BIOL398-04/S15:Class Journal Week 7

William A. C. Gendron

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

Models designed to "discover new knowledge" are just finding the "nodes and edges". I heard about a project for a model just like this at Baylor College of Medicine where they are using an algorithm similar to ones on Facebook to find similarities between various articles to created edges. The other side of this is that models are developed to show that we understand the dynamics of these interactions. This is more like the model that we created. We are trying to pin down how cells work on a mathematical level. Before reading this paper, I was also beginning to align with the idea to merely creating hypotheses, but I can see that being able to create a greater understanding.

• Which point of view resonates with you more? Why?

I believe both tools are quite valuable. I am more impressed with creating a greater understanding of interactions. I hope that this will eventually create a complete model of a cell.

• Discuss your answers to the above two questions with regard to the research project you just completed.

The project follows more along the lines of understanding the exact molecular mechanism. Unfortunately this would never be a pure model and would require external calculations to figure out what the rate constants are. I would hope that eventually we can create models that predict from the ground up using only the most basic physics of each atom.

• William A. C. Gendron 02:55, 5 March 2015 (EST):

Lucia I. Ramirez

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

• Modeling to "understanding" relates more toward the simple cartoon models found in textbooks, while modeling to "discover new knowledge" aims to reconstruct and recreate biological systems into mathematical equations. These both are great, but modeling to "discover new knowledge" in the 21st century can lead to a great discoveries about life.

Which point of view resonates with you more? Why?

• The point the resonated with me was the aspect that mathematicians has developed so much of their knowledge about system of equations that they are now able to transfer their skills to another field, same with a biologist's knowledge.

Discuss your answers to the above two questions with regard to the research project you just completed.

• This article very much correlated with our research project assigned this week. I have seen how Dr. Dahlquist and Dr. Fitzpatrick have collaborated to further understand and create models that better explain large data sets. I also found that my better understanding in the math aspect of the project led me to understand the biological aspect.

Lucia I. Ramirez 01:43, 3 March 2015 (EST)

Lauren M. Magee

• Now that we have closed out the first section of the course and your first modeling project, read the article Lander, AD (2010) The Edges of Understanding. BMC Biology 8:40.
  1. What distinction does Lander draw between modeling to "discover new knowledge" and modeling for "understanding"?
     • Lander argues that comparing new data to existing models is greatly beneficial. He comments that many scientists don’t enter the field to discover new knowledge and that many satisfy themselves by gaining a greater understanding of what we already know. Therefore, testing the relevance of a model and possibly creating a new version of it is an important aspect of biology. He continues on to say that no model is perfect and that there are a wide variety of models to portray the same concepts. No one model is better than the other, as they all offer a different perspective based off of unique data. There are models that may outline the concepts more efficiently, however, and they may be considered more useful than others. Through this type of modeling, no knew concept is being discovered, but as Lander says in the paper, it is extremely difficult to model something completely new to the science community. Personally,
  2. Which point of view resonates with you more? Why?
     • I think it is important to have models that both “discover new knowledge” and “further understanding”. Before we can create something of our own, we need to learn from others and note where they had been successful and were they had failed. The science community provides a wealth of knowledge and the creation of your own model will go much faster if you already have experience testing others. It is also important to criticize and continuously build off of existing models, because nothing is perfect, especially in science, and we never want to remain complacent. A lot of new information can still be gained from revisiting old models, but it is also important to explore other routes to research and use your creativity to conduct your own experiment and compose your own model. Both methods of modeling are essential to the success of the scientific community.
  3. Discuss your answers to the above two questions with regard to the research project you just completed.
     • Our research project highlighted the method of modeling for “understanding”. We were told to build a model off of existing data and then compare it to the pathways that were explained in a previous article. In doing so, you do begin to gain a greater understanding and are able to bring to light a different perspective on the data. I believe this method to be successful in the academic sphere, however, if I were to continue my career in a laboratory, I feel as though I would want to focus more on “discovering new knowledge". I believe this path to modeling is more exciting and leaves you feeling more fulfilled.

Lauren M. Magee 00:33, 3 March 2015 (EST)

Tessa A. Morris

1. Lander explains that discovering new knowledge is finding new information, where understanding is finding different ways to explain or interpret information that has already been discovered.
2. The view about understanding resonates with me more. My career goal is to go into the medical field and conduct research on diseases and disorders of the body. Much is known about the human body, but I want to use mathematical techniques to find new and more effective ways of analyzing different medical disorders
3. In this project, we dealt with understanding, rather than discovering new knowledge. We used Matlab in order to come up with a mathematical model to try and further explain nitrogen metabolism. This research project was interesting to me because it used modeling for understanding, which was the type that resonates more with me.

Tessa A. Morris 19:22, 2 March 2015 (EST)

Kristen M. Horstmann

1. What distinction does Lander draw between modeling to "discover new knowledge" and modeling for "understanding"?
   • Lander believes that gaining factual knowledge about a process or organism is learning, and does not necessarily constitute a full understanding of the how it actually works. Understanding is gaining a deeper knowledge of the topic beyond the facts by utilizing the information already researched and discovered. Lander also seems to feel that scientists in general tend to think knowledge is the final goal, when in reality, there is so much understanding still to be done. Modeling is a way to delve beyond the data and facts and seeing how they interact as a way of understanding.
2. Which point of view resonates with you more? Why?
   • Understanding definitely resonates with me more because I feel like anyone could google or memorize facts about a subject, but it takes a real passion for learning and interest in the topic in order to gain a deeper understanding. In my opinion, pursuing this exploration into understanding over facts is what distinguishes scholars and scientists into who they are. I think it is very admirable to take previous discoveries and expand on them, simply for the sake of yours and other people's full understanding. Although I'm not entirely sure if that's how I want to expand my scientific career, it's interesting and cool when there are new research and understanding into how discoveries function. Plus, I think the scientific community as a whole will see a lot more deeper understanding as the technology improves and scientists realize that they can refine some research in order for everyone to understand better.
3. Discuss your answers to the above two questions with regard to the research project you just completed
   • This project is far more about understanding than learning. Yes, we have had to learn about different biochemical processes, the differential equations, and the different aspects that make up this processes, but it takes a full understanding in order to achieve what we have done. Modeling the differentials, being able to compare it to actual experimental results, and repeating it back to the class all takes an understanding that goes beyond textbook and factual memorization.

Kristen M. Horstmann 23:23, 2 March 2015 (EST)

Alyssa N Gomes

1. The distinction that Lander draws between modeling to "discover new knowledge" and "modeling for understanding" is that discovering new knowledge means using old information to compose something new, and gaining some sort of new unknown unlike before, and modeling for understanding means using old information in a new way, having depth on the topic and being able to apply it in a multitude of ways.
2. I know most people want to say that understanding resonates with them more, but I personally have a great interest in the unknown. There is so much we think we know about the world, and yet there is so so much unknown. I love the idea of using old information in a new and exciting way, but I love the idea of breaking boundaries even more, being able to have a theory and everyone thinking you're crazy, until one day, showing them something new that blows their minds. In relation to biology and mathematics, it's easy to think we know all the answers already, because there are an endless amount of books on each subject, but there are still so many illnesses to be treated, so many ways of modeling things that haven't yet been modeled. As the industry and the amount of information we have ever-expands, we have the opportunity to bring something new to the table.
3. In this project, we had to do a great depth of understanding. There were many terms that were vague and we knew how to define on a baseline level, but as a Math major who has only taken Biology 101, there were methods done here that I never would have originally thought of, Seeing how we used the information from the paper and adapted it into our own project definitely gave me more depth on what types of modeling there are, and that there isn't just one answer to everything.

Alyssa N Gomes 22:29, 2 March 2015 (EST)

Kara M Dismuke

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

• According to Lander, both a molecular biologist and systems biologist view biology through the lens of understanding biology's components and understanding the relationships between these components. However, the molecular biologist focuses more on the former and the systems biologist focuses more on the latter. He distinguishes between knowledge of something that was gained through looking it up on the internet versus actually understanding the thing itself. Lander asserts much of scientific community, to his dismay, seems to focus more on knowledge than understanding. While he acknowledges the difficulty that seeking to understand something may often be "messy,"he addresses this critique by offering up the approach of modeling as a means of creating order amongst the messiness through generalizations. He emphasizes how models are acts of creativity that do not depend on data and that while they can never actually be validated, they can be useful to us. Along this line of thought, Lander does not want scientists to restrict themselves to use models to make predictions with certain data.

Which point of view resonates with you more? Why?

• I think I tend to agree with the points Lander makes. While I certainly have a heart for knowledge, studying mathematics has taught me how to think and the value of understanding. The example that came to mind is that it is easy to plug an equation into Wolfram Alpha and find its derivative. I believe the value lies, however, in being able to understand the process being carried out and why it can be carried out in the first place. As this applies to biology and in my experience, I have found so often biology focuses on memorizing facts as opposed to focusing on understanding the material. However, since I learn (and I believe this is true for most people) better from understanding that I do from memorizing facts/knowledge, I have a tendency to align myself to be in favor of Lander's argument.

Discuss your answers to the above two questions with regard to the research project you just completed.

• Reading this paper after having completed the research project helped me to reflect upon the actual work that I did for the project. It is so easy to get bogged down in the work that we neglect to take a step back and take a larger look at what we are doing (and why we are doing it). In terms of this project, I felt it did seem to align more with what Lander was objecting to, namely using models to make experimental predictions. But, I think for an introductory project in an introductory course, it is necessary for us to go about understanding modeling this way before we seek to create our own models. Also, while this project is ending, I think that upon doing the work we did, there are lots of ways now available for each of us to advance with this project from a modeling-standpoint should we desire to do so.

--Kara M Dismuke 23:52, 2 March 2015 (EST)

Natalie Williams

1. What distinction does Lander draw between modeling to "discover new knowledge" and modeling for "understanding"?
   • Lander states that molecular biologists tend to discover things just for the sake of having that knowledge whereas systems biologists not only have that knowledge, but they want to further their understanding of how and why the subject acts as it does. Modeling to discover new things tends to be pictorial and uses diagrams to show cause and effect. To help us better understand a topic, models incorporate equations or procedural instructions that explain the process that is being done.
2. Which point of view resonates with you more? Why?
   • His distinction between the two uses of models, I now realize how many textbooks use models in a way to see similarities and differences between two concepts. It states the process but does not elaborate or explain the physical changes occurring in the system. However, with systems biology, the modeling uses equations to breakdown what occurs with each step. How system biologists use modeling excites me and interests me more. I want to have models that explain what is occurring so that I can better understand the processes. I also found it interesting how Lander mentioned that many believe models predict outcomes, which is not their sole purpose.
3. Discuss your answers to the above two questions with regard to the research project you just completed.
   • The project that was just completed utilized a model to not only describe but to showcase what occurs when yeast metabolizes nitrogen. In relation to Lander’s message, the model we ran through MATLAB to obtain data was used to help us understand the interactions between alpha-ketoglutarate, glutamate, and glutamine and their rates of conversion. Our model is probably one used by systems biologists because of the differential equations we wrote to describe the production rate of the three molecules.

Natalie Williams 20:26, 4 March 2015 (EST)