Find higher frequencies and flows for industrial applications of your methods
https://www.biorxiv.org/content/10.1101/2024.05.06.592707v1.full
from https://x.com/RichardKCollin2/status/1838458035947090197
My Comments: Find higher frequencies and flows for industrial applications of your methods
When I was at UT Austin and Ilya Prigogine and others were chipping away at chemical clocks, chemical oscillators, talking constantly about “systems far from equilibrium” (his Nobel Prize), it was always dissipative open systems fed by outside energy. An oscillatory solution to a system responding to energy, a system “fed by energy”. Even the same “reaction diffusion” and “periodic oscillations”. I think you are just describing one of the standard solutions. Just not in the same way. I looked through your list of references and did not see him mentioned or any of his group. It might be useful to check.I remember meeting Dilip Kondepudi at the National Academy of Sciences in DC when they were having a conference/symposium on chemical clocks, chemical oscillators. I was working next store in the US State Department building, so that was 1983-1985. I expect Prigogine was there but I was more interested in the topic and presentations which really had not resolved much and to see my friend.
https://en.wikipedia.org/wiki/Ilya_Prigogine – 1977, the Nobel Prize in Chemistry “for his contributions to non-equilibrium thermodynamics, particularly the theory of dissipative structures”.
Now back in college at Case Western Reserve (1968) I worked in the lab for Norman B Rushforth measuring electrical signals from Hydra. Its quasi-periodic contractions were somewhat mysterious so I would record long periods of those contractions and look for statistical patterns, for him. Essentially, in my memory, the energy used in each contraction took a finite time to recover. None of the contractions were exactly the same, so the recovery and initial conditions for the next threshold starting the next contraction was always different. The trigger was sharp and the stored energy released in a cascade.
Now I was interested in the electrical activity of Hydra and periodic contractions because in high school a couple of years previous I was learning about periodic EEG signals in the human brain, and studying and optimizing random neural nets.
I only mention this, not for me, but for a rather large field I have followed for more than 55 years where people have been doing these kinds of systems. Your pictures of reaction diffusion patterns and finding a mechanical (did you do the electrical?) correlate or anti-correlate is part of the same pattern of human groups studying the systems.
You only mention “electrical” once “a loss of synchronization between electrical and mechanical activities, is known to be a potentially life-threatening condition that culminates in sudden cardiac death” which is a well studied, if not always well understood phenomena.
I think you got close to something but I know that using entropy (a slope) is harder than putting the chemical and electrical energy in the same units unless you use sensitive high resolution thermal imaging. There are lots of entropies from information. You did use “calorimetry” but you should be able to use image sensors and proxy measures from them, with your calorimetry calibration” to set a visual entropy measure that works based on measures from the spiral patterns. You did not mention machine learning, but that is the usual way now to help explore non-obvious connections.
Your correlations are a little obscured and jumbled into a too busy “Figure 2”. The autocorrelation frequency is shown as a squared frequency and that is usually a sign that you have found a second order differential equation for a systems, found resonances and excited them. All of those act the same, but it usually means cleaning up and standardizing the signals. And probably not using natural oscillators that are almost always aperiodic because they are soft.
I bet there is a plant (leafy kind) or vat model (industrial plant) that works precisely and still uses organics. An industrial process.
My hunch is that simply counting the pixel patterns in the images would get you somewhere faster.
Even through I tried to read all of what you did, I really did not get a clear picture of what you want to do with what you are finding. Your “computational model” is on GitHub but the details are a bit obscured by the programming style. Computer languages are not standardized yet (I am working on that for the Internet Foundation) and most people are not going to know GitHub. It has no real standards. It is not like they have editors for publication the way text and image documents have readers and editors and standards.
I am fairly certain what you did here would be useful for industrial scale biosynthesis using natural living systems to maximize production of “something”. When you lock them into a periodic process, it is easier to monitor. If you use multispectral high frame rate cameras, you can use much higher frequencies for much higher flow rates. (f^2). And if you use magnetic resonance imaging spectroscopic microscopy and related electromagnetic monitoring tools those almost always have a “reciprocal” control application to modify and control the flows, frequencies, critical points (resonances and transition points).
When I worked at Phillips Petroleum in their Business Intelligence group I read and studied all the global scale industrial process methods and economics to see where more effective monitoring and controls could substantially affect returns on investments.
I think you are close to something very useful, but encourage you to make your “computational model” much more open and interactive and real time. Think “monitoring and control and optimization”.
I apologize for the stories about events in my life, but I can remember details more clearly when I remember the context and time. In a way that is true about your experiments, the more carefully you image, and quantify the images of what you see, the more precisely you can find patterns where “something good” is happening, and you can find out why and how to make it happen more often.
Richard Collins, The Internet Foundation
I was working at USAID in the State Department building from 1983-1985, while I was working for Georgetown University Center for Population Research. I corrected “1984” in my notes but once you post a reply on X there is no way to edit. There was something special about the gathering at National Academy of Sciences. They like to do things formally. There was a formal luncheon.
The focus was on Belousov-Zhabotinsky oscillating chemical reactions.
( “National Academy of Sciences” ” Belousov-Zhabotinsky” ) is fairly rich in some of the key approaches and ideas. But they never seem to hit the target. I expect they are all aiming for a Nobel prize, but sometimes making money is easier. I see “oscillating gel” that looks like people have isolated and built some “ideal systems”. Like those brain cells on a chip, and organs on a chip.
Maybe I should review the field again. They always seem to get close to something but never really hit the target. Mostly groups learn methods but do not know what they can be used for in global industry and society.
For many years I have tried to remember who sponsored that symposium. I was searching again for (“National Academy of Sciences” ” Belousov-Zhabotinsky” “1984”) and noticed Richard Noyes. I heard his name often, but do not remember meeting him. His obituary is at National Academy of Sciences at https://www.nasonline.org/wp-content/uploads/2024/06/noyes-richard.pdf
And it gives a very good summary of Richard Macy Noyes (1919-1997) many years of work on chemical oscillators.
This reinforces my feeling that the spatial frequency is critical. In Reynolds number experiments the critical transitions are spatial frequency dependent.
In 1985 Gordon Research Conference on Oscillations and Dynamic Instabilities Richard Noyes chaired it. I think that was part of that series.
I also happened on Nonlinear chemical dynamics by
Francesc Sagués and Irving R. Epstein. Francesc Sagués was at UT Austin 1985-1986. The paper lays our more of what they were chasing with lots of details. Including the Turing patterns, and effects of gravitational electric, temperature fields. A good review. It confirms that electric fields can be used to control the shapes and timing. I encouraged Dilip Kondepudi and Ilya Prigogine to write a paper on gravitational effects and think it was about that time.
The paper shows the long induction period then the periodic solution. But it can also be a long induction period and then an underdamped or explosive reaction. The shape of the pulses depends on the physical impulse response too. And the oscillations are easier to design if you separate things physically. Control the diffusion, control the feed. Or control the evolution and cascade or both.
I am just writing it out for myself. I store a lot of information and am working on groups who want to rewrite the whole of cell and organ metabolic networks. So reviewing these basics is useful. And remembering some happy times and people.
Fig 6 of this BZ Epstein review the bottom curve occurs in laser self interference and it greatly reduces the cost of interferometers. Because of these papers it is possible to make atom interferometers for that – much more compact and faster. That matters for gravitational wave detection on the desktop and wearables.
I expected to end my life never getting this sorted out. Thanks for your paper.
Richard Collins, The Internet Foundation
