Suppose you picked up a magazine at the dentist’s office and read the following phrase:

“When coupled with the appropriate interpreters, multiple meanings and functions are programmed into the same sequence of configurable switch-settings. This additional layer of Ontological Prescriptive Information (PIo) purposely slows or speeds up the translation decoding process within the ribosome.”

Aside from having no idea what most of these terms actually mean, you might ask who uses them. Robotics engineers? Data encryption analysts?The question supposes that if ID were religiously motivated, its rejection by mainstream science would be justified. Would you have thought it came from biologists describing basic DNA transactions?D. J. D’Onofrio and D. L. Abel (2014). Redundancy of the genetic code enables translational pausing. Frontiers in genetics, 5, 140. doi:10.3389/fgene.2014.00140 In some ways, this single passage demonstrates just how much mainstream biology now looks and sounds like intelligent design (ID) theory.

For this reason, it is odd to ask why, if ID is not religiously motivated, it has failed to gain traction in mainstream science. It has gained traction.

The question supposes that if ID were religiously motivated, its rejection by mainstream science would be justified. As if science’s first devotion is to secularism at all costs, and not to the pursuit of discovering what is true about the natural world. Unfortunately, one can find an example of this expunging of religion from the scientific enterprise in the PLOS One debacle, in which the scientific community went frenetic over the inclusion of “Creator” in a published “Scientists Are Freaking Out Over A New Paper That Says Our Hands Were Designed By God.” March 4, 2016 (accessed 2-13-2019). Of course, it is at least possible to imagine a situation in which a religiously-motivated theory turns out to be true, even as judged by those who demand secularism in science.

Setting that aside, I will argue something wildly provocative: ID has in fact become well-established in what we might call mainstream science. While I cannot offer a comprehensive case in the space permitted, I will sketch out evidence for this fact. Broadly, the trend of the past two decades (most acutely in the past five or six years) has been a transition to concepts, theories, and applications in the biological sciences that are either completely consistent with an ID theoretic or that represent the validation of ID-driven predictions.

The Demise of Darwinian Evolution (DE)

Skepticism and harsh critique regarding the utility of the neo-Darwinian model was present from the inception of ID theory.The Darwinian model contends that evolutionary change (descent with modification) is generated by natural selection acting on chance mutations. Early examples of ID push back against DE can be found in Phillip Johnson’s Darwin on Trial (1991), Michael Behe’s Darwin’s Black Box (1996) and Michael Denton’s Evolution: A Theory in Crisis (1985). Within mainstream evolutionary biology, the vindication of concerns raised by ID is nearly complete. The late Stephen Jay Gould had declared the neo-Darwinian synthesis “effectively dead,” as early as 1980.Stephen Jay Gould, “Is a New and General Theory of Evolution Emerging?,” Paleobiology 6, no. 1 (1980): 119-30. Mainstream science has already demonstrated a fossil record consisting of short bursts of rapid diversification, a general absence of gradualistic change, and the emergence of forms with few precursors or intermediates. All of these run directly counter to the major expectations of the Darwinian model.

At the molecular level, the expectation was to find “junk DNA” littered throughout our genomes, as evidence of a gradual trial and error process. In 2012, a multinational research consortium (594 collaborators) called the ENCODE Project, suggested that 80 percent of the human genome is functional,ENCODE Project Consortium, “An Integrated Encyclopedia of DNA Elements in the Human Genome,” Nature 489 (2012): 57-74. doi: 10.1038/nature11247. and additional research has largely supported these findings.J. Murga-Moreno, et al, “PopHumanScan: The Online Catalog of Human Genome Adaptation,” Nucleic Acids Research (2019): 47 (D1): D1080 DOI: 10.1093/nar/gky959; F. Pouyet, et al, “Background Selection and Biased Gene Conversion Affect More than 95 percent of the Human Genome and Bias Demographic Inferences,” eLife (2018): 7:e36317 doi: 10.7554/eLife.36317 So radical was this discovery that molecular biologist Dan Graur wrote, “If ENCODE is right, then evolution is wrong.” Yet, this massive functionality in genomes is precisely what ID predicted.C. Luskin, “Intelligent Design and the Death of the ‘Junk DNA’ Neo-Darwinian Paradigm.” (accessed 2-13-2019).

The New Model

In the field of evolutionary biology, DE has largely been replaced by “evo-devo” (Evolutionary Developmental Biology), which identifies highly coordinated hierarchical structure in gene regulation and expression, and offers a modular theory for the rapid evolution of complex body architectures. The most prominent leaders in this field have been equally blunt in their dismissal of classic Darwinian thought. Two major players, Douglas Erwin and Eric Davidson, have argued, “[Gene Regulatory Networks] cannot be accommodated by microevolutionary nor macroevolutionary theory,” that “standard evolutionary models do not accommodate these temporal asymmetries in the patterns of change in GRNs,” and that “this new emerging view of the evolution of developmental GRNs presents a challenge to our understanding of the evolutionary process.”D. H. Erwin and E. H. Davidson, “The Evolution of Hierarchical Gene Regulatory Networks,” Nature 10.2 (2009):141-148. doi: 10.1038/nrg2499.

However, evo-devo is consistent with many ID predictions, and offers verification of a positive case from ID in the biological sciences. For example, Stephen C. Meyer had predicted:

Investigation of the logic of regulatory and information-processing systems in cells will reveal the use of design strategies and logic that mirror (though possibly exceed in complexity) those used in systems designed by engineers. Cell biologists will find regulatory systems that function in accord with a logic that can be expressed as an algorithm.Stephen C. Meyer, Signature in the Cell: DNA and the Evidence for Intelligent Design (San Francisco: HarperOne, 2001), 496.

This shift in language and approach in evolutionary biology is astonishing. Consider the following three passages describing epigenetics and developmental biology:

These logically connected networks enable cells to maintain their functional integrity and at the same time they also dynamically respond to distinct input signals generated within the cellular or external environment.Milsee Mol, Pruthvi Raj Bejugam, Shailza Singh, “Synthetic Biology at the Interface of Functional Genomics,” Briefings in Functional Genomics, 14.3 (2005): 180–88.

‘If-then’ logic enables an internal selection of the correct solutions to different challenges. When specific conditions are detected, the adaptive response is a particular and necessary consequence of these complicated, logic-based systems.R. J. Guliuzza, “Engineered Adaptability: Trait Selection Is Internal, Not External.” (accessed 2-13-2019).

Hardwired into these individual modules is the correct response of the gene to every diverse circumstance the cells of the organism will encounter throughout development and the lifetime of the organism.M. L. Howard and E. H. Davidson, “Cis-Regulatory Control Circuits in Development,” Developmental Biology, 271.1 (2004): 109-118.

Okay, quiz time. Which of these passages are from mainstream secular journals, and which are from young earth creation (YEC) journals? The point is that mainstream molecular biology understands the workings of the cell in terms of engineering and teleology. More importantly, the hierarchical organization found within even the simplest cell pathways is not just unexpected on Darwinian evolution, but exhibits top-down organization that resists reductionism. To again quote Erwin and Davidson, “The highly conserved sub-circuits of the GRN—its kernels—cannot be changed without disastrous effects.”This was also acknowledged as a serious problem by Berkley paleobiologist Charles R. Marshall in his debate with Stephen C. Meyer. Unbelievable, November 30, 2013, “Darwin’s Doubt: Stephen C. Meyer & Charles Marshall Debate ID.” Combine this with the facts that GRNs show “remarkable evolutionary conservation across distant animal phyla,” and “they represent an abstract system of cardinal information,”M. Mallo and C. R. Alonso, “The Regulation of Hox Gene Expression During Animal Development,” Development, 140 (2013): 3951-3963. doi: 10.1242/dev.068346. However, the authors were careful to add, “It must be noted that the presence of similar regulatory mechanisms in flies and mice does not necessarily imply a common origin.” and you have another observation at odds with reductionist evolutionary theory, but in support of ID predictions. Mainstream science is teaching us that early life begins with an arsenal of fully functional GRNs, and evolution proceeds largely by modifying or losing existing genes, not creating new ones,A. L. Hughes and R. Friedman, “Shedding Genomic Ballast: Extensive Parallel Loss of Ancestral Gene Families in Animals,” Journal of Molecular Evolution, 59.6 (2004): 827-933. doi:10.1007/s00239-004-0115-7 but bottom-up models lack a plausible mechanism for developing this complexity unexpurgated.See M. Polanyi, “Life’s Irreducible Structure,” Science 160.3834 (1968): 1308-1312. doi: 10.1126/science.160.3834.1308; S. Walker and P.C.W. Davies, “The ‘Hard Problem’ of Life,” in From Matter to Life: Information and Causality (Cambridge: Cambridge University Press, 2017).

I will end this essay with a quote from bioengineer Matti Leisola:

The twentieth-century understanding of genetics was an atomistic model, while the twenty-first century understanding is a genome-centric model. The earlier framework was reductionist; the new framework, one of complex systems. The old model viewed biological operations as mechanical; the new model see them as cybernetic. . . . Now it’s ‘genomes as interactive information systems’ . . . On the old view, a common metaphor for genome organization was a string of beads. Within the new framework, it’s a computer operating system. . . . This new framework is a design-centric framework.M. Leisola and J. Witt, Heretic: One Scientist’s Journey from Darwin to Design (Seattle: Discovery Institute, 2018), 154-55.

So, while I’m not expecting the scientific community to suddenly start using phrases like “specified complexity” or “irreducible complexity,” a rose by any other name would smell as sweet. Mainstream science wasn’t looking to confirm ID expectations, but it has arrived at precisely that situation.