Saturday, July 31, 2010

Order of Systems

I thought that an interesting part of this chapter to discuss was the energy intake discussion for plants and humans. So we know that the energy producing pathways in plants and humans are somewhat spontaneous processes overall, once all the various components of those pathways have been accounted for (i.e. breakdown of food for energy, to then create more ATP helping to create an ordered system, and then a final release of energy through various function), but what is interesting to note is what the systems take from and give back to the surrounding system. That is, as the chapter states, is that they consume order, and not energy, which I find to be a bit of a knockback to my understanding of a systems functioning. By my understanding of this quote, I believe that through the conservation of energy through the systems, what happens is that equal energy is taken in and released, but that the energy is of a different quality (that is a different level of order), and since we're consuming order, that means we release disorded energy back to our surroundings.

What is most interesting about all this is how the organisms take in a high-quality form of energy (sunlight for plants, food for animals) and can use this energy to build up a low-quality form of matter (water, CO2 etc) into high ordered material. Again, this obviously involves an input of energy such as ATP to allow for this reaction to occur, but I still find it amazing how these organisms have their way of making non-spontaneous reactions happen.

The other important point that should be made is in relation to the understanding that the entropy of the universe is always increasing, which can be illustrated through the plant and animal systems. Though both systems take in both high- and low-quality energy, they also both are left at the end of the cycle no more high or low in their quality of matter, and all they will have released back to the surrounding system is low-quality energy (disordered energy) which backs up the theory of ever-increasing disorder (note to mention that when the systems die they only degrade, releasing disorded energy).

I would like to see what others say on this topic, and to see if they may have some more insight to provide.

Friday, July 30, 2010


This is the at least the 3rd time I have been introduced comprehensively to thermodynamics. I think that this is a good thing, as I always forget something in between times that I am being introduced. However, I always find something a little off about the discussion of entropy. I understand that systems go from highly ordered to random if now external work is done on the system. This makes intuitive sense. But I wonder, is it always true? There are always many, many more unordered states that a system can be in than ordered ones, which I have always found is the justification that an ordered system will decay to randomness. Logically, if the particles in the state are moving randomly, then the order is much more likely to be in the lowest state. But my concern is that isn’t it possible for the random movement of particles to happen to find itself, even if only temporarily, in a state higher in entropy than what it started in? Even if it is very very unlikely? Isn’t it possible that a box containing O2 and N2 gas molecules will, after an extremely long period of time, happen across a state where all the O2 molecules are on one side of the box, and all the N2 molecules on the other? Even if that state only lasts for an instant? Furthermore, when this state does occur, does absorption of heat from its surroundings accompany it?

Another case I think of is a body that consists of only a few particles (perhaps 100), at some non-trivial temperature. All the atoms are vibrating in random directions. If the direction of vibration of each atom is independent, and if the object is left for a long enough time, could there be a random synchronisation of the motions of the atoms, even for only a moment, that results in the body moving in a united direction? Obviously this small amount of kinetic energy is quickly turned back to heat energy through friction, but is this a possible example of heat energy spontaneously converting to kinetic energy?

Both these situations are quite trivial. The kinetic energy gained would not be worth harnessing, and the time when the order is achieved in the gas filled box would not be predictable. But it is examples like these which make me sceptical of ‘universal’ laws which state order is never spontaneously gained, or heat energy can never be converted into a more useful form (without an excess of heat energy (i.e. a large amount of heat being used to do the much less work involved in raising a hot-air balloon)).  

Are these situations ignored because they are just so statistically unlikely, or do I have some fundamental flaw in my understanding of the second law of thermodynamics?

Chapter 1 - Biologist or Physicists?

Hello everyone

I have just finished reading the first chapter of Nelson. For anyone who hasn’t started reading it yet, it’s a pretty easy read. It took me an hour and a half, and may take you even less, as I don’t think I am a particularly fast reader. This textbook from what I have seen so far uses quite easy language, and assumes very little background knowledge, which means it explains things in a way that is easy to understand. I have to thank Seth for his choice of textbook for this course.

Regarding this first chapter, there wasn’t much content in it that I hadn’t seen before. In particular section 1.4 which revises units and dimensional analysis was something I presume we all know and have used since high school. But this chapter was very useful for setting up the structure and conventions that I understand will be used in this textbook. I especially appreciate 1.5.4 Track 2, as it explains the conventions used when discussing moles. I would have been quite happy to use the unit mol, but I think the convention in this textbook shouldn’t be too hard to understand. I will be interested to see how this textbook measures quantities like bond energies, which are typically measured in units of kJ/mol.

Anyway, the point of this post was not to discuss the merits of the textbook we are using. I wanted to ask everyone where they perceive themselves in the dichotomy described in section 1.3. This section compares biologists to physicists, suggesting that the former tends to focus on details of a system, whereas the latter simplifies the system and focuses on an overall model. Is this a sentiment that everyone agrees with? I tend to think it is a bit of a generalisation; there would be many physicists that focus on the finer details of a physical system, and many occasions when a biologist can simplify a phenomenon to allow it to be compared to other similar situations. But I can understand where this idea is coming from.

I would place myself towards the big picture side of the scale myself. Coming from a mathematical and physical background, I am comfortable with the idea of extracting the important details of a system, and then attempting to discover the physical relationships which model them. I hope that this does not exclude me from noticing significant finer details about specific situations. I suppose this is something I will have to watch over this semester (and the future).

Where does everyone else perceive themselves on this scale?

Points of Interest in Chapter 1 of Nelson

As you read Chap. 1 of Nelson, here are some interesting points of interest.

Thompson was later named Count Rumford. He married A. Lavoisier's widow after the latter was guillotined. A. Lavoisier is known as the father of modern empirical chemistry.

A popular urban myth holds that Lavoisier's final experiment was to test how long the brain remained concious after beheading, by having an assistant count how many blinks his head could execute following its removal from his torso. The myth maintains that between 12 and 15 blinks were counted. However, an article in the Journal of Chemical Education claims that this myth is groundless, and puts forward some very reasonable arguments.

Examples of pattern formation during non-equilibrium processes abound in nature. A good example are the convection cells that can be seen forming in clouds when you examine them from an airplane. The cells form long repeating stripe patterns. Sand dunes are another example. Another popular example is the Belousov-Zhabotinskii reaction.

Franklin never actually did the calculation. However, Rayleigh redid the experiment later in 1890, and calculated a thickness of 2nm.

The relationship between disorder and information is sometimes hard to grasp, and the connection between the thermodynamical and information-theoretic entropy can be subtle. For more insight, consult:

Swanson. Entropy measures amount of choice. Journal of Chemical Education (1990) vol. 67 (3) pp. 206
Lowe. Entropy: Conceptual disorder. Journal of Chemical Education (1988) vol. 65 (5) pp. 403
Castans. Entropy and Uncertainty. American Journal of Physics (1962) vol. 30 (7) pp. 521-527
Styer. Insight into entropy. American Journal of Physics (2000) vol. 68 (12) pp. 1090-1096

Thursday, July 29, 2010


I sent all of you a copy of the TOC for Nelson's book so you could have a look.

The exercises for Chap. 1 are 1.5,1.6,1.7. Due next Wed.

Bloggers Start Your Engines

Kudos to Mitchell for grabbing the horns of the blogspot bull. Olé!

Assignment will follow tomorrow morning, as will a short summary of what I perceive to the main points left open after today's discussion. I don't have the notes in front of me right now...

Wednesday, July 28, 2010

Adding authors to this blog

Hello everyone

In case you didn't get/notice the e-mail I sent, I am now trying to add you as authors. It's not as easy as I thought it would be. I think I need to invite you to be authors, but to do this I need your e-mail addresses (I pressume the ones linked to your blogging account). If you could send these to me I'll invite you. Also, if someone knows a better way to add you as authors, let me know.