Designing living machines

Read an article the other day in PNAS (A scaleable pipeline for designing reconfigurable organisms) which described an approach to designing and constructing living organisms to perform real world actions. One could call these living machines or biological robots (biobots). There’s an appendix to the paper which provides supplementary information.

The intention of the pipeline is to expand the modern design space from construction materials, chemical process, electronics and mechanical devices to the domain of living things. Thereby create objects that perform functions for mankind, that are operate well with living things, are more resilient and have a benign impact on the environment.

The Biobot design pipeline stage 1

The design process begins using an evolutionary algorithm which takes as input an organism goal or action (i.e., moving so many body lengths for minutes) and the cell types to be used in constructing the organism and randomly generates potential organism designs.

In the current process there are two cell types (red and cyan) one is passive (scaffolding) and the other is active and provides movement power.

Designing and manufacturing reconfigurable organisms. A behavioral goal (e.g., maximize displacement), along with structural building blocks [here, contractile (red) and passive (cyan) voxels], are supplied to an evolutionary algorithm. The algorithm evolves an initially random population and returns the best design that was found.

Once a set of randomized designs using the two cell types have been determined, each undergoes a computerized simulation (in a physics engine that simulates gravity and liquid environment) to see how well the possible organism perform.

All designs are ranked in how well the achieve they performe and the best of these are used as seeds for another round of evolutionary design exploration. This uses these good designs and randomly changes some aspect of them to create another set of organism designs to test out.


Designing reconfigurable organisms. For a given goal, 100 independent evolutionary trials were conducted in silico (A–C). Each colored line represents the velocity of the fastest-moving design within its clade. Each genome (D) dictates anatomy and behavior by determining where and how voxels are combined, and whether they are passive (cyan) or contractile (red; E).

At some point, the evolutionary design exploration-simulation process stops when it has determined a set of workable organism designs which can achieve the goals set out for them.

The workable organism designs are then subjected to two rounds of filtering. The first filter is tests the designs for resilience to noise. This is done by putting the designs through another set of computer simulations that include noise. Some of the workable organism designs will still perform well in noisy environment and others will not.

The organism designs that perform well in noisy environments, are deemed resilient and are then fed into the next filtering stage of the pipeline.

The resilient workable organism designs are then filtered by whether they can be constructed with the current processes. Even though all the organisms are made up of the two cell types, not all of them can be realized given the current process.

After this point we have a set of designs that

a) Achieve the requested goal in simulation;

b) Perform well in noisy environment simulations; and

c) Can be constructed with the current processes and cell types.

The Biobot design pipeline stage 2

The next steps in the organism design pipeline all take place in the real world. The set of selected designs are constructed/manufactured and set into a petri dish to see how well they perform in real life .

The two cell types used in the current process are derived from the Xenobus (frog) embryos and consist of stem cells (passive) and heart muscle cells (active). The building of organism designs is done through layering of stem cells and then surgically or using cauterization to remove cells not part of the design. After the stem cells are placed then heart muscle cells can be layered on in a similar fashion.

There’s no control mechanism whatsoever other than the surfaces designed for the organism. Xenobus heart muscle cells automatically contract and when combined with other heart muscle cells, all the muscle cells contract in waves.

The design of the organism is such that the contractions propel the organism to move and explore the environment (the intended goal). The designed organisms are placed in a Petri dish and then observed over a period of time to see how well the perform the desired action.

Successful designs can then be seeded back into the start of the evolutionary exploration to generate even better designs. Simulations can also be adjusted with feedback from the real world behavior of the designed organisms. At some point the best designed organisms can be used in the real world.

Why biobots

Although the example had a goal to explore its environment. other goals could be readily used as well. Some of the ones mentioned in the paper are manipulating and gathering together some compounds/elements/particles in a volume. These could be used to clear a viscous solution of some impurities.

Another organism could be designed to have a pouch within which they can store and transport objects (or drugs).

Designed organisms could operate together in a solution with some organisms performing one function while others perform other functions. Organism designs could eventually be combined into one organism that performs more functions.

One nice aspect of biobots is that they can be squeezed, perturbed in many ways including being cut and they repair themselves and continue to operate.

One could design an organism to reproduce in a suitable environment or even designed to age and die after a specific time period.

The end goal seems to be to create living machines that can be used to operate in the environment or a body. Biobots could be designed to clear away plaque from a blood vessels or to dismantle malignant tumors. They could conceivably be constructed from a person’s own cells to operate for days-weeks-months in a body and then dissolve to be reused/disposed of just like any other biological material in a human.

So now we can design biobots.

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Just in case you wanted to try your hand at designing living organisms yourself. The researchers have all open sourced thei code for the evolutionary design exploration, computerized simulation, noise and build ability filtering which is available on github. The actual manufacturing/construction of the designed organism would need to be done in a lab.

Photo credit(s): All images are from the paper and its supplementary appendix.

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