Team:Groningen/HP/Silver

CryptoGE®M
Team
Project
Biology
Computing
Human Practice
Acknowledgements

Human Practices Silver

We explored how our project impacts or is impacted by the social environment; for example, with fictional future scenarios that may result from the use of our system.

We did research about the current national and international legislations for the shipping of GMOs.

We got in contact with experts from National Institutions, we performed a global survey and we checked the requirements of a potential user.

We received students to do BioArt and experiments in our laboratory..

We made society part of our exciting journey through the radio, newspapers, and social media.

Hereby you can find more details about our Future scenarios and Outreach projects. A complete discussion of the legal regulations, our contact with experts and society and the outreach activities can be found in the Gold page or in the links in the text.

silver

Future scenarios

“Planning is bringing the future into the present so that you can do something about it” - Alan Lakein

What would be the potential applications of CryptoGErM in the near and far future?

In this part of Human Practices, we explore the future scenarios of the introduction of the CryptoGErM system to the world.

With all these fictional scenarios we give a deep insight on the repercussions, applications and consequences that CryptoGErM would have if introduced as a daily life system.

The scenarios are presented as fictional digital news and articles from a futuristic and unreal city called New Groningen in The Netherlands in the near and far future, where the CryptoGErM system has been introduced, followed by an explanation of the current reasons behind its conceptualization.

We present them as digital news in a mobile device, based on the prediction that the UN Intellectual property agency’s chief made in an interview to La Tribune de Geneve, stating that newspapers will be replaced by digital versions by 2040.

"In a few years, there will no longer be printed newspapers as we know it today” “It’s an evolution. There’s no good or bad about it. There are studies showing that they will disappear by 2040” - Francis Curry
future0

The last existing Public Library has disappeared!

future1
First fictional scenario

What if in the far future we start to run out of space to accommodate the growing world population? Would we be able to find suitable places to inhabit without damaging natural areas? What if we use existent spaces to accommodate the growing population without the necessity of building new human settlements protecting the green areas? Have we thought about it?

According to the UN DESA report; “World Population Prospects: The 2015 Revision”, by 2050 the world population is expected to reach to 9.7 billion; the available living space could not be sustainable to accommodate the rapidly-growing amount of people. Such raising in the population, probably, will see humanity looking for more space to make sustainable the living of new generations, without using the green areas.

Within this fictional scenario, CryptoGErM could offer a potential solution.

CryptoGErM is a system for the storing and safe-sending of information. By making use of the first purpose, we could store the whole current information contained in books, newspapers, articles and other physical paper-based within bacteria to reduce the space needed for the storing of such information. Bacteria, such Bacillus subtilis is able to store up to 1.5 GB of information; furthermore, 1 mm3 of DNA can store up to 109 GB of information. [1]

Just to put an example of this fictional application; it is estimated that the the information contained by the U.S. Library of Congress is equivalent to 200 TB, currently it is stored in a physical space of 186,000 square meter. If this information is stored into DNA, it would only occupy 0.0002 mm3.

Furthermore, storing int DNA is more eco-friendly, because it does not require any specific medium to keep it functional, in contrast with current magnetic and optical storage medium that requires energetic supply to continue working. Just in 2015, 416.2 terawatt hours of electricity were used by world’s data centres. This consumption was “significantly higher than the UK’s total consumption of about 300 terawatt hours.” [2]

future2
Storing information in the DNA of bacteria, will replace the current storing medium (Fictional scenario)

Spores of Bacillus subtilis from 2016 found in the New Groningen

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Second fictional scenario

This fictional scenario was created as an extreme case by using the long-term stability of Bacillus subtilis spores.

One of the advantages of our system is that the spores can survive for several years even if they are exposed to hard conditions. So far, studies have shown that spores exhibit incredible longevity in a broad range of environments on our planet. Actually, there are reports from research groups that have recovered and revived spores from samples as old as 105 years. This data shows the capability of our system to store information for hundreds or thousands of years, even in a hard-conditions environment.

This application seems promising in a near future, as we found out after the interview we had at the Groninger Archives; Jan Jaap Hoogstins, collection manager from the Groninger Archieven, explained us that now most of the documents are being changed from analogous data storage to digital data storage, and one of two most important things that a storage system must fulfil is the durability, which means that the information stored must be conserved for a long period of time.

Spores of Bacillus subtilis are a reliable option since they have shown its long-term resistance. Actually, in 2000, a spore-forming Bacillus strain was isolated from a 250 million years old salt crystals. Moreover, DNA itself is a more stable data storage medium when compared to magnetic and optical medial, because it can remain intact for at least 700 000 years at -4˚C.[3] Even in harsh environments, DNA has a half-life of over 500 years. [4] Contrastly, current magnetic storers of information have lasts at most 30 years.[5]

However, is the DNA that contains the encrypted information in bacteria able to mutate through this period of time?

A complete discussion about mutation in Bacillus subtilis spores can be found in the Modelling Section.

A complete movie has been successfully stored in DNA

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Third fictional scenario

This fictional and extreme scenario provides an example of the future applications of CryptoGErM based on the current files and archives that have been stored successfully in DNA.

Currently, big companies such as Microsoft® have shown interest in the storage of information in DNA. This gives us an idea that DNA storing has started to become one of the most promising methods to store information in the upcoming years. This is mainly given by the capacity of storage that DNA posses; Church, Gao and Kosuri showed that 0.5 exabytes of information can be stored per gram of single-stranded DNA.[6]

A big breakthrough happened in April 2016, when Microsoft published an extensive paper in a joint project with the University of Washington[7] in which they explore the potential application for the use of DNA as storage medium. According to this work, DNA storage has a higher durability in comparison with current systems. Within the applications of storing information in DNA, this group stored in a DNA sequence and recovered succesfully three images that originally were in JPEG format. This shows that nowadays, it is not only possible to store text and information as we did in CryptoGErM; but DNA can be taken to another level of storage.

If now it is possible to store images in DNA, in the near future we might be able to store complete movies on DNA

DNA sequence drops to $0.0002 per Megabase

future5
Fourth fictional scenario

CryptoGErM is designed primordially for information that requires to be stored for a longer period of time and whose accessibility is not required immediately. However, we are pretty sure that this would change in the upcoming years due to the fact that DNA sequencing is becoming faster and cheaper every year. The inclusion of new and modern techniques, like massively parallel DNA sequencing,[8] have resulted in the decrease of the price and time needed for the DNA sequencing parallely to the increasing of the number of megabases that can be read.

Since 2008,[9] it has been predicted that DNA sequencing techniques would evolve till the point that we will be able to obtain the DNA sequence in just a few hours or minutes, even though many technical challenges have to be overcome first.

The National Human Genome Research Institute (NHGRI), a division of the National Institutes of Health (NIH), established to take part on behalf of the NIH within the International Human Genome Project (HGP), has been tracked the costs associated with the DNA sequencing (These tack is done within the Centers founded by the National Institute). This data can be consulted freely on the webpage of the NHGRI, in the section “DNA Sequencing Costs: Data.[10] The following graph contains the data of the costs of DNA Sequencing up to October 2015.

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Cost per Megabase of DNA Sequence

The graph above shows how the cost for the sequencing of DNA has plummeted since the beginning of the 21st century; this is mainly given by the introduction of high-throughput techniques. By October 2015, according to the data provided by the National Human Genome Research Institute, the cost for Megabase base of DNA sequencing was $0.0145. By this year 2016, the cost of the DNA sequencing is expecting to be further reduced. However, until now, not official data has been released.

According to Moore’s Law, that states that the number of transistors in a dense integrated circuit and its computational power doubles approximately every two years, the cost per Megabase at 2015 was expected to be around $50; however, the computational equipment associated with the DNA sequencing has growing exponentially decreasing even further the price, besides the new techniques that allows a faster and more precise analysis.

With all this information, our hypothetical scenario seems to be possible in just a couple of years, in which novel upcoming techniques are available on the market.

However, CryptoGErM is not only a system for the storing of information, our system goes beyond that; rather than just storing encrypted information, our system can be used for physical sending.

And if the system is in the wrong hands?

What would happen if the system would end up in the hands of a criminal? Which impact would it have?

To give an answer to this question, we propose a computational simulation to model the behaviors of some of the agents that could use the CryptoGErM system, within these agents, a potential criminal was included. Please consult the AI Agent Model in The Modelling Section for further information and discussion

References

  • [1] Bornholt, J. et al. A DNA-Based Archival Storage System. ASPLOS’16.
  • [2] Bawden, T. (January 23 2016) Global warming: Data centres to consume three times as much energy in next decadde, experts warm. Retrieved from http://www.independent.co.uk/environment/global-warming-data-centres-to-consume-three-times-as-much-energy-in-next-decade-experts-warn-a6830086.html
  • [3] Ancient DNA: Towards a million-year-old genome - Nature 499, 34-35 (04 July 2013) DOI: 10.1038/nature12263
  • [4] The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils - Proc Biol Sci. 2012 Dec 7; 279 (1748)
  • [5] Bornholt, et al. A DNA-Based Archival Storage System. ASPLOS ’16. April, 2016.
  • [6] Church, G. Gao, Y. Kosuri, S. Next-Generation Digital Information Storage in DNA. Science. 37, 2012, pp. 1628
  • [7] Bornholt, J., Lopez R., Carmean D., Ceze L., Seelig G., Strauss K. A DNA-Based Archival Storage System. ASPLOS ‘16. April 2-6. DOI: 10.1145/2872362.2872397
  • [8] Mardis, E. Next-Generation DNA Sequencing Methods. Annu. Rev. Genomics Hum. Genet. 9, ,2008, , pp. 238
  • [9] Shendure, J. Ji, H. Next-generation DNA sequencing.
  • [10] Wetterstrand, KA. DNA Sequencing Costs: Data from the NHGRI Genome Sequencing Program (GSP) Available at: https://www.genome.gov/sequencingcostsdata/. Accessed September 18th 2016

Outreach

One of the growing (sub)fields of science is science communication. It is key to effectively communicate intricate researches to the general public. Not only when applying for grants, but also to inform the public on ground breaking findings. Good communication is especially important in the field of synthetic biology, because the idea of altering DNA sounds scary to a lot of people. To better communicate CryptoGErM, we tried to make our project accessible by using animations, as you can find in our tour. But also by approaching newspapers, radio- and television stations and giving talks at open-access science events.

Night of Arts and Sciences

Every year, the heart of the city of Groningen transforms into a festival celebrating knowledge, creativity and fun. We were invited to help out at the Aa-church. We got to introduce people to a fungus-operated massage chair. The goal was to let people experience that bacteria, fungi and other microorganisms are not as scary as they are sometimes portrayed to be. It did not take long until word spread about the free massage, and soon people were lining up! This gave us a chance to talk to people about our own project and answer any questions they had!

Netherlands Biotechnology Conference

In April we had the chance to present the first outline of our project at the Netherlands Biotechnology Conference in Wageningen. Enthusiastically, we designed our first poster, t-shirt and business cards. We met some members of current iGEM teams and even had the chance to listen to the presentation of the Delft 2015 team who won last year’s Grand Prize. During this day we made a lot of contacts, tried to find sponsors and got valuable feedback about our ideas. This feedback influenced our project immensely.

Utrecht Campus Party

At the end of May we have been invited to give a presentation about CryptoGErM during the 4th edition of the European Campus Party. We had the chance to explain our idea to people with very different backgrounds and ages which at the end enthusiastically participated in different workshops given by Luis, Marco and Matthia.

By doing so we have been able to collect lots of feedback from different research domains that helped the growing of the project. Moreover, we also had the opportunity to listen to several other interesting talks that helped us to improve our presentation skills.

Radio

Jan van de Meide invited us to their radio studio to talk about our project. Kathinka and Bente went to the studio for their first live-radio performance. The radio show is aimed at a very general public, so we got the challenging task of explaining the project in an understandable manner. A major hurdle here was that we could not use visual support, so we tried to make sure to be as clear as possible. You can hear the result here (in Dutch).

Auction and BBQ

In September we organized an auction to raise money for our project. After giving a presentation of the project itself, the auction started. Every iGEM team member offered some service: lab worker for a day, cake baking, babysitting, lawn mowing, a tour through our lab etc. Researchers of the University of Groningen and friends of our iGEM team members were very eagerly bidding for the offers and thereby helping our project. It was huge success and a lot of fun.

After the auction we had a BBQ together. A local butcher sponsored the meat for it (Thanks to De Groene Weg Slagerij Groningen!). The income of the BBQ also partially funded our project. The evening ended with an exciting tip-stacking competition which peaked in a final between a 2016 iGEMer and an ex-iGEMer.

UK

The university of Groningen publishes its own newspaper, the university paper or UK for short. In order to spread awareness regarding our project and synthetic biology, we approached them to write a piece about us. They were very enthusiastic and curious about our project. To learn more Simone came over to our office to discuss the details of CryptoGErM. She even visited our auction to get a better feeling for the team and witness our presentation. The article can be read here.

Lifeline

Lifeline is a monthly magazine published by study association Idun. This association has members from both the studies Biology and Life Science & Technology. Because of their readers’ background, they were very interested in our project. The magazine is send to Iduns 1700 members and is always very well received. The article in Lifeline will be published at the end of November.

Unifocus

Unifocus is a video magazine that publishes interesting and educational videos concerning the university and its students. We were really excited to have a professional video made. At first we were a little giddy, but soon we got used to the spotlight and continued our work while the interview took place. The video can be viewed on their website, or right here:

New Scientist

On September 15th we were excitedly waiting in front of the iGEM office phone to be interviewed by a New Scientist reporter. The New Scientist is a UK-based weekly English-language international science magazine. Despite minor problems with the phone we are part of this article.

NOS

Our project did not go unnoticed by the Dutch national news agency! After the university posted our unifocus video, we sparked the interest of NOS op 3, the department that makes videos and takes care of social media. To get a better understanding of our project, we gave a few telephone interviews. This resulted in a really nice piece and animation, to explain our project to the general public. The article is available here (in Dutch).

Bionieuws (Bionews)

Thanks to the team of Eindhoven, we got the opportunity to advertise our project in the magazine of the Netherlands Institute of Biology. Together with all the Dutch teams we filled one page. Every team explained themselves in one sentence and included a team logo and contact information. (Translation title picture: The Netherlands is fully represented in Boston at the global iGEM competition.)

The Groningen Biomolecular Sciences and Biotechnology Institute (GBB)

We were invited by Groningen Biomolecular Sciences and Biotechnology Institute (GBB) to present our project at their 24th Annual Symposium. The Symposium was held at the Biotoop, the former Biological Centre. Our audience consisted of postdocs, PhD and MSc students with a Biomolecular or Biotechnology background. This gave us a chance to practice in front of a big audience and to handle critical questions. All in all, this was a valuable learning experience.

Riddle

Besides communicating our project to the general and scientific community, we wanted to do something to bring the iGEM teams together. To let people explore the CryptoGErM system, we developed a game to play during the jamboree. The game explanation can be found here. The idea is for the contestants to find our poster and to interact with our team members.

Interviews with Dagblad van het Noorden & OogTV

On Monday October 17th we had an interview with Dagblad van het Noorden (Local newspaper). In addition, we will still get an interview on Friday 21th of October with of OogTV, the local TV channel of Groningen. Both the article and the TV interview are yet to be published.

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