Science & Faith
2/9/13 at 10:35 PM 14 Comments

Research Supporting Intelligent Design: This is How Science Works

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Many of those commenting on my last post Six Most Frequently Asked Questions about Intelligent Design managed to ignore the respectable track record of research into intelligent design that I documented briefly (I provided a link that many refused to follow, apparently). I shall address this issue more fully here. One should not expect thousands of publications, given that intelligent design (ID), especially in the life sciences, is a new research tradition. Although ID theory may be traced back to at least the ancient Greeks, the recent development of information theory within biology has opened up an impressive new research agenda.

My colleagues at Discovery Institute have provided an annotated list of peer-reviewed ID publications that grows each year. In 2011, the ID movement celebrated its 50th peer-reviewed scientific paper. Note also some of the hubs of ID-related research that are reflected in the annotated list.

  1. Biologic Institute, led by molecular biologist Doug Axe, is "developing and testing the scientific case for intelligent design in biology." Biologic conducts laboratory and theoretical research on the origin and role of information in biology, the fine-tuning of the universe for life, and methods of detecting design in nature.
  2. Another ID research group is the Evolutionary Informatics Lab, founded by senior Discovery Institute fellow William Dembski along with Robert Marks, Distinguished Professor of Electrical and Computer Engineering at Baylor University. Their lab has attracted graduate-student researchers and published multiple peer-reviewed articles in technical science and engineering journals showing that computer programming "points to the need for an ultimate information source qua intelligent designer."
  3. Other pro-ID scientists around the world are publishing peer-reviewed pro-ID scientific papers. These include biologist Ralph Seelke at the University of Wisconsin Superior, Wolf-Ekkehard Lönnig who recently retired from the Max Planck Institute for Plant Breeding Research in Germany, and Lehigh University biochemist Michael Behe.

As the introduction to the annotated list of publications explains:

These and other labs and researchers have published their work in a variety of appropriate technical venues, including peer-reviewed scientific journals, peer-reviewed scientific books (some published by mainstream university presses), trade-press books, peer-edited scientific anthologies, peer-edited scientific conference proceedings and peer-reviewed philosophy of science journals and books. These papers have appeared in scientific journals such as Protein Science, Journal of Molecular Biology, Theoretical Biology and Medical Modelling, Journal of Advanced Computational Intelligence and Intelligent Informatics, Quarterly Review of Biology, Cell Biology International, Rivista di Biologia/Biology Forum, Physics of Life Reviews, Annual Review of Genetics, and many others. At the same time, pro-ID scientists have presented their research at conferences worldwide in fields such as genetics, biochemistry, engineering, and computer science.

This growing network of research results is converging on a consensus: complex functional biological capabilities cannot arise by unguided material mechanisms, but require an intelligent cause.

Here below are just two recent additions to Discovery Institute's annotated list of ID publications. This small sample of research will help you grasp how ID is making progress. Merely pointing out the fact that the majority of scientists reject ID is no substitute for giving ID publications an honest read. Copernicus, Kepler, and Galileo held minority scientific viewpoints in their own day. Judging from the comments of a few of my readers, they have read very little of ID research. They seem to dismiss it primarily because of their own deeply cherished beliefs, rather than based on a fair assesment of the evidence.

Joseph A. Kuhn, “Dissecting Darwinism,” Baylor University Medical Center Proceedings, Vol. 25(1): 41-47 (2012).

This article by Dr. Joseph Kuhn of the Department of Surgery at Baylor University Medical Center appeared in the peer-reviewed journal Baylor University Medical Center Proceedings. It poses a number of challenges to both chemical and biological evolution, including:

  1. Limitations of the chemical origin of life data to explain the origin of DNA
  2. Limitations of mutation and natural selection theories to address the irreducible complexity of the cell
  3. Limitations of transitional species data to account for the multitude of changes involved in the transition.

Regarding the chemical origin of life, Kuhn points to the Miller-Urey experiments and correctly observes that "the experimental conditions of a low-oxygen, nitrogen-rich reducing environment have been refuted." Citing Stephen Meyer's Signature in the Cell, he contends that "the fundamental and insurmountable problem with Darwinian evolution lies in the remarkable complexity and inherent information contained within DNA." Kuhn also explains that "Darwinian evolution and natural selection could not have been causes of the origin of life, because they require replication to operate, and there was no replication prior to the origin of life," but no other known cause can organize the information in life.

Dr. Kuhn then turns to explaining the concept of irreducible complexity, citing Michael Behe's book Darwin's Black Box and noting that "irreducible complexity suggests that all elements of a system must be present simultaneously rather than evolve through a stepwise, sequential improvement, as theorized by Darwinian evolution." Further, "The fact that these irreducibly complex systems are specifically coded through DNA adds another layer of complexity called 'specified complexity.'" As a medical doctor, Kuhn proposes that irreducibly complex systems within the human body include "vision, balance, the respiratory system, the circulatory system, the immune system, the gastrointestinal system, the skin, the endocrine system, and taste." He concludes that "the human body represents an irreducibly complex system on a cellular and an organ/system basis."

Kuhn also explores the question of human/ape common ancestry, citing Jonathan Wells's book The Myth of Junk DNA and arguing:

DNA homology between ape and man has been reported to be 96% when considering only the current protein-mapping sequences, which represent only 2% of the total genome. However, the actual similarity of the DNA is approximately 70% to 75% when considering the full genome, including the previously presumed "junk DNA," which has now been demonstrated to code for supporting elements in transcription or expression. The 25% difference represents almost 35 million single nucleotide changes and 5 million insertions or deletions.

In Dr. Kuhn's view, this poses a problem for Darwinian evolution because the "[t]he ape to human species change would require an incredibly rapid rate of mutation leading to formation of new DNA, thousands of new proteins, and untold cellular, neural, digestive, and immune-related changes in DNA, which would code for the thousands of new functioning proteins."

Kuhn also observes that a challenge to neo-Darwinism comes from the Cambrian explosion:

Thousands of specimens were available at the time of Darwin. Millions of specimens have been classified and studied in the past 50 years. It is remarkable to note that each of these shows a virtual explosion of nearly all phyla (35/40) of the animal kingdom over a relatively short period during the Cambrian era 525 to 530 million years ago. Since that time, there has been occasional species extinction, but only rare new phyla have been convincingly identified. The seminal paper from paleoanthropologists J. Valentine and D. H. Erwin notes that the absence of transitional species for any of the Cambrian phyla limits the neo-Darwinian explanation for evolution.

Despite Texas's call for discussing the scientific strengths and weaknesses of Darwinian evolution, Kuhn closes by noting, "In 2011, when new textbooks were presented to the State Board of Education, 9 out of 10 failed to provide the mandated supplementary curricula, which would include both positive and negative aspects of evolution (44)." Citing Discovery Institute's Report on the Texas Textbooks, he laments:

[S]everal of the textbooks continued to incorrectly promote the debunked Miller-Urey origin of life experiment, the long-discredited claims about nonfunctional appendix and tonsils, and the fraudulent embryo drawings from Ernst Haeckel. In essence, current biology students, aspiring medical students, and future scientists are not being taught the whole story. Rather, evidence suggests that they continue to receive incorrect and incomplete material that exaggerates the effect of random mutation and natural selection to account for DNA, the cell, or the transition from species to species.

Kuhn concludes, "It is therefore time to sharpen the minds of students, biologists, and physicians for the possibility of a new paradigm."

Douglas D. Axe, Philip Lu, and Stephanie Flatau, “A Stylus-Generated Artificial Genome with Analogy to Minimal Bacterial Genomes,” BIO-Complexity, Vol. 2011(3) (2011).

This peer-reviewed paper is a follow-up up to the 2008 PLoS One paper co-authored by Axe and Lu on Stylus, a computer simulation of evolution which is more faithful to biological reality than many others. This 2011 paper explains that the “functions” of the digital organisms in other simulations are often divorced from real-world meaning. They designed Stylus to present a more accurate picture:

The motivation for Stylus was the recognition that prior models used to study evolutionary innovation did not adequately represent the complex causal connection between genotypes and phenotypes.

Stylus aims to correct these deficiencies by simulating Darwinian evolution in a manner that more accurately reflects the biological relationship between genotype and phenotype. It is also more realistic because it solves real-world problems. As the paper explains, “Functional specificity therefore has a structural basis in the Stylus world, just as it does in the real world.” Stylus manipulates digital objects that have real-world meaning: the targets of evolution in Stylus are Chinese characters. As the paper explains:

These translation products, called vector proteins, are functionless unless they form legible Chinese characters, in which case they serve the real function of writing. This coupling of artificial genetic causation to the real world of language makes evolutionary experimentation possible in a context where innovation can have a richness of variety and a depth of causal complexity that at least hints at what is needed to explain the complexity of bacterial proteomes.

These characters not only have real-world meaning, but their function-related shapes bear interesting analogies to proteins. An additional similarity between Chinese characters and proteins is that just as protein domains are re-used throughout many proteins, so particular shapes, called “strokes,” are found commonly throughout Chinese characters.

Basic to life is an information conversion, where the information carried in genes (the genotype) is converted into an organism's observable traits (the phenotype). Those biological structures then perform various functions. Another way of framing this information conversion is therefore: sequence → structure → function. Axe, Lu and Flatau explain that many previous computer programs attempting to simulate evolution achieve part of this conversion, but not the whole thing.

For example, Conway's famous Game of Life starts with a structure, and in some instances that structure can perform a function. But there is no sequence involved in the conversion. Avida starts with a sequence of programming commands, and when successful performs certain logic functions. But in Avida there is no structure to mediate between sequence and function. Stylus, on the other hand, is more advanced in that it simulates the full sequence → structure → function information transfer. It does this by starting with a programmed genome. As the paper explains:

[The] Stylus genome encodes a special kind of text, namely, one that describes how to decode the genome. That is, the desired genome will encode a sequence of Chinese characters (in the form of vector proteins) that tells a reader of Chinese how Stylus genes are translated into vector sequences, and how those sequences are processed to make readable vector proteins.

The paper explains: “What Stylus offers that no other model offers, to our knowledge, is an artificial version of gene-to-protein genetic causation that parallels the real thing.”

In the world of Stylus, a Chinese character is like a protein. So how can we determine if a functional "protein" has evolved? According to the paper, "At the core of Stylus software is an algorithm that quantifies the likeness of a given vector protein to a specified Chinese character." This complicated algorithm is described as follows:

Stylus endows these graphical constructs with interesting similarities to their molecular counterparts by uncovering and exploiting a pre-existing analogy -- the analogy between the set of characters used in Chinese writing and the set of protein structures used in life. Specifically, vector proteins are drawn objects that may function as legible Chinese characters if they are suitably formed. ... Stylus is unique in its use of real function that maps well to molecular biology. It therefore represents a significant advance in the field of evolutionary modeling. (internal citations omitted)

The paper presents a set of Chinese characters that can be used for simulating the evolutionary process in the Stylus world. But can these Chinese character groups, which have many qualities that parallel real-world protein families, evolve by random mutation and natural selection? That's the sort of question the creators of Stylus hope to answer. The results of such simulations will probably be fleshed out in future papers. But the current paper leaves us with a strong sense of where this is all heading:

Evolutionary causation is intrinsically tied to the relationship between genotype and phenotype, which depends on low-level genetic causation. It follows that evolutionary explanations of the origin of functional protein systems must subordinate themselves to our understanding of how those systems operate. In other words, the study of evolutionary causation cannot enjoy the disciplinary autonomy that studies of genetic causation can.

In view of this, the contribution of Stylus is to make evolutionary experimentation possible in a model world where low-level genetic causation has the essential role that it has in the real world. Combined with the free Stylus software, the complete Stylus genome made freely available with this paper paves the way for analogy-based studies on a wide variety of important subjects, many of which are difficult to study by direct experimentation. Among these are the evolution of new protein folds by combining existing parts, the optimality and evolutionary optimization of the genetic code, the significance of selective thresholds for the origin and optimization of protein functions, and the reliability of methods used for homology detection and phylogenetic-tree construction.

There probably will never be a perfect computer simulation of biological evolution, but Stylus brings new and improved methods to the field of evolutionary modeling. This tool will help those interested in testing the viability of Darwinian claims to assess whether complex features can be created by random mutations at the molecular level.

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