Category: Review

Introductory Glimpses of Evolvability for Computer Scientists

By Matthew Andres Moreno on October 27, 2017 in Research, Review / 0 Comments
Introductory Glimpses of Evolvability for Computer Scientists

This is one of a series of posts on evolvability. It is based off my undergraduate thesis, which I wrote at the University of Puget Sound under advisors Dr. America Chambers and Dr. Adam Smith. The original thesis is available here. Introductory Glimpses of Evolvability for Computer Scientists How can the structure of an evolving organism affect the phenotypic outcomes of mutational perturbation? We will walk through a thought example that casts this question in a light more familiar to programmers. Computer scientists who have worked on software understand that two pieces of code that meet identical specifications — return identical output for any input given — can differ vastly in difficulty to extend, modify, or maintain. Software implementation, internal structures largely invisible from the perspective of an external interface, accounts for this discrepancy. Computer scientists […]

Introductory Glimpses of Evolvability for Biologists

By Matthew Andres Moreno on October 20, 2017 in Research, Review / 0 Comments
Introductory Glimpses of Evolvability for Biologists

This is one of a series of posts on evolvability. It is based off my undergraduate thesis, which I wrote at the University of Puget Sound under advisors Dr. America Chambers and Dr. Adam Smith. The original thesis is available here. Introductory Glimpses of Evolvability for Biologists The idea that phenotypic outcomes of mutation are non-arbitrary can be unfamiliar, or even uncomfortable, to biologists [Kirschner and Gerhart, 2005, p 219]. It is consensus among evolutionary biologists that genetic mutation is random. The alternative — the theory of adaptive mutation — is controversial and widely discredited [Sniegowski and Lenski, 1995]. It is therefore essential to note that discussions of evolvability are not predicated on adaptive mutation. The key difference is that adaptive mutation hypothesizes that genetic mutation is non-arbitrary while discussions of evolvability center on the idea […]

Defining Evolvability

By Matthew Andres Moreno on October 13, 2017 in Research, Review / 0 Comments
Defining Evolvability

This is one of a series of posts on evolvability. It is based off my undergraduate thesis, which I wrote at the University of Puget Sound under advisors Dr. America Chambers and Dr. Adam Smith. The original thesis is available here. Defining Evolvability Figure 1 Some of my favorite biological phenotypes… biased towards cooperative photographic subjects! While biological phenotypic adaptation is indeed spectacular, another marvel of biology lurks just below our appreciation for phenotypes well-suited to their respective environments. It is hypothesized that biological organisms exhibit adaptation to the evolutionary process itself, not just to their environment over the course of their lifespans. That is, biological organisms are thought to possess traits that facilitate the evolutionary process. The term evolvability was coined to describe such traits. A general consensus exists in the literature that evolvability stems […]

Blog Series on Evolvability

By Matthew Andres Moreno on October 6, 2017 in Research, Review / 0 Comments

This is one of a series of posts on evolvability. It is based off my undergraduate thesis, which I wrote at the University of Puget Sound under advisors Dr. America Chambers and Dr. Adam Smith. The original thesis is available here. Blog Series on Evolvability I like digital evolution because it necessitates the examination of fundamental assumptions of what is necessary for evolution. Building a digital evolution system, a researcher must work out how the phenotypes that are being evolved should be genetically encoded. This decision raises an interesting question: how do genetic encodings for digital evolution systems influence the evolutionary process within these systems? I think this question is really interesting! Better understanding this question has practical implications for digital evolution, as well. So, I picked it up as the topic for my undergraduate thesis. […]

Overview of Early Avida Work

By Joshua Nahum on November 24, 2015 in Information, Review / 1 Comment
Overview of Early Avida Work

Back in 2005, I was tasked to pick an article written by a science journalist and write a summary of it for my AP Biology class. During those days, I would frequent the library to read science magazines like Scientific American and Popular Science. Little did I know, the article I found would profoundly shape my career to this day. I chose the cover article for the February 2005 edition of Discover titled: “Testing Darwin” by Carl Zimmer. The article described the work done at Michigan State University to study evolution in a completely different system than DNA-based life. Carl Zimmer, who continues to be my favorite science journalist, described experiments studying the rise of complex features, evolution that generated diverse ecologies, altruism, the benefits of sexual recombination, among other ideas, but all using the digital evolution platform, […]