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Systems Biology Cracks Life’s Engineered Intricacies — A Report from CELS

humpback whale
Image via Wikimedia Commons.

Most academic biologists would sooner parasail into Mordor than admit intelligent design beats blind evolution. Modern Darwinism is very much the reigning paradigm in historical biology. Curiously, however, the hottest branch of experimental biology nowadays actually adopts as a working heuristic the view that biological systems are optimally engineered. This hot new approach — systems biology — has proven so fruitful that there is a growing demand for engineers to join biological research groups to help those groups think like engineers.

Recently I had the privilege of attending a scientific conference that took this systems biology approach — the Conference on Engineering in Living Systems (CELS) in Denton, Texas. What makes this gathering stand out is that the biologists and engineers in attendance don’t adopt the design paradigm as merely a working heuristic. They are convinced that the biological systems under review exhibit clever engineering solutions because they really were cleverly engineered. Every CELS talk I attended spotlighted a different ingenious design in biology, or upended some cherished Darwinian assumption, or both.

Smarter than Knitting Machines

In one lecture, internationally distinguished Brazilian chemist Marcos Eberlin discussed the engineering marvels of proteins, ribosomes, and their underlying amino-acid architecture. Ribosomes contain proteins and RNA. They are waterproof, mechanically resistant, flexible, and elastic, with long-lived, connecting units. They work like knitting machines but are much smarter than knitting machines, Eberlin explained. 

Proteins, likewise, are extraordinarily strong, flexible, and elastic — much better than man-made nylons and able to self-fold into the precise four-dimensional structures needed for life. They do so in a myriad of shapes that fulfill a host of challenging tasks. These protein machines, moreover, don’t just work individually; they work together symphonically.

Eberlin said that many of his fellow scientists disbelieve in God but plagiarize him all the time in a research field known as biomimetics. The kicker is that when they manage the copying feat, they usually do so in a way inferior to the original.

A Chicken-and-Egg Problem

Eberlin also pointed out problems with the idea that RNA, proteins, and ribosomes evolved gradually through a mindless process. To get ribosomes and any kind of protein, you need various kinds of amino acids, all left-handed. (No, amino acids don’t have hands. They do, however, have amine groups either on the right-hand or left-hand side.) How did mindless nature sort through the righties and lefties and choose exclusively left-handed amino acids? There is no purely mindless natural process for generating or selecting only left-handed amino acids.

Eberlin warned against slipping into a view of physical laws as having foresight or intentions. The laws of nature were never striving to produce purely left-handed amino acids. Nature’s laws don’t care about nursing life. If anything, the mindless forces of nature want to tear life apart. 

To overcome these buffeting forces, Eberlin says, you need molecular biological machines. One is the ribosome. It’s essential for making proteins, but ribosomes are themselves partially made up of proteins. So, which came first in the evolutionary story? 

You also need very large RNA molecules to make ribosomes. Some origin-of-life researchers say life began as an RNA World, with DNA and proteins arriving later. Others say, no, proteins came first. Others, that no, ribosomes were first to the party. But really you need all three, Eberlin says. None of them can survive without the others.

It’s a classic chicken-and-egg problem, and Eberlin said that overcoming it requires foresight and planning, activities reserved for intelligent agents. Three chemists won a Nobel Prize for mapping the ribosome, and Eberlin said the prize was well deserved. So, what prize, he asked, is due the one who designed the ribosome in the first place?

The Problem of Orphans

In another CELS talk, philosopher of biology Paul Nelson discussed a rising challenge to modern evolutionary theory — the exponential growth in the catalogue of orphan genes. 

Orphan genes are functional DNA sequences without known homologues outside a given species or lineage. A commitment to universal common descent led biologists to expect such genes to be rare. After all, if all species evolved from ancestor species in a gradually branching tree of life, starting with the Last Universal Common Ancestor (LUCA), with genetic changes accumulating only very gradually through small genetic mutations, then novel genes — seemingly without ancestry — should be quite unusual. But as it turns out, they’re not.

Nelson related an experience from years ago when he was called out in a lecture at Dartmouth. He was speaking on the challenge orphan genes pose for evolutionary theory, and his critic complained that we didn’t have enough of a sample — just 122 bacterial species — to conclude that there was any real problem for evolutionary theory. Surely this signal would dissipate, said the critic, once the genomes of more bacterial types were sequenced. 

So, what has occurred in the intervening years? A Polish research team has now surveyed the genomes of more than 60,000 bacterial species and close to 200 million bacterial proteins. In the process they have uncovered 8.5 million orphan proteins. The signal, far from fading, is now loud enough to rattle teeth. Nelson noted that it isn’t just bacteria either. Whenever the DNA of a previously unsequenced plant or animal form is sequenced, many new orphan genes are uncovered.

The pattern clashes with what universal common descent anticipates but meshes well with an intelligent design paradigm. If a feature is closely shared with another species, then we might expect the designer to repurpose a module already in use. If the feature is unique to the species or lineage, then we could expect the designer to write new DNA code for the new feature, much as a software engineer would proceed, with the result being more orphan code. And that is the pattern that is emerging.

The Point of the Pentadactyl

Another CELS speaker was engineering superstar Stuart Burgess, Professor of Engineering Design at Bristol University in England. Burgess is the editor of two bioengineering journals, and a lead designer for the British Olympic Cycling Team. His work there helped the British track cyclists win the top medal haul in both the Rio and Tokyo Olympics. Burgess also has had two research fellowships at Cambridge University and was the lead designer for the European Space Agency’s Metop satellites.

In his CELS talk, Burgess made the case that an understanding of engineering principles well explains the repeated appearance of the pentadactyl (five digit) limb design throughout the animal kingdom.

Evolutionists have long argued that this pattern is due to evolutionary common descent — that is, that a series of mutations constructed the five-digit design in a common ancestral lineage and that the blueprint was passed down to various descendants on the branching limb of animal life, leaving everything from human hands to whale flippers sporting the pentadactyl design. But even a fully paid-up evolutionist such as Harvard paleontologist Stephen Jay Gould conceded that this tidy story breaks down. In his book Eight Little Piggies, he noted various exceptions to the pentadactyl rule before he gamely tried to fit the much messier picture into a Darwinian frame. 

Burgess offered what he sees as a more elegant solution. Namely, an engineering analysis shows that five digits (as opposed to, say, one or three or seventeen) provides an optimal tradeoff between strength and flexibility/dexterity. A single digit would be strongest, and a dozen digits more flexible or dexterous. But if you want an optimal combination of these two virtues, and you graph them with strength decreasing with each additional digit, and flexibility/dexterity increasing with each digit, you find that the two virtues cross at the five-digit point. Five digits thus represent what engineers describe as a constrained optimization of competing attributes. 

The five-digit design appears so often in the animal world, in other words, because the designer was a good engineer and selected it as the best trade-off between competing virtues. Take the five-digit whale flipper. The flipper must be strong but also flexible enough to twist in various subtle ways in the service of making the creature a master swimmer. An engineering analysis found that five digits best achieves that compromise, Burgess said.

Whale Bones of Contention

At this point in the talk Burgess anticipated an objection: Yes, but whales have vestigial pelvic bones, left over from their land-dwelling ancestors, pelvic bones largely useless to the whales. Surely that screams blind evolution, not design. Burgess noted that this oft-recycled argument for evolution is badly outdated, since research has long revealed important functions for these bones. 

The point was conceded in a 2014 paper in the journal Evolution. “Due to their highly reduced state, cetacean pelvic bones are sometimes thought of as ‘useless vestiges’ of their land-dwelling ancestry,” but, the authors continued, these whale bones in fact serve “important roles in male reproductive function.”1 In support of the claim, the article cited more than a dozen corroborating scientific papers stretching from 1881 to 2009. 

As one would expect from an article in the journal Evolution, the authors scrambled to provide an alternative evolutionary explanation for the pelvic bones, but the cherished evolutionary story of “vestigial” pelvic bones joins the growing pile of discredited icons of evolution detailed by biologist Jonathan Wells, first in Icons of Evolution and then further in Zombie Science: More Icons of Evolution

In the case of the pelvic bones of the whale, the Darwinian framework led many scientists astray, whereas the view that these bones are the product of rational and skillful engineering pointed in the right direction.

This pattern of discovery harkens back to the scientific revolution itself. The founders of modern science were theists, tutored in the Judeo-Christian understanding of reality. Their early breakthroughs were fueled by seeing the book of nature as the work of a master author, a great craftsman whose deep designs called for careful study to illuminate their hidden intricacies. So, we shouldn’t be surprised that in recovering this approach to the living world, today’s systems biologists find themselves in the midst of a fresh revolution of discovery.

Editor’s note: This article appeared originally in the journal Salvo. It is republished with the author’s permission.


  1. James P. Dines et al., “Sexual Selection Targets Cetacean Pelvic Bones,” Evolution 68, no. 11 (Nov. 1, 2014), 3296–3306, https://doi.org/10.1111/evo.12516.