The heyday of Darwinism may be coming to an end. Its summer of dominance after neo-Darwinism arose and conquered every field of biology led to an autumn of colorful just-so stories, and now a Narnian rule, where it is always winter and never Christmas. Evolutionary biologists repeat the old dogmas with less and less creative insight, as if cranking out expected boilerplate in a spirit of drudgery. But like a waft of a slightly less-cold breeze, with a slightly higher sun in the sky, hints of a new paradigm may be signaling that biology is about to turn over a new leaf.

One such tender shoot of greenery appeared in Science Magazine, where Maria Clara Zanellati and Sarah Cohen wrote a perspective piece titled, “The endosome as engineer.” It’s an example of an ever-so-slight tendency in mainstream journals — perhaps too early to call a trend — that ignores Darwinism completely while warming up to the engineering paradigm. It is often done without voicing the name of the Enemy, intelligent design.

A hallmark of eukaryotic cells is that they are compartmentalized into membrane-bound organelles. This allows for the spatial separation of biochemically incompatible processes. Nevertheless, organelles must work together for the cell to function. There has been increasing interest in organelle communication at membrane contact sites — where two organelles are anchored in close apposition by “tether” proteins. These contact sites allow the exchange of materials and information between cellular compartments. Intriguingly, organelles can also influence one another’s abundance and morphology. Most studies have focused on the role of the endoplasmic reticulum (ER) in shaping other organelles. However, on page 1188 of this issue, Jang et al. show that the endosome can reengineer ER shape in response to changing nutrient levels, which in turn affects the morphology and function of additional organelles. [Emphasis added.]

The word “engineering” appears briefly in the above-referenced paper by Jang et al., but only in regard to the scientists who engineered the cell lines and their genomes. Still, significantly, evolution was notable for its absence, while engineering terms were used to describe what the endosome is doing: rewiring, signaling, orchestration, function, program, coordination, and regulation.

It’s Logical

Another paper, in Science Advances, is almost comical in its dissing of Darwinism. The paper is all about logic, using the word 18 times. Authors Sun and Horrigan from Baylor College of Medicine describe “A gating lever and molecular logic gate that couple voltage and calcium sensor activation to opening in BK potassium channels.” Sounds like what an IT engineer might do. Here’s their only mention of evolution:

The logic gate–like integration of V and Ca²⁺ signaling by the YFF pathway is a potentially unique mechanismthat raises many interesting questions regarding its physiological role and evolution. While we cannot speculate about the latter, the most obvious role of the mechanism is to enhance both V- and Ca²⁺-dependent coupling, and it may also act paradoxically to simplify the physiological response to V and Ca²⁺, as discussed below.

Forward they proceed into engineering language, leaving Darwinism behind, mumbling in his beard about what “seems to me.” Sun and Horrigan are more interested in couplings and sensors:

In conclusion, our results suggest that coupling mechanisms can be indirect and distributed and that resolving these mechanisms requires structure-function analysis that can distinguish changes in coupling from changes in sensor or gate equilibria, as well as structural information in different states to distinguish static and dynamic interactions.

Nature Feeling the Warmth, Too?

Norman Lockyer founded the journal Nature in the days of the X Club to promote Darwinism. The first issue had a frontispiece by Thomas Huxley, and in the first year there were half a dozen articles “urging Darwin’s scheme, two of which were written by Darwin himself” (Browne, p. 248). That was in 1869. As everyone knows, the Nature Publishing empire proceeded to dominate the journal business and continues its “polemic purpose” in support of materialist science. 

Recently, however, at Scientific Reports, one of Nature’s open-access journals, three scientists wrote a Darwin-free editorial on “3D Genome Organization.” Like the paper described above, this editorial portrays biological engineering without using the word. More importantly, it promotes interdisciplinary research focused on how genomes achieve structure-function relationships from a linear sequence. This opens doors for engineering-based research that scientists weary of Darwinism might find attractive.

We are still a long way from understanding how 3D genome organization is linked precisely to genome function. A concerted multi-disciplinary effort is needed to develop new tools and computational prediction methods, multi-target chromatin imaging techniques in live-cells, and efficient manipulation methods for 3D genome structures. These efforts should be accompanied by the collection of 3D genome data from different diseased and healthy cells and tissues in humans, as well as a range of model organisms. Our increased knowledge of 3D folding of the genome will lead to a better appreciation of the regulatory potential of the linear genetic sequence. 3D genome organization emerges as a cell type specific epigenetic mechanism and gives us clues about the regulatory effect of the non-coding genome in the 3D context. This understanding will allow for enhanced interpretation of genetic variants and their potential phenotypic effects. Finally, such studies will bring new 3D insights into diagnostics and therapies for different conditions including cancer, developmental diseases, ageing, and related disorders.

One can almost sense the excitement at the potential of looking at genomics with an engineer’s eyes.

Disruptors Needed

Nature complained this month that “‘Disruptive’ science has declined — and no one knows why.” Max Kozlov explained, “The proportion of publications that send a field in a new direction has plummeted over the last half-century.” Kozlov gropes for reasons for it. A related paper by Park, Leahey and Funk in the same issue likewise comes to no firm conclusion. All they can suggest are possible ways to stir the embers and ignite something exciting.

Understanding the decline in disruptive science and technology more fully permits a much-needed rethinking of strategies for organizing the production of science and technology in the future.

One factor they ignore is the stupor of consensus. In biology, the aging Darwinian consensus has stifled fresh, disruptive thinking outside the box. Many scientists have contented themselves with describing whatever complex phenomenon is under investigation by saying with a ho-hum that it “evolved” to do what it does. To this day, though, nobody has witnessed a new organ or programmed system come into being by Darwin’s mutation/selection “mechanism” (as if “mechanism” can properly be applied to products of mindless processes). 

People do, by contrast, witness new products coming from engineers. Intelligent minds possess foresight and creativity that can find elegant solutions to problems. That’s what life does. The engineering paradigm is explicitly and effectively applied within the intelligent design community, such as in the new book Your Designed Body by an engineer and an MD. Their interdisciplinary collaboration achieves credible understanding: the body looks designed because it is designed in ways that would make human engineers envious.

Discovery Institute leads the world in design-based initiatives, events, and publications. If the engineering paradigm succeeds in bringing a new leaf to biology after the long Darwinian winter, DI may not get the credit it deserves. It is still hard for scientists to overtly embrace intelligent design because the Darwin empire’s punishment of all who stray from the consensus is legendary. But if, after a century of Darwin’s reign of terror, with its racism, eugenics, meaninglessness, ugliness, and censorship, an engineering-theoretic paradigm offers a new way of doing research, it promises to bring not only superior understanding of how life works, but with it untold practical benefits to the whole world — not the least of which might be great pleasure and satisfaction at rediscovering purpose at the root of life. 

Sources

• Browne, Jane, Charles Darwin: The Power of Place (Princeton, 2002).