Fields Where ID Uses the Scientific Method to Make Scientific Advancements

In a previous post I explained that our recent paper in BIO-Complexity, “The Broad Utility of the Theory of Intelligent Design to Guide Scientific Research,” describes three basic types of ID scientific research:

• ID Theoretical Scientific Research, which focuses on articulating ID-based predictions (expectations) and developing methods for detecting design.
• ID Historical Scientific Research, which tests those predictions / expectations to detect design in the origin of natural features in the past.
• ID Experimental Scientific Research, which tests those predictions / expectations to understand the operation of natural systems in the present.

I also discussed how ID uses the scientific method — starting with observations of what intelligent agents produce when they act, and then using those observations to construct hypotheses, expectations, and predictions about what we should find if intelligent design occurred. Those ID-based expectations / hypotheses / predictions can then be experimentally tested, leading to conclusions.

But what do real-world examples of this method look like? Below are eight case studies, all taken from our paper describing real-world examples of research ID proponents are doing, where ID is using the scientific method to yield scientific advancements.

(It should be noted that not every single paper cited in these examples is written by ID proponents, but each example does represent research that ID proponents are doing.)

Oh yes, and remember how ID can be used to perform both historical and experimental scientific research? The first four examples (biochemistry, paleontology, systematics, and physics) will be examples of ID doing historical scientific research, and the final four examples (genetics, systems biology, comparative anatomy and biomechanics, and neurophysiology) will be examples of ID doing experimental scientific research.

Biochemistry

• Observation: Intelligent agents think with an end goal in mind, allowing them to solve complex problems by taking many parts or symbols and arranging them in intricate patterns that perform a specific function — i.e., they generate high CSI. Intelligent agents also produce irreducibly complex machines.
• Hypothesis / expectation: Finely tuned high-CSI structures will be found in biology, including irreducibly complex systems (like machines) that require multiple components to function.
• Experiment (data collection): Research shows that irreducibly complex molecular machines exist in biology which contain irreducible cores that require multiple protein-parts and / or subsystems to be present in order to function. Research similarly shows that the amino acid sequences of many functional proteins must be highly complex and specified in order to function.

Paleontology

• Observation: Intelligent agents often rapidly infuse large amounts of information into systems, yielding new systems that are different and discontinuous from other systems.
• Hypothesis / expectation: Novel biological forms requiring large amounts of new genetic information will often appear abruptly in the fossil record, “fully formed” and discontinuous from previous designs.
• Experiment (data collection): Discontinuity is prevalent in biology. Biological novelty commonly appears in the fossil record abruptly in a pattern of “explosions.” The Cambrian explosion is a prime example where most of the major animal phyla appear “fully formed” in a geologically abrupt manner, but there are other examples in the fossil record, including a bird explosion, the abrupt appearance of angiosperms, a mammal explosion, and the abrupt appearance of the genus Homo.
• Conclusion: Many higher taxa appear suddenly, without similar direct precursors, indicating design.

Systematics

• Observation:  Intelligent agents reuse functional components in different systems (e.g., wheels for cars and airplanes, or keyboards on cell phones and computers), but do so according to functional needs, where functional dependencies may create some treelike structure in comparative relationships, but ultimately traits need not be distributed in a treelike pattern.
• Hypothesis / expectation:  Genes and other functional parts will be reused in different and unrelated organisms in patterns that match functional needs, and need not match a “tree” or nested hierarchy.
• Experiment (data collection):  Similar morphological traits and genes have been found reused in widely different organisms even where it is believed that the common ancestor did not have the trait in question. Echolocation exists in bats and whales, and similar genes even help produce this trait, though the presumed common ancestor of bats and whales is not thought to have had this ability. Similar genes control eye or limb growth in different organisms, though their presumed common ancestors are not thought to have had such forms of eyes or limbs. Genes and functional parts are frequently not distributed in a “treelike” pattern or nested hierarchy, but rather, show phylogenetic incongruity reflecting reusage of components in a non-nested pattern. As Davalos et al. (2012) acknowledge: “Incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species… phylogenetic conflict is common, and frequently the norm rather than the exception.”
• Conclusion: Phylogenetic incongruity is prevalent throughout life, and this reusage of highly similar and complex parts in non-treelike patterns is best explained by the action of an intelligent agent.

Physics

• Observation: Intelligent agents find extremely rare or highly unlikely solutions to complex problems.
• Hypothesis / expectation: The laws and constants of nature will have rare values that match what is necessary for life to exist (i.e., fine-tuning).
• Experiment (data collection): Multiple physical laws and constants must be finely tuned for the universe to be inhabited by advanced forms of life. These include the strength of gravity (the gravitational constant) compared to the strong nuclear force, which must be fine-tuned to 1 part in 10³⁵; the gravitational force compared to the electromagnetic force, which must be fine-tuned to 1 part in 10⁴⁰; the expansion rate of the universe, which must be fine-tuned to 1 part in 10⁵⁵; the cosmic mass density at Planck time, which must be fine-tuned to 1 part in 10⁶⁰; the cosmological constant, which must be fine-tuned to 1 part in 10¹²⁰; and the initial entropy of the universe, which must be fine-tuned to 1 part in 10^{10^123}. The Nobel Prize-winning physicist Charles Townes observed: “Intelligent design, as one sees it from a scientific point of view, seems to be quite real. This is a very special universe: it’s remarkable that it came out just this way. If the laws of physics weren’t just the way they are, we couldn’t be here at all”.
• Conclusion: The laws of nature are fine-tuned with extremely rare values that allow life to exist in our universe, indicating that the cosmic architecture of the universe was designed.

Genetics

• Observations:
  • About intelligent agents: Intelligent agents generate structures that have a purpose and function.
  • About an unexplained natural feature: Much DNA does not encode proteins and the reason for its existence is unexplained.
• Hypothesis / expectation: “Junk” DNA will perform valuable biological functions.
• Experiment (data collection):  Numerous studies provide evidence of widespread function for “junk DNA,” including evidence of widespread biochemical function in the human genome. Specific examples include functionality in pseudogenes, microRNAs, introns, endogenous retroviruses, and repetitive DNA including LINE, SINE, and Alu elements. A 2021 article in Nature reported that over 130,000 specific genomic elements were “previously called junk DNA,” followed by a paper in Genome Biology and Evolution that concluded, “The days of ‘junk DNA’ are over.”
• Conclusion: Functionality for junk DNA is prevalent, and aligns directly with a strong ID-based prediction that components will have function.

Systems Biology

• Observations:
  • About intelligent agents: Intelligent agents design systems that operate with overarching goals, where every part and subcomponent is oriented towards supporting the overall goal or purpose of the system. Intelligent agents also reuse optimal architectures in multiple systems.
  • About an unexplained natural feature: Glycolysis is a metabolic pathway that is found near-universally in life, and its widespread use remains to be explained.
• Hypothesis / expectation: Glycolysis is nearly ubiquitous among living organisms due to its efficient, goal-oriented design which serves multiple higher-level functions within biological systems.
• Experiment (data collection) Glycolysis is the subsystem found widespread across life whereby glucose is broken down into energy and biomass precursors. This system is subject to higher-level requirements and within glycolysis there are also lower-level processes subject to the requirements of glycolysis itself, showing a goal-directed and top-down design. The glycolytic topology or architecture has also been shown to be pareto-optimized around key cellular requirements, rationalizing why the architecture is used over and over across life. For different tissues of an organism, glycolytic enzymes are unique in that they are optimized for tissue-specific roles while the main architecture of the pathway is the same. The very sequence of glycolysis exhibits foresight in that energy must be invested up front before payoff results at the end of the pathway. This is expected from a top-down design process.
• Conclusion: Glycolysis has an efficient, top-down design that serves multiple higher-level needs of organisms, fulfilling predictions of intelligent design.

Comparative Anatomy and Biomechanics

• Observations:
  • About intelligent agents: Intelligent agents frequently reuse functional and versatile designs in different systems that are optimized to perform functions.
  • About an unexplained natural feature: The limb pattern consisting of a single-bone stylopod (e.g., humerus), two-bone zeugopod (e.g., radius and ulna), and multi-boned autopod with digits (e.g., wrist bones plus fingers) is found throughout nearly all vertebrate tetrapods.
• Hypothesis / expectation:  The vertebrate limb pattern is a highly functional, optimal, and versatile design, explaining its widespread reusage.
• Experiment (data collection):  The limb pattern found reused in virtually all tetrapods is “highly versatile and optimal not just for arms and legs but also for flippers and wings” since it uses “networks of segmented bones that enable smooth morphing of shapes as well as multifunctioning structures” and “linkage mechanisms that fine-tune motions and mechanical advantage.” The similarities between the homologous bones in the vertebrate limb are therefore due to the high functionality of the skeletal pattern.
• Conclusion: The optimality, versatility, functionality, and widespread reusage of the vertebrate limb pattern are highly consistent with the expectations of intelligent design.

Neurophysiology

• Observations:
  • About intelligent agents: Intelligent agents design systems (e.g., circuits) with top-down design, where multiple parts coordinate to achieve a goal, including mechanisms for dampening signals, movement, or vibration.
  • About an unexplained natural feature: Blood flow in the brain does not destroy or damage highly fragile capillaries in the brain.
• Hypothesis / expectation: Signal dampening strategies known from the fields of electrical and mechanical engineering are coordinated in the brain to prevent the pulse of blood flow from damaging fragile capillaries.
• Experiment (data collection): Brain blood flow is controlled by a band-stop filter, and cerebrospinal fluid flow is controlled by a band-pass filter which buffer and absorb blood flow pulses and prevent “unwanted vibration,” preventing damage to capillaries.
• Conclusion: The usage of signal dampening mechanisms known from the fields of electrical and mechanical engineering to control pulsatility of blood flow through the brain shows a top-down, goal-directed design that is highly consistent with the expectations of intelligent design.

In a series of subsequent posts, my co-authors on the paper will elaborate on some of these examples and others to show how ID is being used to make new scientific discoveries.