April 8, 2008 | David F. Coppedge

Darwin on a Chip

PhysOrg, EurekAlert and and Science Daily announced “Evolution on the table top.”  Reporting on a paper in PLoS Biology by Brian Paegel and Gerald Joyce at Scripps, the article claims that the two scientists “have produced a computer-controlled system that can drive the evolution of improved RNA enzymes—biological catalysts—without human input.”  The scientists claim they have achieved “Darwinian evolution on a chip.1
    The press release claims the “evolution machine” demonstrated adaptation via random mutations:

This beautifully illustrates what about evolution is random and what is not.  While the end point is predicted by the selection pressure—i.e., the decreasing concentration of ingredients determines that enzymes will evolve to cope with decreased concentration—the actual mutations that allow this are completely random and cannot be predicted at the outset—i.e., if you bought an “evolution machine” and ran the same experiment, your end product would be an enzyme that could cope with low concentrations too, but the mutations that it acquired to do this might be different.

In the original paper, the authors advertised their experiment as a way to celebrate Darwin’s 200th birthday next year.  “Our microfluidic system allows us to perform Darwinian evolution experiments in much the same way that one would execute a computer program,”  they said.  “The scientific community will soon celebrate the 200th anniversary of the birth of Charles Darwin and the 150th anniversary of the publication of his seminal work On the Origin of Species by Means of Natural Selection,” they continued, ignoring Wallace (03/03/2008) and neglecting the rest of the title: and the Preservation of Favoured Races in the Struggle for Life.  They continued, explaining why their lab experiment can help the celebration:

The principles of Darwinian evolution are fundamental to understanding biological organization at the level of populations of organisms and for explaining the development of biological genomes and macromolecular function.  Darwinian evolution also has become a chemical tool for discovering and optimizing functional macromolecules in the test tube (for recent reviews, see [2�5]).  Laboratory evolution is greatly accelerated compared with natural evolution but requires substantial manipulation by the experimenter, which is imprecise, time consuming, and usually performed in an ad hoc manner.

Their method, they say, combines the best of real-life subjects and laboratory control.  They took an existing RNA enzyme, class 1 RNA ligase, and subjected it to mutations, then added selection pressure in the form of decreased quantity of substrate.  The ones with the most advantageous mutations survived to reproduce.  The abstract explained, “The final evolved enzyme contained a set of 11 mutations that conferred a 90-fold improvement in substrate utilization, coinciding with the applied selective pressure.”  Here’s how they concluded:

The runtime parameters for evolution are established at the outset and are enforced precisely throughout the course of an experiment.  The continuous stream of real-time data provides a high-resolution record of an evolutionary trajectory, which can be obtained as a function of population size, population heterogeneity, growth conditions, and the availability of limiting resources.  Each microchip contains multiple microfluidic circuits that can be addressed independently, and the chip as a whole can be produced at nominal cost.  Thus, Darwinian evolution becomes commoditized, allowing one to perform many evolution experiments with little more difficulty than the execution of a computer program.

The press release advertised this evolution-machine as a teaching tool.  “Evolution has taken another step away from being dismissed as ‘a theory’ in the classroom, thanks to a new paper published this week in the online open-access journal PLoS Biology,” the article began.  “…In the future, this ‘evolution-machine’ could feature in the classroom as well as the lab, allowing students to watch evolution happen in their biology lessons.

1.  Brian Paegel and Gerald Joyce, “Darwinian Evolution on a Chip,” Public Library of Science: Biology, Vol. 6, No. 4, e85 doi:10.1371/journal.pbio.0060085, published 4/8/2008.

Darwin isn’t on this chip.  The chip is on Darwin.  His disciples just put one on his shoulder.  How convenient for Gerald Joyce to start with a complex RNA enzyme.  He has said that the spontaneous appearance of chains of RNA on the early earth would have been a near miracle (02/15/2007).
    Something is very wrong with this picture.  Darwinian evolution experiments are like the way one would execute a computer program?  OK, Baloney Detectors, get busy.  Your assignment is to identify all the ways the scientists snuck information into the system, making this a case of intelligent design, and therefore worthless as an illustration of Darwinian evolution.  How should they have designed the system to really mimic Darwinism?  If you need help, you can re-read the following entries: 07/31/2002, 12/18/2002, 05/08/2003, 10/04/2005, 07/05/2006, 11/14/2006, 08/07/2007.
  Grad students can scrutinize the original open-source paper in detail.
    Before teaching the kiddies about Darwinian evolution on the tabletop, teach them the word TANSTAAFL: There ain’t no such thing as a free lunch.  That will help inoculate them against the scam artists known as evolutionary science reporters.

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Categories: Education

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