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. The basics of scaling.
ReplyDelete1. The dynamic aspects of scaling. Depending on what is being measured then there are a variety of scaling mechanisms such as physiological and mass. Figures 10 and 11 highlight the necessity for researchers to understand what they are are trying to compare before scaling.
2. The article highlights the scaling of mammals but how is the scaling altered in water based on physiological features? I don’t believe that “fish are virtually isometric” because it completely ignores environmental considerations such as salinity and pressure.
3. How does the life style humans now live effect the scaling problem?
4. Once again a nice historical perspective on scaling.
Frank "Edad" Block, Jr.
ReplyDeleteSysBio13 Asgn_5B_Class_05_Article_09_2013_09_05
0. Knew: General ideas of scaling.
1. Learned: Brain size.
2. Pressing: Information about depth is WRONG. Human lungs are not crushed at 5m. Recreational Scuba divers go down to 100 feet!
3. Presentation: Walk-Canter-Trot-Gallop: What's the difference?
4. Thoughts: Major focus of the paper was on muscles, bones, and locomotion. OoC does not include muscle and bone on a chip. In a sense that's good news, because we don't have to worry about scaling something that isn't there! But these are important for mammalian function ...
In terms of gait: for horses the difference is the pattern in which the feet fall.
DeleteWalk: only one foot raised at a time
Trot: two feet raised at once (feet move in diagonal pairs)
Canter: one rear foot pushes off and two feet catch and third foot completes the landing.
Gallup: like a canter except the two feet that hit the ground at the same time in a canter hit the ground at slightly different times in the gallup.
David Wooten
ReplyDeleteSysBio13 Asgn_5B_Class_05_Article_09_2013_09_05
0. Knew: Scaling concepts
1. Learned:
2. Pressing ?: Regarding Fig 10, how would you choose an appropriate "environment" to model your OoC on?
3. Presentation: Different ways environment effects metabolism
4. Thoughts: I'd hate to upset a Baluchitherium! Also, I am beginning to wonder about environmental influences on metabolism, and how to handle then in OoC design. For fun I tried estimating the slopes in Fig 10, then plotting slope vs mass on a log-log plot, and found a scaling coefficient of about -2.3.
0. Scaling in general; Size limits exist for organisms
ReplyDelete1. Smallest organism that can live is an artificial medium is PPLO
2. What are the correlations between brian weight and intelligence within a species and between species?
3. Presentation: prehistoric life
4.Thoughts: Natural history holds many answers to questions of scaling.
Jie Zhao
ReplyDeleteSysBio13 Asgn_5B_Class_05_Article_09_2013_09_05
0. scaling of organs, metabolic rate, muscle character and so on.
1. a. it’s galilei that first point out the nonlinear scale portion between large and small animals.
b. scaling function of physiology,
2. a. I think the fig 3 contradict fig 6?
b. fig 13 is very interesting, but it’s still unclear to me why the data points look more organized after dividing body length instead anything else.
4. it’s such an interesting topic, if one could dig into the explanations for all these phenomena rather than describing and organizing them.
For a broad explanation, there's a (fairly long) video by Geoffrey West on Scaling Laws in Biology (http://www.youtube.com/watch?v=GoHD1ROPiUc). He and some colleagues proposed a mechanism for metabolic scaling laws, and have done quite a bit of math to show that it works pretty well. His talk doesn't really go into the math, but does talk about the assumptions for the model.
Delete0. Knew: General scaling concepts, everything doesn't scale the same way.
ReplyDelete1. Examples of morphological scaling, the history of exploring scaling.
2. If we scale function, will we be able to predict the outcome in larger organs?
3. Presentation: How does scaling affect metabolism
4. As was previously mentioned, we probably won't have to worry about scaling locomotion, the focus of this paper.
0. Knew: Breathing through a long tube under water is really difficult
ReplyDelete1. Learned: The masses of life forms span 10^21 orders of magnitude.
2. Questions: Why did large land animals die out?
3. Presentation: About how various aspects of animals scale with their size.
4. Thoughts: This article is perhaps useful in giving us an intuitive sense of allometric scaling, but it doesn’t seem all that applicable to OoC’s other than mentioning issues like lung surface area, brain scaling, and BMR/body mass. Why are we reading articles about efficiency of movement? Will the OoCs/HoCs be moving?
0. Knew: Basics of scaling.
ReplyDelete1. Learned: Certain functions among different species dictate size, using buoyancy he determined dinosaurs are not aquatic.
2. Pressing: This article reinforces that larger animals are more metabolically efficient, so is it possible to even get close in mimicking a human’s function with an OoC that’s so small?
3. Presentation: Possible reasons why size some physiological units are dictated by function.
4. Thoughts: Covering the history of scaling was interesting and fig. 13 comparing freq. of tail beats to speed vs. to speed over body length was especially convincing.
I think your question is a great one. The idea seems to be to "trick" the OoC cells into thinking they are in a real human, but everything is so dependent on mass! Or maybe it's all based on metabolic rate, but that seems to be dictated by mass. I know A05 suggested limiting O2 supply to force lower metabolic rates, but I wonder if (a) that is effective at all, and (b) if doing so has unintended consequences.
DeleteI suppose there's nothing magical about cells being in a massive creature that causes them to behave more efficiently, but I wonder what specifically causes it, and how we can implement that in OoC?
0 Knew: BMR is important in scaling.
ReplyDelete1 Learned: An animal's habitat has an effect on its maximum body mass.
2 Pressing: This article seems of advocate use of allometric scaling for BMR (p. 298). Is it this simple? Since the size of an organism has so many implications, how reliable is the information we would receive from OoCs?
3 Presentation: scaling effects on dinosaurs.
4 Thoughts: Good scan. It's interesting how much of an impact scaling has on organisms and how they live.
Abigail Searfoss
ReplyDeleteSysBio13 Asgn_5B_Class_05_Article_09_2013_09_05
0. Knew: Basics of scaling from other paper and class. Classification, natural selection, and inheritance.
1. Learned: Where the limits of body size originate. More specifics on animals relative metabolic rates.
2. Pressing Question: Is there any idea why blood (fluid) vs. a respiratory system for gas transport evolved the way it did? Would it be possible to not have an exoskeleton and use the respiratory system as the transporter...or would you loose too much gas without the exoskeleton?
3. Presentation: metabolic rates in relation to sleep cycles/activity
4. Thoughts: Why not use the idea of 3 ways to design larger structures for ways to design smaller structures, and then apply this to OoC thinking.
Rui Wang
ReplyDeleteSysBio13 Asgn_5A_Class_05_Article_09_2013_09_05
0. Knew: The two critical factors, structure and function are important in the size of an organism. Structure determines function while function reflects structure.
1. Learned: The reasons of why dinosaurs live on land but not under water.
2. Pressing: Is there any allometric conclusion from seeds or fruits of vegetables? Another question is that how to apply these allometric analysis to organs on chips, mHu or uHu?
3. Presentation: The importance of mass to allometric scaling
4. Thoughts: Allometric scaling seems not as important as functional scaling in the multi-modeling of organs on chips. But allometric scaling can explain a lot of metabolic questions and present some natural laws when it comes to certain groups of animals. How to keep balance in allometric scaling and functional scaling for OoCs?
Blog Harvested
ReplyDeleteJPW