Biochemical controls: cellular molecular decision making (Introduction)

by David Turell , Thursday, January 18, 2024, 18:59 (100 days ago) @ David Turell

By molecular reactions to stimuli:

https://phys.org/news/2024-01-physical-hidden-neural-network-abilities.html

"...a new study shows how the molecules that build structures, i.e., the muscle, can themselves do both the thinking and the doing. The study, by scientists with the University of Chicago, California Institute of Technology, and Maynooth University, was published in Nature and may suggest avenues for new ways to think about computation using the principles of physics.

"'We show that a natural molecular process—nucleation—that has been studied as a 'muscle' for a long time can do complex calculations that rival a simple neural network," said UChicago Assoc. Prof. Arvind Murugan, one of the two senior co-authors of the paper. "It's an ability hidden in plain sight—the 'doing' molecules can also do the 'thinking.' Evolution can exploit this fact in cells to get more done with fewer parts, with less energy and greater robustness."

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"The traditional view has been that cells might be able to sense and respond in this way using molecular circuits that conceptually resemble the electronic circuits in your laptop; some molecules sense the amount of salt and acid in the environment, other molecules make a decision on what to do, and finally 'muscle' molecules might carry out an action in response, like building an internal protective structure or a pump to remove unwanted molecules.

"Murugan and his colleagues wanted to explore an alternative idea: that all of these tasks—sensing, decision making, response—can be accomplished in one step by the physics inherent to the 'muscle' molecules that build a structure.

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"The scientists tested the robustness of 'phase transitions'–based decision-making using DNA nanotechnology, a field that Erik Winfree (BS'91) helped pioneer. They showed that a mixture of molecules would form one of three structures depending on what concentrations of molecules were present in the beaker.

"'In each case, the molecules came together to build different nanometer-scale structures in response to different chemical patterns—except the act of building the structure in itself made the decision on what to build," Winfree said.

"The experiment revealed that this 'muscle'-based decision making was surprisingly robust and scalable. With relatively simple experiments, the researchers could solve pattern recognition problems involving about a thousand kinds of molecules—nearly a 10-fold larger problem than had been done previously using other approaches that separated 'brain' and 'muscle' components.

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"'Physicists have traditionally studied things like a glass of water, which has many molecules, but all of them are identical. But a living cell is full of many different kinds of molecules that interact with each other in complex ways," said co-author Jackson O'Brien (Ph.D.'21), who was involved in the study as a UChicago graduate student in physics. "This results in distinct emergent capabilities of multi-component systems."

"The theory in this work drew mathematical analogies between such multi-component systems and the theory of neural networks; the experiments pointed to how these multi-component systems can learn the right computational properties through a physical process, much like the brain learns to associate different smells with different actions.

"While the experiments here involved DNA molecules in a test tube, the underlying concepts—nucleation in systems with many kinds of components—applies broadly to many other molecular and physical systems, the authors said.

"'NA lets us experimentally study complex mixtures of thousands of kinds of molecules, and systematically understand the impact of how many kinds of molecules there are and the kinds of interactions they have, but the theory is general and should apply to any kind of molecule," explained Winfree.

"'We hope this work will spur work to uncover hidden 'thinking' abilities in other multi-component systems that currently appear to merely be 'muscles,'" said Murugan."

Comment: this reporter is confused. No real thinking is happening. He is describing molecules recognizing other molecules and reacting accordingly following DNA instuctions. Real thought is in the DNA code.