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.
Wednesday, September 4, 2013
SysBio13 Asgn_5D_Class_05_Article_11_2013_09_05
Scan Article 11:
Vance A. Tucker. The energetic cost of moving about. Sci.Am.
63:413-420, 1975. Be sure to understand Figs. 1-3 and 5, and the concept that energy
has to be expended to stretch active muscle. This is a nice article
that shows the span of spatial scales that we must consider.
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0. Knew the basics of scaling and had a notion of what animals were migratory but Figure 2 puts things into perspective and makes you wonder if there is not some other scaling line in which there is a subset of animals that can be scaled together and others that can’t.
ReplyDelete1. I thought the article but the concept of work and energy expenditures into a nice perspective which highlight the physiological scaling issues that researchers must contend with since a force on a single cell has a different effect than the force on a mass of cells.
2. Since in figure 2 mice are off in a mini-subset are they a good animal for “in vivo” experiments if we are interested in human effects?
3. How does a sea turtle fit into Figure 2? It is a migratory animal but it also expends a great deal of energy so I wonder if it would be an exception to the migratory line?
4. Very interesting article.
David Wooten
ReplyDeleteSysBio13 Asgn_5D_Class_05_Article_11_2013_09_05
0. Knew: Scaling, somewhat of locomotive scaling
1. Learned: The bicyclist is way more efficient than the motorcyclist.
2. Pressing ?: How to account for movement in OoC?
3. Presentation: What accounts for clustering in certain sub-populations? Why are mice separate? Why fish? How does this relate to OoC?
4. Thoughts: Awesome figure! It makes me want a pedal airplane.
Abigail Searfoss
ReplyDeleteSysBio13 Asgn_5D_Class_05_Article_11_2013_09_05
0. Knew: Knew that the wings of birds change the downward motion to forward motion. Also, that the swimbladder uses buoyancy to balance the gravitational force.
1. Learned: Stretching of muscles is the cause of a low mean muscular efficiency.
2. Pressing Question: The treadmill is considered an easier run than on ground(can go further without getting tired). Does this have to do with the momentum of the belt rather than differences in efficiency?
3. Presentation: How much does migrating together affect efficiency? Organs working together compare at all?
4. Thoughts: Really enjoyed this paper!
Frank "Edad" Block, Jr.
ReplyDeleteSysBio13 Asgn_5D_Class_05_Article_11_2013_09_05
0. Knew: Basic principles of metabolism. Basic principles of "work" in physics as opposed to the colloquial term "work."
1. Learned: Minimum cost of transport.
2. Pressing: I do not understand the comment on the bottom left of page 419: "active muscles are not stretched while pedaling." ALL the muscles used in bicycling, or walking, are alternately contracted and stretched. There is also the question of the use of toe clips on bicycle pedals. These allow one leg to push while the other is pulling. Toe clips definitely increase speed and possibly would change the position on Figure 2.
3. Presentation: The physics and physiology of bicycling.
4. Thoughts: LOVE the information on bicycling vs. walking! I'm still struggling to understand the questions I raise in #2 above.
Ya, that's a good point about muscles while bicycling being streched
Delete0. Knew different methods of locomotion had varied efficiency
ReplyDelete1. Learned that P/ (WV) can be used to calculate the cost of transport for a given organism and method of locomotion. Walking and running animals are inefficient due largely to the inefficiency of stretching active muscles.
2. On page 5 the authors state that if human runners could store mechanical energy as elastic energy while moving (without resorting to stretching active muscles) efficiency could be improved. To what extent do running shoes store elastic energy? Could they be designed to store this energy better?
3. Presentation: The effect of running shoes on human running efficiency and storage of mechanical energy.
4. Thoughts: It is not surprising that walking is so inefficient relative to swimming considering the fact that life has had longer to adapt to swimming. It is surprising that flight is so efficient.
Cameron Stewart
ReplyDelete0. Knew: Bicycling is more efficient than jogging/walking.
1. Learned: Flying is more efficient than walking and swimming is more efficient than flying.
2. Pressing: I still don’t see how his analysis adds up. Bicycling uses .25 the energy per unit distance of walking. Part of the reason is that, when walking, the lengthening muscles which are stabilizing the walker are doing work and only a small amount of it is stored in tendons for the next step. So let’s say that for each step the muscles are doing 1.9 times the amount of work necessary. Where is the other wasted going? Is the rest all from the bobbing center of gravity, Mass*delta height*g*(1 – fraction of work from previous step stored in muscles/tendons)
3. Presentation: About efficiency of forms of transportation.
4. Thoughts: No idea how this relates to OoCs
0. Knew: Different means of travel differ in efficiency
ReplyDelete1. Learned: The minimum cost of transport for different types of locomotion fall into groups generally based on the type of locomotion.
2. Why are mice so innefiecent? Do they lose a lot of heat due to their small size and being mammals? I see lizards happen to fall on the line.
3. Efficiency of locomotion
4. It makes sense that runners would have the worst efficiency. The energy cost to move through a fluid(swimmer or flyer) is less. These types of creatures can glide, that is, they receive a further distance traveled for the same input of energy.
Jie Zhao
ReplyDeleteSysBio13 Asgn_5D_Class_05_Article_11_2013_09_05
0. Physics involved in energy cost and so on
1. a. Flying and swimming are very energy efficient.
b. some birds use up 25% body weight as fuel for migrating.
2. I still think the author’s argument against ‘your center of gravity doesn’t go up and down when bicycling’ is not valid. Even if you pedal standing up and down, the total number of ups and downs is less than walking and running.
3. Physiology of Muscle stretching
4. I find the author’s explanation of the efficacy of muscle unconvincing. Not only physics but also lots of biochemistry are involved in the process of muscle doing work, I hope it can be better sort out during the class.
0. Knew: Was aware of topic of energy expenditure/distance traveled.
ReplyDelete1. Learned: Flying mechanism allows changing downward motion forward without stretching or activating muscles.
2. Pressing: If it’s true that evolution hasn’t done a good job of optimizing energy expenditure, what potential costs would be associated with sacrificing other processes for efficient locomotion?
3. Presentation: Possible uses in systems biology
4. Thoughts: I’m still confused on the dynamics of improving biped locomotion, I couldn’t wrap my head around the bit discussing storing energy during deceleration elastically then releasing it in the direction of motion.
0 Knew: Bicycles are more efficient than walking.
ReplyDelete1 Learned: Why bicycles are more efficient than walking - has to do with stretch of active muscles and stability of center of mass
2 Pressing: What does this have to do with OoCs? What is meant by active muscle stretch?
3 Presentation: Maximizing efficiency of locomotion
4 Thoughts: This is cool, but application to OoCs?
Rui Wang
ReplyDeleteSysBio13 Asgn_5A_Class_05_Article_11_2013_09_05
0. Knew: Metabolic rate is a key factor for the cost of transport when comparing two different motions.
1. Learned: An analysis of power for a flying bird
2. Pressing: Can we combine the power input and allometric scaling together to analyze the metabolism of a flying bird?
3. Presentation: good definition of power input for metabolic rate
4. Thoughts: It is a good paper to quantify the cost of transport by applying simple model and explaining the muscle efficiency.
Blog Harvested
ReplyDeleteJPW