E.coli bacteria running the Internet of Things
CAPE TOWN – One of the areas of the Fourth Industrial Revolution (4IR) that has seen phenomenal growth over the past few years is that of bioscience and bioengineering. But when bioscience is combined with computer science, it seems that we may one day have biological computing devices that could partly replace the current hard drives, silicon microprocessors and microchips.
At least this is what some scientists firmly belief is possible.
Through the study of genetics we know that all living organisms consists of genes and deoxyribonucleic acid or DNA. These strings of DNA contains huge amounts of data that can last thousands of years as is evident from the 45 000 year old human femur bone from Siberia that was DNA-sequenced or decoded a few years ago.
It is exactly this remarkable data density and longevity of DNA that got scientists interested. Scientists have therefore been researching a synthetic form of DNA sequencing to store large quantities of data for an indefinite period of time. Recently scientists from Microsoft and the University of Washington announced that they were making very good progress. Already in 2018 they were already able to store 200 MB of data in DNA format and were able to retrieve it with zero errors.
Since 2018 much progress has been made and it seems very likely that DNA storage could complement current data storage methods or even replace some of them in the future. Perhaps Microsoft Research’s target of a DNA storage system functioning within a data centre by the turn of the decade is not so far-fetched.
Due to advances in nano- and biotechnology scientists at the Queen Mary University in London are taking research further and are using microbes to network and communicate at nanoscale, which is of particular interest to the Internet of Things (IoT).
In a 2019 paper by Raphael Kim and Stefan Poslad titled “The thing with E.coli: Highlighting Opportunities and Challenges of Integrating Bacteria in IoT and HCI” the researchers explain that it is not only the minute size, but also the autonomous nature of bacteria that caught their attention and presents interesting possibilities. Bacteria have an embedded, natural propeller motor or whip-like structure, called flagella, that propels them forward.
The research is still at an early stage but the exploitation of similarities between bacteria and computing devices is of great interest to the future of computing. The microbes share interesting similarities with some components of typical IoT devices, which indicate that bacteria could be used as a living form of an IoT device.
A good example would be the field of environmental IoT where bacteria could be programmed and deployed in the sea or in smart cities to detect toxins or pollutants, gather data, and even undertake the biomediation processes.
Likewise, in healthcare and medicine, bacteria could be programmed and deployed to treat specific diseases. The bacteria could swim to a pre-determined destination in the human body, then produce and release encoded hormones when triggered by the microbe’s internal sensor.
Microbes have exceptional chemical sensing, as well as actuating, communication and processing capabilities typical of a computerised IoT and could even outperform the best electronic devices. Bacteria cannot only detect chemicals, but also electromagnetic fields, light, mechanical stress, and temperature, as is normally done by traditional electronic sensors. The bacteria can also respond to these stimuli through movement using their flagella, or through the production of coloured proteins.
In fact bacteria are better than electronic chip-based sensors, since they are much more sensitive, stable and responsive than their digital counterparts. This superior qualities makes bacteria especially useful as a living form of IoT device and also valuable in the field of Human Computer Interaction (HCI).
Just like a digital control unit, memory and processor, the programmed DNA controls the bacteria and functions as a control unit with regard to the collection (sensing), processing and storing of data. Genomic DNA contains the instructions for the functioning of the bacteria, while the smaller circular plasmids (a form of DNA used to introduce genes into organisms) determine the process functions through gene addition and subtraction, as well as the storage of new data.
According to the team from the Queen Mary University the cellular membrane functions as the transceiver and allows for both the transmission and reception of communication. This “molecular communication” or the DNA exchange between cells forms the basis of a bacterial nanonetwork or signalling pathway.
This possibility of bacterial networks as an example of molecular communication such as the widely known E.coli bacterium that could act as an information carrier has in particular excited the IoT community.
The research with digital-to-DNA data and back again from DNA-to-digital data is showing great promise for the future. The idea of the researchers is to use the bacteria to create a potential substrate for the Internet of Bio-Nano Things (IoBNT), which entails the networking and communication through nanoscale and biological entities. Some of the often-despised bacteria may indeed change our connected world of sensors and IoT devices in the future.
Interesting is that the researchers from the Queen Mary University, London closes their research paper with a passionate plea for experimentation with do-it-yourself technology by enthusiasts to promote the IoBNT. They refer to the easily obtainable and affordable educational products like the Amino Labs Kit that are widely available to the public and allow, for example, many bioengineering experiments such as the generation of specific colours from bacteria through the programming of K12 E.coli DNA. Tools, data, and materials of biotechnology that enable the broader public to run small-scale experiments with microorganisms are currently easily accessible and affordable.
The Amino Labs Kit, for instance, caters for people who are interesting in manipulating and genetically engineering E.coli bacteria. The kit enables the user to create customised living colours and smells through the building of genetic circuits that can be triggered through a variety of pre-determined environmental stimuli.
This call by the researchers is not so unusual since technology hobbyists that experimented with very affordable Arduino microcontrollers and Rasberry Pi mini-computers were the very people that significantly advanced the traditional IoT. The mini-computers and the building of sensors and IoT controller devices were the learning space of many very successful technologists and scientists.
Due to the hard work of bioscientists around the world, programming of DNA is improving our quality of life in many instances and is keeping diseases at bay. It is therefore logical that the number of genetically engineered products will continue to rise in the future since it is one of of the 4IR.
Biotechnology en bioengineering will play an increasingly important role as major building blocks of the 4IR. Do-it-yourself and educational bio-kits can therefore teach potential future scientists how to effectively program bacteria. And perhaps some of the young bioengineers, learning the skills and concepts of the future, may one day become the scientists that solve the challenges of cancer, hunger, waste and climate change.
Today’s adventures in science create tomorrow’s innovators. And it all starts with a string of DNA and an unpretentious bacterium.
Professor Louis C H Fourie is a futurist and technology strategist. [email protected]