Even though natural sciences and humanities are often seen as opposite, they are never truly separate from each other. Natural sciences impact humanities and vice versa. For example, the development of machines, such as the internal combustion engine and the spinning jenny, fueled the Industrial Revolution that had tremendous consequences on society in Europe and the USA by releasing people from manual labour and easing transportation. Recent examples are the computer and the internet, whose impact on the world and our field we still witness today. (Duignan, n.d.) Likewise, Cartesian mind and body dualism replaced the orthodox Christian views about mind and body being one, a spiritual being, that must be left untouched in order for human souls’ to ascend to heaven after death. This paradigm shift allowed the study of human anatomy and led to progress in medicine in the 17th century. (Mehta, 2011)
In the past and even present, scientists have made mistakes even resulting in horrible outcomes when not acknowledging or ignoring the social or ethical impact of their science. One of the most horrifying examples is a German chemist Fritz Haber who researched poisonous gases to be used in World War I and later in death camps (Bowlby, 2011). One recent example that resorted to world-wide polemics, is a Chinese researcher, He Jiankui. He used a novel gene-editing technology CRISPR-Cas9 to edit a gene involved with HIV infection in order to create HIV-resistant embryos without the approval of the scientific community, which led to the birth of two HIV-resistant babies and him ending in prison (Mallapaty, 2022).
We realise that our project and synthetic biology in general have an effect on society, sometimes in unforeseeable ways. To make our project as influential, careful and ethical as possible, we selected core values that have guided us through our project and decided to make our Integrated Human Practices as impressive and comprehensive as possible with our resources. Our core values were discussed and re-evaluated monthly.
Wellbeing
Our team spirit and the project overall is deeply impacted by the wellbeing of the team members, which is why we selected wellbeing as one of our core values. Exhaustion and in the most extreme cases, burn out, affect many young people worldwide today. The competitive society puts pressure on youth to excel in every aspect of life, from hobbies to studies and work, at the expense of their own wellbeing. In particular, the pandemic has worsened the exhaustion and the pressure experienced by youth as factors that support everyday life, such as social communities and hobbies, have become scarce. In addition, working in research exposes you to exhaustion because of temporary employment and extreme competition about grants between the researchers, which might encourage overworking.
Sustainability
Sustainability is an aspect that should be included and highlighted in every aspect of modern society in our opinion. Hence we have chosen sustainability as one of our core values. To our team sustainability means constant discussion about ethics and decisions based on these discussions while keeping the UN Sustainable Development Goals (SDGs) in mind. See our Sustainable Development Goals page for SDGs which we particularly wanted to emphasize. To decrease consumption and the environmental impact of our project, we always considered when buying items if we actually needed the item and which option would be the most sustainable. For example, we chose to order organic team hoodies that are more environmentally friendly than the ordinary ones due to the lack of pesticide, chemical and fertilizer use. We dropped the idea to detect MRSA from milk and meat after it raised ethical discussion about if we want to focus on a solution that promotes meat and milk production and consumption, even though in the end, the solution might have improved the overall health of the livestock. We also take care of the biosafety of our project by disposing waste correctly, ensuring that everyone working in the laboratory is following biosafety work practices and making our detection system cell-free to minimize the risk of spread of genetically modified organisms.
Inclusivity
We want to make our project and the fruits it bears as inclusive and accessible as possible for everyone. Our Wiki was planned keeping accessibility in mind - we made it more readable for example by using colour contrast, an accessible font and alternative texts to allow screen readers to read them. In addition, we have kept inclusivity in mind in other project sections, too - from forming a team to planning of proposed implementation. Read more about the inclusivity of our project from our Diversity and Inclusion page.
Cooperation
Teamwork and cooperation with other research groups or agents forms the key to progress in science. Teamwork and cooperation requires you to get along with different kinds of people and learn to appreciate our differences that help to make science diverse and develop it further. We are open-minded and welcoming to everyone, we respect each other and listen to everyone’s opinions. We help each other and do not leave anyone in trouble. We communicate kindly also when giving and receiving criticism. We express our gratitude and give deserved credits to other iGEM teams, research groups and agents and help other teams as much as possible.
In recent years, the COVID-19 pandemic and the crisis in Ukraine have demonstrated how vulnerable our economic system is towards changes in supply and how it fails to secure food availability, especially in low-income countries (World Bank, 2021; World Bank, 2022).
In addition to pandemics and wars, plant diseases pose a threat to global food security, especially now when globalisation and climate change affecting plant-pathogen interactions and their geographical distribution are actual and realistic (Elad & Pertot, 2014). Plant diseases are often an undermined risk to food security, which is not widely understood in Finland since historically, the plant disease situation has been steady so far (Natural Resources Institute Finland n.d.). Even though the plant disease situation in Finland has been good so far, unfortunately, it is not the case globally. For example, Panama disease, also known as Fusarium wilt, is a fungal disease with no cure that threatens the global banana production unless necessary precautions are taken to prevent its spread (Siamak & Zheng, 2018; Australian Government. Department of Agriculture, Fisheries and Forestry, n.d.).
Climate change alters the global plant disease situation, also in Finland (Elad & Pertot, 2014; Natural Resources Institute Finland, n.d.). Its consequences, such as elevated temperatures, drought and increased carbon dioxide concentration in the atmosphere change the interactions between plants and their pathogens (Elad & Pertot, 2014). With our project, we want to highlight food security and the diverse and often unequal effects of climate change on it and promote knowledge around plant diseases to the public.
We decided to focus on detecting plant diseases since early detection of plant diseases could help to prevent crop losses when there are effective and easily laid-out countermeasures against the disease according to the farmers and researchers we contacted (See Integrated Human Practices). In addition, it might also help to decrease pesticide use according to Marja Jalli (See Integrated Human Practices). Pesticides are often used excessively as precaution to avoid crop losses and lost profits. Pesticides cause health problems for humans and harm the environment and other non-target animals, such as birds and fish, and also might contribute to loss of pollinators and other insects, which in turn forms another threat to global food security (Aktar, Sengupta & Chowdhury, 2019; Connolly, 2013).
The laboratory techniques currently used to detect pathogens, RT-PCR and ELISA (Glasa, Hančinský, Šoltys, Predajňa, Tomašechová, Hauptvogel, Mrkvová, Mihálik & Candresse, 2021), are laborious and expensive and in addition, require specific equipment and professionals to perform the test. ELISA also may experience problems with recognition of different viral strains and cross-reactions of antibodies (Rubio, Galipienso & Ferriol, 2020).
To make our detection system more accessible, cheaper and easier to use than currently used techniques, and also safer, we based it on modular toehold switches and cell-free reactions. The cell-free nature of our detection system allows an easy user experience as it doesn’t need any special laboratory equipment or personnel but instead can be done easily on-site. By using cell-free reactions together with following biosafety guidelines, we take care of our responsibility to not release any GMOs or other harmful substances to the environment. Toehold switches are hairpin RNA molecules containing a start codon and ribosomal binding site in their stem-loop. The modularity of the detection systems allows the implementation of the system for different pathogens, enabling global use. Modularity of the system lies in the interchangeable toehold switch sequence that targets a trigger RNA molecule specific to the plant pathogen. Additionally, we aimed to make the detection system paper-based to make it easier to store and thus more accessible for farmers all over the world.
Synthetic biology is a multidisciplinary field that combines the knowledge of different biological fields and engineering principles to produce organisms with new abilities by means of genetic modification. Synthetic biology might revolutionize the way we look at social problems, such as climate change or food security, by providing new technological solutions. However, it creates risks to the environment and specific social groups, such as small-scale farmers and indigenous people. Potential harmful impacts include transfer of genetic material to wild-populations, negative economic effects on small-scale farmers and policymakers, scientists and industry being distracted from addressing the deeper underlying causes of biodiversity loss. (European Environment Agency, 2021.) One could also argue that there lies a risk in technological innovations aiming to improve a societal condition when this condition is actually the result of unsuccessful political decisions.
To decrease the harms associated with synthetic biology, we were determined to focus on cell-free systems that avoid the problems common to the use of living genetically modified organisms, such as spread of genetically modified organisms to the farms. Cell-free systems provide the necessary translational machinery for production without living cells that are able to spread and mutate. We prevent genetically modified organisms used for producing the detection system from spreading outside of the laboratory by necessary precautions, such as correct waste disposal.
We are committed to following the research ethics code, Responsible Conduct of Research (abbr. RCR) approved in Finland (Varantola, Launis, Helin, Spoof & Jäppinen, 2012). This means that we do not manipulate our results, obey the laws of Finland and the European Union and conduct our research responsibly among other things.
See our safety page for further discussion.
As a relatively novel team, we lack established financial and research networks and necessary tools that would help our team to make our project be more sustainable and incorporate diverse aspects to it. For example, we would have liked to estimate the environmental impact of the product and its production process and compare it to other detection systems to see its pros and cons. We think that broad environmental evaluations should be part of every designing process for new technological innovations as technology always comes with a cost.
Travelling from Finland to the conference in France by other means than flying is difficult due to the geographical position of our homeland. Flying by plane is the fastest and cheapest, yet the most polluting travelling option whereas travelling by train is costly and time-consuming and additionally, requires a cruise to Stockholm or another city where it is easier to take a bus or a train to Middle Europe. On top of that, cruises are not an environmentally friendly option either - they pollute the air and the sea. We would have liked to travel more sustainably but due to the financial situation of our team, we were forced to travel by planes. To diminish the emissions, we selected direct flights from Helsinki to Paris. We hope that the future teams in Finland and elsewhere ponder on choosing the most sustainable travelling option to Paris or even ponder whether it is reasonable to travel there due to environmental reasons.
Our human practices work had a significant impact on our project. Throughout the year we had many interviews and discussions with professionals and stakeholders and especially the wet lab and dry lab aspects of our project were heavily influenced by these discussions. Our team values and ethical discussions within the team were also an important part of human practices that we integrated into our project.
On this page, we elucidate how our human practices work influenced and shaped our project from an initial idea to where we are today. This page is divided into three main parts; ideation and design, impact on society and final implementation. Under these headlines we have summarized the discussions we had with professionals in both academia and in agriculture, and how each discussion has formed our project.
We started to ideate our project based on our team values that were established earlier. Discussions about sustainability were held during the ideation of our project, and we discussed ethics and the possible positive or negative impact our project would have. For example, after a discussion about ethics we decided we should not have a project subject that promotes or improves meat and milk production. Even if the solution would improve the quality of the animals' health or the quality of the final product, we do not want to promote meat consumption. This is also one of the reasons we chose to focus on a solution that would solve a problem relating to agriculture.
It was important for us, that every team member's opinions were heard in the ideation-phase, to maintain the motivation and wellbeing in our team. We held wellbeing days to promote team spirit and get to know each other (Fig. 1 and 2). To the best of our knowledge, we also maintained a safe space during our discussions so that everyone could say their opinions freely without being judged or belittled.
During the ideation and design of our project, we also asked for advice from multiple experts and professionals. This was to ensure that we were going into a sensible direction with our project design, as well as to keep in mind what would actually be a realistic undertaking for us.
Discussions with experts were a crucial part of our project design and ideation, and influenced our project tremendously.
In the ideation phase of our project, we had many potential leads for a problem we wanted to solve, and we contacted different experts to learn more about our problem and whether our approach would be effective (Fig. 3). One of these connections was Jukka Hytönen, an Associate Professor at the institute of Biomedicine at the University of Turku. We asked him about the possibility of detecting Lyme Disease biomarkers from sweat. Although we ended up with a different project topic, these initial connections to professionals helped us to shape our project and mindset when searching for the best solution. It also strengthened our will to continue with the topic of developing some form of detection system as our project.
After an intense brainstorming phase, our team decided to shift our focus on creating a cell free detection system. We got inspiration from some earlier iGEM projects, such as team CSMU Taiwan 2020, who used toehold switches for the oral detection of cancer and team EPFL 2019 who showed in their project that toehold switches can be used to detect targets in the cell-free OnePot system.
As we came up with the idea of detecting plant viruses, we approached Kristiina Mäkinen, the group leader of the Plant-virus interactions research group of the University of Helsinki, to ask about potato virus A (PVA) which is the main focus of their research. Discussion with her led us to focus on detection of potato virus Y (PVY) that according to her, might possess a bigger threat to potatoes than PVA. With Mäkinen, we also discussed the possibility to detect the plant siRNAs instead of the virus genome using toehold switches. We explored this idea, but eventually decided that there was not enough previous studies done regarding toeholds and whether it would effectively detect small, 20 nucleotide RNA fragments like siRNA, and we eventually decided to move forwards with detecting pathogen RNA instead.
When doing research on PVY detection, we stumbled upon an article “Decentralizing Cell-Free RNA Sensing With the Use of Low-Cost Cell Extracts” by Arce and colleagues (2021). In this study, the researchers detected Potato Virus Y with toehold sensors. We contacted the corresponding author of the article, Fernán Federici, to ask for their approval to utilize their study in our project as a basis for our project. We also discussed ideas to further develop their project. After the discussion with Federici we decided that the subject of our project is the detection of potato virus Y or other relevant plant pathogens.
We started to explore ways to expand on the work Arce et al presented in their article (2021). We contacted Michael Burgis, a team member from last year’s grand prize winner team, Marburg. He offered insight on how we could meet the novelty requirements of iGEM. We had multiple meetings and email contacts with Burgis during the ideation and design phase of our project. These discussions led us to explore and compare different reporter genes we could use in our design.
We also started to explore the possibility to use the PURE system (Protein synthesis Using Recombinant Elements), a commercial cell-free translation system that EPFL 2019 team also used in their project. PURE system would be very useful for us, since we have quite limited time for our experiments. PURE system is however, quite expensive. We contacted Dr. Tuomas Huovinen from the Department of Life Technologies in the University of Turku for advice on how we could better fit the project to our financial resources by using self-made lysates instead of PURE. He also directed us to Anssi Malinen, who has more experience with RNA assays. After feedback and discussions with both Burgis and Huovinen, we decided to proceed with making our own translation machinery from E. Coli cells. Burgis gave us an idea that we could compare different lysis methods.
After the discussions with Huovinen and Burgis, we came to the conclusion that our project would not be novel enough if we try to optimize the system for PVY detection presented by Arce et al. We instead took a few steps back and started to look for other potential pathogens that we could detect with a cell-free toehold switch mechanism. We started to look into the Barley Yellow Dwarf Virus (BYDV), which is a virus infecting the most cultivated crops in Finland, and is one of the most widespread and serious viral diseases in the world. Later in the fall we re-evaluated our resources, and decided to look into the PURE system again, since we had gotten very minimal results from our own lysate experiments. We reviewed our earlier discussions with Huovinen and Burgis and decided to buy one kit of PURE system, in hopes to get better results from the laboratory.
To optimize the PVY detection system we wanted to try out a few different reporters than those Arce and colleagues presented in their study (2021). Even though we ended up creating a detection mechanism for BYDV, we still wanted to experiment with some different reporters. We contacted Dr. Anssi Malinen from the department of Biochemistry in the University of Turku, who gave us the mScarlett and mScarlett-I fluorescent reporters that they had in their laboratory.
Aditya Jeevannavar, a bioinformatician and data analyst at the department of biology in the University of Turku, helped us with the bioinformatics part of the project. He was already familiar with iGEM, and we introduced him to how iGEM is done in Turku. Jeevannavar helped us through some first hurdles when using and installing the NUPACK python module for designing the toehold switches. He also gave us the initial idea, that we could make our system modular, and easily modifiable for the detection of different pathogens. His help was much appreciated in the early design phase of our project, and helped us move forward with the struggles we were having with NUPACK.
From the beginning, it was clear to the whole team that we wanted to create a project that would have an actual impact on society. We spoke with multiple stakeholders and experts in agriculture to broaden our knowledge around the problem we are solving, as well as to steer the design of our solution to a direction that would best meet the needs of different stakeholders.
We contacted farmers to hear how plant pathogens affect their daily lives. We wanted to find out if there is truly a need for an easy, on-site detection method and what we should take into account when designing our system.
First, we contacted some farmers who want to stay anonymous. In their farm, they grow mainly berries and vegetables. They answered that there would indeed be a market for a simple pathogen test. In their opinion, however, the detection system would only be worthwhile if it does not require too many samples. The detected pathogen should also be one that there are countermeasures against, and the countermeasures are easily laid out so that the farmers can take action.
We wanted to get some more hands-on knowledge on how the early detection of plant pathogens could actually benefit farmers. We had an interview with farmer Petri Riikonen, who farms mostly wheat, oat, rye and barley. He told us that the price paid for producers for crops planted on the fields (such as wheat and barley) is so low in Finland, that the price of our assay would have to be very low for it to actually benefit the farmers. Riikonen also confirmed for us from the farmers’ point of view, that the early detection of pathogens could help to reduce pesticide use.
To get a different angle on farming, we had an interview with Anne-Marie Tuikka, an urban gardener in Turku. She is growing tomatoes, beans, kale, carrots and apples among other things (Fig. 4). The discussion revealed to us that there is definitely interest for a pathogen detection assay amongst urban gardeners, too. They are often very passionate about their plants and take good care of them, and confirming a certain pathogen infection might be crucial to save the yield. We also discussed the future of urban gardening, and how it could become a central factor in securing nutritious food in times of crisis.
Discussions with farmers led us to shift our project from BYDV more towards creating a modular system, where the pathogen-detecting part could be switched and the system easily modified for detection of multiple different pathogens around the world. Moving forwards we would hope to especially target pathogens for which effective countermeasures have been developed. This would maximize the value of our bioassay for the user.
We also wanted a professional opinion on whether the early detection of plant pathogens could actually have a positive effect on food scarcity and decreasing the use of pesticides. We wanted to know if there are any countermeasures after a BYDV infection, and whether there would be any other, better suitable pathogens for our system.
We contacted Johanna Santala who is a laboratory manager in the Finnish Food Authority. We wanted to learn more about the countermeasures after a BYDV infection. Santala did not mention any user-friendly way to fight BYDV after the infection is present. Removing the infected plants would be an option, but it is rather difficult when the farmed crops are on an open field. Thus, diagnosing the diseases of greenhouse-grown plants might be more useful. For example, tomatoes, cucumbers and bell peppers have economically significant plant diseases such as tomato brown rugose fruit virus and cucumber green mottle mosaic virus. After the discussion with Santala, we decided to include more greenhouse-plant infecting viruses to our toehold-switch library. In addition to tomato brown rugose virus and cucumber green mottle virus, we also included pathogens such as pepper mild mottle virus and papaya mosaic virus. Read more from our Design page.
To find out whether the pathogen we had started to work with, BYDV, would really be best suitable for the detection system, we contacted an agronomist working at the University of Helsinki. We wanted to know if the early detection of plant pathogens could improve food security by decreasing crop loss and if including plant disease screening into the cultivation process would be a realistic and a reasonable opportunity in terms of resources. According to them, early detection of plant pathogens could improve food security but only for preventable or curable plant diseases. In the case of BYDV, the only known prevention method is the destruction of aphids transmitting it. In their opinion it might be more useful if it is targeted for the detection of pathogens in some higher-value plants, such as some garden plants.
We also had a meeting with Marja Jalli, a group leader in the Natural Resources Institute Finland (LUKE) and discussed the potential countermeasures against BYDV and our project in general (Fig. 5). We asked her if she knows any alternative methods on how the plants can be treated after a positive BYDV signal, and if she has any insight on whether it would be a good pathogen to detect. According to Jalli, the BYDV is becoming more prevalent with climate change and might be even more relevant in the future. She didn’t have any additional countermeasures, but since BYDV is transmitted by aphids, she gave us an idea that we might be able to detect BYDV from crushed aphids instead of the plants. She also said that an easy detection method could work in reducing the use of unnecessary pesticides. She directed our questions about potential other pathogens to Erja Huusela, who is an expert in farm crops. Huusela, from the Natural Resources Institute Finland (LUKE), told us that oat sterile dwarf virus and wheat dwarf virus could be potential pathogens for our detection system. After the discussion, we decided to include wheat dwarf virus in our toehold switch library. Read more from our Design page.
After extensive discussions with stakeholders and experts, we came to the conclusion that BYDV might not be the best target pathogen to detect in our case mainly due to the lack of countermeasures against it. This realization highlighted to us the importance of Integrated Human Practices.
Including Integrated Human Practices already in the brainstorming phase not only helps you to estimate the influence of your project better and but also prevents the project from coming to a dead-end. After this realization, we focused more intensively on Integrated Human Practices and consulted stakeholders and experts with a lower threshold than before.
Due to the time restrictions, we still decided to continue working with BYDV even after the realization that it might not be the best target pathogen in our case. We decided to still make our experiments in the laboratory using BYDV. However, the extensive discussions with stakeholders and other professionals led us to shift the focus of our project from detecting BYDV to creating a modular system for the detection of plant pathogens.
In relation to this, we decided to create a library of potential target pathogens for our system. In our dry lab, we created toehold switches for some plant pathogens that we thought, based on the discussions with professionals, would benefit farmers around the world. We also got some potential target phytogens from iGEM Patras team from Greece, which we included in our toehold switch library.
From the very start it was clear to us that we want our project to have impact not only on the local scale, but also globally. To estimate the impact our project could have globally, we looked at the United Nations Sustainable Development Goals (SDGs). You can read more about the SDGs and how they are implemented in our project in our Sustainable Development Goals page.
As a part of our collaboration with two iGEM teams, Patras and TecCEM, we had a meeting with three SDG experts (Fig. 6). Alejandra Rentería, Jr consultant in social responsibility and specialist in corporate volunteering, Ana González Castillo, and Karla Muñoz, a consultant in educational experiences and coordinator of the Itinerant MUSEUM of the SDGs, are from Kueponi Consultoría, a company that offers consulting in sustainable strategy and responsibility. Each iGEM team presented their project and we discussed what SDGs would best align with our project, and what more we could do to have a better global impact with our projects. The discussion helped us to better communicate our project to the public and think about what aspects of our project to highlight. The experts also gave us a tip that we could consider dividing the SDGs we are addressing into primary and secondary SDGs based on how well they fit our project. They also said to look more into the details of each SDG and also focus on the smaller subgoals within them.
The discussion with the SDG experts confirmed to us that our project does not only have local, but also global impact.
After the discussions with stakeholders and professionals it became apparent that we will have to carefully think about the implementation of our project. A few aspects that were brought up in many of the discussions with stakeholders were the simplicity and cost-effectiveness of our detection assay.
We wanted to create an assay that could be used on-site by the farmers themselves. While the steps required to conduct our assay are fairly easy, we realized quite early that the amplification of the pathogen’s genetic material might be difficult to conduct on-site. In a study by Pardee and colleagues (2016) they successfully detected NASBA amplified Zika Virus with a toehold switch RNA sensor. With NASBA (Nucleic acid sequence-based amplification), only one temperature is required for the reaction, unlike more traditional amplification methods, such as PCR. We looked into NASBA and decided to include it in our proposed implementation.
To make our final product more user friendly we decided that we would implement our cell-free detection on a paper by freeze drying. This way, it could be stored at room temperature instead of freezers, and the shelf-life would be longer. Cell-free systems have previously been implemented on paper by for example Pardee and colleagues in 2014.
In the final implementation of our detection system, we also have to consider biosafety issues. The cell-free approach ensures that there should be no biosafety risks in regards of GMOs being released to the environment, but we still wanted to know how the legislation in Finland could affect our project. Thus, we contacted a regulatory authority who wants to stay anonymous. According to them, our cell-free detection system itself does not possess a risk for environment and it is not regulated with a gene technology law. However, we should evaluate possible risks related to pathogens, toxins and allergens used in reactions - like in any other project performed in the laboratory.
