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.
Ayeeshik Kole
ReplyDelete13/Kaneko Ch2
0. Knew: To understand complex living systems, we cannot build models for precise phenomena because this approach cannot expose any underlying universal properties.
1. Learned: The current mainstream approach that “X is the A-gene” is flawed because that assumes that it is a necessary condition rather than a sufficient condition. Construction biology, if approached properly, can reveal the sufficient conditions for life.
2. Pressing ?: He says fluid turbulence and the irregular fluctuations both show underlying principles of chaos theory. How does he assume that this will be the case when “unimportant details” are removed from precise life phenomena? What is an “unimportant detail”?
3. Presentation: Zhuangzi philosophy
4. Thoughts: This chapter was very redundant at times. The first few times were useful because he explained the same concept in several ways, but towards the end it diminished his message. Also, he had this pattern of presenting a very bold statement/theory and then slowly stepping back from it by saying things they are not trying to do/be.
Erica Curtis
ReplyDelete13/Kaneko_Ch2
0. Knew: Emergent properties common to all organisms may be the key to discerning the primary universal properties necessary for life.
1. Learned: Small perturbations to the systems studied will not help us to elucidate these fundamental properties. The best way, in the author’s opinion, to uncover these universal properties is through constructive biology. In some ways, single cell studies may be more important for study because we are looking to create systems with only minimal properties.
2. Pressing ?: The author often refers to not only studying the organisms currently living on earth. I understand the reasoning behind wanting to look at all organisms over time as opposed to only those that evolution has selected, but, with the vast number of organisms currently present, would this not be sufficient? I am also not completely clear on the definition of “universality class” and its relation to his argument.
3. Presentation: Protocells
4. Thoughts: The verbosity of the author is beginning to cloud his message. I appreciate his anecdotes referring to Zhuangzi philosophy.
Will Matloff
ReplyDelete13/Kaneko Chapter 2
0. Knew: The idea that simplified models can aid in understanding of complex systems.
1. Learned: In this chapter, Kaneko justifies his use of 'toy models' through the idea of constructive biology. This idea is focused on finding the fundamental principles that are required of life while ignoring all of the history and 'frozen accidents' of evolution. Ideally, constructive biology will reveal principles of life that would be applicable to any life form, including those of extraterrestrial origin.
2. Pressing: Would the Rule 110 automata be an example of a constructive model?
3. Presentation: Successful examples of constructive biology.
4. Thoughts: In terms of dealing with the Leibniz issue, constructive biology seems like a worthwhile endeavor. An abstract understanding of a fundamental function of biology would vastly decrease the solution space in terms of understanding the details of a biological system that implements the function.
Brian Evans
ReplyDelete13/Kaneko Ch. 2
0. Knew: I had a general understanding of "constructive biology" and the studies that it consists of. I also am getting to be quite familiar with the idea of utilizing reductionist views to yield 'universal' understanding.
1. Learned: That sympatric speciation is a fancy way of saying that two species evolve from a common ancestor in the same geographical location.
2. Pressing ?: I feel like a thorough description of "constructive biology" only constitutes half of what systems biology is. Where is "deconstructive biology" and its logic and significance in furthering our understanding what the minimal conditions for life are?
3. Presentation: The Current Biological Universality Class: the phenomena that constitute our understanding of life.
4: Thoughts: When reading about symbiotic development and the mention of studying bacteria, its interesting to think that in terms of cell number each of us is made up of more bacteria than we are of our own cells (e.g. think of the nonpathogenic bacteria in your body, especially the stomach like helicobacter pylori in your stomach, enterococcus and lactobacillus in your small intestine, and tons of types of bacteria in your large intestine ranging from bifidobacteria to sterptococcus)....weird.
Lucas Hofmeister
ReplyDelete13/Kaneko Ch. 2
0. Knew:We need to look beyond present and past to figure out what is fundamental for life
1. Learned: The term Gedanken experiment
2. Pressing ?: Kaneko says that they, "do not seek quantitative agreement, but rather qualitative agreement regarding such questions as the existence of certain properties." Why not, i dont really understand...
3. Presentation: Arsenic DNA controversy http://www.sciencemag.org/content/332/6034/1163
4. Thoughts: Honestly, I'm not really sold on the approach that this book takes (maybe i dont understand it). It reads like a lot of hand waving about the philosophical approach Kaneko is going to take but I'm not really sure that i agree. I'm also not really sure that i am learning anything constructive from this book so far (hopefully this gets better). That said, this writing is so darn wordy that I may have just skimmed over something important.
Zach Eagleton
ReplyDelete13/Kaneko Chapter 2
0 Knew: That the approach to system biology is to find a good abstraction to systems.
1 Learned: Kaneko seeks to identify the basic principles that govern all life. His constructive biology approach then could be used to explain all life. Did a good job laying out current experminets in the table.
2 Pressing ?: If a theory that explained life emerges, could it really apply to extra-terrestrial life?
3 Presentation: Activin-controlled tissue formation
4 Thoughts: Though the philosophy was interesting. Defines his broad approach well, although with too many words.