SynAesthetic biology: science without sight

• Blista
• Visit at Blista
• World of microbiology
• Making movement audible
• Debate
• Taking the eye out of science

iGEM-Team Marburg meets Blista pupils

In one of our iGEM-meetings a discussion about different analysis techniques and the information that can be gained started. We came to the conclusion that for example the UV signal created from an HPLC run does not necessarily contain less information than a picture taken using a fluorescence microscope. Nevertheless due to the more abstract nature it seems to be less reliable than the actual picture which rather makes you feel like you can actually “see” the real facts. Thus we realized what high value and how reliable we estimate our visual experience to be. In a more general sense it is remarkable that even in a field of science like synthetic microbiology which subject of research is not directly accessible by our senses, the paradigm “true means visualisable” is still maintained. Due to the strong influence of this hypothesis on the way research is conducted we feel the need to question this hypothesis. Hence we wanted to create a “human practice” project that allows us to combine our aim of getting others interested in synthetic biology while at the same time consider the fundamental epistemological question of the relation between visual experience and knowledge of nature.

In Marburg is the only school in Germany for visually impaired people where they can reach their Abitur, the final exam of secondary education in Germany. What is really impressive to see is how much their syllabus are just like that of any ordinary school. The pupils even get the chance to participate in practical courses as part of their biology or chemistry classes. Of course there are special safety precautions as they for example do all their experiments in a basin to avoid danger from spilled chemicals. Furthermore they use special equipment, e.g. an “optophone” that transforms a colour into sound so that the pupils can observe colour changes.For these purposes the school employs specially trained teachers that teach only small courses of up to 12 pupils. This also means that they are able to individually support each pupil. Since these pupils do not rely on their visual experience as much as we do we were interested in finding out how they approach certain problems.

Visit at Blista

To get an impression of their daily lessons in school we supported them during their preparations for the Abitur exams and we visited some of their lessons. What we learned is that even if the pupils might be slower in some regards they learn basically in the same way as pupils do at an ordinary school. Obviously there are differences in the way things are taught as for example that there is no black board but everything is printed on a special printer in Braille. Furthermore the pupils use their laptops much more as they have a device connected to them that in combination with a screen-reader software enables them to read texts displayed on their laptop. But it was interesting to see how critical they were towards the facts they were taught. They had many questions that they asked until they really understood instead of learning by heart. On the other hand we also wanted to draw their interest towards the field of synthetic biology. That is why we invited them to visit us in our lab to do some experiments. We started with a presentation as an introduction to the topic synthetic biology which already led to some discussions that indeed showed the great interest of the pupils in our work. Afterwards they did three experiments in small groups that cover basic topics of biochemistry. In this context they learned how to use a pipette and tried to find the mean error of them. Furthermore they learned about the necessity of sterile working and measured a growth curve of bacteria. While we had lunch together in our refectory the pupils asked how we use these techniques in our research. To conclude the day we introduced them to the iGEM competition and our project. The pupils were really interested and impressed by the possibilities synthetic biology offers. In our case especially by the capability to treat such a severe disease such as lung cancer.

The Blista pupils in the lab.

Blista pupils reconnoitre the world of microbiology

A second visit of the pupils was dedicated to microbiology. There was the opportunity of pouring agar-plates and an introduction on how organisms can be cultured using these plates. As an example the pupils could compare how many microorganisms are present on washed and unwashed hands. The pupils were especially interested in preparing the plates because they already learned before how they are used but never had the chance to actually experience how they are made and used in practice. The last experiment dealt with safety aspects of microbiological working. The pupils should think of and got the opportunity to test different methods of sterilizing a liquid sample either by chemical or physical means for example using acids, bases or detergents. Afterwards some of the liquid was plated on LB-Agar plates and incubated over night at 30 °C in order to show which methods were successful. The pupils became aware of the responsibilities scientists have. In a discussion at the end of their visit we recognized that their opinion regarding synthetic biology was a very positive one contrary to our expectation. Although there is of course the danger of misuse still the possible advantages are predominant in their eyes. One girl told us she realized that she does not have to be afraid of bacteria when she saw a documentation on the possibilities of biotechnology and synthetic biology.

But the end of that day does not mean the end of this cooperation.

The Blista pupils discover the world of microbiology in the iGEM lab.

Making movement audible

During the preparation of the experiments for the Blista pupils the question how science could be made visible for visually impaired people was a constant companion. Hence we brood on a possibility to translate bacterial movement into an acoustic signal. A possible advantage of this could be that other information could be gained that have so far been overlooked. The transformation of movement into sound can be done using optical tweezers and dark field microscopy. The optical tweezers are used to keep the cell which movement is meant to be measured in the observed area. This is necessary because otherwise the cell would leave the observed area so quickly that no exact measurement would be possible. If only one LASER-beam is used to keep the cell in place, it can still move around this fixed point. This movement is recorded and if the cell’s displacement from its original orientation is plotted against time, a periodic function can be observed. The frequency of this function can then be interpreted as a sound.

Taking into account all that our work with the visually impaired pupils has shown us, we learned that our visual impressions can lead us to believe that certain results are very reliable when more doubt would be necessary. Furthermore they can lead to misinterpretations that are deducted from our everyday experience even when it might not be applicable.

Synthetic Biology boon or bane

As one part of the cooperation with BLISTA we organized and held 90 minutes of an interactive lecture. Our aim was the presentation of Synthetic Biology especially to promote iGEM and our project SURF. The pupils are in the 11th grade and have only basic knowledge about Synthetic Biology. Our idea was to give the students background information, do interactive group work and end with a debate about the advantages and disadvantages of Synthetic Biology based on recent issues in the public concerning Synthetic Biology.

The main idea was to get an idea about the knowledge and opinion of Synthetic Biology in the public. We had the idea for this cooperation with the BLISTA because we are doing lots of experiments where we can´t see what we are doing. We work with models to visualize molecules, atoms and whole pathways. The interesting point was to explain these things to visually handicapped people and talk and discuss with them about complex topics. During the seven month of our cooperation we asked ourselves how we can explain students who aren’t able to see facts that we can’t even see on our own. Beside this, we wondered if the students would have any concerns, ideas or questions about Synthetic Biology that we did not consider so far.

We started the lesson with a short presentation about Synthetic Biology in general, then we switched to iGEM and our project SURF. Afterwards we explained the pupils a controversial discussed issue that should serve as a base for the following debate. The issue was based on a recent publication that reports about genetic modified tiger mosquitos to fight the dengue fever (Subbaraman, N., Science snipes at Oxitex transgenic mosquito, Nature Biotechnology, 29, 2011). This mosquito is one of the vectors for the virus. Since there are no medications against dengue, the tiger mosquito is a huge threat for humans living in areas where the mosquito is settled. Due to the climate change this mosquito is spreading and so dengue does. Scientists have created a mosquito line via genomic integration which kills all descendants of a breeding if they are not treated with tetracyclin. Successful field trials have already been performed, although there are also several risks that have to be considered though.

Before starting the debate we divided the pupils into two groups that should discuss the advantages and disadvantages of this field trial and Synthetic Biology in general. Each group had support by two experienced iGEM students for preparing the following debate. Afterwards one group was debating pro whereas the other was contra Synthetic Biology.

The pupils were very enthusiastic and there was a lot of discussion which was hard to moderate by the iGEM students. We also realized that the pupils had not enough background information and so they used from time to time stereotypes for their arguments (like it is done in talk shows). In general the topic of the debate was the ecological consequences of the GMO tiger mosquito and the ethical aspects of this issue as well as the dual use character. Nevertheless they also debated about topics like vitamin rice, insulin production, antibiotic development, gene therapy, usage of genetically modified organisms, bioweapons, long-term consequences and last but not least the dual use character in general. At this point we were astonished that the pupils have already got in contact to lots of different Synthetic Biology aspects.

In the end there was a vote for to get a general idea about their opinion. The pupils could choose between three points:

1. Synthetic Biology has no risks and should be applied whenever there is a chance to
2. Synthetic Biology brings new opportunities though the dual use should be kept in mind
3. Synthetic Biology is a risk to humankind and should not be applied

Most of the pupils voted for choice 2 (14), a few were strictly against (3) and a few strictly pro (2) Synthetic Biology. Remarkably one pupil asked “Can I abstain from voting because I feel that I am not enough informed by the media and by the politicians though the iGEM Team changed it in a positive way today”. After this comment more than half of the class followed her opinion.

This shows that there is still a long way for Synthetic Biology to be well accepted in the public. iGEM is a good way to inform the public and we hope that we did our best. Afterwards the teachers of the class were very enthusiastic about the lecture and they asked us for further cooperation in the future. The iGEM Team Marburg agreed and we hope to have further interesting projects in collaboration with the BLISTA.

The discussion about synthetic biology with the Blista pupils.

Taking the eye out of science

During our time with the BLISTA pupils we realized what problems they have to face during their everyday life. We are very visually focussed thus our research is also under this focus. For example even this year’s noble prize for chemistry was awarded to three scientists that found a new method to make small structures visible illustrating the paradigm true means visualisable that is still maintained even in a field of science which subject of research is not perceivable by our visual sense. Even our facilities are composed to suit these needs. For example even though the colour of pipette tips do not even have a colour anymore we still stick to the naming by colours instead of size. We realized that our biology buildings are not clearly arranged and how hard it is to find different rooms. On the other hand the visually impaired already started to adapt to this visually focussed world. For example the colour changes that are used to indicate pH changes can be transformed into sound. But what was even more interesting is that if you are looking for alternatives you even see possibilities where you would not expect them. The autoclave tape for example we always thought to deliver only visual information a blind pupil found out that the shape of the tape changes during autoclavation. This can be transferred to other fields of our research as well. This makes us feel the social injustice even more precarious as there are obviously possibilities even when we are not exactly looking for them. So what could be possible if we actually try to integrate them? We thought about this topic and during several meetings we arranged our laboratory for the needs for visually impaired people. We only needed the simplest methods to reach that aim. For example by marking things with different surface properties that can be felt and thereby giving them the opportunity to find the things they need. We created a barrier free laboratory by removing all triping hazard. The presentations we gave became better adapted to the needs of the visually impaired . We also prepared the scripts telling them what to do in braille. While we started with slides that contained way too much text we learned that it is better to explain things and use only big schematic figures with high contrast. We learned that it is possible if we try to integrate visually impaired people into science. This is especially important as the effort we have to put in it does not only lead to more social justice but can also deliver a contribution to our research as those people that cannot or do not focus on their visual experience might find other information in methods that are already established as it was for example the case with the autoclave tape. From a juristic point of view impaired people should be favored if they have the same ability. But our observations show that this at the moment does not become reality as the facilities do not allow them to reach the same level of ability. All these considerations had also an impact on the way we approached our project. For example instead of only looking at bacterial movement we transformed these movements into sound. We tried to not focus that much on the visual based methods as we found that they suggest a certainty in fields where more doubt would be better.