{"id":9460,"date":"2025-11-07T18:25:51","date_gmt":"2025-11-07T18:25:51","guid":{"rendered":"https:\/\/medical-article.com\/?p=9460"},"modified":"2025-11-07T18:25:51","modified_gmt":"2025-11-07T18:25:51","slug":"life-is-geometry","status":"publish","type":"post","link":"https:\/\/medical-article.com\/?p=9460","title":{"rendered":"Life Is Geometry"},"content":{"rendered":"
\n<\/div>\n

By KIM BELLARD<\/p>\n

In 2025, we\u2019ve got DNA all figured out, right?\u00a0 It\u2019s been over fifty years since Crick and Watson (and Franklin) discovered the double helix structure. We know that permutations of just four chemical bases (A, C, T, and G) allow the vast genetic complexity and diversity in the world. We\u2019ve done the Humam Genome Project. We can edit DNA using CRISPR. Heck, we\u2019re even working on synthetic DNA<\/a>. We\u2019re busy finding other uses for DNA, like computing<\/a>, storage<\/a>, or robots<\/a>. Yep, we\u2019re on top of DNA.<\/p>\n

Not so fast. Researchers at Northwestern University say we\u2019ve been missing something: a geometric code embedded in genomes that helps cells store and process information. It\u2019s not just combinations of chemical bases that make DNA work; there is also a \u201cgeometric language\u201d going on, one that we weren\u2019t hearing.<\/p>\n

Wait, what?<\/p>\n

The research \u2013 Geometrically Encoded Positioning of Introns, Intergenic Segments, and Exons in the Human Genome<\/em><\/a> <\/em>\u2013 was led by Professor Vadim Backman, Sachs Family Professor of Biomedical Engineering and Medicine at Northwestern\u2019s McCormick School of Engineering, and director of its Center for Physical Genomics and Engineering<\/a>. The new research indicates, he says<\/a>, that: \u201cRather than a predetermined script based on fixed genetic instruction sets, we humans are living, breathing computational systems that have been evolving in complexity and power for millions of years.\u201d<\/p>\n

The Northwestern press release<\/a> elaborates:<\/p>\n

The geometric code is the blueprint for how DNA forms nanoscale packing domains that create physical \u201cmemory nodes\u201d \u2014 functional units that store and stabilize transcriptional states. In essence, it allows the genome to operate as a living computational system, adapting gene usage based on cellular history. These memory nodes are not random; geometry appears to have been selected over millions of years to optimize enzyme access, embedding biological computation directly into physical structure.<\/p>\n

Somehow I don\u2019t think Crick and Watson saw that coming, much less either Euclid or John von Neumann.<\/p>\n

Coauthor Igal Szleifer<\/a>, Christina Enroth-Cugell Professor of Biomedical Engineering at the McCormick School of Engineering, adds: \u201cWe are learning to read and write the language of cellular memories. These \u2018memory nodes\u2019 are living physical objects resembling microprocessors. They have precise rules based on their physical, chemical, and biological properties that encode cell behavior.\u201d<\/p>\n

\u201cLiving, breathing computational systems\u201d? \u201cMicroprocessors\u201d? This is DNA computing at a new level.<\/p>\n

The study suggests that evolution came about not just by finding new combinations of DNA but also from new ways to fold it, using those physical structures to store genetic information. Indeed, one of the researchers\u2019 hypothesis is that development of the geometric code helped lead to the explosion of body types witnessed in the Cambrian Explosion<\/a>, when life went from simple single and multicellular organisms to a vast array of life forms.<\/p>\n

Coauthor Kyle MacQuarrie<\/a>, assistant professor of pediatrics at the Feinberg School of Medicine<\/a>, points out that we shouldn\u2019t be surprised it took this long to realize the geometric code: \u201cWe\u2019ve spent 70 years learning to read the genetic code. Understanding this new geometric code became possible only through recent advances in globally-unique imaging, modeling, and computational science\u2014developed right here at Northwestern.\u201d (Nice extra plug there for Northwestern, Dr. MacQuarrie.)<\/p>\n

Coauthor Luay Almassalha, also from the Feinberg School of Medicine, notes: \u201cWhile the genetic code is much like the words in a dictionary, the newly discovered \u2018geometric code\u2019 turns words into a living language that all our cells speak. Pairing the words (genetic code) and the language (geometric code) may enable the ability to finally read and write cellular memory.\u201d<\/p>\n

I love the distinction between the words and the actual language. We\u2019ve been using a dictionary and not realizing we need a phrase book. \u00a0\u00a0<\/p>\n

<\/span><\/p>\n

I recently read about, and was impressed by, something called MetaGraph<\/a>, a tool developed at ETH Zurich to search DNA databases. \u201cIt\u2019s a kind of Google for DNA,\u201d as Professor Gunnar R\u00e4tsch, data scientist at the Department of Computer Science at ETH Zurich, puts it<\/a>. This \u201cDNA search engine\u201d makes it much easier, faster, and cheaper to search for DNA sequences and compare them to other sequences. Cool as that is, the existence of the geometric code means that the ETH Zurich folks may have some additional work to do, as is true of lots of other people working with DNA.<\/p>\n

I hate to say it\u2019s a whole new ball game, but there certainly are some important new rules.<\/p>\n

The presence of this geometric code has implications for our health. It may not always be DNA mutations that cause problems; our DNA structures may sometimes be falling apart. Dr. Almassalha says: \u201cInstead of a puzzle of genetic words, the geometric code lets cells build elaborate tissues, such as brains or skin. But with age, this language loses its fidelity. This decay results in neurodegeneration, cancer, or other diseases of aging.\u201d<\/p>\n

This opens up all sorts of new avenues for research, and, potentially, treatments. \u201cThe next step is to fully learn the engineering principles of the geometric code so we can repair dysregulated cell memories or create entirely new ones,\u201d Professor Backman says. \u201cCurrent approaches to aging try to reset cells back to a factory default state. The geometric code works differently. Cell memories are physical structures enhanced by experience. Revitalizing cells resembles restoring the clarity of a well-loved book \u2014 bringing back the stories our cells already know how to tell.\u201d<\/p>\n

This isn\u2019t CRISPR. This isn\u2019t mRNA. This is a new way of thinking about cells and our genome. This is a whole new step in computational biology, and it may be foundational in 22nd century medicine.<\/p>\n

\u2014\u2014\u2014\u2014-<\/p>\n

If you are a physics or cosmology buff, you may have heard the expression \u201cThe universe is geometry.\u201d E.g., Einstein\u2019s general theory of relativity indicates gravity is not a force but, rather, the result of distortions in spacetime. Similarly, whether the universe is flat (Euclidian), positively curved (spherical), or negatively curved (hyperbolic) has profound implications for the fate of the universe. In fact, some scientists believe<\/a> that geometry may explain everything from the smallest particles to the universe itself.<\/p>\n

So it pleases me to think that life itself may owe much to geometry as well.<\/p>\n

Kim is a former emarketing exec at a major Blues plan, editor of the late & lamented\u00a0<\/em>Tincture.io<\/em><\/a>, and now regular THCB contributor<\/em><\/p>","protected":false},"excerpt":{"rendered":"

By KIM BELLARD In 2025, we\u2019ve got DNA all figured out, right?\u00a0 It\u2019s been over fifty years since Crick and Watson (and Franklin) discovered the double helix structure. We know that permutations of just four chemical bases (A, C, T, and G) allow the vast genetic complexity and diversity in the world. We\u2019ve done the…<\/p>\n","protected":false},"author":0,"featured_media":9459,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[2],"tags":[],"class_list":["post-9460","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-articles"],"_links":{"self":[{"href":"https:\/\/medical-article.com\/index.php?rest_route=\/wp\/v2\/posts\/9460"}],"collection":[{"href":"https:\/\/medical-article.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/medical-article.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"replies":[{"embeddable":true,"href":"https:\/\/medical-article.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=9460"}],"version-history":[{"count":0,"href":"https:\/\/medical-article.com\/index.php?rest_route=\/wp\/v2\/posts\/9460\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/medical-article.com\/index.php?rest_route=\/wp\/v2\/media\/9459"}],"wp:attachment":[{"href":"https:\/\/medical-article.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=9460"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/medical-article.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=9460"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/medical-article.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=9460"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}