I praise you because I am fearfully and wonderfully made; your works are wonderful; I know that full well. – Psalm 139:14
Protein biogenesis in eukaryotic cells proceeds through a highly coordinated series of molecular events that begin in the nucleus. Gene expression initiates with transcription by complex molecular machines mostly composed of proteins, during which a DNA sequence is converted into a precursor mRNA transcript (messenger RNA). This transcript subsequently undergoes essential post‑transcriptional modifications—including capping, splicing, and polyadenylation—before being exported to the cytoplasm. Once in the cytosol, the mature mRNA engages a ribosome, the macromolecular complex responsible for translating nucleotide codons into a linear amino‑acid polymer, thereby producing the nascent polypeptide chain.
The primary structure of a protein—its specific amino‑acid sequence—ultimately dictates its three‑dimensional conformation and functional properties. Many proteins spontaneously adopt well‑defined secondary structures, such as α‑helices, β‑pleated sheets, and irregular loops. The folding process is governed by many factors, including hydrophobic and electrostatic interactions among amino‑acid side chains, entropic and enthalpic considerations, and, in numerous cases, the assistance of molecular chaperones. Additional structural refinement may occur through post‑translational modifications within the endoplasmic reticulum or Golgi apparatus, depending on the protein’s cellular destination and functional role.
Taken as a whole, the multi-step pathway from gene expression in the nucleus to a protein in its final, active form is unfathomably complex—the description above has been simplified—especially when one considers the “chicken or egg” conundrum. Proteins are essential at every step along the way, including initiation.
Think in terms of the tools required to manufacture an assembly line that is designed to manufacture those tools. The process does not begin with either the tools or the assembly line. It begins with information. Engineers and architects generate blueprints, specifications, and workflow diagrams; these informational structures coordinate the activity of construction workers, who in turn apply directed energy through the use of tools to bring the assembly line into existence. In other words, the assembly line is not self‑originating. It is the product of prior planning, prior organization, and prior informational input.
Despite the centrality of folding to classical protein biology, a substantial subset of proteins do not adopt a stable tertiary structure. Instead, these molecules remain conformationally dynamic, sampling a broad ensemble of configurations reminiscent of a flexible, continuously shifting polymer. These intrinsically disordered proteins (IDPs) were historically regarded as nonfunctional or biologically insignificant, i.e., “junk.” Contemporary research, however, has demonstrated that IDPs constitute a significant proportion of the human proteome and participate in diverse regulatory and signaling processes that remain incompletely characterized. Crucially, the structural principles that govern folded proteins do not apply to IDPs, leaving scientists without a systematic framework for designing them.
Addressing this gap, researchers at Syracuse University, in collaboration with Washington University School of Medicine, have developed a computational platform specifically tailored to the design of intrinsically disordered proteins. This tool, termed GOOSE, (Generate disOrdered prOteins Specifying propErties) enables the generation of IDP sequences under rigorously defined constraints.[1] In contrast to traditional protein‑design methodologies—which focus on folded proteins and were central to the 2024 Nobel Prize in Chemistry—GOOSE leverages machine‑learning architectures to produce thousands of candidate sequences that remain disordered yet exhibit targeted functional properties.
With this platform, the team successfully designed new IDPs that can sense cellular environments, self‑assemble, and protect cells from dehydration—demonstrating the first steps toward decoding the functional “rulebook” of intrinsically disordered proteins.
“For decades, these floppy, spaghetti-like proteins were written off as junk,” says Shahar Sukenik, associate professor in the Department of Chemistry at Syracuse University’s College of Arts and Sciences (A&S), who led the project. “But they make up a large portion of the human proteome, and they’re critical to the way many of our proteins function. Despite this, the rules that let us design traditional, folded proteins simply don’t work for them. This study is a first step toward decoding the rules for IDP function.”[2]
“Floppy, spaghetti-like proteins” characterized as “junk” should ring a bell to anyone in the field of molecular biology who is paying attention. It was only several years ago that the same junk-pejorative was casually thrown around to characterize non-coding DNA. But a series of discoveries starting in 2008 forced a major change in thinking about so-called “junk” DNA.[3] Many examples of function have since been identified for the non-coding regions of DNA, and more are being uncovered each year.
Writing in First Things, William Dembski predicted almost thirty years ago it would be just a matter of time before science uncovered function in so-called “junk DNA,”
[Intelligent] design is not a science stopper. Indeed, design can foster inquiry where traditional evolutionary approaches obstruct it. Consider the term “junk DNA.” Implicit in this term is the view that because the genome of an organism has been cobbled together through a long, undirected evolutionary process, the genome is a patchwork of which only limited portions are essential to the organism. Thus on an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function. And indeed, the most recent findings suggest that designating DNA as “junk” merely cloaks our current lack of knowledge about function.[4]
The parallel is hard to miss. Biology has a long history of dismissing what it does not yet understand, only to later uncover layers of unexpected complexity.
And there is something else that is hard to miss. The thoughtful reader should note the vocabulary in the original articles the authors used to describe this elegant research. Words such as develop, design, generate, and defined constraints all point not to some random, blind, unguided process but to a thoughtful mind, information, the use of programmed computer code, and well-defined, controlled experiments with directed outcomes. None of this characterizes an atheistic or naturalistic evolutionary paradigm for the origin or further development of life.
The research team—let’s call them intelligent designers—are not relying on chance to determine empirical outcomes. I have no doubts that similar findings await these researchers as they explore these floppy, spaghetti‑like proteins, originally thought to be non‑functional or biologically insignificant.
Truly we humans are “fearfully and wonderfully made.”
[1] Hunter, Kara, Trevor Brandt, Karina Guadalupe, Kavindu C. Kolamunna, Jeffrey M. Lotthammer, Nora M. Shamoon, Jessica K. Niblo, Brooke Nicholson, Lea M. Day, Alec Martinez, Alex S. Holehouse, Shahar Sukenik, and Ryan J. Emenecker. “Rational Design of Disordered Proteins for Sequence–Function Investigation.” Nature, published July 29, 2026. https://doi.org/10.1038/s41586-026-10849-1.
[2] Tibbetts, John H. “A&S Scientists Design Proteins With No Fixed Shape.” College of Arts & Sciences, Syracuse University, July 29, 2026. https://artsandsciences.syracuse.edu/chemistry/news/as-scientists-design-proteins-with-no-fixed-shape.
[3] Andrew McDiarmid, “Another Case Where ‘Junk’ Myth Impeded Science,” Science and Culture Today, July 19, 2025, https://scienceandculture.com/2025/07/another-case-where-junk-myth-impeded-science.
[4] William A. Dembski, “Science and Design,” First Things, October 1, 1998 as quoted in Casey Luskin, “‘Junk DNA’ from Three Perspectives: Some Key Quotes,” Science and Culture Today, May 2, 2024. https://scienceandculture.com/2024/05/junk-dna-from-three-perspectives-some-key-quotes/
