>Biology is really just an emergent phenomenon after all.
Absolutely, and it enrages me that there are many in the field who don't think like this.
I would point out, however, that the physics/chem we have is likely good enough for the representation biological systems. A more nuanced understanding of QM or fundamental physics in general, while obviously necessary in the end, is not going to do a whole lot to further the biological sciences at this moment. Unless of course, there's some sort of fundamental physics we're missing that is somehow intrinsic to protein/RNA folding, but that's a vanishingly unlikely prospect.
EDIT: oh I see, you do MD stuff, which helps explain your mindset :P I work in developmental genetics and the mindset/goals are very different.
As a (hopefully interesting!) aside, on the scale of most biological molecular dynamics simulations, quantum mechanical contributions can largely be ignored, because the mechanics of the large, heavy nuclei dominate the system. There are a few instances where a hybrid classical/quantum force field is necessary though, like any simulation involving breaking/formation of chemical bonds (where electrons must be treated explicitly).
The computational power needed for the treatment of a very large system (e.g. whole-organism, or even whole-cell) using fundamental physical laws (like QM, and probably even a classical approximation) will be out of reach for at least the next few decades (probably :)). So I would argue that while it's technically true that biology is a phenomenon which emerges from fundamental physical laws, it's sufficient for the time being to treat biology as a field distinct from, but ultimately dependent on, physics.
Yeah, I largely agree. My comment was more to indicate that when Xcelerate thinks about simulating a biological process, he thinks on the level of simulating individual atoms, which is much more likely to make someone think about the fundamental physics of the problem. When I simulate biological processes, I think in terms of chemistry or stat mech. Rather than one molecule I'm dealing with collections of many types of molecules whose interactions are often ill defined anyway, so I'm much more likely to think "eh, the chemistry we have is good enough, let's just get on with it"
Reductionist thinking like this is tempting but not really helpful in the real world, in my experience, and I'm a physicist. More is different, and even though it might be possible to simulate the emergent properties, this is really not feasible at scale. Calculating the wave function of a mole of unordered matter numerically is not possible for example.
I'm not saying that biologists should have to think about QM, just than biologists should think about chemistry. Our understanding of gene regulatory networks (which are definitely an emergent phenomenon), for example, has, until relatively recently been very qualitative, but we're now reaching the point where they can be simulated with relative accuracy from chemical principles. This is great, as it allows us to ground our assumptions about gene function and ask "Could this system really work the way we think it does?" Sometimes the answer is no and models have to be revised.
Absolutely, and it enrages me that there are many in the field who don't think like this.
I would point out, however, that the physics/chem we have is likely good enough for the representation biological systems. A more nuanced understanding of QM or fundamental physics in general, while obviously necessary in the end, is not going to do a whole lot to further the biological sciences at this moment. Unless of course, there's some sort of fundamental physics we're missing that is somehow intrinsic to protein/RNA folding, but that's a vanishingly unlikely prospect.
EDIT: oh I see, you do MD stuff, which helps explain your mindset :P I work in developmental genetics and the mindset/goals are very different.