Empirical ID research

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By coming to understand intelligent design and its subsidiary views, we can see that empirical study in academic research applications and commercial research and development is already underway and more is currently developing. Here we will explore empirical research applications of intelligent design, also known as ID-empirics.

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Empirical research - current

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ID Research Groups

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Biologic Institute

Intelligent Science… The Biologic Institute brings together scientists with diverse expertise, unified by the realization that a revolution in biology—with far reaching implications—is well under way. Like many revolutionary ideas, this one is powerful in its simplicity: The more we learn about the organization of life, the more clearly it reveals design. When you realize that living cells store, transmit, and process information, the similarities with human technology are unavoidable. But when you get a glimpse of the remarkable sophistication of the cellular processes—and the almost unbelievably small scale of the molecular systems performing them—you begin to realize that humans are novices when it comes to complex design. . . .
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Evolutionary Informatics Lab

The Evolutionary Informatics Lab
Evolutionary informatics merges theories of evolution and information, thereby wedding the natural, engineering, and mathematical sciences. Evolutionary informatics studies how evolving systems incorporate, transform, and export information. The Evolutionary Informatics Laboratory explores the conceptual foundations, mathematical development, and empirical application of evolutionary informatics. The principal theme of the lab’s research is teasing apart the respective roles of internally generated and externally applied information in the performance of evolutionary systems.
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Biosteganography

William Dembski asked, "What if organisms instantiate designs that have no functional significance but that nonetheless give biological investigators insight into functional aspects of organisms? Such second-order designs would serve essentially as an 'operating manual,' of no use to the organism as such but of use to scientists investigating the organism."
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Reverse engineering

Reverse engineering has a particularly close relationship with ID-theoretic premises. It also has a particularly close relationship with molecular biology. This is because the living cell is filled with molecular machines that perform various purposeful tasks. At the same time, these biomachines are made of amino acids and proteins, which are derived by direct production from the informational code in the DNA. This yields the cell, its individual parts, and the internal means of production, highly investigable by reverse engineering, which historically is an architectural/engineering/structural method of studying man-made machines and structures.
  • Scott Minnich of the University of Idaho employs reverse engineering as part of his molecular and microbiological research.
  • A researcher studying fluid dynamics in the brain also sees the advantages of design perspectives in biological investigation, especially reverse engineering and principles of fluid dynamics, which were developed to produce better machines and pumps.
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Centrioles

Jonathan Wells looks at the pair of centrioles in the cell, from an intelligent design (ID) perspective.
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ID-innovation detection - Commercial Applications

http://www.genetic-id.com/
This genetics company is utilizing something akin to the informational aspects of specifications and the Explanatory Filter to identify genetic tampering. The company uses several forms of DNA fingerprinting; either by directly investigating the DNA, or indirectly through the proteins and ribosomes.
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Evolvability

Researching the capabilities and theoretical limits of evolution, mutation, and selection from a design perspective.
Michael Behe's proposals of Irreducible Complexity (IC) state that biological structures which show IC cannot evolve from mutations and undirected biological processes. Dr. Behe claims that the bacterial flagellum is one such biological component that exhibits IC. In order test Behe's proposal in the laboratory, scientists are using gene knock-out methods to form a type III system with a missing flagellar component and see if the bacteria, on their own, can assemble the TTS into a functional flagellum. If the flagellum is not irreducibly complex, bacteria should be able to develop one through mass breeding of the bacteria with the disabled flagellum.
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Haldane's Dilemma

Walter ReMine is currently studying Haldane's Dilemma from a design perspective, with some of his recent papers clarifying this issue in population genetics, such as Cost theory and the cost of substitution—a clarification, and More Precise Calculations of the Cost of Substitution.
Haldane's Dilemma "puts a limit on the rate of beneficial evolution. It does not limit the rate of neutral or harmful evolution, which can be far more rapid. However, my book also contributes a style of argument previously unheard of – a serious limit on the rate of expressed neutral substitutions. The argument involves something routinely left out of evolutionary discussions – error catastrophe. By seeing the connection between error catastrophe and plausible substitution rates, I was able to create a new type of argument."[1]


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Mutagenesis

"Can rearrangement of developmental genes produce major, advantageous changes in organisms?" -- from Ralph Seelke's After Darwin’s Black Box
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Morphogenesis

Measures of phenotypic and genotypic divergence: "What are the genetic differences between organisms that have an unknown 'common ancestor'? What would be needed to change one into another?" -- from Ralph Seelke's After Darwin’s Black Box
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Privileged Planet research

Empirically exploring the correlations between habitability and discoverability has been a very successful research project for Guillermo Gonzalez and Jay Richards. This research has broken new ground in the fields of astrobiology and astrophysics, by grappling with an understanding of what type of environment will aid an intelligent race in becoming scientifically and technologically advanced.
Gonzalez, Guillermo, (2005) Habitable Zones in the Universe, Origins of Life and Evolution of Biospheres (Formerly Origins of Life and Evolution of the Biosphere), Volume 35, Issue 6, Pages 555 - 606
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Gonzalez’s lunar research proposals

Gonzalez published a paper with two other researchers on the idea to search the Moon for Earth meteorites that were blasted off the Earth about 3.9 BYA. The rocks should contain relatively unaltered samples from Earth's distant past. The paper was reviewed in Nature.
From The Privileged Planet, p319:
If measurability and discoverability are optimized from our vantage point [Gonzalez and Richards' thesis], however, then we might expect that such information will be preserved somewhere accessible to us. The origin of life is a particularly important question. It would be surprising assuming the correlation, if it could not be investigated. In fact, we might predict that such evidence is available somewhere, if we search diligently enough. It was precisely this prediction that led one of us (Guillermo) to consider the value of lunar exploration for uncovering relatively well-preserved relics of Earthly life from this early period.
From Witt's IDtheFuture.com post:
The Privileged Planet hypothesis motivated him to search for and discover the idea about the moon containing the fossilized remains of life on the early Earth. He isn't claiming that there was no other way to happen upon the idea. To take another example, early scientists like Kepler and Newton were motivated by their belief in a rational designer to search out patterns of mathematical order in the movement of the planets. That alone doesn't prove that such a view was absolutely necessary to the breakthroughs they achieved, but it does strongly suggest that it proved very useful to them.
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Neuroscience

Jeffrey M. Schwartz, research professor of psychiatry at the University of California at Los Angeles.
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Protein evolution

This research gives indirect scientific support to intelligent design by demonstrating inherent limitations to unguided evolutionary processes.
  • Behe, M.J. and Snoke, D.W. (2004), “Simulating Evolution by Gene Duplication of Protein Features That Require Multiple Amino Acid Residues,” Protein Science, 13: 2651-2664.
In this article, Behe and Snoke show how difficult it is for unguided evolutionary processes to take existing protein structures and add novel proteins whose interface compatibility is such that they could combine functionally with the original proteins. By demonstrating inherent limitations to unguided evolutionary processes, this work gives indirect scientific support to intelligent design and bolsters Behe’s case for intelligent design via Irreducible Complexity in answer to some of his critics.
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ID Metrics

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Ontogenetic depth and the ontogenetic network

Marcus Ross and Paul Nelson are developing biological metrics for biological parameters. Ontogenetic depth is the distance, in number of cell divisions, from the egg to the adult capable of reproduction. The ontogenetic network is related to biological parameters like number of genes, number of cells, type and number of tissues, type and number of organs, type and number of organ systems, and body plan.
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Specified Complexity

While not undertaken as an ID application, this research utilizes William Dembski and Paul Davies' understanding of Specified Complexity and puts it to practical use as a Native Intelligence Metric (NIM): Exercising a Native Intelligence Metric on an Autonomous On-Road Driving System
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Genetics

This article examines the role of transposons in the abrupt origin of new species and the possibility of a partly predetermined generation of biodiversity and new species. The authors’ approach is non-Darwinian, and they cite favorably the work of design theorists Michael Behe and William Dembski.
  • Lönnig, Wolf-Ekkehard, Heinz-Albert Becker (2005) "Transposons: Eukaryotic," Encyclopedia of Life Sciences.
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Conceptually related

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Junk DNA

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Empirical demonstrations of causal adequacy/causal specifity.

Experiments demonstrating the possibility of an intelligent origin and diversification of life.

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Design Receptivity, design input, and information receptivity

While not undertaken as an ID application, this kind of research could be modified for the purpose of exploring the malleability and receptivity of organisms to uniquely intelligent processes:
  • Chiu, D.K.Y. & Lui, T.H., “Integrated Use of Multiple Interdependent Patterns for Biomolecular Sequence Analysis,” International Journal of Fuzzy Systems, 4(3) (September 2002): 766-775.
The opening paragraph of this article reads: Detection of complex specified information is introduced to infer unknown underlying causes for observed patterns. By complex information, it refers to information obtained from observed pattern or patterns that are highly improbable by random chance alone. We evaluate here the complex pattern corresponding to multiple observations of statistical interdependency such that they all deviate significantly from the prior or null hypothesis. Such multiple interdependent patterns when consistently observed can be a powerful indication of common underlying causes. That is, detection of significant multiple interdependent patterns in a consistent way can lead to the discovery of possible new or hidden knowledge.”
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Protein folding

Teleological research studying laws of biological form embedded in nature.
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Empirical research - potential

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Irreducible Complexity

  • IC core universality
  • IC malleability - how far, genotypically and phenotypically, can we push an IC core before it loses function? How far can we push the contextual concerns of IC, including formative dynamics, before function is lost? Are there gradations of functionality within it's genotypic or phenotypic context?
  • IC assembly-dependence
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General Purpose Programmable Systems

What is the significance of the presence of "general purpose programmable" systems being found in gene expression machinery as opposed to the expected "specialized" systems?

It appears that far deeper planning is required to create general purpose programmable systems as opposed to specialized systems. The advantage of general purpose programmable systems is that they are very compact in comparison to specialized systems. The reason for this compact size is in the reuse of programmable parts. The advantage of specialized systems on the other hand, is that no program is needed. So in the case of gene expression machinery, no DNA would be required. The disadvantage in specialized systems is that if 100 proteins were needed for the first self replicating cell, then 100 specialized protein production machines would have also been required. This would mean that hte complete system would need to be 100 times larger and therefore, also extremely more physically complex than the programmable system.

If life arose by only natural undirected processes, then shouldn't we expect to see a separate specialized protein production machine for each and every different type of protein in the original living cell so that no other planning would be needed? What is meant by "deeper planning" is this: In a general-purpose programmable system, many levels of extrapolation is required to create such a system that includes anticipated alternate functions or designs. But this general-purpose programmable system is just what we find in the gene expression machinery of cells. Isn't this all the more reason to consider ID far more superior to natural undirected origin of life theories?
In his book "No Free Lunch", William Dembski outlines the design process as follows:

http://www.arn.org/docs/dembski/wd_nfl_intro.htm No Free Lunch

Quote:
Preface
How a designer gets from thought to thing is, at least in broad strokes, straightforward:
(1) A designer conceives a purpose.
(2) To accomplish that purpose, the designer forms a plan.
(3) To execute the plan, the designer specifies building materials and assembly instructions.
(4) Finally, the designer or some surrogate applies the assembly instructions to the building materials.
What emerges is a designed object, and the designer is successful to the degree that the object fulfills the designer's purpose. In the case of human designers, this four-part design process is uncontroversial. Baking a cake, driving a car, embezzling funds, and building a supercomputer each presuppose it. Not only do we repeatedly engage in this four-part design process, but we have witnessed other people engage in it countless times. Given a sufficiently detailed causal history, we are able to track this process from start to finish. [End Quote]

Wouldn't a designer visit steps 1 and 2 many times depending on how flexible he decides to make the general purpose programmable system, before he proceeds further to steps 3 and 4? Isn't this going to require deeper planning, deeper anticipation, deeper foresight, and deeper thinking? Also, why wouldn't step 1 require volition of an intelligent agent to conceive contingent purposes?

If on the one hand abiogenesis is said to begin with specialized protein production machines, then this would obviously require an enormous amount of specialized protein hardware that would have all had to come together by natural undirected processes.

However if on the other hand abiogenesis is said to begin with the far more compact general purpose programmable protein production machines that are actually there today, then wouldn't these systems require planning using many levels of extrapolative behavior to insure the versatility needed to generate all of the hundreds (?) of different proteins required by the first replicating cell?

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See also

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External links

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Searches

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Centriole

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Empirical ID Research

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