ID Friendly Evolution
More and more, I am coming across articles that I consider ID-friendly. I consider them ID friendly because they express ideas and hypotheses that very easily lend themselves to teleological interpretations. As such, I highly recommend them to those interested in using ID. One such article is as follows:
Ann N Y Acad Sci 1999 May 18;870:23-35
Genome system architecture and natural genetic engineering in evolution.
Shapiro JA
Department of Biochemistry and Molecular Biology, University of Chicago, Illinois 60637, USA.
Molecular genetics teaches three lessons relevant to the nature of genetic change during evolution: (1) Genomes are organized as hierarchies of composite systems (multidomain protein-coding sequences; functional loci made up of regulatory, coding, processing, and intervening sequences; and multilocus regulons and replicons) interconnected and organized into specific "system architectures" by repetitive DNA elements. (2) Genetic change often occurs via natural genetic engineering systems (cellular biochemical functions, such as recombination complexes, topoisomerases, and mobile elements, capable of altering DNA sequence information and joining together different genomic components). (3) The activity of natural genetic systems is regulated by cellular control circuits with respect to the timing, activity levels, and specificities of DNA rearrangements (e.g., adaptive mutation, Ty element mobility, and P factor insertions). These three lessons provide plausible molecular explanations for the episodic, multiple, nonrandom DNA rearrangements needed to account for the evolution of novel genomic system architectures and complex multilocus adaptations. This molecular genetic perspective places evolutionary change in the biologically responsive context of cellular biochemistry.
Shapiro is yet another scientist who appears unsatisfied by the current traditional paradigm commonly known as neo-Darwinism.
He writes:
Most of the basic concepts in conventional evolutionary theory predate 1953 when virtually nothing was known about DNA....The conceptual universe of molecular genetics is as different from classical genetics and evolutionary theory as quantum physics is from classical mechanics.
While he accepts evolution, he does not seem to think evolution is simply microevolution + deep time. Instead, he envisions the origin of truly novel biological features quite differently:
One of the most important questions in evolution is: How can new adaptations originate? This is a difficult question, because most evolutionary novelties, such as the eye or the wing, involve the orchestrated expression of many different loci, a number of which act in the expression of multiple
phenotypes. Conventional explanations that randomly generated advantageous changes in complex characters accumulate one locus at a time are unconvincing on both functional and probabilistic grounds, because there is too much interconnectivity and too many degrees of mutational freedom. The genomic reorganization perspective, however, allows us to restate the question of adaptive novelties as : How can a complex multicomponent genomic system be assembled before screening by selection?
Essentially, natural selection is kicked off its throne. It no longer acts as the busy-body overseer who monitors each step of the design, but instead simply gets called upon for final approval when the intra-cellular designers are finished.
Yet how does this work? Shapiro argues that the genome of various organisms possess a "system architecture." Essentially, the various genes in the genome are organized in such a fashion that their expression is tied to such organization. And what plays the crucial role in this organization is the repetitive DNA (commonly called "junk DNA"). Shapiro explains:
From a theoretical perspective, the functional significance of nonprotein coding repetitive DNA elements in transcriptional regulation should not be surprising. Biologically appropriate gene expression is a process of reading those texts (protein coding sequences) suitable for one set of conditions while ignoring the other texts stored in the genome. To accomplish this task, the transcriptional apparatus requires a hierarchical addressing system, which is provided by the right combination of repetitive elements determining both chromatin organization and transcription factor binding.
Shapiro further explains:
Based on their fundamental roles in genome transmission and in determining patterns of gene expression, it can be proposed that repetitive DNA elements set the "system architecture" of each species. The term "system architecture" is used to draw analogy with computers, where programs with the same functionality (e.g., Microsoft Word) are encoded differently according to the requirements of the underlying hardware and operating system (e.g., MacOS or Windows). From the system architecture perspective, what makes each species unique is not the nature of its proteins (a Windows desktop resembles a Mac desktop) but rather a distinct "specific" organization of the repetitive DNA elements that must be recognized by nuclear replication, segregation, and transcriptional functions. In other words, resetting the genome system architecture through reorganization of repetitive DNA content is a fundamental aspect of evolutionary change.
What Shapiro is basically saying is that what makes one organism different from another is not so much its proteins, but the "logic" in which all this material/text (common to all life forms) is expressed and this in turn is a function of the manner in which the "junk DNA" is arranged.
Evolution would then involve the re-wiring of this logical circuit and Shapiro argues that with life comes a toolkit of instruments that can fulfill this function, giving us "natural genetic engineering"
molecular genetics has focused on the ability of cells to carry out recombination between homologous DNA segments, to integrate exogenous DNA (transformation), to transfer DNA from one cell to another (plasmids and phages), to insert and excise episomes (F and lambda), to mobilize defined DNA segments from one location to another (transposons), and to join DNA segments that do not share sequence homology (so-called "illegitimate recombination" involving topoisomerase and transposase activitities).
Shapiro envisions evolution as the deployment of this "natural genetic engineering" toolkit that functions to redesign the system architecture of the genome and thus facilitate rather significant and rapid evolutionary transitions. But what is even more interesting is that such a process of resetting does not need to be envisioned in random terms:
It is widely recognized that a great deal of genetic variation results from the action of cellular biochemical functions...Nonetheless, the conceptual implications of natural genetic engineering are not widely recognized, and most evolutionists try (unrealistically) to model the action of these cellular functions to resemble the random mutational events of conventional evolutionary theory. What distinguishes cellular biochemistry from chemical events outside the living cell is that cellular events are subject to biological regulation by signal transduction networks. There is abundant evidence that DNA biochemistry is no exception to this rule and that natural genetic engineering is also subject to biological regulation controlling both the timing and the localization of changes, as seen in the following cases.
Shapiro also writes:
A distinct mode of regulation of natural genetic engineering activities produces non-random target selection within the genome. A high degree of sequence specificity is inherent in many natural genetic engineering systems.....A growing body of evidence indicates that cellular signal transduction networks can guide natural genetic engineering systems to preferred locations, as seen in the following cases.
Shapiro's vision of evolution is very different from that of Richard Dawkins. Dawkins views are merely an expression of raw reductionism, which I predict will become more and more obsolete (at certain levels) in our post-reductionist age. Shapiro-like views, involving large-scale redesign not necessarily guided by mistakes and selection, but by the cueing of internal programs that work to reset the cell's system architecture, will push aside Dawkinsian views over the next century. For if Shapiro is right, the repetitive DNA so much a part of the so-called junk DNA is an integral component of the genome's system architecture such that this "junk" only just happens to be the very information that makes a cat a cat and not a dog.
It is also noteworthy that Shapiro writes, "Conventional explanations that randomly generated advantageous changes in complex characters accumulate one locus at a time are unconvincing on both functional and probabilistic grounds, because there is too much interconnectivity and too many degrees of mutational freedom."
I find this interesting because Shapiro, from the perspective of molecular biology, is saying much the same as many paleontologists have been saying, including Robert L. Carroll. Carroll recently observed:
large-scale patterns and rates of evolution are not comparable with those hypothesized by Darwin on the basis of extrapolation from modern populations and species
The most striking features of large-scale evolution are the extremely rapid divergence of lineages near the time of their origin, followed by long periods in which basic body plans and ways of life are retained. What is missing are the many intermediate forms hypothesized by Darwin
This explosive evolution of phyla with diverse body plans is certainly not explicable by extrapolation from the processes and rates of evolution observed in modern species, but requires a succession of unique events
This explosive evolution of phyla with diverse body plans is certainly not explicable by extrapolation from the processes and rates of evolution observed in modern species, but requires a succession of unique events
Long-term evolution is not simply the result of selection of alternative alleles controlling specific traits, or the progressive accumulation of new mutations in an additive fashion, as proposed by quantitative genetics.
see http://www.arn.org/ubb/Forum1/HTML/000252.html for more
What all of this means is that the crown jewel of Darwinism, the so-called Modern Synthesis, is becoming more and more irrelevant to a deeper understanding of evolution.
Shapiro's views don't just amount to a important functional role for "junk DNA" and the growing irrelevance of the Modern Synthesis, but they also hold great potential for a very positive fruition of a robust teleological interpretation of life's history. As science moves in this direction, its difference from ID dwindles. This can be appreciated if one begins to ponder the huge implications entailed in the way Shapiro introduced his topic as discussed at a conference:
the debate moved toward thinking of "evolution as biological function" rather than of evolution as accidental changes captured by selection.
I've been thinking and writing about this and may share some opinions later.