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Metaphors for Biology: Time
Posted by Mark Field from Substack in Bio-informatics and Biology
The interior of a cell is densely packed with millions of molecules vibrating, jostling, and moving about. Sugar molecules fly through a cell at 250 miles per hour, ricocheting off of ribosomes, organelles, cytoskeletal fibers, and enzymes. Indeed, every protein in the cell is hit by about 1013 water molecules each second. This chaos makes biology seem hopelessly convoluted. With everything moving so quickly, how can we begin to understand biomolecules' As with other hard-to-intuit quantities in science, one could look up biological rates using resources like PubMed or BioNumbers, to discover facts like 'water flows through aquaporin at 100 million molecules per second,' or 'yeast transcribes RNA at 0.12 molecules per minute.' But knowing a number doesn't necessarily give one a feel for it. Are those rates' fast' How do they compare to protein folding' Or enzymatic activity' Or squeezing a muscle' We can answer this question with a quantitative metaphor, by visualizing the most important goings-on of a typical cell slowed down to speeds that are still accurate relative to one another, but matched to what we experience in the everyday world. The slowdown factor we pick should make it easy to understand the molecular machines that run our cells ' proteins. Ideally, we would scale the fastest functionally important protein event to match the shortest unit of human perception....
Mark shared this article 18hrs
Richard Hynes, a pioneer in the biology of cellular adhesion, dies at 81
MIT Professor Emeritus Richard O. Hynes PhD '71, a cancer biologist whose discoveries reshaped modern understandings of how cells interact with each other and their environment, passed away on Jan. 6. He was 81. Hynes is best known for his discovery of integrins, a family of cell-surface receptors essential to cell'cell and cell'matrix adhesion. He played a critical role in establishing the field of cell adhesion biology, and his continuing research revealed mechanisms central to embryonic development, tissue integrity, and diseases including cancer, fibrosis, thrombosis, and immune disorders. Hynes was the Daniel K. Ludwig Professor for Cancer Research, Emeritus, an emeritus professor of biology, and a member of the Koch Institute for Integrated Cancer Research at MIT and the Broad Institute of MIT and Harvard. During his more than 50 years on the faculty at MIT, he was deeply respected for his academic leadership at the Institute and internationally, as well as his intellectual rigor and contributions as an educator and mentor....
Mark shared this article 6d
Biology-based brain model matches animals in learning, enables new discovery
Posted by Mark Field from MIT in Biology
A new computational model of the brain based closely on its biology and physiology not only learned a simple visual category learning task exactly as well as lab animals, but even enabled the discovery of counterintuitive activity by a group of neurons that researchers working with animals to perform the same task had not noticed in their data before, says a team of scientists at Dartmouth College, MIT, and the State University of New York at Stony Brook. Notably, the model produced these achievements without ever being trained on any data from animal experiments. Instead, it was built from scratch to faithfully represent how neurons connect into circuits and then communicate electrically and chemically across broader brain regions to produce cognition and behavior. Then, when the research team asked the model to perform the same task that they had previously performed with the animals (looking at patterns of dots and deciding which of two broader categories they fit), it produced highly similar neural activity and behavioral results, acquiring the skill with almost exactly the same erratic progress....
Mark shared this article 7d
Read Something Wonderful (about Biology)
Posted by Mark Field from Substack in Biology
One of my favorite websites is called Read Something Wonderful. It's a curated list, compiled by the Matter team, of essays from scattered corners of the Internet on all kinds of topics, with no particular theme. Some of the essays were written by entirely unknown authors, whereas others were written by esteemed figures such as Steve Jobs or Isaac Asimov. None of the essays are newsworthy or timely, but all contain some evergreen idea or insight unlikely to diminish in importance over time. While curation is a contribution that we often regard as less important or impressive than original writing, it is highly valuable. For one, it can lead readers to something they never would have found on their own. When I first found Read Something Wonderful, I spent weeks sifting through its essays and 'discovered' perhaps a dozen writers that I quickly subscribed to (and still read today, more than a year later.) In my planner, I marked a note to read two per day; my small way to spread their wealth over a longer length of time. I feared that, if I read too many essays in one day, they'd jumble together in my brain, and I'd lose track of some of the ideas contained within. (Indeed, I was following advice from another essay, entitled 'Treat your to-read pile like a river, not a bucket.')...
Mark shared this article 2mths