Difference between revisions of "Team:Heidelberg/Sandbox"

iGEM Paris Bettencourt has set up a visual databse that should help various iGEM teams collaborate and find common ground. In that database all teams can enter techniques, keywords, organism and many more thev are knowdledgeable in or have been working on. As common dots are connected automatically, it's easy so see, whom to ask for a collaboration.
Though we came a little late to the party, we really loved the idea and hoped, that the database has helped various teams!

"Rhizi is an open-sourced web of knowledge where nodes are sources of information (e.g. scientific articles, questions, blog posts) and edges are the links between them. The goal of Rhizi is to create information rich links between knowledge, open questions and ideas, through encouraging users to vote, comment, and create new relationships."

It’s done. We’ve finally decided upon a logo. It’s beautiful, it’s blue, it’s fishy *wink*. The next step was to choose a color scheme and a general style for the wiki. As we feared that our own ideas might be too similar we thought of asking a broader public how they would design a website based on our logo. In order to do so, we headed to the ’Neckarwiese’. During summer, a big part of Heidelbergs population decideds to go there and enjoy the sun, have a BBQ or just relax – so we caught them off guard.

We have had prepared a little presentatio with which we introduced them to iGEM and Synthetic Biology. Afterwards we explained them what we planned on doing, showed them our logo and asked, how they would design a website, based on what they’ve just heard. The general consens was to go for a blue theme, maybe add a little algae green and generally stick to maritime iconography. Unexpectedly we actually met someone who knew his stuff: Natalie, a student of the history of arts from Berlin. She gave us useful advice on how play with the different colors, what to avoid and even added a little touch of history to it. Lucky catch!

With fresh ideas we headed back to the lab and continued our experiments, being envious of all the people that could continue to sleep in the sun.

Synthetic biology - engineering life with its most fundamental units by using DNA BioBricks and other modularly combinable parts, has a potential beyond scope and can improve the quality of life for everyone and mankind as a whole. The ultimate goal of researchers in synthetic biology is not only the understanding of life itself and how it functions, but applying the acquired knowledge to make a change within their community.

To investigate the current state of the research and its acceptance in society, we talked to scientists and asked them how their work has influenced their community. Nonetheless, it is of absolute necessity to include the entire society. We decided to do this by organizing a panel discussion evening dedicated to the topic 'Synthetic biology - Bricks for a healthy life?', i.e. synthetic biology in medicine.

As research in general and especially synthetic biology relies on a community, on interaction between researchers and the exchange of ideas and expertise, we asked experts and researchers from different fields to join us for this evening and we distributed flyers and placards to invite the broad society. However, we wanted to go a step further: The panel discussion was not limited to the audience in Heidelberg, it was simultaneously translated from German to English and broadcasted it via a live stream.

Despite the great enhancements synthetic biology can achieve, engineering with building blocks that are so close to the basic principles of life itself comes with a range of ethical questions and security precautions to consider. We see it as our immanent responsibility as iGEM team to address these questions and to take concerns very seriously. Hence, we invited Prof. Dr. Axel Bauer, who has been member of the German ethics council for several years and Dr. Joachim Boldt who works as assessor for the German ethics commitee for ethical implications of synthetic biology. Both of them are highly involved in the field of medical ethics also due to being professor for this subject. In order to review the safety concerns, we were very glad to have Dr. Harald König, who works at the Institute for Technology Assessment and System Analysis, as our guest.

Politics and law play a very big role when discussing the application of synthetic biology in real life. Researchers need to obey the juridical boundaries and on the contrary the legislature has to react to novel developments and find a compromise between many different opinions, some being more conservative, others more progressive. To reflect this interweaving, we additionally invited local politicians, such as Prof. Dr. Nicole Marmé who is member of the city council of Heidelberg. Dr. Stephan Brandt, chairman of the department for Biotechnological Innovation, Nanotechnology and Genetic Engineering, investigates how laws need to be adapted to the most recent findings in synthetic biology and genetics and we are very glad he joined us for this evening. Finally, the topic that stands in the center of this evening is, after all, research in synthetic biology. For that reason, we asked Dr. Dirk Grimm, who works on the CRISPR-Cas system and who knows the cutting edge developments to be the scientific representative in the panel.

After a lot of planning, organization and set up of all the required technical equipment (thanks again to Dr. Jens Wagner from the Physics Department), the discussion evening could start with a brief introduction to the topic given by Jasmin and Max from our team. As we wanted the main part of the evening to be an open discussion, we deliberately made the introduction very compact. For the remaining 1.5 hours of the evening, Tim navigated our guests, as well as the audience through the discussion.

The involvement of the audience was amazing, proving that this topic is indeed highly interesting to a large part of the society. Most eminently, we were very happy that additional to the approximately 100 guests that joined us physically in our institute, we had almost 400 viewers online, among them also other iGEM teams, such as iGEM Team Cambrige (link). Besides watching, our followers on twitter were also very engaged in asking questions that were then addressed by Tim and the invited experts.

The topics discussed ranged from green to red biotechnology and were contemplated in a highly interdisciplinary way (with the focus on medical applications nonetheless). Besides, and in correspondence to the initialization of the “Community lab” track in iGEM, we addressed biohacking and the implications of it on society, the scientific community and the communication between the two entities. Question were asked about ethical problems and implications of in vivo and in vitro technologies, but also about dreams and wishes of the scientists regarding future developments in this field. The question iGEM team Cambridge nicely summarizes the last part of the discussion: “How can synthetic biologists better communicate their research to the public?” This includes the role of politicians and law makers, as well as the responsibility of everyone who is involved in research to put a focus on the outreach and the interaction, not only with the scientific community, but also with the broader public.

So far, many iGEM teams have organized discussion evenings and invited people from the broad society to join an interdisciplinary evening. This approach is great and helps a lot to improve the communication between scientists and the public. Nonetheless, there are still barriers to overcome:

• The interested population of one city is not representing the entire society. Hence, we decided to provide the opportunity to join us online via live stream. This should not be limited to watching the discussion passively, that is why everyone could ask questions via twitter by #askigemheidelberg. These questions were then shown in the discussion, so that our invited guests could reply or reflect on them.
• The lingua franca in research is English, however not everybody is capable of speaking English fluently. Therefore, we deliberately chose German as the language the discussion was held in. This way, everyone who was interested had the possibility to follow. In order to keep the event international and also understandable for those who watched online, we translated the event simultaneously to English.

The use of restriction enzymes is no option for cloning if functional nucleic acids contain the recognition sites for enzymes used in standard restriction cloning, as described in RFC 10, or other suitable restriction enzymes. Although techniques using Type IIs restriction enzymes like Golden Gate assembly do not leave scars after cloning, a Type IIs recognition site within the functional RNA sequence may greatly reduce the efficiency and fidelity of a Golden Gate based cloning attempt. Therefore, the method of choice for reliable assembly of the sequences into a standardized vector has to be based on homology at the interfaces of the parts to be fused. As the DNA templates for functional RNA are commonly synthesized de novo, the addition of overhangs upstream and downstream the functional sequence does not appear to be challenging. Equally those extensions can be added during PCR with primer overhangs.