Evolving Complexity

Anyone analyzing a scientific explanation should evaluate whether it explains the phenomenon or explains it away.  For instance, to say that bats have sonar because they evolved it provides little in the way of understanding of how or why that happened.  Recently, some scientific papers have directly addressed the topic of complex systems in biology.  How good a job are they doing at explaining complexity in an evolutionary context?

1. Very interesting:  Ross and Arkin, in the lead article for a special issue on complex systems in PNAS,¹ started this way: “There is great interest in complex systems in chemistry, biology, engineering, physics, and gene networks, among others.  The complexity comes from the fact that in many systems there are a large number of variables, many connections among the variables including feedback loops, and many, usually nonlinear, equations of motion, or kinetic and transport equations.”  Shortly later, they said, “Nowhere is the importance of complex dynamics and architectures clearer than in biological systems.”  Then they summarized the various papers in the issue: “Topics range from information processing in their signaling network and the organization of their metabolism, to how populations of differentiated cells communicate with one another to coordinate behavior, and to how evolution has arrived at different recurrent motifs of control and linked together different physiological functions.”
       The reader will look in vain, however, for any further mention of the word evolution in Ross and Arkin’s article.  Each summary describes the characteristics of complexity in living systems, such as signal transduction, correlating metabolic flux measurements with functions, and the expressions of genes in networks.  The word design outnumbers evolution three to one: for example, “The boundaries between phenotypic regions yield a method for discussion of the tolerance of a system to large changes of its parameters and the identification of design principles.”
2. Unsolved mystery.  Perhaps the most pertinent recent paper on the evolution of complex systems appeared February in PLoS Biology.²  It’s title sets the stage: “Wings, Horns, and Butterfly Eyespots: How Do Complex Traits Evolve?”  Antonio Monteiro and Ondrej Podlaha set the stage by assuming evolution:
   

   Throughout their evolutionary history, organisms have evolved numerous complex morphological, physiological, and behavioral adaptations to increase their chances of survival and reproduction.  Insects have evolved wings and flight, which allowed them to better disperse, beetles have grown horns to fight over females, and moths and butterflies have decorated their wings with bright circles of colored scales to scare off predators.  The way that most of these and other adaptations first evolved, however, is still largely unknown.  In the last two decades we have learned that novel traits appear to be built using old genes wired in novel ways, but it is still a mystery whether these novel traits evolve when genes are rewired de novo, one at a time, into new developmental networks, or whether clusters of pre-wired genes are co-opted into the development of the new trait.  The speed of evolution of novel complex traits is likely to depend greatly on which of these two mechanisms underlies their origin.  It is important, thus, to understand how novel complex traits evolve.

   Their presentation is like the chef who offers two choices on the menu: fish sticks, or fish cubes.  Both mechanisms they offered to explain complex systems were fully evolutionary.  Either the animals evolved their wings, horns and eyespots de novo, or they co-opted the equipment from previous complex systems with other functions and applied them in new ways.  They seem to like co-option better.  “Creating a developmental program de novo would involve linking many genes one-by-one, requiring each mutation to drift into fixation, or to confer some selective advantage at every intermediate step in order to spread in the population,” they said in the Darwinian spirit.  “While this lengthy process is not completely unlikely, it could be circumvented with fewer steps by recruiting a top regulator of an already existing gene network, i.e., by means of gene network co-option.”  The rest of the paper leaned toward this approach, since it apparently requires fewer miracles, as long as one accepts the prime miracle of the “already existing gene network.”
       It’s interesting that this paper appeared the month of the 200th birthday of Darwin in the category “Unsolved Mystery.”  Articles in the Unsolved Mystery series, the heading explained, “discuss a topic of biological importance that is poorly understood and in need of research attention.”  One might think that this is the very mystery Darwin solved 150 years ago.  Monteiro and Podlaha made it look like evolutionary biologists are still at square one: “There is still much to do in order to fully understand how novel complex traits evolve,” their final paragraph began, before giving a final plug to their favored gene network co-option hypothesis.  Their paper did little more, though, than offer an experimental framework for distinguishing innovation from co-option.  Then they said, “This work is difficult and time consuming, but the question at its core—the genetic origin of new and complex traits—is probably still one of the most pertinent and fundamental unanswered questions in evolution today.”

3. In the beginning, Genetics:  A specific example of evolutionary theory applied to a complex system may shed light on the effectiveness of evolutionary explanations.  Michael Rosbash attempted to explain biological circadian clocks in PLoS Biology last month.³  His article, “The Implications of Multiple Circadian Clock Origins,” started with a take-off on the Genesis creation story.  “In the beginning… Genetics has had an awesome impact on our understanding of basic processes like circadian rhythms,” he teased.  But understanding how the clocks emerged is a different matter.  Circadian clocks exist in cyanobacteria and maybe earlier: “These relationships indicate that a similar, basic clock mechanism was present in a common ancestor, before the separation of insects and mammals more than 500 million years ago,” he noted.  “Some argue that the relationship of basic clock mechanism and proteins extends to Neurospora, which would push back the common ancestor date even further.”
       Rosbash noted the differences between the circadian clock systems of cyanobacteria and those of mammals.  This could either mean the function emerged early in the evolution of life, or that it arose twice: “the strong suggestion is that circadian rhythms have arisen at least twice, once in an ancestor of present-day cyanobacteria and then again in an ancestor of animals.”  While we’re speculating, let’s up the ante: “More than two evolutionary origins are also possible, as the different set of plant circadian proteins may indicate a third independent origin” (though he doubts this actually happened).
       So how did these complex systems evolve?  He appealed to selective advantages.  “Finally, what were the original selective advantages, the driving forces, for the origins/development of rhythms in the eukaryotic and bacterial systems?” he asked.  It appears that living cyanobacteria and mammals make good use of diurnal cycles and timekeeping to regulate their motions.  In the end, though, all he could do was speculate: “So although circadian transcription may not be essential for some cyanobacterial timekeeping features, its temporal organization may have provided a progenitor with a sufficient selective advantage to drive the development of rhythms.”  He almost attributed purpose and will to the ancestors.  Don’t most orchestrators work on purpose with a design and a plan?  In a “photosynthetic progenitor of current-day cyanobacteria,” he imagined that transcription factors “developed the capacity to orchestrate transcription in response to the ever-present light�dark cycle, and eventually to anticipate that cycle in a transcription- and even light-independent manner.”
       He ended by speculating that DNA repair mechanisms (involving multiple complex systems) linked light cycles to emerging clock systems: “Given the important role played by signal transduction in DNA repair, the relationship of DNA damage and repair to rhythms may have additional explanatory power, namely, the origin of circadian kinases.”

Explanatory power – that is the question.  To what extent does speculative appeal to imaginary ancestors, comparisons between functioning gene networks, and the assumption of the creative power of natural selection provide explanatory power for the origin of these systems?

1.  John Ross and Adam P. Arkin, “Complex systems: From chemistry to systems biology,” Proceedings of the National Academy of Sciences USA, published online before print April 20, 2009, doi: 10.1073/pnas.0903406106.
2.  Antonio Monteiro and Ondrej Podlaha, “Wings, Horns, and Butterfly Eyespots: How Do Complex Traits Evolve?” Public Library of Science: Biology, Vol. 7, No. 2, e37 doi:10.1371/journal.pbio.1000037.
3.  Michael Rosbash, “The Implications of Multiple Circadian Clock Origins,” Public Library of Science: Biology, Vol. 7, No. 3, e62 doi:10.1371/journal.pbio.1000062.

The tricks the Darwinians play should be obvious.  Over and over, evolution is the assumption, not the explanation: it evolved because it evolved.  Some PhD biochemist with a good grasp of philosophy of science and good baloney detecting skills should grab that second paper by Monterio and Podlaha and make it a poster child of the emptiness of evolutionary explanations.  Here, on the 200th birthday of the guy who made evolution famous, who supposedly explained everything, so that nothing in biology makes sense except in the light of evolution, they had nothing to offer but unsolved mysteries, just-so stories, miracles and futureware.  It’s disgusting.  And remember – just last month there was a huge uproar in Texas about whether students should be able to learn the “strengths and weaknesses” of evolutionary theory.  Now you understand why the NCSE was so up in arms.  Teaching those things in their actual proportions would require a whole semester on the weaknesses, and a nanosecond on the strengths.
    The news media, the school boards, the textbook writers and the courts are all resting on the quicksand of assumption that our academic labs are daily providing the solid evidence for Darwin’s theory needed to make it the sole dogma of the culture.  Day after day, week after week, month after month, year after year, Creation-Evolution Headlines has been bringing you the Darwin Party’s very best evidence.  We take you down under the superstructure, the gigantic monument to Darwin that pervades our culture, so that you can see the rotting pilings in quicksand on which it rests.  Would you want to trust it with your life?