William Paley’s Intelligent Contrivance

It is no secret that intelligent design is a reiteration of centuries millienia old ideas. All that is really new is that its proponents are less than sincere in what they are peddling and perhaps ignorant of the history of natural theology.

While natural theology has a long history, it seems (to this newbie in the field anyway) it was most well-articulated by the late 18th century Anglican theologian William Paley. Paley was not known for his original ideas, apparently, but for his ability to write well and convey ideas to the public. His last book, Natural Theology (1802), historically speaking, seems like a triumphant last gasp of the field.

On the Rotatability of Evolutionary Branches, or On Life’s Little Joke, or On Why We Ain’t Special

“It is obvious to common sense that some organisms are higher than others – that a dog is higher than his fleas, or a fish higher than a jellyfish.” – Julian Huxley, in Evolutionary Humanism

It may be common sense, but common sense isn’t always right.

The most rampant misconceptions of how evolution works all coincide with how we humans perceive ourselves. Many believe we are the ultimate goal of evolution, that our existence is inevitable, and that we are superior to all other species – we are perched at the top of the ladder: the Ascent of Man.

Alan Turing’s Reaction-Diffusion Model – Simplification of the Complex

The following post is what I wrote for the first 2-day essay in my developmental biology course. It covers the potential limitations of mathematical modeling in developmental biology – specfically, the reaction-diffusion systems of the computer scientist, Alan Turing. Perhaps the larger point I try to make is that ideas that are initially and blatantly disregarded as irrelevant seem to reappear later on as actually important! The post is a bit bulky but hopefully you find it of interest!

Senior Seminar: The Deterioration of the Mammalian Y Chromosome

So I just gave my senior seminar the other day in which I gave a ~40-minute talk on the deterioration of the Y chromosome.

The Case of the Y Chromosome: Will It Disappear and Spell the End of Man? (Google Docs).

I have uploaded my PowerPoint as a PDF on Google Docs for all to view. I even included the typed out notes I had so you can make the leaps between the slides! Hope you like it!

Let me know if you have any questions – I’ll be happy to answer them!

The Mario Genome!

Evolutionary algorithms can be used to solve problems that would take humans forever to do, but they can also be used to see if a computer can match what a human can do. A great example of this is “The Mario Genome,” a program developed by Oddball at the TIGSource forums. What it does is take a group of Marios with certain traits and uses evolution to navigate the course in as little time as possible.

This popped up at Reddit, apparently, but I have no memory of where I found it (sorry!). While I am sort of familiar with the idea of genetic algorithms, and many are cooler than what this does, I think the Mario Genome easily illustrates what the idea is all about to someone with little prior knowledge. The analogies to biological evolution are easily made here.

Drift as Biology’s First Law

Synopsis: Robert Brandon agrees with the “evolutionary theory as a ‘theory of forces’ ” framework established by Elliott Sober but disagrees with Sober’s choice of Hardy-Weinberg as a zero-force law. Instead, Brandon believes genetic drift is to evolution as inertia is to Newtonian mechanics, i.e., drift is the “first law of biology.”

Evolutionary Theory as a Theory of Forces

In a post a few weeks back, I expressed skepticism towards labeling evolutionary processes such as selection, drift, migration and mutation as “forces.” At this point I’m not even sure what to call them – “processes” doesn’t seem right either. So I decided to read up on the topic.

As far as I know, the first formulation of selection, drift, migration and mutation as forces is Elliott Sober’s “Evolutionary Theory as a Theory of Forces,” the first chapter of his book, The Nature of Selection (1984). The chapter serves both as an argument for treating evolution as a theory of forces as well as introducing some of the basics of evolutionary theory. I will try to distill the “theory of forces” in this post.

While Sober never explicitly says what exactly a “theory of forces” entails, he mentions multiple prerequisites throughout the text. These include vector quantities that can resolve in a single direction, a zero-force state, and a differentiation between source laws and consequence laws. I will first describe these requirements specifically and show how they are reflected in a Newtonian theory of forces. I will then describe why Sober believes evolution can be seen as a “theory of forces.”

Learning mutation bias

So.

I have been reading about mutational bias primarily through the work of Arlin Stoltzfus and it’s been a bit difficult to decipher so far. For some reason I cannot find a source that provides a good explanation of how the different biases work and the relevant research. If anyone can recommend a source (a review article, a book, a web site, etc.), I would appreciate it!

In this post though, I will describe what I have taken away from my readings, however, and show you what progress I have made while I haven’t been posting. Basically, mutations ain’t random!