One thing that has always interested me about computer simulated evolution of networks is that virtually (pun intended) all of them turn out to be non-modular. This has been pointed out in the literature (Thompson et. al 1998).

Modularity itself is something that the front-loading hypothesis predicts:

If life was designed and our analogy to human design is substantial, then we would predict life would be modular…Modularity enhances evolution and thus the perpetuation of design.
The Design Matrix p.167-168

The researchers running these sort of simulations make use of duplication, recombination, mutation, selection until they see the relevant result. However, there is a lot more to the evolution of life-like networks.

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Check this story out…

DNA is Blueprint, Contractor and Construction Worker for New Structures

In the Northwestern study, gold nanoparticles take the place of atoms. The novel part of the work is that the researchers use DNA to drive the assembly of the crystal. Changing the DNA strand's sequence of As, Ts, Gs and Cs changes the blueprint, and thus the shape, of the crystalline structure. The two crystals reported in Nature, both made of gold, have different properties because the particles are arranged differently.

"We are now closer to the dream of learning, as nanoscientists, how to break everything down into fundamental building blocks, which for us are nanoparticles, and reassembling them into whatever structure we want that gives us the properties needed for certain applications," said Chad A. Mirkin, one of the paper's senior authors…

Several years back I thought that the Darwinian theory was probably the best explanation for the emergence of biotic structures. That was before the stunning details of molecular machines were discovered. As the details of these remarkable machines rolled in, I became more and more skeptical that the random step-by-step process of mutations propounded by Darwinian theory could, in fact, account for what we see. It wasn't common descent (which I accept) or the increase of complexity over time that bothered me. It was the idea that the complex machines we see could come about with no planning or some sort of cognitive factor. Having been a machine designer for many years and designed many complex machines and systems, the probability that such remarkable machines could come about unplanned just seemed beyond rationality.

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We here at TT often make light of the outlandish 'emo' [emotive] gloom and doom prophesies of the many erstwhile spokespersons of big-s Science in their attempts to sell failed or highly debatable theories to the public for ideological or political reasons. We focus primarily on the stalwart defenders of Neodarwinian Orthodoxy, but the tendency for groups of like-minded scientists to propagandize in favor of their pet theories and projects as if there were no alternatives - or simple facts - to get in the way, crosses all the disciplinary borders.

This blog is intended to highlight how this propagandizing - a.k.a. "spin" - works in other areas of science, engineering and government, on an issue I am familiar with. It's a bit of a departure from the usual biological focus, but the information herein may serve to promote a little skepticism of "authority" in the perennial science wars that Telic Thoughts so often challenges.

As the new century's propaganda push to re-invest in "clean, safe, too-cheap-to-meter" nuclear energy kicks into high gear, a new PR effort to address issues related to the 1979 accident at Three Mile Island has also taken flight. The Massachusetts Institute of Technology held a 2-day seminar on January 22-23 entitled Three Mile Island - failure of science or spin?

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In this post I would like to explore some of the implications of evolutionary algorithms (EA's) and what they can (and can't) tell us about design. While I think what I say is relevant to all EA's, I am going to focus specifically on the Avida software program. I'm doing this for a number of reasons - the software and documentation are available online, Avida is often used in debates about design and evolution, and Robert Pennock made some claims about Avida during the Dover trial that I want to explore.

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[Albert de Roos is a cell biologist from Amsterdam, who has previously graced Telic Thoughts with this guest post about applying engineering principles to evolution. We've invited him to write about his latest article, published in the journal Artificial Life. Not because we agree with everything he has to say (nor vice versa), but because we find it to be an interesting approach, which may jolt researchers into thinking about evolution in new terms. Don't forget to check out Albert de Roos' blog]

A design hypothesis for the evolution of the nucleus
By Albert de Roos, Ph.D. Cell Biology

Recently, I published an article about the origin of the nucleus. Basically, I pose that the nucleus arose in evolution when a nucleus-like cell generated an extra plasma membrane around itself. Or in other words, when we take the current nucleus, we are looking at the direct descendent of a free living ancestor cell. Genetic material that is wrapped in a double membrane with large simple pores in them that keeps macromolecules such as DNA, RNA and proteins inside, while nutrients and waste is free to diffuse in and out.

This article is not 'just another theory' about the origin of the nucleus, but it is derived from an engineering framework named 'design by contract'. This concept is used in the development of software where components of systems communicate according to defined interfaces or contracts. As long as you don't change existing interfaces, you can extend the system. You can directly apply that to evolution: you can add new functionality, as long as you keep existing interfaces intact. The conserved mechanisms for translation, transcription, splicing etc. can be considered to reflect these constant interfaces in this engineering view. Conservation is thus regarded as an inevitable consequence of extension since any evolutionary process that would require extensive rework in critical systems would never survive because of the direct fitness costs.

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Discuss whatever you want. If you need some inspiration, here's a few discussable topics:

An article in Physics Today, titled "The Biological Frontier of Physics". From the article:

Molecular machines are the basis of life. DNA, a long molecule that encodes the blueprints to create an organism, may be life's information storage medium, but it needs a bevy of machines to read and translate that information into action. The cell's nanometer-scale machines are mostly protein molecules, although a few are made from RNA, and they are capable of surprisingly complex manipulations. They perform almost all the important active tasks in the cell: metabolism, reproduction, response to changes in the environment, and so forth. They are incredibly sophisticated, and they, not their manmade counterparts, represent the pinnacle of nanotechnology.

At the University of Montana, Dr. Dane Scott, director for The Center for Ethics, is teaching the eight-day course "Ethics, Education and the Evolution Debate", which promises to "clarify the confusion surrounding the long debate over teaching evolution by recognizing that this debate is fundamentally ethical, not exclusively scientific or religious." Critics of the current approach to teaching evolution "believe it promotes an atheistic, materialist philosophy", whereas those defending the current approach "believe that teaching intelligent design theory and its criticisms of evolutionary theory amount to state sponsorship of religion and undermine science education."

It seems there's a wave of new books warning us of the Coming Theocracy. Among them are American Theocracy by Kevin Phillips, Kingdom Coming by Michelle Goldberg, and finally Intelligent Thought, the John Brockman-edited volume on why the intelligent design movement is "the gravest of threats to the American economy". Mind you, I haven't read any of these books, so reviews and recommendations are welcome.

[At Telic Thoughts, we're proud to announce our first guest post, by Albert de Roos of Amsterdam. Although he considers his approach completely Darwinian, de Roos finds design and engineering principles useful in explaining evolution. To give his interesting ideas a wider audience, we asked him to describe his recent article in Bioinformatics (abstract available here) in layman's terms. Fortunately, Albert de Roos was happy to obliege.]

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Intelligent design detractors often claim that certain designs in nature could not have come from intelligence because they are not optimal. Although I addressed this from the standpoint of design motifs here there is another aspect of design that is pertinent to this issue, namely the design space.

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Source: Wired News

It has long been held that self-replication is one of the fundamental processes separating the living from the nonliving. To watch a robot make it happen is a bit spooky.

A robot that makes functional copies of itself was announced this week in the journal Nature. Researchers at Cornell University's Computational Synthesis Lab say their robot is a working example of machine self-replication and evidence that self-reproduction is not unique to biology.

What do we see here? At least two important points can be derived from this story.

1. Biology as a heuristic for human design (we want machines that are self-sustaining and adaptive). Adaptation as a design feature.
2. The engineering of life-like artifacts by natural intelligences. Does intelligent activity fall out of our explanatory toolkit in this case?