John Long: Darwin’s Devices

You can find the details of the digi-Tad3 simulation in this paper: J. H. Long Jr., M. E. Porter, C. W. Liew, and R. G. Root, “Go Reconfigure: How Fish Change Shape as They Swim and Evolve,” Integrative and Comparative Biology 50, no. 6 (2010): 1120–1139.

This is a line spoken by Miss Vance, played by Katherine Hepburn in the film Bringing Up Baby , as she walked awkwardly following the loss of just one of her high-heeled shoes. I do not mean to imply that Tadro3 limped or wore high heels.

Spoken upon the airborne release of an egg trapped in its container by extraterrestrial Mork, played by Robin Williams, in the television sitcom Mork and Mindy .

By the way, we are always trying to find ways to automate video analysis. I’ll spare you the details, but suffice it to say that we run into three kinds of problems with feature-tracking algorithms: (1) false positives from the light reflected off of the water’s surface, (2) abrupt contrast changes as the Tadros pass into and out of regions of high light intensity, and (3) needing to double-check every automatically processed frame for errors. The closest we’ve come to a nifty solution is to have each Tadro emit an ultrasonic signal that an array of fixed receivers then reads. We simply ran out of money to make this work.

For rules, regulations, and results, see www.worldsolarchallenge.org/.

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.

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.

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, The Beak of the Finch: A Story of Evolution in Our Time (New York: Alfred A. Knopf, 1994).

In fishes the vertebral column is seen to have two main sections, the precaudal and the caudal. The precaudal section is what we haughty mammals might be tempted to call “abdominal” because each vertebra is associated with ribs and an underlying visceral cavity. The caudal section comes after (posterior) the precaudal and, in bony fishes, stops at the caudal fin. In sharks, skates, and rays, however, the vertebral column continues all the way up to the tip of the upper lobe of the caudal fin. Thus, in these cartilaginous fishes it’s not clear where the “caudal” vertebrae stop—at the anterior or posterior margin of the caudal fin? Although I’m sure that this is a fascinating topic for most of you, we have to stop. When I say “caudal” here I mean from the last precaudal vertebra to the anterior margin of the caudal fin.

Kurt and Keon presented our work on biomimetic vertebral columns at the Annual Meeting of the Society for Integrative and Comparative Biology: K. Bantilan, K. Combie, J. Schaeffer, D. Pringle, J. H. Long Jr., and T. Koob, “Building Biomimetic Backbones: Modeling Axial Skeleton Morphospace,” Integrative and Comparative Biology 46, suppl. 1 (2006): e8.

From the Metallica song, “Enter Sandman” on the album Metallica . Rock on!

For a detailed comparison of model 3 and model 1 versions, see the following paper: J. H. Long Jr., T. Koob, J. Schaefer, A. Summers, K. Bantilan, S. Grotmol, and M. E. Porter, “Inspired by Sharks: A Biomimetic Skeleton for the Flapping, Propulsive Tail of an Aquatic Robot,” Marine Technology Society Journal 45, no. 4 (2011): 119–129.

The presence of a lateral line is debated, but examination of the different specimens of Drepanaspis shows small canals that may have housed neuromast cells. See D. K. Elliot and E. Mark-Kurik, “A Review of the Lateral Line Sensory System in Psammosteid Heterostracans,” Revista Brasileira de Paleontologia 8, no. 2 (2005): 99–108.

C. E. Brett and S. E. Walker, “Predators and Predation in Paleozoic Marine Environments,” in The Fossil Record of Predation, edited by M. Kowalewski and P. H. Kelley, Paleontological Society Special Papers 8 (2002): 93–118.

Westneat, an expert on the biomechanics of fish feeding, produced this jaw-dropping analysis: P. S. L. Anderson and M. W. Westneat, “Feeding Mechanics and Bite Force Modeling of the Skull of Dunkleosteus terrelli , an Ancient Apex Predator,” Biology Letters 3, no. 1 (2007): 77–80.

An important point to keep in mind here, if you want to try this system in your own Evolvabot, is that because Tadros are surface swimmers, the IR sensors mounted above the water line are working in air.

To beat a dead horse, as the saying goes, keep in mind that correlated evolution can turn out to be either concerted or mosaic. In spite of this flogging, you shouldn’t be deterred from investigating this character evolution approach. Here’s a great place to start: Michael I. Coates and Martin J. Cohn, “Developmental and Evolutionary Perspectives on Major Transformation in Body Organization—Vertebrate Axial and Appendicular Patterning: The Early Development of Paired Appendages,” American Zoologist 39, no. 3 (1999): 676–685. Also: Robert A. Barton and Paul H. Harvey, “Mosaic Evolution of Brain Structure in Mammals,” Nature 405, no. 6790 (2000): 1055–1058.

D.-G. Shu, S. Conway Morris, J. Han, Z.-F. Zhang, K. Yasui, P. Janvier, L. Chen, X.-L. Zhang, J.-N. Liu, Y. Li, and H.-Q. Lui, “Head and Backbone of the Early Cambrian Vertebrate Haikouichthys ,” Nature 421, no. 6922 (2003): 526–529.

The term “Kutta condition” describes the physical situation at the trailing edge that is used in the Runge-Kutta theorem of inviscid flow. Runge-Kutta is used to estimate the pattern of flow around a body, including the so-called separation and stagnation points. The pattern of flow around a fish’s body is constantly changing as the fish undulates its body, and the caudal fin is the place where water that has interacted with the body is shed rearward, creating a wake. The wake, in turn, can be thought of as evidence of the momentum that the fish has transferred from its body in order to move forward, thanks to Newton’s third law.

When they started the predator-prey trials for generation six, the students noticed a change in the behavior of the robots that turned out to be related to the servo motors breaking down. The wisdom of their observations had been informed, in part, by the fact that at the start of every generation they ran positive controls on PreyRo and Tadiator, using a fixed “control tail” to assess any degradation in the hardware. Although we normally keep spare and identical parts on hand for just such a breakdown, we were fresh out of servos and so was the supplier. This pause in evolutionary activities allowed us to analyze this first run, which we published: N. Doorly, K. Irving, G. McArthur, K. Combie, V. Engel, H. Sakhtah, E. Stickles, H. Rosenblum, A. Gutierrez, R. Root, C.-W. Liew, and J. H. Long Jr., “Biomimetic Evolutionary Analysis: Robotically-Simulated Vertebrates in a Predator-Prey Ecology,” Proceedings of the 2009 IEEE Symposium on Artificial Life (2009): 147–154.