The Historical Importance of Modularity

I am currently sitting in on a graduate philosophy of biology seminar and the theme of this semester’s seminar is evo-devo and we recently discussed the concept of modularity. I’m also sitting in on a history of biology course and we have talked a little about the early 19th century French scientist, Georges Cuvier. While attending the seminar, I was delighted to make a historical link between the two! (And oddly enough, one of the works we read in the seminar was a chapter from a book on modularity co-authored by Gunther Wagner which opens with the same link I had made.)

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“Niche construction” before “niche construction” was cool?

One of the most useful aspects of being aware of the history of science is that much like literature and the arts, one can trace the historical origins of ideas and make connections among various thinkers who lived at different times. Last week’s post was a great example of such a connection: the arguments of Gould & Lewontin were articulated over 70 years before 1979 by TH Morgan, and more astoundingly, William Bateson (who even nailed down the idea of a “spandrel”). While there may be no link between Gould & Lewontin and Morgan & Bateson, this example shows us that biologists have had to argue against adaptationism since at least 1903. We can see a clear historical trend.

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“Spandrels” before “spandrels” were cool

In 1979, Stephen Jay Gould and Richard Lewontin famously attacked what they called the “Adaptationist Program.” They accused evolutionary biologists and sociobiologists of concocting “just-so stories” in which scientists would claim a particular trait, an adaptation, was a result of natural selection without rigorously testing their hypotheses. If they did test the claim and it turned out the claim was false, the scientist would create another just-so story, rarely questioning whether the trait was an adaptation or possibly a byproduct or fixed by non-adaptive processes. Most readers are familiar with this argument, so I won’t expand any further.

Upon reading material for my history major paper, I came across some arguments by the biologists T.H. Morgan and William Bateson that seemed oddly familiar…

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Favorite Arguments from Paley I: Day & Night

Busy busy busy! To buffer against the death of my blog, my next few posts will focus on various arguments from Paley that I am particularly fond of (aside from the few arguments I discussed in my previous post). The first argument I chose is not related to intelligent design as we normally think of it; instead, Paley’s awe towards the relation of living organisms to the cycles of day and night evokes a wider sense of design in the universe than the narrowly constructed “God must have designed the bacterial flagellum.” Paley sees design in the construction of the heavens itself. As Paley points out, this relation is quite wondrous!

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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.

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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.

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Conversation with Arlin Stoltzfus

In the comments of my August 17th post, Learning mutation bias, Arlin Stoltzfus, Perplexed in Peoria, and I have been discussing the meaning and implications of his work. Since this conversation is buried in a month-and-a-half old post, I thought I would bring it up to the front of the blog for more exposure. Below I will quote the fairly long discussion in full. As Perplexed notes, the conversaion may be hard to follow if you have not read Stoltzfus’ research articles or his blog series at Sandwalk, The Curious Disconnect: The Mutationism Myth.

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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.”

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The Problem of Language in Biology Part II

A couple weeks ago I posted an opinion piece more-or-less on how I think biologists should work on a more precise language, one example being the language of dominance/recessiveness in genetics. Douglas Allchin is skeptical as to the usefulness of such language and believes we should “dissolve dominance.” Most of the comments agreed with me, but Graves asked me to clarify a bit.

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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!

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