# BIOL398-03/S13:Class Journal Week 2

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## Contents

- 1 Week 2 questions
- 1.1 Reflection on Work
- 1.2 Read and Reflect
- 1.3 Kasey E. O'Connor Week 2 Journal Entry
- 1.4 James P. McDonald Week 2 Journal
- 1.5 Paul N. Magnano week 2 Journal entry
- 1.6 Salman Ahmad Week 2 Journal
- 1.7 Matthew E. Jurek Week 2
- 1.8 Laura Terada
- 1.9 Ashley Rhoades Week 2
- 1.10 Elizabeth Polidan Week 2 Journal
- 1.11 Anthony J. Wavrin Week 2 Journal
- 1.12 Helena Olivieri Week 2 Journal

# 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?
- This assignments purpose was to help familiarize us with matlab, and the modeling process.

- What aspect of this assignment came most easily to you?
- I would honestly say non of this assignment came easy to, I spent roughly 4 hours throughout the day trying to figure out matlab and work through my many mistakes.

- What aspect of this assignment was the most challenging for you?
- The coding part if this assignment was really hard. I am terrible with computers, and this was a nightmare for me. I would compare it to giving someone from china a chinese to english dictionary and asking them to use it to translate the odessy in 24 hours.

- What (yet) do you not understand?
- The entirety of proper coding, and matlab as a whole.

### Read and Reflect

- What distinction does Lander draw between modeling to "discover new knowledge" and modeling for "understanding"?
- Landers discerns that modeling to discover new knowledge and modeling for understanding entail the same process but have different outcomes. if one models to discover new knowledge it is like they are simply gather new data, like when early scientists performed dissections to learn how the bodies of certain organisms functioned. They simply learned something new. But when one models for understanding it is like they are a med student dissecting cadavers, they are doing it so they can better understand how a body works, knowledge they already have. This results in greater comprehension and retention. Modeling will have the same process but can yield different outcomes for the one modeling, is the general jist of what Landers paper states.

- Which point of view resonates with you more?
- Personally the ideal of modeling for understanding resonates with me more. I would say I use models to understand things more in my life than to discover new knowledge. for example when I am working on my motorcycle and I need to perform a new maintenance procedure, I can read a step by step guide, and have not too much of an idea of what to do. But after I look at the schematics, and watch a video, then do the maintenance myself, I have that knowledge instilled in me because I know how each step goes and why each part must go into its place. The process of modeling, for me helps me to connect concepts together and get a much better understanding of it, vs simply "learning" or "hearing" about it.

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)

## Ashley Rhoades Week 2

### Reflection on Work

- The purpose of this assignment was to introduce MATLAB and therefore the basic idea of differential equations. The assignment allows looked at general principles behind population modeling and how those differential equations and MATLAB can be used.
- Once I had a collection of graphs and looked what was happening it was easy to reason out why the cell population and nutrient level were behaving the way they were depending on what parameter I changed.
- Using differential equations in MATLAB was challenging at first. I’m used to them on paper and MATLAB has certain requirements to put the equations in correctly.
- I feel that I have more to understand with regards to how MATLAB works with more practice. Also I took a course on differential equations and I understand what is happening generally but there is much I feel that I don’t remember as well as I’d like to.

### Read and Reflect

- Lander uses an example to explain his views on knowledge and understanding. He says that a student may have the right answer but looking it up on their cell phone does not mean they understand it. This relates to his distinction between modeling for knowledge and understanding. Modeling for knowledge aims to generate a hypothesis or validate experimental results. Essentially modeling for knowledge looks for an answer to a question but modeling for understanding looks to explain what it’s modeling. If a model is just for a hypothesis or matching the model to experimental results that all that’s obtained is some kind of answer, just like the student has an answer. A model for understanding can provide more than that.
- Modeling for understanding definitely resonates more with me. Maybe that is due to the author’s bias towards that type of modeling but I know that in my experience in previous classes that is what has interested me. I’ve done experiments in labs where the answer is obvious and the teacher just wants you to do the experiment to prove an answer you already know. I’ve enjoyed experimenting in the classroom more when I didn’t know what I was going to find and neither did the teacher.

Ashley Rhoades 22:53, 24 January 2013 (EST)

## Elizabeth Polidan Week 2 Journal

### Reflection on Work

- What was the purpose of this assignment?
- To get us used to the ideas of the chemostat, the models, and Matlab.

- What aspect of this assignment came most easily to you?
- The models and Matlab were easy for me. I have already done some of this work.

- What aspect of this assignment was the most challenging for you?
- The biggest challenge for me was remembering the chemistry and biology -- it's been a while

- What (yet) do you not understand?
- I could play around with these models all day. I did come across behavior I did not understand. I uploaded a file with plots and it is in figure 11.

### Read and Reflect

- What distinction does Lander draw between modeling to "discover new knowledge" and modeling for "understanding"?
- Modeling to discover new knowledge is done through cartoons or diagrams, and is used for things like validating the results of a process. Modeling for understanding is done with mathematical equations. It is used to find connections between pieces of knowledge, or to better understand abstract concepts. It is a way to understand complex systems or systems one cannot even see.

- Which point of view resonates with you more?
- I definitely resonate more with the second approach. If one simply gathers sets of information, but does not attempt to synthesize all of the information in a way that explains systems, there is little real progress being made. This is why I left Biology in the first place. It was presented as just gathering a bunch of facts. I want to understand!

Elizabeth Polidan 02:56, 25 January 2013 (EST)

## Anthony J. Wavrin Week 2 Journal

### Reflection on Work

- What was the purpose of this assignment?
- The purpose of this assignment was to get us involved in making a system. It is really easy to watch someone do it on the computer but, forcing us to make it on Matlab and attempt to change the parameters forced us to learn and explore more about modeling. Also, it was a good intro for using the functions in Matlab.

- What aspect of this assignment came most easily to you?
- The part of the assignment that came easy to me was changing the parameters and looking at the results. From these results I was able to come up with very plausible and reasonable ideas of why the chemostat population and nutrient concentration was affected.

- What aspect of this assignment was the most challenging for you?
- The hardest part was the writing and coding in Matlab. I am not used to the language and if there were any errors, I was unable to decipher what they meant.

- What (yet) do you not understand?
- The biggest thing that I don’t understand is controlling Matlab and making it do what I want to do. If we did not get help making the equation for the model of a chemostat in class I think I would have had a very hard time with the assignment.

### Read and Reflect

- What distinction does Lander draw between modeling to "discover new knowledge" and modeling for "understanding"?
- Lander makes a rather large distinction between the two ‘types’ of modeling. In modeling to discover new knowledge, one is attempting to design a model that can solve a specific problem. That is, design a system that can test a specific hypothesis or approach a certain problem to either prove or disprove an idea. This is the more commonly known type of modeling. The other type is modeling for “understanding”. This means that you are learning from the model itself rather than posing a question and a designing the model around that question. There is an abundant amount of knowledge one can learn from models such as patterns and tendencies, essentially gaining a better understanding of something through a model instead of finding one fact.

- Which point of view resonates with you more? Why?
- I personally believe that the modeling to “discover new knowledge” resonates with my personality more. I am one that typically sets out to find an exact answer. I want to know if something is right now wrong. It is not that I don’t like understanding how things work because that is how I actually learn material but, I am not one that likes to “stop and smell the roses”. I believe my lack of patience is what leans me more towards the modeling to “discover more knowledge”.

Anthony J. Wavrin 00:34, 25 January 2013 (EST)

## Helena Olivieri Week 2 Journal

### Reflection on Work

- What was the purpose of this assignment?
- The purpose of this assignment was to reinforce the calculus behind the functioning of the chemostat and population dynamics.

- What aspect of this assignment came most easily to you?
- The aspect of this assignment that came most easily for me was the population dynamics section, especially the Malthus section. Population dynmaics has been a topic that has been drilled in various math and biology classes since high school, so the topic seems to come pretty naturally.

- What aspect of this assignment was the most challenging for you?
- The aspect of this assignment that was the most challenging was understanding the role of concentration in the chemostat, as well as following along with some of the derivations.

- What (yet) do you not understand?
- I'm still a little shaky with how to incorporate the calculus of the chemostat and population dynamics in MatLab. But I expect that to come with time and practice.

### Read and Reflect

- What distinction does Lander draw between modeling to "discover new knowledge" and modeling for "understanding"?
- The distinction that Lander makes between modeling to "discover new knowledge" and modeling for "understanding" is that modeling to "discover new knowledge" tends to seek answers to questions that lack depth. While modeling to discover new knowledge may bring to light new and unforeseen biological findings, it frequently regurgitates facts and fails to connect these discoveries to other relevant biological questions. Modeling for understanding, on the other hand, uses critical reasoning to connect questions regarding one's biological discoveries.

- Which point of view resonates with you more? Why?
- Modeling for "understanding" is a view that resonates much more with me. While at times it can be easy to overly focus on the details of math and science, making the connections to better understand biological concepts is significantly more important. I would argue that, in order for Biology to truly be understood to its fullest, it needs to be incorporated as an interdisciplinary study. Not only are there various areas of study within Biology, Biology by nature offers the potential of dialogue through critical reasoning. For example, by incorporating one's understanding of Biology with Political Sciences researchers may have the chance to influence the direction of law, or by encouraging dialogue between Biologists and Theologians and Philosophers, scientists may better communicate their understanding of Bio-ethics. Only through "understanding" will society be able to appreciate the findings of Biology. Helena M. Olivieri 02:39, 25 January 2013 (EST)