Category: Review

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, […]

Review of “Why do bacteria regulate public goods by quorum sensing?”

By Anya Vostinar on November 3, 2015 in Review / 0 Comments
Review of “Why do bacteria regulate public goods by quorum sensing?”

Bacteria flourish in nearly every place on Earth imaginable including in and on humans. They also reproduce and therefore evolve much more quickly than we do, so understanding their evolution is vital to every aspect of our lives. A surprisingly common strategy for bacteria ­- controlling everything from virulence to production of useful resources such as cellulase -­ is a form of communication called quorum sensing. Bacterial cells using quorum sensing consistently produce a signal molecule and then detect the concentration of that molecule in the surrounding area. The bacteria generally have a signal­-molecule density threshold, called a quorum, that triggers them to start performing a new behavior. The behaviors controlled by quorum sensing are usually only useful if there are enough organisms doing them at the same time. Producing public goods such as light or enzymes […]

After Man: A Zoology of the Future by Dougal Dixon

By Anya Vostinar on July 21, 2015 in Review / 2 Comments
After Man: A Zoology of the Future by Dougal Dixon

After Man: A Zoology of the Future by Dougal Dixon is a fictional non-fiction book proposing possible evolutionary tracks for the species that remain 50 million years after the Age of Man. As a fan of sci-fi and evolution, I couldn’t resist asking Dr. Ofria if I could borrow it when I spotted After Man on his shelf. As with most popular audience books, After Man doesn’t do a perfect job describing evolutionary events, but it is highly entertaining to read through. I also suspect that a very fun unit could be created around After Man for a high school or intro biology course.

Public Goods Paper Round-Up

By Anya Vostinar on June 16, 2015 in Review / 0 Comments
Public Goods Paper Round-Up

One of the nice things about summer is catching up on everything that got put to the side during the semester, right? It seems like reading literature is always one of the first things to go, so I’ve been spending some time reading a number of papers that I had set aside to be read “sometime” since they’ll definitely feature in a background section in my future. I’m quite interested in the evolution of cooperation, and one type of cooperative “game” is the production and use of public goods. A public good is a product that is useful to an organism, but is for some reason physically outside of the organism’s control and so must be shared with surrounding organisms. In the simplest systems, a “tragedy of the commons” scenario can occur in which organisms that don’t […]

Identifying Field-of-Origin Bias

By Emily Dolson on March 3, 2015 in Review / 0 Comments

The other day, I was reading a paper (paywall) on using graph and network theory to quantify properties of ecological landscapes, by Rayfield et al. It is a review summarizing: what properties of landscape networks we might want to measure, structural levels within networks that we might want to measure these properties at (e.g. node, neighborhood, connected component, etc), and metrics that can be used to measure a given property at a given structural level. The authors found that there was dramatic variation in the number of metrics available in these different categories. I was particularly struck by this comment, offering a potential explanation for the complete lack of component-level route redundancy metrics: “This omission could be attributed to, first, the importation of measures from other disciplines that prioritized network efficiency over network redundancy…”