Not So Suboptimal After All

Will Collaboration Between Engineers and Biologists Affirm Optimal Design?

As a framework for explaining the origin of life and organismal diversity, materialism has enjoyed a long-standing reign, buttressed not so much by the weight of evidence in its favor, but rather by the momentum it enjoys riding a wave of post-enlightenment skepticism. Yet materialism’s not-so-enlightened reign over the sciences is loosening as research models resulting from a partnership between biologists and engineers are challenging its assumptions.

At the 2022 Dallas Conference on Science and Faith, Dr. Brian Miller, Research Coordinator at Discovery Institute’s Center for Science and Culture, reported on how collaborations between biologists and engineers are causing many biologists to reconsider the predictive powers of evolution and the veracity of its underlying assumptions. What many of them are realizing is that the predictions an intelligent design (ID) framework advances are not only worthy of consideration but are useful in ascertaining how biological systems work.

For those not familiar with the debate between the frameworks of ID and evolutionary biology, following is a characterization of Darwinian evolution’s claims, the implications of those claims, and what that framework would predict for living systems. Then we can contrast those with the model scientists ID theorists are advancing.

An Evolution Primer

Evolutionary biologists argue that the origin of life likely started with an ancestral bacterial cell emerging from what Darwin characterized as some “warm little pond” bearing all manner of ammonia and phosphoric salts with just the right amount of energy in the form of light, heat, or perhaps electricity some 3.5 billion years ago.

From this single prokaryotic cell, more complex cells developed by means of endosymbiosis (one cell engulfing another, resulting in a symbiotic relationship and options for more complex metabolic pathways).[1] From these innovations, multicellularity evolved, leading the way for more complex organisms over geological time to appear, ultimately gracing Earth’s surface with a rich biome of organisms that can be grouped into the five kingdoms of life (Monera, Protista, Fungi, Plantae, and Animalia).

From this single cell ancestral line, then, organisms grew in complexity by way of very gradual, step-by-step changes in their genetic codes (genetic mutations). These changes gave way to variations conferring upon some the ability to not only survive, but to out-reproduce other members of their own species (conspecifics), thus enhancing what Darwin famously termed as “fitness.” Contrary to popular usage, the term fitness does not necessarily denote an organism’s ability to merely survive, but rather its ability to reproduce and leave more viable offspring to the next generation, than its conspecifics.

In evolutionary biology, the simple-to-complex evolution of life is the consequence of many, many mutations on an organism’s genome, with each changing a protein or regulatory pathway so that the organism expresses a novel or modified characteristic (“phenotype”) that is either deleterious or adaptive. Whether the innovation succeeds or fails is determined by the organism’s ecological niche (environment). If the new phenotype enables the organism to out-reproduce its conspecifics, that phenotype is extended into the next generation. If the innovation fails in this regard, it becomes an evolutionary dead end. And so, over the course of 3.5 billion years, this “bottom-up” mechanism drives phenotypic variation and ultimately, the remarkable diversity we see on Earth today. That is the Darwinian evolutionary framework in a nutshell.

Darwinism’s Assumptions

If Darwinism’s bottom-up approach is accurate, there are certain things we should expect to see in the natural world. One of those is suboptimal design. In 2014, through powerful modeling, David Snoke and colleagues concluded that certain systems should be replete with vestigial structures if in fact innovations giving rise to increased complexity are the consequence of proverbial evolutionary “stabs in the dark.” [2] This is because the blind processes of evolution (possessing no foreknowledge of the challenges the organism would face in the business of life) should yield structures that appear randomly “cobbled” together, something like a Rube Goldberg machine.

By way of analogy, an everyday example of cobbled-together design is what we might expect to see emerge from the workbench of a geeky kid, tasked with making a slingshot from borrowed materials. We can imagine the haphazard assemblage of a pencil, a string of rubber bands, perhaps some paper clips (as ammo) and duct tape (to hold everything together). Any rapscallion who has made a slingshot from school supplies can attest to the pitfalls of this sort of suboptimal design.

Contrast this with the slingshot that Amazon can deliver; one rising from the CAD software of a weapons engineer, fabricated from stainless steel, bearing a walnut grip, and durable rubber bands of just the right width and thickness to launch a projectile with great momentum and precision. Such a prize as this exemplifies top-down design, as the engineer(s) started with the end in mind, and with judicious selection of materials appropriate to the slingshot’s purpose, delivered specs for an end product of optimal design.

Granted, this analogy is not perfect: the geeky kid cobbling materials from his school supplies still suggests intellectual agency. To make the bottom-up analogy perfect, you would have to imagine a sling shot over geological time self-assembling without the involvement of the geek.

Now, if Darwinian assumptions are correct, in the natural world, suboptimal design should be normative; but this is not the testimony of nature. If one considers the complexity of a bacterial flagellum ,with its 30-plus number of different proteins fitting together to form a rotor, stator, driveshaft, U-joint, bushings, bearings, and a whip-like tail, propelling it at 100,000 rpm, we might suppose that all those structures were not formed in one fell swoop (that is, after all, the way a human engineer or intelligent designer would work).

Instead, the evolutionary paradigm would suggest most or nearly-most of these proteins having had some function or purpose in the bacteria’s ancestor – say as members functioning as part of a secretory system which would have enabled its progenitor to inject bacterial proteins directly into host cells (enabling those proteins to commandeer host cell function)[3]. We might imagine that over time through a materialistic sleight of hand, that fruitful “stab in the dark” resulted in a very fortunate individual boasting a fully-functioning motor from several borrowed or even vestigial parts.

Yet the flagellum does not resemble a structure like the geeky kid’s slingshot – parts cobbled together. In fact, the complexity of the structure, with its functionality and optimal design, suggests something far more sophisticated than any slingshot Amazon (or perhaps even the Department of Defense) could deliver.

The Language of Design

Scientific models are only as good as the predictive frameworks they can advance. In the sciences, prediction is power. This is how hypotheses driving research are developed. Consider the question, “What might a top-down assemblage of life predict?” The answer is, it would largely predict what we already observe in nature: that many structures, functions, and systems work together in symphonic harmony. Whether we are looking at something as small as a photosynthetic pathway, or the larger-scale systems characteristic of the interaction of organisms with one another and their ecological niches, what we see is optimal design. This is what we would expect as a consequence of intelligent agency.        

In contrast to a bottom-up approach, then, top-down design involves a body plan originating in the mind of a designer, who then brings together tools and materials that are optimal to execute this plan. That prize slingshot exemplifies such design. It’s not hard to imagine engineers drafting plans informed from an idealized model, which takes into account the amount of force the Y-shaped frame would have to support, other design constraints, the availability and suitability of materials, and of course ergonomic design.

What results from a process such as this? A blueprint for a powerful weapon fashioned from durable materials, perhaps even bearing an ergonomically friendly design, and capable of carrying out the purpose for which the designer intended. To the rapscallion’s glee – this represents optimal design.

Returning to Dr. Miller, he reported that many biologists are conceding to the need to adopt design language in order to understand complex systems in biology. One textbook author even remarked, “A hope for understanding complexity in biology then is to uncover operational principles through ‘calculus of purpose’. . .” which is accomplished by “asking teleological questions such as why cellular networks are organized as observed, given their known or assumed function.” [4]

While these authors are not necessarily appealing to a creator here, they are certainly affirming the value of design-based assumptions for ascertaining how complex systems work.

A New Openness to Design?

It would be naïve to believe that this marks an about face in the field of biology and that biologists are willing to dethrone materialism for good. But this collaboration does signal an openness to design. We can all hope that the fruit of this collaboration will advance more research in the body of design literature, and at least in our lifetimes we might see a more peaceful coexistence between mainstream science and the ID framework.

For those of us who recognize the existence of a transcendent designer, we have wide-ranging scientific reasons to marvel at the natural world. His awesome power is manifest in structures ranging from the tiny bacterial flagellum to the larger systems comprising the mammalian immune system, to the very large-scale design evident in entire ecosystems.

Over time the evidence will reveal that whether the systems constituting life are nanoscale or astronomical, their Creator used materials and tools to sustain an extensive variety of life demonstrating optimal design.


[1] For an excellent history of the theory of evolution, see

[2] David W. Snoke, Jeffrey Cox, and Donald Petcher, “Suboptimality and Complexity in Evolution,” Complexity 21.1 (2015):322-327.

[3] Bryan Coburn, Inna Sekirov, and B. Brett Finlay, “Type III Secretion Systems and Disease,” Clinical Microbiology Reviews, 20.4 (2007): 535-549.

[4]  Zoltan Szallasi, Jörg Stelling, and Vipul Periwal. System Modeling in Cellular Biology: From Concepts to Nuts and Bolts, (Cambridge: MIT Press, 2006), 24.

graduated summa cum laude from California State University, Fresno, with a BS in molecular biology and a minor in cognitive psychology. As an undergraduate, she conducted research in immunology, microbiology, behavioral and cognitive psychology, scanning tunneling microscopy and genetics - having published research in the Journal of Experimental Psychology, and projects in scanning tunneling microscopy. Having recently completed an M.Ed. from University of Cincinnati and a Certificate in Apologetics with the Talbot School of Theology at Biola University, Emily is currently an instructional designer/content developer for Moody Bible Institute and teaches organic chemistry and physics. As a former Darwinian evolutionist, Emily now regards the intelligent design arguments more credible than those proffered by Darwinists for explaining the origin of life.

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