# BIOL368/F16:Class Journal Week 2

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## Contents

## Will Fuchs

**Before**

- What is the definition of a model?
- A tool that can be used to create predictions or emulate a phenomena, supported by data and substantiated observations.

- What is the definition of modeling?
- The manipulation of a model through the change of parameters and to evaluate the output of that process.

- How does modeling relate to the scientific method?
- It can be used to support findings and can be involved in future repetitions of the same experiment; it can also be used to lead to new observations in a system.

**After**

- What is the main take-home message of this paper?
- The purpose of this paper is to unify the different ideas of models across fields into a succinct and clear definition of the purpose of models and the tools they provide. This paper also achieves in creating a multifaceted description of the modeling system.

- What is the definition of a model?
- According to the paper a model is known “as a simplified, abstract or concrete representation of relationships and/or processes in the real world” which fall under one or more representations: Experimental, Numerical, Visual, Symbolic, and/or Verbal.

- What is the definition of modeling?
- The paper defines modeling as the process of moving from observations of the real world to a model, moving from one model representation to another model representation, or comparing different models.

- Were you engaged in modeling for this week's assignment? If so, how? If not, why not?
- We employed a categorically visual model and performed interactive modeling while observing the various amino acid interactions when they folded and displayed pigments. I feel that we modeled on an experimental level because of the process of trial and error through animated simulations as we watched the protein folds change to our manipulation.

William P Fuchs 01:31, 12 September 2016 (EDT)

## Zachary T. Goldstein

*Before:*

- What is the definition of a model?
- A simplified, abstract, or concrete representation of a relationship and/or process in the real world; a caricature of reality.

- What is the definition of modeling?
- The process of moving from observations of the real world to a model, moving from one model to another, and comparing different models.

- How does modeling relate to the scientific method?
- Modeling relates to the scientific method in the sense that they are both fluid processes. There is no "right" order to either modeling or the scientific method, and many times it will take more than one shot to reach your end goal.

*After:*

- What is the main take-home message of this paper?
- This paper aims to explain the importance of integrating mathematics into less math-intensive areas of study (such as biology). The paper details five types of model representations and states that modeling surrounds us everywhere we go. The final message of the paper is that modeling should be taught in school curriculums because it makes students more adaptable and capable to preform at a higher level across all career fields.

- What is the definition of a model?
- A simplified, abstract, or concrete representation (Experiential, Verbal, Numerical, Visual, and Symbolic -5) of relationships and or processes in the real world

- What is the definition of modeling?
- The process of moving from observations of the real world to a model, moving from one model to another, and comparing different models.

- Were you engaged in modeling for this week's assignment? If so, how? If not, why not?
- This week's assignment required two types of representations: experiential and verbal. Aipotu was a virtual lab that allowed us to directly experience, visualize, and experiment on the genetics of flowers. Similarly, the collaborative aspect of this lab enabled our group to form hypotheses, design experiments, and predict outcomes. We took observations and wrote descriptions about the interactions between flowers and their subsequent alleles.

Zachary T. Goldstein 18:19, 10 September 2016 (EDT)Zachary T. Goldstein

## Anindita Varshneya

In class group was made up of myself, Colin Wikholm, and Courtney Merriam.

*Before:*

- What is the definition of a model?
- Personal definition: a model is a simplified representation of a complex set o data/observations; can exist as a graph, chart, or other diagram.
- Group definition: a representation of something complex.

- What is the definition of modeling?
- Personal definition: the process of taking actual data to observe patters and outcomes, and using those patterns to predict outcomes on theoretical data.
- Group definition: the act of describing something through a representation.

- How does modeling relate to the scientific method?
- Modeling relates to the scientific method because it is a form of presenting data such that analysis is more easily/efficiently done.

*After:*

- What is the main take-home message of this paper?
- The main take-home message of this paper is to explain the "Rule of Five" and apply it to models and modeling to allow interdisciplinary understanding and use of models and modeling.

- What is the definition of a model?
- A model is "a simplified, abstract or concrete representation of relationships and/or processes in the real world" (Eaton et al., 2016). In other words, a model provides a new reduced representation of a real world concept.

- What is the definition of modeling?
- Modeling is the process of moving from observations to a model, a model to a model, or comparing different models (Eaton et al., 2016).

- Were you engaged in modeling for this week's assignment? If so, how? If not, why not?
- I was engaged in modeling for this week's assignment because, as a member of the Evolution Group, we used colored boxes to represent organisms in a population and their genotypes. Therefore, this program was a visual representation of the more complex process of evolution. The process of modeling occurred as we modified the relative fitness of each of the organisms in the bank and grew them for many generations in order to see how different organisms would react to different conditions. This is an example of modeling because we moved from observations to model in order to create each situation (i.e. no mutation, random mating, no/some natural selection), and we compared models to each other in order to see why different situations allowed some organisms to succeed while others did not.

-- Anindita Varshneya 22:42, 12 September 2016 (EDT)

## Courtney L. Merriam

**Before**

- What is the definition of a model?
- A representation of a complex process or system.

- What is the definition of modeling?
- The understanding of a process or system by organizing it into a model.

- How does modeling relate to the scientific method?
- The scientific method uses all the types of model such as experiments, verbal, numerical, visual, and symbolic, to go from hypothesis to results as a process of modeling.

**After**

- What is the main take-home message of this paper?
- To develop a common denominator between multiple fields of study such as mathematics statistics and biology to prepare the student for real world that is comprised of all studies.

- What is the definition of a model?
- A simplified, abstract, or concrete representation (Experiential, Verbal, Numerical, Visual, and Symbolic) of relationships and or precesses in the real world.

- What is the definition of modeling?
- The process of moving from observations of the real world to a model
- Moving from one model representation to another representation
- Comparing diffrent models

- Were you engaged in modeling for this week's assignment? If so, how? If not, why not?
- Yes, my assignment incorporated may different types of models. The visual representation of alleles were present with colors. The numerical model was brought in with the equation for HWE. The experimental model was used to perform generations under specific conditions. Using all these models allowed me to come to a conclusion.

**Courtney L. Merriam 23:38, 7 September 2016 (EDT)**:

## Avery Vernon-Moore

**Before**

- What is the definition of a model?
- A graphical representation of a concept or object for the purpose of understand it's functions.

- What is the definition of modeling?
- The creation of said model to most accurately show an understanding of the functions.

- How does modeling relate to the scientific method?
- I think that modeling is the act of carrying out the scientific method for the experiment that you have set up. You create a hypothesis and follow some methods and then convert the data and results you have found into a model for the experiment.

**After**

- What is the main take-home message of this paper?
- This paper provides a framework for models and modeling by defining each term in detail and creating subunits of models. Within model the paper goes into depth to explain how models can be created numerically, visually, verbally, numerically, and most recently experimentally. The paper is meant to show how unifying these frameworks can help people within different fields (mathematics, biology, etc) come together to create better retention, structure and learning environment for students.

- What is the definition of a model?
- Simplified abstract or concrete representation of a relationship and/or processes in the real world.

- What is the definition of modeling?
- (1)Process of moving from observations of the real world to a model
- (2)Moving from one model to another
- (3)Comparing different models

- Were you engaged in modeling for this week's assignment? If so, how? If not, why not?
- Yes, we used models which were already made for us and analyzed and compared them. We also created visual models within the Aipotu system. The models in this assignment were used to gather the information to ultimately create a purple flower.

Avery Vernon-Moore 01:39, 7 September 2016 (EDT)

## Shivum Desai

**Before**

- What is the definition of a model?
- A built representation of an imaginary idea, concept, or real object.

- What is the definition of modeling?
- The process of building a representation of an imaginary idea, concept, or real object

- How does modeling relate to the scientific method?
- Modeling is the process of analytically building somthing out of many different pieces or ideas. The scientific method is very similar to that because the results of the scientific method could be seen as the resulting model itself, while the different segments of the method (i.e. hypothesis, methods, results, conclusion etc.) are the different pieces that go into building a model to fruition.

**After**

- What is the main take home message of this paper?
- Basically this paper talks about how to bring mathematics into other fields such as biology where it can be used at a lower level to help students understands concepts better while they are learning.

- What is the definition of a model?
- Simplified abstract or sometimes concrete representation of relationships and processes in the real world.

- What is the definition of modeling?
- There are three parts. The first is moving from a real world observation to a model. Then being able to move that representation to another representation. And then being able to compare those models.

- Were you engaged in modeling for this week's assignment? If so, how? If not, why not?
- I believe I was engaged in modeling in this weeks lab because the process of having to compare and compatriots representations (amino acid sequences) took a good amount of work. Then finding the little differences in between the models was a process in itself, which eventually led to the combination of different representations to create a final model (purple coloring protein).

**Kam D. Dahlquist 12:09, 12 September 2016 (EDT)**:

## Mia Huddleston

**Before:**

- What is the definition of a model?
- A tool that can be used to explain what we know about a certain a phenomenon, object, etc. that is supported by data.

- What is the definition of modeling?
- Modeling is creating a model based on your knowledge of the object or phenomenon.

- How does modeling relate to the scientific method?
- Modeling can be used to represent the knowledge that has been discovered through the scientific method.

**After:**

- What is the main take-home message of this paper?
- This paper grants an understanding as to why the integration of mathematical modeling is imperative to develop a deeper learning and understanding of biology and other such fields while also building framework for how these models can be used by defining models and modeling and what types of models can and should be used.

- What is the definition of a model?
- A model is a “simplified, abstract or concrete representation of relationships and/or processes in the real world (Eaton et al. 2016)” according to the paper. There are five different types of representations described in this paper; experiential, verbal, numerical, visual, and symbolic.

- What is the definition of modeling?
- Modeling is a process of using observations in the real world to create a model, using the information of one model to influence another model, and/or the act of comparing one model to another.

- Were you engaged in modeling for this week's assignment? If so, how? If not, why not?
- I believe we were engaged in modeling, especially with the use of the definition of using one model to influence another. Using aipotu we were looking at the models of proteins they gave us and using those models, were trying to create our own models of the new flower.

Mia Huddleston 17:01, 12 September 2016 (EDT)

## Jordan T. Detamore

**Before:**

- What is the definition of a model?
- A representation of a concept or idea used to teach or display the concept or idea

- What is the definition of modeling?
- Creating representations of a concept or idea to teach or display the concept or idea

- How does modeling relate to the scientific method?
- Modeling can be used to portray different aspects of the scientific method including observations, methods, and results.

**After:**

- What is the main take-home message of this paper?
- The aim of this paper was to give an overarching definition of what a model and modeling is and how they can be used effectively in education. The paper calls for an implementation of the "rule of 5" for all models in all subjects in order to give students and teachers a guideline for all models.

- What is the definition of a model?
- A model is defined as "as a simplified, abstract or concrete representation of relationships and/or processes in the real world" (Eaton et al. 2016).

- What is the definition of modeling?
- Modeling is defined as "the process of moving from observations of the real world to a model, moving from one model representation to another model representation, or comparing different models" (Eaton et al. 2016).

- Were you engaged in modeling for this week's assignment? If so, how? If not, why not?
- Yes, crossing flowers and creating new colors using the software is an example of taking a real world concept and working with it on the computer. The models helped to come up with hypotheses for new experiments.

**Jordan T. Detamore 18:26, 12 September 2016 (EDT)**:

---

## Colin Wikholm

**Reflection before reading**

- What is the definition of a model?
- my definition: refers to something meant to represent, describe, or exemplify
- group definition: a representation of something complex.

- What is the definition of modeling?
- my definition: the act of creating something which is meant to represent, describe, or exemplify
- group definition: the act of describing through representation.

- How does modeling relate to the scientific method?
- Modeling relates to the scientific method in that it can act as mode of learning and investigating questions and achieve a new understanding of a subject. Like the scientific method, which is a method of uncovering new knowledge, models can be used to learn.

**Reflection after reading**

- What is the main take-home message of this paper?
- This paper attempts to explore the use of modeling across disciplines. It proposed the use of five part method to allow for sharing of models between mathematics and biology. Finally, it argues that modeling between disciplines can benefit the fields of biology and mathematics (Eaton et al., 2016).

- What is the definition of a model?
- The author defines a model as the following in context of the paper: "For our discussions below, we define model as a simplified, abstract or concrete representation of relationships and/or processes in the real world." A model is a more basic description of that which occurs in reality. (Eaton et al., 2016).

- What is the definition of modeling?
- Based on the definition of model in the paper, modeling is creating some kind of representation of a manifestation that really exists (Eaton et al., 2016).

- Were you engaged in modeling for this week's assignment? If so, how? If not, why not?
- Evolution occurs in the real world. I worked with a software to create a simplified representation of this real life process. Therefore, I did indeed engage in modeling of evolution in this week's assignment.

Colin Wikholm 00:56, 13 September 2016 (EDT)

## Matthew R Allegretti

### Before

- What is the definition of a
*model*?- A representation of an ideo or concept that is created to better understand its processes, intricacies, etc.

- What is the definition of
*modeling*?- Generating representations of ideas or concepts in order to simulate possible outcomes of the idea/concept being represented.

- How does
*modeling*relate to the*scientific method*?- Modeling allows scientists to share their information with the rest of the scientific community, as well as with a more general audience. It also allows predictions to be made ahead of time for how something being studied might potentially work before testing.

### After

- What is the main take-home message of this paper?
- Modeling is becoming an increasingly more useful skill in learning environments. It allows educators to effectively convey information in a variety of manners, and allows students to better grasp the material they are learning by building their own models. By being able to change between types of models, both students and educators are capable of demonstrating greater knowledge of a subject. It is also necessary for all disciplines to have a common framework for what models and modeling is in order to promote interdisciplinary conversation about models.

- What is the definition of a
*model*?- According to the paper, a model is "a simplified, abstract or concrete representation of relationships and/or processes in the real world." (Eaton et al., 2016, p. 8). It is a representation of the real world because it is merely depicting a larger concept, not serving as a perfect, all encompassing example for what it represents.

- What is the definition of
*modeling*?- Modeling is "1) the process of moving from observations of the real world to a model, 2) moving from one model representation to another model representation, or 3) comparing different models" (Eaton et al., 2016, p.9). Both 1) and 2) effectively create a new model by transitioning from one object to a model of it, while 3) is essentially explaining how one model could become another, or the process of modeling as defined by 2).

- Were you engaged in
*modeling*for this week's assignment? If so, how? If not, why not?- Yes. I effectively engaged in modeling. I know this because I moved from an experiential model (the simulation) to a verbal model (creating hypotheses, designing experiments, sharing results). In this way I was performing the second definition of modeling.

Matthew R Allegretti 22:33, 12 September 2016 (EDT)

## Matthew K. Oki

**Before**

- What is the definition of a
*model*?- A model is a simplistic graphical or visual explanation of a complicated system.

- What is the definition of
*modeling*?- Modeling is the recreation of an object to convey some idea about its function for the purpose of study or understanding.

- How does
*modeling*relate to the*scientific method*?- You can use modeling to display your data in a way that is simple and concise. This takes care of a major step of the scientific method. It can also appeal to not only the scientific community and the non-scientist population.

**After**

- What is the main take-home message of this paper?
- The take home message of this paper was about the separation between mathematical modeling and fields such as biology. It calls forward a need to merge the two fields in some capacity, even though a merger would be difficult because of the separation of the definition of modeling in the two different fields.

- What is the definition of a
*model*?- A model is defined in this article as "a simplified, abstract or concrete representation of relationships and/or processes in the real world." (Eaton et al., 2016)

- What is the definition of
*modeling*?- This article defines modeling in three ways, "1) the process of moving from observations of the real world to a model, 2) moving from one model representation to another model representation, or 3) comparing different models (Figure 2, arrows)." (Eaton et al., 2016)

- Were you engaged in
*modeling*for this week's assignment? If so, how? If not, why not?- We were engaged in modeling for this week's assignment, as our model included the protein structure and creating an output of a colored flower.

**Matthew K. Oki 23:16, 12 September 2016 (EDT)**:

## Isai Lopez

**Before**

- What is the definition of a model?
- A model is a representation of a concept or object that allows for understanding of the basic ideas behind the role or characteristics of said object/ concept.

- What is the definition of modeling?
- Modeling is the recreation of an object to convey some idea about its function for the purpose of study or understanding.

- How does modeling relate to the scientific method?
- Modeling relates to the scientific method because it can serve as evidence to lend support for or against a certain idea, thereby leading to a revision of earlier models and hypotheses.

**After**

- What is the main take-home message of this paper?
- The paper is meant to bring awareness to the necessity for having more unity in their definitions and uses of models. The fields of math and biology can benefit greatly from an increase in communication, and efforts should be made to provide a framework that allows the two to be more interconnected.

- What is the definition of a model?
- The article defines a model as, "a simplified, abstract, or concrete representation of relationships and/or processes in the real world.” (Eaton et al., 2016)

- What is the definition of modeling?
- The article defines modeling in three steps, those being: “1) the process of moving from observations of the real world to a model, 2) moving from one model representation to another model representation, or 3) comparing different models” (Eaton et al. 2016).

- Were you engaged in modeling for this week's assignment? If so, how? If not, why not?
- I think that, yes, I was engaged this week in modeling for the assignment. As defined in the article, because we went from representing the data using simulations to graphs to making predictions and back again, I was in fact, engaged in modeling.

**Isai Lopez 23:14, 12 September 2016 (EDT)**: