Interlude 5 - The Micro to Macro Connection

Much of what we have done so far — the Newtonian framework, describing the properties of solids and liquids, and the concepts of heat and temperature — are macroscopic concepts: they describe things we see, feel, and experience. They express the regularities and consistencies of the behavior of physical systems. Much of this was well known by the middle of the nineteenth century.

But one of the most extraordinary and important pieces of knowledge that humanity has garnered since then is the idea of the microscopic.  By this, physicists don't mean "what you can see in a microscope", but rather the fact that everything we regularly experience is made up of a small number of different kinds of atoms (91 in the natural world, a few more that have been created by humans).*

The essential point about this is that we believe that all properties of the macroscopic world are ultimately due to the properties and interactions of those 91 distinct elements. Although some phenomena require a description at a higher level (see the discussion of emergent phenomena), at some level (even if it's not convenient or useful for us to explicate), everything we see is a result of atomic properties.

A major component of modern biology is working at the microscopic — atomic and molecular — level and learning what are the critical elements that underlie basic biological mechanisms. Much of the research and development that can be expected to transform both biology and medicine over the next few decades will depend on making sense of the micro to macro connection. In this class, we will develop a few of the basic tools needed for making this connection.

One set of tools involves statistical physics. Since there is a huge amount of energy distributed in all objects at common temperatures, and since these energies tend to be randomly distributed among the atoms and molecules of a substance as a result of molecular collisions sharing and resharing energy, the science of figuring out the implications of randomness is critical for understanding many biological phenomena.

We've already looked at one emergent macroscopic phenomenon that arises as a result of molecular motion: diffusion. What we have learned there give us our first insight into the value of random motion models.

We begin our study of the implications of molecular motion for our understanding of thermodynamics with kinetic theory. It looks a lot like our analysis of diffusion, but in a uniform rather than a non-uniform situation. Kinetic theory applied to gases helps us make source of the concepts of pressure and temperature. We build simple molecular models of gases whose properties lead to our observed everyday observed macroscopic observations of temperature and pressure and give us deeper insights into the mechanisms responsible for the phenomena we observe.

But the real power of the molecular model is in helping us to understand "thermal dynamics" — what controls the spontaneous flow and distribution of thermal energy. This involves the less macroscopically intuitive concepts of entropy, enthalpy, free energy and fluctuations, all of which play critical roles in the understanding of the functioning of biological system.

* The molecular scale is really nanoscopic rather than microscopic. That is, it is at the scale of nanometers (10^-9 m) rather than micrometers (10^-6 m). A typical microscope that you might use in a bio lab, allows you to view objects that are micrometers in size (cells) but not nanometers in size (molecules). But there are now electron and atomic force microscopes that can see down to the molecular level, so we will use the term "microscopic" to mean "anything too small to see with the naked eye".

Julia Gouvea 8/21/13, Joe Redish 3/27/19