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. From previous class discussions and reading I understood the basics of scaling.
ReplyDelete1. I learned more of the history that led to the development of scaling laws and some of the equations initially developed for scaling. I also found the determinants of size in different species interesting.
2. I suppose the pressing question regarding scaling is what is the most dominant means of scaling if all things are equal? I recognize that scaling depends on the system and what one is trying to study but what factors whether mechanical or physiological are more dominant since this could help when understanding scaling.
3. Does the mouse to elephant curve always hold up?
4. I found the information interesting and provides some nice history.
Frank "Edad" Block, Jr.
ReplyDeleteSysBio13 Asgn_5A_Class_05_Article_08_2013_09_05
0. Knew: Basics of scaling
1. Learned: Frogs grow isometrically. Springiness and gaits. Locomotion in fluids.
2. Pressing: Water animals are operating at the pressure of depth. This affects all kinds of physiology. Same comment applies to high-flying birds (some documented above 20,000 feet) and insects.
3. Presentation: Changes in physiology at depth and at altitude. Also the question of acclimatization we mentioned on Tuesday.
4. Thoughts: The issue of habitat is mentioned but the animals in any given habitat also depend upon the OTHER animals in the habitat (predators and prey).
Jie Zhao
ReplyDeleteSysBio13 Asgn_5A_Class_05_Article_08_2013_09_05
0. Knew: organ scaling laws in various animals
1. Learned: scaling law in mascle characteristic and legged locomotion.
2. Pressing: why it’s always power law relation?
3. Presentation: mechanical limitations of organ size
4. Thoughts: I’m looking forward to more explanations for such phenomena so that it’ll be useful for the design of HoC.
David Wooten
ReplyDeleteSysBio13 Asgn_5A_Class_05_Article_08_2013_09_05
0. Knew: The basics of metabolic scaling and city scaling
1. Learned: About locomotive allometry
2. Pressing ?: How can you understand differing scaling exponents for different organs?
3. Presentation: Causes of variation from the predicted allometry line
4. Thoughts: In designing and OoC, is metabolism the main consideration? If so, can we assume that allometry causes metabolic rates to naturally get out-of-whack on OoC's? Then, in order to force a micro tissue sample to match human metabolic rates, what can we learn from organisms that fall outside the typical allometry curve?
Austin Oleskie
ReplyDelete0. Knew: Organs scale at different exponents.
1. Learned: How the constants are generally determined. Relationship between body mass and metabolic rate.
2. How can we apply the proper scaling exponents to HoC as to maintain the proper metabolic rate scaling? How will scaling human organs affect their metabolic rate and will they obey this law?
3. How to scale human organs
4. This really brings up an applicable question to organs on a chip that the review on scaling covered, that is, what's the best method to scale the organs?
0. Knew that allometry was used to reconcile relative organ size at different scales.
ReplyDelete1. Learned: Behavior was a component of allometric scaling
2. What is Froude-number analysis?
3. Modeling gait allometrically.
4. There is so much data and analysis available for allometric scaling. It is too bad it is not more consistent with metabolic scaling.
Abigail Searfoss
ReplyDeleteSysBio13 Asgn_5A_Class_05_Article_08_2013_09_05
0. Knew: Idea of scaling and that organs do not scale in the same manner as each other.
1. Learned: How the scaling is determined. In fluid locomotion, a larger body size is more favorable when comparing metabolic expenditure.
2. Pressing Question: There is a lot of scaling but we always come back to the same question as to which is best for OoC. Is there another component we have not thought to scale, or are we just going to have to pick one and go with it? None individually seem to be the answer...how about combining the scales?
3. Presentation: Scaling to the number of cells. Find out how few cells you can reach before the scale falls apart.
4. Thoughts: Found the article helpful in explaining the equations/exponents of scaling.
Cameron Stewart
ReplyDelete0. knew: If an animal's size scales allometrically, it's mass will increase more quickly than its lungs' surface area or bones cross sectional area.
1. Learned: The log of mass vs log of cruising speed for insects, birds and planes forms a rough line.
2. pressing: A former article had emphasized that the difference in BMR between mice and humans is a large reason why animal studies are not effective. Do animal studies ever use deer or other animals with similar BMR's to humans?
3.Presentation: Allometry. How organs scale with respect to each other in order to serve their necessary functions.
4. Thoughts: Very applicable to what we’re learning. The main idea was has been conveyed in the other articles that we've read.
0 Knew: Allometric scaling can be used to predict organ sizes as well as other variables in relation to body mass.
ReplyDelete1 Learned: I learned how allometric scaling actually works and how it can be used to compare different species.
2 Pressing: So, other articles have argued allometric scaling is not a reliable scaling procedure... Do the scaling coefficients scale across species? Humans are the size we are for a reason; if we try to minimize a human, should we try to mimic human scaling or that of a species on the same size scale of our OoC? Is this why allometry breaks down?
3 Presentation: Allometric Scaling: Applications to OoCs?
4 Thoughts: Thank you! I understand this much better now. I'm starting to see why this idea doesn't work, and we need to scale more for function.
0. Knew: Allometric scaling of organs produces organs out of scale with each other and not proportional to the original.
ReplyDelete1. Learned: Using power laws and gathered data, many functions and structures have been modelled.
2. Pressing: What does the allometric v. functionality interface look like, which values are most important in recreating in OoC’s?
3. Presentation: What other teams have done in making allometrically scaled models.
4. Thoughts: Mammals BMR’s display negative allometry with increasing size, so presumably just to sustain themselves their metabolic complexity per cell must increase, systems are more adept at using energy, so going back a few articles to the figure comparing BMR’s in vitro v. in vivo does the lack of system integration in the in vitro cells account for the disparity in BMR’s, is this an inescapable problem/what is the limit of in vitro metabolic mimicry, the two have to be related but what else is there to consider?
Rui Wang
ReplyDeleteSysBio13 Asgn_5A_Class_05_Article_08_2013_09_05
0. Knew: A way to analyze data in scaling is to use log-transformation. This is very common in astronomy. This is how people found the stellar evolution.
1. Learned: Large marine mammals or large fly animals can migrate much more distance in the fluid than small ones because of the metabolic allometric mechanics inside.
2. Pressing: Are these allometric analyses helpful to research the metabolic law for dinosaurs?
3. Presentation: Allometry of legged locomotion
4. Thoughts: Allometry analysis can help us macroscopically understand the evolution of species and the metabolic organism. Does this microscopically connect with the genes or genomes? In other words, different animals behave different allometric aspects in organs, locomotion or other factors because of different microscopic quantities in genes, genomes or other chemicals?