BIOL398-01/S11:Class Journal Week 5

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Part One: Reflection on Chemostat Model

  1. What was the purpose of this assignment?
  2. What aspect of this assignment came most easily to you?
  3. What aspect of this assignment was the most challenging for you?
  4. What (yet) do you not understand?

Part Two: Landers Paper

  1. What distinction does Lander draw between modeling to "discover new knowledge" and modeling for "understanding"?
  2. Which point of view resonates with you more? Why?

Class Responses

Sarah Carratt's Journal Entry


  1. This assignment is designed to help us understand how to better create models for real life biological systems. It gives us practice with different equations.
  2. The easiest part of this project was understanding the background material and working with the IT rep at the hotel help desk to get the internet to actually work.
  3. The hardest element for me continues to be Matlab. I'm not sure why I have such a hard time starting each program, but it has been really difficult for me.
  4. Sorry Jaimz and Dr. Fitzpatrick, but I can't confidently say that I understand Matlab. The programing is getting easier, as is understanding the programs, but knowing where to start and if I'm correct is frustrating.


  1. Landers says that to "discover new knowledge" is a misleading phrase that lures people to the field of biology. The way he views the world, "understanding" is much more appropriate because the term acknowledges that rejecting/approving hypotheses is not satisfactory. Understanding requires a scientist to look into the "hows" and "whys" of a mystery, and is the better way to learn.
  2. I think that Lander draws an interesting distinction, but I'm not convinced that understanding is always best. I think sometimes "discovery" and simply being able to acknowledge truths can be highly satisfying. While it would be cool to understand more about the world, I know that I will be happier if I don't spend all my time exploring truths.

Carmen E. Castaneda's Journal Entry

Chemostat Model

  1. The purpose of this assingment was to allow us to put into use the newly aquired knowledge on mathematical modeling in MATLAB and apply it towards the chemostat model.
  2. From this assingment i found it easiest to read the assignment and the actual writing of the program was a little easier this time around.
  3. However debugging the program was challenging. I also ran into a a bit of a snag when first writing the program trying to understand how each equation worked.
  4. I still don't have a great understanding of MATLAB but I feel like I'm getting there. Sometimes it also takes me a while to try to understand what exactly is happening in the equations.

Landers Paper

  1. Lander believes that modeling for the "discovery of new knowledge" should not be the reason to practice modeling. He also believes that very few might actually model to discover new knowledge but instead they model in oreder to gain understanding. Through understanding we gain a knowledge, the likes in which we are given an opportunity to explain things in a simpler manner.
  2. As for me, I believe that modeling for understanding is what resonates with me the most because I believe that through modeling we will gain an insight to how a specific function, activity or the world works.

--Carmen E. Castaneda 02:47, 14 February 2011 (EST)

James C. Clements' Journal Entry

Chemostat Response

  1. The purpose of this assignment was for the students to observe the effects of varying the parameters for the Malthus and Logistic models of population for the Chemostat model.
  2. The MatLab modeling came most easily to me. One problem that I was having thought was that I had written "clear" beneath my statement declaring my global parameters. This caused the global statement to be undone and caused much frustration when the model was not working.
  3. The most challenging part of the assignment was communicating the effects of varying the parameters. It's difficult to describe a plot concisely.
  4. I'm starting to wonder what would happen if we took differential equations for the logistic model into the laplace domain and did an analysis of the differential equations. The parameter values appear to change the damping of the system for the logistic model. In some cases (such as varying the feed concentration) the plot of nutrient concentration appeared to start out as over damped at U = 1 and then transition into being under damped as U increased.

James C. Clements 02:04, 14 February 2011 (EST)

Landers Response

  1. The distinction is that modeling for the sake of discovering new knowledge is the creation of models designed to increase the accumulation of facts by helping to develop new hypotheses and make predictions about the use of different parameters; modeling for understanding, on the other hand, is modeling for the purpose of being able to visualize/conceptualize the phenomenon at hand. The former will tell you which proteins will bind together, the latter sheds light on the process of binding.
  2. Modeling for understanding resonates with me most because it is from understanding that we are able to make the best predictions and hypotheses. I actually think that Landers' argument is one of semantics; a model that does not bring about understanding is incapable of performing the functions of creating predictions, creating hypothesis, and validating data.

James C. Clements 02:31, 14 February 2011 (EST)

Nicholas A. Rohacz's Journal Entry

Chemostat Modeling

  1. The purpose of this assignment was for us to make our own model of the Chemostat equilibrium.
  2. Once I got some help on the Matlab it actually came pretty easily to me, I'm still working on a format for how to start scripts.
  3. However, the most frustrating part of this homework was still trying to set up the model from scratch, Jame's comments helped a great deal in getting started.
  4. I am trying my best to understand Matlab but it is still coming slowly to me.

Lander's Reading

  1. The distinction that Landers places on modeling for "knowledge" and modeling for "understanding" is understanding. The distinction asks whether the biologist uses models to find an answer to a question, or to better understand how something works.
  2. The point that resonates with me the most is when Lander distinguishes between the "thrill of discovering new knowledge" and the "challenge of understanding the world", I start to try and categorize myself within this distinction. This self reflection definitely made me think about my future and if I want to make any changes to my plans.

Nicholas A. Rohacz 02:22, 14 February 2011 (EST)

Alondra Vega's Journal Entry

Reflection on Chemostat Assignment

  1. The purpose of this assignment was to understand how the nutrient/ cell population works, when different constants are put in place. It shows us how the system behaves. We were also able to see how the system shapes differently when it is shaped to the logistic model.
  2. The easiest part of this assigment was reading the simple chemostat model of nutrients and population growth that was written by Dr. Fitzpatrick. It was easy to see how the equations interacted with each other and how the system worked step-by-step.
  3. The hardest part of this assignment was working with matlab, since it took me forever to get the program right, or what I think is right.
  4. I think I am starting to begin to understand how the nutrient income works. For now, I think i understand everything.

Landers Paper

  1. Landers says that to modeling to "discover new knowledge" is wrong for a lack of better terms. Scientists should not model to test their hypotheses, they should model to understand what is going on. When modeling a person should be answering the questions why and how. He says that a person should not characterize models just as a form to test hypotheses because they have an even greater function now more than ever towards understanding biology.
  2. I think that learning in general is the best way to go. If it is believed that understanding models and their functions is of greater help than just discovery, then we should focus on them. I like discovering new knowledge and seeing how people used to think how things work. Going further into making models for grearter understanding is great, but I think that it is hard for many people to apply new ideas when the old are still being taught. When we look at the curriculum, there are more "discovering new knowledge" classes than there are "understanding" courses. the emphasis is still greater in the discovery department, which is the one I like best.

Alondra Vega 00:47, 13 February 2011 (EST)