BIOL398-05/S17:Class Journal Week 4
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Margaret J. ONeil Reflection Questions
Question Answers
Before
- The purpose of modeling at its core is to model the processes of complex systems. Modeling allows for controlling variables in usually complex environments, such as GRNs, and being able to perform large-scale experiments rapidly in silico. This allows for a better understanding of how an increase or decrease in variables (ie food source) have on living organisms. These modeling-based experiments are cheaper and allow for more experimentation to be done in a short period of time.
After
- According to Lander, the purpose of modeling is create useful models in which hypotheses can be framed and models that can be vehicles for understanding biological processes. Lander also argues that modeling should not be about validating or invalidating models, as models that are deemed to not fit data don't necessarily correlate to a lack of utility. He is looking at modeling from a systems biology perspective, and seems to agree to an extent with the Occam's razor approach in that sometimes the simplistic is more useful than the complex, citing George Box as saying "all models are wrong; some are useful," and then backing up his explanation for the utility of models and modeling as a whole.
- Odenbaugh describes models as being used/useful for 5 things. (1) Models are used to explore possibilities, (2) Models give scientists simplified means by which they can investigate more complex systems. (3) Models provide scientists with conceptual frameworks. (4) Models can be used to generate accurate predictions. (5) Models can be used to generate explanations. To elaborate on some of these points, Odenbaugh goes on to say:
- "Models act as tools that help biologists realize possible relationships between natural phenomena through tracking relationships between variables and parameters." (Odenbaugh, 2005)
- "Models also allow scientists to investigate systems that are more complex than the model used. Scientists often employ models that clearly do not display a statistically significant goodness-of-fit to the phenomena. Nonetheless, these models serve as a ‘baseline’ for recognizing the important ways in which more complex phenomena deviate from these simpler representations." (Odenbaugh, 2005)
- "Models can provide concepts which can be used independently of models to raise important questions. Ultimately, the concepts outstrip the application of the model and have lives that are independent of their mathematical counterparts and directly contribute to experimental research." (Odenbaugh, 2005)
- Odenbaugh then concludes by saying modeling must be measured against the functional rules of the models instead of against "jobs they are not designed to carry out."
- The fields of systems biology and theoretical biology seem to have a somewhat similar view of models, as both fields seem to recognize that no models are perfect, and that both have uses beyond simply serving as models. Both Odenbaugh and Lander seem to argue that models also serve as ways to better understand concepts and get a general feel for how simpler systems work in order to better understand more complex systems. I don't really see any tensions between the two articles per say, however both seem to address the notion that models must be validated or invalidated based on how they fit the data, and seem to suggest that one shouldn't be looking into validation of models, but whether concepts are grasped or an understanding is made through modeling.
- Yes these two papers provided insight into what we are doing in this course, because in learning how different models work and the impact of changing parameters of those models, we as students can get a better understanding of the concepts being modeled. For example, for this week's assignment, in playing around with the different parameters and variables, I gained a better understanding of growth models might work in an open system like a chemostat. I look forward to modeling other processes (like GRN's) to gain a better understanding of how those systems might operate.
Acknowledgements
- For this assignment, the two readings, Lander 2010 and Odenbaugh 2005 were used and referenced in the answers.
- Except for what is noted above, this individual journal entry was completed by me and not copied from another source
Margaret J. Oneil 18:46, 8 February 2017 (EST)
References
Lander, A. D. (2010). The edges of understanding. BMC biology, 8(1), 40. DOI: 10.1186/1741-7007-8-40
Odenbaugh, J. (2005). Idealized, inaccurate but successful: a pragmatic approach to evaluating models in theoretical ecology. Biology and Philosophy, 20(2-3), 231-255. DOI: 10.1007/s10539-004-0478-6
Margaret J. Oneil 18:06, 8 February 2017 (EST)
Lauren M. Kelly Reflection Questions
Before
- On your honor, before you do the readings, answer: what is the purpose (or utility) of models/modeling? List as many as you can think of.
- Models allow us to manipulate different parameters outside of a typical lab setting. If one were to try to obtain a large amount of data on population growth by doing experiments, it would take an extremely long time and be very expensive. By modeling the populations in programs like MATLAB, there is no need to do a tiresome amount of experiments and the parameters can be manipulated to extremes that would otherwise be impossible in real life.
After
- According to Lander (2010), what is the purpose (or utility) of models/modeling?
- According to Lander (2010), the purpose of models is to promote understanding. He argues that we create models when we grasp an understanding of more complex processes. We use different types of models depending on what will best help us make connections between different sets of knowledge. Lander also goes on to say that invalidating models because they are found to be inconsistent is not a good practice. Models are meant to "approximate reality" (Lander 2015), and therefore are more useful than more complicated models. The overall goal of modeling is to understand and approximate reality, not to construct an exact replica.
- According to Odenbaugh (2005), what is the purpose (or utility) of models/modeling?
- According to Odenbaugh (2005), modeling is the first step in understanding the extremely complex world that we live in. There are five main ways in which models are used: to explore possibilities, to investigate more complex systems, to provide conceptual frameworks, to generate accurate predictions, and to generate explanations. He also argues that model building is inescapable. Models lead us to ask the important questions that lead to further investigations. He also makes an important point that models should not be evaluated based on things they are not designed to do. Every model is different.
- Do the fields of systems biology and theoretical biology seem similar or different in their uses of models? Are the "tensions" the same or different? Explain your answer.
- Both Lander and Odenbaugh seem to argue that models are used to understand a complex reality. They also seem to agree that models are not meant to be 100% accurate. The "tensions" brought up in both of the articles are centered around the misconceptions that the authors feel that others have about models. Lander and Odenbaugh seem to feel that the value that comes from models is not based solely in their accuracy. Inaccurate models can also lead to significant findings.
- Do these readings provide you with any new insight as to what we are doing in this course? Why or why not?
- These readings provided me with new insight as to what we are doing in this course. By using a variety of different models, even ones that may not have the greatest accuracy, we can gain an understanding of how larger, more complex systems work. We do not have an actual chemostat that we can observe in class, but this weeks modeling assignment allowed us to work with a variety of parameters and observe how the chemostat would behave under different conditions. While modeling, we can also be led to develop other models based on the behavior of the previous model.
Acknowledgements
- The two readings, Lander (2010) and Odenbaugh (2005), were used and referenced in the answers.
- Except for what is noted above, this individual journal entry was completed by me and not copied from another source
- Lauren M. Kelly 00:27, 9 February 2017 (EST)
References
- Dahlquist, Kam D. (2017) BIOL398-05/S17:Week 4. Retrieved from http://www.openwetware.org/wiki/BIOL398-05/S17:Week_4 on 8 February 2017.
- Lander, A. D. (2010). The edges of understanding. BMC biology, 8(1), 40. DOI: 10.1186/1741-7007-8-40
- Odenbaugh, J. (2005). Idealized, inaccurate but successful: a pragmatic approach to evaluating models in theoretical ecology. Biology and Philosophy, 20(2-3), 231-255. DOI: 10.1007/s10539-004-0478-6
Nika Vafadari Reflection Questions
Before
- The purpose of creating models and modeling is to create a simplified representation or version of relationship or process that may otherwise be difficult to understand or learn about. Therefore modeling acts as a learning process that enables a person to understand the components, structure and function of the relationship or process they are making into a model. In addition, modeling allows researchers to explore relationships and processes that may be hard to replicate within a lab setting.
After
- According to Lander, the purpose of modeling is to promote an understanding of complex processes and relationships. It enables us to connect various areas of expertise and knowledge and make predictions or hypotheses about how something works. Therefore, the purpose of modeling is to hypothesize about the results of various experiments and then test the predictions made.
- According to Odenbaugh, modeling is a process that enables us to understand the complexity of the world. Furthermore it can be used to make predictions, look at various outcomes and provide a framework for understanding a system.
- Both fields seem to have similar uses for models and the process of modeling, since both stress the importance of modeling in bringing about a greater understanding of something complex. In addition both, discuss that the so called accuracy of a model should not be the only thing that is stressed. Since any outcome of a model, even if it may be deemed inaccurate can bring about a new understanding or enable researchers to explore new options and make new predictions.
- Yes, as the both articles explain, in this course we will be utilizing the process of modeling to gain a greater understanding of various systems, such as the growth of yeast in a chemostat. While many of us our introduced to the concepts of population models in our other biology and mathematics courses, the hands on experience of modeling within the course will increase our understanding ben more and provide us with the skills needed to tackle other complex systems and make predictions about the various outcomes.
Acknowledgments
- I certify that this individual journal entry was completed by me and not copied from another source
- Nika Vafadari 17:17, 8 February 2017 (EST):
References
- Lander, A. D. (2010). The edges of understanding. BMC biology, 8(1), 40.
- Odenbaugh, J. (2005). Idealized, inaccurate but successful: a pragmatic approach to evaluating models in theoretical ecology. Biology and Philosophy, 20(2-3), 231-255.
Conor Keith Reflection Questions
Before
- The purpose of modeling is to make a complex concept easier to understand. Models can be visual mathematical or graphical.
After
- According to Lander modeling is the act of replacing the messy with the simple to promote understanding.
- According to Odenbaugh, model building is a strategy for coping with an extraordinarily complex world.
- Models for both disciplines share a similar goal. Biologists across all disciplines use models to seek understanding. Systems biologists and theoretical biologists merely differ In the elements used in their models. Systems biologists construct quantitative mathematical models of biological systems, while theoretical biologists use more simplistic diagrams. They share a common goal but differ in their methods to achieve it.
- These readings provided me new insight into this course. I now realize that biologists share a common goal with their modeling, even if their techniques differ. Using different models helps promote better understanding, and their is a benefit to the 'tensions' between disciplines.
Conor Keith 00:58, 9 February 2017 (EST)
Cameron M. Rehmani Seraji Reflection Questions
Before
- On your honor, before you do the readings, answer: what is the purpose (or utility) of models/modeling? List as many as you can think of.
- The purpose of modeling is to understand how a system works and to change variables to see the affect they have on the system. It is best to change variables in the system to make it behaved in a desired way. Modeling allows for large scale experiments to be performed on a small scale in a shorter period of time.
After
- According to Lander (2010), what is the purpose (or utility) of models/modeling?
- According to Lander (2010), the purpose of models/modeling is to predict outcomes of experiments and then validate or invalidate them. Creating models is a way to understand a more complex process and different types of models can be used to make connections between different information sets. Furthermore, Lander says that it is not a good practice to invalidate model that they are found to be inconsistent because all models are not going to be perfect the situation. An imperfect model is necessary to help find the correct model.
- According to Odenbaugh (2005), what is the purpose (or utility) of models/modeling?
- According to Odenbaugh (2005), modeling is the first strategy to understand the detailed world we live in. Models are used to explore possibilities, to investigate more complex systems, to provide conceptual frameworks, to generate accurate predictions, and to generate explanations. Lastly, every model is different and they should not be evaluated on whether or not they are right. Every model serves a purpose and can lead to questions being asked that further the investigation process.
- Do the fields of systems biology and theoretical biology seem similar or different in their uses of models? Are the "tensions" the same or different? Explain your answer.
- The two readings argue that models are used to understand complex problems and environments and that there is no such thing as an imperfect model. One "tension" brought up in both articles is a model is bad if it does not support the idea it was designed for. Lander and Odenbaugh both talk about models being useful if they do not necessarily answer the question. They are useful because they can lead to other questions being asked.
- Do these readings provide you with any new insight as to what we are doing in this course? Why or why not?
- These readings have provided me with new insight as to what we are doing in this course. We can gain a better understanding of how systems work by doing many different types of models. We will be able to manipulate complex systems to see how they work and what affect changing something will have on it.
Acknowledgements
- I certify that this individual journal entry was completed by me and not copied from another source
- Cameron M. Rehmani Seraji 01:25, 9 February 2017 (EST):
References
Dahlquist, Kam D. (2017) BIOL398-05/S17:Week 4. Retrieved from http://www.openwetware.org/wiki/BIOL398-05/S17:Week_4 on 8 February 2017.
Lander, A. D. (2010). The edges of understanding. BMC biology, 8(1), 40. DOI: 10.1186/1741-7007-8-40
Odenbaugh, J. (2005). Idealized, inaccurate but successful: a pragmatic approach to evaluating models in theoretical ecology. Biology and Philosophy, 20(2-3), 231-255. DOI: 10.1007/s10539-004-0478-6
