Tuesday, June 27, 2017

The Happy Path and genome sizes

In software engineering, the Happy Path refers to the case when execution of the code happens with no problems or exceptions or possible errors. This scenario could also apply to other areas of engineering. For example, in chemical manufacturing, the unit operations are designed to give the desired output when the inputs are just as expected. But sometimes, disturbances upset the unit operation, so operating parameters like steam pressure, cooling water flow, etc., must be changed "on the fly" to make sure the product is up to specification. (That is what process control is for.)

The same principle is also true of other engineered systems. For example, while a car is designed to operate in a wide range of weather conditions, most of the time, you are on the Happy Path. But when it rains, it is a good thing the engineers built a subsystem of the car (wipers) to keep the water on your windshield from obscuring your view. An even more extreme case is your airbag. Hopefully, you'll never need to see your airbag in operation, but when you get off the Happy Path by crashing into something, you'll be glad the airbag is in place. Indeed, I am sure that careful inspection of the car's components, including the programming in the car's onboard computer, will show that a sizable fraction of the car is dedicated to situations that are not on the Happy Path.

In biology, "Happy Path" could be envisioned as when cells are grown under pristine laboratory conditions. If cells are kept at the just right conditions, with the just right amounts of nutrients, they will only execute the most basic sets of code and subroutines (the Happy Path). Under these cases, researchers have been able to strip down the genome to about 10% of its normal size. On the other hand, under wild (or uncontrolled) conditions, cells might face a myriad of challenges, and must execute various subroutines to proceed with growth/division. In this way, the vast majority of DNA code within the cell is there to ensure the cell continues to grow and divide, even when faced with unpredictable, suboptimal conditions.

Both the cell and man-made systems display this hallmark of complex, engineered systems: that a large fraction of the system's make-up is in place to provide robustness in the face of many disturbances.

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