Mutation Bias as an Evolutionary Driver

By Matthew Rupp on December 15, 2015 in Research / 0 Comments
Mutation Bias as an Evolutionary Driver

If mutation is the ultimate source of genetic novelty, can a bias of mutation inflow alter the evolutionary trajectory of a population? On the surface, it would appear the answer should be yes. Intuitively, the path through genotype space should be influenced by the manner in which mutations are introduced into the population. For an easy to digest analogy, consider a rephrased thought experiment proposed by Stoltzfus and Yampolsky called “Climbing Mount Probable” [Stoltzfus, A., & Yampolsky, L. Y. (2009). Climbing mount probable: Mutation as a cause of nonrandomness in evolution. Journal of Heredity, 100(5), 637–647]. Beginning with the 80 year old fitness-landscape as a mountain analogy, we can envision a population of haploid organisms clustered about the face of a mountain with the organisms’ elevation representing their absolute fitnesses. Genetic novelty introduced through mutation during […]

Avida-ED for classroom research

By Mike Wiser on December 8, 2015 in Education, Research / 1 Comment
Avida-ED for classroom research

Laboratory components are often integral parts of both K-12 and college science courses. I certainly had a lot over the course of my science education; 5 courses with labs in high school, 8 in college. But for the overwhelming majority of them, I was essentially following a recipe and doing by rote things which had already been done and where the answers were already known. It was only in science-fair-style projects that I typically had any control over the questions I was asking, or how I would go about trying to answer them. But science education doesn’t have to be like that. Inquiry-based science practice is a growing part of the recommendations for science education1 2.  Thankfully, computational tools are making these practices more accessible. NGSS Lead States. (2013). Next Generation Science Standards: For States, By […]

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, […]

Writing in the Sciences Online Class

By Anya Vostinar on November 17, 2015 in Information / 0 Comments
Writing in the Sciences Online Class

I recently finished taking an online course through Stanford’s Lagunita online learning site. The course was “Medicine: SciWrite Writing in the Sciences” and was an online version of a class that is offered in person at Stanford from what I can tell. This was the first online class I had ever taken and I decided to try it originally because I’m done with taking classes for my PhD and honestly craved a bit of structure as I started my first semester of pure research. I also hear on a regular basis how important strong writing skills are to scientists no matter where you end up, so this class seemed a good thing to try. While the class is apparently through the medical school and the examples made that clear, I found that the information pertained to […]

What goes on in a closed-door defense session?

By Mike Wiser on November 10, 2015 in Graduate School, Information / 0 Comments
What goes on in a closed-door defense session?

Last week, I defended my dissertation. While I knew how to prepare the written dissertation, and the public talk, the third component – the closed-door session in which my committee examined me – was mysterious. I’d asked about 8 people over the years what their closed-door sessions were like, and all of them told me that they couldn’t remember. So, while my experience might not be typical, it is at least an experience, and thus potentially a useful data point. Your mileage may vary.