Class content > The micro to macro connection

Thermodynamics is the study of the energy associated with temperature

Thermodynamics (from the Greek words meaning "heat" and "strength") is the study of the energy associated with temperature. It is what develops our understanding of what happens when objects heat up or cool down. From the physics point of view, it tells us that when resistive forces deplete the mechanical energy that we have defined as a part of our Newtonian framework, that the energy is not destroyed but transformed into another form -- an energy internal to matter (thermal energy) by virtue of its temperature. Thermodynamics shows us that even matter at normal temperatures contain huge amounts of thermal energy. This field of physics develops laws for the behavior of this energy and tells us under what circumstances the hidden thermal energy may be tapped to do useful work.

Thermal energy is associated with the random motion of molecules

Our understanding of what this thermal energy actually is -- the kinetic and potential energies of the small particles of which matter is made -- arises from studying how the macroscopic laws of thermodynamics arise from considering the motion of those particles. The critical difference between the motions we studied under the Newtonian framework and those we will study under the thermodynamic framework is this:

The energy associated with the motion of a macroscopic object studied using Newton's laws is coherent; that is, all parts of the object (or the segment of the object we are considering) move in the same way. The object has a net momentum associated with the kinetic energy we are considering.

The energy associated with the thermal energy of an object is incoherent; that is, the molecules of the object are moving in all directions randomly. Although the molecules have kinetic energy and momentum, the net momentum of the object as a result of its thermal energy is zero.

The study of how the macroscopic thermal behavior of objects arises from the motion of its molecules is called statistical mechanics.

The biological implications

The flow and control of thermal energy are of considerable interest and importance to organisms, in part since the rate at which some of the critical chemical reactions of life take place depends on the temperature of the system. As a result, many organisms may spend a lot of the energy they harvest to regulate their temperatures. (See the Thermal Regulation activity.) Understanding the thermal energy that is necessarily associated with chemical reaction chains such as photosynthesis, respiration, and the Krebs cycle is an important component of the energy balance of the reactions.

But perhaps even more important for modern biology is the understanding the statistical mechanics of biological systems. The random motion of molecules plays a huge role in how the basic molecular mechanisms of biological systems take place, for example, the motion of uneven distributions of chemicals (chemical gradients, Fick's law, etc.), the self-assembly of viruses, and the replication of DNA. Our treatment of thermodynamics will therefore blend with a statistical mechanical description of the phenomena and an extended description of the role played by random molecular motions.

Physics, chemistry, and biology

A word of warning: Thermodynamics (and occasionally some elements of statistical mechanics) is discussed in physics, chemistry, and biology classes. This might seem as if it would help, but in fact it often creates problems. The three fields each have their own "most important" aspects of these topics for their interests and they therefore may make different starting assumptions. Biologists often assume everything happens at constant pressures; chemists ignore coherent motions; physicists suppress chemical changes. While these may be perfectly reasonable assumptions for the examples they are each considering, often these assumptions are not highlighted. The choice of which thermodynamic variables to use and how to express the laws may be different. This means that the "laws of thermodynamics" may look different in your different classes! Here, we will do our best to include all forms of energy -- at least as a basis for discussion -- and to be explicit about what we choose to ignore in our various discussions.

Systems

Thermodynamics is about the forms energy can take and how it is transferred from one form to another. Since we presently believe that we know all the forms of energy that are relevant for biological processes* and we know that for the universe as a whole energy is conserved, the key thing is not that energy is conserved, but rather where does it go? This means that to study energy transformations we have to divide our universe into parts and look at how energy (and other thermodynamic variables such as entropy) are transferred between the parts. We have to divide the universe into the part we are paying attention to and the rest of the universe. The part we are paying attention to is called the system (of interest).

In some cases, we will be considering parts of a system that only exchange material and energy with each other. In this case, we refer to is as an isolated system. If energy can flow between the system but not matter, we refer to it is a closed system. If the system we are looking at can exchange both matter and energy with the rest of the universe, we refer to it as an open system. While isolated systems are useful in order to get a sense of how energy flows, real biological systems typically have to be considered as open as they exchange both energies and matter with their environments. This is less true when when considers large biological systems, such as ecosystems.  Ecosystems may be considered open or closed depending on whether you include the soil or oceans as part of the system. If you do, then they mostly a lot of exchanging of materials among themselves (food chains, soil, etc.), but the sun provides an outside source of energy that is critical to the functioning of the system.

* This is probably an excellent assumption. Molecular systems are so well studied that it is hard to imagine a new form of energy being discovered. On the other hand, the 2011 Nobel Prize in Physics was given for discovering that distant galaxies seem to be speeding up as they go away from us, not slowing down as the increases in their gravitational potential energy (it gets less negative as you get farther away) would predict. This suggests that either there is a new form of energy affecting the bigger-than-galactic scale or that on those (extremely large) distance scales, energy conservation no longer holds. Stay tuned!

Joe Redish 11/29/11