand them. In this case I had some difficulty applying them because my understanding of differential equations it is not fresh in my mind.

- What (yet) do you not understand?
- I do not fully understand using MATLAB and how to input differential equations into it correctly. I have never used the program before and I rarely have done math on computer software. With some more practice I feel that I will be able to understand it better as we use it more in class.

### Read and Reflect

- What distinction does Lander draw between modeling to "discover new knowledge" and modeling for "understanding"?
- Lander explains that there is more to understanding than there is to simply discovering new knowledge. Discovery new knowledge can simply be identifying a new fact. He states that factual discovery does not always accompany a full understanding, using the example that a student can discover new knowledge by looking up an answer on their phone while that student actually has no understanding of the fact. Lander supports modeling for understanding. He is interested in understanding the world in new ways rather than just discovering new facts about it. He believes that modeling is not simply a way to make predictions or hypotheses but can be useful in further understanding concepts.

- Which point of view resonates with you more? Why?
- Modeling for understanding resonates more with me. To me, understanding lays a foundation that you can continue to learn on. If one is just discovering new facts without a foundation of understanding, that knowledge can go to waste. When I understand something, I will always know it and then I can relate it and apply it. When I know just the facts I am unable to apply the knowledge. Also, I think modeling for understanding can lead to new discoveries because once the foundation is in place, one can use it guide themselves towards making new discoveries.

James P. McDonald 00:46, 24 January 2013 (EST)

## Paul N. Magnano week 2 Journal entry

### Reflection on Work

- What was the purpose of this assignment?

- What aspect of this assignment came most easily to you?

- What aspect of this assignment was the most challenging for you?

- What (yet) do you not understand?

### Read and Reflect

- What distinction does Lander draw between modeling to "discover new knowledge" and modeling for "understanding"?

- Which point of view resonates with you more?

User:Paul Magnano 01:48, 24 January 2013 (EST)

## Salman Ahmad Week 2 Journal

### Reflection on Work

- What was the purpose of this assignment?
- I think the purpose of this assignment was to learn about and understand better how a chemostat works. It was also helpful to see the equations again and try to understand how each variable was connected and what it meant to the cell population.

- What aspect of this assignment came most easily to you?
- The easiest part of this assignment for me was probably the use of MATLAB. The syntax of the MATLAB language is similar to other languages I have used. It was also easy for me to understand a chemostat from a biological point of view.

- What aspect of this assignment was the most challenging for you?
- The hardest part for me was to understand all the math that was involved. It was hard to use the differential equations in MATLAB because I have not had to do any serious math in the last few years. I think the more I use MATLAB and work with the equations, the more I will remember how to use these equations.

- What (yet) do you not understand?
- Putting in the differential equations into MATLAB is something I think I do not fully understand yet. I was able to do it because I followed the template we used in class, but I do not think I could make a new differential equation from scratch and get it to work.

### Read and Reflect

- What distinction does Lander draw between modeling to "discover new knowledge" and modeling for "understanding"?
- Lander explains the difference between "discovering knowledge" and "understanding". It is simple to discover knowledge by reading information presented in a book, or looking up information on a phone (an example Lander uses). Discovering this knowledge does not also mean, however, that one has truly understood it. When I was reading this it reminded me of something that happens every once in a while in class. When following along on a problem with a professor, I feel like I know how to do it. What I have done is discovered new knowledge. When I go back, however, and try to solve the same problem from the beginning without help from notes, I am not able to. This is because I have not fully understood the problem. Lander believes modeling should be done to promote understanding instead of just discovering new knowledge.

- Which point of view resonates with you more? Why?
- I think modeling for "understanding" is more important. I believe this because of the example I gave above about following along with a professor. Without really understanding something, I don't think there is any point in discovering the new knowledge.

Salman Ahmad 20:04, 24 January 2013 (EST)

## Matthew E. Jurek Week 2

### Reflection on Work

- What was the purpose of this assignment?
- This assignment allowed for a hands-on experience involving modeling. Via matlab, the various variables within a chemostat were manipulated and the impact of each variable was observed. This provided an introduction to modeling which will be used throughout the semester.

- What aspect of this assignment came most easily to you?
- Understanding the biology behind the chemostat was rather easy to follow. Looking at the graphs created by matlab was also easier as it expressed the relationship between cell growth and nutrients within a system. Part 2 introduced carrying capacity and explored how this impacted cell growth which is something I've seen before.

- What aspect of this assignment was the most challenging for you?
- Deriving the equations used within matlab. I haven't seen math in a while so I'm desperately trying to recall the ins and outs of calculus. Generating the equations to use within matlab was difficult. Also, once the equations were derived, entering them in to matlab was not easy. I'm still trying to figure out this computer program.

- What (yet) do you not understand?
- Seeing that I've only used matlab twice now (Tuesday and today), I'm hoping to further my understanding of this program as it seems like a powerful tool in the world of modeling.

### Read and Reflect

- What distinction does Lander draw between modeling to "discover new knowledge" and modeling for "understanding"?
- He compares discovering new knowledge to something we all do today; looking something up on the internet. As he explains, this may help a student answer a question on a given assignment. However, this does not mean the student understands the answer. The big difference is regurgitation versus retention. Understanding something allows for retention years later, simply regurgitating a fact makes it hard to remember the subject in the future (or at all). As explained on the first day of this class, the process is more important than the end result. That's why our assignments are all contained within this fully editable site. The end product does not imply a level of understanding, however a process does.

- Which point of view resonates with you more?
- As a student, I would be lying if I said they both don't resonate within my life. However, I can make a distinction between when I use each. I find myself seeking to "discover new knowledge" in classes outside my major. In core classes that I have little interest in, it's easy to simply look up answers online to complete the assignment. The are of "understanding" is more prevalent in my science classes. I feel this is true because everything builds on the subject before it. For example, an understanding of general chemistry is needed for organic chemistry which is then needed for biochemistry. The same is true for all biology classes, math classes, etc. Although I'm familiar with both, I would say "understanding" is more important as I want to work within the field of science following my education.

**Matthew E. Jurek 22:07, 24 January 2013 (EST)**:

## Laura Terada

### Reflection on Work

- What was the purpose of this assignment?
- The purpose of this assignment was to develop my MATLAB skills. While doing so, developing a general understanding about the chemostat was also involved. This assignment allowed me to work with equations and how changing the variables affect the results, or growth rate.

- What aspect of this assignment came most easily to you?
- Understanding the properties of cell growth in a chemostat made the most sense to me because I have learned about growth patterns, including the concept of carrying capacity, in other courses.

- What aspect of this assignment was the most challenging for you?
- The most challenging part was understanding MATLAB and if I was doing the assignment correctly. I also had a hard time understanding the equations and how the variables relate to each other.

- What (yet) do you not understand?
- I'm still uncomfortable using MATLAB because it generally takes me awhile to understand computer programs.

### Read and Reflect

- What distinction does Lander draw between modeling to "discover new knowledge" and modeling for "understanding"?
- Lander contends that most biologists seek to both discover new knowledge and to develop an understanding of scientific concepts. Understanding is when one can similarly treat two different phenomena in some way, which is what most biologists hope for. Lander argues that in order to comprehend pieces of data and facts, one must build a model aimed for "understanding." Towards the end of the paper, Lander suggests that models can not only generate predictions and hypotheses, but it can also be a vehicle of understanding.

- Which point of view resonates with you more?
- It is clear that Lander supports the modeling for understanding concept. I believe that understanding concepts is more important than knowing the facts. When I'm able to understand a concept, I can then relate it to larger concepts. For example, I previously learned about different functions of the kidney; however, an understanding of how the kidney relates to and affects other organs is of greater significance.

Laura Terada 22:46, 24 January 2013 (EST)