Computer scientist and engineer Dean Schulz has published two papers in the journal BIO-Complexity that describe his top-down and bottom-up analyses of the bacterial flagellum (here, here). He recently published his final paper in the series, “An Engineering Perspective on the Bacterial Flagellum: Part 3 — Observations,” which synthesizes the two approaches. Schulz’s observations and conclusions demonstrate the explanatory and predictive power of engineering-based models of living systems.
The Rotary System
The bacterial flagellum functions as a rotary propulsion system in bacteria. It employs many stunningly complex subsystems. To name but a few, assembly is directed by a genetic network that ensures the manufacture of the right proteins in the right quantities at the right time. The proteins that compose the propeller are transported across the cell membrane through a transport gate that only allows the correct ones through at the correct time based on protein signal sequences. Other proteins assemble the hook and propeller (here, here). Another protein acts as a ruler that coordinates with the gate to ensure that the flagellar hook extends to the correct length. And a navigational control system controls the rotation of the rotary motor.
The Investigative Approach
Schulz investigated the design of the flagellum with a method that could be described as groundbreaking. He first outlined what he expected would be the most efficient architecture for a nanotechnology rotary propulsion system based on engineering principles. He started with the highest level in the organizational hierarchy and mapped the expected overarching design of the core processes including manufacturing, assembly, energy production, torque generation, environmental tracking, and directional control. He graphed the minimal components and their functional relationships. He also anticipated design requirements and constraints.
He then reviewed the literature on actual flagellar operations starting with the processes and structures at the bottom organizational level (see Figure 1). Finally, he compared the top-down and bottom-up analyses. Schulz’s expectations for the design architecture, interrelationships, and constraints matched to a remarkable extent the actual operations.
In addition, he identified numerous tight constraints that must be met for the flagellum to function at an efficiency that would provide any benefit to the cell. The constraints include over 80 requirements for the interactions between the individual proteins (see Figure 2). For instance, some proteins must bind together permanently, others temporarily, others must never bind. If any one of these criteria is not met, the flagellum would provide no benefit to the cell, but it would disadvantage it by wasting resources.
Nearly every aspect of the flagellar system contradicts what evolutionary theory would predict. Any cellular propulsion system resulting from an undirected process should not strongly resemble human creations. In particular, it should display a bottom-up design logic where components are clumsily thrown together as seen in Rube Goldberg machines. (See previous, “How Engineers Helped Save Biology from Evolutionary Theory.”)
In addition, if the motor evolved incrementally, removing different pieces should degrade operations but not entirely disable them. Finally, vast numbers of other solutions to the problem of rotary propulsion should exist, or else a random search through the space of all possibilities would never have discovered any of them. Schulz’s investigation reveals that the flagellum displays the opposite features.
His success in anticipating so many flagellar details based on engineering principles demonstrates that the flagellum was engineered around a clear overarching top-down design logic. Every system and component are optimally designed to integrate with multiple other systems and components in symphonic harmony. Each of the core systems must coordinate with each other at extremely high efficiency. Thus, their construction and integration require foresight and goal direction. In addition, few other general architectures exist that could effectively operate at a comparable efficiency, or else Schulz would not have accurately predicted either the overarching architecture or the individual features.
Equally important, the system is comprised of an irreducibly complex set of subsystems constructed and interconnected according to the same design logic seen in comparable human-designed systems. And each subsystem (e.g., navigation) corresponds to an irreducibly complex set of components, some of which require transport processes and assembly tools, just as seen in human manufacturing. The number of essential components, interrelationships, requirements, constraints, and the similarity with the most advanced human engineering prove that the system could not have evolved gradually. Instead, it must have originated at once through the actions of an intelligent agent.
Biologists have only begun to tap into engineering models’ explanatory and predictive power. Schulz’s application of engineering principles to analyzing the flagellum greatly expands scientists’ understanding of its operations and its design logic. He presented his research at the Conference on Engineering in Living Systems, and his insights stunned and mesmerized even biologists with intimate knowledge of the related technical literature. As his top-down/bottom-up approach is applied to other systems, investigators will increasingly recognize that the only viable framework for understanding life starts from the assumption of design.