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CHEMICAL CARCINOGENS IN THE ATHABASCA RIVER

The Alberta Oil Sands and Increasing Cancer Rates

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CHEMICAL CARCINOGENS IN THE ATHABASCA RIVER

The Alberta Oil Sands and Increasing Cancer Rates

Assessing a 3D molecular animation as a tool to inform the public regarding the health impacts of carcinogenic PAH molecules and their link to oil sands exploitation

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A master’s research project by Stefanie Joelle Kuzmiski

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Declaration Abstract

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Aims and Project Overview

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List of Images and Figures Introduction I. Chemical Carcinogens in the Athabasca River: Increasing Rates of Cancer II. Chemical Carcinogens: An Introduction to Polycyclic Aromatic Hydrocarbons III. PAH’s Link to Cancers: the Underlying Metabolic Pathways IV. Animation as a Tool for Advancing Public Understanding

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Materials and Methodology I. Programs II. Preproduction III. Production i. Modelling ii. Animating iii. Texturing and Lighting iv. Rendering IV. Post Production i. After Effects ii. Narration and Sound iii. Final Production V. Questionnaire

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Conclusions

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Glossary

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Appendix

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References

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Acknowledgements

Results Discussion I. Discussion of Method and Limitations II. Discussion of Results

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Declaration I confirm that this assignment is my own work and that I have read and understood the University of Dundee Code of Practice on Plagiarism and Dishonesty. I have clearly referenced, in the text and reference list, all sources of information used in the text (including figures, tables, pictures) and used inverted commas around all sections of text that have been directly quoted. I have not used the work of others (including work from books, journals and websites) without acknowledgement nor used the work of another student (past or present) without acknowledgement. I have not used work of my own that has been previously submitted for another assessment, in this University or any other educational institution, and not used any external agencies to produce this work. I understand that any false claim about this work will be penalised according to the University of Dundee Regulations on Plagiarism and Dishonesty. Copyright in text of this thesis rests with the author. Copyright on illustrations, of any form, in this thesis rests with the author. Copies, by any process, either full or of extracts, may be made only in agreement with instructions given by the author and lodged in the University of Dundee Library. Details may be obtained from the librarian. This page must form part of any such copies. Further copies made in accordance with such instructions may not be made without the explicit permission of the author. The ownership of intellectual property described herein is vested with the University of Dundee, subject to prior agreement to the contrary, and may not be made available for use by third parties without the written permission of the University, which will prescribe the terms and conditions of any such agreement. Further information on the conditions under which enclosure or exploitation may take place is available from the Head of the Centre of Anatomy and Human Identification.

Declaration

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Abstract Alberta industry is largely dependent on oil sands development, which also represents a huge force in the Canadian national economy. This has obvious implications for affecting government interest and environmental policy. Studies have shown that specific chemical carcinogens known as polycyclic aromatic hydrocarbons (PAHs) play a huge role in the development of human cancers (Luch 2005). PAHs contaminate soils and aquifers and are derived from the combustion of fossil fuels such as coal, shale, and petroleum. The link between PAH and cancers has been widely established and there is growing concern that these carcinogens are contributing to the elevated cancer rates in communities surrounding the Athabasca oil sands (Luch 2005; Kelly et al. 2009). Many papers published within the past decade report rising levels of PAHs in the Athabasca River and its tributaries (Kelly et al.; McLauchan 2014). Additionally, incidences of lymphomas and leukemias have been linked to exposure to volatile components of petroleum products, gasoline, and benzene (Nordlinder et al. 1997; Michael et al. 2006). Alberta Health Services responded to claims of higher cancer rates in areas surrounding the oil sands with an investigation into the types and incidences of cancers present within Fort Chipewyan, near the Athabasca River. The paper’s overall findings show there was a 30% increase in cancers in the Fort Chipewyan population over the past twelve years, a threefold increase in leukemias and lymphomas, a seven-fold increase in bileduct cancers, and a small increase in other cancers such as soft tissue sarcomas and lung cancers in women (Alberta Health Services 2009). There is a pressing need to inform the public about the devastating health impacts of bitumen extraction, and animations have been shown to be an extremely effective educational tool (O’Day, 2005). This research project involved the creation of a short bio-molecular 3D animation that shows the breakdown of PAHs in the body, as well as how PAH molecules exert their carcinogenic effects through binding to DNA. The discussion about the growth and development of the oil sands requires an awareness of the toxicological implications and the environmental impact of bitumen extraction, as well as an understanding of cancer development. Scientific learning tools, such as 3D animation, can offer an alternative method through which scientists and activists can communicate the key scientific concepts at the centre of this difficult and urgent issue. The final animation was to be viewed alongside an

Abstract

Image source: one river news

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online survey presented through Survey Monkey. The survey participants were asked to first view the animation and then complete a short survey regarding the content as well as their experience of the animation. The survey included some basic information about the individual such as age range. The survey collected a total of 57 responses, with 9 responses originating from self-identified experts in the fields of toxicology and public health. Overall, the survey responses were positive and were very supportive of the project. The fields of computers and 3D animation are constantly expanding, and the possibilities for medical animation to enhance public understanding are endless. This study provides support for the use of new technologies, specifically computer animation, for instruction and public engagement. The animation was successful in reaching out across Canada, as well as globally. Scholars from the University of Ottawa and filmmakers from the Athabasca region have been interested in further development of the project, offering suggestions for improvements to the animation itself, as well as expressing a desire to expand the project to include personal stories from affected individuals in the Athabasca region.

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Image source: one river news

Abstract

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Aims and Project Overview There is growing concern that the increased cancer rates around the Athabasca oil sands in Alberta are a result of the increasing development and byproducts of oil sands extraction. Many papers published within the past decade report increasing levels of Polycyclic Aromatic Hydrocarbons (PAHs) in the Athabasca River and its tributaries. The link between PAHs and cancers is widely established. This project involves the creation of a short bio-molecular 3D animation that depicts the complex events underlying the pathophysiology specific to the types of cancers associated with increased PAHs. This animation is geared towards the general public, and attempts to present complicated scientific information to individuals who do not necessarily have a scientific background. The animation seeks to increase knowledge and stimulate public interest in potential developments of new public policy surrounding the oil sands.

Image source: Garth Lenz

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List of Images 38 40 44 44 45 46 47 48 48 50 52 56 58 60 60 62 63 64 64 66 70 72 73 74 76 76 77 82 82 84 86 88 90 91 92

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Image 01: Workflow Chart Image 02: Storyboard Image 03: Hypergraph and Outliner Image 04: Project Window Image 05: The Channel Box and Attribute Editor Image 06: Introduction Vertebrae Image 07: Completed Introduction Vertebrae Image 08: Nucleus and NPC Holes Image 09: Rough Endoplasmic Reticulum Image 10: Completed Cell Nucleus and RER Image 11: PAH to Diol Epoxide Image 12: DNA Helix Image 13: Chromatin Nucleosomes Image 14: nParticle PDB Image 15: Smooth vs. Tight PDB Image 16: NPC with Long Tendrils Image 17: NPC with Short Tendrils Image 18: Chromatin Movement Image 19: DNA Movement Image 20: PAH Turning Image 21: Camera Path Image 22: Floating nParticle Image 23: Pond and Wake System Image 24: Colour Test Image 25: Render Layers Image 26: Hypershade Window Image 27: Fog Light Image 28: After Effects Composite Editor Image 29: Wave World Simulation Image 30: Font Tests Image 31: Audition Sound Editing Image 32: Final Vimeo Upload Image 33: Image Still: DNA Adduct Image 34: Image Still: Enzymatic Conversion Image 35: Image Still: The Cell

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List of Figures 97 100 102 103 104

Figure 01: Collected Responses Figure 02: Likert Scale Collected Responses Figure 03: Yes/No Collected Responses Figure 04: Age of Survey Paticipants Figure 04: Good vs. Poor Biology Responses

Lists of Images and Figures

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INTRODUCTION Image source: Garth Lenz

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I. Chemical Carcinogens in the Athabasca River: Increasing Rates of Cancer The Alberta oil sands are large bitumen deposits in Northern Alberta, comprised of three main sites: the Peace River oil sands, the Cold Lake oil sands, and the Athabasca oil sands, which is the largest of the three. They are located on land covered by Treaties 6, 7, and 8, representing 44 First Nations communities (Droitsch & Simieritsch 2010). Together, the oil sands represent one of the largest crude oil reservoirs in the world, trailing only Saudi Arabia and Venezuela in terms of proven oil resources. The oil sands have received global attention for their devastating environmental impact; and yet supporters argue that the oil sands’ role in driving the Canadian economy offsets their hazardous repercussions. Despite well-publicized research, the Albertan government continues to draft legislation based upon the premise that the oil sands are not damaging the environment, and have negligible health implications for the surrounding communities and the individuals employed by the industry. Aboriginal groups in these areas rely on the land, water and wildlife to sustain their communities. For decades these Aboriginal communities have been raising concerns regarding water and air quality, the escalating impact the oil sands have on wildlife populations, and potential health consequences such as elevated levels of cancers (Droitsch & Simieritsch 2010). Recent studies show that elevated levels of pollution in the Athabasca River are strongly linked to oil sands development. With Alberta’s strong drive for industry, these studies’

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findings are going largely unnoticed. To further complicate the matter, a 2008 study published by the Regional Aquatic Monitoring Program (RAMP), the group that government and industry rely most heavily on in the creation of public policy, reported that oil sands development and extraction had a minimal effect on the quality of water in the Athabasca River; rather, the RAMP study suggested that elevated levels of polycyclic aromatic hydrocarbons (PAHs) and other contaminants were naturally occurring, and a result of the Athabasca River’s proximity to the oil sands (RAMP, 2008). Peer reviewed scientific papers have since contested the RAMP study. In addition to RAMP’s troubling conclusions, the Alberta Health Services (AHS) has investigated the reports of elevated cancer levels within the nearby communities, finding that overall cancer rates had increased by 30%. The study, however, failed to link the elevation with any concrete cause, as this was not part of their experimental design (Alberta Health Services 2009). In addition, the press release by AHS downplayed the increased rates of cancer and chose instead to focus its attention on a rare form of cancer that was seen to be at normal levels within the Fort Chipewyan population. Further controversy with RAMP has arisen due to the fact that, since 1997, the program has been funded primarily by industry and directed by a multistakeholder committee (Kelly et al. 2009). There is a drastic need for transparent research to shed light on the serious health impacts of the Athabasca oil sands on neighboring aboriginal communities. Studies have shown that specific chemical carcinogens, known as PAHs, play a huge role in the development of human cancers. PAHs

Introduction

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contaminate soils and aquifers and are derived from the combustion of fossil fuels such as coal, shale, and petroleum (Grasso et al. 2001). They have been found at elevated levels in the Athabasca River and its tributaries as a result of oil sands development (Kelly et al. 2009; McLauchlan 2014). Additionally, incidences of lymphomas and leukemias, which were reportedly elevated by three times the expected level in the Fort Chipewyan communities surrounding the Athabasca River, have been linked to exposure to volatile components of petroleum products, gasoline, and benzene (Nordlinder et al. 1997). Repeated exposure to these contaminants presents a serious threat to the surrounding wildlife and potentially to the people relying on the land for food and water (Rogers 2002). Taken together, these studies put into question whether the economic gains of the industry outweigh the negative impacts. The need to educate and inform the public surrounding these issues of toxicology and public health is of radical importance. *** II. Chemical Carcinogens: An Introduction to Polycyclic Aromatic Hydrocarbons A chemical carcinogen is any chemical agent that has the capacity to cause the development of cancer in human tissue. Chemical carcinogens vary widely in their configurations, modes of action, pathways, and the various organs in which they can produce tumors. Chemical carcinogens have been

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categorised into various subclasses based primarily on the functional groups in the compound itself (Warshwasky 2006). A specific subclass of chemical carcinogen is PAHs. They are defined as hydrocarbon molecules containing three or more fused benzene rings. They contain two or more aromatic rings fused together in a linear or angular configuration (Luch 2005). The more severely carcinogenic PAH molecules usually range from four to six rings (Warshwasky 2006). PAHs that are present in the environment usually originate from human sources. The most prolific source of anthropogenic PAH is coal tar products, derived from the coking of bituminous coal. PAHs are most often emitted in the workplace through evaporation during the process of heating raw and oily PAH-containing matter, or formed via pyrolysis and incomplete combustion. Coke production and aluminum smelting, iron and steel sintering and foundry operations, and petrochemical and petroleum processing are amongst the most common industries where PAH exposures occur (Luch 2005). Studies have reported PAH levels as high as 200 mg/ kg of dried soil when the soil was collected from areas in close proximity to oil refinery plants; in comparison, rural soil samples have averaged levels of 2µg/kg dried soil (Warshwasky 2006). Samples of water taken near the Athabasca oil sands show levels of up to 34 µg/g of total alkylated PAHs; uncontaminated rivers should have concentrations of <2 µg/g (Akre et al. 2004). Although there have not been any documented human cases of

Introduction

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cancers that were exclusively caused by PAHs, there is tremendous evidence for the contribution of PAHs to the overall carcinogenic risks for occupational workers who are exposed to complex mixtures of bitumen emissions (Warshwasky 2006). The role of PAHs in the development of cancers was recognized as early as 1775. Observation of cancers in chimney sweeps lead to the discovery of the first environmental origin for one particular type of cancer; a prevalence of scrotal tumors was linked to soot contamination on the skin of the chimney sweeps (Luch 2005). The first two PAHs were isolated from coal tar in 1930; it was not until 1960, however, that the metabolic pathways of PAHs were finally described (Warshwasky, 2006; Besaratinia & Pfeifer 2005). Some of the other compounds which have been isolated include: Anthracene Benz[a]anthracene (Weak carcinogen) Benz[c]acridine Benz[a]pyrene (Strongly carcinogenic) Benzo[b]fluoranthene (Carcinogenic) Benzo[c]phenanthrene(Strongly carcinogenic) Benzo[e]pyrene Benzo[j] fluoranthene (Carcinogenic) Dibenzo[a,1]pyrene(Strongly carcinogenic) Chysene (Weak carcinogen) Bibenz[a,h]acridine (Carcinogenic) Bibenz[a,j]acridine (Carcinogenic) Bibenz[a,h]anthreacene (Strongly carcinogenic)

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7H-Dibenzo[c,g]carbazole (Strongly carcinogenic) 7,12-Dimethylbenz[a]anthracene Fluoranthene Indeno[1,2,3-cd]pyrene (Carcinogenic) Naphthalene Pyrene (Warshwasky, 2006) (See appendix for complete IARC classification of PAH and related occupational exposures.) Chemical carcinogens can react with distinct levels of the body, affecting DNA or specific cells in tissues and organs. The level of toxicity is dependent on the concentration of the toxicant at the site of action as well as the rate of absorption, access to target cells, the degree to which bioactivation occurs, and the rate of elimination (Richards & Bourgeois 2014). PAHs are chemical agents that damage the genetic information within a cell by forming covalent bonds with DNA. If PAHs are not removed from the DNA properly by DNA repair enzymes, then subsequent formation of PAH DNA adducts can result in nucleobase mispairings and introduce mutations to cancer-related genes, such as protooncogenes or tumor suppressor genes. This nucleobase mispairing is therefore generally considered the crucial event during the process of tumor formation. ***

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III. PAH’s Link to Cancers: the Underlying Metabolic Pathways The process of chemical carcinogenesis is divided into three distinct stages: initiation, promotion, and progression. Firstly, initiation involves a precise and permanent conversion of normal cells into latent tumor cells. These cells remain in a quiescent phase unless there is further stimulus by promoting agents (Luch 2005). The process of tumor formation is “initiated” either by the activation of proto-oncogenes, or by an interaction between chemical carcinogens and tumor suppressor genes that renders the suppressor genes inactive. Once the process has been initiated, the cells still appear normal, and will need to evade DNA repair in order for the carcinogenic process to proceed (Richards & Bourgeois 2014). A tumor suppressor gene encodes proteins that are normally involved in restraining cell proliferation and are genetically recessive. Protooncogenes are genes that encode growth regulating proteins (Nelson & Cox 2008). Repeated exposure to chemicals that stimulate cell proliferation leads to an outgrowth of initiated cells and to the propagation of altered cells, which enhances tumor formation (Luch 2005). The final stage in malignant tumor production, or metastasis, is progression. During this stage, some cells may migrate from the cloned cell into the lymphatic or vasculature systems (Richards & Bourgeois 2014). All carcinogenic PAHs are initiators; many of them, however, have the capacity for both initiation and promotion and are considered “complete carcinogens,” which makes PAH exposure all the more damaging and problematic. Studies that repeatedly treat animals with high doses of potent PAH over an extended period of time have

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always resulted in tumor production without the need for any additional application of standard promoters such as TPA (Luch 2005). PAHs would not be carcinogenic if it were not for the way the body metabolized them (Richards & Bourgeois 2014). They are generally metabolized in the endoplasmic reticulum by two distinct groups of enzymes (Besaratinia & Pfeifer 2005). PAHs undergo enzymatic conversion into electrophilically reactive derivatives in order to exert their genotoxic effects. The conversion of chemically inactive PAHs into hydrophilic water-soluble molecules is a multistep process, which is facilitated by multiple different enzymes (Luch & Baird 2005). Epoxide rings (cyclic ethers with three ring atoms) neighboring to the bay region on a hydrocarbon have the highest electrophilic reactivity and, therefore, would be the preferred position for covalent interaction with nucleophiles, also known as electron donors, such as purine bases in genomic DNA (Luch & Baird 2005). The initial oxidation of PAHs is catalyzed by a Cytochrome P450 dependent monooxygenase, also known as a CYP molecule, which is usually located in the endoplasmic reticulum. CYP enzymes are particularly prevalent in the liver but are also found in other organs such as the lungs, kidneys, and the gastrointestinal tract (Hirvonen 2005). Diol epoxides are created by the addition of two hydroxyl groups to a PAH with an epoxide ring. The activation pathway leading to bay diol epoxides requires two additional enzymatic hydrolase interactions after the initial monooxygenation, or epoxide

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creation (Luch & Baird 2005). The formation of diol epoxides is considered one of the foremost pathways of metabolic activation that produces the mutagenic and carcinogenic properties of PAHs (Warshwasky 2006). *** IV. Animation as a Tool for Advancing Public Understanding There is growing evidence that animations are more effective educational tools than still, chronological images. Animations allow insight into complex cellular events that static images cannot convey (Oâ&#x20AC;&#x2122;Day 2005). Animations have been shown to be most effective when text is incorporated and used to highlight physical structures, and when narration corresponds to specific events occurring simultaneously onscreen. In terms of facilitating and reinforcing the learning process, successful animations most often integrate visual, textual, and aural information synchronously (Oâ&#x20AC;&#x2122;Day 2007). Currently, animations often accompany textbooks, with many molecular biology courses reinforcing learning through visualizations. Documented video microscopy has been incorporated into classroom lectures for decades, but computer animation represents a far more versatile teaching tool, and has only recently gained in popularity. Simplification, infinite resolution and magnification, emphasis of symbols, dynamic motion control, colour and aesthetic changes, and the integration of textual cues with

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verbal dialogue are just some of the advantages of computer animation (Stith 2004). Vision is allotted more of the cerebral cortex than all the other senses combined (Bromberg et al. 2010). To visualize can mean to make (something) visible to the eye, which is an important concept for the sciences (Sharpe, 2008). When words and pictures are combined (‘multimedia effect”) it allows the learner to more readily absorb the information (O’Day 2005). Sharpe (2008) has described visualization as existing within a “design-space” graph, with “level of interpretation” along one axis and “level of complexity” along another. As the level of complexity increases, so must the level of interpretation; therefore, the design and complexity must match its audience. Animations that move too quickly or that contain unnecessary and unrelated detail or a high level of realism might actually hinder the transfer of knowledge (O’Day 2005). The issue of chemical carcinogens in the Athabasca River is one that requires a deep knowledge of toxicology, cancer development, and public health. This could leave many affected individuals unequipped with the language to discuss these issues further. By presenting this information through animation, I hope to better inform the public about chemical carcinogens and their origins. Representing these phenomena as an animated sequence with a temporal component will enhance learning and allow the oils sands debate to be more inclusive.

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MATERIALS AND METHODOLOGY

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I. Programs

Image 01 PG 38

The production process was conceived in 3 distinct phases (see Image 1) consisting of the preproduction, production, and postproduction stages. During the preproduction phase, images were predominantly hand drawn. Some sketches were made in Photoshop CC and storyboards were put together using Illustrator CC. In the production stage, 3D modelling software such as Maya Autodesk 2014 was used extensively, as well as Mudbox and Blender. Some tasks required 2D illustration software such as Photoshop CC and Illustrator CC. In the postproduction phase, After Effects CC and Audition CC were used as well as Handbrake. The animation was uploaded to Vimeo for public access. *** II. Preproduction

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The preproduction phase consisted of project conceptualisation and the storyboarding process. The decision to create an animation was based off of research, conducted by Dr. Oâ&#x20AC;&#x2122;Day at the University of Toronto, concerning information retention and student engagement with molecular animations. The script was written and revised before 2D illustrations and storyboards were created to approximate the animation (see Image 2). These were shared with experts in the field of chemistry and public health for their feedback, verification, and critiques.

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*** III. Production The production stage consisted of modelling and animating with continuous room for revising these structures after test renders. Once the final animation was set, the animation underwent texturing and lighting before the final render passes. i. Modelling Through the Virtual Training Company (VTC), introductory tutorials that described the navigation and the interface of the Maya viewport were completed. These provided baseline information regarding Mayaâ&#x20AC;&#x2122;s data organisation. The videos described how to create and edit nodes, which are the individual components that complete an animated scene, and which can include objects, textures, lights, etc. Within a Maya scene, these nodes are set up in a hierarchy called the Dependency Graph (DG). Understanding the intricacies of the DG allows for a better grasp of the possibilities and the limits of animation production in Maya. Maya has multiple ways to view the hierarchy. These include the Hypergraph and the Outliner (see Image 3), which was a staple in the animation workflow. The Hypergraph shows node connections and has a similar navigation setup to that of the main canvas viewport. Rarely was such a detailed view of the network of connections needed. The Outliner gives a comprehensive hierarchical list of all the nodes in the scene,

Materials and Methodology

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Image 01: Workflow Chart This image depicts the typical animation workflow along with some of the major points where revision occurs.

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Materials and Methodology

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Image 02: Storyboard A sample of a storyboard draft with an older version of the script. This script underwent further development and the storyboard was rearranged to create the final animation.

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even if their visibility is turned off. Unlike the Hypergraph, it does not show connections between nodes, which made the workflow less complicated.

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Setting and creating new projects is also an aspect of animation production that requires some practice. Setting a project is a process that ensures files will not be lost and that the resulting animation will run smoothly. When starting a new scene or animation, it is necessary to open the Project Window and create a new file through the resulting menu. This automatically produces a directory that stores image files, render data, sounds, clips, and scenes (see Image 4). Modelling nodes requires firstly the actual creation of objects as well as understanding of the Move, Scale, and Rotate Tools, which are very basic and yet crucial to the modelling process. In addition, The Channel Box and Attribute Editor become important menus to quickly modify the objectâ&#x20AC;&#x2122;s characteristics (see Image 5). The Channel Box is a list of all of the nodesâ&#x20AC;&#x2122; attributes and can be modified and used as a tool to animate through keyframes. Crude shape nodes were created and smooth, wireframe, and shaded preview shortcuts were tested. The basics of polygon vs. NURBS geometry was assessed along with the merits of each while working on introductory projects (see Image 6 and Image 7). The nucleus model began as a polygon sphere. The b shortcut key was used to change the fall off radius and smooth bumps were created around the spherical surface.

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The polygon subdivisions were increased and a polygon face on each of the newly created bumps was deleted. These holes in the mesh later became a slot for the nuclear pore complex (NPC) (see Image 8). To construct the endoplasmic reticulum, the Face Component Mode was used to remove individual faces from a number of different long rectangles. The Append to Polygon Tool was used to reshape the rectangles by closing the holes. A similar method was employed to create the outer tube structures, representing vesicles; however, instead of rectangles, cylinders were used (see Image 9). This model was eventually deleted and a new model was made by extruding surfaces on a rectangular shape node instead of the previous method of joining two separate meshes (see Image 10).

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To create a model of the Polycyclic Aromatic Hydrocarbon, a molecular model set was used as a real life reference for benzene ring structure. Within Maya, a hexagonal cylinder polygon was created that was viewable from the top down viewport window, and the vertices were aligned on the grid points as a guide. Spheres were then placed at each of the hexagonâ&#x20AC;&#x2122;s vertices using the Snap to Grid Tool. A small cylinder was then linked to each sphere and outward projecting oxygen molecules were attached in a similar fashion. The initial PAH was modified slightly to create the diol, the epoxide, and the diol epoxide; this allowed the geometry to be contained in a single file (see Image 11). To build the DNA, base pairs were constructed using 4 polygon cubes. The helical frame was created using NURBS circles and an animated sweep, which was used to build a

Materials and Methodology

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Image 03: Hypergraph and Outliner These windows show the Outliner and the Hypergraph hierachy displays. The Outliner provides a more functional list of the nodes.

Image 04: Project Window The file structure automatically created by using Mayaâ&#x20AC;&#x2122;s Project Window creation.

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Image 05: The Channel Box and Attribute Editor These windows show the many different attributes of the node and allow for quick manipulation.

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Image 06: Introduction Vertebrae Introduction to modelling with polygon primitives and NURBS curves.

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Image 07: Completed Introduction Vertebrae Final rendering of vertebrae showing organic topology through contour rendering.

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Image 08: Nucleus and NPC Holes Showing rough nucleus structure with holes for NPCs.

Image 09: Rough Endoplasmic Reticulum The first RER constructed with the Append to Polygon Tool.

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Materials and Methodology

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Image 10: Completed Cell Nucleus and RER The final RER constructed using the Extrude Tool, with textures applied from Mudbox.

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Materials and Methodology

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Image 11: PAH to Diol Epoxide The various molecules which the PAH transforms into during the enzymatic conversion to a diolexpoide.

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lofted surface between a series of circles that rotated 360 degrees and translated upwards (see Image 12). Later, the polygon cubes were replaced with more refined cylinders. Image 12 PG 56

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The chromatin was created with a cylinder and by deleting selected faces in Component Mode, until one quarter of the geometry was left. Then, using the Append to Polygon Tool, a solid object was created. Using the smooth preview, edge loops were inserted until the desired shape was achieved. A sharp quality was maintained near the center of the nucleosome, where the individual histones intersect. Each histone was duplicated until they were arranged in a fourleaf clover pattern. This pattern was then duplicated until the nucleosome was complete with eight histones (see Image 13). The enzymes involved in the PAH to diol epoxide conversion, Cytochrome P450 and Methyl Epoxide Hydrolase, were imported into Maya using the mMaya add-on. In mMaya, the PDB file is imported as a particle cloud (see Image 14). These nParticles were converted into polygon meshes. The nParticle cloud PDB contains a number of different nodes that are used to determine its geometry. These proteinsâ&#x20AC;&#x2122; meshes were then tightened to better show the rough structure of the protein (see Image 15). Like the endoplasmic reticulum, modelling the nuclear pore complex took two trials. The first attempt was constructed using a polygon pipe. The subdivision was then increased and every other edge on either side was extruded to create the nuclear basket and the cytoplasmic filaments. The

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initial tendrils were not well conceived, and a more stylized structure was decided on as it would be less complex and still meet the goal for the overall animation (see Image 16 and Image 17). The second model was constructed in a similar fashion with a polygon pipe and extruded faces. The tendrils were modified to point inwards and were much shorter and wider.

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ii. Animating Initial animation tests began by working with rigging and dynamic systems. In order to rig the Chromatin model, joint systems and Inverse Kinematics (IK) handles were made, which were then turned into a soft body. From here, basic Maya Embedded Language (MEL) scripting techniques were used to add a field effect (see Image 18) (Iwasa & McGill 2008). Several of the DNA strands had the same techniques applied to them as the chromatin model. The diol epoxide molecule was imported into the scene and then animated to come into contact with the DNA base pairs (see Image 19). The opening sequence of the revolving PAH molecule was made by rotational keyframes. The camera zooming toward the PAH was completed with positional keyframes (see Image 20).

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In Maya, there are three different types of cameras: the Camera, Camera and Aim, and Camera, Aim, and Up. The Camera and Aim was used to allow for a continuous focal point on the nucleus as the camera moved around the cell. A

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Image 12: DNA Helix DNA helix created by lofted surfaces in an animated sweep.

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Image 13: Chromatin Nucleosomes The topology of individual histones created initally from polygon cylinders. Polygon faces were split using the Insert Edge Loop Tool.

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Image 14: nParticle PDB The inital nParticle imported by mMaya from the PDB.

Image 15: Smooth vs. TIght PDB Showing the difference between smooth and tight meshes created in mMaya.

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Image 16: NPC with Long Tendrils The inital NPC made with long tendrils and a small basket.

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Image 17: NPC with Short Tendrils Tendrils were shortened and simplified for viewers unfamilliar with cell biology.

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Image 18: Chromatin Movement Depicts the subtle movement of the chromatin strands set up by the turbulence field.

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Image 19: DNA Movement Depicts the subtle movement of DNA strands set up by the turbulence field.

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Image 20: PAH Turning The turning PAH was achieved through rotational keyframing.

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curve was created and the camera was attached to the path (see Image 21) (Autodesk Maya 2014). Image 21 PG 70

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Particles were made using nParticles and turbulence fields (Dryer 2014). The CC snow option in After Effects was also used (Grayson 2010). Ultimately, neither method worked and, therefore, no floating particle systems were used at all (see Image 22). Creation of the coal transforming into a water droplet was achieved by using Blend Shapes in Maya. Keyframes were used to coordinate the transformation from the coal object to the droplet object (Koning 2011). nCloth and Pond Simulations with a Wake System were used first to attempt to create the droplet simulation. While nCloth did not furnish the desired effect, the Simulations required too much memory, and made proper rendering impossible (Harbinger Arts 2013; Anon. 2010; Autodesk Maya 2014). Methods from an older tutorial were also attempted (see Image 23) (Estrada n.d.). Ultimately, the initial idea was modified, and the ripple effect was accomplished later in After Effects and incorporated into the background of the scene. iii. Texturing and Lighting

Image 23 PG 73

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Colour tests were created in Photoshop CC by taking simple occlusion renders of the cell and painting them with different photo filters applied. A dark blue-purple was chosen, in order to give the scene an unnerving and mysterious look and feel (see Image 24). A rendering layer technique, a fairly standard technique within the 3D modelling community, was

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modified from tutorials presented on the molecular movies website (Anon. n.d.; Keller 2011). Each layer is created and separated in Maya. They are rendered out into .tiff footage files with Alpha Channels, and then imported into After Effects where different blend modes are applied to combine the layers (see Image 25). A number of different shaders were composed in the hypershader. This included flat colour, occlusion, and luminescent shaders. The luminescent shaders were the most complicated, and were made by creating a flat surface shader and connecting a Ramp Shader to the incandescence field. This shader was applied to all objects throughout the animation, with different colours used for the incandescence (see Image 26). One light was employed for this project, using a method that only works when rendering through Maya Software and not Mental Ray (see Image 27) (Autodesk Maya 2014; jnaps098 2013).

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iv. Rendering Each individual scene was rendered overnight because, even in the smaller scenes, each render layer was taking approximately 3 hours. The cell scene was the largest and was sent to the University of Dundee Render Farm for rendering.

Image 27 PG 77

***

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Image 21: Camera Path Camera and Aim was used to allow for a continuous focal point on the nucleus as the camera moved around the cell. This image depicts the curve that was created for the camera to be attached to. It shows the rough path the camera followed.

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Image 22: Floating nParticle The floating nParticle clouds in a turblence field.

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Image 23: Pond and Wake System The pond and wake system that can be adapted to create ripples and waves.

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Image 24: Colour Test Colour tests were occlusion images rendered from Maya and brought into Photoshop where different colour palettes created in Kuler were tested.

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Image 25: Render Layers Each individual texture and colour is assigned its own layer and later combined to create the completed image.

Image 26: Hypershade Window Depicts the node structure associated with creating a shading network for textures and shaders. This Xray shader has a RAMP shader applied to the the luminescence field.

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Image 27: Fog Light Fog light test made using a volumetric light and rendered out in Maya Software.

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IV. Post Production i. After Effects

Image 28 PG 82

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The rendered image sequences were taken from their folders into After Effects where they were automatically placed in sequence (Keller 2011). Another way to do this would have been through Mayaâ&#x20AC;&#x2122;s FCheck. However, FCheck is used predominantly for single layer test renders. Using different blend mode sets, each layer was combined and modified to create a completed composite. Solids were used with masks to create colour gradients and a sophisticated blurring effect was completed with depth maps (see Image 28). Sections of the animation in which the camera movement did not seem to flow properly were slowed down to help give the illusion that the animation was much smoother. This created a long pause in the middle of the animation. Once all the render layers were blended properly, the ripple effect was made using a Wave World Simulation (see Image 29) (Hadley 2013). Lastly, text and fonts were tested in Illustrator and were later applied to the animation itself (see Image 30). ii. Narration and Sound

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Narration was recorded using a sound card device that takes an analogue audio signal and transfers it to a digital file by sampling it, using GarageBand as a recording intermediate. The sound was then brought into Adobe Audition where the noise in the background was cleaned and the narration

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volume was amplified (see Image 31) (Sengstack 2013). Music was brought into the animation through After Effects and the output volumes and fade-ins were adjusted using keyframes. Music clips were taken from Godspeed You! Black Emperor’s “09-15-00,” Erokia’s “Elementary Wave,” Stk’s “Life Line,” Erokia’s “ambient sound,” Bell Orchestre’s “The Bells Play the Band,” and Broken Social Scene’s “Superconnected.” Levels of music and narration were adjusted in After Effects. iii. Final Production

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Video was rendered in After Effects and brought into Handbrake in order to reduce the file size for upload to Vimeo (see Images 32-35). Image 33 PG 90

*** V. Questionnaire The final animation was shared publically using Vimeo as a hosting platform. The animation was to be viewed alongside an online survey presented through Survey Monkey. The survey was made available to the public over an 8-day period from July 6th until July 14th. The survey reached out to the general public as well as experts via social networking sites such as Twitter, Facebook, Tumblr, Reddit, as well as direct personal e-mails. Along with a brief introduction of the

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project and the video URL (https://vimeo.com/100138173), the survey link URL (www.surveymonkey.com/s/ athabascathesis) was provided with an initial consent form on the first page of the survey. Outlined in the consent form was the approximate time to complete the survey, the option to skip questions, and the option to withdraw participation or information at any time during or after the study was completed. Confidentiality concerns were addressed and secure data protection was explained. A “Continue” button appeared at the bottom of the page. It was clearly explained that by clicking “Continue,” participants were agreeing to all conditions within the consent form. No restrictions were made on age, sex, or education level. The survey participants were asked to first view the animation and then complete a short survey regarding the content as well as their experience of the animation. The survey included some basic information about the individual such as age range. The survey collected a total of 57 responses, with 9 responses originating from self-identifying experts in the fields of toxicology and public health. Examples of the survey can be found in the appendix. General Public: I assumed the general public to be anyone below a Master’s level without a specific research interest in public health, environmental toxicology, and cancer developments. These individuals were directed to respond to Questions 1-12, which employed either a 1-5 Likert

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evaluation scale or a yes/no/neutral rating system. There were two additional questions that invited comments or suggestions. Experts: Experts in the fields of PAH and cancer developments, public health, and environmental toxicology were contacted primarily by e-mail. They were directed to answer the same questions as the general public, with the addition of two more Likert scalar rated questions.

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Image 28: After Effects Composite Editor Showing the indivual layers in After Effects to create a complete composite including the rendered footage files, solids, and adjustment layers.

Image 29: Wave World Simulation Showing the 3D view of how the subtle Wave World pond ripple was created.

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Image 30: Font Tests Different fonts were tested in Illustrator CC. Evetually, Helvetica was chosen for a clean and modern look.

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Image 31: Audition Sound Editing Sound was imported into Audition from Garageband where the sound levels were adjusted and hiss and noise was removed.

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Image 32: Final Vimeo Upload The final video was uploaded to Vimeo and was viewable on desktop, ipads, and iphones.

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Image 33: Image still: DNA Adduct Showing the formation.

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Image 34: Image Still: Enzymatic Conversion Showing the PAH transformation to a diol epoxide.

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Image 35: Image Still: The Cell Depicting the cell structure highlighting the nucleus and rough endoplasmic reticulum.

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RESULTS

Image source: peter essick

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The surveys for both groups were conducted through surveymonkey.com and the results were calculated as percentages for each question individually. All questions are shown on the table below, with the exception of the open questions in which participants were asked to describe or comment about their general experience and areas for improvement.

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Q1. What is your age?

15 and Under

16-25

26-35

36-45

46+

Percentage

0.00%

36.84%

35.09%

12.28%

15.79%

Participant Number

0

21

20

7

9

Q2. How would you rate your current knowledge about cell biology?

Very Poor

Poor

Percentage

12.28%

31.58%

31.58%

17.52%

7.02%

Participant Number

7

18

18

10

4

Q3. How would you rate your current knowledge about genetics?

Very Poor

Poor

Very Good

Good

Very Good

Good

Excellent

Excellent

Percentage

5.28%

43.86%

29.82%

15.79%

5.26%

Participant Number

3

25

17

9

3

Q4. How would you rate the videoâ&#x20AC;&#x2122;s success at transferring information?

Very Poor

Poor

Good

Very Good

Excellent

Percentage

0.00%

5.36%

39.29%

42.86%

12.50%

Participant Number

0

3

22

24

7

Q5. How would you rate the overall aesthetic of the video?

Very Poor

Poor

Good

Very Good

Excellent

Percentage

0.00%

7.02%

36.84%

33.33%

22.81%

Participant Number

0

4

21

19

13

Results

Total 57

Total 57

Total 57

Total 56

Total

57

Average Rating n/a

Average Rating 2.75

Average Rating 2.72

Average Rating 3.63

Average Rating 3.72

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Q6. How would you rate the level of visual detail in the animation?

Very Poor

Poor

Very Good

Good

Excellent

Percentage

0.00%

7.02%

40.35%

40.35%

12.28%

Participant Number

0

4

23

23

7

Q7. How would you rate the verbal dialogue in the animation?

Very Poor

Poor

Very Good

Good

0.00%

7.02%

33.33%

36.84%

22.81%

Participant Number

0

4

19

21

13

Very Poor

Poor

Very Good

Good

0.00%

1.75%

43.86%

36.84%

17.54%

Participant Number

0

1

25

21

20

Yes

No

66.67%

10.53%

22.81%

Participant Number

38

6

13

Yes

No

Total 57

87.72%

5.26%

7.02%

Participant Number

50

3

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Average Rating 3.58

Average Rating 3.75

Average Rating 3.70

Total

57

Neutral

Percentage

98

57

Neutral

Percentage Q10. Do you believe that this video has improved your understanding of the links between PAHs and cancers?

Total

Excellent

Percentage Q9. Do you believe that this video has improved your understanding of how cancer forms?

57

Excellent

Percentage Q8. How would you rate your overall experience with the animation?

Total

Total

57

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Q11. Was it helpful to have this information presented as a video?

Yes

No

Neutral

Percentage

92.98%

0.00%

7.02%

Participant Number

53

0

4

Q12. Do you believe the content of the video is appropriate for the general public?

Yes

No

57

Neutral

Percentage

77.19%

8.77%

14.04%

Participant Number

44

5

8

Q15. (For Experts) Do you believe videos like this will improve public understanding?

Yes

No

81.82%

9.09%

9.09%

Participant Number

9

1

1

Q16. (For Experts) How does this video rate against current visual learning aids in this area?

Very Poor

Poor

Very Good

Good

Excellent

Percentage

10.00%

0.00%

30.00%

60.00%

0.00%

Participant Number

1

0

3

6

0

Total

57

Neutral

Percentage

Total

Total 11

Total

10

Average Rating 3.40

Figure 01: Collected Responses Overall responses collected from the online questionnaire on surveymonkey.com.

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Figure 02: Likert Scale Collected Responses Graph of responses for questions 1-8. These questions used a Very Poor-Excellent Likert scale rating system.

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Figure 03: Yes/No Collected Responses Graph of responses for questions 9-12. These questions requested a Yes/No/Neutral response.

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Figure 04: Age of Survey Participants Graph depicting the age range of the 57 survey participants.

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Figure 05: Good vs. Poor Biology Responses Graph of difference between results of individuals who reported their biology and genetics knowledge to be good, very good, or excellent (in green) and individuals who reported their biology and genetics knowedge to be poor or very poor (in orange).

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DISCUSSION

Image source: Healing WAlk 2014

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I. Discussion of Method and Limitations Most importantly, areas for improvement lie primarily within organization. The Outliner became very unorganized throughout the modelling and animating process and proper labelling, grouping, and parenting could have minimized issues in the long term. Acknowledging processor limitations to begin with would also have saved time. Many attempts at modelling and rigging were made without a clear understanding of what the limitations were for processor-heavy actions and high-density polygon meshes. This was certainly the case for the cell scene and was the primary reason why complications arose when the scene was outsourced to the render farm in Dundee. All layers came back from the render farm, with the exception of the occlusion layer, which would have brightened the scene significantly. A similar aesthetic was achieved throughout the animation by darkening other scenes. This homogeneity, of course, was at the cost of detail. A deeper understanding of nParticle node structure and the imported PDB node structure would have also contributed to improved organization. The nSolver nodes created many issues throughout the animation process, resulting in the need for multiple reanimations of the metabolic process. Having more than one nSolver with the same name causes errors within the Maya script. In addition to having issues with the nSolver of the PDB files, it was also not discovered until very late in the production process that there was a way within the mMaya software to create a much tighter polygon mesh from the nParticle cloud that would offer a higher quality appearance overall.

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Time constraints and familiarity with software packages lead to a great deal of limitations within the context of this project. These limitations were reflected in the quality of the final product as well as in the responses and comments received by the questionnaire. *** II. Discussion of Results Overall, the results of the questionnaire highlighted the many limitations that arose during the production phase, as well as pointing out positive aspects of animation as a learning tool. Out of 57 participants, 77% felt that the video was appropriate for the general public and 92% felt as though it was helpful to have the information presented in a video. The animation itself attempted to address many of the suggestions for molecular animation put forward by Dr. O’Day in “Animated Cell Biology: A Quick and Easy Method for making Effective, High-Quality Teaching Animations” (2005), such as a clear narrative and an integration of the narration with the events shown on-screen. The animation employed conversational narration with the intent that it would be easy to understand and follow for individuals with varying levels of knowledge in biology and genetics. There was a large spread in perceived background knowledge, with 12% of respondents feeling that their biology knowledge was very poor, while 7% felt theirs was

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excellent. 5% thought their genetics knowledge was very poor and only 5% thought theirs was excellent. The majority of respondents felt their background knowledge was either poor or good. Further limitations that should be addressed include a difference in Internet connection speeds between urban centres and smaller, more remote towns, such as those in northern Alberta affected by oil sands development. In future, videos should be made smaller and uploaded on multiple different video hosting sites in order to make the video more accessible and run more smoothly. The animation was very dark, which on some computers may not have appeared as bright as it did on my Mac retina display. This was not considered until the survey had started. It would have been beneficial to ask about different types of browsers and monitors in order to know what the animation should look like to remain aesthetically pleasing across multiple different platforms. This could account for the four individuals who rated the visual aesthetic of the animation as poor: “Brighter, it is quite dark as if designed on a Mac (but replayed on a PC). The result is spending time trying to see the picture and missing the narrative. I would have liked a few more “shots” of things relating to the area, as with the map, to drive home what causes the pollution as opposed to see in [sic] animations of cells and other internal gadgets.” “The video is quite dark, especially the PAH molecule itself. Sometimes it’s hard to see what’s going on…” “Its a bit dark, and the speaker was kind of monotone, but the video would be really good for schools.”

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The other biggest critique was regarding the pauses between narration. This was initially used as a way to make the animation appear less jerky, and to add a break in narration for the viewer to process the information. This break was too long and in the future should be shortened: “Speed up the video, feels like long gaps where nothing is being said.” “In the first part there is a longer speech without any change of the animation, I would change the scene or make the speech shorter.” “Fewer black screens, fewer pauses.” “Right as the video starts and maybe a minute into it, there are a couple of long pauses during which I found myself distracted and losing the thread.” “There are long periods the animation without any dialogue….” “Long shots of the same thing with no voiceover is boring...” “Between 2:00 and 2:40 there is no dialogue, and I’m not sure what part of the image on-screen I’m meant to be focusing on. Perhaps the zoom-in could be quicker, or dialogue could be added to explain the image? The silence broke the flow a little.” “Personally, I think it could be sped up a little bit, but that’s just me!” “Some unnecessary pauses in places which could be eliminated to make the video more ‘punchy’.” “There is one moment in the video with a blackout for a couple seconds. Keep the image there to continue engaging the audience!”

Many of the respondents said they would have benefitted from labels on the enzymes and the different parts of the cell, which is consistent with research conducted by Dr. Stith and Dr. O’Day. Other suggestions mentioned that zooming in from a macroscopic level to the microscopic would have given more context for viewers who were unfamiliar with what a cell looks like.

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“A non biologist may not recognize the inner structure of a cell, or may not know what a cell is. What about zooming in from a whole organism into a random organ and then into a cell and into a cell’s nucleus? (for perspective).” “Details are very technical and will not be understood by many non scientists in the public.” “… people may not realize the link between DNA and cancer; I feel your video presumes the audience knows of what cancer is. I like the way you did not go into too much detail with the way the enzymes work. That allowed the video to retain its focus.” “More explanation of the 3 types of cancer causing pathogens and also better graphics...” “Not sure what it shows- conveys no information to topic. Animation of reactions is good but script too technical.” “… If possible maybe (if possible) simplify it further some of the words were a bit to [sic] academic and may be difficult to understand for the general public with no past knowledge of cellular structure of science. But apart from that good.” “I didn’t know what some of the animations were, eg. The thing that looked like a cabbage with a tumour, and the moving blob at the end (was it a something to do with infectd [sic] water becoming clean? I didnt [sic] understand some of the language. There may be too much information/ science for the “general public” ( i.e. Someone who doesnt [sic] have cancer/ close friend with cancer and somoeone who doesn’t live in the affected area - for these people slightly more depth may be good).” “Although PAHs are explained and shown as visual text, the other terms, ie: Diely... the red and yellow blobs, etc., are not and this makes them harder to grasp and retain. And it would be good to know how to spell these terms. It would also be good to have the aural narration supported by visual emphasis and labels identifying the parts of the cell and cancerous phenomena. As well, visually and narratively, the PAH chain should not remain just black after its contact with the yellow and red blobs, as that is a transformative process that makes it cancerous, no? Why wouldn’t the PAH chain look slightly different once it has become cancerous?”

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“Small labels to distinguish the enzymes that modify PAHs may be useful for the viewer so the names are easier to remember (and therefore the process).” “This is too complex for general public (GP) - reading age about 11 years -reference The Sun. They may be interested if presented more simply - long chemical names although later reduced to initials (too many & so confusing) are a turn off to GP This level of ‘science’ is too advanced for the motivated environmentalist from road sweeper to bank teller.”

Aesthetically there was definite room for improvement. In addition to the animation being quite dark, respondents pointed out that they were unable to tell that the PAH had changed. The model does change from the PAH to a diol epoxide, but perhaps it would help to have the camera moving even closer to the reaction. Another possibility for visually signifying the reaction could be to use some sort of light rather than simply showing the enzyme touching the particle. “…3) It’s sometimes unclear how the video relates to the dialogue. For example, we zoom in through an atom in PAH to see...a cell’s nucleus, I think? But I’m not sure. Also, we hear that the PAH is transformed by three enzymes but I couldn’t see a transformation? 4) After hearing about the 3 transformations required to make PAH carcinogenic I was left with the impression that it should be rare and unlikely to occur. But we know it’s not so rare so I presume that the enzymes are prevalent and these interactions are common. It might help to show that somehow. Just some ideas to improve on an alreadyimpressive video!”

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There were also limited critiques regarding the narration. “Narration needs a little polish. Content was good but inflection is a really difficult skill and it takes alot of practise so that the narrator does not sound as if they are reading a script”

Despite the pitfalls of the animation, it appears as though it was successful overall in starting a conversation about this issue. Many of the additional comments were simply respondents expressing a desire for more information about the people affected, what they can do to help, and how they can protect themselves for the future: “very interesting. Any data on actual cancer rates changing in this region of Alberta?” “great job, good luck.” “Very well done! I have learned something new.” “good job!” “I particularly liked the sequences with DNA.” “Really, really excellent and informative!” “Very well done.” “Loved your RER.” “Overall, the visuals are carefully considered and restrained and the transformations are paced to be easy to follow. I just think the whole could be improved to appeal to a variety of viewers. Some folk learn better aurally, others visually, most of us would likely benefit from the narration and the visuals working together more closely. The sequence where the oily black molecule transforms into the water drop is very effective - even darkly poetic!” “Overall the content is very informative and I wish you the best of luck with this project.” “Very important message for the general public. I think it would be more valuable if you could demonstrate the conceptual jump between the DNA adducts, and the formation of a tumour. Perhaps it is beyond the scope here, but to make it a complete piece for the audience you are trying to reach this link between the abstractions of cell/molecular bio/genetics and the experienced reality of cancer would make it more powerful.”

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“Interesting and engaging. Never busy or confusing. Really well done.” “less details on the DNA and molecular biology level, more detail on the how do we get that, how can we protect ourselves, etc. The video needs to focus more on the health education aspect rather than explaining scientific details.” “Suggestions about what can be done about it.”

Individual learning styles may have affected overall user experience, with the resource primarily catering to visual learning. However, with the use of narration, auditory learners may have found the animation useful as well. Unfortunately, the comments from experts were not clear, leading me to wonder if respondents from the general public had missed the disclaimer at the top of the page, which outlined which questions they were supposed to fill out and which they were supposed to leave blank. Some experts also did not understand the phrasing of the expert questions, thinking that the animation had been geared towards experts, when the project was seeking expert opinions for an animation geared towards the public. For these reasons, the comments have been discussed cumulatively. “I’m not sure what you mean. This seems very clearly to be for the general public. It can’t really serve two masters - not sure what type of experts you mean. Experts in this field would probably gain little from it.”

Overall feedback was fairly positive. 88% of respondents felt that the video had improved their understanding of the links between PAHs and cancers, while 98% of respondents reported they had a positive experience with the animation.

Discussion

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CONCLUSIONS Image source: peter essick 117


The aim of this research project was to design a molecular animation that described health hazards associated with the oil sands developments for Canadians living in the Athabasca region. The animation was intended to educate individuals about the health risks most commonly associated with exposure to the byproducts of bitumen production and to open a dialogue about public policy surrounding water contamination. This work has shown the pedagogical importance of molecular animations for the general public. These animations can be uploaded to the web through Youtube or Vimeo and could also be played through Quicktime in classroom settings. The key to effective knowledge transfer in animation production lies in having conversational narration synchronous with onscreen animated events and having a suitable level of detail for the target audience. The overall responses were positive and were very supportive of the project. Computer and 3D animation is a constantly expanding and developing field, and the possibilities for medical animation to enhance public understanding is immeasurable. Incorporating these animations into curriculum in schools, however, would require more planning and structure. Visual animation should most certainly be incorporated more into basic genetics learning at a high school level. The animation successfully reached people not only across Canada, but also globally; the Vimeo upload surpassed 275 views in only 10 days. Scholars from the University of Ottawa and filmmakers from the Athabasca region have

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been interested in helping to develop the project, offering suggestions for improvements to the animation itself, as well as expressing a desire to expand the project to include personal stories from affected individuals in the Athabasca region. This study provides support for the use of new technologies, specifically computer animation, for instruction and public engagement. Limitations to do with cost of creation as well as widespread use of computer software are understandably problematic; however, these issues will likely diminish with time.

Conclusion

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GLOSSARY Image source: Garth Lenz

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B

of cancer in human tissue.

Bay region: The space between the aromatic rings of the PAH molecule. Base pair: Two nitrogenous bases (a purine and a pyrimidine) held together by weak bonds. In DNA the pairs consist of adenine and thyamine or guanine and cytosine. In RNA uracil replaces thyamine. Two strands of DNA are held together in the shape of a double helix by the covalent bonds between the base pairs. Benzene: The simplest ringed compound consisting of 6 carbons and 6 hydrogen atoms. Exposure to benzene can increase the risk of cancer and lead to anemia and a decrease in blood platelets.

C Cancer: A group of approximately 100 diseases characterized by uncontrolled cellular growth and divisions. Most cancers are named for the type of cell or the organ of origin. Chemical carcinogens: Any chemical agent that has the capacity to cause the development

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Complete carcinogens: Have the capacity for both initiation and promotion, and do not need any immediate promotor chemical carcinogen. Covalent bonds: A chemical bond that involves the sharing of electron pairs between atoms. The stable balance of attractive and repulsive forces between atoms when they share electrons is known as covalent bonding.

D DNA (deoxyribonucleic acid): The molecule that encodes genetic information. DNA is a doublestranded molecule held together by weak bonds between base pairs of nucleotides. DNA adducts: A piece of DNA covalently bonded to a (cancercausing) chemical. This process could be the start of a cancerous cell, or carcinogenesis. DNA repair enzymes: Proteins that function to correct improper DNA sequences.

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E Enzymes: A macromolecule, usually a protein that speeds the rate of chemical reactions in the body without altering the direction or nature of the reaction. Epoxide rings: Cyclic ethers with three ring atoms.

G Gene: The functional and physical unit of heredity composed of a sequence of DNA that occupies a position or locus on a DNA strand.

I Initiation: A precise and permanent conversion of normal cells into latent tumor cells.

M Metabolic pathways: The sum of anabolic and catabolic processes in the body. Metastasis: Describes the movement of diseased cells, particularly cancer cells, from the

Glossary

site of origin to another location in the body. Multimedia effect: When words and pictures are combined.

N Nucleophiles: Electron donors.

O Oxidation: A change in a chemical characterized by the addition of oxygen, the loss of hydrogen, or the loss of total electrons.

P Polycyclic aromatic hydrocarbons: Hydrocarbon molecules containing three or more fused benzene rings. Progression: Further growth and expansion of the tumor cells into normal cells. Proliferation: The continuous reproduction of similar forms, especially of cells. Promotion: When mutated cells are stimulated to grow and divide faster and become a population of

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cells. Proto-oncogenes: Repress genes that are essential for the continuing of the cell cycle. If they are not expressed, the cell cycle does not continue, effectively inhibiting cell division. Pyrolysis: Decomposition brought about by high temperatures.

R Recessive: A gene expressed only if there are two identical copies.

T Tumor suppressor genes: A class of genes which, when mutated, predispose an individual to cancer by causing the loss of function of the particular tumor suppressor protein encoded by the gene.

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APPENDIX

Image source: Gath Lenz

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Consent Forms

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Questionnaire: General Public

Appendix

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Questionnaire: General Public

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Questionnaire: Experts

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IARC Classification of PAHs and Related Occupational Exposures IARC Group

Exposure/Substance

1 (Carcinogenic to Humans)

Occupational exposure during: Coal gasification Coke Production Coal tar Distillation Paving and roofing with coal tar pitch Aluminum production Substance Benco[a]pyrene

2A (Probably Carcinogenic to humans

Occupational exposure during: Carbon electrode manufacture Substances Creosotes Cyclopenta[cd]Pyrene Dibenz[a,h]Anthracene Dibenzo[a,l]pyrene Dibenz[a,j]acridine

2B (Possibly carcinogenic to humans)

Substances 5-Methylchrysene Benz[j]aceanthrylene Benz[a]anthracene Benzo[b]fluoranthene Benzo[j]fluoranthene Benzo[k]fluoranthene Benzo[c]phenanthrene Chyrsene Dibenzo[a,h]pyrene Dibenzo[a,i]pyrene Indeno[1,2,3-cd]pyrene Dibenz[a,h]acridine Dibenz[c,h]acridine Carbazole 7H-Dibenzo[c,g]carbazole

3 (Not classifiable re: carcinogenicity to humans)

All other PAHs

(Carex 2014)

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REFERENCES Image source: peter essick 135


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Acknowledgements I would like to thank all the research participants, my friends and family, and all the people who have supported and helped me throughout the development of this research project. Many thanks to Caroline Erolin, for all her guidance and words of encouragement. Thank you to Chris Ogan and Sang-Hun Yu for their transAtlantic help with rendering and 3D modelling assistance in Maya, and thank you to Miriam Waite for taking this booklet to the printers. Finally, a big thank you to Max Karpinski for all your edits, your voice, your time and support, without which I might not have completed my project at all.

Acknowledgements

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Profile for Medical and Forensic Art

Stefanie Kuzmiski MSc Medical Art  

I have created a short bio-molecular 3D animation that shows the breakdown of PAHs in the body, as well as how PAH molecules exert their car...

Stefanie Kuzmiski MSc Medical Art  

I have created a short bio-molecular 3D animation that shows the breakdown of PAHs in the body, as well as how PAH molecules exert their car...

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