My iGEM Experience - by Ogaga Sim-Ifere

Having come to the UK from Nigeria when I was just 15, it was quite difficult as I had to adapt to a new system of teaching and learning. I had done several biology experiments both in my Nigerian high school, and in the UK during my A levels and as a medic, but none of these truly prepared me for what I was going to face in iGEM.

I was told about iGEM during the second year of my A levels by my friend Fatemeh who had participated the year before me. Although I applied to St Andrews to study medicine, I looked forward earnestly to iGEM, with a vague idea of the work ahead of me. So far, I have learnt a lot, not just about biology, but also about working in a team. As a team member, I learnt the importance of division of labour and learning to work with others, as well as trusting them to do their very best knowing that we all have the same interest in mind and we’re all working together to achieve it. I have also become versed in the use of various lab equipment and basic lab protocols such as ligation, transformations, amongst others, most of which I had only a very fundamental knowledge of before iGEM. Neither my Nigerian high school, nor my A level biology knowledge, had prepared me for the skill needed in the lab.

In Nigeria, the biology lab work consisted mainly of drawing, identifying and classifying organisms such as earthworms. In the UK however, it was a bit more hands on as we grew microorganisms on agar plates, but we never had to make one ourselves and most of the lab work involved sampling insects or other organisms.

We were taken through a basic tutorial of how to use the lab instruments before the start of iGEM, including making agar gels, pouring plates, amongst an abundance of other things and this helped greatly to bridge the gap in my knowledge. Nevertheless, my knowledge of Biology from A levels as well as my first year of medicine did make a major difference in understanding the theory behind the different procedures we had to carry out.

In retrospect, I am delighted that I did this project, as I intend to do a research project as part of my dissertation in the third year of my preclinical training, and this has most definitely boosted my interest in research as a whole. Also, being a part of a new and exponentially growing branch of science is definitely a privilege I am very grateful to have.

Musings of a Modeller - by Christina Samson

I’m a mathematician. Am I a modeller?

What does it take to be a synthetic biology modeller?

I don’t believe that there’s any particular answer to this dilemma. There are engineers, mathematical biologists and computer scientists amongst the field that delve into the realm of modeling, but what, I wonder, does it take to be a modeller? And what are the obstacles that an aspiring modeller can expect to face?

In the preliminary stages of modelling, there are a few articles and journals which consider the basics of the modelling premise. The ideas that are discussed in "Modeling and Simulation of Genetic Regulatory Systems: A Literature Review" (De Jong, 2002) or "Stochastic mechanisms in gene expression" (McAdams, 1997), provide some of the foundations for the basic equations required. The subsequent step involved is to decide which method to investigate your particular system with; deterministic, stochastic and then, perhaps, consequentially parameter sensitivity analysis.

From my novice modeller’s viewpoint this has been a minefield of theory and a swamp of biological knowledge to have ploughed through. I have found that, although I have a background in applied mathematics, the synthetic biology discipline is like embarking into a completely unfounded territory. Alongside this, I have a limited knowledge of biology which was an obvious obstacle at the beginning of the iGEM project. Consequently within our own working system, I have been on a steep learning curve in the attempt to produce the workings of a model.

Throughout this educatory experience, there have been several frustrating moments in conjunction with various ‘eureka’ moments.

One of the exasperating factors is that, from a mathematician’s vantage point, I require precision, accuracy and, quite often, numerical values. However for the duration of the iGEM competition, there has been a continuous struggle to acquire the relevant data (including parameters) that can be applied to our system. This annoying state of affairs could easily be rectified with an readily available database of facts and figures (such as Bionumbers). What can also be infuriating is that even whilst researching these numbers, I explored and analysed various past iGEM competitors’ modelling and they, like ourselves, have had to estimate constraints in order to proceed. Not only has there been a limited set of resources but, due to this constraint, there has been a quite a large proportion of estimation involved in the parameters and even the composition of equations. These parameters are among mystical legends (rather like Nessie); you believe they exist but their presence is shrouded in mystery.

These approximations and assumptions loosely compose the already precarious fundamentals of the modelling. Due to the absence of experimental documentation at the time of writing, I'm slightly wary of our outcomes and predictions which have been placed upon our model. This opinion is based upon my previous mathematical experience, which involves several years of utilizing vigorous proofs and being able to view thorough examinations of methods describing the validity of the data. Without the robust strength of a strong foundation, my faith is slightly fractured in our modelling.

There have been numerous disheartening moments when much time has been spent on the equation and code development of the system, only to find that there’s an inconsistency between your own thoughts and the model’s eventual outcome. Conversely, these are far outweighed when compared to the momentous occasions where a beautiful curve miraculously appears on the screen, just as you theorised it.

Overall the modelling can be a rewarding venture, even with the rocky predictions, that can, quite remarkably and fairly accurately, follow the biology to present the system rather effectively. Successful modelling can complement the biology and, in some instances, can provide assistance in the experimental side of the project. Throughout iGEM, the aspect of modelling has developed my abilities and I have appreciated the incomparable opportunity to learn the variety of skills that have I have utilised. I believe that with the right mindset and basic intuitive knowledge of the particular working biological system that the team is working in, that any person could learn about modelling.

So what’s necessary to be a modeller? I believe three things are key: some coding and biology knowledge, an eagerness to learn and, but most importantly, motivation. I have been able to produce important graphs and understand biological trends before my fellow biologists have even performed their key experiments, ensuring that modelling has not only been an important skill to learn, but is a fundamental part of the iGEM project experience.

Presentation vs. Usability? - by Max

Originally tasked exclusively with modelling, I found myself quickly engaged in other matters. My computer science background quickly pulled me into tasks related to computers. Funny as it may sound, developing programs does not actually help you with using programs. I was eventually tasked with designing the wiki, the team logo and occasionally running some simulations.

Having done very little web design and never used wiki markup language, I started reading about wiki engines and checking out previous team's wikis. After familiarizing myself with the use of the mediawiki engine it struck me that most teams' wikis were far too advanced to be using the wiki mark up language. A closer look into the source code confirmed my beliefs. Practically all "wikis" are not really using wiki markup language at all, they were mainly HTML websites using very little wiki mark up language. More pointedly, most of them had JavaScript animations and the more advance ones even had Flash.

Being a typical run of the mill computer science student, web design was never something I cared too much about, always thinking about efficiency and usability does not really go hand in hand with designing and making things look aesthetically pleasing and so until not very long ago I had never written a whole website, I simply never had the need to. Working on the wiki or website (as I like to call it) alongside other things got me to think differently. My colleagues seem to know a lot more than me about what it should look like, so I concentrated on mainly making it look pretty. Only when we started to collect information from previous wikis as part of our Human Practices projects it got to me.

The wikis being designed in the last 2 years look nothing like the wikis that teams were producing when the iGEM competition started. The original wikis were actually done in wiki markup language, nothing else, no fancy animations or flash. They were simple, but clear and all the layouts were fairly standard. The latter became very noticeable when we started to collect information from the wikis; finding specific information across all the wikis was proving to be time consuming as their was no longer a standard navigational layout.

iGEM is a competition where scientific research is meant to be carried out and then showcased in a presentation and documented on a wiki, at least that is the premise. However as years have gone past, it seems to be that more emphasis has been put on how the information is presented, and how good it looks like than the actual quality of the information and how available it is.

I don't know how iGEM will evolve, it would be silly to try to make a prediction now. However the purpose of this essay is to draw some attention at how sometimes goals get confused. iGEM started as as a scientific competition, aimed at giving its participants research experience, at least that's why I entered it. The overall aim should be no different than the one of professional researchers, where the importance is place on the quality and relevance of the work being produced more than on how it is presented. Professional researchers publish their work through academic papers, we use wikis instead. Despite that our vehicle of presentation is far from being as homogeneous as theirs. I just hope that in a society where plasticity seems to be taking over, where things seem to be valued more for how they feel like and the associations attached to them, instead of what they actually are and their real intrinsic value. Ideologies of this kind should not hinder scientific research.

All in all I would say that wikis should be used to document the work being produced, instead of being used to showcase specific projects with funky colour schemes, animations and sounds. Wikis should be written with a focus on simplicity, clarity and usability. Good work will clearly stand out, no harm will be done and I am sure judges and future teams will be glad that they can find the information they want easily and quickly.

My experience at iGEM- by Lamya

Being a first year medical student on the iGEM team is no easy task particularly because for me the world of promoters, ligation protocols and PCR reactions was completely unexplored territory. At the beginning of the summer I was apprehensive about my primitive knowledge of synthetic biology and though the learning curve was steep this summer, it was definitely a rewarding experience, as it allowed me to broaden my perspective and it introduced me to aspects of synthetic biology that I was otherwise unaware of. Growing up in Dubai our main focus was learning the subject matter without allocating time to develop an understanding of concepts or considering how to apply these concepts in practical matters. Thus being a part of an iGEM team was a unique experience as it forced me to think about life at a cellular level and the responsibilities that we as biologists face when we embark on projects which could potentially solve the problems plaguing our generation.

There are many ethical issues and concerns involved in synthetic biology and the human practices component of iGEM allowed us to evaluate our project and consider questions about its possibility to misuse, bio-safety and biosecurity. As a part of the iGEM project we also had to study the public view of synthetic biology and the various ethical dilemmas associated with experiments concerning synthetic organisms. The beauty and curse of ethical issues are that nothing is black or white but instead a unique shade of grey and to solve these issues they must be critically considered and addressed. Here we were given the opportunity to address misplaced concerns that people may have and encourage the acceptance of synthetic biology as a valuable asset in science and technology.

This summer was a rewarding experience as it taught me valuable lessons about interdisciplinary teamwork and how members from every subject area can contribute and work together in a iGEM project. I was able to learn a lot about biology and statistics and am grateful to the lab team for bearing with my primitive biological knowledge and explaining the concepts as simply as possible. I gained valuable insights which I hope could benefit me in the future when I’m writing dissertations or experiment protocols. Overall this summer was a valuable experience, as it allowed me to delve further into all aspects of synthetic biology and gain knowledge about biological systems, ethics and teamwork.

Overall this summer was a valuable experience as it allowed me to delve further into all aspects of synthetic biology and gain knowledge about biological systems, ethics and teamwork.

References:

De Jong, H (2002), "Modeling and Simulation of Genetic Regulatory Systems: A Literature Review", Journal of Computational Biology, Vol 9, pg67-103. Link to paper.

McAdams, H and Arkin, A (1997), "Stochastic mechanisms in gene expression", Proc. Natl. Acad. Sci. USA, Vol 94, pg814-819. Link to paper.