Bac-net: freedom to communicate

CONCEPT

In many countries and regions of the world, freedom of expression is still not a legal right of people. The communication was controlled by the governments and powerful groups. Seriously, even in the free areas, they still have their own problems of free expression. The recent scandal of Facebook and Cambridge Analytica exposed that our private information on the Facebook was sold to some organizations and companies. This personal information may be used to control our filter bubble. According to Samples (2018), “The harms of filter bubbles and echo chambers should be much more than alleged to justify government actions to “improve” our debates.”

The Bac-net envisions a decentralized network to express and communicate in the near future. We chose bacteria as a future media to exchange information and communicate. Because the bacteria is everywhere in the environment and they are very active in exchange of genetic information, and the genetic information carried in the DNA can be transferred from one cell to another ( Encyclopedia Britannica, 2018 ). According to Tang & Liu ( 2018),

the information can be erased and re-recorded in multiple cycles in the bacterias. This posed a great possibility that the Bac-net can be common in the future.

BIOLOGICAL MECHANISM

The Bac-net is divided into three major steps. In the first step, we use the “encoder” to translate the information into the bacteria’s DNA. It involves the translation of the text into the binary code of ones and zeroes and further converted to pairings of DNA bases. For instance, Adenine (A) is 00, Guanine (G) is 01, Cytosine (C) is 10, and Thymine (T) is 11. DNA strands are then synthesized based on the combination of bases obtained from the translation process, using Agilent’s Oligo Library Synthesis microarray platform (Church, Gao, & Kosuri, 2012). Compared to another method which translates text to binary code, triplet code, and genetic bases codes consecutively (Goldman et al., 2013), the former method has lesser procedure steps and thus more time efficient. The GC-content of each 8 bases substring is then balanced using specialized constrained coding techniques coupled with homopolymer check codes to reduce synthesis error and correct sequencing deletion errors (Yazdi, Gabrys, & Milenkovic, 2017). Implementation of Reed-Solomon code can also minimize the sequencing redundancy while retaining a logical data density in the DNA (Organick et al., 2018). 

The genetic bases are then scattered over numerous individual synthetic protospacer oligonucleotides which are electroporated into a population of living BL21-AI Escherichia coli. The bacteria contain a functional endogenous CRISPR array and overexpress the Cas1-Cas2 integrase complex that allows them to incorporate the oligonucleotides into their genome (Shipman, Nivala, Macklis, & Church, 2017). the oligonucleotides into their genome (Shipman, Nivala, Macklis, & Church, 2017). 

These bacteria then act as information vector which can easily be transferred from one place to another. The proposed system is that bacteria will be ‘sprayed’ all over the person’s clothes to allow wider exposure. In addition, they also overexpress fluorescent proteins (GFP) in aerobic condition (Thorn, 2017) to allow easier detection of the bacteria prior to collection for information extraction. 

The third stage utilizes nanopore sequencing technology like MinION where an ionic current and DNA strands are passed through the nanopore. The current change indicates different genetic bases passing through the pore (“A nanopore is a very small hole,” 2017). The sequenced data run in different multiple sequence alignment algorithms to identify high-quality reads. Following that, iterative and BWA alignment is performed consecutively to ensure minimum error occurrence, which continued by deletion correction step in order to reduce redundancy (Yazdi et al., 2017).   

PROTOTYPE AND USAGE

First, we need to drop some bacteria into the Encoder and then link the encoder  to the computer. We chose the information we want to communicate on the computer and input it to the encoder by USB cable. The encoder will convert the information into the DNA of bacteria and then we collect the information bacteria from the Encoder.  We add the bacteria contained the information into the perfume and spray the perfume on the clothing allow wider exposure. 

When we bring the information bacteria to the public environment, it easy to spread.  As the same time, we also get information bacteria from other users.

The information bacteria will glow by the fluorescent protein after a period time.  We collect them by the loop and drop them into the “sequencer”. The sequencer translates the information from DNA code to a readable format.

The Bac-net will not replace the recent information system, but provide a new way to communicate which is not centralized and controlled. Everyone will have the right to speak out and receive information.  However, it may also bring negatives, for instance, some dangerous and criminal information will be easily spread.

Reference

A nanopore is a very small hole. (2017). Retrieved April 24, 2018, from https://nanoporetech.com/how-it-works

Bacteria – Exchange of genetic information. (2018). Encyclopedia Britannica. Retrieved 24 April 2018, from https://www.britannica.com/science/bacteria/Exchange-of-genetic-information

Church, G. M., Gao, Y., & Kosuri, S. (2012). Next-generation digital information storage in DNA. Science (New York, N.Y.), 337(6102), 1628. http://doi.org/10.1126/science.1226355  

Goldman, N., Bertone, P., Chen, S., Dessimoz, C., LeProust, E. M., Sipos, B., & Birney, E. (2013). Towards practical, high-capacity, low-maintenance information storage in synthesized DNA. Nature, 494(7435), 77.

Organick, L., Ang, S. D., Chen, Y.-J., Lopez, R., Yekhanin, S., Makarychev, K., … Strauss, K. (2018). Random access in large-scale DNA data storage. Nature Biotechnology. http://doi.org/10.1038/nbt.4079  

Shipman, S. L., Nivala, J., Macklis, J. D., & Church, G. M. (2017). CRISPR–Cas encoding of a digital movie into the genomes of a population of living bacteria. Nature, 547(7663). http://doi.org/10.1038/nature23017  

SAMPLES, J. (2018). The Case for Government Control of Internet Speech Grows Weaker: Filter Bubble Edition. Cato Institute. Retrieved 12 March 2018, from https://www.cato.org/blog/case-government-control-internet-speech-grows-weaker-filter-bubble-edition

Tang, W., & Liu, D. (2018). Rewritable multi-event analog recording in bacterial and mammalian cells. Science, 360(6385), eaap8992. http://dx.doi.org/10.1126/science.aap8992

Thorn, K. (2017). Genetically encoded fluorescent tags. Molecular Biology of the Cell, 28(7), 848–857. http://doi.org/10.1091/mbc.E16-07-0504

Yazdi, S. M. H. T., Gabrys, R., & Milenkovic, O. (2017). Portable and Error-Free DNA-Based Data Storage. Scientific Reports, 7, 5011. http://doi.org/10.1038/s41598-017-05188-1