This left us with our old indirect fitness nemesis: calculate a host of performance metrics and put them together to yield a single number, the individual’s evolutionary fitness. With the addition of predator-avoidance to the mix, we obviously needed to shake things up a bit. Based on what we’d learned about Tadro3 in Chapter 4, we reasoned that feeding behavior was measured well by two sub-behaviors: (1) average speed throughout the trial and (2) average distance from the light.[118] We took Rob’s point about acceleration to heart and added three additional sub-behaviors we thought were critical for avoiding predators: (3) peak acceleration during an escape, (4) number of escapes, and (5) average distance from the predator.
Rob had also made the point that we needed to scale each of these sub-behaviors by how much they varied among the individuals we were testing. For those of you who know and care about statistics, he suggested we use what’s called a z-score. In our case, we start by taking the difference between, say, individual 5’s peak acceleration and the average peak acceleration of all six of the Tadro4 individuals in that generation. That difference is then scaled by dividing by the standard deviation of the peak acceleration for all individuals in that population. For the predator-prey world, then, an individual’s evolutionary fitness is the sum of the z-scores from the five sub-behaviors.
In that explanation of z-scores you can see that we also addressed another of Rob’s criticisms of Tadro3: we expanded the population size from three to six for Tadro4. When we told this to Rob, he burst out laughing: “Wow! Six individuals. That’s a really big population, John.” Where would we be without friends to point out sarcastically the ridiculous? But here, again, the ugly anterior extremity of actually running the experiment rears up. When we double the population size, we double the amount of tail building and video analysis that we have to do. We thought we’d give six a try and see if we could survive. We did, and as you’ll see, we’re darn proud of all of that work!
The work that we do is also multiplied by the number of generations that we run. Rob wanted more generations because he knew that evolutionary change is usually slow and gradual. Also, he had seen that our populations of digi-Tad3s needed, at a minimum, one hundred generations to find the equilibrium of optimal stiffness. But given that we were already doubling the work by doubling the population size, the best we could promise here was to try to make it to ten generations.
The final criticism—no vertebrae—was one that we all knew from the start of the whole Evolvabot project. When Joe Schumacher had made Tadro2 he had used a long eraser as the notochord and snapped tube clamps around it to simulate rigid vertebrae. This was a great solution at the time. When we designed Tadro3 we had focused on building a biomimetic axial skeleton, in part to deal with the kind of criticism that Bob Full had about our mechanistic accuracy at the level of the skeleton. Because the notochord of the biomimetic skeleton was built from molecular collagen, the stuff of real animal connective tissues, we were pleased as punch on the accuracy side of things. However, as soon as we tried to put Joe’s tube clamps on the biomimetic notochord, we destroyed it. The gelatin just was too brittle to withstand much in the way of squeezing or clamping; it would form small cracks that would then propagate into wholesale and catastrophic notochordal failure during swimming.
“Damn the torpedoes—full speed ahead!”[119] We had to have vertebrae. In Chapter 3 we talked about why building a vertebral column was a challenge: we have to attach dry and rigid structures, the vertebrae, to wet and flexible ones, the intervertebral joints. The composite assembly of alternating vertebrae and joints needs to be mechanically robust enough to be used as the propulsive tail of a Tadro. In addition, the joints, where the bending occurs, have to be of a biologically realistic stiffness. At the time of Tadro3 we’d been unable to meet this design specification, so we compromised by building the continuous hydrogels of different material stiffnesses.
Our failures with Tadro3 taught us that we needed to come up with some new tricks for Tadro4. Because we knew that working in isolation can sometimes produce creative and unexpected results, we decided to split our multi-institutional team in two.[120] Our first marine platoon was led by Tom Koob at the Shriners Hospital for Children in Tampa, Florida. Working with Adam Summers, associate professor and associate director of the Friday Harbor Laboratories at the University of Washington, and Adam’s PhD student, Justin Schaefer, Tom’s team took the high road. First, they created beautiful double cup–shaped vertebrae, just like the kinds you find in sharks, in a software program engineers use called SolidWorks. They then used a rapid prototyping machine to convert the three-dimensional software objects into 3-D physical objects (Figure 6.2).
A single vertebra is composed of a number of structures: a vertebral centrum, the cylinders shown in Figure 6.2 that form a chain of bones separated by the intervertebral joints; a neural arch, a rigid structure running along the top of the centra that forms a c-shaped covering over the nervous system’s spinal cord (note: the spinal cord does not run through the intracentral canal, the hole that runs through the centrum shown in Figure 6.2); sometimes a neural spine, a spike of bone that shoots up off the top of the neural arch; a hemal arch, the mirror opposite of the neural spine, covering the major veins and arteries that run under the centra posterior to the anus; sometimes a hemal spine, a spike of bone that shoots down from the bottom of the hemal arch.
FIGURE 6.2. Biomimetic vertebral centra. Based on the structure of vertebrae seen in sharks, these biomimetic centra were designed by Adam and Justin in a software called SolidWorks. Centra varied in terms of the angle of the cup-like surfaces that attach to the flexible material of the intervertebral joint. Compared to the joints, the centra are rigid. The rigidity is created by adding cyanoacrylate glue to the powder matrix out of which the vertebrae are made. The centra are not arranged here as they will be in the biomimetic vertebral column.
FIGURE 6.3. Biomimetic vertebral column, model 1. Using the vertebral column of the bonnethead shark, Sphyrna tiburo, as our biological target, Justin and Tom assembled the realistically shaped vertebrae (see Figure 6.2) into a column. Horse hairs were glued to the outsides of the centra to hold the column together in a manner similar to real intervertebral ligaments. Gelatin was injected in between to create the intervertebral joints. To keep the gelatin stable and to adjust its stiffness, it was chemically cross-linked, a procedure that preserves this soft and wet material.
118
Because wobble and speed were correlated, as we saw in Chapter 4, it didn’t make sense to use that pair. Also, we did not keep all of the four feeding metrics and then add new predator-avoidance ones on top because we wanted to keep low the number of metrics in order to help us interpret after all was said and done. Finally, average distance from the light is arguably the closest behavioral metric we have to actual light harvesting.
119
This quote is attributed to David Farragut, naval commander during the US Civil War. Although historians question its veracity, it is, no matter its origin, a damn good quote.
120
Interestingly, isolation also works in the same way for evolution. It’s on isolated islands, like the Galapagos or the Hawaiian archipelago, that we see rapid evolutionary changes. For a fantastic introduction to rapid evolution on islands and evolutionary processes in general, I recommend this book, mentioned earlier: Jonathan Weiner,