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I ask myself a few questions every day: How do we feed 10 billion people without creating deserts where we once had farms? How can we ensure that we don’t all die from disease without limiting health to those who can afford luxuries? How can we expand manufacturing output to enable higher living standards for more people around the world, while reducing ecological impact and halting climate change? To me, these are the big questions of the 21st century. They all have biotech answers. The only problem is that today we are not creating biotech answers fast enough to meet our overwhelming demand for solutions. That’s why we need the Synbio Stack. We need a technology ecosystem that increases humanity’s ability to build biotech solutions a hundred or even a thousand times. This article is about that ecosystem—the “technology stack” being created that will help us create the world-saving biological solutions we need.

What is a technology stack?

A "stack" is a combination of technologies that can make enormous complexity manageable. They mask some of the complexity by dividing parts of large systems into "layers of abstraction," so designers can focus on the parts that need to be designed at the moment without having to think about all the other complex parts. Stephen Wolfram elaborated on this idea in 1986:

"The components of a system should be arranged in some form of hierarchy. Components higher in the hierarchy should provide overall control to the set of components lower in the hierarchy, which can be viewed as individual units or modules. This principle Crucial for software engineering, where modules are often subroutines, this is also reflected in the existence of organs and specific body parts, apparently reflected by subroutine-like structures in the genetic code." — —Complexity Engineering Methods (Stephen Wolfram, 1986)

For something as complex as a CPU with billions of transistors or a cell with trillions of molecules, organizing things in this hierarchical way is crucial to any kind of engineering work. Wolfram continued:

"An important aspect of modularity is that it enables abstraction. Once the construction of a particular module is complete, that module can be treated as a single object, and no matter where the module appears, only its overall behavior needs to be considered. Therefore, modules ization divides the problem of building or analyzing a system into multiple levels, making it possible to make each level manageable” - Complexity Engineering Methods (Stephen Wolfram, 1986).

By breaking a large complex problem into smaller, simpler parts and stacking them on top of each other, complex problems become easier to solve. A famous example of web development is the LAMP stack (Linux, Apache, MySQL, PHP). If you do a Google search, you'll find many tutorials on how to create web applications using the LAMP Stack, along with diagrams explaining it like this:

Figure 1: LAMP stack. The magic of the LAMP stack is that if you are making a web application, you can stay on top and write some PHP scripts without having to think about controlling the process at the underlying operating system layer. Now you don't need to be a professional computer scientist to make a website, just know some simple scripts. This points us to another important thing about stacks: the same abstraction layer can be populated by different technologies. In our LAMP example, the abstraction layers are (from bottom to top) operating system, web server, database server, and scripting language; the technologies that populate these abstraction layers are Linux, Apache, MySQL, and PHP.

These same abstraction layers can be populated by different technologies to create other stacks, such as the widely used MEAN Stack, which uses MongoDB, Express.js, AngularJS, and Node.js as specific technologies stacked together. The modern web development stack is largely a thing of the past. LAMP and MEAN are a thing these days, but LAMP remains one of the most common technology combinations on the internet (source) because it was the first to make it possible for almost anyone to Technology portfolio for building websites. That’s the power of the stack: it lets people do things they couldn’t handle without it, gives people access to technology that was previously out of reach of many, and accelerates development by orders of magnitude.

Why are "stacks" important to biology?

Biology is so complex that our only chance of engineering it is to use a stack (or stacks). Drew Endy was the first to articulate this idea in his 2003 Nature review "Fundamentals of Engineering Biology." There, he identified "standardization, decoupling, and abstraction" as key elements that make up the new discipline of "synthetic biology." These three engineering concepts build on genetic engineering tools that have been developed since the first restriction enzymes were used to reprogram DNA in the 1970s, and together they create a new biotech approach we call for "synbio". This video shows Drew making this argument on a whiteboard in 2007.

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Rob Carlson further developed this ideain his 2010 book Biology is Technology. Carlson traces the history of the development of abstraction layers that enabled the design and engineering of the incredibly complex aircraft and integrated circuits we take for granted today. Here he quotes one of the internet’s earliest developers, Ginkgo Bioworks co-founder Tom Knight:

"We have an opportunity to leverage our complexity and information management tools to modularize, abstract and understand biological systems. Just as we simplify and abstract components from physics to allow us to build billions of component processors, we can and will Can modularize, abstract, and understand biological components with the explicit goal of building artificial biochemical and biological systems." - Tom Knight, quoted in Biology is Technology (Rob Carlson, 2010).

The creation of the Synbio Stack will free people from thinking about individual DNA base pairs so they can focus on designing new biological applications. It will become easier than ever for more people to use biotechnology to create new applications, allowing them to find solutions to the huge existential problems facing humanity today.

What is Synbio Stack?

If layers of abstraction are so important to engineering biology, what are all the different layers? What technologies can fill these gaps? There are many ways to slice the pie, and each Synbio lab may be using a slightly different configuration of the technology. That said, I think there are four (very broad) levels:

Figure 2: Synbio stack

• Application layer:有價值的產(chǎn)品新型儲能，從食品到藥品再到時尚紮實。
• Bio CAD/CAM layer:計算機輔助設計和/或制造 (CAD / CAM) 軟件不久前，用于設計應用程序并規(guī)劃它們的構建方式。
• Process execution layer:自動化 Bio CAD/CAM 軟件描述的流程的硬件服務品質，以操縱試劑和生物學的發生。
• Biological reagent layer:組合生物部件以創(chuàng)建應用程序。

Each of these layers can be broken down into further layers and sub-layers. However, even through this 30,000-foot view of the Synbio stack, we can see the advantages of layers of abstraction for people building with biology. Stacks divide the large and complex work of creating a new organism into several smaller, less complex tasks. This makes what was once impossible now possible. There are opportunities for people and organizations to specialize at different levels to build the capabilities needed there. With a synbio stack like this, someone using CAD software to design a DNA part, for example, wouldn't have to think about the step-by-step process a robot would perform to create its design. This means they can focus on the very difficult job of designing functional parts of DNA. Organizing the creation of new biological products in this way makes it possible to build teams and solve problems that were previously impossible.