WannabeNewton said:
I would ask for this thread to be closed because at this point it is akin to a cowering cat cornered by a gang of dogs closing in for the kill but I feel like too many people are getting entertainment value out of it.
Well I'm enjoying this thread so I hope it continues.
Firstly my apologies to jergen, micromass, and others for not examining each and every application in detail. I promise I'm not trying to cherry pick applications which are easiest for me to argue with. However, it is much easier for me to choose applications I'm
familiar with, and if the applications I was familiar with did not conform to my point, I wouldn't believe it (although I may merely be misinterpreting them). More importantly, if you merely mention an application or post a textbook, it puts the ball in my court to construct the argument for you. I'm not saying you're lazy, but I am saying this thread would likely progress much more rapidly if you were to construct more thorough arguments around your evidence.
Secondly, I have been accused of waving my hands and not really providing concrete arguments. This is duly noted and I have consistently attempted to increase the rigor (...ha!) of my arguments with each post. However, I have not observed many concrete arguments from my (admittedly numerous) foes. Mostly I am told "if you only read this textbook" or "surely this must be the case", which may very well be true, but it is extremely challenging for me to read every paper, extract the argument you imply with said paper, and then respond to it.
Finally, I think we should concentrate on one of these topics at a time. Either it will constitute evidence that the mathematician's theories are very helpful and the thread will die a peaceful death, or it will not, and we will proceed onto the next application.
I would prefer we begin with algebraic topology as applied to protein structure since I presently work in a computational biophysics lab and have been pondering more theoretical approaches to the problem of protein conformational change for several years now. The problem space appears to admit itself very well to a geometric or topological approach, yet protein conformational change prediction or first principles predictions of protein folds are extremely challenging unsolved physics problems (some colleagues of mine are currently engaged in CASP, a refinement/prediction challenge and advanced mathematical trickery which gave them an edge would certainly be interesting ;)). I have repeatedly explored more esoteric approaches and have been unimpressed.
The laboratory in which I work (surprise surprise) relies heavily on brute force, running molecular dynamics simulations on protein systems where the trajectories for every atom are simulated, although I work on algorithmic/more theoretical approaches. What is interesting to me is just how far out of our reach conformational change actually is; just obtaining a microsecond of simulation, significantly below the timescales for full conformational change, can take several months.
So what I would like to know is, what are these approaches, what pure mathematics do they rely upon,and how do they perform?