Unlocking the code of life: mRNA, cybersecurity, and additive manufacturing

Exploring the building blocks of human life

The cells in our bodies are amazing pieces of finely tuned molecular machinery — working in sync with each other, interacting and producing every millisecond of the day.

Decoding our molecular machinery

Even more amazing is the protein assembly line within ribosomes. Ribosomes link amino acids together in the appropriate sequence to make different types of proteins needed by our bodies. In fact, they are extremely versatile 3D printers that we use to produce the essentials needed by our bodies.

Need hemoglobin to transport oxygen? Perhaps some antibodies to combat invaders? Insulin to keep those sugar levels in check? Our ribosomes will produce any of the above and myriad others, if we provide the instructions. All that needs to be conveyed is the specific sequence of amino acids.

This information comes from our DNA, which is the equivalent of a hard drive that contains all our protein assembly data. In multicellular organisms, this data is so important that there is a backup in the nucleus of every cell. Such a decentralized data storage system is highly resilient. One corrupted copy does not mean it’s game over. We can rebuild it from the remaining copies.

For single-celled organisms that only have one copy... that’s another story.

When we need a specific protein, a partition in our DNA hard drive (simply known as a gene) is activated and a specific sequence is copied by the file system and stored on a temporary medium called messenger-RNA (mRNA). This messenger now carries the information to our ribosomes, which read it and assemble amino acids in the right order to make whatever protein was ordered. Amazing, right?

Identifying attack surfaces

Looking at this system from a red team perspective, we can already spot the attack surfaces. If one wants to subvert the system to print their own stuff, they easily can. This type of attack has been seen in the IT world before, with a hacker targeting over 150,000 exposed printers and instructing them to print ASCII art.

Back to microbiology: Viruses are infectious agents that carry encoded genetic information in a hull that is equipped with protein “keys.” The key is designed to bind with a specific receptor on a cell, which acts as a door to let the virus in. Once inside, the virus will release its genetic information, corrupting the cell’s data storage and instructing its ribosomes to assemble virus proteins that will be combined to form new viruses. These will, in turn, be released to attack other cells. In malware lingo, this is not just a virus but a computer worm that replicates itself and spreads — one of the most feared occurrences that can cause colossal damage. Similarly, in our bodies, if a virus is not stopped it could very well infect all the cells!

Thankfully the immune system has some nifty ways of stopping infections from spreading.

Antibodies are key assets in this fight against infections. These proteins bind to the keys on the hull of the virus, rendering it harmless. The trussed-up virus will float around until it is removed by macrophages, the body’s clean-up crew. Having specific antibodies in our blood is the equivalent of patching a system vulnerability, or at least adding the virus signature to our endpoint protection.

Viruses have been interfering with our protein assembly line for millions of years, penetrating our defenses, injecting malicious code into our cell data storage and using our 3D printers to replicate themselves. Our immune system applies patch after patch whenever a new threat is encountered and neutralized. The relatively new technologies of genome sequencing, mRNA synthesis or CRISPER-Cas9 give us read-write access to genetic data storage and transmission. The consequences are tremendous and, as always with powerful technology, it has the potential to be used for good and bad.

Modern-day real life applications

Throughout the COVID-19 pandemic, we have all heard of PCR the technique of exponential amplification of trace DNA, allowing it to be detected and manipulated, and mRNA vaccines. These new vaccines are the equivalent of a code injection attack where code is introduced into the last step of the protein assembly line, instructing our ribosomes to manufacture the SARS-CoV-2 spike protein.

Without being associated with the malicious virus code, this protein is harmless since it is only the key that a virus uses to penetrate cells. However, since our printers are now flooding our system with this protein because of the mRNA code injection, our immune system believes there is a live virus attack and starts designing and manufacturing antibodies – a time-consuming process. Once the defenses are ready, our immune system can stop the real virus in its tracks when it arrives, trying to flaunt the same spike protein.

The idea of code injection to attain immunity is straightforward, and exploits several tools already in place. Namely, our 3D printers (ribosomes) and our adaptive immune systems. The amazing part is that there is no need for a complicated traditional drug discovery process.

Here’s how it works:

  1. Sequence the virus DNA. The initial Sars-Cov-2 sequence was available as early as January 2020.
  2. Isolate the code for the spike protein. This is a digital process, since we are only manipulating data.
  3. Manufacture mRNA from that sequence. This is the equivalent of loading it on to a USB drive.
  4. Inject it to the host. This is similar to plugging in the USB drive and hitting enter.
  5. The existing molecular machinery of our bodies takes it from there.

These mRNA vaccines are the first time that medicine-as-code has been used on such a large scale, and it is just the beginning.

Ribosomes, which are around 20 nanometers in size, were first observed in 1938. Their complete molecular structure was still unknown at the turn of the millennium but it has since been discovered. By harnessing the ribosome printers, we will be able to design code that instructs them to produce whatever protein we want. Combining this with advanced analytics and the fact that protein design is becoming possible (thanks to high performance computing), the possibilities are virtually endless. Correcting gene-induced deficiencies and new cancer therapies will just be the start.

Unlocking our digital evolution

By accessing the information technology that underlies the protein assembly chain, we have unlocked a new virtual dimension: The code of life. This is the true digital transformation of medicine the ability to access, understand, repair and improve genetic information, then inject and execute it. By opening a virtual dimension so closely connected to our physical being, we may have truly reached the era of our own digital evolution.

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About Simon Ulmer
Business Development Cybersecurity and Strategic partnership with Siemens at Atos and member of the Scientific Community
Simon Ulmer is a graduate of the Ecole Normale Supérieure Paris-Saclay and of the Ecole des Mines de Paris, he holds the rank of Ingénieur en Chef of the Corps des Mines. From 2011 to 2014 he was Economic advisor to the Prefect of the Rhône-Alpes region, working for the French Ministry of Economy and Finance. In 2014 he was appointed as Counselor for Economic Affairs at the Embassy of France in Berlin. In December 2017 he joined Atos SE being a technology enthusiast and globalized European himself. As a Franco-German he is developing the Siemens Global Alliance and as a computer geek (and maybe a bit of a control freak) he is enjoying promoting cybersecurity.