Team:Kent/Human Practices

Education and Public Engagement


Our first public engagement activity, was aimed at educating pupils (16-17 years of age) at the Simon Langton Grammar School for Boys. We presented our talk on the subjects “Synthetic Biology and iGEM”, “Magnetotactic bacteria”. We were at the early stages of our project at the time of this event. It was extremely useful to see how the 'public' viewed our project ideas and how we could use these ideas to shape our project.



Here are examples of the questions asked by the pupils in each class:

Year 12 Physics class:
  1. What is a feasible time for a working and functioning product?
  2. How do you extract magnetic compounds?
  3. What are the sizes of magnetosomes/magnetite?
    • What are the differences between nanoparticles and microparticles?
  4. Did we come up with our own idea?
  5. How long does it take to produce a viable amounts of nano-particles?
  6. Are there other methods to make magnetite?
    • Other than biological method?
    • Why use biological method?
  7. How does magnetite clean waste water?
  8. Could we use magnetite to extract shrapnel from human body?
  9. Could we use hoverboards for travel with magnetite on roads?
  10. Are there liquid magnets? -> imaging application
  11. How powerful are the magnets?
  12. How does it feels to collaborate with people with different scientific backgrounds?
  13. What is the grand prize?
Year 12 Biology class:
  1. Why E. coli?
  2. Why not use organisms other than E.coli?
  3. Magnetosome - what role does it play? Why is it important to organisms?
    • How does this work?
  4. Are there organelles similar to magnetosomes?
  5. Why generate nano-magnetic using bacteria not other standard methods?
  6. What type of culture are the nano-particles grown in?
    • How do we optimize growth?
  7. What nutrients do we need to provide the media?
  8. What would contaminate our samples?
  9. How would the drug delivery work?
  10. Is solid state storage better than magnetic storage?
  11. Can it also be used to clear oil spillages in water?
  12. How does iGEM work?
    • How are we funded?
    • Do we receive supervisor support?
    • Do we aim to publish a paper?
  13. Method of extraction?
  14. How does it work?

We summarized all question into a venn diagram for easier analysis:

As expected, the physics students were focused on the applications side of our whereas the biology students were focused on the biological aspect of our project. Common questions asked by both classes was about the feasibility of our project in real world.

Upon reflection of this outreach it was indeed a valuable tool that allowed us to direct project and consider the chemical synthesis of magnetite nano-particles.

Following the outreach to A-level biology and physics pupils we decided to chemically synthesise magnetite to compare to the samples that proteins produced in order to intergrate the some of the central questions from the feedback we got from the pupils. This would allow us to expand our project to see if the nanoparticles differ in terms of size and shape.



We contact Dr Marc Williams from the University of Kent who is an expert on magnetic nanoparticles applications. Dr Williams completed his PhD on the uses of magnetic nanoparticles in chemotherapy. Together we looked at the methods and papers we had gathered. Dr Williams suggested to follow an ethylene glycol reduction method. This method was attempted unsuccessfully. We returned to Dr Williams to troubleshoot, he then recommended a co-precipitation method. This second method was successful and we produced magnetic nanoparticles. Therefore, talking to the expert has influenced how we approached our project, we were able to decide biological synthesis was preferred to the chemical synthesis because we have better control of the particles produced, it provides a renewable source.



Quantitative analysis of human practices - “Human practice-Bricks”


Introduction

Our main aim is to set a new standard for human practices with an approach that is unique. We hope to achieve this by introducing a new type of mathematical modelling called ‘Topic

Modelling’, which was is a Big Data approach invented just over a decade ago. As far as we know, according to Google and Yahoo search engines, no iGEM team to date has applied topic models to quantitatively analyze the context and the impact of their project as part of their integrated human practices.

Furthermore, we would also like to show that our novel modelling approach is a powerful and useful quantitative tool for iGEM projects. From this we hope to inspire future iGEM teams and show topic modelling has no limits by using them in their project as we live in an information age. For more information about our topic model and learn what topic mode is, please click here! (link to modelling page)

Results from our Topic Model


iGEM team Human practices/Policy and Practices

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Figure 1 shows the mapping of 15 topics which was computed by our topic model. The size of the circle indicates the probability of that topic appearing in each of the documents that were introduce to our model. The thickness and darkness of the lines connecting each topic is affected by the distance between each topic. As you can see shorter distance equals darker and thicker line and vice-versa for longer distance.

Human practice/Policy and Practice texts of all the teams from 2013 to 2015 were collected and there was total of 572 text files.

It shows that the topic with the biggest probability of appearing in each documents is the dark blue circle and it contains only 1 word, “communication”. Which essentially is its own topic and the distance with synthetic biology is quite far. This could be something that is expect due to either the general public still lacks understanding of synthetic biology or mode public engagement needs to be done for the scientists side. Communication can go both ways.

Seeing that the communication has strong connection (closest distance) with topic which contains the word team perhaps signifies strong collaboration betweens.

It should be noted that absence of the words “ethics” or “policy” might signify these are topics that are not very popular. Yet we also have to take into account that the input data are from 3 years back, where the rules for Human Practices were not so stringent, and teams mostly focused on just communicating their scientific ideas to the public. Possibly, future iGEM teams could explore these these further or do more under the more stringent iGEM rules in working on more novel ways to explore HP, thereby, enhancing the significance of SynBio in a grander societal context.

Several world problems that are popular among iGEM teams are: health, antibiotic resistance, cancer, energy, environmental. We can argue that iGEM has probably made an impact in these areas. Perhaps there are more areas which we can look at in the future, such as poverty, world hunger, etc.

‘Biosensor’ has been a popular topic in iGEM competition too, probably due to it being a concept that can easily be understood by the audience - to detect something and emit a signal in response.

Absence of the terms that are related to “economic” or “financial”, could signify that synthetic biology is still not economically feasible to solve certain problems. However with the exponential reduction of the cost of gene synthesis and sequencing, this might change soon.



PubMed entries with the keyword “Magnetosome”

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Figure 2 shows the mapping of 15 topics which was computed by our topic model. Abstract of 429 PubMed articles under the search keyword “Magnetosome” were scraped for the model.

This analysis was used to evaluate the science behind our project. Immediately it is interesting to look that the topic with the highest probability. Words like “genes”, “genomics”, “sequence”, “genome” are all related and expected to be seen under the same topic. However, the most interesting thing about this topic is the word “novel”. This is very good for our project because this indicates that analysing, sequencing, or genomic study of magnetosome are considered novel and needs to be explored. This topic has the closes relationship with the topic containing the words “magnetite” and “crystal” which could also mean it is novel.

The orange topic in the middle of the map tells that microorganisms such as magnetotactic and its magnetotaxis behavior is unique which was to be expected.

Looking at keywords, smallest purple circle at the left bottom of the map, the protein ‘mamK’ is the only protein that has appeared in our map and this topic suggests that it is a stable and a domain protein to work with. Importantly, non of our proteins is represented in the topic, suggesting that our project could represent an important unexplored area in magnetosome research.

iGEM team abstracts

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Figure 3 shows the mapping of 25 topics which was computed by our topic model.

Abstract of all the teams from 2013 to 2015 were collected and there was total of 693 text files. The presence of this topic “open community” and it being connected with the topic “iGEM” is very encouraging. It shows that teams are working towards democratization of biology, in lie with the iGEM organisation ethos of having DNA repository where everyone can submit a Biobrick and have access to it.

Yet again, problems popular among teams are antibiotic resistance, environmental problems, water pollution. This agrees with Human Practices/Practice & Policy topics, which is not surprising.

The word or terms related to “magnetic” is not there, which could possibly signify that iGEM Kent is solving a very novel problem.

PubMed entries with the keyword “Synthetics Biology”

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Figure 4 is mapping of 15 topics from PubMed keyword search “Synthetic biology”. Abstract of 9628 PubMed articles under the search keyword “Synthetic Biology” were scraped for the model.

Interestingly, the topic “cancer” appears here again, similar to HP topics, suggesting it is not only a popular subject for iGEM teams but also for the synthetic Biology community.

The red circle located at the right side of the map contains a topic of “organ regeneration” might implies that synthetic biology could be a promising field for this. In contrast with “cancer”, this topic is exclusive to synthetic biology researchers, possibly due to the time needed to work on such challenge.

Conclusion

In general, topic model has proven itself to be a very useful and powerful tool as our results show the area of magnetosome is a novel topic. Thus, our well integrated quantitative approach to human practices approach has feedbacks to our project and informed us where it is placed in current research and in the iGEM communities. It has also shown important areas that need to be discovered such as application of magnetosomes and ethics and policy for Human Practices. Our model has also shown popular iGEM projects and iGEM teams in the future can utilise the approach we pioneered to help choose their projects. For this reason, as an analogy to BioBricks, our results could be called ‘Human Practice-Bricks’.

HMM LDA is one of the algorithms that LDA topic model uses, and LDA is one of several several topic models. In this age of ever increase contents of information, it is exciting to wait and see what future iGEM teams will do with their topic models and larger sample of data. They could improve our/other topic models and produce better results. Hopefully, our efforts to HP using topic modelling shows that even at early stage is a powerful tool with growing potentials, and convince future iGEM teams that is newly opened door is worth walking through.





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