October 5, 2005 | David F. Coppedge

Stupid Evolution Quote of the Week:  Network Evolution Trumps ID

This entry will make more sense after reading yesterday’s story on the evolution of modular networks (10/04/2005).  A reader sent in a reference to a very similar article from scientists at Johns Hopkins published in PLoS Biology.1  It must be Network Evolution Week.  Before awarding the SEQOTW prize, some background is necessary.
    Like the Weizmann team, the Johns Hopkins team sought to explain biological network organization in terms of material mechanisms of mutation and natural selection.  They reasoned that “constraints” (the environment) dictate the dynamic character of network motifs and their interrelationships.  By awarding a “structural stability score” (SSS) to biological motifs in fruit flies and worms based on their ability to recover from perturbations, they found stable motifs cluster in a non-random way that determine the overall network structure.  They suggested, with apparent trepidation, that the environment therefore constrains biological networks to take a predictable form through pure mechanistic “forces” –

Do common “driving forces” underlie the organization of biological networks?  It seems fantastic to suggest that such forces could exist, considering that the biological entities involved are as diverse as genes, enzymes, and whole cells.  Nevertheless, even functionally unrelated systems may have evolved under fundamental constraints.  The analysis presented here suggests that the dynamic properties of small network motifs contribute to the structural organization of biological networks.  In particular, robustness of small regulatory motifs to small perturbations is highly correlated with the non-random organization of these networks.   (Emphasis added in all quotes.)

That their explanatory toolkit is limited to material causes is clear in a subsequent paragraph:

An evolutionary argument may help explain the overrepresentation of structurally stable motifs in real networks compared to random graphs.  Evolutionary pressure may select for network innovations that are structurally stable because these configurations are robust to variations in the strength of the connections.  A high SSS indicates that it is likely that randomly assigned connection strengths and signs will result in a stable equilibrium, while a low SSS indicates that stability is possible although it requires precisely weighted connection strengths.  Easily parameterized network designs that are predisposed to dynamical stability can be advantageous considering the evolutionary mechanisms of random mutation and natural selection.  Of course, stability to small perturbations is by no means the only functional constraint on network performance and structure.  For instance, in the developmental transcriptional regulation network in Drosophila [fruit fly] considered here, irreversible switching of transcriptional circuits involving feedback regulation is an important determinant of irreversibility of the developmental progress, which might lead to selection of relatively unstable network motifs with feedbacks.  The C. elegans [roundworm] neuron network, which strays the furthest from structural stability in our analysis, may also have functional constraints leading to overrepresentation of oscillators and memory switchesNevertheless, the correlation between network motif overrepresentation and the SSS suggests that stability of small functional circuits may be a basic constraint common to all networks, which along with other functional requirements can significantly bias the likelihood that a given motif is selected for.

Functional constraints, in their context, can only come from the environment – not from design.  This was made clear in an earlier statement: “Regulation of gene expression is dependent on the particular demands of a cell with respect to its environment.”  In their experiments, environmental perturbations governed the “structural stability score” awarded the network motifs.  The reader is referred to yesterday’s discussion (10/04/2005) about whether the environment can generate robust, modular network design.
    Now to the Stupid Evolution Quote of the Week.  Liza Gross, commenting on this paper in the same issue of PLoS Biology,2 used this paper to flaunt the superiority of Darwinian evolution over intelligent design:

While intelligent-design proponents enjoy their 15 minutes of fame denying the role of evolutionary forces in generating complex networks in nature, scientists are probing the organizing principles that govern these networks.  Traditional models of complex networks assumed that connections between units—such as genes, proteins, neurons, or species—occur randomly.  These notions changed as studies of protein interaction networks and other biological systems revealed “small world” features—characterized by short paths between nodes and highly clustered connections—and varying levels of organization, with certain patterns of local connections occurring more frequently in complex networks than in random networks.  What determines the abundance of these so-called network motifs in specific networks is not known….
….Discerning the global dynamics of these network structures has proved a major challenge…..
[She summarizes the paper by Prill, Iglesias and Levchenko.]
These results suggest that both global constraints on the network and properties of network motifs themselves influence the abundance of motifs and the overall structure of a given network.  While the authors caution that their networks are stripped-down versions of those found in biological systems, they point out that their approach can incorporate more complicated interactions as understanding of living networks increases.  And with this new understanding, scientists can test the hypothesis that selective pressures favor motifs with particular dynamic properties.

In short, who’s on the net?  Certainly not a designer.  Networks are things that just happen from time to time.  Maybe some day, after we have studied the networks in more detail, we can test that idea.
    The Runner-Up prize could go to another paper in the same issue of PLoS Biology.3  Skerker et al. marveled at the abilities of cells to process information and execute programs.  They didn’t try to explain how the systems evolved.  They just declared that they did:

Cells have the remarkable ability to sense, respond to, and adapt to their internal and external environments in order to maximize survival or accurately execute a developmental program.  Such behavior requires the ability to process information, and cells have evolved complex regulatory and signaling systems capable of sophisticated information-processing tasks.

1Prill, Iglesias and Levchenko, “Dynamic Properties of Network Motifs Contribute to Biological Network Organization,” Public Library of Science Biology, Volume 3, Issue 11, November 2005 (published 10/04/2005), DOI: 10.1371/journal.pbio.0030343.
2Liza Gross, “Charting the Interplay between Structure and Dynamics in Complex Networks,” Public Library of Science Biology, Volume 3, Issue 11, November 2005 (published 10/04/2005), DOI: 10.1371/journal.pbio.0030369.
3Skerker et al., “Two-Component Signal Transduction Pathways Regulating Growth and Cell Cycle Progression in a Bacterium: A System-Level Analysis,” Public Library of Science Biology, Volume 3, Issue 11, November 2005 (published 10/04/2005), open access article.

Prill et al. subscribe to the same goofy theory as the 10/04/2005 attempt, and the same comments apply.  Friends, Romans, and First Corinthians, and all reasonable, thinking people, let us understand two principles that undermine the whole premise of this claim and others like it:

  1. Requirements do not build a system.  They only specify what a system must have to work.  NASA publishes many requirements.  The requirements for a small robotic spacecraft can fill hundreds of pages.  Do these requirements create “evolutionary forces” and “selective pressures” that produce functional, interacting parts?  If requirements were sufficient, NASA could just produce lots of requirements and let the spacecraft assemble itself out of the dust of the ground.
  2. Properties of existing structures do not explain their origin.  A spacecraft, once assembled, has hundreds of pages of specifications.  These specs, if they met the design requirements, ensure that the spacecraft will reach the target and accomplish the mission objectives.  The spacecraft is observable; the specs are measurable and verifiable, but the hands that did the work can only be inferred.  Does Liza Graz expect us to believe that the requirements produced the specifications of a finished spacecraft, without any help from intelligent physicists, machinists, fabricators, assemblers, quality control engineers, software designers, testers and managers?

Mutation and natural selection cannot be called in as designer proxies.  Neither is a “force,” and neither connects requirements to specifications.  Neither has any direction, energy, or concern about the outcome.  Nature would be just as content with a black hole – a very stable structural motif – as with a biological clock.  Misfolded proteins are just as beautiful to Mother Nature as properly-folded ones.  Mechanistic processes have no stake in generating complex networks of molecular machines; they couldn’t care less.
    When a highly-ordered, functional, interrelated, robust, information-rich system is observed, the design inference is compelling to the point of being uncontestable.  Yet Liza Gross had the gall to scorn the intelligent design proponents in her victory speech praising the myths of the Darwinists.  ID proponents may only get 15 minutes of fame, but better that with sound science and logic than 146 years of totalitarian rule by fatuous charlatans wearing lab coats.
    When the usurpers are eventually toppled, they can still have a future.  They can compete in the National Storytelling Festival (see National Geographic report).  The best can graduate to the West Virginia Liar’s Contest and win a golden shovel.  They’ll have plenty of stuff to use it on.

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