The Systems Biology of COVID-19 and the SARS-CoV-2 virus. The class will build a foundation that includes the emergence of complexity, simple biological subsystems, their reductionist and equivalent toy and organ-chip models, and the measurements required to specify model architecture and parameters. Applications to biology, physiology, medicine, chemical and biological defense, pharmacology, drug discovery, and toxicology. UGrad: PHYS 240 01 and BME 290B; Grad: PHYS 326 and BME 395C.
0. I knew the basics of control from the readings and the other point point.
ReplyDelete1. I learned about the basic control loops and found the example loops interesting and am curious as to what was other factors went into the loop that were later removed more so because they may not be significant in one system loop but critical in another and these could be how loops cross talk to maintain overall homeostasis.
2. Slide 18 discusses the electrical control of cellular feedback as a critical external control but what about the electrical that mimics in vivo controls? Is it the electron flow that mimics a free radical that could have a critical component in vivo.
3. A topic for presentation might be how chemical oscillations provide a spring for homeostatic response.
4. Several interesting concepts presented that take a bit to take in and understand.
0 Knew: basic concepts of biological control (homeostasis, gene transcription)
ReplyDelete1 Learned: The opening of feedback loops is an important tool for the control of biological systems.
2 Pressing: Slide 17 asks how we study cellular-level responses to stimuli... why do we need to control the feedback loops? Why can't we just provide stimuli and see what the cell does in response? If we open the feedback loops then aren't we controlling the cell? I thought we wanted to see what the cell does on its own... On slide 20 when it's discussing oscillations - why does the time delay create oscillations? Why do we want oscillations? Are these examples of natural control by the cell itself or of external control?
3 Presentation: Oscillations in Biological Systems: What this means for control
4 Thoughts: Still confused about the point of control... I don't understand why we want to manipulate the feedback loops to observe cell response.
SysBio13 Asgn_8B_Class_08_PPT_02_2013_09_14
ReplyDelete0. Knew: Basics of control
1. Learned: Various systems in the body and how they maintain control through feedback.
2. Questions: How is the Hodgkin-Huxley loop being opened in slide 15?
3. Presentation: How chemical dynamics drive the electric properties in a cell
4. Thoughts: It was a lot of information that was not necessarily clear with just diagrams and little text. Brought more confusion than clarification for me.
Frank "Edad" Block, Jr.
ReplyDeleteSysBio13 Asgn_8B_Class_08_PPT_02_2013_09_14
0. Knew: Some basics of physiological control. Some models of physiological investigation.
1. Learned: Gain and delay of feedback control can lead to oscillations or loss of control.
2. Pressing: How does something as complex as a cell or an organism remain in control when so many things are being controlled?
3. Presentation: Principles of control with questions of gain and delay. Also, human compensations to moving to live at high altitude.
4. Thoughts: Some level of oscillations is the norm. Health = oscillations and Disease = lack of oscillations. Homeostasis as such does not exist, because the result is always variable and changing.
Also note that many processes have multiple levels and abilities of control. I have previously mentioned the short-, medium-, and long-term compensations for moving to live at high altitude.
David Wooten
ReplyDeleteSysBio13 Asgn_8B_Class_08_PPT_02_2013_09_14
0. Knew: Feedback, basics of control.
1. Learned: Specific examples of control experiments in biology.
2. Pressing ?: Regarding oscillations in biology: what good does it do to find them? What have we learned from observing oscillators today?
3. Presentation: Interactions between electrical, mechanical, chemical, and cell-to-cell feedbacks. Can chemical be controlled by electrical? Or mechanical?
4. Thoughts: I'm looking forward to class this week so we can talk about some of these different concepts.
0. Knew: Control and feedback from the readings
ReplyDelete1. Learned: A series of different mechanisms have been devised to open a feedback loop, how to read a control diagram
2. Pressing: Can anything be learned from ‘divergent behavior’ when a cell is exposed to a stimuli outside of its normal bounds?
3. Presentation: Uncopuling, coupling dynamics as a product of feedback loops
4. Thoughts: Putting tangible processes to these ideas was a fresh way to look at these ideas.
0. Knew: Biological systems are often composed of feedback loops which work to maintain homeostasis.
ReplyDelete1. Learned: Great advances in physiology have been made by opening the feedback loop. I think this hypothesis is true.
2. Pressing ?: To learn how to create your algorithm for external control of an OoC, why not start by having that "algorithm" be a mouse's body. IE Connect the OoC(would need to be larger than milli) liver to a liverless mouse, and let the mouse's body control the OoC. Then incorporate sensors between the connection in order to find out what is happening.
3: Presentation: An explanation of how what numerical analysis of a black-box system is/how it works.
4: Thoughts: This presentation was the answer to my previous presentation suggestion. It gives satisfying examples.
0. Knew: complexity of gene transcription and feedback mechanisms.
ReplyDelete1. Learned: Khoo experiment; Hodgkin-Huxley in terms of electrical circuitry.
2. Pressing ?: It is surprising that we have achieved electrical control before mechanical, cell-cell, and mechanical control. Why is this?
3. Presentation: Heterodyne Chemistry
4. Thoughts: Understanding metabolic and chemical oscillations seem to be key to establishing chemical control of cells.
0. Knew: Some of the elements of control, basics of gene transcription
ReplyDelete1. Spatially restricted calcium oscillations, ways to open the feedback loop.
2. The idea of oscillators is interesting. What can we learn from perturbations to the system and how can utilize the body's natural oscillating systems.
3. Understanding natural oscillators
4. How can we model these oscillating systems? Are we still short on the knowledge to do this?
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