March 12, 2024

Engineering Life Through Code: The Intersection of Computer Science and Synthetic Biology

Ognjen Koprivica, Director of Engineering
Imagine a world where biologists write genetic code as programmers write software, thereby changing the fundamental rules of life. This is not science fiction but the concept of synthetic biology. In this revolutionary field, engineering principles intersect with the fundamental rules of organic life.  
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Born at the end of the 20th century, synthetic biology rested on the idea of rewriting genetic code and creating new organisms. Today, this idea has become a reality. The world witnessed the birth of the first synthetic organism in 2008, in the form of a simple bacterium with a minimal but artificially created genome. This success marked the beginning of a series of endeavors, from producing yeast that produces insulin to engineering bacteria to remediate oil spills in oceans. Such achievements would not have been possible without the creation of two key elements of synthetic biology, the first of which is The Human Genome Project. In short, this can be considered a map of every gene contained within the human body. This comprehensive atlas, completed in 2003, is considered one of the most complex and important scientific undertakings of all time. Regardless of how impressive mapping and understanding the genetic code may be, synthetic biology could not be a realistic concept without a way to manipulate these genes.

Enter CRISPR, a revolutionary gene-editing tool that can be compared to a molecular scalpel. It's no surprise that the discovery of this technology warranted a Nobel Prize as it allows scientists to precisely rewrite specific parts of DNA, unlocking the ability to finely tune cellular function. The combination of these two tools creates an essential, powerful synergy, and they are considered the foundations of genetic engineering.

Science Against Diabetes

The concept of synthetic biology is not just about creating new forms of life but also about adapting existing ones. One of the best examples is the first major success in this domain, the creation of synthetic insulin, a beacon of hope for millions of people struggling with diabetes. Traditionally, extracting insulin from animal pancreas was an extremely laborious and expensive process. Even disregarding the ethical issues of this approach, a significant challenge lay in the fact that the world was practically running out of an adequate number of suitable animals (mostly cows) to be used for insulin production. Taking into account the current state and number of diabetics worldwide, it would have been impossible to produce enough insulin to cover even a fifth of the demand, turning this disease into arguably the biggest cause of mortality globally. However, thanks to the wonders of synthetic biology, scientists can compel genetically modified bacteria to produce insulin identical to that of humans, reliable and affordable. This is truly a moment to pause and consider how incredible such an achievement is, where the metabolism of simple bacteria is literally "hacked" to convert industrial sugar into insulin.

These feats are just some insights into the enormous potential of synthetic biology. However, like any uncharted frontier, it faces significant challenges. Designing and manipulating biological systems are complex processes that, besides being time-consuming, are extremely costly and inflexible, with a maze of unpredictable hurdles and outcomes. Fortunately, the explosion in the development of computer science, exponential growth in computing power, and impressive advances in artificial intelligence have created a perfect opportunity to address many of the mentioned challenges. To better understand how these digital partners can assist in the field of synthetic biology, we must understand the basic building blocks of life. DNA is the blueprint of life, whose role is to store genetic instructions that guide every cell function. Each DNA sequence is, in fact, a very complex code, written in a four-letter language consisting of the letters A, T, C, and G. RNA is the messenger of genetic instructions that decipher the DNA code, translating it into instructions for protein construction. Proteins are versatile molecules that perform countless tasks, from enzymes that catalyze reactions to structural components that cells are made of. Understanding the interaction between these components is crucial for designing and manipulating biological systems. The enormous complexity of living systems makes predicting how changes in one component will affect the entire system a very challenging process. This is where artificial intelligence comes into play and represents the final component needed for synthetic biology to become the most significant technology of this century. Using artificial intelligence can help in many ways.

AI can design DNA sequences and assist scientists in creating optimized genetic circuits for specific tasks by predicting how changes in DNA will affect protein function and cell behavior. By modeling and simulating life, AI can create virtual models of cells and organisms, allowing researchers to test and refine their designs before embarking on laboratory work, saving time and resources. AI robots can conduct experiments and analyze data autonomously, speeding up the research process and providing valuable insights.

AlphaFold, The Key To The Future

Today's key AI invention is AlphaFold. To understand how proteins function, biologists need to know their 3D structure. Predicting the 3D structure of proteins from their genetic sequences has been a long-standing challenge for biologists because there are many ways amino acids can come together to form a protein, and each of these ways can result in a different structure. This is precisely the problem that AlphaFold has helped solve. Using a combination of evolutionary optimization and computer simulation, AlphaFold can predict the 3D structure of proteins with incredible precision. That's why many consider it the greatest success of artificial intelligence, even in the age of the enduring excitement and widespread use of LLM technology. AlphaFold can accelerate the development of new proteins with targeted functions, which has the potential for a wide range of applications, including biofuels (AlphaFold can be used to design proteins that more efficiently convert sunlight into biofuels), drugs (it can be used to design proteins that target specific diseases), and bioremediation (it can be used to design proteins that degrade harmful substances like plastics). Besides artificial intelligence, the development of computer systems has also played a significant role. Decoding the first human genome took thirteen years, and the total project costs exceeded $3.2 billion. If the same project were to be launched again in 2003, it would cost $50 million and be completed in less than a year.

In addition to manipulating existing biology, scientists are exploring the possibility of building biocomputers based on organic cells, which can perform calculations using their molecular machinery. Today's electronic computers, despite their impressive achievements, leave a very weak impression compared to these potential biological counterparts. They consume energy, are fragile, cannot self-repair or produce on their own, and cannot produce anything tangible without connecting to a printer. Cells, on the other hand, have the ability to self-repair, work on different sources of energy, and produce tangible things such as proteins and enzymes. DNA has the potential to completely change the way data is stored. Its information density surpasses traditional electronic memory, with the potential to store millions of times more data in the same volume. For example, the set of information stored on 200 million DVDs could be compressed into just one sugar cube. Additionally, unlike electronic disks, whose lifespan is relatively short, DNA can retain data for millions of years.

Computers Of The Future

The combination of synthetic biology, computer science, and artificial intelligence opens new horizons in redefining the very core of technology. We are entering the era of biomimetic computers, inspired by the genius and efficiency of natural processes. Imagine computers that not only function but also "breathe," adapt to the environment, perhaps even replicate, constantly evolving in synergy with human creators. This vision brings with it numerous ethical dilemmas due to its enormous impact, but its potential to change the way we understand and use technology is unquestionable. This young field holds the key to addressing some of humanity's greatest challenges. The use of CRISPR and other gene modification technologies is key to developing ways to prevent and treat many modern diseases. This includes the development of personalized cancer vaccines by companies like BioNTech, the use of CRISPR to correct genetic defects and the potential for growing human tissues for organ transplants and therapeutic treatments. Innovations in synthetic biology can lead to more sustainable and efficient agriculture. Examples include synthetic organisms that produce plant oil, nuts that require less water, and bacteria to improve soil fertility. Additionally, lab-grown meat offers a sustainable alternative to traditional livestock farming.

The development of an artificial leaf that converts CO2 and oxygen into organic forms is an excellent example of how synthetic biology can address environmental challenges. This technology not only increases yields but also sequesters CO2 underground, thereby helping to combat climate change. Synthetic biology also plays a vital role in public health. Take, for example, genetic modifications of mosquitoes that prevent the spread of malaria without the need to kill trillions of individuals of the same species. Creating self-renewing materials and bio-based coatings can revolutionize various industries by making products more durable and sustainable. The development of transparent biofilms for touch-sensitive screens and bio-based ultra-tough coatings can significantly reduce waste and improve product lifespan. If any technology has the potential to fundamentally change the course of our civilization, giving us what many consider divine abilities to manipulate life, it is synthetic biology. Many influential technological entities are starting to take notice. Investors and companies are finally realizing the value of research in this area, while governments are rushing to optimize infrastructure and regulations. In particular, I expect the greatest strides to be made in China. The world has finally turned its attention to this field, which could not be said for most of its history. The ethical implications are enormous, but it is a topic that warrants a discussion of its own. Predicting the future is an ungrateful task, but a strong argument can be made as to why synthetic biology will be the technology that defines the 21st century, much like the semiconductor industry and computer science defined the past.