Team:William and Mary/Education
Education
Although a relatively new discipline, the field of synthetic biology impacts every aspect of society, and has the potential to address many of the pressing global problems facing the planet. It is imperative that the discipline of synthetic biology be integrated into mainstream education at all levels. Not only do we want to inspire students about the prospect of working in this exciting field, but we want to ensure a well-informed citizenry. It is also essential that the knowledge of this field be accessible to all students, not just an elite who have the opportunity to attend well-resourced schools. However, the field of synthetic biology is currently almost non-existent in the K-12 and college level introductory biology curriculum. A survey of currently used textbooks devote only a few sentences to synthetic biology, if even that. Additionally, educational materials are often inaccessible for educators with limited resources. These educational materials need to be made open source, accessible, and easy to use for everyone so all students have opportunities to learn about new technologies. This year our education project aimed to address these needs. Working closely with educators at all levels (as described in our Integrated Human Practices section), we created: (1) an open source curriculum to accompany the section on synthetic biology in the state standards of learning; (2) educational materials to supplement each of the chapters in the leading OpenStax introductory textbook that will introduce students to synthetic biology and allow them to understand its connections to every aspect of biology; (3) materials that integrate data science and synthetic biology hosted by QUBES; and (4) software tools based on web scraping and machine learning that update a database (first constructed in 2017) of iGEM projects in an automated manner, thus ensuring a current and sustainable database of iGEM outreach projects for community use. It provides enhanced accessibility for others’ educational materials.
Open Source Curriculum for State Standards of Learning
Many students are not exposed to synthetic biology until they reach some level of specialized higher education. Students should be introduced to key topics in genetics and synthetic biology earlier in their education. Our team is pioneering this effort by participating in the process of updating our state learning standards to include synthetic biology developing resources to streamline the implementation of these updates.
In 2018, the state of Virginia called for public input on updating their Science Standards of Learning (SOL). The SOLs are the basic guidelines for Virginia public schools which detail what students should learn by the end of the course. Our 2018 team submitted a proposal during the public input session to include synthetic biology and other important topics in genetic engineering in the updated SOLs. This proposal was approved and in October 2018 the updated SOLs were approved which successfully integrated synthetic biology into state standards (see the original SOL proposal here). The new standard of learning says:
BIO.5 The student will investigate and understand that there are common mechanisms for inheritance. Key ideas include:
- DNA has structure and is the foundation for protein synthesis;
- the structural model of DNA has developed over time;
- the variety of traits in an organism are the result of the expression of various combinations of alleles;
- meiosis has a role in genetic variation between generations; and
- synthetic biology has biological and ethical implications.
The full list of updated science standards of learning can be found here:
Integrating synthetic biology into our state standards will affect the 1, 265, 419 high school students enrolled in Virginia public high schools. However, these new standards of learning take years to fully implement. Based on the Science and Standards Review Timeline published by the Virginia Department of Education, the new Science Standards of Learning won’t be implemented until the 2020-2021 school year. In order to streamline this implementation process, we created a curriculum which covers key topics in genetics in order to introduce students to synthetic biology. Our curriculum aims to address topics presented in the curriculum framework which can be found here
Our curriculum consists of six discussion and collaboration based lesson plans. The topics for the lesson plans are DNA Structure and Function, DNA Replication, Gene Expression, Genetic Engineering, Synthetic Biology, and Synthetic Biology Ethics. These lessons engage students through videos and encourage research and collaboration. The lessons consist of a background to discuss basic information related to the topic, directions for instructors, an in class activity to synthesize learning, and an optional lab activity. Schools may not have the resources to perform advanced experiments, but there are a plethora of online videos and resources which can still show students these processes.
Click here for full curriculum document
Our next steps to further implement this curriculum are to engage more educators and experts in curriculum development and put our curriculum into effect through our high school outreach programs. We also shared this curriculum with Virginia iGEM, and their feedback influenced our final draft.
To accompany our curriculum, we created a circuit builder activity to give students real experience using the design, build, test strategy employed in synthetic biology. This enrichment features the connection between technology and synthetic biology by illustrating the synthetic biology concept that complex biological systems can be broken into parts like computer engineering. This activity leads students through the process of designing a circuit by using network motifs seen in electrical engineering, and recently adapted to E. Coli, as templates for biological circuit design.
This curriculum and enrichment material aligns with our goals of increasing the availability for comprehensive open source educational materials. While the curriculum and enrichment are designed for Virginia state education system, they are broadly applicable and available for anyone to use and could affect synthetic biology education worldwide.
OpenStax Biology 2e Synthetic Biology Supplementary Materials
Textbook prices have been rising extensively. Currently, the average college student spends hundreds of dollars on textbooks each year with some textbooks costing upwards of $200! This price crisis exposes the need for open source access to textbooks in key higher level topics. This issue has been tackled by OpenStax. OpenStax is an open source education company that creates high quality textbooks and education materials. Their textbooks are now used in over half of the universities in the United States, and their impact on the textbook industry is causing prices for mainstream textbooks to decline for the first time in 50 years! Students and teachers were satisfied with the quality and cost of the OpenStax Biology textbook. (Watson et. Al. 2017) We saw an opportunity this open source access to synthetic biology educational materials by integrating synthetic biology topics into chapters of the OpenStax Biology 2e Textbook. Synthetic biology is not covered extensively in mainstream materials, but integrating synthetic biology into the topics covered in the textbook would could greatly increase knowledge of and appreciation for synthetic biology. Their mission aligns with our goal to improve access to synthetic biology by dovetailing with open source materials.
The topics in the textbook span everything from biological macromolecules to ecosystems, but synthetic biology is such a broad field with an incredible amount of research and applications which can be integrated into every topic. Being able to write a synthetic biology supplement for each of the 47 chapters proves the expansive reach synthetic biology has to effect all biological topics. These supplements integrate easily into the OpenStax textbook framework. They can be understood by students and educators alike who may be using this material to create lesson plans.
Our supplements for each chapter can be seen below. In the future, we hope to work with OpenStax to publish these materials and find new ways to incorporate synthetic biology into mainstream educational materials.
Synthetic Biology Materials for the QUBES/BioQuest Workshop and Website
Participating in the QUBES/BioQuest Workshop inspired our team to create activities which use synthetic biology topics as a hook to introduce data science into the undergraduate classroom. Synthetic biology occupies a unique place to integrate big data into biology as a crossroads between engineering, genetics, and data science. The discipline increasingly requires more integration with data science as the availability of sequence data and modular synthetic DNA parts grows. Many of these sequences and parts are available for anyone through databases and tools such as BLAST, GenBank, and the iGEM Registry of Standard Biological Parts serve as open-source learning tools for students to begin using big data to identify, build, and apply circuits. Based on this, we created 5 activities intended for introductory biology students in undergraduate and upper level classes. These activities can be adapted to all levels of learning and employ the exciting field of synthetic biology to introduce students to meaningful data mining, analysis, and application to engineering novel biological constructs The activities are:
- Identifying Applications of In Class Learning by Examining Past iGEM Projects
- Building a Synthetic Biology “Circuit” Using Network Motif Models
- Promoter Engineering with Big Data
- Using DNA for Digital Storage
- (Re)Building a Synthetic Minimal Cell Using Bioinformatics Insights
The five activities can be easily completed in the classroom or outside of the classroom. These activities are comprehensive because their complexity can be adapted to many levels of learning. The only materials needed to complete the activities are an internet connected device and creative thinking. These activities and our rationale behind creating them are all publicly available through the QUBES community website. Since the publishing of our materials on the QUBES resources database, our materials have been viewed 131 times and downloaded by 58 users.
Software Tools for Automated Updating of our iGEM Outreach Database
With hundreds of iGEM teams developing innovative pedagogical tools and outreach practices for synthetic biology, there is an obvious need for a database similar to the iGEM Parts Registry that promotes dissemination of teams' outreach projects. This database should document these achievements and be easily searchable to promote widespread accessibility so future teams could draw inspiration from past projects to better serve their communities. To facilitate this process, the W&M iGEM team created an outreach database in 2017 and manually updated it in 2018. However, updating via manual curation was a major challenge. It requires hundreds of person hours each year, is inefficient, and not in line with available technology. The question of how to keep databases updated and current actually dissuades iGEM teams from constructing databases for other iGEM activities (e.g. modeling), despite the usefulness of these databases for the community.
To address this problem, we created software to automate this process through the use of groundbreaking web scraping and natural language processing techniques. Specifically, our web scraper is able to visit team sites, locate relevant pages, and group and extract contents from different pages. Our machine learning models can summarize the events, then identify their audiences, categories, and goals based on automatically collected textual descriptions. This software will obviously be beneficial for the teams that utilize it to improve their own outreach projects in future years. Equally important, our software will hopefully provide the framework for future teams who are considering making a searchable database to make other aspects of iGEM teams' projects more accessible to the community. The software description as well as the database can be found under the database tab.