# BIOL398-03/S13:Class Journal Week 14

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#*After all the class assignments, I would consider myself both a biologist and mathematician, even though I did not consider myself a mathematician during the first week of class. In the Stewart reading, a mathematician is one that can not only see patterns in various settings, but is one who can mathematically justify why these patterns occur. The class assignments helped me to understand the mathematical theories that can support biological concepts. Through statistical analysis and modeling, I now understand how applicable the field of biomathematics can be. In regards to being a biologist, I previously considered myself one and I still do after doing all the assignments. However, I now see how biological concepts can be aided by math to produce an alternative way of understanding science. | #*After all the class assignments, I would consider myself both a biologist and mathematician, even though I did not consider myself a mathematician during the first week of class. In the Stewart reading, a mathematician is one that can not only see patterns in various settings, but is one who can mathematically justify why these patterns occur. The class assignments helped me to understand the mathematical theories that can support biological concepts. Through statistical analysis and modeling, I now understand how applicable the field of biomathematics can be. In regards to being a biologist, I previously considered myself one and I still do after doing all the assignments. However, I now see how biological concepts can be aided by math to produce an alternative way of understanding science. | ||

[[User:Laura Terada|Laura Terada]] 19:38, 25 April 2013 (EDT) | [[User:Laura Terada|Laura Terada]] 19:38, 25 April 2013 (EDT) | ||

+ | |||

+ | ==Salman Ahmad Week 14== | ||

+ | [[User:Salman Ahmad| Salman Ahmad]] | ||

+ | |||

+ | #What is the value of combining biological and mathematical approaches to scientific questions? | ||

+ | #*Biology helps us understand the concepts of life. The pathways we looked at in this class were pathways that are studied in biology classes. What these pathways give us, however, are more questions than answers. The combination of math and biology helps us find answers to these questions. Research papers would hold little meaning if observations were recorded and no mathematical analysis was done to them. Math helps us see what ideas are significant and what may concretely be happening in biology. This helps further the concepts in biology. Together, both disciplines allow us to pose questions and also answer those questions with greater certainty. | ||

+ | #Looking back on your reflections on the Janovy and Steward readings from the Week 1 Class Journal, do you have any further insights to share? Have your answers changed to those original reflection questions? Why or why not? | ||

+ | #*I definitely still consider myself a biologist because biology is a part of all of my classes and what I study. As far as math goes, I still wouldn't necessarily call myself a mathematician. I definitely have a greater understanding of biomath and statistics, but I still have trouble following how all of the equations came about in class. I've realized how connected biology and math really are, especially in biological research. The class helped me start seeing mathematical patterns in biology and because of that I think I am more of a mathematician now than I was at the beginning of the class. | ||

+ | |||

+ | [[User:Salman Ahmad|Salman Ahmad]] 21:24, 25 April 2013 (EDT) | ||

+ | |||

+ | ==Matthew E. Jurek Week 14== | ||

+ | [[User: Matthew E. Jurek| Matthew E. Jurek]] | ||

+ | #What is the value of combining biological and mathematical approaches to scientific questions? | ||

+ | #*All scientific questions contain numerous layers. That's what makes science so exciting. There's a long list of factors involved in even the simplest scientific processes. In our case, we are looking at transcription factors. More importantly, we are looking at a network of transcription factors. Ultimately we want to see how a long list of transcription factors relate/ cooperate while impacting gene regulation. Not only that, we are interested in how certain transcription factors respond to cold. Based on the biology alone, this is a complex problem. Seeing that we are working with a network, there are clearly mathematical relationships relating one transcription factor to another. Mathematical approaches will allow us to better understand these relationships via modeling. Without a mathematical-based model it would be impossible to fully explore the network. | ||

+ | #Looking back on your reflections on the Janovy and Steward readings from the Week 1 Class Journal, do you have any further insights to share? Have your answers changed to those original reflection questions? Why or why not? | ||

+ | #*While looking at my responses from Week 1, it seems like I was really trying to keep mathematician and biologist separate. Honestly, it's funny to re-read because in my writing I can tell how hard I was working to differentiate the two things. Sitting here now, the line between the two is far from direct. It's a lot more blurred as the two things overlap way more than I initially wanted to admit. I'll still call my self a biologist first, but now I'd say you have to be a mathematician in order to be a biologist. Obviously our various projects throughout the year have proved that to be true. It's hard to fully explore biological questions without math. That is something I would never admit weeks ago, but now it's hard not to admit. Looking back on this class, we've done some amazing things integrating math and biology to solve a scientific question. Something that comes to mind is our first group project. I never thought it'd be possible to create a model of metabolism like we did. That model required a firm understanding of the biological process but would have been impossible without math. My answers have changed due to the fact that I now understand how much overlap is required in order to answer scientific questions. | ||

+ | *'''[[User:Matthew E. Jurek|Matthew E. Jurek]] 22:38, 25 April 2013 (EDT)''': | ||

+ | |||

+ | ==Anthony J. Wavrin Week 14== | ||

+ | [[User: Anthony J. Wavrin| Anthony J. Wavrin]] | ||

+ | #What is the value of combining biological and mathematical approaches to scientific questions? | ||

+ | #*I think the largest benefit from this method is the fact that there are different methods between the two practices. Biologically it is understanding it but mathematically it is about transforming it into a numerical fashion. It is a little difficult to answer this question unbiased as math is intimately involved in biology. Overall, I think the real value is to create these types of models, essentially taking observations and turning them into a form in which they can be more easily explored and explained. | ||

+ | #Looking back on your reflections on the Janovy and Steward readings from the Week 1 Class Journal, do you have any further insights to share? Have your answers changed to those original reflection questions? Why or why not? | ||

+ | #*I believe the answers have changed as in how they both relate to each other. As a person who likes both subjects, I have never actually combined them in a manner like this, essentially I’ve only done it in statistics. I believe there is a lot of unappreciated math behind some of the big findings in biology that is overlooked by biologists, at least at the undergraduate student level. With regards to the questions in the original journal, the only answer I would change would be if I considered myself a mathematician. While the answer would still be that I do not consider myself to be one but, I think my overall ability to utilize mathematics is much higher than I originally thought. However, I still would not consider myself a master of mathematics, which is the other prerequisite I set for being considered a mathematician. | ||

+ | [[User:Anthony J. Wavrin|Anthony J. Wavrin]] 00:06, 26 April 2013 (EDT) | ||

+ | |||

+ | ==Elizabeth Polidan Week 14== | ||

+ | [[User: Elizabeth Polidan| Elizabeth Polidan]] | ||

+ | #What is the value of combining biological and mathematical approaches to scientific questions? | ||

+ | #*I had no clue what complicated detective work is involved in studying gene regulatory networks. There is so much wet work involved in producing the data, and then there is an overwhelming amount of information to explore. Mathematics helps make the problem approachable. Without the statistical analysis to give you some semblance of confidence in a part of the data, you might just throw your hands up and go home. | ||

+ | |||

+ | #*At the beginning of this class, I was only interested in larger scale ecological questions, and did not think I would ever be interested in functions at the subcellular level. But I have been fascinated with the work we have done, and have added another area of interest. | ||

+ | |||

+ | ==Paul Magnano Week 14== | ||

+ | [[User: Paul Magnano| Paul Magnano]] | ||

+ | #What is the value of combining biological and mathematical approaches to scientific questions? | ||

+ | #*I believe there is great value in this, by applying mathmatics to biological concepts and questions we have, we can quantify discoveries in the biological realm. Quantifying new discoveries in mathmatical terms allows us to have data that is comparable and helps us better understand the answers to our questions. | ||

+ | |||

+ | #*No not particularly, although I will say that I have become somewhat more of a mathmatician and I have started to view aspects of my life from a more mathmatical approach. | ||

+ | [[User:Paul Magnano|Paul Magnano]] 02:14, 26 April 2013 (EDT) | ||

+ | |||

+ | ==Helena M. Olivieri Week 14== | ||

+ | [[User: Helena M. Olivieri| Helena M. Olivieri]] | ||

+ | #What is the value of combining biological and mathematical approaches to scientific questions? | ||

+ | #*The value of combining biological and mathematical approaches to scientific questions is that through this interdisciplinary study, one is better able to delve into the details and specifics of concrete and developing research. The two areas of study encourage a deepening of scientific knowledge. Biology provides a concrete context for mathematical studies, while math is able to guide the direction of future biological quests. | ||

+ | |||

+ | #*In terms of Janovy's and Steward's writings, I have a much better understanding of the significance of math in relation to biology. We have specifically studied mathematics on a molecular level, if math is possible in such unrecognizable examples, then it is very much believable that mathematical examples are occurring all around us. While I certainly consider myself a Biologist, I still struggle to some extent in considering myself a mathematician. Math has never really been my strong suit. But, I have developed a greater understanding for the importance of honing in on the mathematical abilities I do have. |

## Current revision

## Contents |

## Reflection

- Kevin McKay
- I feel that there is mathematics behind every phenomena in life that one could ever hope to study or understand, this obviously includes the science of life or biology. If one wishes to understand or make connections between data or observations of biology, a great way to analyse this data is with math. Using math in biological questions allows us to see the randomness and the orderliness of life.
- Looking back at the readings and the answers I gave to the questions for week 1, I have no new insights or answers to share. My answers remain the same, I still see myself as a biologist and a mathematician. Although over the past weeks in this class, my outlook on bio math has changed. I have gained a sense of the reality of biomath and the hard work that goes into it. I have gained an appreciation for how difficult this field of study really is. Analyzing biology with math seems to me a bit more complicated now as compared with analyzation of physical properties such as gravity. Biology is always changing, whereas gravity is a constant 9.81 Newtons per kilogram downwards. I have also learned that this type of work that involves this much use of computers is not really for me (although I did have an idea of this before the class).

Kevin Matthew McKay 15:28, 25 April 2013 (EDT)

## James P. McDonald Week 14

- What is the value of combining biological and mathematical approaches to scientific questions?
- Combining biological and mathematical approaches gives multiple perspectives on a question and allows for a more complete solution to a scientific problem. A very important aspect of combining biological and mathematical approaches is that it allows for both qualitative and quantitative analysis and solutions. Math has the ability to take a biological observation or result and put it into a equation. A math equation can take a qualitative observation and make it into a quantitative explanation, which can easily be manipulated and analyzed to answer scientific questions. This can be very beneficial in doing research because you can make predictions and experiments can be reproduced with ease.

- Looking back on your reflections on the Janovy and Steward readings from the Week 1 Class Journal, do you have any further insights to share? Have your answers changed to those original reflection questions? Why or why not?
- When it comes to being a mathematician I now understand more of what Stewart was talking about. Stewart states that a mathematician more often sees the math that is taking place all the time around us. This class has shown me that math can be used, in addition to biology, to analyze and solve scientific questions. I originally would not have recognized the potential math that could be used in the biological processes we have looked at. In regards to the answers in my original reflection, my answer to the biologist question has not changed. I tend to thing of science in biological terms before anything else and this has not changed. But in regards to being a mathematician I am still not sure whether I would say I am one, but I have definitely seen the potential that mathematical approaches have. I have tried to learn to think more in mathematical terms and I think I will start to think more in terms of mathematical approaches in the future.

James P. McDonald 18:55, 25 April 2013 (EDT)

## Ashley Rhoades Week 14

- What is the value of combining biological and mathematical approaches to scientific questions?
- I think another perspective is allows welcomed and mathematics allows us to look at biological systems differently. Additionally I think using mathematical approaches is a very powerful tool for problem solving. Maybe after scientific experimentation you know the why and how but a mathematical model may be more apt for discovering trends and patterns. Also recently we've been doing a lot of statistis. One point that has been emphasized is that these statistical test allow us to see the possibility that trends in the data are just by chance. Biological systems are not often predictable and the statistical examination can express the likelihood that there actually is a pattern among other things. Additionally in biology sometimes you don't know the how or the why and math can still be helpful.

- Looking back on your reflections on the Janovy and Steward readings from the Week 1 Class Journal, do you have any further insights to share? Have your answers changed to those original reflection questions? Why or why not?
- I would change my answer to the question that asks if I consider myself a biologist and I now understand more what Janovy and Stewart were saying. They talked about math and biology in the context of personal experiences and perspectives. Over the course of this semester in this class as well as others I think I've really come to realize my unique perspective. I see people not as individuals but as super organisms with crucial microbiomes and when we go to the beach I'm thinking about the potential thymine dimers forming in my genome. When I hear a statistic I ask about the methodology behind that figure rather than accepting it as a fact and when a teacher puts the bell curve for the last exam on the board I think of the normal distribution. For whatever reason I have finally become aware of how different my perspective is from my biology and mathematics studies.

Ashley Rhoades 19:35, 25 April 2013 (EDT)

## Laura Terada

- What is the value of combining biological and mathematical approaches to scientific questions?
- While biological approaches seek to explain scientific principles through description and qualitative analysis, mathematics explains science through numbers quantitatively. Biology can explain a certain scientific idea; however, math simply puts that idea into the form of equations that produce either a significant or insignificant result. Thus, the two different approaches work together to explain science in a more complete and thorough way.

- Looking back on your reflections on the Janovy and Steward readings from the Week 1 Class Journal, do you have any further insights to share? Have your answers changed to those original reflection questions? Why or why not?
- After all the class assignments, I would consider myself both a biologist and mathematician, even though I did not consider myself a mathematician during the first week of class. In the Stewart reading, a mathematician is one that can not only see patterns in various settings, but is one who can mathematically justify why these patterns occur. The class assignments helped me to understand the mathematical theories that can support biological concepts. Through statistical analysis and modeling, I now understand how applicable the field of biomathematics can be. In regards to being a biologist, I previously considered myself one and I still do after doing all the assignments. However, I now see how biological concepts can be aided by math to produce an alternative way of understanding science.

Laura Terada 19:38, 25 April 2013 (EDT)

## Salman Ahmad Week 14

- What is the value of combining biological and mathematical approaches to scientific questions?
- Biology helps us understand the concepts of life. The pathways we looked at in this class were pathways that are studied in biology classes. What these pathways give us, however, are more questions than answers. The combination of math and biology helps us find answers to these questions. Research papers would hold little meaning if observations were recorded and no mathematical analysis was done to them. Math helps us see what ideas are significant and what may concretely be happening in biology. This helps further the concepts in biology. Together, both disciplines allow us to pose questions and also answer those questions with greater certainty.

- Looking back on your reflections on the Janovy and Steward readings from the Week 1 Class Journal, do you have any further insights to share? Have your answers changed to those original reflection questions? Why or why not?
- I definitely still consider myself a biologist because biology is a part of all of my classes and what I study. As far as math goes, I still wouldn't necessarily call myself a mathematician. I definitely have a greater understanding of biomath and statistics, but I still have trouble following how all of the equations came about in class. I've realized how connected biology and math really are, especially in biological research. The class helped me start seeing mathematical patterns in biology and because of that I think I am more of a mathematician now than I was at the beginning of the class.

Salman Ahmad 21:24, 25 April 2013 (EDT)

## Matthew E. Jurek Week 14

- What is the value of combining biological and mathematical approaches to scientific questions?
- All scientific questions contain numerous layers. That's what makes science so exciting. There's a long list of factors involved in even the simplest scientific processes. In our case, we are looking at transcription factors. More importantly, we are looking at a network of transcription factors. Ultimately we want to see how a long list of transcription factors relate/ cooperate while impacting gene regulation. Not only that, we are interested in how certain transcription factors respond to cold. Based on the biology alone, this is a complex problem. Seeing that we are working with a network, there are clearly mathematical relationships relating one transcription factor to another. Mathematical approaches will allow us to better understand these relationships via modeling. Without a mathematical-based model it would be impossible to fully explore the network.

- Looking back on your reflections on the Janovy and Steward readings from the Week 1 Class Journal, do you have any further insights to share? Have your answers changed to those original reflection questions? Why or why not?
- While looking at my responses from Week 1, it seems like I was really trying to keep mathematician and biologist separate. Honestly, it's funny to re-read because in my writing I can tell how hard I was working to differentiate the two things. Sitting here now, the line between the two is far from direct. It's a lot more blurred as the two things overlap way more than I initially wanted to admit. I'll still call my self a biologist first, but now I'd say you have to be a mathematician in order to be a biologist. Obviously our various projects throughout the year have proved that to be true. It's hard to fully explore biological questions without math. That is something I would never admit weeks ago, but now it's hard not to admit. Looking back on this class, we've done some amazing things integrating math and biology to solve a scientific question. Something that comes to mind is our first group project. I never thought it'd be possible to create a model of metabolism like we did. That model required a firm understanding of the biological process but would have been impossible without math. My answers have changed due to the fact that I now understand how much overlap is required in order to answer scientific questions.

**Matthew E. Jurek 22:38, 25 April 2013 (EDT)**:

## Anthony J. Wavrin Week 14

- What is the value of combining biological and mathematical approaches to scientific questions?
- I think the largest benefit from this method is the fact that there are different methods between the two practices. Biologically it is understanding it but mathematically it is about transforming it into a numerical fashion. It is a little difficult to answer this question unbiased as math is intimately involved in biology. Overall, I think the real value is to create these types of models, essentially taking observations and turning them into a form in which they can be more easily explored and explained.

- Looking back on your reflections on the Janovy and Steward readings from the Week 1 Class Journal, do you have any further insights to share? Have your answers changed to those original reflection questions? Why or why not?
- I believe the answers have changed as in how they both relate to each other. As a person who likes both subjects, I have never actually combined them in a manner like this, essentially I’ve only done it in statistics. I believe there is a lot of unappreciated math behind some of the big findings in biology that is overlooked by biologists, at least at the undergraduate student level. With regards to the questions in the original journal, the only answer I would change would be if I considered myself a mathematician. While the answer would still be that I do not consider myself to be one but, I think my overall ability to utilize mathematics is much higher than I originally thought. However, I still would not consider myself a master of mathematics, which is the other prerequisite I set for being considered a mathematician.

Anthony J. Wavrin 00:06, 26 April 2013 (EDT)

## Elizabeth Polidan Week 14

- What is the value of combining biological and mathematical approaches to scientific questions?
- I had no clue what complicated detective work is involved in studying gene regulatory networks. There is so much wet work involved in producing the data, and then there is an overwhelming amount of information to explore. Mathematics helps make the problem approachable. Without the statistical analysis to give you some semblance of confidence in a part of the data, you might just throw your hands up and go home.

- Looking back on your reflections on the Janovy and Steward readings from the Week 1 Class Journal, do you have any further insights to share? Have your answers changed to those original reflection questions? Why or why not?
- At the beginning of this class, I was only interested in larger scale ecological questions, and did not think I would ever be interested in functions at the subcellular level. But I have been fascinated with the work we have done, and have added another area of interest.

## Paul Magnano Week 14

- What is the value of combining biological and mathematical approaches to scientific questions?
- I believe there is great value in this, by applying mathmatics to biological concepts and questions we have, we can quantify discoveries in the biological realm. Quantifying new discoveries in mathmatical terms allows us to have data that is comparable and helps us better understand the answers to our questions.

- Looking back on your reflections on the Janovy and Steward readings from the Week 1 Class Journal, do you have any further insights to share? Have your answers changed to those original reflection questions? Why or why not?
- No not particularly, although I will say that I have become somewhat more of a mathmatician and I have started to view aspects of my life from a more mathmatical approach.

Paul Magnano 02:14, 26 April 2013 (EDT)

## Helena M. Olivieri Week 14

- What is the value of combining biological and mathematical approaches to scientific questions?
- The value of combining biological and mathematical approaches to scientific questions is that through this interdisciplinary study, one is better able to delve into the details and specifics of concrete and developing research. The two areas of study encourage a deepening of scientific knowledge. Biology provides a concrete context for mathematical studies, while math is able to guide the direction of future biological quests.

- Looking back on your reflections on the Janovy and Steward readings from the Week 1 Class Journal, do you have any further insights to share? Have your answers changed to those original reflection questions? Why or why not?
- In terms of Janovy's and Steward's writings, I have a much better understanding of the significance of math in relation to biology. We have specifically studied mathematics on a molecular level, if math is possible in such unrecognizable examples, then it is very much believable that mathematical examples are occurring all around us. While I certainly consider myself a Biologist, I still struggle to some extent in considering myself a mathematician. Math has never really been my strong suit. But, I have developed a greater understanding for the importance of honing in on the mathematical abilities I do have.