Author: Kim Berard
By 2025, we'll have DNA figured out, right? It had been more than fifty years since Crick and Watson (and Franklin) discovered the double helix. We know that the arrangement of just four chemical bases (A, C, T, and G) enables the world's vast genetic complexity and diversity. We have completed the Human Genome Project. We can use CRISPR to edit DNA. Heck, we're even working on synthetic DNA. We are busy finding other uses for DNA, such as computing, storage or robotics. Yes, we are on top of DNA.
Not so fast. Researchers at Northwestern University say we've been missing something: a geometric code embedded in the genome that helps cells store and process information. DNA is more than just a combination of chemical bases at work; there's a “geometric language” that we don't hear.
Wait, what?
The study – Geometric coding positioning of introns, intergenic segments, and exons in the human genome – Led by Professor Vadim Backman, Sacks Family Professor of Biomedical Engineering and Medicine and Director of the Center for Physical Genomics and Engineering at Northwestern University’s McCormick School of Engineering. He said new research shows that “we humans are not predetermined scripts based on a fixed set of genetic instructions, but are living, breathing computing systems whose complexity and capabilities have evolved over millions of years.”
A press release from Northwestern University elaborates:
The geometric code is a blueprint for how DNA forms nanoscale packaging domains that create physical “memory nodes” – functional units that store and stabilize transcriptional states. Essentially, it allows the genome to operate as a living computational system, adjusting gene usage based on the cell's history. These memory nodes are not random; the geometries appear to have been chosen over millions of years to optimize enzyme access, embedding biological computation directly into the physical structure.
Somehow I don't think Crick and Watson anticipated this, let alone Euclid or John von Neumann.
Co-author Igal Szleifer, professor of biomedical engineering at the McCormick School of Engineering, added: “We are learning to read and write the language of cellular memory. These 'memory nodes' are living physical objects similar to microprocessors. They have precise rules based on the physical, chemical and biological properties that encode the cell's behavior.”
“Living, breathing computing system”? “microprocessor”? This is a new level of DNA computing.
The study shows that evolution occurs not only by finding new combinations of DNA, but also by new ways of folding DNA, using these physical structures to store genetic information. In fact, one of the researchers' hypotheses is that the development of the geometric code helped lead to the explosion of body types witnessed during the Cambrian explosion, when life developed from simple single- and multi-celled organisms to a vast array of life forms.
Co-author Kyle MacQuarrie, assistant professor of pediatrics at the Feinberg School of Medicine, points out that we shouldn't be surprised that it took so long to recognize the geometric code: “We have spent 70 years learning to decipher the genetic code. Understanding this new geometric code has only been possible through recent advances in globally unique imaging, modeling and computational science developed at Northwestern.” (Extra plug from Dr. MacQuarrie, Northwestern University.)
Co-author Luay Almassalha, also from the Feinberg School of Medicine, noted: “While the genetic code is much like words in a dictionary, the newly discovered 'geometric code' turns words into a living language that all of our cells speak. Pairing words (genetic code) and language (geometric code) may ultimately enable the ability to read and write cellular memory.”
I love the difference between words and actual language. We use dictionaries all the time without realizing we need a phrasebook.
I recently read about MetaGraph, a tool developed at ETH Zurich for searching DNA databases, and I was impressed. “It’s a kind of DNA Google,” says Professor Gunnar Rätsch, a data scientist at ETH Zurich’s Department of Computer Science. This “DNA search engine” makes it easier, faster and cheaper to search for DNA sequences and compare them to other sequences. As cool as that is, the existence of the geometric code means that the folks at ETH Zurich probably have some extra work to do, as do many others studying DNA.
I don’t want to say it’s a whole new ball game, but there are definitely some important new rules.
The presence of this geometric code has implications for our health. It's not always DNA mutations that cause problems; our DNA structure can sometimes break down. Dr. Almassalha said: “The geometric code is no longer a puzzle of genetic letters, but allows cells to build complex tissues such as the brain or skin. But as we age, this language loses fidelity. This decline can lead to neurodegenerative diseases, cancer or other diseases of aging.”
This opens up a variety of new avenues for research and potential treatments. “The next step is to fully learn the engineering principles of the geometric code so that we can repair dysregulated cellular memories or create entirely new cellular memories,” said Professor Backman. “Current aging methods try to reset cells back to their factory default state. Geometric codes work differently. Cellular memories are physical structures that are enhanced through experience. Restoring cellular vitality is like restoring the clarity of a well-loved book—bringing back the story our cells already know how to tell.”
This is not CRISPR. This is not mRNA. It's a new way of thinking about cells and genomes. This is a completely new step in computational biology and it could be 22ND Century Medicine.
——————
If you're a fan of physics or cosmology, you've probably heard the phrase “the universe is geometry.” For example, Einstein's theory of general relativity shows that gravity is not a force but the result of a distortion of space-time. Likewise, whether the universe is flat (Euclidean), positively curved (spherical), or negatively curved (hyperbolic) has profound consequences for the fate of the universe. In fact, some scientists believe geometry can explain everything from the smallest particles to the universe itself.
So it pleased me to think that life itself might also owe a great deal to geometry.
Kim is a former electronics marketing executive for a large blues program and editor of The Late and Regretful tincture.ionow a regular THCB contributor
