The Synthetic Biology Tech Stack
The Emergence of the New Biology
Introduction
We have been through five technological revolutions in 240 years, starting with the Industrial revolution and currently being part of the Age of Information Technology and Telecommunications revolution. Each revolution led to a techno-economic paradigm shift that has changed the direction of innovation in our economy and society (“a change in the direction of change”) (1). Each paradigm shift brought far-reaching transformations in the way we live, produce, work and consume. Once the Age of Information comes to a conclusion and establishes a well-adopted set of paradigms, a simple yet intriguing question arises: What comes next?
The Age of Biotech, Nanotech, Bioelectronics and New Materials.
What comes next are not metallic, electronic driven devices but rather biological machines enabled by computation — biological applications (bApps). All this will be made possible by a new platform/tool/technology which is known as synthetic biology — the New Biology.
Synthetic Biology went through four major revolutions, the fourth one being the New Biology. It was enabled by a trend referred to as Convergence (2), which is the integration of engineering, physical sciences, computation, and life sciences.
Arguably the first revolution took place during the Neolithic era about 12,000 years ago and characteristic for it was the domestication of plants and animals (3). The second revolution was based on molecular and cellular biology — namely the discovery of DNA structure. The third one was in genomics, more precisely the evolution of genetic engineering tools, which led to the human genome project. All these revolutions within biology were accommodated by groundbreaking discoveries. To name a few: 9000 BC — selective breeding of cereal with higher yield, 1953 — the discovery of DNA by Watson and Crick, 1969 — Salvador Luria discovered the replication mechanism and the genetic structure of viruses; 1980 — a method to sequence DNA rapidly developed by Frederick Sanger; 2001 — Human Genome Project — Craig Venter sequences the first whole human genome; 2009 — Next Generation Sequencing — Illumina comercializes high-accuracy DNA sequencing and many more.
We are now at a stage where a new type of biology is emerging. Characteristics for this new biology are scientific integration and a deeper understanding of biological systems. The more the understanding of biological systems progresses, the more we are able to use this understanding and deliver something valuable to the economy and society. This enables an era of biology-based solution to social problems (Next-Generation Bioeconomy) such as health, food, environment and energy (4).
To build these solutions we require a set of tools or an infrastructure that will enable and accelerate the build-up. This structure is the synthetic biology technology stack. Similar notions were brought forward by Will Canine (5), Calvin Schmidt (6) and Drew Endy (7). I propose a different view on the synbio tech stack that tries to capture some further relations and involves a broader view.
The Tech Stack
In general, a tech stack consists of three main layers: infrastructure, middleware and application (8). Some principles that govern the tech stack evolution are universal and industry agnostic and, like in every industry, once the tech stack is evolved sufficiently enough, the main focus shifts towards the application layer. The discussion around the application layer is mainly governed by market demand and problem-solution-fit. If we blend out the discussion around which application is relevant and only focus on the structural set up of such a tech stack we will be confronted with one key questions: What components and structures are needed to build biology-based solutions?
The source of the question lies in the fact that individual applications cannot be considered in isolation when discussing innovation and technology evolution. We need to consider a system of interrelated technologies and drivers that influence the evolution of a given application — in our case synthetic biology applications. To understand the interrelatedness of these individual technologies, we first need to identify specific layers with specific characteristics.
The SynBio Tech Stack
The technology stack below is specific for the synthetic biology space. This is simply a categorization of various layers. The categorization is forward-looking and tries to establish an end result rather than a snapshot. In particular, the synbio stack can be characterized as follows:
Layer 1: The Application Layer
The SynBio Application layer consists of the product interface — and product — block.
Product Interface Layer: Solutions that offer interaction with products and increase the value of products. Primarily consumer focused, it refers to products that are ready to be distributed. Product Interface finds its way into the consumer good class.
Products Layer: Chemicals or proteins as well as complex systems that are ready to be processed for end consumer. (E.g. leather, vanillin extract…)
Layer 2: The Component Layer
bApps Layer: Bio parts or finalized biosystems that are commercializable, as well as materials, drugs, industrial chemicals. This class is similar to components that are part of the process of a more complex solution. Examples are chassis, bioparts, cells and pathways.
Layer 3: The Middleware Layer
The middleware layer consists of Engineering Platform- and Enabling Infrastructure — block.
Engineering Platforms Layer: Especially Organism Engineering Platforms provide finalized organisms or bigger systems built from different bio parts and synthesized molecules (e.g. proteins) that can be used in different fields with different applications.
Enabling Infrastructure Layer: It refers to technologies that help enable synbio applications and are a combination of hardware, software and bApps (e.g. cloud labs or organism test platforms).
Layer 4: The Infrastructure Layer
Software Infrastructure Layer: It includes Software solution such as design, data analytics, lab project management, modeling, knowledge management, visualization tools and data mining solutions.
Hardware Infrastructure Layer: It includes tangible lab equipment such as hardware, robotics, microfluidics, liquid handling systems, cloning and picking equipment.
Conclusion
This tech stack might be a guide in developing a market view on this space and help to give structure and a common denominator. The difficult question is whether the technology stack is mature enough to drive synthetic biology application as envisioned. But what did we envision? And if we are not there yet, how long will it take us? In which way is the synthetic biology tech stack growing and what is the current state of the tech stack.
If you are a founder, researcher, industry expert or just curious and excited about this field as I am, then please reach out to me via twitter @kapeugen or Linkedin.
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Footnotes
(1) Following Carlota Perez. The five revolutions are: 1771 The Industrial Revolution (machines, factories and canals), 1829 Age of Steam, Coal, Iron and Railways, 1875 Age of Steel and Heavy Engineering (electrical, chemical, civil, naval) 1908 Age of the Automobile, Oil Petrochemicals and Mass Production, 1971 Age of Information Technology and Telecomunications
(2) http://www.convergencerevolution.net
(3) Its similar to today’s intention to attempt to “domesticate” microbes and genomes of plants, animals and humans
(4) https://www.nap.edu/resource/12764/new_biology_final.pdf
(5) https://synbiobeta.com/the-synbio-stack-part-1/
(6) https://synbiobeta.com/synthetic-biology-companies-raised-over-650-million-in-q1/
(7) https://www.youtube.com/watch?v=XIuh7KDRzLk
(8) A good primer into tech stacks in the software world: https://blog.hubstaff.com/technology-stack/