Hello World!

 Any sufficiently advanced technology is indistinguishable from magic

                                                                                                                                        -  Arther C. Clarke

Technology is advancing faster than ever and is taking less time to get widely adopted. Each time we invent a powerful technology, we open new, untapped domains which are far beyond the horizon of human imagination. 

To grasp the rate of acceleration by which technology is improving, consider this case. It took $3 billion and 15 years to sequence the first human genome during the human genome project. Shortly after that, in 2003, the cost of sequencing a human genome for the second time was $50 million. Now you can get your genome sequenced for less than $1000.

The living systems work in an intricate, mysterious, but also intriguing manner. Several reactions, processes, transport, packaging, and coordination are taking place in the living organism every second. It would be foolish to say that all these things are occurring randomly. There must be a program, or a code to be specific, which must be working behind the curtains, ensuring synchrony in the midst of chaos. 

The living system and the computer systems are much more alike than we think. Computers work on a binary code- 0 and 1, while biological systems work on nucleotides- A, T, G and C. A compiler reads the 0s and 1s in computer code and gives an output, while a combined effort of several enzymes during replication, transcription and translation results in the formation of proteins from the As, Ts, Gs, and Cs. Humans now have the ability to manipulate, add, or remove the genomic code. But, what’s next? 

The next advancement would revolve around the nexus between computer programming and biology. Human health and well being is the key reason why we study Biology in the first place. The immense potential of programming combined with biology can result in a colossal change in healthcare. 

How do we treat diseases? We take medicine, which goes into our bodies, and inhibits certain chemical pathways which halts imperative processes of the pathogen necessary for its reproduction and survival. This is undoubtedly a revolutionary milestone that humanity has achieved, but that should not stop us from innovating, especially when the entire pharmacopeia in medicinal chemistry can only act on a tiny fraction of all chemical reactions in the body. And even once the medicine is inside our body, we have really less control over it. What if we can engineer our cells to detect and cure diseases? That’s what professor Timothy Lu, Associate Professor of Biological Engineering and Electrical Engineering and Computer Science and a core faculty member at the synthetic biology center in MIT is working on. By leveraging our ability to read and manipulate the DNA, we can program cells which can incorporate artificial multigene constructs, known as gene circuits, so that the cells can make decisions and produce a desirable response. To oversimplify, a simple gene circuit contains these three modules:

1. A sensing module that takes inputs by detecting the biomarkers of pathogens.
2. A computational module that evaluates the situation using the boolean logic, where a combination of different inputs leads to a specific output which is either true or false (just like 1 or 0 in the computational world). Think of this as “And”, “OR”, and “NOT” gates. 
3. An output module that executes one or more therapeutic functions depending on the outcome of the input.

Programming cells to store information is the other end of the spectrum of synthetic biology. Data is the currency of the 21st century. Since the internet revolution, we have been generating a huge amount of data every single second. You generate data every time you purchase a product from Amazon, like a post on Instagram, visit a website and accept its cookies. Data is the reason behind effective contact tracing and the google ads that you see about a product you were thinking of buying. But where does this exponentially growing amount of data get stored? For now, we have a lot of means of storing data, but in the beginning of 2021, scientists discovered another storage of data- Genome of a living organism. 

DNA data storage is lucrative given its edge over other data storages. First of all, storage devices like floppy discs and pen drives become unreadable when a powerful technology supersedes them. The information stored in old devices can’t be read by new machines. However, the information is going to be safe in the DNA, and everytime an organism replicates, the information is going to be copied exactly to the daughter cells. Secondly, DNA is compact, and obviously, occupies less space.

The First Hard Drive of IBM of 5 MB (1956)

A team led by Harris Wang in Columbia University electrically encoded “Hello World!” in E. Coli bacteria. They zapped the organism with electricity to make changes in the genome. The patterns made by “Electricity on” and “Electricity off” are equivalent to the 1s and 0s in computer. By sequencing the genome, we can recover our data. 

This break-through, however, cannot compete with the data storage devices of today. Nonetheless, it’s premature to underestimate the potential of DNA data storage. Think about the first hard drive of IBM which could only store 5 MB of data back in the day. This is just the beginning of a new era, or to reference the two widely known words used to begin something new in the computational world given by Brian Kernighan, “Hello world”.

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References:

1. https://www.sciencemag.org/news/2021/01/scientists-program-living-bacteria-store-data
2. https://www.nature.com/articles/d41586-021-00092-1
3. https://www.genengnews.com/insights/gene-circuits-empower-next-generation-cell-and-gene-therapies/#:~:text=Gene%20Circuits%20Empower%20Next%2DGeneration%20Cell%20and%20Gene%20Therapies,-Senti%20Biosciences%20describes&text=Over%20the%20past%20few%20decades,and%20writing%20(synthesizing)%20DNA.&text=Now%20they%20are%20allowing%20us,therapies%20that%20reprogram%20genetic%20code.