I really enjoyed this, thanks for putting it all together! As a neurobiologist, I am always curious to know how these equations get implemented in living systems. Beyond guiding the development of technology, these principles or methods of representing matter via their physics should hold the keys to biological form and function, so thanks for making this accessible! I would be curious to know if you have done any work on biological modeling?
Hi Daniel - no problem and no, I haven't done a lot of work in regards to biological modelling, but that's one of the topic I've always been hugely interested in and curious about, so it's definitely on my future to-do list. Are there any specific biological models that you're working with or interested in reading about?
Hi Nick — thanks for the reply. I work on bioenergetics + brain dynamics, and I’m curious whether whole-organism energy budget models can be extended to treat the brain as an explicitly costly control module instead of a black box? My hunch (from coarse-graining in physics) is you often end up with history dependence—memory terms—when you compress a complex driven system down to a few state variables. If you were to explore biological modeling, which level sounds most fun: cells/neurons, animals, ecosystems?
Wow - that sounds super interesting I'll definitely check out your research when I have more time! If I had to choose, I'd probably choose between 1) trying to model the brain / neurons or 2) finding out how cell differentiation occurs (i.e. how is the information for the entire human system / body encoded within a cell). I'm more interested in how things work at the very-low level (bottom-up) rather than the top-down approach and looking and dynamics from the top-level. I've been interested in Michael Levin's research as well and I believe in most of his thesis (i.e. bioelectricity encodes a lot more than we think it does). Btw, it looks to me like you work at University of Illinois - is that correct? The reason I ask is because my brother is a professor there: https://etrl.mechanical.illinois.edu/people.html
Hi Nick — thanks, I appreciate that! I was at UIUC until recently, and I’m in a transition doing independent work now. Small world — I probably missed your brother since my overlap was mostly with BioE/neuro circles, but his lab looks like it’s doing solid foundational work! I’m with you on the bottom-up approach, and Levin’s bioelectric patterning results are exactly the kind of thing that feels feasible to bridge the biophysics of cell signaling during development. I’d be curious what your first swing at a differentiation model would look like?
Hey Daniel - apologies for the long delay - and it is a small world indeed haha. Either way I wish you the best of luck on the independent work and on the question: I'm not quite sure what you're asking here? I normally don't use differentiation models -- I try to do procedural bottom up modelling and if i do use differential equations I normally code it using difference equation modelling. On the human brain side Im mostly interested in hobbian / associative learning right now. I don't really have a good model on cellular differentiation im currently still reading about and studying this - here microtubule networks interest me as well as cellular membranes.
No worries, I'm relatively new to bioenergetics which is where I think our interests may overlap. As a biologist delving into differential equations for the first time really in depth beyond some forays with information theory, I’m mostly curious what others are trying and simultaneously exploring social media, so I appreciate the conversation, and look forward to hearing more!
I really enjoyed this, thanks for putting it all together! As a neurobiologist, I am always curious to know how these equations get implemented in living systems. Beyond guiding the development of technology, these principles or methods of representing matter via their physics should hold the keys to biological form and function, so thanks for making this accessible! I would be curious to know if you have done any work on biological modeling?
Hi Daniel - no problem and no, I haven't done a lot of work in regards to biological modelling, but that's one of the topic I've always been hugely interested in and curious about, so it's definitely on my future to-do list. Are there any specific biological models that you're working with or interested in reading about?
Hi Nick — thanks for the reply. I work on bioenergetics + brain dynamics, and I’m curious whether whole-organism energy budget models can be extended to treat the brain as an explicitly costly control module instead of a black box? My hunch (from coarse-graining in physics) is you often end up with history dependence—memory terms—when you compress a complex driven system down to a few state variables. If you were to explore biological modeling, which level sounds most fun: cells/neurons, animals, ecosystems?
Wow - that sounds super interesting I'll definitely check out your research when I have more time! If I had to choose, I'd probably choose between 1) trying to model the brain / neurons or 2) finding out how cell differentiation occurs (i.e. how is the information for the entire human system / body encoded within a cell). I'm more interested in how things work at the very-low level (bottom-up) rather than the top-down approach and looking and dynamics from the top-level. I've been interested in Michael Levin's research as well and I believe in most of his thesis (i.e. bioelectricity encodes a lot more than we think it does). Btw, it looks to me like you work at University of Illinois - is that correct? The reason I ask is because my brother is a professor there: https://etrl.mechanical.illinois.edu/people.html
Hi Nick — thanks, I appreciate that! I was at UIUC until recently, and I’m in a transition doing independent work now. Small world — I probably missed your brother since my overlap was mostly with BioE/neuro circles, but his lab looks like it’s doing solid foundational work! I’m with you on the bottom-up approach, and Levin’s bioelectric patterning results are exactly the kind of thing that feels feasible to bridge the biophysics of cell signaling during development. I’d be curious what your first swing at a differentiation model would look like?
Hey Daniel - apologies for the long delay - and it is a small world indeed haha. Either way I wish you the best of luck on the independent work and on the question: I'm not quite sure what you're asking here? I normally don't use differentiation models -- I try to do procedural bottom up modelling and if i do use differential equations I normally code it using difference equation modelling. On the human brain side Im mostly interested in hobbian / associative learning right now. I don't really have a good model on cellular differentiation im currently still reading about and studying this - here microtubule networks interest me as well as cellular membranes.
No worries, I'm relatively new to bioenergetics which is where I think our interests may overlap. As a biologist delving into differential equations for the first time really in depth beyond some forays with information theory, I’m mostly curious what others are trying and simultaneously exploring social media, so I appreciate the conversation, and look forward to hearing more!